Researchers have new evidence that suggest Neanderthals died out much earlier than previously thought, and possibly before modern humans arrived.
Carbon-dated Neanderthal remains from a cave in the foothills of the Caucasus Mountains in Russia were found to be 10,000 years older than previous research had suggested. The new evidence contradicts the popular theory that Neanderthals and modern humans interacted for thousands of years before the archaic species became extinct.
Instead, the researchers believe any co-existence between the two species is likely to have been far more restricted, perhaps at most a few hundred years. It is quite possible in some areas Neanderthals became extinct before modern humans moved out of Africa.
The remains from the cave, known as Mezmaiskaya, were dated with a precise carbon-dating technique, said paleoanthropologist Thomas Higham of the University of Oxford, UK, a co-author of a study published in the Proceedings of the National Academy of Sciences.
Higham’s team says the implication is that Neanderthals and humans may never have met in Europe. However, the Neanderthal genome, decoded by scientists last year, suggests that the ancestors of all humans, except those from Africa, interbred with Neanderthals somewhere.
“DNA results show that there was admixture probably at some stage in our human ancestry, but it more than likely happened quite a long time before humans arrived in Europe,” says Ron Pinhasi, an archaeologist at University College Cork in Ireland, who is lead author of the latest study. “I don’t believe there were regions where Neanderthals were living next to modern humans. I just don’t find it very feasible.”
The researchers found the fossil in question to be 39,700 years old, instead of the previous assigned 30,000 years old. The dating implies that Neanderthals did not survive at the cave site beyond that time.
The research suggests that if we are going to have accurate chronologies the data needs to be improved so possible associations between Neanderthals and early modern humans can be properly assessed. The previous dating processes seem to have “systemically underestimated” the true age of Late Middle Paleolithic and Early Upper Paleolithic deposits, artifacts and fossils by up to several thousand years, says the research report.
“The latest dating techniques mean we can purify the collagen extracted from tiny fragments of fossil very effectively without contaminating it,” said Higham. “Previously, research teams have provided younger dates which we now know are not robust, possibly because the fossil has become contaminated with more modern particles.”
“This latest dating evidence sheds further light on the extinction dates for Neanderthals in this key region, which is seen by many as a crossroads for the movement of modern humans into the wider Russian plains. The extinction of Neanderthals here is, therefore, an indicator we think, of when that first probably happened,” said Higham.
Carbon dating of stone tools characteristic to both humans and Neanderthals, as well as their remains, has previously suggested that the first humans to reach Europe, between 40,000 and 30,000 years ago, shared the land with Neanderthals that were believed to have been long established there.
However, carbon dating of remains older than 30,000 years is tricky because nearly all the radioactive carbon in the remains has decayed, said Higham.
The overlap in dating could also be the result of contamination of older finds with younger finds. “What we are finding is that the careful and patient excavation work of many archaeological sites has not been supported by accurate and reliable radiocarbon dating,” Higham said.
But, using the most up-to-date carbon-dating techniques, Pinhasi and his team were able to date the remains of two Neanderthal infants from the cave to close to 40,000 years old. The infants’ bones were found above the cave’s other Neanderthal remains, so they must have been the most recent, Higham explained.
Higham’s conclusion fits with another discovery made by David Reich, a geneticist at Harvard Medical School in Boston, Massachusetts, whose team found that all contemporary humans, except those who trace their roots back to Africa, owe about 1 to 4 percent of their DNA to interbreeding between early modern humans and Neanderthals.
Reich’s team did not find any proof that Neanderthals ever mated with the ancestors of modern Europeans specifically, however.
Yet he said that new, more sensitive methods for detecting interbreeding, as well as genome sequences from late Neanderthals could change that conclusion. “Absence of evidence isn’t evidence of absence,” said Reich.
Chris Stringer, a paleoanthropologist at the Natural History Museum in London, agrees that Neanderthals were rare in Europe after 40,000 years ago, but added that they might not have completely disappeared.
“It does seem that if Neanderthal populations existed after that time, they must have been small and scattered remnants,” he said.
There is evidence of more recent Neanderthal settlements. Clive Finlayson, director of the Gibraltar Museum, and his colleagues have dated a Neanderthal settlement in Gorham’s Cave in Gibraltar to as recently as 24,000 years ago.
“Eurasia is a big place and there doesn’t seem to be any reason why populations of Neanderthals may not have survived somewhere,” said Higham.
The University of Oxford and University College Cork researchers collaborated with the Laboratory of Prehistory at St Petersburg, Russia. The study was funded by Science Foundation Ireland.
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• University of Oxford
• Proceedings of the National Academy of Sciences
• University College Cork

It’s not quite Christmas, but the DNA sequence of a small plant that resembles the seasonal conifers is providing biofuels researchers with information that could influence the development of candidate biofuel feedstock plants and offering botanists long-awaited insights into plant evolution.

“When you burn coal, you’re burning Selaginella’s ancestors,” said Purdue University botanist Jody Banks, who originally proposed that the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) sequence the plant more commonly known as spikemoss as part of the DOE JGI’s 2005 Community Sequencing Program.

Published online May 5 in Science Express, a team of researchers from over 60 institutions, that included DOE JGI’s Dan Rokhsar and Igor Grigoriev, the senior authors of this work, reported the genome sequence of Selaginella moellendorffii and used a comparative genomics approach to identify the core genes that are likely to be present in a common ancestor to land plants.

Grigoriev noted that the Selaginella genome helps fill in a large gap in plant evolution from the unicellular green alga Chlamydomonas, sequenced at the DOE JGI and published in 2007, to flowering plants with vascular systems. “Selaginella occupies a phylogenetically important position for which we had no reference,” he said. “On one end of the spectrum we had mosses such as Physcomitrella” “” the first moss to have its genome sequenced and published by DOE JGI “” “and on the other are angiosperms such as grasses including Brachypodium,” whose genome was published by DOE JGI last year.

Spikemoss stands tall like grasses, but because it diverged from flowering plants more than 400 million years ago, it doesn’t have the roots and leaves like later plants. To help understand these relationships, the researchers compared the genome of Selaginella against those of Chlamydomonas, Physcomitrella and 14 angiosperms (flowering plants), including Arabidopsis and rice to identify common genes.

Banks said having the spikemoss genome revealed that the transition from mosses to plants with vascular systems didn’t involve as many genes as going from a vascular plant that doesn’t produce flowers to one that does. “We have a much better idea with Selaginella which genes evolved only in angiosperms. Plants need vascular tissues to be tall, to transport nutrients from roots to leaves,” she said. “That’s fairly complicated, but it turns out that process just didn’t need that many genes compared to inventing flowers.”

To help vascular tissues to stay upright, plants rely on lignin, a polymer biofuels researchers are targeting for investigation because its rigid structure is challenging to break down, impeding their use as potential bioenergy feedstocks. Banks’ colleague Clint Chapple, a coauthor on the paper and a Purdue colleague, has been using the Selaginella genome to study the pathways by which three different types of lignin are synthesized in plants.

“What we learned is that Selaginella not only invented the S type of lignin independently, maybe even earlier, than angiosperms but that they go about doing it through a related but different chemical route,” Chapple said. He described a recent project [funded by the National Science Foundation] in which enzymes from the lignin-synthesizing pathway in Selaginella were used to modify the canonical lignin-producing pathway in Arabidopsis to produce the polymer. Having the genome sequence offers strategic research opportunities, he said. “We’ve known for some time that if you alter the lignin building blocks you can improve biomass for agricultural and industrial uses.”

Banks also noted that the Selaginella research community has grown up around the availability of the genome, which was made publicly available through the DOE JGI’s plant portal Phytozome in 2009.  One metric she cites is the number of researchers who’ve contributed to the Selaginella Genomics wiki she helps maintain, whose existence spread solely by word of mouth. “There are more than 100 coauthors now just because people are interested in the genome,” she said. “There have been a large number of recent papers, all including Selaginella genes because it really helps the researcher understand the evolution of their favorite gene family. Selaginella represents a whole branch of the plant evolutionary tree that no one has sampled before, and it is really important. The lignin story is just one example.”

The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow DOE JGI on Twitter.

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On the Net:

• Doe Joint Genome Institute
• Science Express

Pontifical Academy of Sciences working group of leading scientists to present report to Pope Benedict XVI

Scripps Institution of Oceanography / University of California, San Diego

A panel of some of the world’s leading climate and glacier scientists co-chaired by a Scripps Institution of Oceanography, UC San Diego researcher issued a report today commissioned by the Vatican’s Pontifical Academy of Sciences citing the moral imperative before society to properly address climate change.

The co-authors of “Fate of Mountain Glaciers in the Anthropocene” list numerous examples of glacial decline around the world and the evidence linking that decline to human-caused changes in climate and air pollution. The threat to the ways of life of people dependent upon glaciers and snow packs for water supplies compels immediate action to mitigate the effects of climate change and to adapt to what changes are happening now and are projected to happen in the future.

“We are committed to ensuring that all inhabitants of this planet receive their daily bread, fresh air to breathe and clean water to drink as we are aware that, if we want justice and peace, we must protect the habitat that sustains us,” the authors write in a declaration prefacing the report. “The believers among us ask God to grant us this wish.”

Scripps Climate and Atmospheric Scientist Veerabhadran Ramanathan co-chaired the working group with Nobel Laureate Paul Crutzen, formerly affiliated with Scripps and Lennart Bengtsson, former head of the European weather forecasting center. The group also included Nobel Laureate Carlo Rubbia, former director general of the CERN Laboratory. Among the rest of the 24 authors are Lonnie Thompson of Ohio State University, Wilfried Haeberli from Switzerland, Georg Kaser from Austria and Anil Kulkarni from India, considered among the world’s foremost experts on glacial change. Former Scripps Director Charles Kennel and Scripps Professor of Atmospheric Chemistry Lynn Russell are also members of the working group.

“The widespread loss of snow and ice in the mountain glaciers is one of the most visible changes attributable to global climate change. The disintegration of many small glaciers in the Himalayas is most disturbing to me since this region serves as the water tower of Asia and since both the greenhouse gases and air pollutants like soot and ozone contribute to the melting,” said Ramanathan, who has been a member of the Pontifical Academy of Sciences since 2004.

Report authors met at the Vatican from April 2 to April 4, 2011 under the invitation of Chancellor Marcelo Sanchez Sorondo of the pontifical academy. The report was issued by the Vatican today and will be presented to Pope Benedict XVI.

Though scientists usually refrain from proposing action, Ramanathan said the circumstances warranted advancing suggestions from the working group. The authors recommend pursuit of three measures: immediate reduction of worldwide carbon dioxide emissions, reduction of concentrations of warming air pollutants such as soot, ozone, methane and hydroflurocarbons by up to 50 percent, and preparation to adapt to climate changes that society will not be able to mitigate.

The report title refers to the term coined by Crutzen to describe what is considered a new geologic epoch that began when the impacts of mankind on the planet became a major factor in environmental and climate changes.

“The recent changes observed in glacial behavior are due to a complex mix of causal factors that include greenhouse gas forcing together with large scale emissions of dark soot particles and dust in ‘brown clouds’, and the associated changes in regional atmospheric energy and moisture content, all of which result in significant warming at higher altitudes, not least in the Himalayas,” the authors write.

“Changes of mountain glaciers all around the world are rapid and impacts are expected to be detrimental, particularly in the high mountains of South America and Asia,” said Kaser, of the Institute for Meteorology and Geophysics at the University of Innsbruck. “Yet, our understanding about glacier changes in these regions is still limited and ambitious and joint efforts are required to respond to these problems. With its report, the pontifical academy contributes considerably to raising awareness.”

“Glaciers are one of our most visible evidences of global climate change,” added Thompson. “They integrate many climate variables in the Earth system. Their loss is readily apparent and they have no political agenda. Glaciers remind us of the stunning beauty of nature and in turn the urgency of doing everything in our power to protect it.”

The authors conclude: “We appeal to all nations to develop and implement, without delay, effective and fair policies to reduce the causes and impacts of climate change on communiÂties and ecosystems, including mountain glaciers and their watersheds, aware that we all live in the same home. By acting now, in the spirit of common but differentiated responsibility, we accept our duty to one another and to the stewardship of a planet blessed with the gift of life.”

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On the Net:

• Scripps Institution of Oceanography

F1000 Biology Reports takes a look at the story behind the invention of optogenetics

Commenting on Edward Boyden’s article, Ben Barres, Head of the Neuronal & Glial Cell Biology Section of Faculty of 1000 and Professor at Stanford University School of Medicine said: “There will probably be a Nobel prize for optogenetics someday as it has revolutionized our attempts to understand how the brain works. This article provides a fascinating insight into the birth of optogenetics and the roles of the major players.”

The invention of optogenetics literally sheds light on how our brains work. Published in the May 2011 issue of F1000 Biology Reports, Edward Boyden’s revealing article gives a unique perspective on the birth of optogenetics tools, new resources for analyzing and engineering brain circuits. These ‘tools’ take the form of genetically encoded molecules that, when targeted to specific neurons in the brain, enable their activity to be driven or silenced by light, thus revealing how entire neural circuits operate.

By driving or quieting the activity of defined neurons embedded with an intact neural network, Boyden and his colleagues are able to determine what behaviors, neural computations, or pathologies those neurons were sufficient to cause or what brain functions, or pathologies, these neurons are necessary for.

These tools are also being explored as components of neural control prosthetics capable of correcting neural circuit computations that have gone awry in brain disorders. Part of a systematic approach to neuroscience that is empowering new therapeutic strategies for neurological and psychiatric disorders, optogenetic tools are widely accepted as one of the technical advances of the decade, and could one day be used to treat neurological disorders such as Parkinsons.

Using primary sources and his own experiences at Stanford, Boyden reconstructs a compelling case study of the development of optogenetic tools, providing an insight into the hard work and serendipity involved.

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On the Net:

• Faculty of 1000: Biology and Medicine

To find out what motivates pigs to frolic around in the mud, a scientist in the Netherlands looked at the wallowing behavior of its wild relatives.

Marc Bracke from Wageningen University and Research Centre carried out the study that suggests a pig’s love of mud is not just a way to keep cool, but is vital for the animals’ well-being.

Pigs are known to wallow in order to keep cool because they do not have normal sweat glands to regulate their body temperature.

Bracke searched through scientific literature for any evidence of what might motivate other animals to carry out the similar behavior.

He looked at animals such as the hippo, a pig’s close relative, who spend much of their time in the water in order to keep cool; and the deer because they roll around on the ground, not to keep cool, but to “scent mark” in order to attract a mate.

From these analyses, Bracke proposed that mud wallowing, similar to rolling, may be hardwired in pigs and could play a role in their reproduction.

“If so, wallowing could be an important element of a good life in pigs,” says Bracke.

Bracke also suggests that the rolling behavior of pigs was possibly evolved from its ancient relatives.

“Pigs are genetically related to particularly water-loving animals such as hippos and whales,” Bracke says.

“It seems to me that this preference to be in shallow water could have been a turning point in the evolution of whales from land-dwelling mammals,” he adds.

Watering holes are ideal places for predators to ambush their prey, and for many animals wallowing would be dangerous.

“But pigs, like many carnivores, are relatively large animals with enlarged canine teeth, so they would be better able to fend off an attack,” says Bracke.

In conclusion, Bracke thinks that pigs “did not evolve functional sweat glands like other ungulates because they liked wallowing so much,” and not because they need the mud to cool down because pigs do not have [functional] sweat glands.

The study is published in the journal Applied Animal Behaviour Science.

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• Wageningen University and Research Centre
• Applied Animal Behaviour Science

A novel way to ramp up biodiversity

Bruce Carlson stands next to a fish tank in his lab, holding a putty colored Radio Shack amplifier connected to two wires whose insulation has been stripped. At the bottom of the tank a nondescript little fish lurks in a sawed-off section of PVC pipe.

Carlson sticks the two bare wires into the tank. Suddenly we hear a rapid-fire pop, pop, pop, pop, pop, pop. The pops, which are surprisingly loud, sound rather like the static on an old-fashioned tube radio tuned between stations.

“When there are many fish in a tank,” Carlson says, “it sounds like a frying pan”.

Carlson, PhD, assistant professor of biology in Arts & Sciences, is studying the African family of weakly electric fishes called the Mormyridae, or mormyrids.

Each fish in this family has an electric signal distinctive to its species, but also, to its sex, dominance status and even its individual identity.

The shape of the discharge is the fish’s “face,” says Carlson. “It’s how they recognize one another.”

The sensory pathway that detects and analyzes the electric discharges in the Mormyridae had been well studied, but only in two or three species, Carlson says, and the family has more than 200. Given its diversity Carlson asked whether changes in electrical communication might have influenced rates of speciation.

Three anatomical advances underlie the ability to send and receive diverse electrical signals: cells able to produce different discharges, a global distribution of the sensors that detect the discharges’ shape, and a more complex signal-processing area of the brain to analyze them.

In 2008 the National Science Foundation awarded Carlson a grant to travel to Gabon (where many mormyrid species are found) to study the mormyrid brain, and how brain anatomy maps onto the evolutionary tree of the fishes.

His team found that changes in brain anatomy and the resulting ability to fully exploit electric signal space did indeed lead to rapid speciation, a result published in the April 29 issue of Science.

The electric organ

Each pop is one discharge of an electric organ located at the base of a fish’s tail. The organs consist of stacks of disk-like cells called electrocytes, “pretty much like watch batteries in series,” says Carlson.

The electrocytes all fire action potentials simultaneously, and so their tiny action potentials sum to produce a discharge that is typically about a few volts.

“These signals don’t propagate as electromagnetic waves,” Carlson explains. “Instead they exist as an electrostatic field, just like you’d get by sticking a battery in the water.

“That’s why these fish are so good at recognizing pulses with different shapes,” he says. Waves are distorted during transmission, so that their fine temporal structure is smeared.

“The discharges are not distorted. They get weaker with distance, but their temporal structure stays the same. That’s one reason mormyrids evolved to be exquisitely sensitive to small timing differences in electric signals,” Carlson explains.

Detecting the pulse

Weakly electric fish have several types of electroreceptors but the ones important for communication are called knollenorgans, from the German word “Knolle,” or tuber, because they consist of bulbous cells buried just under the fish’s skin.

The knollenorgans respond to a voltage rise, firing a time-locked spike in response to outside positive-going voltage changes.

The knollenorgans on one side of a fish’s body respond to the start of a discharge and those on the opposite side respond to the end of a discharge. This lets a fish recognize a species-specific discharge by comparing the intervals between spikes coming from opposite sides of its body.

The spike time comparison occurs within the central nervous system, in a part of the brain called the extero-lateral nucleus, or EL.

Signal processing

When we began our work, the “standard anatomy” for the “mormyrid” brain””what you’d find if you looked in a textbook– says Carlson, was a two-part EL, with separate nuclei, or clumps of cells, in the anterior and posterior portions.

“We collected lots of brains in Gabon, and two collaborators, Saad Hasan, a former undergraduate at Washington University, who is now a medical student at Cornell, and Derek Miller, who is an undergraduate at Washington University, did all the histology on the brains.

“In addition to the standard anatomy, we were amazed to see another anatomy, where the EL is substantially smaller and not split into two portions.

“All the fish we looked at either had the large EL that was divided into anterior and posterior halves, or they had the small undifferentiated EL.

Working with collaborator Matthew Arnegard, PhD, a postdoctoral fellow at the Fred Hutchinson Cancer Research Center in Seattle, WA, the scientists mapped the brain anatomy onto a phylogenetic tree (an evolutionary tree based on the similarity of DNA sequences), and they could see that there were two equally parsimonious ways to reconstruct the fishes’ evolutionary history.

Either the complex brain was ancestral and the simpler brain evolved twice or the simpler brain was ancestral and the complex brain arose twice. To solve this riddle, they did what evolutionary biologists do, which is look at the “next outgroup member,” the closest related fish that’s not part of the Mormyridae family.

This fish has an area in the midbrain that is similar to a small, undifferentiated EL. This suggested the EL brain was probably the ancestral brain, and the more complex divided ELa/ELp evolved twice, once within the subfamily Mormyrinae and once within the subfamily Petrocephalinae.

Did fancy anatomy lead to rapid diversification?

If a communication system is to promote species diversity it must have both the capacity to create new signals (flexible stalk morphology) and the ability to distinguish those new signals from other signals (the broad distribution of knollenorgans and the complex brain).

“The only fish that have all three is a group of mormyrids we ended up calling Clade A for simplicity’s sake,” Carlson says.

To test the importance of these traits on signal divergence we analyzed the discharges of fish collected in two locales: the Ivindo River of Gabon, home to the largest known assemblage of the subfamily Mormyrinae; and Odzala National Park in the Republic of the Congo, home to the largest known assemblage of the subfamily Petrocephalinae.

“Statistical analysis showed us that the rate of signal divergence in Clade A was 10 times higher than among other fish within the Mormyridae,” Carlson says. Further analysis by collaborator Luke Harmon, PhD, assistant professor of biology at the University of Idaho, revealed that the number of species in clade A has been increasing three to five times faster than the number of species in other mormyrid lineages.

In other words, the fancier the fishs’ communication kit, the more likely it was to come up with new electric discharges and new species that identified one another by those discharges.

Putting it to the test

It all worked out statistically and logically but was it what the fish actually experienced?

“After all,” says Carlson, “this sensory world is totally foreign to us. I’ve worked with these fish a long time, so I can tell a few of the discharges apart by ear. But for the most part I need an oscilloscope to see the differences.

Can the Clade A fish tell the difference between discharges? To test them, Carlson ran behavioral playback experiments on fish caught in Gabon.

“A fish would be going pop, pop, pop and we’d pulse it. Depending on the fish, it would either discharge more rapidly, brrrrrrrrr, or stop discharging altogether.

“But if we repeated the stimulus again and again the fish would stop responding. Once it stopped responding, we hit it with a phase-shifted version of the same pulse. If the fish could tell the difference, the discharge rate or pause duration would increase. If it couldn’t tell the difference, there would be no change.

The experiments showed that mormyrid fish in Clade A were able to distinguish among pulses, but other mormyrids (those with the EL brain) were not.

Did the evolution of a fancy signal-processing brain drive speciation in the Mormyridae? “It’s always difficult with evolutionary studies to say that any one trait is the cause or the trigger for another,” Carlson says. “But in this case we were able to show that the complex signal-processing brain evolved before a burst of speciation, that signal variation was higher among fishes with that brain, and that these fishes could distinguish among subtly different pulses, whereas others could not.

“Together it adds up to a strong case for brain evolution triggering increased diversification.”

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On the Net:

• Washington University in St. Louis

Like people with a big choice to make, stem cells have a process to “decide” whether to transform into a specific cell type or to stay flexible, a state that biologists call “pluripotency.” Using a technology he invented, Brown researcher William Fairbrother and colleagues have discovered new molecular interactions in the process that will help regenerative medicine researchers better understand pluripotency.

In a paper published in advance online in the journal Genome Research, Fairbrother’s team showed that different proteins called transcription factors compete and cooperate in the cells to produce complex bindings along crucial sequences of DNA. This game of molecular “capture the flag,” played in teams and amid shifting alliances, appears to be a necessary part of what determines whether stem cells retain their pluripotency and whether specialized, or differentiated, cells can regain it.

In recent years scientists have reported spectacular successes in turning fully differentiated cells back into pluripotent stem cells, a process called reprogramming. But the animals derived from these cells often suffer higher rates of tumors and other problems, Fairbrother said. The reason may be because the complex details of the reprogramming process haven’t been fully understood. He said there are many misconceptions about how reprogramming transcription factors interact with DNA.

“Most people think of a protein binding to DNA as a single, surgical thing where you have this isolated binding event,” Fairbrother said. “But in fact we show that sometimes these binding events occur over hundreds of nucleotides so they seem more like great greasy globs of proteins that are forming. In addition, the proteins interact with each other, diversifying their function by appearing in complexes with with different partners at different places.”

By employing a high-throughput, high-resolution binding assay that he’s dubbed MEGAShift, Fairbrother and his colleagues, who include pathology researchers from the University of Utah School of Medicine, were able to analyze the interactions of several key transcription factors in a region of 316,000 letters of DNA with a resolution as low as 10 base pairs. Through hundreds of thousands of array measurements, lead authors Luciana Ferraris and Allan Stewart, Fairbrother, Alec DeSimone, and the other authors learned previously unspotted patterns of protein interactions.

“How do stem cells stay in the state where they can keep their options open?” Fairbrother said. “A key player is POU5F1. But what are the key players that could interact with it and modulate its function? We’ve developed technology to look at that question.”

One of several findings in the paper concerned POU5F1 and its archrival, POU2F1, which binds to exactly the same eight-letter DNA sequence. Which protein binds to the sequence first influences whether a stem cell specializes or remains pluripotent. Experiments showed that a determining factor was a third protein called SOX2. SOX2 helped both proteins bind, but it helps POU2F1 more than POU5F1. In contrast, the team found that another player, NANOG, exclusively helps POU5F1.

“Who binds next to a protein is a determinant of who ends up binding to a sequence,” Fairbrother said.

With support from the National Institutes of Health, Fairbrother’s group is also applying MEGAShift to other questions, including how protein-protein interactions affect the formation of RNA-protein complexes, which can be even more complicated than binding DNA.

They will also look at the problem of narrowing the field of hundreds of genomic sequence variations that exist naturally in the population down to the real genetic “causal variants” of disease risk. MEGAShift can sort through which variants associated with disease result in an altered binding event that results in a clinical manifestation, such as diabetes or lupus.

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• Brown University
• Genome Research

MIT reported on Monday that researchers have a used genetically modified virus to produce structures that improve solar-cell efficiency by about one-third.

MIT researchers said they have found a way to make significant improvements to the power-conversion efficiency of solar cells by using a tiny virus to perform detailed assembly work at the microscopic level.

Sunlight hits a light-harvesting material in a solar cell, which releases electrons that can produce an electric current. 

The research of this new study is based on findings that carbon nanotubes can enhance the efficiency of electron collection from a solar cell’s surface.

However, previous attempts to use the nanotubes had been thwarted by two problems.

The first problem is that creating carbon nanotubes generates a mix of two types, some of which act as semiconductors and some as metals.

The new research has shown that the effects of these two types tend to be different. 

The second problem is that nanotubes clump up together, which reduces their effectiveness.

Graduate students Xiangnan Dang and Hyunjung Yi – working with Angela Belcher, the W. M. Keck Professor of Energy, and several other researchers – found that a genetically engineered version of a virus called M13 can be used to control the arrangement of the nanotubes on a surface, keeping the tubes separate so they cannot short out the circuits.

The system the researchers tested used a type of solar cell called dye-sensitized solar cells, which is a lightweight and inexpensive type where the active layer is composed of titanium dioxide.

The researchers said the same technique could be applied to the types as well. 

During the study the team enhanced the power conversion efficiency to 10.6 percent from 8 percent by adding the virus-built structures.

This improvement takes place even though the viruses and the nanotubes make up just 0.1 percent by weight of the finished cell.

“A little biology goes a long way,” Angela Belcher said in a press release.

The first step is for the energy of the light to knock electrons loose from the solar-cell material.  After this, those electrons need to be funneled toward a collector, from which they can form a current that flows to charge a battery or power a device.

The team has previously used differently engineered versions of the same virus to enhance the performance of batteries and other devices.  However, Belcher said that the method used to enhance solar cell performance is different.

The research was funded by the Italian company Eni, through the MIT Energy Initiative’s Solar Futures Program. 

It was published online this week in the journal Nature Nanotechnology.

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Image Caption: In this diagram, the M13 virus consists of a strand of DNA (the figure-8 coil on the right) attached to a bundle of proteins called peptides “” the virus coat proteins (the corkscrew shapes in the center) which attach to the carbon nanotubes (gray cylinders) and hold them in place. A coating of titanium dioxide (yellow spheres) attached to dye molecules (pink spheres) surrounds the bundle. More of the viruses with their coatings are scattered across the background. Image: Matt Klug, Biomolecular Materials Group 

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On the Net:

• MIT
• Nature Nanotechnology
• Angela Belcher
• Biomolecular Materials Group
• MIT Energy Initiative

The British government said this week that a species of parakeet which threatens wildlife and crops will be removed from the wild.

The Department for Environment, Food and Rural Affairs (DEFRA) said in a statement that the monk parakeet was an invasive species.

It announced measures to either rehouse the birds, remove their nests or shoot them.

DEFRA said there are about 100 of the birds in the U.K., mainly in the southeast of England.

DEFRA said that they have the potential to threaten “national infrastructure,” even though they have not caused any damages yet.

It said extensive damage to crops had been reported in both North and South America, and the birds could cause power cuts when their nests were built on electricity pylons.

A spokesman for DEFRA said it would try to rehouse the birds in aviaries and if that fails their nests would be moved.

“In extreme cases, it could mean we have to shoot some, but we haven’t tried that yet,” he said.

The 1ft-tall parakeet builds huge communal nests and are identified by their green body, yellowish belly, pale grey face and breast and pale bill.

“Control work is being carried out as part of a DEFRA initiative to counter the potential threat monk parakeets pose to critical national infrastructure, crops and native British wildlife,” a DEFRA spokesman said in a statement.

“This invasive species has caused significant damage in other countries through nesting and feeding activity and we are taking action now to prevent this happening in the UK.”

A spokesman for the RSPB bird conservation group said “Our understanding is that they are going to be brought into captivity; we don’t see it’s necessary for them to be culled.

“We’re happy action is taking place in that they’re being removed from the wild.

“It’s a small population at large, as the birds are colonial and are concentrated in one or two sites, so it will be possible to deal with as we think it could be a problem.”

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On the Net:

• DEFRA

Berkeley Lab nuclear scientists join with their international colleagues in the latest record-breaking discovery at RHIC

Eighteen examples of the heaviest antiparticle ever found, the nucleus of antihelium-4, have been made in the STAR experiment at RHIC, the Relativistic Heavy Ion Collider at the U.S. Department of Energy’s Brookhaven National Laboratory.

“The STAR experiment is uniquely capable of finding antihelium-4,” says the STAR experiment’s spokesperson, Nu Xu, of the Nuclear Science Division (NSD) at Lawrence Berkeley National Laboratory (Berkeley Lab). “STAR already holds the record for massive antiparticles, last year having identified the anti-hypertriton, which contains three constituent antiparticles. With four antinucleons, antihelium-4 is produced at a rate a thousand times lower yet. To identify the 18 examples required sifting through the debris of a billion gold-gold collisions.”

Collisions of energetic gold nuclei inside STAR briefly recreate conditions in the hot, dense early universe only millionths of a second after the big bang. Since equal amounts of matter and antimatter were created in the big bang they should have completely annihilated one another, but for reasons still not understood, only ordinary matter seems to have survived. Today this excess matter forms all of the visible universe we know.

Roughly equal amounts of matter and antimatter are also produced in heavy-ion (gold nuclei) collisions at RHIC. The resulting fireballs expand and cool quickly, so the antimatter can avoid annihilation long enough to be detected in the Time Projection Chamber at the heart of STAR.

Ordinary nuclei of helium atoms consist of two protons and two neutrons. Called alpha particles when emitted in radioactive decays, they were found in this form by Ernest Rutherford well over a century ago. The nucleus of antihelium-4 (the anti-alpha) contains two antiprotons bound with two antineutrons.

The most common antiparticles are generally the least massive, because it takes less energy to create them. Carl Anderson was the first to find an antiparticle, the antielectron (positron), in cosmic ray debris 1932. The antiproton (the nucleus of antihydrogen) and the antineutron were created at Berkeley Lab’s Bevatron in the 1950s. Antideuteron nuclei (“anti-heavy-hydrogen,” made of an antiproton and an antineutron) were created in accelerators at Brookhaven and CERN in the 1960s.

Each extra nucleon (called a baryon) increases the particle’s baryon number, and in the STAR collisions every increase in baryon number decreases the rate of yield roughly a thousand times. The nuclei of the antihelium isotope with only one neutron (antihelium-3) has been made in accelerators since 1970; the STAR experiment produces many of these antiparticles, having baryon number 3. The antihelium nucleus with baryon number 4, just announced by STAR based on 16 examples identified in 2010 and two examples from an earlier run, contains the most nucleons of any antiparticle ever detected.

“It’s likely that antihelium will be the heaviest antiparticle seen in an accelerator for some time to come,” says STAR Collaboration member Xiangming Sun of Berkeley Lab’s NSD. “After antihelium the next stable antimatter nucleus would be antilithium, and the production rate for antilithium in an accelerator is expected to be well over two million times less than for antihelium.”

NSD’s Maxim Naglis adds, “Finding even one example of antilithium would be a stroke of luck, and would probably require a breakthrough in accelerator technology.”

If antihelium made by accelerators is rare, and heavier antiparticles rarer still, what of searching for these particles in space? The Alpha Magnetic Spectrometer (AMS) experiment, scheduled to be launched on one of the last space-shuttle missions to the International Space Station, is an instrument designed to do just that. A principal part of its mission is to hunt for distant galaxies made entirely of antimatter.

“Collisions among cosmic rays near Earth can produce antimatter particles, but the odds of these collisions producing an intact antihelium nucleus are so vanishingly small that finding even one would strongly suggest that it had drifted to Earth from a distant region of the universe dominated by antimatter,” explains Hans Georg Ritter of Berkeley Lab’s NSD. “Antimatter doesn’t look any different from ordinary matter, but AMS finding just one antihelium nucleus would suggest that some of the galaxies we see are antimatter galaxies.”

Meanwhile the STAR experiment at RHIC, which has shown that antihelium does indeed exist, is likely to hold the world record for finding the heaviest particle of antimatter for the foreseeable future.

This work was supported by the DOE Office of Science.

NOTES:

STAR’s Time Projector Chamber is a cylinder filled with dilute gas and placed in a uniform (solenoidal) magnetic field (STAR stands for Solenoidal Tracker at RHIC). Charged particles created in beam collisions ionize the gas as they streak through it; how much the trails bend in the magnetic field reveals their momentum. Detecting antihelium also depends on measuring particle mass, which can be learned from how much energy the particles lose in flight and how long it takes them to reach the sides of the cylinder.

A series of “event triggers” picks out particles matching the specifications of those the researchers are looking for. The data generated by STAR travel to the National Energy Research Scientific Computing Center (NERSC), managed by Berkeley Lab, via DOE’s high-bandwidth Energy Sciences Network (ESnet).

Time projection chambers were invented by David Nygren of Berkeley Lab’s Physics Division and are used at accelerators around the world; the time-projection-chamber principle inspired the original proposals for the STAR experiment within Berkeley Lab’s NSD. STAR’s Time Projection Chamber was designed by NSD’s Howard Wieman, built by Berkeley Lab physicists and engineers, and shipped to Brookhaven on a C-5 cargo plane.

The installation of a large time-of-flight detector in 2009 added measurement capabilities to STAR that were vital to the identification of antihelium-4. It was constructed jointly by U.S. and Chinese institutions and jointly funded by DOE’s Office of Science and the National Natural Science Foundation of China, China’s Ministry of Science and Technology, and the Chinese Academy of Sciences.

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Image 1: Roughly equal amounts of matter and antimatter are created in the collision of energetic gold nuclei inside STAR, but because the fireball expands and cools quickly, antimatter can survive longer than that created in the big bang. In this collision an ordinary helium-4 nucleus (background) is matched by a nucleus of antihelium-4 (foreground). Credit: STAR Collaboration and Lawrence Berkeley National Laboratory

Image 2: The track of an antihelium-4 nucleus, highlighted in red, appears in a myriad of tracks produced by a gold-gold collision inside the STAR detector at RHIC. STAR’s Time Projection Chamber measures the momentum and mass of the collision events, which are sifted to select particles with specific characteristics. Credit: STAR Collaboration

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On the Net:

• DOE/Lawrence Berkeley National Laboratory
• For more about the discovery of the antihelium-4 nucleus, read the Brookhaven press release

Researchers from six countries are in the Arctic studying the potential role that soot, or black carbon, has on the rapidly changing Arctic climate.

Although the Arctic is typically viewed as a vast white wasteland, scientists believe a thin layer of soot is causing it to absorb more heat. They want to find out if that is the main reason for the recent rapid warming of the Arctic, which could have an impact on the world’s climate for years to come.

Black carbon is produced by vehicle engines, aircraft emissions, burning forests and wood- and coal-burning stoves.

“Carbon is dark in color and absorbs solar radiation, much like wearing a black shirt on a sunny day. If you want to be cooler, you would wear a light-colored shirt that would reflect the sun’s warmth,” said Tim Bates, a research chemist at NOAA’s Pacific Marine Environmental Laboratory (PMEL) in Seattle and co-lead of the U.S. component of the study.

“When black carbon covers snow and ice, the radiation is absorbed, much like that black shirt, instead of being reflected back into the atmosphere,” explained Bates.

Scientists from The United States, Norway, Russia, Germany, Italy and China are a participating in the Coordinated Investigation of Climate-Cryosphere Interactions (CICCI) project. The team’s goals are to coordinate more than a dozen research activities so they are done in tandem providing, for the first time, a vertical profile of black carbon’s movement through the atmosphere, its deposition on snow and ice surfaces, and its affect on warming in the Arctic.

“The Arctic serves as the air conditioner of the planet,” said Patricia Quinn of the National Oceanic and Atmospheric Administration (NOAA), and research chemist at Pacific Marine Environmental Laboratory (PMEL).

Heat from other regions of the Earth moves to the Arctic via circulating air and ocean currents, where some of that warmth does radiate into space along its journey. At the same time, some of the incoming heat from the sun that tends to be absorbed in other regions is reflected by ice and snow, allowing the polar regions to help cool the planet.

But soot in the Arctic could be changing that game.

In recent years, the Arctic has been warming more rapidly than other areas of the planet and the “warming of the Arctic has implications not just for polar bears, but for the entire planet,” Quinn told the Associated Press (AP).

“We need to better understand the behavior of black carbon in the Arctic,” said Quinn. “This coordinated study will give us a snapshot so we can see all of it at once.”

For the NOAA part of the study, called Soot Transport, Absorption, and Deposition Study (STADS), conducted between April 7 and May 6, researchers are using two small unmanned aircraft outfitted with sensors to take samples of the air in the Arctic. 

The aircraft will measure aerosol size, number, light absorption and chemical composition. A PMEL sensor will also be outfitted on the aircraft for the first time.

Also, a Norwegian unmanned aircraft will measure incoming radiation from the sun and the reflectivity of snow and ice covered surfaces.

NOAA will also collect falling and newly fallen snow to check levels of black carbon and for chemical tracer analysis. Chemical tracers yield information on the source of the black carbon, which is necessary for creating strategies on how best to deal with the impact black carbon has on the Arctic climate.

Also, Robert Stone of the Cooperative Institute for Research in Environmental Sciences will lead a study to measure reflectivity using a snowmobile-pulled sled on Svalbard at the Holtadalfohna Plateau, Kongsfjord fast ice, and the sea ice north of Spitsbergen.

Cutting carbon dioxide and other greenhouse gases is the mainstay of any effort to fight global warming, especially within the Arctic, said Quinn.

But studies suggest that cutting the concentration of short-lived pollutants, such as soot, will reduce the rate of warming in the Arctic faster than cuts in carbon dioxide and other greenhouse gases, which last much longer in the atmosphere, she said.

The UN Environmental Program urged for cuts in soot emissions in February. The call came for a variety of reasons, including the threat to human health from inhaling it and the potential warming of the polar regions.

The Arctic Council, which represents eight countries that border the Arctic, is deciding whether to seek reductions in soot from other nations and will be using data from the new research project to help make its decisions.

The surface air temperature in the Arctic has increased about twice as fast as the global average rate over the past 100 years, Quinn told AP in an interview by email. “Over the past 50 years, annual average surface air temperatures have increased from 2 to 3 degrees Celsius (3.6 to 5.4 degrees Fahrenheit) in Alaska and Siberia. The annual average temperature globally has increased by about 0.7 degree C (1.3 F) over the same time period.”

The Arctic warming has resulted in an earlier spring melt, a longer melting season, and a decrease in the extent of sea ice, she said. That raises concerns for polar bears, which depend on sea ice to hunt for food. When the highly reflective snow and ice melt, the darker surfaces of land and water that are beneath absorb more heat, adding to the growing global warming problem.

Soot’s greatest effect in the Arctic is likely to be warming caused by the particles floating in the atmosphere, according to Jack Dibb, an atmospheric chemist at the University of New Hampshire. It may also reduce the reflectivity of the snow and ice enough to cause warming, but that is going to be harder to document, he said in a telephone interview with AP.

The NOAA team includes leaders Bates and Quinn, as well as PMEL engineers Scott Stalin, Nick Delich, and Dirk Tagawa; Joint Institute for the Study of Atmosphere and Ocean scientists Jim Johnson and Drew Hamilton, and NOAA scientist Derek Coffman.

Participating institutions and research centers include the Arctic and Antarctic Research Institute, the Alfred Wegner Institute, the Institute of Atmospheric Sciences and Climate of the Italian National Research Council, the Chemistry Department of Florence University, the Norwegian Institute for Air Research, the Northern Research Institute, the Norwegian Institute for Polar Research, and the Chinese Academy of Meteorological Sciences.

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Image 2: Trish Quinn shows off the first snow pit. Credit: NOAA-STAD

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On the Net:

• NOAA Pacific Marine Environmental Laboratory
• Coordinated Investigation of Climate-Cryosphere Interactions Project
• Soot Transport, Absorption, and Deposition Study
• Cooperative Institute for Research in Environmental Sciences
• UN Environmental Program
• Arctic Council
• Joint Institute for the Study of Atmosphere and Ocean

The harmful effects of ozone that exist at low levels in the earth’s atmosphere can be reduced when charging is done at night for electric vehicles, a new study has found.

In the stratosphere, ozone becomes a protective layer of film that filters out ultraviolet rays that can cause skin cancer and DNA mutations in plants, reports AFP.

However, ozone that is formed from the reaction between hydrocarbons and nitrogen oxide with sunlight can irritate the airways of people with cardiac or respiratory, in addition to harming sensitive plants.

The popularity of Plug-in Hybrid Electric Vehicles (PHEVs) resulted from high gasoline fuel costs, increased inefficiency, and positive impact on the environment due to the lack of exhaust fumes.

It is already known that charging PHEVs at night is much more cost-effective and reliable, and research has also found that nighttime charging can lead to lower levels of pollution on average.

Researchers at the Massachusetts Institute of Technology (MIT) and the University of Texas published their study in IOP Publishing’s journal Environmental Research Letters. They modeled the effects of replacing 20% of the vehicle miles travelled (VMT) by gasoline-run cars with PHEVs.

In the study, their computer model predicted the emissions of nitrogen oxides for 2018 in three different scenarios and in four major Texas cities: Dallas/Ft. Worth, Houston, Austin and San Antonio. Nitrogen oxide is the basic ingredient for ground-level ozone.

AFP reports that the power generation for this grid in 2009 was provided by 46% gas, 35% coal, 13% nuclear and 4.5% wind.

The first scenario involved charging the car at off-peak time in the night. The second scenario was based on charging to maximize battery life, which means charging just before use and only the amount of charge needed to complete the trip); and the third scenario was charging the battery when it was a convenient time for the driver, which is usually just after vehicle use.

As a result, the study showed that the overall levels of pollution were lower from the electricity generating unit emissions associated with charging than the level of pollution that resulted from emissions associated with 20% of gasoline VMT.

Although nighttime charging yielded the highest amount of nitrogen oxides, it produced the least amount of ozone on average across all the cities because there was no sunlight to react with the emissions, the study showed.

By morning, pollutants are dispersed and diluted by wind and other processes.

“The results in general show positive air quality results due to the use of PHEVs regardless of charging scenario with the nighttime charging scenario showing the best results on average by a small margin,” says lead author Dr. Tammy Thompson of MIT.

“This further supports efforts to develop regulation to encourage nighttime charging; an example would be variable electricity pricing. As more of the fleet switches over to PHEVs and a larger demand is placed on the electricity grid, it will become more important that we design and implement policy that will encourage charging behaviors that are positive for both air quality and grid reliability.”

The researchers hope that the study’s findings will guide policies on how to encourage cleaner cars.

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On the Net:

• Environmental Research Letters Article
• Massachusetts Institute of Technology
• University of Texas
• Image Courtesy Wikipedia

Lee Rannals for RedOrbit.com

Just days before Earth Day, tropical dry forests in the Brazilian state of Minas Gerais received good news as members of the Superior Court of Minas Gerais overturned a state law that altered the status of the 6,000 square-mile forest’s protection.

The tropical dry forests can thank a project called Tropi-Dry for the success of overturning the law that left the area unprotected from logging.

The effort taken by these scientists rings of truth that man can still make a difference on this planet.  The state law that was overturned would have allowed a 70 percent clearing of Minas Gerais’ forests.

However, despite the victory in Minas Gerais, many of the world’s forests still face the threat of deforestation.

A National Geographic report said that land the size of Panama is stripped of its trees each year.

According to NASA, about half of all species on Earth live in only about 7 percent of the Earth’s tropical forests.

Experts believe that in less than 40 years, our planet has lost 8 percent of its rainforests.

Brazil led the pack of countries between the years of 1990 and 2005 by clearing over 42 million hectares of tropical forest regions. 

Let us all take an extra step this Earth Day by learning a little bit more about what we can do to help stop deforestation.

How can I help?

The simplest step to take for most would be to recycle the paper we use on a daily basis. 

According to A Recycling Revolution, if every American recycled just one-tenth of their newspapers, we would save about 25,000,000 trees a year.

The same source also said that about 1 billion trees worth of paper are thrown away every year in the U.S.

One step further would be to do more research into companies to determine which ones plant trees in place of those that were cut down to help print that receipt you threw away.

Though deforestation remains a problem, acts taken by projects like Tropi-Dry deserve a big thumbs-up for helping this Earth Day look a little greener.

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Image Caption: A Brazilian tropical dry forest during the rainy season, which can last 4-6 months. Credit: Diego Brandao

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On the Net:

• Earth Day 2011
• Tropi-Dry
• National Geographic
• NASA
• A Recycling Revolution

Federal wildlife officials said on Friday that they will take over 1,300 gray wolves in the Northern Rockies off the endangered species list in the next 60 days.

An attachment to the budget bill signed into law Friday by President Barack Obama has taken away the wolves’ protection in five Western states.

This will be the first time Congress has taken a species off the endangered list.

Idaho and Montana are planning public wolf hunts this fall.  The states had a similar mindset last year until a judge ruled that the species still remained at risk.

Wolves in Wyoming are still at risk because of its shoot-on-sight law for the canine-species.

Oregon and Washington have not announced immediate plans to hunt the wolf populations.