Global human genomes reveal rich genetic diversity shaped by complex evolutionary history

A new study has provided the most comprehensive analysis of human genetic diversity to date, after the sequencing of 929 human genomes by scientists at the Wellcome Sanger Institute, the University of Cambridge and their collaborators. The study uncovers a large amount of previously undescribed genetic variation and provides new insights into our evolutionary past, highlighting the complexity of the process through which our ancestors diversified, migrated and mixed throughout the world.

The resource, published in Science (20 March), is the most detailed representation of the genetic diversity of worldwide populations to date. It is freely available to all researchers to study human genetic diversity, including studies of genetic susceptibility to disease in different parts of the world.

The consensus view of human history tells us that the ancestors of present-day humans diverged from the ancestors of extinct Neanderthal and Denisovan groups around 500,000-700,000 years ago, before the emergence of 'modern' humans in Africa in the last few hundred thousand years.

Around 50,000-70,000 years ago, some humans expanded out of Africa and soon after mixed with archaic Eurasian groups. After that, populations grew rapidly, with extensive migration and mixture as many groups transitioned from hunter-gatherers to food producers over the last 10,000 years.

This study is the first to apply the latest high-quality sequencing technology to such a large and diverse set of humans, covering 929 genomes from 54 geographically, linguistically and culturally diverse populations from across the globe. The sequencing and analysis of these genomes, which are part of the Human Genome Diversity Project (HGDP)-CEPH panel, now provides unprecedented detail of our genetic history.

The team found millions of previously unknown DNA variations that are exclusive to one continental or major geographical region. Though most of these were rare, they included common variations in certain African and Oceanian populations that had not been identified by previous studies.

Variations such as these may influence the susceptibility of different populations to disease. However, medical genetics studies have so far predominantly been conducted in populations of European ancestry, meaning that any medical implications that these variants might have are not known. Identifying these novel variants represents a first step towards fully expanding the study of genomics to underrepresented populations.

However, no single DNA variation was found to be present in 100 per cent of genomes from any major geographical region while being absent from all other regions. This finding underlines that the majority of common genetic variation is found across the globe.

Dr Anders Bergström, of the Francis Crick Institute and an alumnus of the Wellcome Sanger Institute, said: "The detail provided by this study allows us to look deeper into human history, particularly inside Africa where less is currently known about the timescale of human evolution. We find that the ancestors of present-day populations diversified through a gradual and complex process mostly during the last 250,000 years, with large amounts of gene flow between these early lineages. But we also see evidence that small parts of human ancestries trace back to groups that diversified much earlier than this."

Hélène Blanché, Head of the Biological Resource Centre at the Centre d'Etude du Polymorphisme Humain (CEPH) in Paris, France, said: "The Human Genome Diversity Project resource has facilitated many new discoveries about human history in the past two decades. It is exciting to see that with the latest genomic sequencing technology, these genomes will continue to help us understand our species and how we have evolved."

The study also provides evidence that the Neanderthal ancestry of modern humans can be explained by just one major 'mixing event', most likely involving several Neanderthal individuals coming into contact with modern humans shortly after the latter had expanded out of Africa. In contrast, several different sets of DNA segments inherited from Denisovans were identified in people from Oceania and East Asia, suggesting at least two distinct mixing events.

The discovery of small amounts of Neanderthal DNA in west African people, most likely reflecting later genetic backflow into Africa from Eurasia, further highlights how human genetic history is characterised by multiple layers of complexity. Until recently, it was thought that only people outside sub-Saharan Africa had Neanderthal DNA.

Read more at Science Daily

The strange orbits of 'Tatooine' planetary disks

ALMA radio antennas at night.

Astronomers using the Atacama Large Millimeter/submillimeter Array (ALMA) have found striking orbital geometries in protoplanetary disks around binary stars. While disks orbiting the most compact binary star systems share very nearly the same plane, disks encircling wide binaries have orbital planes that are severely tilted. These systems can teach us about planet formation in complex environments.

In the last two decades, thousands of planets have been found orbiting stars other than our Sun. Some of these planets orbit two stars, just like Luke Skywalker's home Tatooine. Planets are born in protoplanetary disks -- we now have wonderful observations of these thanks to ALMA -- but most of the disks studied so far orbit single stars. 'Tatooine' exoplanets form in disks around binary stars, so-called circumbinary disks.

Studying the birthplaces of 'Tatooine' planets provides a unique opportunity to learn about how planets form in different environments. Astronomers already know that the orbits of binary stars can warp and tilt the disk around them, resulting in a circumbinary disk misaligned relative to the orbital plane of its host stars. For example, in a 2019 study led by Grant Kennedy of the University of Warwick, UK, ALMA found a striking circumbinary disk in a polar configuration.

"With our study, we wanted to learn more about the typical geometries of circumbinary disks," said astronomer Ian Czekala of the University of California at Berkeley. Czekala and his team used ALMA data to determine the degree of alignment of nineteen protoplanetary disks around binary stars. "The high resolution ALMA data was critical for studying some of the smallest and faintest circumbinary disks yet," said Czekala.

The astronomers compared the ALMA data of the circumbinary disks with the dozen 'Tatooine' planets that have been found with the Kepler space telescope. To their surprise, the team found that the degree to which binary stars and their circumbinary disks are misaligned is strongly dependent on the orbital period of the host stars. The shorter the orbital period of the binary star, the more likely it is to host a disk in line with its orbit. However, binaries with periods longer than a month typically host misaligned disks.

"We see a clear overlap between the small disks, orbiting compact binaries, and the circumbinary planets found with the Kepler mission," Czekala said. Because the primary Kepler mission lasted 4 years, astronomers were only able to discover planets around binary stars that orbit each other in fewer than 40 days. And all of these planets were aligned with their host star orbits. A lingering mystery was whether there might be many misaligned planets that Kepler would have a hard time finding. "With our study, we now know that there likely isn't a large population of misaligned planets that Kepler missed, since circumbinary disks around tight binary stars are also typically aligned with their stellar hosts," added Czekala.

Still, based on this finding, the astronomers conclude that misaligned planets around wide binary stars should be out there and that it would be an exciting population to search for with other exoplanet-finding methods like direct imaging and microlensing. (NASA's Kepler mission used the transit method, which is one of the ways to find a planet.)

Czekala now wants to find out why there is such a strong correlation between disk (mis)alignment and the binary star orbital period. "We want to use existing and coming facilities like ALMA and the next generation Very Large Array to study disk structures at exquisite levels of precision," he said, "and try to understand how warped or tilted disks affect the planet formation environment and how this might influence the population of planets that form within these disks."

"This research is a great example of how new discoveries build on previous observations," said Joe Pesce, National Science Foundation Program Officer for NRAO and ALMA. "Discerning trends in the circumbinary disk population was only made possible by building on the foundation of archival observational programs undertaken by the ALMA community in previous cycles."

Read more at Science Daily

Public health leadership paramount to emerging coronavirus pandemic

For decades, public health officials have directed the containment of emerging pandemics -- perhaps most notably -- the worldwide eradication of smallpox starting in the early to mid-1960s. Since then, surveillance systems have increased in number and sophistication with advances in data collection, analysis, and communication. From influenza to smallpox, the establishment of systematic reporting systems and prompt action based on results have enabled public health officials to lead the charge in containing emerging pandemics.

Researchers from Florida Atlantic University's Schmidt College of Medicine and Christine E. Lynn College of Nursing, in collaboration with the Christine E. Lynn Women's Health & Wellness Center, Boca Raton Regional Hospital/ Baptist Health South Florida and the University of Wisconsin School of Medicine & Public Health, have published a commentary online ahead of print in the American Journal of Medicine about the urgent need for public health leadership in the wake of the emerging coronavirus (COVID-19) pandemic.

Their message? Public health leaders, namely, Anthony S. Fauci, M.D., director of the United States National Institute of Allergy and Infectious Diseases, whom they liken as the "Babe Ruth" of virology, should guide the nation and other comparable world leaders through this pandemic and ensure preparedness for the challenges ahead.

Over the course of a decade spanning the tenures of U.S. presidents John F. Kennedy, Lyndon B. Johnson, Richard Nixon and Gerald Ford, using evidence-based leadership, public health officials led the U.S. and worldwide efforts that resulted in smallpox becoming the first human disease ever eradicated from the face of the earth. At the helm of this effort were Alexander D. Langmuir, M.D., who created the Epidemic Intelligence Service (EIS) and Epidemiology Program at the U.S. Centers for Disease Control and Prevention (CDC), and Donald A. Henderson, M.D., chief of the Virus Disease Surveillance Program at the CDC in the 1960s.

"Based on the existing totality of evidence, it appears that coronavirus is comparable in communicability to influenza but with perhaps a tenfold higher case fatality rate," said Charles H. Hennekens, M.D., Dr.P.H., first author and first Sir Richard Doll Professor in FAU's Schmidt College of Medicine, who trained under Langmuir when he was a lieutenant commander in the U.S. Public Health Service as an EIS medical epidemiologist with the CDC. "The anticipated number of deaths due to coronavirus may become comparable to the most lethal epidemic of influenza in U.S. history, which occurred in 1918 when approximately 675,000 Americans died."

In contrast, with respect to usual outbreaks of influenza, the 2018-19 flu season affected about 42.9 million Americans, of which 647,000 were hospitalized and about 61,200 died.

Hennekens and co-authors Safiya George, Ph.D., dean of FAU's Christine E. Lynn College of Nursing; Terry A. Adirim, M.D., M.P.H., M.B.A., senior associate dean for clinical affairs, chair of the Department of Integrated Medical Sciences and professor of pediatrics in FAU's Schmidt College of Medicine; Heather Johnson, M.D., preventive cardiologist/cardiologist at the Christine E. Lynn Women's Health & Wellness Center, Boca Raton Regional Hospital/Baptist Health South Florida; and Dennis G. Maki, M.D., professor of medicine, University of Wisconsin School of Medicine & Public Health, and an internationally renowned infectious disease clinician and epidemiologist who was a fellow EIS officer with Hennekens under Langmuir and Henderson.

"U.S. health care workers today are appropriately confused about current and future issues concerning COVID-19, an infectious disease that is caused by the severe acute respiratory syndrome coronavirus known as SARS-coV2, which is now responsible for an emerging pandemic," said Adirim, who recently served as deputy assistant secretary of defense for health affairs at the Department of Defense and a senior medical official at the Department of Homeland Security during the 2009-H1N1 Pandemic. "Appropriate concerns and not fear should play a major role in the emerging pandemic, and public health efforts should focus on public health issues, not political or economic considerations."

More than 80 percent of symptomatic individuals will experience only mild flu-like symptoms. However, more alarmingly, approximately 15 percent of affected patients will become seriously ill and 5 percent will need critical care. Younger and healthier people will represent a larger proportion of the population with mild to moderate symptoms. Those at highest risk -- the elderly, those with certain chronic diseases such as cardiovascular disease and lung disease as well as those receiving chemotherapy or who are otherwise immunocompromised through illness or therapies.

"The good news is that the majority of those infected with the virus will recover, however, the most vulnerable are not projected to fare as well. It is therefore, extremely important that we all take an active role in not only protecting ourselves, but also those among us who are the most vulnerable," said George, who specializes in immunology, oncology and HIV/AIDS. "In only eight days, Florida went from 18 cases and two deaths on March 9 to 314 positive cases and seven deaths on March 18. However, these numbers are still less than 10 percent of the rising number of cases in New York and still much less than California and Washington. Therefore, education, social distancing, staying away from others when symptomatic and continued handwashing and vigilance remain key in minimizing transmission."

The authors note that the staggering estimates of the potential numbers of hospitalizations could paralyze the U.S. health care delivery system. Moreover, the overcrowding of hospitals by patients with coronavirus could make it more difficult to provide care to those with life threatening conditions.

"The first case was reported in Wuhan, China on Dec. 31, 2019 and in the U.S. on Jan. 22," said Adirim. "During that interval, containment was potentially achievable in the U.S. but required collaborative efforts such as widespread utilization of rapid testing kits available from the World Health Organization. Now, however, we must employ strategies to flatten the curve to decrease avoidable morbidity and mortality."

By March 8, South Korea, which has a population of about one-sixth that of the U.S., had tested more than 240,000 (1 per 250) compared to the U.S., which had tested about 13,662 (3,903 from the CDC and 9,721 from public health laboratories). In both South Korea and the U.S., only about 3 percent of these cases tested positive for coronavirus.

Read more at Science Daily

Maize, not metal, key to native settlements' history in NY

New Cornell University research is producing a more accurate historical timeline for the occupation of Native American sites in upstate New York, based on radiocarbon dating of organic materials and statistical modeling.

The results from the study of a dozen sites in the Mohawk Valley were recently published in the online journal PLoS ONE by Sturt Manning, professor of classical archaeology; and John Hart, curator in the research and collections division of the New York State Museum in Albany.

The findings, Manning said, are helping to refine our understanding of the social, political and economic history of the Mohawk Valley region at the time of early European intervention.

The work is part of the Dating Iroquoia Project, involving researchers from Cornell, the University of Georgia and the New York State Museum, and supported by the National Science Foundation.

The new paper continues and expands upon research on four Iroquoian (Wendat) sites in southern Ontario, published by the project team in 2018. Using similar radiocarbon dating and statistical analysis methods, the 2018 findings also impacted timelines of Iroquoian history and European contact.

"The Mohawk case was chosen because it is an iconic series of indigenous sites and was subject to one of the first big dating efforts in the 1990s," said Manning. "We have now examined a southern Iroquois (Haudenosaunee) case as well as a northern Iroquois (Wendat) case, and we again find that the previous dating scheme is flawed and needs revision."

The Mohawk and Hudson river valleys were key inland routes for Europeans entering the region from the coast in the 16th and early 17th centuries. Colonization of the new world enriched Europe -- Manning has described this period as "the beginning of the globalized world" -- but brought disease and genocide to indigenous peoples, and their history during this time is often viewed in terms of trade and migration.

The standard timeline created for historical narratives of indigenous settlement, Manning noted, has largely been based on the presence or absence of types of European trade goods -- e.g., metal items or glass beads. Belying this Eurocentric colonial lens, trade practices differed from one native community to another, and not all of them accepted contact with, or goods from, European settlers.

To clarify the origins of metal goods found in the upstate New York settlements, the team used portable X-ray fluorescence (pXRF) analysis to determine whether copper artifacts were of native or European origin. They then also re-assessed the dates of the sites using radiocarbon dating coupled with Bayesian statistical analysis.

Bayesian analysis, Manning explained, is "a statistical method that integrates prior knowledge in order to better define the probability parameters around a question or unknown. In this case, archaeological and ethno-historic information was combined with data from a large set of radiocarbon dates in order to estimate occupation dates for a set of Mohawk villages across the 13th to early 17th centuries."

The focus was on the period from the late 15th to the early 17th century, he said, or "the long 16th century of change in the northeast."

The results "add to a growing appreciation of the interregional variations in the circulation and adoption patterns of European goods in northeastern North America in the 16th to earlier 17th centuries," Manning said.

In previous indigenous site studies, where artifacts indicated trade interactions, researchers might assume "that trade goods were equally available, and wanted, all over the region," and that different indigenous groups shared common trade practices, he said.

Direct radiocarbon dating of organic matter, such as maize kernels, tests those assumptions and removes the colonial lens, allowing an independent timeframe for historical narratives, Manning said.

At several major Iroquois sites lacking close European connections, independent radiocarbon studies indicate substantially different date ranges from the previous estimates based on trade goods.

"The re-dating of a number of Iroquoian sites also raises questions about the social, political and economic history of indigenous communities from the 14th to the 17th centuries," Manning said. "For example ... a shift to larger and fortified communities, and evidence of increased conflict," was previously thought to have occurred around the mid-15th century.

But the radiocarbon findings from some larger sites in Ontario and their cultivated maize fields ¬- 2,000 acres or more in some instances -- date the sites from the mid-16th to the start of the 17th century, he said.

"However, as this New York state study shows, other areas had their own and differing trajectories. Thus with direct dating we start to see real, lived, histories of communities, and not some imposed generic assessment," Manning said. "The emerging new and independent timeframe for northeast North America will now form the basis of a wider indigenous history," Manning said, "free from a Eurocentric bias, with several past assumptions open for an overdue rethink."

Read more at Science Daily

On the origin of massive stars

A scene of stellar creation, captured by the NASA/ESA Hubble Space Telescope, sits near the outskirts of the famous Tarantula Nebula. This cloud of gas and dust, as well as the many young and massive stars surrounding it, is the perfect laboratory to study the origin of massive stars.

The bright pink cloud and the young stars surrounding it in this image taken with the NASA/ESA Hubble Space Telescope have the uninspiring name LHA 120-N 150. This region of space is located on the outskirts of the Tarantula Nebula, which is the largest known stellar nursery in the local Universe. The nebula is situated over 160,000 light-years away in the Large Magellanic Cloud, a neighbouring irregular dwarf galaxy that orbits the Milky Way.

The Large Magellanic Cloud has had one or more close encounters in the past, possibly with the Small Magellanic Cloud. These interactions have caused an episode of energetic star formation in our tiny neighbour -- part of which is visible as the Tarantula Nebula.

Also known as 30 Doradus or NGC 2070, the Tarantula Nebula owes its name to the arrangement of bright patches that somewhat resemble the legs of a tarantula. It measures nearly 1000 light-years across. Its proximity, the favourable inclination of the Large Magellanic Cloud, and the absence of intervening dust make the Tarantula Nebula one of the best laboratories in which to study the formation of stars, in particular massive stars. This nebula has an exceptionally high concentration of massive stars, often referred to as super star clusters.

Astronomers have studied LHA 120-N 150 to learn more about the environment in which massive stars form. Theoretical models of the formation of massive stars suggest that they should form within clusters of stars; but observations indicate that up to ten percent of them also formed in isolation. The giant Tarantula Nebula with its numerous substructures is the perfect laboratory in which to resolve this puzzle as in it massive stars can be found both as members of clusters and in isolation.

With the help of Hubble, astronomers try to find out whether the isolated stars visible in the nebula truly formed alone or just moved away from their stellar siblings. However, such a study is not an easy task; young stars, before they are fully formed -- especially massive ones -- look very similar to dense clumps of dust.

LHA 120-N 150 contains several dozen of these objects. They are a mix of unclassified sources -- some probably young stellar objects and others probably dust clumps. Only detailed analysis and observations will reveal their true nature and that will help to finally solve the unanswered question of the origin of massive stars.

Read more at Science Daily

Fine-tuning radiocarbon dating could 'rewrite' ancient events

Tree rings

Radiocarbon dating, invented in the late 1940s and improved ever since to provide more precise measurements, is the standard method for determining the dates of artifacts in archaeology and other disciplines.

"If it's organic and old -- up to 50,000 years -- you date it by radiocarbon," said Sturt Manning, the Goldwin Smith Professor of Classical Archaeology in the College of Arts and Sciences.

Manning is lead author of a new paper that points out the need for an important new refinement to the technique. The outcomes of his study, published March 18 in Science Advances, have relevance for understanding key dates in Mediterranean history and prehistory, including the tomb of Tutankhamen and a controversial but important volcanic eruption on the Greek island of Santorini.

Radiocarbon dating measures the decomposition of carbon-14, an unstable isotope of carbon created by cosmic radiation and found in all organic matter. Cosmic radiation, however, is not constant at all times. To account for fluctuations of cosmic radiation in the Earth's atmosphere, the radiocarbon content of known-age tree rings was measured backward in time from the 20th century, for thousands of years.

Tree-ring calibrated radiocarbon started to be widely used 50 years ago. A standard calibration curve was introduced in 1986 and is updated every few years as more data are added.

"A single Northern Hemisphere calibration curve has formed the basis of radiocarbon dating in Europe and the Mediterranean for five decades, setting the time frame for prehistory," Manning and co-authors write. "However, as measurement precision increases, there is mounting evidence for some small but substantive regional (partly growing season) offsets in the same-year radiocarbon levels."

In their study, Manning and co-authors question the accuracy of a single calibration curve for all of the Northern Hemisphere. Using data collected by only one lab to control for interlaboratory variation, they compared radiocarbon data from northern Europe (Germany) and from the Mediterranean (central Turkey) in the 2nd and 1st millennia B.C. They found that some small but critical periods of variation for Mediterranean radiocarbon levels exist. Data from two other radiocarbon labs on samples from central Italy and northern Turkey then provided consistency.

Growing seasons play a role, the paper says. The radiocarbon level on Earth varies according to the season; there's a winter low and a summer high, Manning said. The carbon in a tree ring reflects when the tree was photosynthesizing and, therefore, taking carbon out of the atmosphere.

"In northern Europe or in North America, a tree is going to be doing this in April through September. But a tree in Jordan or Israel does that October through April -- almost the opposite time of the year," he said.

These variations, although small, potentially affect calendar dates for prehistory by up to a few decades, the paper concludes.

Even small date offsets -- 50 years or less -- are important for building the timeline of the Mediterranean region, which, in the last two millennia B.C., was a hotbed of interrelated cultures.

The adjusted dates confirm previously awkward timelines, where radiocarbon and history did not seem to agree for some historical landmarks, including the death and burial of Egyptian pharaoh Tutankhamen, which is dated around the 1320s to 1310s B.C., according to recent Egyptology.

The study also addresses a debate over the date of a massive volcanic eruption on Santorini. This much-studied event is dated around 1500 B.C. by archaeologists but earlier -- 1630 to 1600 B.C. -- by scientists. Manning said the new findings rule out the date of 1500 B.C., but may also modify the science. A 1630-1600 B.C. date remains possible, but a later date in the range 1600-1550 B.C. now becomes plausible, and even works better with existing archaeological and historical records, including writings from Egypt.

The study also has ramifications for understanding which culture influenced the Minoans and Mycenaeans, which led to ancient Greece.

"Getting the date right will rewrite and get our history correct in terms of what groups were significant in shaping what then became classical civilization," Manning said. "An accurate timeline is key to our history."

Read more at Science Daily

Late cretaceous dinosaur-dominated ecosystem

A topic of considerable interest to paleontologists is how dinosaur-dominated ecosystems were structured, how dinosaurs and co-occurring animals were distributed across the landscape, how they interacted with one another, and how these systems compared to ecosystems today. In the Late Cretaceous (~100-66 million years ago), North America was bisected into western and eastern landmasses by a shallow inland sea. The western landmass (Laramidia) contained a relatively thin stretch of land running north-south, which was bordered by that inland sea to the east and the rising Rocky Mountains to the west. Along this ancient landscape of warm and wet coastal plains comes an extremely rich fossil record of dinosaurs and other extinct animals.

Yet, from this record, an unexpected pattern has been identified: Most individual basins preserve an abundant and diverse assemblage of dinosaur species, often with multiple groups of co-occurring large (moose- to elephant-sized) herbivorous species, yet few individual species occur across multiple putatively contemporaneous geological formations (despite them often being less than a few hundred kilometers apart). This is in fairly stark contrast to the pattern seen in modern terrestrial mammal communities, where large-bodied species often have very extensive, often continent-spanning ranges. It has therefore been suggested that dinosaurs (and specifically large herbivorous dinosaurs) were particularly sensitive to environmental differences over relatively small geographic distances (particularly with respect to distance from sea level), and may have even segregated their use of the landscape between more coastal and inland sub-habitats within their local ranges.

In their new study published in Geology, Thomas Cullen and colleagues sought to test some of these hypotheses as part of their broader research reconstructing the paleoecology of Late Cretaceous systems.

One of the methods they're using to do that is stable isotope analysis. This process measures differences in the compositions of non-decaying (hence, "stable") isotopes of various common elements, as the degree of difference in these compositions in animal tissues and in the environment have known relationships to various factors such as diet, habitat use, water source, and temperature. So the team applied these methods to fossilized teeth and scales from a range of animals, including dinosaurs, crocodilians, mammals, bony fish, and rays, all preserved together from a relatively small region over a geologically short period of time in sites called vertebrate microfossil bonebeds.

By analyzing the stable carbon and oxygen isotope compositions of these fossils they were able to reconstruct their isotopic distributions in this ecosystem -- a proxy for their diets and habitat use. They found evidence of expected predator-prey dietary relationships among the carnivorous and herbivorous dinosaurs and among aquatic reptiles like crocodilians and co-occurring fish species.

Critically, says Cullen, "What we didn't see was evidence for large herbivorous dinosaurs segregating their habitats, as the hadrosaurs, ceratopsians, and ankylosaurs we sample all had strongly overlapping stable carbon and oxygen ranges. If some of those groups were making near-exclusive use of certain parts of the broader landscape, such as ceratopsians sticking to coastal environments and hadrosaurs sticking to more inland areas, then we should see them grouping distinctly from each other. Since we didn't see that, that suggests they weren't segregating their resource use in this manner. It's possible they were doing so in different ways though, such as by feeding height segregation, or shifting where in the landscape they go seasonally, and our ongoing research is investigating some of these possibilities."

Another important part of their study was comparing the fossil results to an environmentally similar modern environment in order to examine how similar they are ecologically. For a modern comparison, they examined the animal communities of the Atchafalaya River Basin of Louisiana, the largest contiguous wetland area in the continental U.S. The landscape of this area is very similar to their Cretaceous system, as are many elements of the plant and animal communities (not including the non-avian dinosaurs, of course).

From their comparisons, the team found that the Cretaceous system was similar to the Louisiana one in having a very large amount of resource interchange between the aquatic and terrestrial components of the ecosystem, suggesting that fairly diverse/mixed diets were common, and food being obtained from both terrestrial and aquatic sources was the norm. They also found that habitat use differences among the herbivorous mammals in the Louisiana system was more distinct than among those large herbivorous dinosaurs in the Cretaceous system, lending further evidence to their results about their lack of strict habitat use preferences.

Lastly, the team used modified oxygen stable isotope temperature equations to estimate mean annual temperature ranges for both systems (with the Louisiana one being a test of the accuracy of the method, as they could compare their results to directly measured water and air temperatures). The team found that in their Late Cretaceous ecosystem in Alberta, mean annual temperature was about 16-20 degrees C, a bit cooler than modern day Louisiana, but much warmer than Alberta today, reflecting the hotter greenhouse climate that existed globally about 76 million years ago.

Read more at Science Daily

Bone analyses tell about kitchen utensils in the Middle Ages

Clay pots? Wooden spoons? Copper pots? Silver forks? What materials has man used for making kitchen utensils throughout history? A new study now sheds light on the use of kitchen utensils made of copper.

At first thought, you would not expect hundreds of years old bones from a medieval cemetery to be able to tell you very much -- let alone anything about what kinds of kitchen utensils were used to prepare food.

But when you put such a bone in the hands of Professor Kaare Lund Rasmussen, University of Southern Denmark, the bone begins to talk about the past.

A warehouse full of bones

"For the first time, we have succeeded in tracing the use of copper cookware in bones. Not in isolated cases, but in many bones over many years, and thus we can identify trends in historical use of copper in the household," he explains.

The research team has analyzed bones from 553 skeletons that are between 1200 and 200 years old. They all come from nine, now abandoned cemeteries in Jutland, Denmark and Northern Germany. The skeletons are today kept at Schloss Gottorf in Schleswig, Germany and at the University of Southern Denmark.

Some of the bones examined are from Danish cities such as Ribe and Haderslev, while others are from small rural communities, such as Tirup and Nybøl.

Your body needs copper

The element copper can be traced in bones if ingested. Copper is needed for the body to function; it is, among other things, involved in a number of metabolic processes, such as the function of the immune system -- so without copper, the individual would not be able to live.

The need for copper is usually met through the food we eat and most of us probably never think about this.

It is different with the high concentrations of copper now revealed to have been ingested by our predecessors in the Viking Age and the Medieval Times. Much of this copper must have come from the kitchen utensils with which the daily meals were prepared, the researchers believe.

How did the copper get into the body?

One possibility is that the copper pots were scraped by metal knives, releasing copper particles, and that these particles were ingested with the food.

Or maybe copper was dissolved and mixed with food, if the pot was used for storing or cooking acidic foods.

"The bones show us that people consumed tiny portions of copper every day throughout their lives. We can also see that entire cities have been doing this for hundreds of years. In Ribe, the inhabitants did this for 1000 years," says Kaare Lund Rasmussen.

Who ate the copper?

Apparently, the copper intake was at no time so great that it became toxic. But the researchers can't say for sure.

However, they can with certainty say that some people never ingested copper enough for it to be traceable in the bones. Instead, they ate food prepared in pots made of other materials.

These people lived in the countryside. The bones reveal that inhabitants in the small villages of Tirup and Nybøl did not prepare their food in copper pots.

Rely less on written sources

But how do these findings go with historical accounts and pictures of copper cookware used in in country kitchens?

"A copper pot in a country kitchen may have been so unusual that the owner would tell everybody about it and maybe even write it down. However, such an account should not lead to the conclusion that copper cookware was commonly used in the countryside. Our analyses show the opposite," says Kaare Lund Rasmussen.

Contrary, the use of copper pots was evident in the towns of Ribe, Horsens, Haderslev and Schleswig.

1000 years of constant copper ingestion

"The cities were dynamic communities and homes of rich people who could acquire copper items. Wealthy people probably also lived in the countryside, but they did not spend their money on copperware," concludes Kaare Lund Rasmussen.

208 of the skeletons originate from a cemetery in Ribe, covering a period of 1000 years from AD 800 to AD 1800, spanning from the Viking Age over the Middle Ages to recent times.

"These skeletons show us there was a continuous exposure of copper throughout the period. Thus, for 1000 years, the inhabitants consumed copper via their daily diet."

Read more at Science Daily

Black hole team discovers path to razor-sharp black hole images

Last April, the Event Horizon Telescope (EHT) sparked international excitement when it unveiled the first image of a black hole. Today, a team of researchers have published new calculations that predict a striking and intricate substructure within black hole images from extreme gravitational light bending.

"The image of a black hole actually contains a nested series of rings," explains Michael Johnson of the Center for Astrophysics | Harvard and Smithsonian (CfA). "Each successive ring has about the same diameter but becomes increasingly sharper because its light orbited the black hole more times before reaching the observer. With the current EHT image, we've caught just a glimpse of the full complexity that should emerge in the image of any black hole."

Because black holes trap any photons that cross their event horizon, they cast a shadow on their bright surrounding emission from hot infalling gas. A "photon ring" encircles this shadow, produced from light that is concentrated by the strong gravity near the black hole. This photon ring carries the fingerprint of the black hole -- its size and shape encode the mass and rotation or "spin" of the black hole. With the EHT images, black hole researchers have a new tool to study these extraordinary objects.

"This is an extremely exciting time to be thinking about the physics of black holes," says Daniel Kapec from the Institute for Advanced Study. "Einstein's theory of general relativity makes a number of striking predictions for the types of observations that are finally coming within reach, and I think we can look forward to lots of advances in the coming years. As a theorist, I find the rapid convergence between theory and experiment especially rewarding, and I hope we can continue to isolate and observe more universal predictions of general relativity as these experiments become more sensitive."

The research team included observational astronomers, theoretical physicists, and astrophysicists.

"Bringing together experts from different fields enabled us to really connect a theoretical understanding of the photon ring to what is possible with observation," notes George Wong, a physics graduate student at the University of Illinois at Urbana-Champaign. Wong developed software to produce simulated black hole images at higher resolutions than had previously been computed and to decompose these into the predicted series of sub-images. "What started as classic pencil-and-paper calculations prompted us to push our simulations to new limits."

The researchers also found that the black hole's image substructure creates new possibilities to observe black holes. "What really surprised us was that while the nested subrings are almost imperceptible to the naked eye on images -- even perfect images -- they are strong and clear signals for arrays of telescopes called interferometers," says Johnson. "While capturing black hole images normally requires many distributed telescopes, the subrings are perfect to study using only two telescopes that are very far apart. Adding one space telescope to the EHT would be enough."

Read more at Science Daily

Sea otters, opossums and the surprising ways pathogens move from land to sea

Sea otter eating clam

A parasite known only to be hosted in North America by the Virginia opossum is infecting sea otters along the West Coast. A study from the University of California, Davis, elucidates the sometimes surprising and complex pathways infectious pathogens can move from land to sea to sea otter.

For the study, published in the journal Scientific Reports, researchers tested sea otters ranging from Southern California to Alaska for the presence of Sarcocystis neurona, a parasite and important cause of death in sea otters.

They were surprised to find several infected sea otters in the northern part of Vancouver Island in British Columbia, where Virginia opossums -- also known as the North American opossum -- are not known to live. They wondered: Could this parasite travel very long distances in water, or is there an additional unknown host for this pathogen?

To answer this question, the scientists examined spatial patterns and previous research into pathogen transmission, diet and movement of otters. Their results suggest the pathogen may be carried by water runoff from land to sea, where it can be concentrated through ocean movement and prey species, such as clams.

Learning from Otters and Cats

A related parasite, Toxoplasma gondii, is also known to kill sea otters. Decades of research by a consortium of scientists led by UC Davis School of Veterinary Medicine and the California Department of Fish and Wildlife traced that parasite to another land-based mammal -- wild and domestic cats near watersheds.

"We know S. neurona kills sea otters, and we were pretty sure it comes from the land, but we didn't really know how this pathogen finds them," said lead author Tristan Burgess, a doctoral student in the lab of Christine Kreuder Johnson at the UC Davis One Health Institute at the time of the study. "This new research suggests that there may be a long and complex transmission pathway, a little like the way Toxoplasma finds sea otters, but with a different cast of characters."

Risk Factors

Most infections occurred in California and Washington, more so than Alaska and British Columbia. The study found that higher risks of exposure were associated with:

• Adult male otters.
• Human-dense habitats, some wetlands and croplands.
• Wetlands can help filter and deactivate some pathogens, but the study noted they may be potential opossum habitat, as well.
• Habitats of soft sediment, like the mouths of rivers and estuaries.
• Otters consuming a diet rich in clams, where the parasite may be concentrated.

Marine Mammal Sentinels

This study highlights risk factors for one species' exposure to one parasite. But it also provides a better understanding of how parasites and infection can move from land to sea to marine mammals.

"Seemingly unimportant species can be important in unexpected ways," Burgess said. "We should also remember the value of marine mammals as sentinels, not just of the health of their marine habitat, but of nearby terrestrial environments, too."

Read more at Science Daily

New telescope design could capture distant celestial objects with unprecedented detail

Researchers have designed a new camera that could allow hypertelescopes to image multiple stars at once. The enhanced telescope design holds the potential to obtain extremely high-resolution images of objects outside our solar system, such as planets, pulsars, globular clusters and distant galaxies.

"A multi-field hypertelescope could, in principle, capture a highly detailed image of a star, possibly also showing its planets and even the details of the planets' surfaces," said Antoine Labeyrie, emeritus professor at the Collège de France and Observatoire de la Cote d'Azur, who pioneered the hypertelescope design. "It could allow planets outside of our solar system to be seen with enough detail that spectroscopy could be used to search for evidence of photosynthetic life."

In The Optical Society's (OSA) journal Optics Letters, Labeyrie and a multi-institutional group of researchers report optical modeling results that verify that their multi-field design can substantially extend the narrow field-of-view coverage of hypertelescopes developed to date.

Making the mirror larger

Large optical telescopes use a concave mirror to focus light from celestial sources. Although larger mirrors can produce more detailed pictures because of their reduced diffractive spreading of the light beam, there is a limit to how large these mirrors can be made. Hypertelescopes are designed to overcome this size limitation by using large arrays of mirrors, which can be spaced widely apart.

Researchers have previously experimented with relatively small prototype hypertelescope designs, and a full-size version is currently under construction in the French Alps. In the new work, researchers used computer models to create a design that would give hypertelescopes a much larger field of view. This design could be implemented on Earth, in a crater of the moon or even on an extremely large scale in space.

Building a hypertelescope in space, for example, would require a large flotilla of small mirrors spaced out to form a very large concave mirror. The large mirror focuses light from a star or other celestial object onto a separate spaceship carrying a camera and other necessary optical components.

"The multi-field design is a rather modest addition to the optical system of a hypertelescope, but should greatly enhance its capabilities," said Labeyrie. "A final version deployed in space could have a diameter tens of times larger than the Earth and could be used to reveal details of extremely small objects such as the Crab pulsar, a neutron star believed to be only 20 kilometers in size."

Expanding the view

Hypertelescopes use what is known as pupil densification to concentrate light collection to form high-resolution images. This process, however, greatly limits the field of view for hypertelescopes, preventing the formation of images of diffuse or large objects such as a globular star cluster, exoplanetary system or galaxy.

The researchers developed a micro-optical system that can be used with the focal camera of the hypertelescope to simultaneously generate separate images of each field of interest. For star clusters, this makes it possible to obtain separate images of each of thousands of stars simultaneously.

The proposed multi-field design can be thought of as an instrument made of multiple independent hypertelescopes, each with a differently tilted optical axis that gives it a unique imaging field. These independent telescopes focus adjacent images onto a single camera sensor.

The researchers used optical simulation software to model different implementations of a multi-field hypertelescope. These all provided accurate results that confirmed the feasibility of multi-field observations.

Read more at Science Daily

Mysterious bone circles made from the remains of mammoths reveal clues about Ice Age

Illustration of mammoths.

Mysterious bone circles made from the remains of dozens of mammoths have revealed clues about how ancient communities survived Europe's ice age.

About 70 of these structures are known to exist in Ukraine and the west Russian Plain.

New analysis shows the bones at one site are more than 20,000 years old, making it the oldest such circular structure built by humans discovered in the region. The bones were likely sourced from animal graveyards, and the circle was then hidden by sediment and is now a foot below current surface level.

The majority of the bones found at the site investigated, in the Russian Plains, are from mammoths. A total of 51 lower jaws and 64 individual mammoth skulls were used to construct the walls of the 30ft by 30ft structure and scattered across its interior. Small numbers of reindeer, horse, bear, wolf, red fox and arctic fox bones were also found.

Archaeologists from the University of Exeter have also found for the first time the remains of charred wood and other soft non-woody plant remains within the circular structure, situated just outside the modern village of Kostenki, about 500km south of Moscow. This shows people were burning wood as well as bones for fuel, and the communities who lived there had learned where to forage for edible plants during the Ice Age. The plants could also have been used for poisons, medicines, string or fabric. More than 50 small charred seeds were also found -- the remains of plants growing locally or possibly food remains from cooking and eating.

Dr Alexander Pryor, who led the study, said: "Kostenki 11 represents a rare example of Palaeolithic hunter-gatherers living on in this harsh environment. What might have brought ancient hunter gatherers to this site? One possibility is that the mammoths and humans could have come to the area on masse because it had a natural spring that would have provided unfrozen liquid water throughout the winter -- rare in this period of extreme cold.

"These finds shed new light on the purpose of these mysterious sites. Archaeology is showing us more about how our ancestors survived in this desperately cold and hostile environment at the climax of the last ice age. Most other places at similar latitudes in Europe had been abandoned by this time, but these groups had managed to adapt to find food, shelter and water."

The last ice age, which swept northern Europe between 75-18,000 years ago, reached its coldest and most severe stage at around 23-18,000 years ago, just as the site at Kostenki 11 was being built. Climate reconstructions indicate at the time summers were short and cool and winters were long and cold, with temperatures around -20 degrees Celsius or colder. Most communities left the region, likely because of lack of prey to hunt and plant resources they depended upon for survival. Eventually the bone circles were also abandoned as the climate continued to get colder and more inhospitable.

Previously archaeologists have assumed that the circular mammoth bone structures were used as dwellings, occupied for many months at a time. The new study suggests this may not always have been the case as the intensity of activity at Kostenki 11 appears less than would be expected from a long term base camp site.

Read more at Science Daily

Early evolution of the brain's cortex revealed in new study

Lamprey

A new study on the lamprey brain has enabled researchers at Karolinska Institutet in Sweden to push the birth of the cortex back in time by some 300 million years to over 500 million years ago, providing new insights into brain evolution. The study is published in the scientific journal Nature Ecology & Evolution.

The human brain is one of the most complex structures that evolution has created. It has long been believed that most of the forebrain evolution took place largely in mammals and that the brains of simpler, pre-mammalian animal groups such as fish and amphibians lack a functional cortex. The cortex, which is the outer layer of the brain, controls the more complex cerebral functions like vision and movement and higher skills such as language, memory and emotion.

"We've spent a long time studying brain evolution using the lamprey, which is one of the oldest groups of extant vertebrates," says Sten Grillner, last author of the study and professor of neurophysiology at the Department of Neuroscience, Karolinska Institutet. "Here we've made detailed studies of the lamprey brain, combining neurophysiological analyses with histochemical techniques."

In the study, the researchers show that even the lamprey, which existed hundreds of millions of years before mammals, possesses a detailed blueprint for the development of the cortex, the basal ganglia and the dopamine system -- all the vital ingredients of integrative cerebral function.

The researchers also found that the lamprey's cortex has a visual area on which different parts of its visual field are represented. Sensory and motor areas have also been discovered.

"This shows that the birth of the cortex has to be pushed back about 300 million years," says Professor Grillner. "This, in turn, means that the basic plan of the human brain was defined already over 500 million years ago, that's to say before the lamprey branched off from the evolutionary line that led to mammals and humans."

The study shows that all the main components of the human brain are also to be found in the lamprey brain, albeit with much fewer nerve cells in each part.

"That vital parts of the lamprey brain are conserved and organised in the same way as in the human brain was unexpected," he continues. "These findings are crucial to our understanding of how the brain evolved and how it has been designed through evolution."

Read more at Science Daily

COVID-19 coronavirus epidemic has a natural origin

Coronavirus illustration

The novel SARS-CoV-2 coronavirus that emerged in the city of Wuhan, China, last year and has since caused a large scale COVID-19 epidemic and spread to more than 70 other countries is the product of natural evolution, according to findings published today in the journal Nature Medicine.

The analysis of public genome sequence data from SARS-CoV-2 and related viruses found no evidence that the virus was made in a laboratory or otherwise engineered.

"By comparing the available genome sequence data for known coronavirus strains, we can firmly determine that SARS-CoV-2 originated through natural processes," said Kristian Andersen, PhD, an associate professor of immunology and microbiology at Scripps Research and corresponding author on the paper.

In addition to Andersen, authors on the paper, "The proximal origin of SARS-CoV-2," include Robert F. Garry, of Tulane University; Edward Holmes, of the University of Sydney; Andrew Rambaut, of University of Edinburgh; W. Ian Lipkin, of Columbia University.

Coronaviruses are a large family of viruses that can cause illnesses ranging widely in severity. The first known severe illness caused by a coronavirus emerged with the 2003 Severe Acute Respiratory Syndrome (SARS) epidemic in China. A second outbreak of severe illness began in 2012 in Saudi Arabia with the Middle East Respiratory Syndrome (MERS).

On December 31 of last year, Chinese authorities alerted the World Health Organization of an outbreak of a novel strain of coronavirus causing severe illness, which was subsequently named SARS-CoV-2. As of February 20, 2020, nearly 167,500 COVID-19 cases have been documented, although many more mild cases have likely gone undiagnosed. The virus has killed over 6,600 people.

Shortly after the epidemic began, Chinese scientists sequenced the genome of SARS-CoV-2 and made the data available to researchers worldwide. The resulting genomic sequence data has shown that Chinese authorities rapidly detected the epidemic and that the number of COVID-19 cases have been increasing because of human to human transmission after a single introduction into the human population. Andersen and collaborators at several other research institutions used this sequencing data to explore the origins and evolution of SARS-CoV-2 by focusing in on several tell-tale features of the virus.

The scientists analyzed the genetic template for spike proteins, armatures on the outside of the virus that it uses to grab and penetrate the outer walls of human and animal cells. More specifically, they focused on two important features of the spike protein: the receptor-binding domain (RBD), a kind of grappling hook that grips onto host cells, and the cleavage site, a molecular can opener that allows the virus to crack open and enter host cells.

Evidence for natural evolution

The scientists found that the RBD portion of the SARS-CoV-2 spike proteins had evolved to effectively target a molecular feature on the outside of human cells called ACE2, a receptor involved in regulating blood pressure. The SARS-CoV-2 spike protein was so effective at binding the human cells, in fact, that the scientists concluded it was the result of natural selection and not the product of genetic engineering.

This evidence for natural evolution was supported by data on SARS-CoV-2's backbone -- its overall molecular structure. If someone were seeking to engineer a new coronavirus as a pathogen, they would have constructed it from the backbone of a virus known to cause illness. But the scientists found that the SARS-CoV-2 backbone differed substantially from those of already known coronaviruses and mostly resembled related viruses found in bats and pangolins.

"These two features of the virus, the mutations in the RBD portion of the spike protein and its distinct backbone, rules out laboratory manipulation as a potential origin for SARS-CoV-2" said Andersen.

Josie Golding, PhD, epidemics lead at UK-based Wellcome Trust, said the findings by Andersen and his colleagues are "crucially important to bring an evidence-based view to the rumors that have been circulating about the origins of the virus (SARS-CoV-2) causing COVID-19."

"They conclude that the virus is the product of natural evolution," Goulding adds, "ending any speculation about deliberate genetic engineering."

Possible origins of the virus

Based on their genomic sequencing analysis, Andersen and his collaborators concluded that the most likely origins for SARS-CoV-2 followed one of two possible scenarios.

In one scenario, the virus evolved to its current pathogenic state through natural selection in a non-human host and then jumped to humans. This is how previous coronavirus outbreaks have emerged, with humans contracting the virus after direct exposure to civets (SARS) and camels (MERS). The researchers proposed bats as the most likely reservoir for SARS-CoV-2 as it is very similar to a bat coronavirus. There are no documented cases of direct bat-human transmission, however, suggesting that an intermediate host was likely involved between bats and humans.

In this scenario, both of the distinctive features of SARS-CoV-2's spike protein -- the RBD portion that binds to cells and the cleavage site that opens the virus up -- would have evolved to their current state prior to entering humans. In this case, the current epidemic would probably have emerged rapidly as soon as humans were infected, as the virus would have already evolved the features that make it pathogenic and able to spread between people.

In the other proposed scenario, a non-pathogenic version of the virus jumped from an animal host into humans and then evolved to its current pathogenic state within the human population. For instance, some coronaviruses from pangolins, armadillo-like mammals found in Asia and Africa, have an RBD structure very similar to that of SARS-CoV-2. A coronavirus from a pangolin could possibly have been transmitted to a human, either directly or through an intermediary host such as civets or ferrets.

Then the other distinct spike protein characteristic of SARS-CoV-2, the cleavage site, could have evolved within a human host, possibly via limited undetected circulation in the human population prior to the beginning of the epidemic. The researchers found that the SARS-CoV-2 cleavage site, appears similar to the cleavage sites of strains of bird flu that has been shown to transmit easily between people. SARS-CoV-2 could have evolved such a virulent cleavage site in human cells and soon kicked off the current epidemic, as the coronavirus would possibly have become far more capable of spreading between people.

Study co-author Andrew Rambaut cautioned that it is difficult if not impossible to know at this point which of the scenarios is most likely. If the SARS-CoV-2 entered humans in its current pathogenic form from an animal source, it raises the probability of future outbreaks, as the illness-causing strain of the virus could still be circulating in the animal population and might once again jump into humans. The chances are lower of a non-pathogenic coronavirus entering the human population and then evolving properties similar to SARS-CoV-2.

Read more at Science Daily

Mysterious ancient sea-worm pegged as new genus after half-century in 'wastebasket'

When a partial fossil specimen of a primordial marine worm was unearthed in Utah in 1969, scientists had a tough go identifying it. Usually, such worms are recognized and categorized by the arrangement of little knobs on their plates. But in this case, the worm's plates were oddly smooth, and important bits of the worm were missing altogether.

Discouraged, researchers placed the mystery worm in a "wastebasket" genus called Palaeoscolex, and interest in the lowly critter waned for the next 50 years.

That all changed recently when Paul Jamison, a teacher from Logan, Utah, and private collector, and his student Riley Smith were hunting fossils in the Spence Shale in Utah, a 506-million-year-old geologic unit housing a plethora of exceptionally preserved soft-bodied and biomineralized fossils. (Paleontologists call such a mother lode of fossils a "Lagerstätte.") There, Smith discovered a second, more thoroughly preserved example of the worm.

Eventually, thanks to Jamison's donation, the new fossil specimen arrived at the University of Kansas Biodiversity Institute, where Anna Whitaker, a graduate student in museum studies, researched and analyzed the worm with scanning electron microscopes, energy-dispersive X-ray spectrometry and optical microscopy.

At last, Whitaker determined the worm represented a new genus of Cambrian sea worm heretofore unknown to science. She's the lead author of a description of the worm just published in the peer-reviewed paleontological journal PalZ.

"Before the new species that we acquired there was only one specimen known from the Spence Shale," she said. "But with our new specimen we discovered it had characteristics that the original specimen didn't have. So, we were able to update that description, and based on these new characteristics -- we decided it didn't fit in its old genus. So, we moved it to a new one."

Whitaker and her colleagues -- Jamison, James Schiffbauer of the University of Missouri and Julien Kimmig of KU's Biodiversity Institute -- named the new genus Utahscolex.

"We think they're closely related to priapulid worms that exist today -- you can find them in the oceans, and they are very similar to priapulids based on their mouth parts," Whitaker said. "What's characteristic about these guys is that they have a proboscis that can evert, so it can turn itself inside out and it's covered with spines -- that's how it grabs food and sucks it in. So, it behaved very similarly to modern priapulid worms."

While today, Utah is not a place you'd look for marine life, the case was different 506 million years ago, when creatures preserved in the Spence Shale were fossilized.

"The Spence Shale was a shelf system, and it's really interesting because it preserves a lot of environments -- nearshore to even deeper offshore, which is kind of unusual for a Lagerstätte, and especially during the Cambrian. These animals were living in kind of a muddy substrate. This worm was a carnivore, so it was preying on other critters. But there would have been whole diversity of animals -- sponges, and trilobites scuttling along. We have very large, for the time, bivalve arthropods that would be predators. The Spence has a very large diversity of arthropods. It would have looked completely alien to us today."

Whitaker hopes to complete her master's degree this spring, then to attend the University of Toronto to earn her doctorate. The description of Utahscolex is Whitaker's first academic publication, but she hopes it won't be her last. She said the opportunity to perform such research is a chief reason for attending KU.

"I came for the museum studies program," she said. "It's one of the best in the country, and the program's flexibility has allowed me to focus on natural history collections, which is what I hopefully will have a career in, and also gain work experience in the collections and do research -- so it's kind of everything I was looking for in the program."

While ancient sea worms could strike many as a meaninglessly obscure subject for such intense interest and research, Whitaker said filling in gaps in the fossil record leads to a broader understanding of evolutionary processes and offers more granular details about the tree of life.

Read more at Science Daily

Bacterial enzyme could become a new target for antibiotics

MIT and Harvard University chemists have discovered the structure of an unusual bacterial enzyme that can break down an amino acid found in collagen, which is the most abundant protein in the human body.

The enzyme, known as hydroxy-L-proline dehydratase (HypD), has been found in a few hundred species of bacteria that live in the human gut, including Clostridioides difficile. The enzyme performs a novel chemical reaction that dismantles hydroxy-L-proline, the molecule that gives collagen its tough, triple-helix structure.

Now that researchers know the structure of the enzyme, they can try to develop drugs that inhibit it. Such a drug could be useful in treating C. difficile infections, which are resistant to many existing antibiotics.

"This is very exciting because this enzyme doesn't exist in humans, so it could be a potential target," says Catherine Drennan, an MIT professor of chemistry and biology and a Howard Hughes Medical Institute Investigator. "If you could potentially inhibit that enzyme, that could be a unique antibiotic."

Drennan and Emily Balskus, a professor of chemistry and chemical biology at Harvard University, are the senior authors of the study, which appears today in the journal eLife. MIT graduate student Lindsey Backman and former Harvard graduate student Yolanda Huang are the lead authors of the study.

A difficult reaction

The HypD enzyme is part of a large family of proteins called glycyl radical enzymes. These enzymes work in an unusual way, by converting a molecule of glycine, the simplest amino acid, into a radical -- a molecule that has one unpaired electron. Because radicals are very unstable and reactive, they can be used as cofactors, which are molecules that help drive a chemical reaction that would otherwise be difficult to perform.

These enzymes work best in environments that don't have a lot of oxygen, such as the human gut. The Human Microbiome Project, which has sequenced thousands of bacterial genes from species found in the human gut, has yielded several different types of glycyl radical enzymes, including HypD.

In a previous study, Balskus and researchers at the Broad Institute of MIT and Harvard discovered that HypD can break down hydroxy-L-proline into a precursor of proline, one of the essential amino acids, by removing the hydroxy modification as a molecule of water. These bacteria can ultimately use proline to generate ATP, a molecule that cells use to store energy, through a process called amino acid fermentation.

HypD has been found in about 360 species of bacteria that live in the human gut, and in this study, Drennan and her colleagues used X-ray crystallography to analyze the structure of the version of HypD found in C. difficile. In 2011, this species of bacteria was responsible for about half a million infections and 29,000 deaths in the United States.

The researchers were able to determine which region of the protein forms the enzyme's "active site," which is where the reaction occurs. Once hydroxy-L-proline binds to the active site, a nearby glycine molecule forms a glycyl radical that can pass that radical onto the hydroxy-L-proline, leading to the elimination of the hydroxy group.

Removing a hydroxy group is usually a difficult reaction that requires a large input of energy.

"By transferring a radical to hydroxy-L-proline, it lowers the energetic barrier and allows for that reaction to occur pretty rapidly," Backman says. "There's no other known enzyme that can perform this kind of chemistry."

New drug target

It appears that once bacteria perform this reaction, they divert proline into their own metabolic pathways to help them grow. Therefore, blocking this enzyme could slow down the bacteria's growth. This could be an advantage in controlling C. difficile, which often exists in small numbers in the human gut but can cause illness if the population becomes too large. This sometimes occurs after antibiotic treatment that wipes out other species and allows C. difficile to proliferate.

"C. difficile can be in your gut without causing problems -- it's when you have too much of it compared to other bacteria that it becomes more problematic," Drennan says. "So, the idea is that by targeting this enzyme, you could limit the resources of C. difficile, without necessarily killing it."

The researchers now hope to begin designing drug candidates that could inhibit HypD, by targeting the elements of the protein structure that appear to be the most important in carrying out its function.

Read more at Science Daily

Even a limited India-Pakistan nuclear war would bring global famine, says study

Illustration of nuclear bomb explosion.

The concept of nuclear winter -- a years-long planetary freeze brought on by airborne soot generated by nuclear bombs -- has been around for decades. But such speculations have been based largely on back-of-the-envelope calculations involving a total war between Russia and the United States. Now, a new multinational study incorporating the latest models of global climate, crop production and trade examines the possible effects of a less gargantuan but perhaps more likely exchange between two longtime nuclear-armed enemies: India and Pakistan. It suggests that even a limited war between the two would cause unprecedented planet-wide food shortages and probable starvation lasting more than a decade. The study appears this week in the journal Proceedings of the National Academy of Sciences.

Of an estimated 14,000 nuclear warheads worldwide, close to 95 percent belong to the United States and Russia. India and Pakistan are thought to have about 150 each. The study examines the potential effects if they were to each set off 50 Hiroshima-size bombs -- less than 1 percent of the estimated world arsenal.

In addition to direct death and destruction, the authors say that firestorms following the bombings would launch some 5 million tons of soot toward the stratosphere. There, it would spread globally and remain, absorbing sunlight and lowering global mean temperatures by about 1.8 degrees C (3.25 F) for at least five years. The scientists project that this would in turn cause production of the world's four main cereal crops -- maize, wheat, soybeans and rice -- to plummet an average 11 percent over that period, with tapering effects lasting another five to 10 years.

"Even this regional, limited war would have devastating indirect implications worldwide," said Jonas Jägermeyr, a postdoctoral scientist at the NASA Goddard Institute for Space Studies who led the study. "It would exceed the largest famine in documented history."

According to the study, crops would be hardest hit in the northerly breadbasket regions of the United States, Canada, Europe, Russia and China. But paradoxically, southerly regions would suffer much more hunger. That is because many developed nations in the north produce huge surpluses, which are largely exported to nations in the Global South that are barely able to feed themselves. If these surpluses were to dry up, the effects would ripple out through the global trade system. The authors estimate that some 70 largely poor countries with a cumulative population of 1.3 billion people would then see food supplies drop more than 20 percent.

Some adverse effects on crops would come from shifts in precipitation and solar radiation, but the great majority would stem from drops in temperature, according to the study. Crops would suffer most in countries north of 30 degrees simply because temperatures there are lower and growing seasons shorter to begin with. Even modest declines in growing-season warmth could leave crops struggling to mature, and susceptible to deadly cold snaps. As a result, harvests of maize, the world's main cereal crop, could drop by nearly 20 percent in the United States, and an astonishing 50 percent in Russia. Wheat and soybeans, the second and third most important cereals, would also see steep declines. In southerly latitudes, rice might not suffer as badly, and cooler temperatures might even increase maize harvests in parts of South America and Africa. But this would do little to offset the much larger declines in other regions, according to the study.

Since many developed countries produce surpluses for export, their excess production and reserves might tide them over for at least a few years before shortages set in. But this would come at the expense of countries in the Global South. Developed nations almost certainly would impose export bans in order to protect their own populations, and by year four or five, many nations that today already struggle with malnutrition would see catastrophic drops in food availability. Among those the authors list as the hardest hit: Somalia, Niger, Rwanda, Honduras, Syria, Yemen and Bangladesh.

If nuclear weapons continue to exist, "they can be used with tragic consequences for the world," said study coauthor Alan Robock, a climatologist at Rutgers University who has long studied the potential effects of nuclear war. "As horrible as the direct effects of nuclear weapons would be, more people could die outside the target areas due to famine."

Previously, Jägermeyr has studied the potential effects of global warming on agriculture, which most scientists agree will suffer badly. But, he said, a sudden nuclear-caused cooling would hit food systems far worse. And, looking backward, the the effects on food availability would be four times worse than any previously recorded global agriculture upsets caused by droughts, floods, or volcanic eruptions, he said.

The study might be erring on the conservative side. For one, India and Pakistan may well have bombs far bigger than the ones the scientists use in their assumptions. For another, the study leaves India and Pakistan themselves out of the crop analyses, in order to avoid mixing up the direct effects of a war with the indirect ones. That aside, Jägermeyr said that one could reasonably assume that food production in the remnants of the two countries would drop essentially to zero. The scientists also did not factor in the possible effects of radioactive fallout, nor the probability that floating soot would cause the stratosphere to heat up at the same time the surface was cooling. This would in turn cause stratospheric ozone to dissipate, and similar to the effects of now-banned refrigerants, this would admit more ultraviolet rays to the Earth's surface, damaging humans and agriculture even more.

Much attention has been focused recently on North Korea's nuclear program, and the potential for Iran or other countries to start up their own arsenals. But many experts have long regarded Pakistan and India as the most dangerous players, because of their history of near-continuous conflict over territory and other issues. India tested its first nuclear weapon in 1974, and when Pakistan followed in 1998, the stakes grew. The two countries have already had four full-scale conventional wars, in 1947, 1965, 1971 and 1999, along with many substantial skirmishes in between. Recently, tensions over the disputed region of Kashmir have flared again.

"We're not saying a nuclear conflict is around the corner. But it is important to understand what could happen," said Jägermeyr.

Read more at Science Daily

New coronavirus stable for hours on surfaces

Virus illustration

The virus that causes coronavirus disease 2019 (COVID-19) is stable for several hours to days in aerosols and on surfaces, according to a new study from National Institutes of Health, CDC, UCLA and Princeton University scientists in The New England Journal of Medicine.

The scientists found that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detectable in aerosols for up to three hours, up to four hours on copper, up to 24 hours on cardboard and up to two to three days on plastic and stainless steel. The results provide key information about the stability of SARS-CoV-2, which causes COVID-19 disease, and suggests that people may acquire the virus through the air and after touching contaminated objects. The study information was widely shared during the past two weeks after the researchers placed the contents on a preprint server to quickly share their data with colleagues.

The NIH scientists, from the National Institute of Allergy and Infectious Diseases' Montana facility at Rocky Mountain Laboratories, compared how the environment affects SARS-CoV-2 and SARS-CoV-1, which causes SARS. SARS-CoV-1, like its successor now circulating across the globe, emerged from China and infected more than 8,000 people in 2002 and 2003. SARS-CoV-1 was eradicated by intensive contact tracing and case isolation measures and no cases have been detected since 2004. SARS-CoV-1 is the human coronavirus most closely related to SARS-CoV-2. In the stability study the two viruses behaved similarly, which unfortunately fails to explain why COVID-19 has become a much larger outbreak.

The NIH study attempted to mimic virus being deposited from an infected person onto everyday surfaces in a household or hospital setting, such as through coughing or touching objects. The scientists then investigated how long the virus remained infectious on these surfaces.

The scientists highlighted additional observations from their study:

• If the viability of the two coronaviruses is similar, why is SARS-CoV-2 resulting in more cases? Emerging evidence suggests that people infected with SARS-CoV-2 might be spreading virus without recognizing, or prior to recognizing, symptoms. This would make disease control measures that were effective against SARS-CoV-1 less effective against its successor.
• In contrast to SARS-CoV-1, most secondary cases of virus transmission of SARS-CoV-2 appear to be occurring in community settings rather than healthcare settings. However, healthcare settings are also vulnerable to the introduction and spread of SARS-CoV-2, and the stability of SARS-CoV-2 in aerosols and on surfaces likely contributes to transmission of the virus in healthcare settings.

Read more at Science Daily

Plastic building bricks could survive in ocean for up to 1,300 years, study suggests

A LEGO brick could survive in the ocean for as many as 1,300 years, according to new research.

A study led by the University of Plymouth examined the extent to which items of the ever-popular children's toy were worn down in the marine environment.

By measuring the mass of individual bricks found on beaches against equivalent unused pieces and the age of blocks obtained from storage, researchers estimated that the items could endure for anywhere between 100 and 1,300 years.

They say it once again reinforces the message that people need to think carefully about how they dispose of everyday household items.

The research, published in the journal Environmental Pollution, focused on bricks of LEGO found washed up on the coastlines of South West England.

Over the past decade, voluntary organisations from Cornwall -- including Rame Peninsula Beach Care and the LEGO Lost at Sea Project -- have retrieved thousands of pieces and other plastic waste during regular beach cleans.

Previous studies have indicated that many of these could have either been lost during beach visits or entered the environment via the household waste process.

For this particular study, 50 pieces of weathered LEGO -- constructed of acrylonitrile butadiene styrene (ABS) and collected from beaches -- were washed and then weighed in labs at the University, with the size of the studs also being measured.

The chemical characteristics of each block were then determined using an X-ray fluorescence (XRF) spectrometer, with the results used to confirm the age of individual pieces based on the presence of certain elements no longer in use.

By pairing those items with unweathered sets purchased in the 1970s and 80s, researchers were able to identify levels of wear and -- as a result -- how long the pieces might continue to endure in the marine environment.

The study was led by Dr Andrew Turner, Associate Professor (Reader) in Environmental Sciences, who has previously conducted extensive research into the chemical properties of items washed up as marine litter.

He said: "LEGO is one of the most popular children's toys in history and part of its appeal has always been its durability. It is specifically designed to be played with and handled, so it may not be especially surprising that despite potentially being in the sea for decades it isn't significantly worn down. However, the full extent of its durability was even a surprise to us.

"The pieces we tested had smoothed and discoloured, with some of the structures having fractured and fragmented, suggesting that as well as pieces remaining intact they might also break down into microplastics. It once again emphasises the importance of people disposing of used items properly to ensure they do not pose potential problems for the environment."

From Science Daily

Ancient mantis-man petroglyph discovered in Iran

A unique rock carving found in the Teymareh rock art site (Khomein county) in Central Iran with six limbs has been described as part man, part mantis. Rock carvings, or petroglyphs, of invertebrate animals are rare, so entomologists teamed up with archaeologists to try and identify the motif. They compared the carving with others around the world and with the local six-legged creatures which its prehistoric artists could have encountered.

Entomologists Mahmood Kolnegari, Islamic Azad University of Arak, Iran; Mandana Hazrati, Avaye Dornaye Khakestari Institute, Iran; and Matan Shelomi, National Taiwan University teamed up with freelance archaeologist and rock art expert Mohammad Naserifard and describe the petroglyph in a new paper published in the open access Journal of Orthoptera Research.

The 14-centimetre carving was first spotted during surveys between 2017 and 2018, but could not be identified due to its unusual shape. The six limbs suggest an insect, while the triangular head with big eyes and the grasping forearms are unmistakably those of a praying mantid, a predatory insect that hunts and captures prey like flies, bees and even small birds. An extension on its head even helps narrow the identification to a particular genus of mantids in this region: Empusa.

Even more mysterious are the middle limbs, which end in loops or circles. The closest parallel to this in archaeology is the 'Squatter Man,' a petroglyph figure found around the world depicting a person flanked by circles. While they could represent a person holding circular objects, an alternative hypothesis is that the circles represent auroras caused by atmospheric plasma discharges.

It is presently impossible to tell exactly how old the petroglyphs are, because sanctions on Iran prohibit the use of radioactive materials needed for radiocarbon dating. However, experts Jan Brouwer and Gus van Veen examined the Teymareh site and estimated the carvings were made 40,000-4,000 years ago.

One can only guess why prehistoric people felt the need to carve a mantis-man into rock, but the petroglyph suggests humans have linked mantids to the supernatural since ancient times. As stated by the authors, the carving bears witness, "that in prehistory, almost as today, praying mantids were animals of mysticism and appreciation."

From Science Daily

Soft corals near Virgin Islands recover from hurricanes, but stony corals declining

Soft corals at three sites in the U.S. Virgin Islands were able to recover from the destructive effects of nearly back-to-back Category 5 storms in 2017, but the story of these apparently hardy communities of colorful marine life is part of a larger, rapidly shifting narrative surrounding the future of coral reefs, according to a new study led by a University at Buffalo marine ecologist.

The recently realized resilience of the soft corals is an important development toward our increasing understanding of these complex ecosystems, but the findings published in the journal Scientific Reports puts that seemingly good news in the context of an ecosystem that is dramatically changing.

"These soft corals are resilient," says Howard Lasker, a professor in the Department of Environment and Sustainability and the Department of Geology, and an expert on the ecology of coral reef organisms.

"But right now in the Caribbean we're seeing a drastic decline of stony corals, and the soft corals are not a simple replacement for what's being lost."

Soft corals, also known as octocorals, are branching colonial organisms. The colonies with their impressionistic tree-like appearance sway in ocean currents like trees in a storm. The stony corals, which also form colonies, produce rigid skeletons and create the framework of coral reefs. The living animal sits atop the structure they create, slowly secreting calcium carbonate, essentially limestone, to build up the reef.

These screen saver favorites are inspiring tourist destinations that on a more practical level play diverse ecological, economic and environmental roles, everything from protecting shorelines from erosion to providing habitats for a diverse populations of marine life.

The soft corals are doing fine while the stony corals have declined as much as 40% in recent decades, according to Lasker, whose team examined three reefs on the south shore of St. John (part of the U.S. Virgin Islands) following Hurricanes Irma and Maria, storms that passed within two weeks of one another in September 2017. They compared data from the storm's aftermath with sampling that began in 2014 and continued in 2018.

"The octocoral communities we studied suffered dramatic declines with the passage of these hurricanes. In that sense, they weren't resistant to the effects of severe storms," says Lasker. "However they showed resilience -- the ability to recover.

"We found that many colonies were killed, but two years later it hadn't changed the nature of species distribution, and as importantly new colonies were developing making up for the losses" says Lasker.

This pattern of loss and recovery was emblematic historically of stony corals as well, but that's no longer the case for the scleractinians, and Lasker says their soft coral counterparts while providing shelter for many reef animals will not build the hard physical structure of reefs.

"One of the big questions in marine ecology is what we should be doing," says Lasker. "Should we be trying to remediate the damage and attempt to prevent species loss by creating protected environments?"

There is a range of opinions about taking the curator's approach to the reefs, but what certain is that these systems are already dramatically different from descriptions made during the 1950s. And those observations from the '50s stand in obvious contrast to what European explorers would have seen when they encountered the reefs centuries ago.

"Humans are responsible for the changes," says Lasker. "It's really pretty simple: land use, sediments, sewage, agricultural runoff, overfishing, and now climate change."

As the stony corals wane the soft corals are replacing them, but the reason the stony corals aren't recovering comes back to us, according to Lasker.

Read more at Science Daily

Coronavirus spreads quickly and sometimes before people have symptoms, study finds

Virus illustration

Infectious disease researchers at The University of Texas at Austin studying the novel coronavirus were able to identify how quickly the virus can spread, a factor that may help public health officials in their efforts at containment. They found that time between cases in a chain of transmission is less than a week and that more than 10% of patients are infected by somebody who has the virus but does not yet have symptoms.

In the paper in press with the journal Emerging Infectious Diseases, a team of scientists from the United States, France, China and Hong Kong were able to calculate what's called the serial interval of the virus. To measure serial interval, scientists look at the time it takes for symptoms to appear in two people with the virus: the person who infects another, and the infected second person.

Researchers found that the average serial interval for the novel coronavirus in China was approximately four days. This also is among the first studies to estimate the rate of asymptomatic transmission.

The speed of an epidemic depends on two things -- how many people each case infects and how long it takes for infection between people to spread. The first quantity is called the reproduction number; the second is the serial interval. The short serial interval of COVID-19 means emerging outbreaks will grow quickly and could be difficult to stop, the researchers said.

"Ebola, with a serial interval of several weeks, is much easier to contain than influenza, with a serial interval of only a few days. Public health responders to Ebola outbreaks have much more time to identify and isolate cases before they infect others," said Lauren Ancel Meyers, a professor of integrative biology at UT Austin. "The data suggest that this coronavirus may spread like the flu. That means we need to move quickly and aggressively to curb the emerging threat."

Meyers and her team examined more than 450 infection case reports from 93 cities in China and found the strongest evidence yet that people without symptoms must be transmitting the virus, known as pre-symptomatic transmission. According to the paper, more than 1 in 10 infections were from people who had the virus but did not yet feel sick.

Previously, researchers had some uncertainty about asymptomatic transmission with the coronavirus. This new evidence could provide guidance to public health officials on how to contain the spread of the disease.

"This provides evidence that extensive control measures including isolation, quarantine, school closures, travel restrictions and cancellation of mass gatherings may be warranted," Meyers said. "Asymptomatic transmission definitely makes containment more difficult."

Meyers pointed out that with hundreds of new cases emerging around the world every day, the data may offer a different picture over time. Infection case reports are based on people's memories of where they went and whom they had contact with. If health officials move quickly to isolate patients, that may also skew the data.

"Our findings are corroborated by instances of silent transmission and rising case counts in hundreds of cities worldwide," Meyers said. "This tells us that COVID-19 outbreaks can be elusive and require extreme measures."

Zhanwei Du of The University of Texas at Austin, Lin Wang of the Institut Pasteur in Paris, Xiaoke Xu of Dalian Minzu University, Ye Wu of Beijing Normal University and Benjamin J. Cowling of Hong Kong University also contributed to the research. Lauren Ancel Meyers holds the Denton A. Cooley Centennial Professorship in Zoology at The University of Texas at Austin.

Read more at Science Daily