Taking a deep look into animals

VIENNA UNIVERSITY OF TECHNOLOGY

IMAGE: LIGHT-SHEET IMGES OF DIFFERENT DEEP-CLEAR PROCESSED ANIMALS LABELLED WITH NEUROSYSTEM SPECIFIC MARKERS. view more 

CREDIT: TU WIEN / MAX PERUTZ LABS

Advances in neuroscience research and microscopy: a collaborative project driven by researchers of the Max Perutz Labs Vienna, a joint venture of the University of Vienna and the Medical University of Vienna, and the TU Wien (Vienna) allows researchers to look deep into organs and nervous systems of animals, ranging from squids and worms to fish and salamanders.

Analyses of individual cells in the context of whole organs or tissues is becoming increasingly important in biology. A standard approach so far was to cut larger tissues into thin layers, study each of these sections, and then piece the information again together into a 3D model. However, this is a laborious process, and often yields incomplete results. For instance, the cells that make up our nervous systems possess long extensions that can reach through the entire body. Reconstructing such projections from small slices is extremely challenging.

An elegant solution to avoid this is provided by tissue clearing techniques that can render opaque tissues transparent. When applied to complex tissues, including the brain, such techniques allow to visualize individual cells and their extensions, enabling scientists to capture 3D images of cells and tissues without the need of sectioning. However, existing clearing techniques so far were not optimized to remove a variety of pigments that are present in tissues, and that limit how deeply these specimens can be imaged. Therefore, despite the power of tissue clearing approaches, they have essentially remained restricted to specific unpigmented organs like the brain, and a handful of model species that have reduced pigmentation.

In a team effort, researchers from the Max Perutz Labs, the Medical University of Vienna and the TU Wien (Vienna) and their collaborators have now developed a new method that combines tissue clearing with the removal of various pigment types as they are characteristic for most animals. This new approach - dubbed "DEEP-Clear" - has now been published in the international journal Science Advances.


Depigmentation and tissue clearing enable 3D reconstruction with Light-sheet of squid nervous system.

A toolkit for imaging biomolecules in the nervous systems of a broad panel of species

An important observation that helped to develop the new method was that the combination of different chemical treatments had a synergistic effect, allowing for fast depigmentation and tissue clearing. "Shortening chemical processing preserves the integrity of tissues and organisms, so that the molecules and internal structures of interest are more likely to be retained", explains Marko Pende, the developer of the clearing method, from the lab of Hans-Ulrich Dodt at the TU Wien and the Center for Brain Research (CBR) of the Medical University of Vienna, and one of the first authors of the study. This way multiple organisms could be imaged from different clades ranging from mollusks to bony fish to amphibians. "These are just a few examples. We believe that the method is applicable to multiple organisms. It was just not tried yet", explains Prof. Hans Ulrich Dodt, senior author of the study.

The team then systematically explored which types of molecules could still be marked and detected in DEEP-Clear-processed samples, investigating species ranging from squids and worms to fish and salamanders. This work - largely performed by PhD student Karim Vadiwala in the lab of Florian Raible at the Max Perutz labs - showed that DEEP-Clear was compatible with the detection with a variety of important biomolecules, allowing to image specific proteins, DNA markers and RNA in intact specimens. "This versatility of DEEP-Clear makes it a highly attractive tool to explore a range of animals for which standard tissue clearing techniques currently would not be sufficient", explains Karim Vadiwala (Max Perutz Labs).

A 3D view of whole animal nervous systems to explore neural stem cell biology

Besides its compatibility with many species, another attractive feature of DEEP-Clear is that the transparency of the processed organisms allows to image samples across scales: On the one hand, the team looked into very small details such as contact points between neurons, or individual clusters of dividing cells. On the other hand, they took advantage of the latest generation of so-called light-sheet microscopes developed by the Dodt lab, in which two-dimensional laser light is used to rapidly scan a whole sample, resulting in a full three-dimensional model created on the computer. "Using a very thin light-sheet enables us to overcome a lot of optical limitations and allows us to generate such high-resolution images, even from samples that are several millimeters thick", says the designer of the microscopes, Dr. Saiedeh Saghafi (TU Wien).


Light-sheet images of DEEP-Clear processed zebrafish showing proliferative cells (pink) and the nervous system (green).

The expectation of the team is that "DEEP-Clear" will serve to popularize tissue clearing, allowing researchers around the world to intensify molecular and cellular research in a variety of species that exhibit highly interesting, but poorly explored neuroscientific features. For instance, worms, fish, and salamanders can regenerate parts of their central nervous system, suggesting that they possess molecular capacities that humans and other mammals have lost. "Visualizing the responsible stem cells, and investigating their molecular make-up, or their contribution to regenerated tissue, will be greatly facilitated by DEEP-Clear", believes Dr. Florian Raible (Max Perutz Labs), who coordinated the study that also involved additional researchers in the groups of Dr. Oleg Simakov (Uni Vienna) and Dr. Elly Tanaka (Institute for Molecular Pathology).

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Solution to century-old math problem could predict transmission of infectious diseases

UNIVERSITY OF BRISTOL

A Bristol academic has achieved a milestone in statistical/mathematical physics by solving a 100-year-old physics problem - the discrete diffusion equation in finite space.

The long-sought-after solution could be used to accurately predict encounter and transmission probability between individuals in a closed environment, without the need for time-consuming computer simulations.

In his paper, published in Physical Review X, Dr Luca Giuggioli from the Department of Engineering Mathematics at the University of Bristol describes how to analytically calculate the probability of occupation (in discrete time and discrete space) of a diffusing particle or entity in a confined space - something that until now was only possible computationally.

Dr Giuggioli said: "The diffusion equation models random movement and is one of the fundamental equations of physics. The analytic solution of the diffusion equation in finite domains, when time and space is continuous, has been known for a long time.

"However, to compare model predictions with empirical observations, one needs to study the diffusion equation in finite space. Despite the work of illustrious scientists such as Smoluchowski, Pólya, and other investigators of yore, this has remained an outstanding problem for over a century--until now.

"Excitingly, the discovery of this exact analytic solution allows us to tackle problems that were almost impossible in the past because of the prohibitive computational costs."

The finding has far-reaching implications across a range of disciplines and possible applications include predicting molecules diffusing inside cells, bacteria roaming in a petri dish, animals foraging within their home ranges, or robots searching in a disaster area.

It could even be used to predict how a pathogen is transmitted in a crowd between individuals.

Solving the conundrum involved the joint use of two techniques: special mathematical functions known as Chebyshev polynomials, and a technique invented to tackle electrostatic problems, the so-called method of images.

This approach allowed Dr Giuggioli to construct hierarchically the solution to the discrete diffusion equation in higher dimension from the one in lower dimensions.

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Study: Integrating satellite and socioeconomic data to improve climate change policy

UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN, NEWS BUREAU

 

IMAGE: ATUL JAIN LED A STUDY THAT USED A COMBINATION OF SATELLITE AND CENSUS DATA TO IDENTIFY DEFORESTATION AND EXPANDING SALTWATER FARMING AS THE KEY PHYSICAL AND SOCIOECONOMIC DRIVERS OF CLIMATE... view more 

CREDIT: PHOTO BY L. BRIAN STAUFFER

CHAMPAIGN, Ill. -- Bangladesh is on track to lose all of its forestland in the next 35-40 years, leading to a rise in CO2 emissions and subsequent climate change, researchers said. However, that is just one of the significant land-use changes that the country is experiencing. A new study uses satellite and census data to quantify and unravel how physical and economic factors drive land-use changes. Understanding this relationship can inform climate policy at the national scale in Bangladesh and beyond.

The study, led by University of Illinois at Urbana-Champaign atmospheric sciences professor Atul Jain and postdoctoral researcher Xiaoming Xu, is published in the journal Regional Environmental Change.

"Land usage changes when biophysical factors like temperature and soil quality change, but also when the economic needs of people change," Xu said. The study identifies two key areas where land use and cover have shifted because of biophysical and socioeconomic activities in Bangladesh - and suggests policies to mitigate their influence on climate change.

First, the team found that approximately 11% of the forests in Bangladesh have shifted to shrub land, cropland and urban land from 2000-10.

"Extreme climate events, such as drought and flood, changes in urban and rural population and economic conditions are driving the changes from forest to shrub land in the southeast region of Bangladesh," Jain said. "Here, the locals earn their livelihood by using land, lumber and fuel resources from forests. However, deforestation may be controlled by implementing simple policies such as road improvement, which can provide the people with a means to obtain alternative fuels and livelihoods that are not as dependent on forests."

The study also found that from 2000-10, the area of standing water bodies such as ponds, lakes and reservoirs increased by approximately 9%. This change occurred in the coastal southwest part of the country, where worsening floods during monsoon months have pushed aquaculture expansion at the cost of cropland in recent decades, the researchers said.

"The rapid conversion of traditional rice-farming land to saltwater shrimp ponds is now a well-established practice in the southwest coastal area of Bangladesh," Xu said. "Shrimp farming is 12 times more profitable than rice cultivation in this country."

The flooding and expansion of saltwater farming have led to increased soil salinity, spoiling the soil for farming purposes, the researchers said. "Policies need to be developed that encourage the development of saltwater aquaculture only in the regions with favorable conditions to prevent further soil degradation," Jain said.

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The U.S. Department of Energy supported this research.

Editor's notes:

To reach Atul Jain, call 217-333-2128; email jain1@illinois.edu.

To reach Xiaoming Xu, email xuxm@illinois.edu.

The paper "Dynamics and drivers of land use and land cover changes in Bangladesh" is available online and from the U. of I. News Bureau. DOI: 10.1007/s10113-020-01650-5

Scientists develop sorbent for purifying water from radioactive elements

FAR EASTERN FEDERAL UNIVERSITY

 

IMAGE: SEM IMAGES OF TUNGSTEN OXIDE SAMPLES, A WO3-100, B WO3-300, C WO3-600, D WO3-900. view more 

CREDIT: FEFU PRESS OFFICE, THE INSTITUTE OF CHEMISTRY FEB RAS

Scientists from Far Eastern Federal University (FEFU) in collaboration with colleagues from the Institute of Chemistry FEB RAS come up with a smart technology for the synthesis of sorbent based on a "tungsten bronze" compound powder (Na2WO4) aimed to purify industrial and drinking water from hazardous radionuclides cesium (137Cs), and strontium (90Sr), as well as for effective processing of liquid radioactive waste. A related article appears in the Journal of Materials Science.

The new sorbent is appropriate when the concentration of hazardous radioactive elements is extremely higher than the acceptable level, i.e. for processing of liquid radioactive waste from nuclear plants and to eliminate the consequences of technological accidents.

The development resolves one of the pressing problems of modern radioecology, which is to completely or down to the level of regulative standards extract the hazardous radioactive elements cesium (137Cs) and strontium (90Sr) capable of accumulating in the body, replacing potassium and calcium.

The waste sorbent is supposed to convert into high-density ceramics with subsequent safe disposal.

"We propose to apply a sorbent in several ways. First, in the static version, granules based on tungsten bronze powder can simply be introduced into the volume of contaminated water bodies. Second, in a dynamic mode, porous sorbent tablets can be a component of flow filters. The high filtration efficiency registered by calculation methods determining the residual amount of radionuclides in sorbent-purified solutions, as well as the number of radionuclides retained in the sorbent body. We appreciate the Institute of Chemistry FEB RAS for the partial development of these methods in the frame of state assignment. We have studied physicochemical properties of the sorbent material via high-class Shimadzu equipment (Japan) and do believe that the operational properties of the material are up to analogs produced by more expensive technologies. Thus, we hope that our synthesis method will be recognized by the industry as most practical and technologically effective," says Arthur Drankov, a member of the creative team, postgraduate student of FEFU School of Natural Science.

The scientist points out that, if regenerated, the sorbent can serve five or more cycles. However, re-using of "tungsten bronze" sorbents is not the main idea, given that its absorbing abilities with respect to 137Cs and 90Sr radionuclides are well known.

The advantage proposed by researchers of FEFU School of Natural Science and FEB RAS is to convert waste granules or sorption tablets to high-density ceramics for further safe disposal during the half-life of hazardous radioactive elements. For cesium, this period is about 30 years, for strontium is about 29 years.

Scientists will develop a transforming-to-ceramics technology at the next stage of the work supported by a grant of the Russian Foundation for Basic Research (Grant chief is I. G. Tananaev, Director of FEFU School of Natural Science, corresponding member of the Russian Academy of Sciences).

Researchers suggest that the total outcome will be a cost-effective technology that guarantees environmental safety when dealing with radioactive waste.

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Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

Paid sick leave mandates hold promise in containing COVID-19

Mandates like those found in the federal government's Families First Coronavirus Response Act may be helping to slow the pandemic

GEORGIA STATE UNIVERSITY

 

ATLANTA--Paid sick leave (PSL) mandates like those found in the federal government's Families First Coronavirus Response Act may be helping to slow the spread of COVID-19, according to a new study by health economists at Georgia State and Tulane universities.

Since 2007, several state and local governments have enacted laws requiring employers to provide their workers with paid sick leave. Michael Pesko, an associate professor in Georgia State's Andrew Young School of Policy Studies, and co-author Kevin Callison studied the effects of these staggered mandate adoptions using multiple government-collected survey data sources from 2005 to 2018.

The mandates were effective in increasing the number of workers holding Paid Sick Leave coverage, particularly those in low-wage industries who were unlikely to have previously received PSL benefits from their employers, they found. Women and racial/ethnic minorities benefitted disproportionately from the PSL mandates.

"These mandates reduced the number of people attending work while sick, which is similar to an earlier study showing influenza-like disease rates decreased after employees gained access to paid sick leave," said Pesko. "If paid sick leave helps stop people from attending work while sick and prevents the spread of disease as a result, this has important policy implications in today's fight to contain COVID-19."

Paid Sick Leave reduces the rate of those working while sick by 4.5 percentage points on average for workers in industries with historically low rates of PSL, such as the accommodation and food service industries. PSL mandates are particularly likely to increase work absences among women and households with children, where workers may be using their benefits to care for a sick child or other family obligations.

"What are the policy implications? The Families First Coronavirus Response Act, which went into effect April 1, is the first congressionally passed bill that provides Paid Sick Leave for employees in medium- and small-sized businesses with coronavirus issues," Pesko said. "We believe that the bill will reduce people attending work with COVID-19 because it pays for them to stay home and recover. This bill is, therefore, an important component in COVID-19 containment efforts."

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Study: Public health campaigns can do better on cannabis harm reduction

UB, University of Michigan researchers surveyed cannabis enthusiasts about their knowledge of effective harm reduction strategies

UNIVERSITY AT BUFFALO

 

IMAGE: JESSICA KRUGER, PHD, IS A CLINICAL ASSISTANT PROFESSOR IN THE DEPARTMENT OF COMMUNITY HEALTH AND HEALTH BEHAVIOR IN THE UNIVERSITY AT BUFFALO'S SCHOOL OF PUBLIC HEALTH AND HEALTH PROFESSIONS. view more 

CREDIT: UNIVERSITY AT BUFFALO

BUFFLO, N.Y. -- Harm reduction strategies have proven effective for use of opioids, alcohol, and tobacco products. University at Buffalo and University of Michigan researchers say harm reduction techniques also have potential for cannabis users - but first, public health practitioners and organizations need to do a better job of making cannabis users aware of those strategies.

Researchers assessed harm reduction awareness by surveying nearly 500 participants at the 2019 Hash Bash, a popular marijuana advocacy event on the campus of the University of Michigan.

The research team has published a series of papers in recent years based on data collected by surveying Hash Bash attendees. Their latest study, published in Health Promotion Practice, shows that frequent cannabis users aren't as knowledgeable as they should be about harm reduction strategies, such as not driving within six hours of using cannabis. And that, the researchers argue, falls more squarely on public health's failure to properly provide that knowledge.

"Our findings should serve as a wake-up call to public health professionals to integrate harm reduction strategies into practice," said Jessica Kruger, PhD, the study's lead author and a clinical assistant professor of community health and health behavior in UB's School of Public Health and Health Professions.

"As more states legalize medicinal and recreational use of cannabis, it's important that public health equip people with proper knowledge about using cannabis. We know that abstinence just isn't realistic or desirable for some users. We can minimize the costs and risks of cannabis use by creating awareness around harm reduction strategies," Kruger added.

Fewer than half of the study participants believed that any of the listed strategies reduced the harm of using cannabis. Only 42% identified avoiding use when pregnant as an effective harm reduction strategy. Even less, 36%, identified avoiding driving within six hours of using cannabis as an effective strategy.

"This is really remarkable, given that both of these are common warnings for a variety of psychoactive and pharmaceutical substances," said co-author Daniel Kruger, PhD, a research associate professor of community health and health behavior in UB's School of Public Health and Health Professions. He is also a research investigator with the Population Studies Center at the University of Michigan.

About one-quarter of participants believed that using strains with high cannabidiol (CBD) CBD to tetrahydrocannabinol (THC) ratios, using a concentrate or dab without plant material, and putting ice in a bong to reduce cannabis potency were effective harm reduction techniques. Only using strains with a high CBD to THC ratio has been empirically supported, the researchers note.

Less than half of participants reported using any harm reduction strategy, and 39% reported using no effective strategy.

Although knowledge doesn't guarantee behavior or behavior change, the researchers note that providing cannabis users with accurate information on the risks and benefits of the drug will at least help users make informed decisions.

They point to two public health campaigns in Colorado, a state where cannabis is legal for adult use. That state's "Good to Know" campaign educated Colorado residents on new cannabis laws. The state's "Responsibility Grows Here" campaign shares information about the potential risks for teens and pregnant and breastfeeding women, and calls on users to consume cannabis responsibly.

"As more and more people have legal access to medical and recreational cannabis, the importance of effective cannabis-specific health education increases," said study co-author R. Lorraine Collins, PhD, associate dean for research in UB's School of Public Health and Health Professions and a professor of community health and health behavior.

Bangladeshi eggplant farmers reap rewards via genetics

CORNELL UNIVERSITY  RELEASE 29-MAY-2020

Farmers in Bangladesh achieved significantly higher yields and revenues by growing insect-resistant, genetically engineered eggplant, a new Cornell study has found.

The four genetically engineered (Bt) varieties yielded, on average, 19.6% more eggplant - known as brinjal in Bangladesh - than non-Bt varieties and earned growers 21.7% higher revenue, according to the study, published May 25 in Frontiers in Bioengineering and Biotechnology.

The additional revenue per hectare (1 hectare is approximately 2 ½ acres) is the equivalent of around $664, a substantial sum for resource-poor farmers in Bangladesh.

The paper is the first to document the economic benefits of the four existing Bt brinjal varieties though the Bangladeshi market chain and their acceptability to farmers and consumers, said lead author Tony Shelton, professor of entomology and former director for the Feed the Future South Asia Eggplant Improvement Partnership based in Cornell's Department of Global Development. The study was based on a 2019 survey of Bt and non-Bt brinjal farmers.

Bt brinjal was developed by the Bangladesh Agricultural Research Institute (BARI) in conjunction with Mahyco (an India-based agricultural company), Cornell and the U.S. Agency for International Development, in an effort to stop the losses caused by eggplant fruit and shoot borer (EFSB) larvae caterpillars, and reduce pesticide use.

"The EFSB causes between 30% and 60% yield loss, even when insecticides are frequently sprayed," Shelton said. "Farmers typically apply insecticides more than 80 times during the four- to five-month brinjal growing season, a process that is both expensive and harmful to farmers, who spray without protective equipment."

Of Bt brinjal growers, 83% were satisfied with the yields obtained and 80% were satisfied with the quality of the plant; 59% of non-Bt brinjal growers were pleased with their yields. Some 28% of the non-Bt farmers also indicated that a large portion of their fruit was infested with EFSB larvae. This was not a concern for Bt brinjal, because it provides genetically inherent resistance.

"Bt brinjal varieties provide farmers a more sustainable crop that protects food security and the environment," said Maricelis Acevedo, director of the project since March 2020. "This study provides more evidence that Bt brinjal is being accepted in the market, but more work is needed to develop new varieties better adapted to local conditions and market preferences."

Because of the higher yields, increased revenue and fruit quality, about three-quarters of Bt brinjal farmers said they planned to grow the crop again next season. Brinjal is the second-most important vegetable grown in Bangladesh, cultivated by about 150,000 resource-poor farmers on 50,955 hectares, and consumed by the public on a daily basis.

The survey was conducted in the five most important brinjal producing districts in Bangladesh - Rangpur, Bogra, Rajshahi, Jessore and Tangail - through face-to-face interviews with 195 Bt farmers and 196 non-Bt farmers. Farmers made their own choices about which crop to grow.

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Other authors include Sayed H. Sarwer and Md J. Hossain of the Feed the Future South Asia Eggplant Improvement Partnership; Graham Brooks of PG Economics, Stafford House, in the U.K.; and Vijay Paranjape of Sathguru Management Consultants Pvt. Ltd. in Hyderabad, India.

A rising tide of marine disease? How parasites respond to a warming world

UNIVERSITY OF WASHINGTON

 

IMAGE: SEA STAR WASTING DISEASE, PICTURED HERE, IS LIKELY CAUSED BY THE SEA STAR ASSOCIATED DENSOVIRUS. view more 

CREDIT: OREGON STATE PARKS

Warming events are increasing in magnitude and severity, threatening many ecosystems worldwide. As the global temperatures continue to climb, it also raises uncertainties as to the relationship, prevalence, and spread of parasites and disease.

A recent study from the University of Washington explores the ways parasitism will respond to climate change, providing researchers new insights into disease transmission. The paper was published May 18 in Trends in Ecology and Evolution.

The review builds upon previous research by adding nearly two decades of new evidence to build a framework showing the parasite-host relationship under climate oscillations. Traditionally, climate-related research is done over long timescales, however this unique approach examines how increasingly frequent "pulse warming" events alter parasite transmission.

"Much of what is known about how organisms and ecosystems can respond to climate change has focused on gradual warming," said lead author Danielle Claar, a postdoctoral researcher at the UW School of Aquatic and Fishery Sciences. "Climate change causes not only gradual warming over time, but also increases the frequency and magnitude of extreme events, like heat waves."

Claar explained that both gradual warming and pulse warming can and have influenced ecosystems, but do so in different ways. Organisms may be able to adapt and keep pace with the gradual warming, but an acute pulse event can have sudden and profound impacts.

The 2013-2015 "blob" is one such extreme heat pulse event which has been linked to a massive die-off of sea stars along the Pacific coast of the U.S. and Canada. Many species of sea stars, including the large sunflower sea star, were decimated by a sudden epidemic of wasting disease. Five years later, populations in the region are still struggling to recover. The abnormally warm waters associated with the blob are thought to have favored the spread of the sea star-associated densovirus, the suggested cause of the disease.

The authors compare the prevalence of these marine diseases to a rising tide, an ebbing tide, or a tsunami. Disease transmission can rise or ebb in concert with gradual warming or a series of pulse warming events. However, a severe pulse warming event could result in a tsunami, "initiating either a deluge or drought of disease," as was observed with sea stars along the Pacific Northwest.

However, not all pulse heat events will cause the same response. What may benefit a particular parasite or host in one system can be detrimental in another. Warming can alter a parasite's life cycle, limit the range of suitable host species, or even impair the host's immune response. Some flatworms which target wildlife and humans cannot survive as long in warmer waters, decreasing their window for infecting a host. Another recent UW study found that parasites commonly found in sushi are on the rise with their numbers increasing 283-fold in the past 40 years, though the relationship between heat pulse events and their abundance is not yet clear.

"The relationships between hosts, parasites, and their corresponding communities are complex and depend on many factors, making outcomes difficult to predict," said Claar, who recommends researchers make predictions on a case-by-case basis for their individual systems.

The authors conclude that rather than a straightforward tidal prediction, they would expect pulse warming to cause "choppy seas with the occasional rogue wave."

"It is important that we are able to understand and predict how parasitism and disease might respond to climate change, so we can prepare for, and mitigate, potential impacts to human and wildlife health," said Claar.

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The paper's co-author is Chelsea Wood, a UW assistant professor of aquatic and fishery sciences.

This research was supported by the NOAA Climate and Global Change Postdoctoral Fellowship Program, administered by UCAR's Cooperative Programs for the Advancement of Earth System Science (CPAESS); the National Science Foundation; a Sloan Research Fellowship from the Alfred P. Sloan Foundation; a UW Innovation Award from the UW President's Innovation Imperative; and a UW Royalty Research Fund Award.

Grant numbers: NA18NWS4620043B (CPAESS), OCE-1829509 (NSF)

For more information, contact Claar at danielle.claar@gmail.com.

Heightened interaction between neolithic migrants and hunter-gatherers in Western Europe

Analyzing the first archaeogenetic data from the Mesolithic-Neolithic transition in Western Europe, a team of French and German researchers documents levels of admixture between expanding early Neolithic farmers and local hunter-gatherers seen nowhere els

MAX PLANCK INSTITUTE FOR THE SCIENCE OF HUMAN HISTORY

NEWS RELEASE 29-MAY-2020

 

IMAGE: THE BURIAL OF PENDIMOUN F2 (5480-5360 BC), WOMAN CARRYING ABOUT 55% OF HUNTER-GATHERER COMPONENT. view more 

CREDIT: HENRI DUDAY

The Neolithic lifestyle, including farming, animal domestication and the development of new technologies, emerged in the Near East around 12,000 years ago and contributed profoundly to the modern way of life. The Neolithic spread rapidly across Europe, mainly along the Danube valley and the Mediterranean coastline, reaching the Atlantic coast around 5000-4500 BCE. The existing archaeogenetic data from prehistoric European farmers indicates that the spread of farming is due to expanding populations of early farmers who mixed little, if at all, with indigenous hunter-gatherer groups. However, until now, no archaeogenetic data were available for France.

"France is where the two streams of the Neolithic expansion overlapped, so understanding how these groups interacted would fill in a big piece of the puzzle," says Wolfgang Haak, senior author of the study. "The data we're collecting suggests a more complex scenario than elsewhere in Europe, with more interaction between early farmers and hunter-gatherers."

These interactions seem to vary greatly from one region to another, attesting to a diverse cultural mosaic in early Neolithic Western Europe. In order to document the biological interactions during this transition period, researchers from the Max Planck Institute for the Science of Human History teamed up with colleagues from the PACEA laboratory (1*) in Bordeaux, the CEPAM laboratory (2*), the RGMZ (3*), and other international partners (4*). The study, published in Science Advances, reports new genome-wide data for 101 prehistoric individuals from 12 archaeological sites in today's France and Germany, dating from 7000-3000 BCE

High levels of hunter-gatherer ancestry in early farmers from France

The new results showed evidence for a higher level of admixture, or the combination of genetic information from genetically distant populations, between early migrant farmers and local hunter-gatherers in France. The genetic mixture in this region is unprecedented in the rest of Europe for the early stages of the Neolithic expansion. The genetic contribution of hunter-gatherers is particularly high in the south of France, roughly 31% on average, compared with 3% in Central Europe or 13% in the Iberian Peninsula.

Intriguingly, in an individual from the Pendimoun site in Provence (5480-5360 BCE), the genetic contribution of local hunter-gatherers was as high as 55%. The team could show that the admixture in this individual occurred recently, about four generations before, shortly after the first Neolithic farmers settled on that part of the French coast. "These findings suggest continuous contacts between both groups for at least a century," says Maïté Rivollat, postdoc in the INTERACT project and lead author of the study.

Genetic evidence for the two routes of the Neolithic expansion

Leveraging the genetic substructure observed in European hunter-gatherers, the team was able to retrace the dynamics of admixture in various European regions. Neolithic farmers in central Europe carry a very small hunter-gatherer component, which had already been mixed in and brought in from southeastern Europe. This accounts for the rapid spread of Neolithic groups with a negligible amount of interaction with local hunter-gatherers. On the other hand, Neolithic farmers from west of the Rhine river (in France, Spain, Great Britain) carry a genetic component inherited from local Mesolithic groups, implying a process of late and local admixture.

The new data highlight the complexity and regional variability of biological and cultural interactions between farmer and hunter-gatherer communities during the Neolithic expansion. "This study shows that we can add a lot more detail with focused sampling and unravel the regional dynamics of the farmer-forager interactions," concludes Rivollat. "With the increasing amount of genetic data, we gain the much-needed resolution to investigate biological processes in the past and to understand their relations with observed cultural phenomena."

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(1*)de la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie. Bordeaux, France

(2*)Cultures et environnements. Préhistoire, Antiquité Moyen Âge. Nice, France

(3*)Roemisch-Germanisches Zentralmuseum / Leibniz Research Institute for Archaeology. Mainz, Germany

(4*)See list of authors. This study was funded by the Fyssen Foundation (MR, post-doctoral fellowship, 2017-2018), the New Faculty Startup Fund of the National University of Seoul (CJ), the Max Planck Society, the French (ANR) and German (DFG) Research Foundations, via the INTERACT project, ANR-17-FRAL-0010, DFG-HA-5407/4-1, 2018-2021 (MFD, WH, MR), and the European Research Council (ERC, 771234 - PALEoRIDER (WH, ABR)).

Evolution of pandemic coronavirus outlines path from animals to humans

The virus's ability to change makes it likely that new human coronaviruses will arise

DUKE UNIVERSITY MEDICAL CENTER

DURHAM, N.C. -- A team of scientists studying the origin of SARS-CoV-2, the virus that has caused the COVID-19 pandemic, found that it was especially well-suited to jump from animals to humans by shapeshifting as it gained the ability to infect human cells.

Conducting a genetic analysis, researchers from Duke University, Los Alamos National Laboratory, the University of Texas at El Paso and New York University confirmed that the closest relative of the virus was a coronavirus that infects bats. But that virus's ability to infect humans was gained through exchanging a critical gene fragment from a coronavirus that infects a scaly mammal called a pangolin, which made it possible for the virus to infect humans.

The researchers report that this jump from species-to-species was the result of the virus's ability to bind to host cells through alterations in its genetic material. By analogy, it is as if the virus retooled the key that enables it to unlock a host cell's door -- in this case a human cell. In the case of SARS-CoV-2, the "key" is a spike protein found on the surface of the virus. Coronaviruses use this protein to attach to cells and infect them.

"Very much like the original SARS that jumped from bats to civets, or MERS that went from bats to dromedary camels, and then to humans, the progenitor of this pandemic coronavirus underwent evolutionary changes in its genetic material that enabled it to eventually infect humans," said Feng Gao, M.D., professor of medicine in the Division of Infectious Diseases at Duke University School of Medicine and corresponding author of the study publishing online May 29 in the journal Science Advances.

Gao and colleagues said tracing the virus's evolutionary pathway will help deter future pandemics arising from the virus and possibly guide vaccine research.

The researchers found that typical pangolin coronaviruses are too different from SARS-CoV-2 for them to have directly caused the human pandemic.

However, they do contain a receptor-binding site -- a part of the spike protein necessary to bind to the cell membrane -- that is important for human infection. This binding site makes it possible to affix to a cell surface protein that is abundant on human respiratory and intestinal epithelial cells, endothelial cell and kidney cells, among others.

While the viral ancestor in the bat is the most closely related coronavirus to SARS-CoV-2, its binding site is very different, and on its own cannot efficiently infect human cells.

SARS-CoV-2 appears to be a hybrid between bat and pangolin viruses to obtain the "key" necessary receptor-binding site for human infection.

"There are regions of the virus with a very high degree of similarity of amino acid sequences among divergent coronaviruses that infect humans, bats and pangolins, suggesting that these viruses are under similar host selection and may have made the ancestor of SARS-CoV-2 able to readily jump from these animals to humans," said lead co-author Xiaojun Li from Duke.

"People had already looked at the coronavirus sequences sampled from pangolins that we discuss in our paper, however, the scientific community was still divided on whether they played a role in the evolution of SARS-CoV-2," said study co-lead author Elena Giorgi, staff scientist at Los Alamos National Laboratory.

"In our study, we demonstrated that indeed SARS-CoV-2 has a rich evolutionary history that included a reshuffling of genetic material between bat and pangolin coronavirus before it acquired its ability to jump to humans," Giorgi said.

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In addition to Gao, Li and Giorgi, study authors include, Manukumar Honnayakanahalli Marichannegowda, Brian Foley, Chuan Xiao, Xiang-Peng Kong, Yue Chen, S. Gnanakaran and Bette Korber

SARS-CoV-2 possibly emerged from shuffling and selection of viral genes across different species

Emergence of SARS-CoV-2 through recombination and strong purifying selection

AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE

 

A combination of genetic shuffling and evolutionary selection of near-identical genetic sequences among specific bat and pangolin coronaviruses may have led to the evolution of SARS-CoV-2 and its introduction into humans, a new study suggests. The results also showed that the virus' entire receptor binding motif (RBM), a component that plays a key role in viral entry into host cells, was introduced through recombination with pangolin coronaviruses. The study joins ongoing efforts to identify the source of the virus that causes COVID-19, which is critical for informing efforts to establish proper animal models, discover new drugs and vaccines, and ultimately prevent the rise of future zoonotic diseases. While the precise origin of SARS-CoV-2 remains a mystery, this study makes clear "that reducing or eliminating direct human contact with wild animals is critical to preventing new coronavirus zoonoses in the future," the authors say. Proximity of different species in a wet market setting, for example, may increase the potential for cross-species spillover infections, by enabling recombination between more distant coronaviruses and the emergence of mutations, the authors say. By analyzing 43 complete genome sequences from three strains of SARS-CoV-2-like coronaviruses from bats and pangolins, Xiaojun Li and colleagues delineated which strains were most and least similar to the novel coronavirus, with a special focus on genes related to the virus' spike protein complex, a critical component that facilitates viral entry into host cells. They found evidence of strong evolutionary selection around the RBM - part of the spike's amino acid sequence that directly contacts host cell receptors - among the bat, pangolin, and human coronaviruses they studied. Amino acid sequences from these viruses and SARS-CoV-2 were identical or nearly identical in the regions adjacent to the RBM, suggesting that common evolutionary mechanisms shaped these distinct viral strains. The scientists also demonstrated that SARS-CoV-2's entire RBM was introduced through recombination with coronaviruses from pangolins. Together, evolutionary selection and frequent recombination among coronaviruses from bats, pangolins, and humans may have allowed the closely related viruses to readily jump between species, the authors postulate, leading to the introduction of SARS-CoV-2 in humans.

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Largest study of its kind of women in labor finds nitrous oxide safe, side effects rare

Additionally, women in labor who had a prior vaginal birth had low rates of converting to other pain management techniques such as epidural or opioids

UNIVERSITY OF COLORADO ANSCHUTZ MEDICAL CAMPUS

 

AURORA, Colo. (May 29, 2020) - Researchers at the University of Colorado College of Nursing and the School of Medicine Department of Anesthesiology at the Anschutz Medical Campus found that the use of nitrous oxide (N2O) as a pain relief option for individuals in labor is safe for newborn children and laboring individual, and converting to a different form of pain relief such as an epidural or opioid is influenced by a woman's prior birth history and other factors.

The study, out today in Journal of Midwifery & Women's Health, surveyed 463 women who used nitrous oxide during labor. The study is the largest and first of its kind in the United States to report rates of side effects from N2O use during labor, as well as reasons for women in labor after cesarean to convert to other forms of pain relief. Of the women who began using N2O as an initial pain relief technique, 31% used only N2O throughout labor and 69% transitioned to another pain relief method such as epidural and/or opioids. "Nitrous oxide is a useful, safe option for labor analgesia in the United States. And for some laboring mothers, that's all the pain relief they need. Understanding predictors of conversion from inhaled nitrous oxide to other forms of analgesia may assist providers in their discussions with women about pain relief options during labor," said lead author and Associate Professor with the University of Colorado College of Nursing Priscilla M. Nodine, PhD, CNM.

The reason most often cited (96%) for converting from N2O to an alternative therapy was inadequate pain relief. The odds of conversion from N2O increased approximately 3-fold when labor was augmented with oxytocin and when labor was induced. Also, those who had a history ofcesarean section and experienced labor post-cesarean had more than a 6-fold increased odds of conversion to neuraxial analgesia or epidural. The odds of conversion to neuraxial analgesia decreased by 63% for individuals who had given birth previously relative to those who were giving birth for the first time.

Approximately 4 million women in the United States give birth each year, and for many, coping with laborp is a significant concern. Epidurals and spinal blocks, also known as neuraxial analgesia, are the most frequently used pain management tools in the United States, with the main alternative being systemic opioids, which can be associated with both maternal and fetal adverse effects. Recently reintroduced as a pain relief option during labor in the United States, N2O has a long history of use in many developed nations and is increasingly available in the US. "While there is a fair body of anecdotal evidence of safety and effectiveness for how nitrous oxide affects pain during labor, few systematic analyses of outcomes are available from US-based cohorts," said Nodine.

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About the University of Colorado Anschutz Medical Campus

The University of Colorado Anschutz Medical Campus is a world-class medical destination at the forefront of transformative science, medicine, education, and patient care. The campus encompasses the University of Colorado health professional schools, more than 60 centers and institutes, and two nationally ranked hospitals that treat more than 2 million adult and pediatric patients each year. Innovative, interconnected and highly collaborative, together we deliver life-changing treatments, patient care, professional training, and conduct world-renowned research powered by more than $550 million in research awards. For more information, visit http://www.cuanschutz.edu.

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New study finds cannibalism in predatory dinosaurs
NEWS RELEASE 28-MAY-2020

UNIVERSITY OF TENNESSEE AT KNOXVILLE

IMAGE: BIG THEROPOD DINOSAURS SUCH AS ALLOSAURUS AND CERATOSAURUS ATE PRETTY MUCH EVERYTHING -- INCLUDING EACH OTHER, ACCORDING TO A NEW STUDY. view more 

CREDIT: PLOS ONE

Big theropod dinosaurs such as Allosaurus and Ceratosaurus ate pretty much everything--including each other, according to a new study, "High Frequencies of Theropod Bite Marks Provide Evidence for Feeding, Scavenging, and Possible Cannibalism in a Stressed Late Jurassic Ecosystem," published last month in the journal PLOS ONE.

"Scavenging, and even cannibalism, is pretty common among modern predators," said lead author Stephanie Drumheller, a paleontologist in the University of Tennessee, Knoxville's Department of Earth and Planetary Sciences. "Big theropods, like Allosaurus, probably weren't particularly picky eaters if it meant they got a free meal."

Researchers surveyed more than 2,000 bones from the Jurassic Mygatt-Moore Quarry, a 152-million-year-old fossil deposit in western Colorado, looking for bite marks. They found more than they were expecting.

There were theropod bites on the large-bodied sauropods whose gigantic bones dominate the assemblage, bites on the heavily armored Mymoorapelta, and lots of bites on theropods, too, especially the common remains of Allosaurus. There were hundreds of them, in frequencies far above the norm for dinosaur-dominated fossil sites.

Some were on meaty bones like ribs, but researchers discovered others on tiny toe bones, far from the choicest cuts. Pulled together, the data paints a picture of an ecosystem where dinosaur remains lay out on the landscape for months at a time--a stinky prospect, but one that gave a whole succession of predators and scavengers a turn at eating.

But why were there so many bites on the Mygatt-Moore bones? That question is a little harder to answer, at least without similar surveys from other dinosaur sites for comparison.

The Mygatt-Moore Quarry itself is a little unusual.

Volunteer members of the public have excavated most of the fossils found at the quarry. Julia McHugh, curator of paleontology with the Museums of Western Colorado and a co-author of the study, decided to continue this tradition of outreach by bringing students into the lab to help with the project. Now two of them, Miriam Kane and Anja Riedel, are co-authors on the new study as well.

"Mygatt-Moore is such a unique place," McHugh said. "Science happens here alongside hands-on STEM education with our dig program and volunteers."

Having so many marks on hand let the researchers really dig into details that are sometimes harder to study in smaller collections. For example, theropod teeth are serrated, and once in a while the tooth shape is reflected in the bite marks they make. Another co-author, Domenic D'Amore of Daemen College, had earlier figured out a way to translate those striated tooth marks into body size estimates.

"We can't always tell exactly what species were marking up the Mygatt-Moore bones, but we can say many of these marks were made by something big," D'Amore said. "A few may have been made by theropods larger than any found at the site before."

For more than 30 years, researches and others have worked the Mygatt-Moore Quarry intensively, but even after all that time, each season brings new discoveries in the field and in the lab. This snapshot of dinosaur behavior is proof that old bones can still hold scientific surprises.

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Read the full study online.

Amanda Womac (865-974-2992, awomac1@utk.edu)