Digitally diagnosing dinosaurs

Researchers from the University of Manchester have teamed up with the New Jersey State Museum and the University of Massachusetts to diagnose a dinosaur from the USA with a horrific medical condition.

First case of septic arthritis found in a dinosaur 
[Credit: University of Manchester]

The prehistoric patient is a Hadrosaur�a duck-billed dinosaur�which seems to have suffered from septic arthritis, a condition seen in modern birds and crocodiles as well as humans. The septic arthritis affected the elbow joint, resulting in a fused joint covered in bony growths.

"The condition would have made it almost impossible for the animal to move its elbow, making it look a bit like the hobbling pigeons you see today. It's almost humbling to think that the same conditions that affect the pigeons on the street might have also affected their impressive dinosaur relatives," said Dr. Jennifer Ann�, lead author of the study.

Paleopathologies - ancient diseases and injuries - are fairly rare in the fossil record. Even rarer are dinosaurs from the East Coast of North America. The combination of both is an extremely significant find, which allows for a look at the harsher side of life for dinosaurs on the eastern seaboard 70 million years ago.

The specimen was found was found in a former New Jersey quarry by David Parris of New Jersey State Museum. Like many fossils from this site, the specimen suffers from a geological condition called pyrite disease which makes it very fragile and can lead to it crumbling into dust. Therefore, the team used the microCT scanning facilities at Harvard University's Center for Nanoscale Systems to do an internal diagnosis without the need for saws.

"By microCTing the specimen, we not only ensured an accurate diagnosis of the pathology, but also the preservation of the specimen for future scientific studies" said co-author Dr Brandon Hedrick.

"The fact that such a fossil was preserved is difficult to comprehend" said co-author Jason Schein of the New Jersey State Museum. "It's exciting to think that New Jersey is still producing scientifically important finds after over 200 years of paleontological discoveries."

Details of this research will appear in the Royal Society Open Science journal.

Source: University of Manchester [August 03, 2016]

Digitally diagnosing dinosaurs

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Population boom preceded early farming in North America

University of Utah anthropologists counted the number of carbon-dated artifacts at archaeological sites and concluded that a population boom and scarce food explain why people in eastern North America domesticated plants for the first time on the continent about 5,000 years ago.

New research backs eastern North America plant domestication theory 
[Credit: WikiCommons]

"Domesticated plants and animals are part of our everyday lives, so much so that we take them for granted," says Brian Codding, senior author of the study published online by the British journal Royal Society Open Science. "But they represent a very unique thing in human history. They allowed for large numbers of people to live in one place. That ultimately set the stage for the emergence of civilization."

Graduate student Elic Weitzel, the study's first author, adds: "For most of human history, people lived off wild foods -- whatever they could hunt or gather. It's only relatively recently that people made this switch to a very different method of acquiring their food. It's important to understand why that transition happened."

The study dealt not with a full-fledged agricultural economy, but with the earlier step of domestication, when early people in eastern North America first started growing plants they had harvested in the wild, namely, squash, sunflower, marshelder and a chenopod named pitseed goosefoot, a pseudocereal grain closely related to quinoa.

Codding, an assistant professor of anthropology, says at least 11 plant domestication events have been identified in world history, starting with wheat about 11,500 years ago in the Middle East. The eastern North American plant domestication event, which began around 5,000 years ago, was the ninth of those 11 events and came after a population boom 6,900 to 5,200 years ago, he adds.

For many years, two competing theories have sought to explain the cause of plant domestication in eastern North America: First, population growth and resulting food scarcity prompted people to grow foods on which they already foraged. Second, a theory called "niche construction" or "ecosystem engineering" that basically says intentional experimentation and management during times of plenty -- and not immediate necessity -- led people to manage and manipulate wild plants to increase their food supply.

"We argue that human populations significantly increased prior to plant domestication in eastern North America, suggesting that people are driven to domestication when populations outstrip the supply of wild foods," Weitzel says.

"The transition to domesticating food allowed human populations to increase drastically around the world and made our modern way of life possible," he adds. "People start living near the fields. Whenever you've got sedentary communities, they start to expand. Villages expand into cities. Once you have that, you have all sorts of social changes. We really don't see state-level society until domestication occurs."

When early North Americans first domesticated crops

The region of eastern North America covered by the study includes most of Missouri, Illinois, Indiana, Ohio, West Virginia, Kentucky, Tennessee and Arkansas, and portions of Oklahoma, Kansas, Iowa, Virginia, North Carolina, South Carolina, Georgia, Mississippi and Louisiana.

This map shows the area covered by a new University of Utah study that concludes a population boom and resulting 
scarcity of wild foods are what caused early people in eastern North America to domesticate wild food plants for
 the first time on the continent starting about 5,000 year ago. The triangles and names represent archaeological 
sites previously identified as locations where one or more of the these plants first were domesticated: squash, 
sunflower, marshelder and pitseed goosefoot, a relative of quinoa. The small circles are sites where 
radiocarbon-dated artifacts have been found, with a single circle often representing many dated artifacts.
 The study area includes much of eastern North America inland from the Atlantic and Gulf coasts 
[Credit: Elic Weitzel, University of Utah]

"This is the region where these plant foods were domesticated from their wild variants," Weitzel says. "Everywhere else in North America, crops were imported from elsewhere," particularly Mexico and Central America.

Four indigenous plant species constitute what scientists call the Eastern Agricultural Complex, which people began to domesticate about 5,000 years ago.

Previous research shows specific domestication dates were 5,025 years ago for squash at an archaeological site named Phillips Spring in Missouri, 4,840 years ago for sunflower seeds domesticated at Hayes in Tennessee, 4,400 years ago for marshelder at the Napoleon Hollow site in Illinois, and 3,800 years ago for pitseed goosefoot found in large quantities at Riverton, Illinois, along with squash, sunflower and marshelder.

Three more recent sites also have been found to contain evidence of domestication of all four species: Kentucky's Cloudsplitter and Newt Kindigenash rockshelters, dated to 3,700 and 3,640 years ago, respectively, and the 3,400-year-old Marble Bluff site in Arkansas.

Sunflower and squash -- including acorn and green and yellow summer squashes -- remain important crops today, while marshelder and pitseed goosefoot are not (although the related quinoa is popular).

Deducing population swings from radiocarbon dates

"It's really difficult to arrive at measures of prehistoric populations. So archaeologists have struggled for a long time coming up with some way of quantifying population levels when we don't have historical records," Weitzel says.

"People have looked at the number of sites through time, the number of artifacts through time and some of the best work has looked at the effects of population growth," such as in the switch from a diet of tortoises to rabbits as population grew in the eastern Mediterranean during the past 50,000 years, he adds.

Codding says that in the past decade, archaeologists have expanded the use of radiocarbon-dates for artifacts to reconstruct prehistoric population histories. Weitzel says radiocarbon dates in the new study came from artifacts such as charcoal, nutshells and animal bones -- all recorded in a database maintained by Canadian scientists.

The University of Utah anthropologists used these "summed radiocarbon dates" for 3,750 dated artifacts from eastern North America during the past 15,000 years.

"The assumption is that if you had more people, they left more stuff around that could be dated," Weitzel says. "So if you have more people, you conceivably should have more radiocarbon dates."

"We plotted the dates through time," namely, the number of radiocarbon dates from artifacts in every 100-year period for the past 15,000 years, he adds.

The analysis indicated six periods of significant population increase or decrease during that time, including one during which population nearly doubled in eastern North America starting about 6,900 years ago and continuing apace until 5,200 years ago -- not long before plant domestication began, Codding says.

Codding notes that even though plant domestication meant "these people were producing food to feed themselves and their families, they're still hunting and foraging," eating turtles, fish, water fowl and deer, among other animals.

The other theory

Weitzel says the concept of niche construction is that people were harvesting wild plants, and "were able to get more food from certain plants." By manipulating the environment -- such as transplanting wild plants or setting fires to create areas favorable for growth of wild food plants -- they began "experimenting with these plants to see if they could grow them to be bigger or easier to collect and consume," he adds. "That kind of experimentation then leads to domestication."

Codding says: "The idea is that when times are good and people have plenty of food then they will experiment with plants. We say that doesn't provide an explanation for plant domestication in eastern North America." He believes the behavioral ecology explanation: increasing population and-or decreasing wild food resources led to plant domestication.

Source: University of Utah [August 02, 2016]

Population boom preceded early farming in North America

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Where there's smoke and a mutation there may be an evolutionary edge for humans

A genetic mutation may have helped modern humans adapt to smoke exposure from fires and perhaps sparked an evolutionary advantage over their archaic competitors, including Neanderthals, according to a team of researchers.

A genetic mutation that is now ubiquitous in humans may have increased our tolerance to smoke, leading to an 
evolutionary advantage over other hominins, such as Neanderthals [Credit:Web]

Modern humans are the only primates that carry this genetic mutation that potentially increased tolerance to toxic materials produced by fires for cooking, protection and heating, said Gary Perdew, the John T. and Paige S. Smith Professor in Agricultural Sciences, Penn State. At high concentrations, smoke-derived toxins can increase the risk of respiratory infections. For expectant mothers, exposure to these toxins can increase the chance of low birth weight and infant mortality.

The mutation may have offered ancient humans a sweet spot in effectively processing some of these toxins -- such as dioxins and polycyclic aromatic hydrocarbons -- compared to other hominins.

"If you're breathing in smoke, you want to metabolize these hydrophobic compounds and get rid of them, however, you don't want to metabolize them so rapidly that it overloads your system and causes overt cellular toxicity," said Perdew.

The researchers, who released their findings in the current issue of Molecular Biology and Evolution, suggest that a difference in the aryl hydrocarbon receptor -- which regulates the body's response to polycyclic aromatic hydrocarbons -- between humans, Neanderthals and other non-human primates may have made humans more desensitized to certain smoke toxins. The mutation in the receptor is located in the middle of the ligand-binding domain and is found in all present-day humans, Perdew added.

Ligands are small molecules that attach to receptor proteins in certain areas in much the same way that keys fit into locks.

Troy Hubbard, Ph.D candidate in molecular biology, left, reviews as chart of proteins collected from a sample 
with Dr. Gary Perdew in their Life Sciences Lab at Penn State [Credit: Patrick Mansell]

"For Neanderthals, inhaling smoke and eating charcoal-broiled meat, they would be exposed to multiple sources of polycyclic aromatic hydrocarbons, which are known to be carcinogens and lead to cell death at high concentrations," said Perdew. "The evolutionary hypothesis is, if Neanderthals were exposed to large amounts of these smoke-derived toxins, it could lead to respiratory problems, decreased reproductive capacity for women and increased susceptibility to respiratory viruses among preadolescents, while humans would exhibit decreased toxicity because they are more slowly metabolizing these compounds."

There is evidence that both humans and Neanderthals used fire, according to George Perry, assistant professor of anthropology and biology, Penn State, who worked with Perdew.

"Our hominin ancestors -- they would technically not be called humans at that time -- were likely using fire at least a million years ago, and some infer an earlier control and use of fire approximately 2 million years ago," said Perry.

Fire would have played an important role for both humans and Neanderthals.

"Cooking with fire could have allowed our ancestors to incorporate a broader range of foods in our diets, for example, by softening roots and tubers that might otherwise have been hard to chew," Perry said. "Cooking could also help increase the digestibility of other foods, both in chewing time and reduced energetic investment in digestion."

Adding cell culture media to cells in Gary Perdew's Life Sciences Laboratory 
[Credit: Patrick Mansell]

Fire also provided warmth, particularly in the higher latitudes, according to Perry.

"Besides heating and cooking, humans used -- and still use -- fire for landscape burning and as part of hunting and gathering, and now as part of agriculture," said Perry.

The study may also lend support to a recent theory that the invention of cooking may have helped humans thrive, according to Perdew.

He also suggested that the receptor might give humans a better tolerance for cigarette smoke, allowing people to smoke, but also putting them at risk of cancer and other chronic diseases.

"Our tolerance has allowed us to pick up bad habits," Perdew said.

The researchers used computational and molecular techniques to examine the difference in the genetics of polycyclic aromatic hydrocarbon tolerance between humans and Neanderthals. They examined a genomic database of humans, Neanderthals and a Denisovan, a hominin more closely related to Neanderthals than humans.

"We thought the differences in aryl hydrocarbon receptor ligand sensitivity would be about ten-fold, but when we looked at it closely, the differences turned out to be huge," said Perdew. "Having this mutation made a dramatic difference. It was a hundred-fold to as much of a thousand-fold difference."

In contrast, the sensitivity of the aryl hydrocarbon receptor for some endogenous -- produced in the body -- ligands is the same between human and Neanderthal, which further illustrates that modern humans may have adapted to specific environmental toxin exposures through this critical mutation in the aryl hydrocarbon receptor.

Author: Matt Swayne| Source: Penn State University [August 02, 2016]

Where there's smoke and a mutation there may be an evolutionary edge for humans

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Tracking down the first chefs

Archaeological sites speak about the everyday lives of people in other times. Yet knowing how to interpret this reality does not tend to be straightforward. We know that Palaeolithic societies lived on hunting and gathering, but the bones found in prehistoric settlements are not always the food leftovers of the societies that lived in them. Or they are not exclusively that. Peoples of this type were nomads and used to be constantly on the move across the territory, so other predators, such as hyenas or wolves, lurking around in search of food remains left by humans would be a common occurrence. Or even at a specific moment, carnivores could have sheltered in a cave abandoned by Prehistoric peoples and there raise their puppies and bring in the bones of the animals caught to feed them. These predators used to bite the bones leaving their teeth marks on them.

A piece of experimental research has shown that human bites on bones have distinctive features 
allowing them to be differentiated from the bites made by other animals, and that cooking the meat
 in advance influences the appearance of these marks. This study provides valuable conclusions
 for analyzing food remains found on sites [Credit: Antonio J. Romero/UPV/EHU]

So it is very difficult to identify, for example, a roasted shoulder of mouflon eaten several thousand years ago from a few bone fragments that remain of it today. To be able to identify cases like this one, a novel way is to analyse the marks that we humans leave on bones when eating meat today. Human beings not only alter the bones when using stone knives on them and exposing them to fire to cook them, but like other animals, we also leave bite marks on the surface of the bone when we remove the meat to feed ourselves.

In this respect, the researcher at the UPV/EHU's Department of Geography, Prehistory and Archaeology of the Faculty of Arts Antonio J. Romero has led a piece of experimental research in which ninety lamb bones -- phalanges, radii and scapulae -- were studied and the meat of which was consumed by ten volunteers using only hands and teeth. To control the variables resulting from the processing of the food beforehand, a third of the sample was eaten raw, another third roasted and the rest boiled.

What did they eat and how?

The results, published in the Journal of Archaeological Science: Reports, show that over half of the bones bore the marks of human bites, teeth marks as well as fractures caused by chewing. These marks, analysed under a binocular magnifying glass have a set of characteristics (size and morphology) that allows them to be differentiated from those produced by other animals. Furthermore, as the researcher explained, "although the men produced more marks than the women, according to these data, it is not possible as yet to differentiate between them." On the other hand, cooking the meat beforehand affects the appearance of marks: "the teeth marks tend to appear more regularly in the roasted or boiled specimens," pointed out the researcher, "while the damage on the tips, edges and crushing tends to be more usual in the bones eaten raw."

"There are various similar studies that have explored in depth the damage caused by animals on bones when feeding, but not dealing with the marks that we humans leave behind," explained Antonio Romero. Studies of this type have a clear application in the analysis of archaeological remains, in particular for historical eras. So in each case a whole set of characteristics is studied, such as the location of the damage left on the bones, its morphology and dimensions, which is not always easy to apply to the archaeological record, but "together with other prints of human activity that are more reliable, such as the marks of stone knives, etc., it is possible to complete the interpretation," he insisted. This research constitutes a real breakthrough in the possibility of finding out what kind of meat foods hominids consumed and in what circumstances (whether or not they cooked the meat before they ate it). "It allows us to find out more about human beings in the past and the origin of our modern behaviour, about the way we process foods (cooking them or not) and about our way of eating," he concluded.

Source: University of the Basque Country [August 02, 2016]

Tracking down the first chefs

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China to crack down on damage to Great Wall

The State Administration of Cultural Heritage (SACH) will launch a campaign to crack down on criminal damage to the Great Wall.

Visitors to the Great Wall of China just north of Beijing 
[Credit: AFP/Getty Images]

The campaign will involve regular inspections and random checks on protection efforts by authorities in 15 provinces, autonomous regions and municipalities.

The SACH will open a special tip line for information about violations and damage to the Great Wall from the public.

Built from the third century B.C. to the Ming Dynasty (1368-1644), the Great Wall stretches over 21,000 kilometers from the northwestern province of Gansu to north China's Hebei Province.

According to SACH statistics, about 30 percent of a 6,200-km section of the wall built in the Ming Dynasty has disappeared, and less than 10 percent is considered well-preserved.

The Great Wall has faced threats from both nature and humans. Earthquakes, rain, wind and other natural elements have left the wall with many decayed and crumbling bricks.

Human activities, such as reckless development by some governments and theft of bricks by local villagers for use as building materials, as well as agriculture near the wall, have damaged the landmark, according to research by the China Great Wall Society.

A lack of protection efforts in remote regions and a weak plan for protection have also contributed to the damage, the society added.

In 2006, China released a national regulation on Great Wall protection. However, Great Wall experts have urged local authorities to draw up more practical measures to better implement the regulation.

This year, Inner Mongolia Autonomous Region included Great Wall protection expenditures in its budget. The government of Fangcheng City, Henan Province, began a campaign for conservation experts and local residents to work together to protect the wall.

Source: Xinhua Net [August 02, 2016]

China to crack down on damage to Great Wall

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'Red gene' in birds and turtles suggests dinosaurs had bird-like colour vision

Earlier this year, scientists used zebra finches to pinpoint the gene that enables birds to produce and display the colour red.

Dinosaurs would have had the same ability to see a wide spectrum of redness as birds and turtles, 
according to a new study [Credit: Web]

Now, a new study shows the same 'red gene' is also found in turtles, which share an ancient common ancestor with birds. Both share a common ancestor with dinosaurs.

The gene, called CYP2J19, allows birds and turtles to convert the yellow pigments in their diets into red, which they then use to heighten colour vision in the red spectrum through droplets of red oil in their retinas.

Birds and turtles are the only existing tetrapods, or land vertebrates, to have these red retinal oil droplets. In some birds and a few turtle species, red pigment produced by the gene is also used for external display: red beaks and feathers, or the red neck patches and rims of shells seen in species such as the painted turtle.

The scientists mined the genetic data of various bird and reptile species to reconstruct an evolutionary history of the CYP2J19 gene, and found that it dated back hundreds of millions of years in the ancient archelosaur genetic line - the ancestral lineage of turtles, birds and dinosaurs.

The findings, published today in the journal Proceedings of the Royal Society B, provide evidence that the 'red gene' originated around 250 million years ago, predating the split of the turtle lineage from the archosaur line, and runs right the way through turtle and bird evolution.

Scientists say that, as dinosaurs split from this lineage after turtles, and were closely related to birds, this strongly suggests that they would have carried the CYP2J19 gene, and had the enhanced 'red vision' from the red retinal oil.

This may have even resulted in some dinosaurs producing bright red pigment for display purposes as well as colour vision, as seen in some birds and turtles today, although researchers say this is more speculative.

The painted turtle, widespread across North America, is one of the turtle species that uses red pigment for external display 
as well as colour vision. Samples from this species were used in the new study [Credit: Nicole Valenzuela]

"These findings are evidence that the red gene originated in the archelosaur lineage to produce red for colour vision, and was much later independently deployed in both birds and turtles to be displayed in the red feathers and shells of some species, going from seeing red to being red," says senior author Dr Nick Mundy, from the University of Cambridge's Department of Zoology.

"This external redness was often sexually selected as an 'honest signal' of genuine high quality in a mate," he says.

The previous research in zebra finches showed a possible link between red beaks and the ability to break down toxins in the body, suggesting external redness signals physiological quality, and there is some evidence that colouration in red-eared terrapins is also linked to honest signalling.

"The excellent red spectrum vision provided by the CYP2J19 gene would help female birds and turtles pick the brightest red males," says Hanlu Twyman, the PhD student who is lead author on the work.

The structure of retinas in the eye includes cone-shaped photoreceptor cells. Unlike mammals, avian and turtle retinal cones contain a range of brightly-coloured oil droplets, including green, yellow and red.

These oil droplets function in a similar way to filters on a camera lens. "By filtering the incoming light, the oil droplets lead to greater separation of the range of wavelengths that each cone responds to, creating much better colour sensitivity," explains Mundy.

"Humans can distinguish between some shades of red such as scarlet and crimson. However, birds and turtles can see a host of intermediate reds between these two shades, for example. Our work suggests that dinosaurs would have also had this ability to see a wide spectrum of redness," he says.

Over hundreds of millennia of evolution, the CYP2J19 gene was independently deployed to generate the red pigments in the external displays of some bird species and a few turtle species. The scientists say their data indicate that co-option of CYP2J19 for red colouration in dinosaurs would also have been possible.

The ancestral lineage that led to scaly lizards and snakes split from the archosaur line before turtles, and, as the findings suggest, before the origin of the red gene. These reptiles either lack retinal oil droplets, or have yellow and green but not red.

However, the crocodilian lineage split from the archelosaur line after turtles, yet crocodiles appear to have lost the CYP2J19 gene, and have no oil droplets of any colour in their retinal cones.

Mundy says there is some evidence that oil droplets were lost from the retinas of species that were nocturnal for long periods of their genetic past, and that this hypothesis fits for mammals and snakes, and may also be the case with crocodiles.

Source: University of Cambridge [August 02, 2016]

'Red gene' in birds and turtles suggests dinosaurs had bird-like colour vision

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Buried oxygen rose to the occasion as Earth's early atmosphere formed

Research by geoscientists at Yale, Arizona State University, and Bayerisches Geoinstitut in Germany suggests that convection in Earth's mantle�the slow movement of rocks circulating beneath the surface, caused by heat from inside the Earth�is affected by the distribution of oxygen in those minerals.

Oxygen buried deep underground in minerals may have prompted the churning of Earth's rocky mantle 
billions of years ago and helped transform the planet's early atmosphere, according to a new study 
[Credit: Yale University]

"When there's less oxygen present in the rock, it's denser than when there is more oxygen present, even though the rest of the elements are the same. The more oxidized rock preferentially rises over the reduced rock," said Kanani Lee, the study's principal investigator and an associate professor of geology and geophysics at Yale.

This process had consequences both above and below the surface. Deep below the surface, the more oxygen-depleted rocks sank to the bottom of the rocky mantle, leading to the creation of massive, dense piles just above the Earth's core such as those found deep beneath the Pacific and Atlantic oceans.

"This is the first time anyone has shown that the relative amount of oxygen deep in the Earth influences the minerals that rocks are made of and how it changes their densities," Lee said.

Tingting Gu, a former Yale postdoctoral associate and the paper's lead author, added, "The mantle is not entirely isolated from the surface. For example, gases from volcanic eruptions connect the mantle with the atmosphere. Our model predicts that early in Earth's history, the shallow mantle was less oxidized and thus released gases such as methane that would consume oxygen produced by photosynthesis. But as time progressed and the less dense oxidized material rose in the mantle, biotic oxygen could be preserved and accumulate in the atmosphere. This process could be unique among the terrestrial planets because of their different compositions."

The findings appear online in the journal Nature Geoscience.

Author: Jim Shelton | Source: Yale University [August 02, 2016]

Buried oxygen rose to the occasion as Earth's early atmosphere formed

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