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Monday, May 25, 2015

Special Fats Proven Essential for Brain Growth

Research led by a Duke-NUS Graduate Medical School Singapore (Duke-NUS) scientist has proved that certain special fats found in blood are essential for human brain growth and function.

Duke-NUS Associate Professor David Silver co-led two Nature Genetics published studies which showed that mutations in the protein Mfsd2a causes impaired brain development in humans. Mfsd2a is the transporter in the brain for a special type of fat called lysophosphatidylcholines (LPCs) -- composed of essential fatty acids like omega-3. These studies show, for the first time, the crucial role of these fats in human brain growth and function.

The difference between a brain with a normal Mfsd2a gene and a brain with a mutated Mfsd2a gene.
Credit: Duke University

In the first study, two families in Libya and Egypt with Mfsd2a mutations were identified with severely reduced brain size, or microcephaly. Their mutations eliminated Mfsd2a's ability to transport LPCs, which meant not enough LPCs were absorbed by the brain. In these families, children affected by these mutations died between one and six years of age. The study not only establishes a link between the transport of LPCs by Mfsd2a and human brain growth and function, it is also the first time a genetic disease has been related to LPC transport in humans. The research was co-led by senior author Professor Joseph Gleeson from Rockefeller University.

In a second, separate study, a family in North Pakistan was found to have another type of mutation in the Mfsd2a gene which reduced its transport activity. The individuals with this mutation also had microcephaly, but in this case it was not lethal. However, they did have intellectual disabilities, impaired control of their limbs, and absent speech. Like the first study, findings are proof of the importance of LPCs in brain development and function. The research was co-led by senior author Professor Andrew H. Crosby from Exeter University.

In 2014, Dr. Silver published a landmark study in Nature which served as a basis for these two studies. He and his team discovered that Mfsd2a is the transporter for LPCs. Prior to this breakthrough, LPCs were known to be found at high concentrations in our blood but their function was a mystery. Dr. Silver's team showed that mice genetically engineered without Mfsd2a failed to transport LPCs into their brains - which resulted in microcephaly. 

Since DHA deficiency in animals does not result in microcephaly, this meant that LPCs are critical factors in brain growth and function. Also, while it was previously believed the brain made all the fat it needed, Dr. Silver's research showed that LPCs are transported there from the blood past the blood-brain barrier. His work with Rockefeller and Exeter prove this in humans.

"Our work confirms the essential role of LPCs in brain development and function in humans, and indicates that brain uptake of LPCs during foetal development and in adult life is important," said Dr. Silver, co-lead on both studies, based in the Cardiovascular and Metabolic Disorders Programme at Duke-NUS. 

"Now we are studying the functions of LPCs in the brain, and the implications for application are very exciting. We might be able to develop therapeutics in the future that could prevent and treat neurological disorders, and improve brain growth and function. We may even be able to target better brain nutrition for babies, mothers, and the aged."


Contacts and sources: 
Dharshini Subbiah
Duke University 

11 New Species Discovered in Madagascar

Madagascar is home to extraordinary biodiversity, but in the past few decades, the island's forests and associated biodiversity have been under greater attack than ever. Rapid deforestation is affecting the biotopes of hundreds of species, including the panther chameleon, a species with spectacular intra-specific colour variation. 

Shown here is a panther chameleon.
Credit: © Michel Milinkovitch

A new study by Michel Milinkovitch, professor of genetics, evolution, and biophysics at the University of Geneva (UNIGE), led in close collaboration with colleagues in Madagascar, reveals that this charismatic reptilian species, which is only found in Madagascar, is actually composed of eleven different species. The results of their research appear in the latest issue of the Molecular Ecologyjournal. They also discuss the urgent need to protect Madagascar's habitats.

In collaboration with professor Achille Raselimanana of the University of Antananarivo, researchers from the Department of Genetics and Evolution in the UNIGE Faculty of Sciences, led by Michel Milinkovitch, sought to find the genetic keys behind panther chameleon's incredible colour palette. Their analyses, performed on site in Madagascar, reveal the presence of 11 rather than a single species.

A Talkative Drop of Blood

It took two expeditions led from East to West for the scientists to collect a drop of blood from each of 324 individuals and document them through colour photographs. The DNA (mitochondrial and nuclear) of each of the specimens were sequenced and analysed in the laboratory according to the hypothesis that a chameleon's dominant colour might be related to the geographic zone where it is found. Most importantly, the genetic material indicated strong genetic structure among geographically-restricted lineages, revealing very low interbreeding among populations.

Shown here is a panther chameleon.
Credit: © Michel Milinkovitch

A Key for Turning Genetics into Color

The mathematical analyses of the 324 colour photographs demonstrated that subtle colour patterns could efficiently predict assignment of chameleon individuals to their corresponding genetic lineage, confirming that many of the geographical populations might need to be considered separated species. The scientists then simplified their analyses of the colour diversity into a classification key, which allows to link most chameleons to their corresponding species using only the naked eye. This case of hidden speciation confirms a major characteristic of Madagascar: it is amongst the most diverse places for life on Earth; a biodiversity hotspot.

Madagascar, Unique but Precarious Conservatory

Each of the new chameleon species requires individual management, given that they each constitute a different part of the biodiversity of the whole. The visual classification key devised by the researchers could assist local biologists and trade managers to avoid local population over-harvesting. The task of biodiversity management is daunting because of the widespread destruction of the forest habitat for agricultural practices as well as for firewood and charcoal production by populations with very low living standards. These human activities threaten the survival of 400 species of reptile, 300 species of amphibians, 300 species of birds, 15,000 species of plants and countless species of invertebrates. In addition, approximately 80 to 90% of all living species found in Madagascar are endemic, meaning they exist nowhere else on earth.

Given the charismatic nature of chameleons, Milinkovitch hopes that, beside a better understanding of the genetic basis of colour variation in chameleons, his collaborative study with his Malagasy colleagues will help his colleague, Professor Raselimanana, to continue his difficult enterprise: raising awareness for the staggering but fragile biodiversity hosted by Madagascar.


Contacts and sources:
Michel Milinkovitch
University of Geneva (UNIGE)

From Chicken To Dinosaur: Scientists Experimentally Reverse The Evolution Of The Perching Toe

Aunique adaptation in the foot of birds is the presence of a thumb-like opposable toe, which allows them to grasp and perch. However, in their dinosaur ancestors, this toe was small and non- opposable, and did not even touch the ground, resembling the dewclaws of dogs and cats. 
Remarkably, the embryonic development of birds provides a parallel of this evolutionary history: The toe starts out like their dinosaur ancestors, but then its base (the metatarsal) becomes twisted, making it opposable. Brazilian researcher Joâo Botelho, working at the lab of Alexander Vargas at the University of Chile, decided to study the underlying mechanisms. Botelho observed that the twisting occurred shortly after the embryonic musculature of this toe was in place.
Credit: University of Chile
“This is one of the clearest examples of how indirect the morphological consequences of genetic change are mediated”, Gunter Wagner, evolutionary geneticist and professor at Yale.
Bird embryos move a lot inside the egg during development, and the onset of movement at this toe coincided with the twisting of its base. Botelho also demonstrated that in this toe, genes of cartilage maturation were expressed at a much later stage than other digits: It retains many rapidly dividing stem cells for a much longer period. Such immature cartilage is highly plastic and easily transformed by muscular activity.

These observations suggested the toe is twisted as a result of mechanical forces imposed on it by the embryonic musculature. Definitive proof, however, would come from experiments. When Botelho applied Decamethonium bromide, a pharmacological agent capable of paralyzing embryonic musculature, the result was a non-opposable toe with a straight, non-twisted base identical to that of their dinosaur ancestors. 
Only a few experiments are known to recover dinosaur traits in birds (such as a dinosaur-like shank and tooth-like structures). The undoing of the perching digit is thus an important new addition, and the results have now been published in Scientific Reports, an open-access journal of the Nature Publishing Group.

The significance of this experiment, however, goes beyond the fact that a dinosaur-like toe is being retrieved. Evolutionary research often centers on mutations, but the development and evolution of the perching toe cannot be understood without the forces of embryonic muscular activity. 
The study is described as “true developmental mechanics” by Gunter Wagner, an evolutionary geneticist and professor at Yale. “This is one of the clearest examples of how indirect the morphological consequences of genetic change are mediated. The experiments prove that interactions about organ systems channel the directions of organismal evolution.” 


Contacts and sources:
University of Chile

Citation: João Francisco Botelho,Daniel Smith-Paredes, Sergio Soto-Acuña,Jorge Mpodozis, Verónica Palma & Alexander O. Vargas, “Skeletal plasticity in response to embryonic muscular activity underlies the development and evolution of the perching digit of birds”, Scientific Reports, 5, Article number: 9840, published 14 may 2015. doi:10.1038/srep09840. Link to article, images and supplementary info: http://www.nature.com/srep/2015/150514/srep09840/full/srep09840.html

The Viking's Grave and the Sunken Ship

Mapping archaeological digs takes plenty of time and a lot of measuring, photographing, drawing and note taking. Now, most of this work can be done with a technique called photogrammetry.

Photogrammetry is a method that uses two-dimensional images of an archaeological find to construct a 3D model.

Detailed image of a shield boss found in what is likely a Viking’s grave in Skaun. 
Photo: NTNU University Museum

You don’t need and special glasses or advanced equipment to use make use of this new technique. Together with precise measurements of the excavation, photogrammetry can create a complete detailed map of an archaeological excavation site.

“This is still a very new technique,” say archaeologists Raymond Sauvage and Fredrik Skoglund of the Norwegian University of Science and Technology's University Museum.

Photogrammetry is in many ways much more precise than older, more time-consuming methods.

Viking graves
This method is already being put to use by archaeologists. When a possible Viking grave was found in Skaun in Sør-Trøndelag in 2014, the excavation site was mapped using photogrammetry.

The manner in which artefacts are found, how deeply the are buried and where they are placed in relation to each other can provide a lot of information to archaeologists studying a site.

A Viking archaeological site

Credit: NTNU

Photogrammetry also makes it easier for archaeologists to share their findings with others. The 3D models that are produced can be saved as normal PDF files, which can be sent to colleagues for input.

Saving time
The two archaeologists are very enthusiastic. A Russian company has developed the program that they’re using at the museum. The program is easy to use and gives good results. The development and use of the technique has exploded in recent years.

“There’s a lot more interest in photogrammetry now. The new program is readily available and inexpensive,” says Sauvage.

He explains that it provides the kind of quality and detail that you could only dream of a few years ago. Even though the method requires some work, it still saves a lot of time.
“In one day, you can get three million measurement points. Before, we were satisfied with 3000,” he says.

And those 3000 points could take a long time to find. This method can save archaeologists weeks of work with tape measures, sketching paper and cameras. The practical work in the field goes much quicker.

“This frees up a lot more time for things like research,” Skoglund says.

Old finds
Similar results have been achieved in the past using laser equipment and early versions of a photogrammetry program. But this has been very expensive, and takes a lot of time and resources.

The new program only costs a few hundred euros, meaning that it is much more widely available.

With a photogrammetry program, three or four pictures from different angles are enough to make a simple 3D model, although more images will provide a higher quality model. You can use any normal camera.

“The more images, the better the quality,” Sauvage says.

It is also possible to use images of old finds to build a 3D model based on them. For example, you could make a model using photos from previous excavations of Viking graves, and use this to explore how an excavation site changes over time.

Shipwreck
Marine archaeologist Skoglund has tried this with the Dutch ship “De Grawe Adler” (the Grey Eagle), which sank in 1696 by Strømsholmen in Hustadvika, on the coast of central Norway and was discovered in 1982 when dredging for sand destroyed parts of the ship.

“I swam along the whole length of the wreck a few years ago and took pictures,” Skoglund says.

He did so with out ever considering the possibility of making a 3D model of the wreck. The fact that the photos were taken underwater makes it slightly harder to put them together, but it is by no means impossible.

If the results are precise enough, they can be used to monitor the decomposition of the ship. Finds under water tend to be particularly fragile, but decomposition can be difficult to see. You can’t just dive down every few years to make sure that everything is OK. With this new method, the decomposition can be measured much more precisely, and appropriate protection measures can be put in place.

The future
The next step is likely to be able to put on a pair of 3D-glasses and virtually walk into an excavation site, although that may be a few years in coming.

There is one challenge, however — storing measurements digitally in a manner that will be useful for generations to come. Archaeologists working today are behind measurements and notes on excavations that may be used hundreds of years in the future. A paper photo taken 100 years ago is just as good now as it was then, as long as you have it on hand. But nobody knows if a PDF file will be of use in year 2115. But this is a challenge facing all information that is stored digitally. And it’s something that we can’t overcome.


Contacts and sources:

Go Fish! Ancient Birds Evolved Specialist Diving Adaptations

A new study of some primitive birds from the Cretaceous shows how several separate lineages evolved adaptations for diving.

Living at the same time as the dinosaurs, Hesperornithiform bird fossils have been found in North America, Europe and Asia in rocks 65–95 million years old. Dr Alyssa Bell and Professor Luis Chiappe of the Dinosaur Institute, Natural History Museum of Los Angeles County, publishing in the Journal of Systematic Palaeontology, have undertaken a detailed analysis of their evolution, showing that separate lineages became progressively more adept at diving into water to catch fishes, like modern day loons and grebes.

Evolution of diving specializations within the Hesperornithiformes.
Credit:   Taylor & Francis

The Hesperornithiformes are a highly derived but very understudied group of primitive birds from the Cretaceous period. This study is the first comprehensive phylogenetic analysis, or evaluation of evolutionary relationships, to ever be undertaken on the entire group.

The results of this study confirm that the Hesperornithiformes do form a single group (or clade), but that within this group the inter-relationships of the different taxa are more complex than previously thought. Additionally, this study finds that anatomical changes were accompanied by enlargement in overall body size, which increased lung capacity and allowed deeper diving.

Overall, this study provides evidence for understanding the evolution of diving adaptations among the earliest known aquatic birds.


Contacts and sources:
Taylor & Francis

Researchers Find The 'Key' To Quantum Network Solution

Scientists at the University of York’s Centre for Quantum Technology have made an important step in establishing scalable and secure high rate quantum networks.

Working with colleagues at the Technical University of Denmark (DTU), Massachusetts Institute of Technology (MIT), and the University of Toronto, they have developed a protocol to achieve key-rates at metropolitan distances at three orders-of-magnitude higher than previously.

Credit: Quantum Theory - Full Documentary HD

Standard protocols of Quantum Key Distribution (QKD) exploit random sequences of quantum bits (qubits) to distribute secret keys in a completely secure fashion. Once these keys are shared by two remote parties, they can communicate confidentially by encrypting and decrypting binary messages. The security of the scheme relies on one of the most fundamental laws of quantum physics, the uncertainty principle.

Today's classical communications by email or phone are vulnerable to eavesdroppers but quantum communications based on single particle levels (photons) can easily detect eavesdroppers because they invariably disrupt or perturb a quantum signal. By making quantum measurements, two remote parties can estimate how much information an eavesdropper is stealing from the channel and can apply suitable protocols of privacy amplification to negate the effects of the information loss.

However, the problem with QKD protocols based on simple quantum systems, such as single-photon qubits, is their low key-rate, despite their effectiveness in working over long distances. This makes them unsuitable for adaptation for use in metropolitan networks.

The team, led by Dr Stefano Pirandola, of the Department of Computer Science at York, overcame this problem, both theoretically and experimentally, using continuous-variable quantum systems. These allow the parallel transmission of many qubits of information while retaining the quantum capability of detecting and defeating eavesdroppers. The research is published in Nature Photonics.

Dr Pirandola said: “You want a high rate and a fast connection particularly for systems that serve a metropolitan area. You have to transmit a lot of information in the fastest possible way; essentially you need a quantum equivalent of broadband.

“Continuous-variable systems can use many more photons but are still quantum based. Our system reaches extremely high speeds by three orders of magnitude higher than ever before over a distance of 25 kilometres. Its effectiveness above that distance decreases rapidly however.

“Nevertheless, our protocol could be used to build high-rate quantum networks where devices securely connect to nearby access points or proxy servers.”

Dr Pirandola was funded by the Engineering and Physical Sciences Research Council.

The University of York leads a unique collaboration to exploit fundamental laws of quantum physics for the development of secure communication technologies and services for consumer, commercial and government markets.

The Quantum Communications Hub is one of four in the EPSRC’s new £155m National Network of Quantum Technology Hubs.

Contacts and sources:
University of York


Citation:  The paper ‘High-rate measurement-device independent quantum cryptography’ by Stefano Pirandola, Carlo Ottaviani, Gaetana Spedalieri, Christian Weedbrook, Samuel L Braunstein, Seth Lloyd, Tobias Gehring, Christian S Jacobsen and Ulrik L Andersen is published in Nature Photonics.

Friday, May 22, 2015

First Drug Approved For Radiation Exposure

As a result of research performed by scientists at the University of Maryland School of Medicine (UM SOM), the U.S. Food and Drug Administration has approved the use of a drug to treat the deleterious effects of radiation exposure following a nuclear incident. The drug, Neupogen®, is the first ever approved for the treatment of acute radiation injury.


Credit: Oregon State University

The research was done by Thomas J. MacVittie, PhD, professor, and Ann M. Farese, MA, MS, assistant professor, both in the University of Maryland School of Medicine (UM SOM) Department of Radiation Oncology's Division of Translational Radiation Sciences. The investigators did their research in a non-human clinical model of high-dose radiation.

"Our research shows that this drug works to increase survival by protecting blood cells," said Dr. MacVittie, who is considered one of the nation's leading experts on radiation research. "That is a significant advancement, because the drug can now be used as a safe and effective treatment for the blood cell effects of severe radiation poisoning."

Radiation damages the bone marrow, and as a result decreases production of infection-fighting white blood cells. Neupogen® counteracts these effects. The drug, which is made by Amgen, Inc., was first approved in 1991 to treat cancer patients receiving chemotherapy. Although doctors may use it "off label" for other indications, the research and the resulting approval would speed up access to and use of the drug in the event of a nuclear incident.

This planning is already under way. In 2013, the Biomedical Advanced Research and Development Authority (BARDA), an arm of the Department of Health and Human Services, bought $157 million worth of Neupogen® for stockpiles around the country in case of nuclear accident or attack.

Neupogen® is one of several "dual-use" drugs that are being examined for their potential use as countermeasures in nuclear incidents. These drugs have everyday medical uses, but also may be helpful in treating radiation-related illness in nuclear events. Dr. MacVittie and Ms. Farese are continuing their research on other dual-use countermeasures to radiation. They are now focusing on remedies for other aspects of radiation injury, including problems with the gastrointestinal tract and the lungs.

The research builds on 40 years of work that Dr. MacVittie and his team have conducted in the field of radiation research, during which they have helped to define the field. The Neupogen study is also part of a broad portfolio of research being conducted by faculty in the Department of Radiation Oncology. Among these are Minesh Mehta, MD, the medical director of the Maryland Proton Treatment Center, who is focusing on research into thoracic oncology, neuro-oncology, integrating imaging advances with radiation therapy, and innovative applications of new radiation therapy technologies to test biological concepts. 

Another researcher in the department is Zeljko Vujaskovic, MD, PhD, director of the Division of Translational Radiation Sciences; he is doing research on identifying potential biomarkers predicting individual patient risk for injury, and to develop novel therapeutic interventions/strategies to prevent, mitigate, or treat radiation injury.

"In terms of both research and treatment, our department is leading the way in developing the most effective discovery-based clinical applications to help protect and heal patients," says William F. Regine, MD, professor and Isadore & Fannie Schneider Foxman Endowed Chair in Radiation Oncology at the UM SOM.

He added that research has served as the foundation for the Department of Radiation Oncology's recent development of four clinical modalities for the treatment of cancer through radiation:

Proton Treatment, a precise approach to cancer, which targets tumors while minimizing harm to surrounding tissues. Proton treatment uses protons traveling at about two-thirds the speed of light to precisely deliver beams of radiation to the tumor. This treatment will be available in the new 110,000 sq ft Maryland Proton Treatment Center before the end of the year;

Selective Internal Radiation Therapy, a precision modality for treating patients with particularly difficult to remove tumors involving the liver such as those from colorectal cancers;

Gammapod, a new, high-precision, noninvasive method of treating early-stage breast cancer;

Thermal Therapies, the use of "heat" in treating a broad spectrum of malignancies.

"The Department of Radiation Oncology's work is just one example of how the School of Medicine is discovering innovative ways to repurpose existing drugs that are able fight a broader array of critical diseases," said Dean E. Albert Reece, MD, PhD, MBA, who is also the vice president for Medical Affairs, University of Maryland, and the John Z. and Akiko K. Bowers Distinguished Professor and Dean of the School of Medicine. "We are particularly proud of the Neupogen research as it is not only important scientifically; it is crucial for our country's public health and its national security."


Contacts and sources: 
David Kohn

Machine learning can pinpoint rodent species that harbor diseases and geographic hotspots vulnerable to new parasites and pathogens. So reports a new study in the Proceedings of the National Academy of Sciences led by Barbara A. Han, a disease ecologist at the Cary Institute of Ecosystem Studies.

Most emerging infectious diseases are transmitted from animals to humans, with more than a billion people suffering annually. Safeguarding public health requires effective surveillance tools.

A majority of new reservoir and hyper-reservoir rodent species are predicted to occur in the upper latitudes.

Credit: Han et al.


Han comments: "Historically, emerging infectious diseases have been dealt with reactively, with efforts focused on containing outbreaks after they've spread. We were interested in how machine learning could inform early warning surveillance by revealing the distribution of rodent species that are effective disease reservoirs."

With University of Georgia Odum School of Ecology colleagues John Paul Schmidt, Sarah E. Bowden, and John M. Drake, Han employed machine learning, a form of artificial intelligence, to reveal patterns in an extensive set of data on more than 2,000 rodent species, with variables describing species' life history, ecology, behavior, physiology, and geographic distribution.

The team developed a model that was able to predict known rodent reservoir species with 90% accuracy, and identified particular traits that distinguish reservoirs from non-reservoirs. They revealed over 150 new potential rodent reservoir species and more than 50 new hyper-reservoirs - animals that may carry multiple pathogens infectious to humans.

"This study shows the value of bringing new analysis techniques together with big data," commented study co-author John Drake. "By combining ecological and biomedical data into a common database, Barbara was able to use machine learning to find patterns that can inform an early warning system for rodent-borne disease outbreaks."

Flying squirrels are a known reservoir for anaplasmosis and one the 50+ hyper-reservoir species predicted to carry additional pathogens infectious to humans.
Credit: Holly B. Vuong, Cary Institute of Ecosystem Studies/Rutgers University

With Han explaining, "Results equip us with a watch list of high-risk rodent species whose intrinsic traits make them effective at carrying infections transmissible to people. Such a list is increasingly important given accelerating rates of environmental change."

Among the take home messages: rodents are not created equal in their ability to transmit disease. The riskiest reservoir species are those that mature quickly, reproduce early and often, and live northern temperate areas with low levels of biodiversity. The paper adds to the growing body of knowledge that 'pace of life' affects infection tolerance in animals.

"Biologically-speaking, species that bear as many offspring as possible in a shorter period of time may tend to invest fewer resources in immune response compared to slower-living animals. This could make certain rodent species more effective disease reservoirs," notes Han.

Geographic areas found to have a high diversity of rodent reservoirs included North America, the Atlantic coast of South America, Europe, Russia, and parts of Central and East Asia. Predicted future hotspots of rodent reservoir diversity spanned arctic, temperate, tropical, and desert biomes, including China, Kazakhstan, and the Midwestern United States. A majority of new reservoir and hyper-reservoir species are predicted to occur in the upper latitudes.

"It was surprising to find more emerging rodent-borne diseases predicted for temperate zones than the tropics--given assumptions that the tropics are where new diseases originate," Drake commented. "This result shows how data-driven discovery can correct such stereotypes."

Findings provide a basis for targeted surveillance efforts, which are vital given the cost of monitoring for emerging infectious diseases. Han notes, "Turning our predictions into preventative measures will require collaboration with experts on the ground. It's where the real work begins. A start would be to look at the newly predicted rodent reservoirs and assess which have increasing contact with people through activities like urbanization, agricultural and hunting practices, and displacement from political or climate instability."



Contacts and sources:
Lori Quillen

Human and Dog Bond Goes Back Beyond 27,000 years

Dogs' special relationship to humans may go back 27,000 to 40,000 years, according to genomic analysis of an ancient Taimyr wolf bone reported in the Cell Press journal Current Biology on May 21. Earlier genome-based estimates have suggested that the ancestors of modern-day dogs diverged from wolves no more than 16,000 years ago, after the last Ice Age.

This is an ancient Taimyr Wolf bone from the lower jaw. The animal lived approximately 27,000 to 40,000 years ago.
Credit: Love Dalén

The genome from this ancient specimen, which has been radiocarbon dated to 35,000 years ago, reveals that the Taimyr wolf represents the most recent common ancestor of modern wolves and dogs.

"Dogs may have been domesticated much earlier than is generally believed," says Love Dalén of the Swedish Museum of Natural History. "The only other explanation is that there was a major divergence between two wolf populations at that time, and one of these populations subsequently gave rise to all modern wolves." Dalén considers this second explanation less likely, since it would require that the second wolf population subsequently became extinct in the wild.

This image compares an ancient Taimyr Wolf bone from the lower jaw to a modern pipette.
Credit: Love Dalén

"It is [still] possible that a population of wolves remained relatively untamed but tracked human groups to a large degree, for a long time," adds first author of the study Pontus Skoglund of Harvard Medical School and the Broad Institute.

The researchers made these discoveries based on a small piece of bone picked up during an expedition to the Taimyr Peninsula in Siberia. Initially, they didn't realize the bone fragment came from a wolf at all; this was only determined using a genetic test back in the laboratory. But wolves are common on the Taimyr Peninsula, and the bone could have easily belonged to a modern-day wolf. On a hunch, the researchers decided to radiocarbon date the bone anyway. It was only then that they realized what they had: a 35,000-year-old bone from an ancient Taimyr wolf.

The DNA evidence also shows that modern-day Siberian Huskies and Greenland sled dogs share an unusually large number of genes with the ancient Taimyr wolf.

DNA from this small piece of a rib bone from an ancient Taimyr wolf suggests that dogs may have been domesticated 27,000 years ago.
Credit: Love Dalén

"The power of DNA can provide direct evidence that a Siberian Husky you see walking down the street shares ancestry with a wolf that roamed Northern Siberia 35,000 years ago," Skoglund says. To put that in perspective, "this wolf lived just a few thousand years after Neanderthals disappeared from Europe and modern humans started populating Europe and Asia."


Contacts and sources: 
Joseph Caputo
Cell Press

Citation: Current Biology, Skoglund et al.: "Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds" http://dx.doi.org/10.1016/j.cub.2015.04.019

Sight Without Eyes: Octopus Sees With Skin

The octopus has a unique ability. It can change the color, pattern and even texture of its skin not only for purposes of camouflage but also as a means of communication. The most intelligent, most mobile and largest of all mollusks, these cephalopods use their almost humanlike eyes to send signals to pigmented organs in their skin called chromatophores, which expand and contract to alter their appearance.

This is a a California two-spot octopus hatchling.
Credit: UCSB

A new study by UCSB scientists has found that the skin of the California two-spot octopus (Octopus bimaculoides) can sense light even without input from the central nervous system. The animal does so by using the same family of light-sensitive proteins called opsins found in its eyes -- a process not previously described for cephalopods. The researchers' findings appear in the Journal of Experimental Biology.

UCSB Researchers Study Octopus Camouflage from UC Santa Barbara on Vimeo.


"Octopus skin doesn't sense light in the same amount of detail as the animal does when it uses its eyes and brain," said lead author Desmond Ramirez, a doctoral student in the Department of Ecology, Evolution and Marine Biology (EEMB). "But it can sense an increase or change in light. Its skin is not detecting contrast and edge but rather brightness."

These are chromatophores in their contracted state (left) and at maximum expansion (right).

Credit: UCSB

As part of the experiment, Ramirez shone white light on the tissue, which caused the chromatophores to expand and change color. When the light was turned off, the chromatophores relaxed and the skin returned to its original hue. This process, Ramirez noted, suggests that light sensors are connected to the chromatophores and that this enables a response without input from the brain or eyes. He and his co-author, Todd Oakley, an EEMB professor, dubbed the process Light-Activated Chromatophore Expansion (LACE).

In order to record the skin's sensitivity across the spectrum, Ramirez exposed octopus skin to different wavelengths of light from violet to orange and found that chromatophore response time was quickest under blue light. Molecular experiments to determine which proteins were expressed in the skin followed. Ramirez found rhodopsin -- usually produced in the eye -- in the sensory neurons on the tissue's surface.

According to Oakley, this new research suggests an evolutionary adaptation. "We've discovered new components of this really complex behavior of octopus camouflage," said Oakley, who calls cephalopods the rock stars of the invertebrate world.

"It looks like the existing cellular mechanism for light detection in octopus eyes, which has been around for quite some time, has been co-opted for light sensing in the animal's skin and used for LACE," he explained. "So instead of completely inventing new things, LACE puts parts together in new ways and combinations."

Octopuses are not the only marine mollusks whose skin can sense light, but scientists don't know yet whether the skin of those other animals contains the light-sensitive opsins. If they do, Ramirez wants to understand how these two groups are related."Do they all come from the same ancestral source or did they evolve multiple times?" he asked. "What kind of behaviors do the different groups share and what kind of behaviors does the skin sensing light underlie?"

Ramirez and Oakley are conducting new experiments that will seek to answer those questions and more.


Contacts and sources:
Julie Cohen
University of California - Santa Barbara  

Thursday, May 21, 2015

Weird One-of-a-Kind Star Called "Nasty 1"

Astronomers using NASA's Hubble Space Telescope have uncovered surprising new clues about a hefty, rapidly aging star whose behavior has never been seen before in our Milky Way galaxy. In fact, the star is so weird that astronomers have nicknamed it "Nasty 1," a play on its catalog name of NaSt1. The star may represent a brief transitory stage in the evolution of extremely massive stars.

Astronomers using NASA's Hubble Space Telescope have uncovered surprising new clues about a hefty, rapidly aging star whose behavior has never been seen before in our Milky Way galaxy. Astronomers have nicknamed it 'Nasty 1,' a play on its catalog name of NaSt1.

Credit: NASA/Space Telescope

First discovered several decades ago, Nasty 1 was identified as a Wolf-Rayet star, a rapidly evolving star that is much more massive than our sun. The star loses its hydrogen-filled outer layers quickly, exposing its super-hot and extremely bright helium-burning core.

But Nasty 1 doesn't look like a typical Wolf-Rayet star. The astronomers using Hubble had expected to see twin lobes of gas flowing from opposite sides of the star, perhaps similar to those emanating from the massive star Eta Carinae, which is a Wolf-Rayet candidate. Instead, Hubble revealed a pancake-shaped disk of gas encircling the star. The vast disk is nearly 2 trillion miles wide, and may have formed from an unseen companion star that snacked on the outer envelope of the newly formed Wolf-Rayet. Based on current estimates, the nebula surrounding the stars is just a few thousand years old, and as close as 3,000 light-years from Earth.

"We were excited to see this disk-like structure because it may be evidence for a Wolf-Rayet star forming from a binary interaction," said study leader Jon Mauerhan of the University of California, Berkeley. "There are very few examples in the galaxy of this process in action because this phase is short-lived, perhaps lasting only a hundred thousand years, while the timescale over which a resulting disk is visible could be only ten thousand years or less."

In the team's proposed scenario, a massive star evolves very quickly, and as it begins to run out of hydrogen, it swells up. Its outer hydrogen envelope becomes more loosely bound and vulnerable to gravitational stripping, or a type of stellar cannibalism, by a nearby companion star. In that process, the more compact companion star winds up gaining mass, and the original massive star loses its hydrogen envelope, exposing its helium core to become a Wolf-Rayet star.

Another way Wolf-Rayet stars are said to form is when a massive star ejects its own hydrogen envelope in a strong stellar wind streaming with charged particles. The binary interaction model where a companion star is present is gaining traction because astronomers realize that at least 70 percent of massive stars are members of double-star systems. Direct mass loss alone also cannot account for the number of Wolf-Rayet stars relative to other less-evolved massive stars in the galaxy.

"We're finding that it is hard to form all the Wolf-Rayet stars we observe by the traditional wind mechanism, because mass loss isn't as strong as we used to think," said Nathan Smith of the University of Arizona in Tucson, who is a co-author on the new NaSt1 paper. "Mass exchange in binary systems seems to be vital to account for Wolf-Rayet stars and the supernovae they make, and catching binary stars in this short-lived phase will help us understand this process."

But the mass transfer process in mammoth binary systems isn't always efficient. Some of the stripped matter can spill out during the gravitational tussle between the stars, creating a disk around the binary.

"That's what we think is happening in Nasty 1," Mauerhan said. "We think there is a Wolf-Rayet star buried inside the nebula, and we think the nebula is being created by this mass-transfer process. So this type of sloppy stellar cannibalism actually makes Nasty 1 a rather fitting nickname."

The star's catalogue name, NaSt1, is derived from the first two letters of each of the two astronomers who discovered it in 1963, Jason Nassau and Charles Stephenson.

Viewing the Nasty 1 system hasn't been easy. The system is so heavily cloaked in gas and dust, it blocks even Hubble's view of the stars. Mauerhan's team cannot measure the mass of each star, the distance between them, or the amount of material spilling onto the companion star.

Previous observations of Nasty 1 have provided some information on the gas in the disk. The material, for example, is travelling about 22,000 miles per hour in the outer nebula, slower than similar stars. The comparatively slow speed indicates that the star expelled its material through a less violent event than Eta Carinae's explosive outbursts, where the gas is travelling hundreds of thousands of miles per hour.

Nasty 1 may also be shedding the material sporadically. Past studies in infrared light have shown evidence for a compact pocket of hot dust very close to the central stars. Recent observations by Mauerhan and colleagues at the University of Arizona, using the Magellan telescope at Las Campanas Observatory in Chile, have resolved a larger pocket of cooler dust that may be indirectly scattering the light from the central stars. The presence of warm dust implies that it formed very recently, perhaps in spurts, as chemically enriched material from the two stellar winds collides at different points, mixes, flows away, and cools. Sporadic changes in the wind strength or the rate the companion star strips the main star's hydrogen envelope might also explain the clumpy structure and gaps seen farther out in the disk.

To measure the hypersonic winds from each star, the astronomers turned to NASA's Chandra X-ray Observatory. The observations revealed scorching hot plasma, indicating that the winds from both stars are indeed colliding, creating high-energy shocks that glow in X-rays. These results are consistent with what astronomers have observed from other Wolf-Rayet systems.

The chaotic mass-transfer activity will end when the Wolf-Rayet star runs out of material. Eventually, the gas in the disk will dissipate, providing a clear view of the binary system.

"What evolutionary path the star will take is uncertain, but it will definitely not be boring," said Mauerhan. "Nasty 1 could evolve into another Eta Carinae-type system. To make that transformation, the mass-gaining companion star could experience a giant eruption because of some instability related to the acquiring of matter from the newly formed Wolf-Rayet. Or, the Wolf-Rayet could explode as a supernova. A stellar merger is another potential outcome, depending on the orbital evolution of the system. The future could be full of all kinds of exotic possibilities depending on whether it blows up or how long the mass transfer occurs, and how long it lives after the mass transfer ceases."


Contacts and sources:
Ray Villard
NASA/Goddard Space Flight Center 

Bronze Age Egtved Girl Found in Denmark Came From Germany's Black Forest


The Bronze Age Egtved Girl came from far away, as revealed by strontium isotope analyses of the girl's teeth. The analyses show that she was born and raised outside Denmark's current borders, and strontium isotope analyses of the girl's hair and a thumb nail also show that she travelled great distances the last two years of her life.

The wool from the Egtved Girl's clothing, the blanket she was covered with, and the oxhide she was laid to rest on in the oak coffin all originate from a location outside present-day Denmark.

This is the Egtved Girl's grave, from 1370 BC.
Credit:  The National Museum of Denmark

The combination of the different provenance analyses indicates that the Egtved Girl, her clothing, and the oxhide come from Schwarzwald ("the Black Forest") in South West Germany - as do the cremated remains of a six-year-old child who was buried with the Egtved Girl. The girl's coffin dates the burial to a summer day in the year 1370 BC.

It is senior researcher Karin Margarita Frei, from the National Museum of Denmark and Centre for Textile Research at the University of Copenhagen, who has analysed the Egtved Girl's strontium isotope signatures. The analyses have been carried out in collaboration with Kristian Kristiansen from the University of Gothenburg and the Department of Geosciences and Natural Resource Management and the Centre for GeoGenetics, both University of Copenhagen.

The research has been possible through the support of The Danish National Research Foundation, European Research Council, the Carlsberg Foundation and L'Oréal Denmark-UNESCO For Women in Science Award.

The results have just been published in Scientific Reports.

The girl's movements mapped month by month

Strontium is an element which exists in the earth's crust, but its prevalence is subject to geological variation. Humans, animals, and plants absorb strontium through water and food. By measuring the strontium isotopic signatures in archaeological remains, researchers can determine where humans and animals lived, and where plants grew because of their strontium isotope signatures. In that sense, strontium serves as a kind of GPS for scientists.

"I have analysed the strontium isotopic signatures of the enamel from one of the Egtved Girl's first molars, which was fully formed/crystallized when she was three or four years old, and the analysis tells us that she was born and lived her first years in a region that is geologically older than and different from the peninsula of Jutland in Denmark," Karin Margarita Frei says.

Karin Margarita Frei has also traced the last two years of the Egtved Girl's life by examining the strontium isotopic signatures in the girl's 23-centimetre-long hair. The analysis shows that she had been on a long journey shortly before she died, and this is the first time that researchers have been able to so accurately track a prehistoric person's movements.

"If we consider the last two years of the girl's life, we can see that, 13 to 15 months before her death, she stayed in a place with a strontium isotope signature very similar to the one that characterizes the area where she was born. Then she moved to an area that may well have been Jutland. After a period of c. 9 to 10 months there, she went back to the region she originally came from and stayed there for four to six months before she travelled to her final resting place, Egtved. Neither her hair nor her thumb nail contains a strontium isotopic signatures which indicates that she returned to Scandinavia until very shortly before she died. As an area's strontium isotopic signature is only detectable in human hair and nails after a month, she must have come to "Denmark" and "Egtved" about a month before she passed away," Karin Margarita Frei explains.

The Black Forest Girl

If the Egtved Girl was not born in Jutland, then where did she come from? Karin Margarita Frei suggests that she came from South West Germany, more specifically the Black Forest, which is located 500 miles south of Egtved.

Considered in isolation, the Egtved Girl's strontium isotope signature could indicate that she came from Sweden, Norway or Western or Southern Europe. She could also come from the island Bornholm in the Baltic Sea. But when Karin Margarita Frei combines the girl's strontium isotopic signatures with that of her clothing, she can pinpoint the girl's place of origin relatively accurately.

"The wool that her clothing was made from did not come from Denmark and the strontium isotope values vary greatly from wool thread to wool thread. This proves that the wool was made from sheep that either grazed in different geographical areas or that they grazed in one vast area with very complex geology, and Black Forest's bedrock is characterized by a similarly heterogeneous strontium isotopic range," Karin Margarita Frei says.

That the Egtved Girl in all probability came from the Black Forest region in Germany comes as no surprise to professor Kristian Kristiansen from the University of Gothenburg; the archaeological finds confirm that there were close relations between Denmark and Southern Germany in the Bronze Age.

"In Bronze Age Western Europe, Southern Germany and Denmark were the two dominant centres of power, very similar to kingdoms. We find many direct connections between the two in the archaeological evidence, and my guess is that the Egtved Girl was a Southern German girl who was given in marriage to a man in Jutland so as to forge an alliance between two powerful families," Kristian Kristiansen says.

According to him, Denmark was rich in amber and traded amber for bronze. In Mycenaean Greece and in the Middle East, Baltic amber was as coveted as gold, and, through middlemen in Southern Germany, large quantities of amber were transported to the Mediterranean, and large quantities of bronze came to Denmark as payment. In the Bronze Age, bronze was as valuable a raw material as oil is today so Denmark became one of the richest areas of Northern Europe.

"Amber was the engine of Bronze Age economy, and in order to keep the trade routes going, powerful families would forge alliances by giving their daughters in marriage to each other and letting their sons be raised by each other as a kind of security," Kristian Kristiansen says.

A great number of Danish Bronze Age graves contain human remains that are as well-preserved as those found the Egtved Girl's grave. Karin Margarita Frei and Kristian Kristiansen plan to examine these remains with a view to analysing their strontium isotope signatures.


Contacts and sources:

Senior researcher Karin Margarita Frei
National Museum of Denmark and University of Copenhagen

Professor Kristian Kristiansen
University of Gothenburg

Exploring the Mysteries of Cosmic Explosions

An automated software system developed at Los Alamos National Laboratory played a key role in the discovery of supernova iPTF 14atg and could provide insight, a virtual Rosetta stone, into future supernovae and their underlying physics.

A Los Alamos National Laboratory simulation of an exploding white dwarf, in which the supernova drives an expanding shock wave that collides with a torus of material accreted from a companion star. 
Credit: Los Alamos National Laboratory

"Over the past decade, rapid advances in imaging and computing technology have completely transformed time-domain astronomy," said Przemek Wozniak, the principal investigator of a Laboratory Directed Research and Development (LDRD) project that funds the Laboratory's contributions to the research. "The Intermediate Palomar Transient Factory (iPTF) is a leader among the new breed of data-intensive sky monitoring surveys that seek to discover and understand transient events of astrophysical origin."

The Laboratory is partnering with an international consortium, led by the California Institute of Technology, to conduct the iPTF project.

Type Ia supernovae, such as supernova iPTF 14atg, occur in binary systems, when two stars orbit one another and one of the stars is a dense white dwarf. This supernova demonstrated a rarely observed phenomenon that allowed scientists to understand the underlying physics of type Ia supernovae.

"The challenge in this work is to select transients from the torrent of images and quickly identify the ones that deserve further attention," Wozniak said. "Too many transients compete for scarce resources such as observing time on large telescopes. We are developing new machine learning technology that will allow us to tackle these big data challenges."

Researchers at Los Alamos developed an automated software system based on machine learning algorithms to reliably separate real astronomical transients from false detections. Wozniak said without machine learning technology, it is impossible to find events such as iPTF 14atg before it is too late for detailed follow-up observations that tell scientists about the broad spectral energy distribution of radiation emitted by supernovae.

An important piece of the puzzle in the case of iPTF 14atg came from NASA's Swift satellite, which detected the supernova in time to catch rapidly fading ultraviolet radiation from a young supernova.

"This excess UV emission is strong evidence that the supernova is interacting with its surrounding medium, such as an exploding white dwarf colliding with its companion star in the so-called single degenerate scenario," said Chris Fryer, a computational scientist at Los Alamos who leads the supernova simulation and modeling group at the Laboratory.

In this model, the ejecta from an exploding degenerate object called a white dwarf collide with a normal companion star, producing a UV transient lasting at most a few days. The competing double-degenerate model, which uses a pair of merging white dwarfs, predicts no UV excess.

Wozniak said Los Alamos is at the forefront of this fast-evolving field and well equipped to make important contributions in the future. He said the main idea is to automate and optimize the entire process of selecting, vetting and prioritizing transients in order to collect the most effective follow-up observations for events that matter.




Contacts and sources:
Nancy AmbrosianoLos Alamos National Laboratory

Supernova Ignition Surprises Astronomers


Scientists have captured the early death throes of supernovae for the first time and found that the universe's benchmark explosions are much more varied than expected.

The scientists used the Kepler space telescope to photograph three type 1a supernovae in the earliest stages of ignition. They then tracked the explosions in detail to full brightness around three weeks later, and the subsequent decline over the next few months.

Supernova SN2012fr, just below the center of the host galaxy, outshone the rest of the galaxy for several weeks.
       
Credit: Brad Tucker and Emma Kirby

They found the initial stages of a supernova explosion did not fit with the existing theories.

"The stars all blow up uniquely. It doesn't make sense," said Dr Brad Tucker from The Australian National University (ANU).

"It's particularly weird for these supernovae because even though their initial shockwaves are very different, they end up doing the same thing."

This is a timelapse compilation of the brightness of SN 2012fr over several weeks.  
Credit: ANU

Before this study, the earliest type 1a supernovae had been glimpsed was more than 2.5 hours after ignition, after which the explosions all followed an identical pattern.

This led astronomers to theorise that supernovae, the brilliant explosions of dying stars, all occurred through an identical process.

Astronomers had thought supernovae all happened when a dense star steadily sucked in material from a large nearby neighbour until it became so dense that carbon in the star's core ignited.

"Somewhat to our surprise the results suggest an alternative hypothesis, that a violent collision between two smallish white dwarf stars sets off the explosion," said lead researcher Dr Robert Olling, from the University of Maryland in the United States.

At the peak of their brightness, supernovae are brighter than the billions of stars in their galaxy. Because of their brightness, astronomers have been able to use them to calculate distances to distant galaxies.

Dr. Brad Tucker discusses the first observations of supernova ignition which are challenging theories of how they form.  
Credit: ANU

Measurements of distant supernovae led to the discovery that some unknown force, now called dark energy, is causing the accelerated expansion of the universe. Brian Schmidt from the ANU, Saul Perlmutter (Berkeley) and Adam Reiss (Johns Hopkins) were awarded the Nobel prize in 2011 for this discovery.

Dr Tucker said the new results did not undermine the discovery of dark energy.

"The accelerating universe will not now go away - they will not have to give back their Nobel prizes," he said.

"The new results will actually help us to better understand the physics of supernovae, and figure out what is this dark energy that is dominating the universe."

The findings are published in Nature.

Contacts and sources:
Dr. Brad Tucker
Australian National University

Infections Can Lower I.Q.

New research shows that infections can impair your cognitive ability measured on an IQ scale. The study is the largest of its kind to date, and it shows a clear correlation between infection levels and impaired cognition.

Anyone can suffer from an infection, for example in their stomach, urinary tract or skin. However, a new Danish study shows that a patient's distress does not necessarily end once the infection has been treated. In fact, ensuing infections can affect your cognitive ability measured by an IQ test:

"Our research shows a correlation between hospitalisation due to infection and impaired cognition corresponding to an IQ score of 1.76 lower than the average. People with five or more hospital contacts with infections had an IQ score of 9.44 lower than the average. The study thus shows a clear dose-response relationship between the number of infections, and the effect on cognitive ability increased with the temporal proximity of the last infection and with the severity of the infection. 

An example of one kind of IQ test item, modeled after items in the Raven's Progressive Matrices test
Credit: Life of Riley

Infections in the brain affected the cognitive ability the most, but many other types of infections severe enough to require hospitalisation can also impair a patient's cognitive ability. Moreover, it seems that the immune system itself can affect the brain to such an extent that the person's cognitive ability measured by an IQ test will also be impaired many years after the infection has been cured," explains MD and PhD Michael Eriksen Benrós, who is affiliated with the National Centre for Register-Based Research at Aarhus BSS and the Mental Health Centre Copenhagen, University of Copenhagen.

He has conducted the research in collaboration with researchers from the University of Copenhagen and Aarhus University.

190,000 Danes participated in the study

The study is a nationwide register study tracking 190,000 Danes born between 1974 and 1994, who have had their IQ assessed between 2006 and 2012. 35% of these individuals had a hospital contact with infections before the IQ testing was conducted.

According to Senior Researcher Michael Eriksen Benrós, part of the explanation of the increased risk of impaired cognition following an infection may be as follows:

"Infections can affect the brain directly, but also through peripheral inflammation, which affects the brain and our mental capacity. Infections have previously been associated with both depression and schizophrenia, and it has also been proven to affect the cognitive ability of patients suffering from dementia. This is the first major study to suggest that infections can also affect the brain and the cognitive ability in healthy individuals."

"We can see that the brain is affected by all types of infections. Therefore, it is important that more research is conducted into the mechanisms which lie behind the connection between a person's immune system and mental health," says Michael Eriksen Benrós.

He hopes that learning more about this connection will help to prevent the impairment of people's mental health and improve future treatment.

Experiments on animals have previously shown that the immune system can affect cognitive capabilities, and more recent minor studies in humans have also pointed in that direction. Normally, the brain is protected from the immune system, but with infections and inflammation the brain may be affected. 

Michael Eriksen Benrós' research suggests that it may be the immune system that causes the cognitive impairment, not just the infection, because many different types of infections were associated with a decrease in cognitive abilities. This is the first study to examine these correlations in this manner. 

The results suggest that the immune system's response to infections can possibly affect the brain and thereby also the person's cognitive ability. This is in line with previous studies, some of which have also been conducted by Dr. Michael Eriksen Benrós, which show that infections are associated with an increased risk of developing mental disorders such as depression or schizophrenia.

The researchers behind the study hope that their results may spur on further research on the possible involvement of the immune system in the development of psychiatric disorders and whether the discovered correlations contribute to the development of mental disorders or whether they may be caused by e.g. genetic liability toward acquiring infections in patients with reduced cognitive ability. 

The study has been adjusted for social conditions and parental educational levels; however, it cannot be ruled out that heritable and environmental factors associated with infections might also influence the associations.


Contacts and sources:
Michael Eriksen Benrós, MD, PhD, Senior Researcher
Mental Health Centre Copenhagen, University of Copenhagen
National Centre for Register-Based Research, Aarhus University

Ancient Snakes Had Tiny Limbs Complete with Ankles and Toes


The ancestral snakes in the grass actually lived in the forest, according to the most detailed look yet at the iconic reptiles.

A comprehensive analysis by Yale University paleontologists reveals new insights into the origin and early history of snakes. For one thing, they kept late hours; for another, they also kept their hind legs.

This is an artist's rendering of an ancient snake, with tiny hind limbs.

Credit: Julius T. Csotonyi

"We generated the first comprehensive reconstruction of what the ancestral snake was like," said Allison Hsiang, lead author the study published online May 19 in the journal BMC Evolutionary Biology. Hsiang is a postdoctoral researcher in Yale's Department of Geology and Geophysics.

"We infer that the most recent common ancestor of all snakes was a nocturnal, stealth-hunting predator targeting relatively large prey, and most likely would have lived in forested ecosystems in the Southern Hemisphere," Hsiang said.

Snakes have always captured the imagination of humans. Their long and sinuous body, fearsome reputation, and great diversity -- with more than 3,400 living species -- make them one of the most recognizable groups of living vertebrate animals. Yet little has been known about how, where, and when modern snakes emerged.

The Yale team analyzed snake genomes, modern snake anatomy, and new information from the fossil record to find answers. In doing so, the researchers generated a family tree for both living and extinct snakes, illuminating major evolutionary patterns that have played out across snake evolutionary history.

"Our analyses suggest that the most recent common ancestor of all living snakes would have already lost its forelimbs, but would still have had tiny hind limbs, with complete ankles and toes. It would have first evolved on land, instead of in the sea," said co-author Daniel Field, a Yale Ph.D. candidate. "Both of those insights resolve longstanding debates on the origin of snakes."

The researchers said ancestral snakes were non-constricting, wide-ranging foragers that seized their prey with needle-like hooked teeth and swallowed them whole. They originated about 128.5 million years ago, during the middle Early Cretaceous period.

"Primate brains, including those of humans, are hard-wired to attend to serpents, and with good reason," said Jacques Gauthier, senior author of the study, a Yale professor of geology and geophysics, and curator of fossil vertebrates at the Yale Peabody Museum of Natural History. "Our natural and adaptive attention to snakes makes the question of their evolutionary origin especially intriguing."

Contacts and sources:
Jim Shelton
Yale University

3.3 Million Year Old Tools Oldest Yet Found


The discovery is the first evidence that an even earlier group of proto-humans may have had the thinking abilities needed to figure out how to make sharp-edged tools. The stone tools mark "a new beginning to the known archaeological record," say the authors of a new paper about the discovery, published today in the leading scientific journal Nature.

The finds were made in the desert badlands near Lake Turkana, Kenya. Many other important discoveries of fossils and artifacts have been made nearby.

Credit: West Turkana Archaeological Project

"The whole site's surprising, it just rewrites the book on a lot of things that we thought were true," said geologist Chris Lepre of the Lamont-Doherty Earth Observatory and Rutgers University, a co-author of the paper who precisely dated the artifacts.

The tools "shed light on an unexpected and previously unknown period of hominin behavior and can tell us a lot about cognitive development in our ancestors that we can't understand from fossils alone," said lead author Sonia Harmand, of the Turkana Basin Institute at Stony Brook University and the Universite? Paris Ouest Nanterre.

Hominins are a group of species that includes modern humans, Homo sapiens, and our closest evolutionary ancestors. Anthropologists long thought that our relatives in the genus Homo - the line leading directly to Homo sapiens - were the first to craft such stone tools. But researchers have been uncovering tantalizing clues that some other, earlier species of hominin, distant cousins, if you will, might have figured it out.

The researchers do not know who made these oldest of tools. But earlier finds suggest a possible answer: The skull of a 3.3-million-year-old hominin, Kenyanthropus platytops, was found in 1999 about a kilometer from the tool site. A K. platyops tooth and a bone from a skull were discovered a few hundred meters away, and an as-yet unidentified tooth has been found about 100 meters away.

Sammy Lokorodi, a resident of Kenya's northwestern desert who works as a fossil and artifact hunter, led the way to a trove of 3.3 million-year-old tools.
Credit: Credit: West Turkana Archaeological Project

The precise family tree of modern humans is contentious, and so far, no one knows exactly how K. platyops relates to other hominin species. Kenyanthropus predates the earliest knownHomo species by a half a million years. This species could have made the tools; or, the toolmaker could have been some other species from the same era, such as Australopithecus afarensis, or an as-yet undiscovered early type of Homo.

Lepre said a layer of volcanic ash below the tool site set a "floor" on the site's age: It matched ash elsewhere that had been dated to about 3.3 million years ago, based on the ratio of argon isotopes in the material. To more sharply define the time period of the tools, Lepre and co-author and Lamont-Doherty colleague Dennis Kent examined magnetic minerals beneath, around and above the spots where the tools were found.

Sonia Harmand and Jason Lewis examine stone artifacts at the Lomekwi dig in Kenya. 
Credit: West Turkana Archaeological Project

The Earth's magnetic field periodically reverses itself, and the chronology of those changes is well documented going back millions of years. "We essentially have a magnetic tape recorder that records the magnetic field ... the music of the outer core," Kent said. By tracing the variations in the polarity of the samples, they dated the site to 3.33 million to 3.11 million years.

Lepre's wife and another co-author, Rhoda Quinn of Rutgers, studied carbon isotopes in the soil, which along with animal fossils at the site allowed researchers to reconstruct the area's vegetation. This led to another surprise: The area was at that time a partially wooded, shrubby environment. Conventional thinking has been that sophisticated tool-making came in response to a change in climate that led to the spread of broad savannah grasslands, and the consequent evolution of large groups of animals that could serve as a source of food for human ancestors.

Chris Lepre of Columbia University's Lamont-Doherty Earth Observatory (back to camera) precisely dated the artifacts by analyzing layers above, around and below them for reversals in earth's magnetic field.
Credit: West Turkana Archaeological Project

One line of thinking is that hominins started knapping - banging one rock against another to make sharp-edged stones - so they could cut meat off of animal carcasses, said paper co-author Jason Lewis of the Turkana Basin Institute and Rutgers. But the size and markings of the newly discovered tools "suggest they were doing something different as well, especially if they were in a more wooded environment with access to various plant resources," Lewis said. The researchers think the tools could have been used for breaking open nuts or tubers, bashing open dead logs to get at insects inside, or maybe something not yet thought of.

"The capabilities of our ancestors and the environmental forces leading to early stone technology are a great scientific mystery," said Richard Potts, director of the Human Origins Program at the Smithsonian's National Museum of Natural History, who was not involved in the research. The newly dated tools "begin to lift the veil on that mystery, at an earlier time than expected," he said.

Potts said he had examined the stone tools during a visit to Kenya in February.

"Researchers have thought there must be some way of flaking stone that preceded the simplest tools known until now," he said. "Harmand's team shows us just what this even simpler altering of rocks looked like before technology became a fundamental part of early human behavior."

Photos of selected Lomekwi 3 stones accompanying the paper show both cores and flakes knapped from the cores that the authors say illustrate various techniques.
Credit: West Turkana Archaeological Project

Ancient stone artifacts from East Africa were first uncovered at Olduvai Gorge in Tanzania in the mid-20th century, and those tools were later associated with fossil discoveries in the 1960s of the early human ancestor Homo habilis. That species has been dated to 2.1 million to 1.5 million years ago.

Subsequent finds have pushed back the dates of humans' evolutionary ancestors, and of stone tools, raising questions about who first made that cognitive leap. The discovery of a partial lower jaw in the Afar region of Ethiopia, announced on March 4, pushes the fossil record for the genus Homo to 2.8 million years ago. Evidence from recent papers, the authors note, suggests that there is anatomical evidence that Homo had evolved into several distinct lines by 2 million years ago.

There is some evidence of more primitive tool use going back even before the new find. In 2009, researchers at Dikika, Ethiopia, dug up 3.39 million-year-old animal bones marked with slashes and other cut marks, evidence that someone used stones to trim flesh from bone and perhaps crush bones to get at the marrow inside. That is the earliest evidence of meat and marrow consumption by hominins. No tools were found at the site, so it's unclear whether the marks were made with crafted tools or simply sharp-edged stones. The only hominin fossil remains in the area dating to that time are from Australopithecus afarensis.



The new find came about almost by accident: Harmand and Lewis said that on the morning of July 9, 2011, they had wandered off on the wrong path, and climbed a hill to scout a fresh route back to their intended track. They wrote that they "could feel that something was special about this particular place." They fanned out and surveyed a nearby patch of craggy outcrops. "By teatime," they wrote, "local Turkana tribesman Sammy Lokorodi had helped [us] spot what [we] had come searching for."

By the end of the 2012 field season, excavations at the site, named Lomekwi 3, had uncovered 149 stone artifacts tied to tool-making, from stone cores and flakes to rocks used for hammering and others possibly used as anvils to strike on.

The researchers tried knapping stones themselves to better understand how the tools they found might have been made. They concluded that the techniques used "could represent a technological stage between a hypothetical pounding-oriented stone tool use by an earlier hominin and the flaking-oriented knapping behavior of [later] toolmakers." Chimpanzees and other primates are known to use a stone to hammer open nuts atop another stone. But using a stone for multiple purposes, and using one to crack apart another into a sharper tool, is more advanced behavior.

The find also has implications for understanding the evolution of the human brain. The toolmaking required a level of hand motor control that suggests that changes in the brain and spinal tract needed for such activity could have occurred before 3.3 million years ago, the authors said.

"This is a momentous and well-researched discovery," said paleoanthropologist Bernard Wood of George Washington University, who was not involved in the study. "I have seen some of these artifacts in the flesh, and I am convinced they were fashioned deliberately." Wood said he found it intriguing to see how different the tools are from so-called Oldowan stone tools, which up to now have been considered the oldest and most primitive.

Lepre, who has been conducting fieldwork in eastern Africa for about 15 years, said he arrived at the dig site about a week after the discovery. The site is several hours' drive on rough roads from the nearest town, located in a hot, dry landscape he said is reminiscent of Arizona and New Mexico. Lepre collected chunks of sediment from a series of depths and brought them back to Lamont-Doherty for analysis. He and Kent used a bandsaw to trim the samples into sugar cube-size blocks and inserted them into a magnetometer, which measured the polarity of tiny grains of the minerals hematite and magnetite contained in the sediment.

"The magnetics pretty much clinches that the age is something like 3.3 million years old," said Kent, who also is a professor at Rutgers.

Earlier dating work by Lepre and Kent helped lead to another landmark paper in 2011: a study that suggested Homo erectus, another precursor to modern humans, was using more advanced tool-making methods 1.8 million years ago, at least 300,000 years earlier than previously thought.

"I realized when you [figure out] these things, you don't solve anything, you just open up new questions," said Lepre. "I get excited, then realize there's a lot more work to do."


  
Contacts and sources:
David FunkhouserColumbia University's Lamont-Doherty Earth Observatory

Galaxy's Cannibalistic Feeding Habits Revealed


A team of Australian and Spanish astronomers have caught a greedy galaxy gobbling on its neighbours and leaving crumbs of evidence about its dietary past.

Galaxies grow by churning loose gas from their surroundings into new stars, or by swallowing neighbouring galaxies whole. However, they normally leave very few traces of their cannibalistic habits.

This is a chemical enrichment map of the NGC 1512 and NGC 1510 galaxy system showing the amount of oxygen gas in the star-forming regions around the two galaxies.

Credit: Ángel R. López-Sánchez (AAO/MQU) and Baerbel Koribalski (CSIRO/CASS)

A study published today in Monthly Notices of the Royal Astronomical Society (MNRAS) not only reveals a spiral galaxy devouring a nearby compact dwarf galaxy, but shows evidence of its past galactic snacks in unprecedented detail.

Australian Astronomical Observatory (AAO) and Macquarie University astrophysicist, Ángel R. López-Sánchez, and his collaborators have been studying the galaxy NGC 1512 to see if its chemical story matches its physical appearance.

The team of researchers used the unique capabilities of the 3.9-metre Anglo-Australian Telescope (AAT), near Coonabarabran, New South Wales, to measure the level of chemical enrichment in the gas across the entire face of NGC 1512.

Chemical enrichment occurs when stars churn the hydrogen and helium from the Big Bang into heavier elements through nuclear reactions at their cores. These new elements are released back into space when the stars die, enriching the surrounding gas with chemicals like oxygen, which the team measured.

This is a multiwavelength image of galaxies NGC 1512 and NGC 1510 combining optical and near-infrared data (light blue, yellow, orange), ultraviolet data (dark blue), mid-infrared data (red), and radio data (green).

Credit: Ángel R. López-Sánchez (AAO/MQU) and Baerbel Koribalski (CSIRO/CASS)

"We were expecting to find fresh gas or gas enriched at the same level as that of the galaxy being consumed, but were surprised to find the gases were actually the remnants of galaxies swallowed earlier," Dr López-Sánchez said.

"The diffuse gas in the outer regions of NGC 1512 is not the pristine gas created in the Big Bang but is gas that has already been processed by previous generations of stars."

CSIRO's Australia Telescope Compact Array, a powerful 6-km diameter radio interferometer located in eastern Australia, was used to detect large amounts of cold hydrogen gas that extends way beyond the stellar disk of the spiral galaxy NGC 1512.

"The dense pockets of hydrogen gas in the outer disk of NGC 1512 accurately pin-point regions of active star formation", said CSIRO's Dr Baerbel Koribalski, a member of the research collaboration.

When this finding was examined in combination with radio and ultraviolet observations the scientists concluded that the rich gas being processed into new stars did not come from the inner regions of the galaxy either. Instead, the gas was likely absorbed by the galaxy over its lifetime as NGC 1512 accreted other, smaller galaxies around it.

Dr Tobias Westmeier, from the International Centre for Radio Astronomy Research in Perth, said that while galaxy cannibalism has been known for many years, this is the first time that it has been observed in such fine detail.

"By using observations from both ground and space based telescopes we were able to piece together a detailed history for this galaxy and better understand how interactions and mergers with other galaxies have affected its evolution and the rate at which it formed stars," he said.

The team's successful and novel approach to investigating how galaxies grow is being used in a new program to further refine the best models of galaxy evolution.

For this work the astronomers used spectroscopic data from the AAT at Siding Spring Observatory in Australia to measure the chemical distribution around the galaxies. They identified the diffuse gas around the dual galaxy system using Australian Telescope Compact Array (ATCA) radio observations. In addition, they identified regions of new star formation with data from the Galaxy Evolution Explorer (GALEX) orbiting space telescope.

"The unique combination of these data provide a very powerful tool to disentangle the nature and evolution of galaxies," said Dr López-Sánchez.

"We will observe several more galaxies using the same proven techniques to improve our understanding of the past behaviour of galaxies in the local Universe."

Contacts and sources:
Pete Wheeler
International Centre for Radio Astronomy Research