Friday, February 28, 2020

How Mars May Have Once Hosted Oceans and Life

Scientists have devised new analytical tools to break down the enigmatic history of Mars’ atmosphere — and whether life was once possible there.

Jezero Crater, landing site for the upcoming Mars 2020 rover mission.
Credit: NASA/JPL/JHUAPL/MSSS/Brown University 

A paper detailing the work was published today in the journal Science Advances. It could help astrobiologists understand the alkalinity, pH and nitrogen content of ancient waters on Mars, and by extension, the carbon dioxide composition of the planet’s ancient atmosphere.

Mars of today is too cold to have liquid water on its surface, a requirement for hosting life as we know it.

“The question that drives our interests isn’t whether there’s life on present-day Mars,” said Tim Lyons, UCR distinguished professor of biogeochemistry. “We are driven instead by asking whether there was life on Mars billions of years ago, which seems significantly more likely.”

However, “Overwhelming evidence exists that Mars had liquid water oceans roughly 4 billion years ago,” Lyons noted.

The central question astrobiologists ask is how that was possible. The red planet is farther from the sun than Earth is, and billions of years ago the sun generated less heat than it does today.

“To have made the planet warm enough for liquid surface water, its atmosphere would likely have needed an immense amount of greenhouse gas, carbon dioxide specifically,” explained Chris Tino, a UCR graduate student and co-first-author of the paper along with Eva Stüeken, a lecturer at the University of St. Andrews in Scotland.

Since sampling Mars’ atmosphere from billions of years ago to learn its carbon dioxide content is impossible, the team concluded that a site on Earth whose geology and chemistry bear similarities to the Martian surface might provide some of the missing pieces. They found it in southern Germany’s Nordlinger Ries crater.

A sample of suevite rock formed nearly 15 million years ago by the Ries Crater meteorite impact. Similarly impact-generated rocks exist on the rims of ancient crater lakes on Mars.
Credit: NASA

Formed roughly 15 million years ago after being struck by a meteorite, Ries crater features layers of rocks and minerals better preserved than almost anywhere on Earth.

The Mars 2020 rover will land in a similarly structured, well-preserved ancient crater. Both places featured liquid water in their distant past, making their chemical compositions comparable.

According to Tino, it’s unlikely that ancient Mars had enough oxygen to have hosted complex life forms like humans or animals.

However, some microorganisms could have survived if ancient Martian water had both a neutral pH level and was highly alkaline. Those conditions imply sufficient carbon dioxide in the atmosphere — perhaps thousands of times more than what surrounds Earth today — to warm the planet and make liquid water possible.

While pH measures the concentration of hydrogen ions in a solution, alkalinity is a measure dependent on several ions and how they interact to stabilize pH.

“Ries crater rock samples have ratios of nitrogen isotopes that can best be explained by high pH,” Stüeken said. “What’s more, the minerals in the ancient sediments tell us that alkalinity was also very high.”

However, Martian samples with mineral indicators for high alkalinity and nitrogen isotope data pointing to relatively low pH would demand extremely high levels of carbon dioxide in the past atmosphere.

The resulting carbon dioxide estimates could help solve the long-standing mystery of how an ancient Mars located so far from a faint early sun could have been warm enough for surface oceans and perhaps life. How such high levels could have been maintained and what might have lived beneath them remain important questions.

“Before this study, it wasn’t clear that something as straightforward as nitrogen isotopes could be used to estimate the pH of ancient waters on Mars; pH is a key parameter in calculating the carbon dioxide in the atmosphere,” Tino said.

Funding for this study came from the NASA Astrobiology Institute, where Lyons leads the Alternative Earths team based at UCR.

Included in the study were Gernot Arp of the Georg-August University of Göttingen and Dietmar Jung of the Bavarian State Office for the Environment.

When samples from NASA’s Mars 2020 rover mission are brought back to Earth, they could be analyzed for their nitrogen isotope ratios. These data could confirm the team’s suspicion that very high levels of carbon dioxide made liquid water possible and maybe even some forms of microbial life long ago.

“It could be 10-20 years before samples are brought back to Earth,” Lyons said. “But I am delighted to know that we have perhaps helped to define one of the first questions to ask once these samples are distributed to labs in the U.S. and throughout the world.”

Contacts and sources:
Holly Ober
University of California Riverside (UCR)

Publication: Nitrogen isotope ratios trace high-pH conditions in a terrestrial Mars analog site
Eva E. Stüeken1,2,*,†, Christopher Tino3,*, Gernot Arp4, Dietmar Jung5 and Timothy W. Lyons2,3

1. School of Earth and Environmental Sciences, University of St. Andrews, St. Andrews, Fife, KY16 9AL Scotland, UK.
2. Virtual Planetary Laboratory, University of Washington, Seattle, WA 98195, USA.
3. Department of Earth Sciences, University of California, Riverside, CA 92521, USA.
4. Georg-August-Universität Göttingen, Geowissenschaftliches Zentrum, Goldschmidtstrasse 3, 3.7077 Göttingen, Germany.
5. Bayerisches Landesamt für Umwelt, Geologischer Dienst, Hans-Högn-Straße 12, 95030 Hof/Saale, Germany.
* These authors contributed equally to this work.
Science Advances 26 Feb 2020:
Vol. 6, no. 9, eaay3440 DOI: 10.1126/sciadv.aay3440

Cannabigerol (CBG): Researchers Uncover Hidden Antibiotic Potential of Cannabis

McMaster University researchers have identified an antibacterial compound made by cannabis plants that may serve as a lead for new drug development.

An interdisciplinary team of McMaster researchers found that the chemical compound, or cannabinoid, called cannabigerol (CBG) is not only antibacterial but also effective in mice against a resilient family of bacteria known as methicillin-resistant Staphylococcus aureus (MRSA).

Photo caption: Professor Eric Brown (left); research associate Maya Farha (centre), and postdoctoral fellow Omar El-Halfawy, are authors of the study and members of the Michael G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences at McMaster University. 
Photo courtesy McMaster University

The findings were published in the journal American Chemical Society Infectious Diseases.

"In this study, we investigated 18 commercially available cannabinoids and they all showed antibiotic activity, some much more than others," said study lead Eric Brown, professor of biochemistry and biomedical sciences at McMaster.

"The one we focused on was a non-psychoactive cannabinoid called CBG, as it had the most promising activity. We synthesized that cannabinoid in mass quantity which gave us sufficient compound to go deep into the research."

The research team found that CBG had antibacterial activity against drug-resistant MRSA. It prevented the ability of that bacteria to form biofilms, which are communities of microorganisms that attach to each other and to surfaces; and it destroyed preformed biofilms and cells resistant to antibiotics. CBG achieved this by targeting the cell membrane of the bacteria.

These findings in the laboratory were supported when mice with an MRSA infection were given CBG.

"CBG proved to be marvellous at tackling pathogenic bacteria," Brown said. "The findings suggest real therapeutic potential for cannabinoids as antibiotics."

One caveat noted by the research team is the toxicity of CBG on the host cells which makes the study's findings an important lead rather than a likely final product, Brown said.

"It opens a therapeutic window, but a narrow one, to develop this into a drug," he said. "The next steps are to try to make the compound better in that it is more specific to the bacteria and has a lower chance of toxicity."

The Brown lab has been studying the antibiotic potential of cannabis for the past two years since the legalization of marijuana in Canada.

"This research became top of mind for us, in part, because we are in Canada," Brown said. "There has been some stigma of investing in this kind of research, but there's increasing anecdotal evidence of the medicinal use of cannabis. The stigma seems to be waning."

Brown said the study was reliant on his collaborator, Jakob Magolan, a McMaster associate professor of biochemistry and biomedical sciences who specializes in drug development using organic synthetic chemistry.

"The labs of Jake and I are just steps away from each other and our teams are talking to each other all the time," Brown said. "This is just one of many exciting projects we're involved with that combine scientists with very different but complementary expertise."

The study was funded by McMaster's Michael G. DeGroote Centre for Medicinal Cannabis Research, Faculty of Health Sciences and Michael G. DeGroote Institute for Infectious Disease Research.

Contacts and sources:
Veronica McGuire
McMaster University

Far Side Of The Moon: Chang'E-4 Probes 40 Meters Into Lunar Surface

A little over a year after landing, China's spacecraft Chang'E-4 is continuing to unveil secrets from the far side of the Moon. The latest study, published on Feb.26 in Science Advances, reveals what lurks below the surface.

Chang'E-4 (CE-4) landed on the eastern floor of the Van Kármán crater, near the Moon's south pole, on Jan. 3, 2019. The spacecraft immediately deployed its Yutu-2 rover, which uses Lunar Penetrating Radar (LPR) to investigate the underground it roams.

The subsurface stratigraphy seen by Yutu-2 radar on the farside of the moon.

"We found that the signal penetration at the CE-4 site is much greater than that measured by the previous spacecraft, Chang'E-3, at its near-side landing site," said paper author LI Chunlai, a research professor and deputy director-general of the National Astronomical Observatories of the Chinese Academy of Sciences (NAOC). "The subsurface at the CE-4 landing site is much more transparent to radio waves, and this qualitative observation suggests a totally different geological context for the two landing sites."

LI and his team used the LPR to send radio signals deep into the surface of the moon, reaching a depth of 40 meters by the high frequency channel of 500 MHz - more than three times the depth previously reached by CE-3. This data allowed the researchers to develop an approximate image of the subsurface stratigraphy.

"Despite the good quality of the radar image along the rover route at the distance of about 106 meters, the complexity of the spatial distribution and shape of the radar features make identification of the geological structures and events that generated such features quite difficult," said SU Yan, a corresponding author who is also affiliated with NAOC.

The researchers combined the radar image with tomographic data and quantitative analysis of the subsurface. They concluded that the subsurface is essentially made by highly porous granular materials embedding boulders of different sizes. The content is likely the result of a turbulent early galaxy, when meteors and other space debris frequently struck the Moon. The impact site would eject material to other areas, creating a cratered surface atop a subsurface with varying layers.

The results of the radar data collected by the LPR during the first 2 days of lunar operation provide the first electromagnetic image of the far side subsurface structure and the first 'ground truth' of the stratigraphic architecture of an ejecta deposit.

"The results illustrate, in an unprecedented way, the spatial distribution of the different products that contribute to from the ejecta sequence and their geometrical characteristics," LI said, referring to the material ejected at each impact. "This work shows the extensive use of the LPR could greatly improve our understanding of the history of lunar impact and volcanism and could shed new light on the comprehension of the geological evolution of the Moon's far side."

This work was a collaboration with the Key Laboratory of Lunar and Deep Space Exploration at NAOC, the University of the Chinese Academy of Sciences, the Mathematics and Physics Department of Roma Tre University in Italy, the School of Atmospheric Sciences at the Sun Yat-sen University, and the Insituto per il Rilevamento Elettromagnetico dell'Ambiente IREA-CNR in Italy.

Contacts and sources:
Xu Ang
Chinese Academy of Sciences

Publication: The Moon’s farside shallow subsurface structure unveiled by Chang’E-4 Lunar Penetrating RadarChunlai Li1,2, Yan Su1,2,*, Elena Pettinelli3,*, Shuguo Xing1,*, Chunyu Ding4, Jianjun Liu1,2, Xin Ren1, Sebastian E. Lauro3, Francesco Soldovieri5, Xingguo Zeng1, Xingye Gao1, Wangli Chen1, Shun Dai1, Dawei Liu1, Guangliang Zhang1, Wei Zuo1,2, Weibin Wen1, Zhoubin Zhang1, Xiaoxia Zhang1 and Hongbo Zhang1

1 Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100101, China.
2 University of Chinese Academy of Sciences, Beijing 100049, China.
3 Mathematics and Physics Department of Roma Tre University, Roma 00146, Italy.
4 School of Atmospheric Sciences, Sun Yat-sen University, Zhuhai 519000, China.
5 Istituto per il Rilevamento Elettromagnetico dell’Ambiente IREA-CNR, I-80124 Naples, Italy.
Science Advances 26 Feb 2020:
Vol. 6, no. 9, eaay6898  DOI: 10.1126/sciadv.aay6898

The First Salmonella: Transition from Hunter-Gather to Farmer Brought New Diseases

The oldest bacterial genomes that have been reconstructed to date show that agriculture and animal husbandry brought new diseases with them

On the basis of the genomes of the Salmonella enterica bacterium , which were obtained from skeletons up to 6,500 years old, an international research team was able to find new evidence for a central hypothesis for the development of diseases. Accordingly, the transition from a hunter-gatherer culture to agriculture and animal husbandry favored the emergence of new human pathogens that still exist today.

Dangerous proximity: Research has long suspected a connection between the emergence of agriculture and animal husbandry and the development of pathogens that jump from animals to humans. The analysis of the genetic material of salmonella that is thousands of years old confirms this thesis for the first time.

Credit: © Annette Günzel

The Neolithic Revolution and with it the beginning of agriculture stands for one of the key moments in the history of mankind. It was long believed that this was also the reason for the emergence of many new human diseases.

In a current study, a team led by Felix M. Key, Alexander Herbig and Johannes Krause from the Max Planck Institute for Human History examined human remains from western Eurasia and reconstructed eight ancient genomes from Salmonella enterica . All reconstructed genomes are part of a related group within the much larger variety of today's Salmonella pathogen. The results shed light on what was probably a serious health problem in the past and show how the bacterial pathogen developed over a period of 6,500 years.

Humans, pigs, and the origin of Paratyphi C

The analysis showed that the six salmonella genomes from farmers and ranchers are precursors of the Paratyhpi C bacterial strain - a strain that specifically infects humans, but is now rare. It triggers typhoid-like symptoms that can be fatal if left untreated.

The historical Salmonella, however, were probably not yet adapted to humans and infected animals as well as humans. This suggests that the new cultural habits associated with the introduction of agriculture have facilitated the emergence of these precursors and thus human-specific diseases.

So far, it has been assumed that the Salmonella strain spread to humans via domesticated pigs 4,000 years ago. However, the discovery of the predecessor strain in skeletons more than 5,000 years old suggests that it originated earlier than previously thought and may have spread from humans to pigs. However, the authors of the study advocate the more moderate hypothesis that both human and pig-specific Salmonella developed independently from unspecific precursors within an environment of close contact between humans and animals.

The difficult search for historical pathogens

When examining fossil finds, it is usually difficult to tell whether or not an individual was infected with a pathogen during his lifetime. Because only a few pathogens leave permanent traces on human remains such as bones or teeth. In order to be able to reliably identify previous pathogens and reconstruct their history, research is now using genetic techniques.

In the current work, the team around Key helped a new computer-controlled process called HOPS to overcome these obstacles in the search for historical pathogens in the metagenomic data. "With our newly developed methods, we were able to examine thousands of archaeological samples for traces of Salmonella DNA," explains Alexander Herbig, research group leader at the Max Planck Institute for Human History.

The research team examined a total of 2,739 human remains and was able to use them to construct eight salmonella genomes up to 6,500 years old. These are the oldest reconstructed bacterial genomes to date.

The relationship between the samples examined and the reconstructed genomes illustrates another hurdle in the field of historical pathogen research. Hundreds of samples are often required to decode only one pathogen genome. In the case of the present study, the genetic material of the pathogen could be extracted from the teeth of the human remains. The finding of S. enterica in the teeth suggests that individuals had systemic salmonella infection at the time of their death.

The people examined came from various European regions, from Russia to Switzerland, and were late hunters and gatherers, nomadic ranchers or early farmers. "This broad temporal, geographical and cultural spectrum enabled us, for the first time, to use molecular genetics to link the evolution of pathogens with the advent of a new human lifestyle," explains Herbig.

Contacts and sources: 
Petra Mader, Alexander Herbig, Prof. Dr. Johannes Krause
Max Planck Institute for Human History

Publication: Emergence of human-adapted Salmonella enterica is linked to the neolithization process Felix M. Key et al. Nature Ecology and Evolution (2019)

The Genetic Secret of Night Vision

One of the most notable features of the vertebrate eye is its retina on the inside of the eye. Surprisingly, the sensitive parts of the photoreceptor cells are on the back of the retina. Therefore, the light has to travel through living nerve tissue before it can be perceived. A special DNA organization could help improve vision in nocturnal mammals. Researchers at the Max Planck Institute for Molecular Cell Biology and Genetics in Dresden are now showing that the optical quality of the retina in mice increases in the first month after birth. This leads to an improved visual sensitivity in difficult lighting conditions. This is caused by the compact organization of the genetic material in the cell nucleus of rod photoreceptor cells.

Seeing at night is one of the most difficult and important tasks in evolution. This explains the complexity of the eye and its light-sensitive retina.[fewer]

Credit: © Ernie Janes / Alamy Stock Photo

The retina is perhaps the most amazing part of the vertebrate eye. This light-sensitive fabric layer lines the back of the eyeball and serves as a projection surface for the images projected by the lens. The retina has a thickness of 130 to 500 micrometers, which corresponds to the thickness of several sheets of paper, and consists of five layers of dense nerve tissue. Since the sensitive parts of the photoreceptor cells are on the back of the retina, the light has to travel through this dense nerve tissue to reach the photoreceptors. Researchers have long suspected that a certain compact arrangement of DNA in the nucleus of the rod photoreceptors could improve vision in nocturnal animals, but it has remained unclear

Scientists led by research group leader Moritz Kreysing at the Max Planck Institute for Molecular Cell Biology and Genetics wanted to find out together with colleagues from the TU Dresden and the bio center of the Ludwig Maximilians University in Munich whether and why cells of the retinal nerve cells are optically special and what effects this has on the transparency of the retina. In this context, transparency means that each rod cell scatters less light and is therefore more transparent.
DNA rearrangement improves transparency

The researchers particularly focused on the importance of DNA densification in the rod photoreceptor cells and whether changes in the optical properties of the retina are strong enough to improve mouse vision under difficult lighting conditions. Kaushikaram Subramanian, the lead author of the study, explains: “When examining mice, we found that the optical quality of the retina increased during the first month after birth. There is a twofold improvement in retinal transparency caused by the compact rearrangement of the genetic material in the cell nucleus. With behavioral tests under moonlight conditions, we were also able to show that mice with this DNA adjustment could see better under poor light conditions than mice that lacked such an arrangement.

Research not only reveals the function of this unusual DNA organization in the retina. Furthermore, the work shows that image clarity is not only a question of the image projection lens, but also depends on the optical quality of the retina. Moritz Kreysing, who supervised the study and is also a member of the Center for Systems Biology Dresden, summarizes: “Our study further indicates that genetics methods could be used to change the optical properties of cells and tissues. It would be exciting to see whether genetics can be used to improve the transparency of cells and tissues, which would greatly benefit biological microscopy of living tissues. ”

Contacts and sources:

Katrin Boes, Dr. Moritz Kreysing

Max Planck Institute for Molecular Cell Biology and Genetics

Publication: Kaushikaram Subramanian, Martin Weigert, Oliver Borsch, Heike Petzold, Alfonso Garcia, Eugene Myers, Marius Ader, Irina Solovei, Moritz Kreysing:
Rod nuclear architecture determines contrast transmission of the retina and behavioral sensitivity in mice eLife, December 11, 2019 DOI

Thursday, February 27, 2020

Mystery Surrounding Dinosaur Footprints on A Cave Ceiling in Central Queensland Solved

The mystery surrounding dinosaur footprints on a cave ceiling in Central Queensland has been solved, in article published in Historical Biology, after more than a half a century.

University of Queensland palaeontologist Dr Anthony Romilio discovered pieces to a decades-old puzzle in an unusual place - a cupboard under the stairs of a suburban Sydney home.

"The town of Mount Morgan near Rockhampton has hundreds of fossil footprints and has the highest dinosaur track diversity for the entire eastern half of Australia," Dr Romilio said.
Credit: Copyright STAINES

"Earlier examinations of the ceiling footprints suggested some very curious dinosaur behavior; that a carnivorous theropod walked on all four legs.

"You don't assume T. rex used its arms to walk, and we didn't expect one of its earlier predatory relatives of 200 million years ago did either."

Researchers wanted to determine if this dinosaur did move using its feet and arms, but found accessing research material was difficult.

"For a decade the Mount Morgan track site has been closed, and the published 1950s photographs don't show all the five tracks," Dr Romilio said.

However Dr Romilio had a chance meeting with local dentist Dr Roslyn Dick, whose father found many dinosaur fossils over the years.

"I'm sure Anthony didn't believe me until I mentioned my father's name - Ross Staines," Ms Dick said.

"Our father was a geologist and reported on the Mount Morgan caves containing the dinosaur tracks in 1954.

"Besides his published account, he had high-resolution photographs and detailed notebooks, and my sisters and I had kept it all.

"We even have his dinosaur footprint plaster cast stored under my sister's Harry Potter cupboard in Sydney."

Dr Romilio said the wealth and condition of 'dinosaur information' archived by Ms Dick and her sisters Heather Skinner and Janice Millar was amazing.

"I've digitized the analogue photos and made a virtual 3D model of the dinosaur footprint, and left the material back to the family's care," he said.

"In combination with our current understanding of dinosaurs, it told a pretty clear-cut story."

The team firstly concluded that all five tracks were foot impressions - that none were dinosaur handprints.

Also the splayed toes and moderately long middle digit of the footprints resembled two-legged herbivorous dinosaur tracks, differing from prints made by theropods.

"Rather than one dinosaur walking on four legs, it seems as though we got two dinosaurs for the price of one - both plant-eaters that walked bipedally along the shore of an ancient lake," Dr Romilio said.

"The tracks lining the cave-ceiling were not made by dinosaurs hanging up-side-down, instead the dinosaurs walked on the lake sediment and these imprints were covered in sand.

"In the Mount Morgan caves, the softer lake sediment eroded away and left the harder sandstone in-fills."

Contacts and sources:
Simon Wesson
Taylor and Francis

Coronavirus Fatality Rate Estimated

Imperial researchers have released estimates on the proportion of people who may die from the disease.

According to the latest estimates from the team, from the MRC Centre for Global Infectious Disease Analysis at Imperial, one percent of people with the disease will die from their infection.

This is the fourth report from the team, who are also part of J-IDEA, the Abdul Latif Jameel Institute for Disease and Emergency Analytics.

Since the emergence of the new coronavirus (COVID-19) in December 2019, the team have adopted a policy of immediately sharing research findings on the developing pandemic. The new report presents an assessment of the severity of the likely health impact of COVID-19.

Credit: Imperial College London.

A key measure of severity of any outbreak is the case fatality ratio (CFR) - the proportion of people with a disease who will eventually die as a result of infection. Quantifying this can be challenging.

Cases of infection are detected through surveillance, which typically occurs when ill people seek healthcare. Depending on the demands a healthcare system is under, and the capacity to undertake testing, confirmed case numbers reported during an outbreak only ever represent a fraction of the true levels of infection in the community.

In addition, it can take weeks for the final clinical outcome of someone infected with a respiratory virus such as COVID-19 to be known and reported.

For the new report, the researchers used statistical models that combined data on deaths and recoveries reported in China and in travellers outside mainland China, as well as infections in repatriated citizens.

Dr Ilaria Dorigatti, co-author of the report, said: “The estimates published in today’s report rely on limited data and the next few weeks will provide valuable information on the outcome of current infections, which will allow us to refine our estimates and fill our knowledge gaps on the severity of this new virus.”

Dr Lucy Okell, report co-author, added: "It's critical to work out the chance of dying from COVID-19 for those who become infected, and who is most at risk, but our estimates remain uncertain at the current time. Most cases reported so far remain in hospital or quarantine and we don’t yet know how many will eventually recover or die. Deaths tend to be reported promptly but there is less information on how many people have recovered from the virus. We are likely to be missing cases who have milder symptoms but there is limited information on how common these are. However, our team has tried to account for these factors, and we are continuing to compile as much data as possible on the outbreak to reduce uncertainty about this critical issue."

 Credit: Imperial College London.

Professor Neil Ferguson, co-author of the report, explained: “Understanding the likely impact of the unfolding pandemic caused by the COVID-19 virus on human health will be critical to informing the decisions made by countries in the coming weeks in how best to respond to this new public health threat. Our estimates – while subject to much uncertainty due to the limited data currently available – suggest that the impact of the unfolding epidemic may be comparable to the major influenza pandemics of the twentieth century. It is therefore vital that countries across the world continue to work together to accelerate the development and testing of effective treatments and vaccines, on the fastest possible timescale. Surveillance and data sharing also need to be further enhanced to allow the spectrum of disease severity caused by this virus to be better understood.”
Fatalities among severe cases

The team estimate that people dying now from the virus on average first developed symptoms three weeks ago. This means the numbers of deaths reported today should be compared with the numbers of cases reported over two weeks ago, to gain insight into the true proportion of people who might die from their infection.

Professor Azra Ghani, report co-author, said: “Assessing the severity of an emerging disease is always challenging. This is because we generally detect those that are most ill first and only later get a sense of how many people may have milder disease or carry the infection but not have any symptoms. However, by piecing together data from various sources – including from the most severe cases reported from China, from international travellers to Wuhan who return infected, and from testing undertaken on repatriated citizens – and by correcting for delays in reporting, we estimate a fatality ratio for all infections of approximately 1%. It is important to remember that this estimate remains very uncertain. However, by monitoring the outcome in some of these populations in the coming days and weeks we should very soon be in a position to get more precise estimates that can inform public health planning.”

The team’s analysis presents estimates of the CFR for three bands of symptom severity. In Hubei province in China, only people with relatively severe symptoms are being prioritised for testing. Their central estimate of CFR for these cases is 18%, but with high uncertainty.
Only one in 19 people infected are being tested

Many countries have been looking for COVID-19 cases in travellers returning from mainland China and have been testing not just people with pneumonia (a key criterion for testing in China), but also with fever or other milder respiratory symptoms. Therefore, the severity of infections detected in travellers is lower than seen in reported cases in Hubei. The central estimates for CFR in cases detected in travellers outside mainland China lie in the range 1.2%-5.6% depending on the methods and data used. However, given the limited data so far available, there is substantial uncertainty around these values.

To make an overall assessment of the potential global health impact of this pandemic, the team needed to estimate the CFR across all people who will be infected, irrespective of symptom severity.

Global cooperation is essential to fighting the threat from coronavirus
Credit: Imperial College London.

This required estimates of the number of people currently infected, including those with mild or no symptoms. From the results of testing of all passengers (irrespective of symptoms) on several repatriation flights to Japan and Germany, the team estimate that 1.3% of the population of Wuhan currently had the infection on January 31st.

Comparing this figure with reported case numbers, the team estimate only about 1 in 19 people infected with COVID-19 in Wuhan are being tested for infection and therefore being reported as confirmed cases. In turn this allowed them to estimate that the CFR of COVID-19 in people with detectable infection (including some who may never develop symptoms) is approximately 1% (uncertainty range: 0.5-4%).

Professor Christl Donnelly, report co-author, said: "At the end of an epidemic that is completely observed, the case fatality ratio is simply the number of deaths divided by the number of cases. However, understanding the severity of a newly discovered pathogen is much more difficult, despite being an urgent priority. To get an estimate during an ongoing epidemic, we have had to allow for mild cases being less likely to be detected in symptom-based surveillance as well as the fact that the clinical outcome (death or recovery) is not yet known for some confirmed cases that remain hospitalised. Assumptions are always required to underpin our estimation methods, so we have explored the impact of alternatives. Our best estimate is that the fatality ratio for all infections is roughly 1%, but there remains uncertainty and we will update our analyses as further data become available."
Lower fatality ratio than Ebola

All CFR estimates should be interpreted cautiously at the current time as the proportion of both deaths and cases being detected is unclear. Not all infected people may have symptoms and severe cases are more likely to be detected. All estimates rely on currently limited data on the time intervals from symptom onset to death or recovery. Additional studies to assess the extent of mild or asymptomatic infection will also allow estimates of CFR to be refined. The next two weeks will allow refinement of the CFR estimates presented here.

Professor Steven Riley , report co-author added: "As more data becomes available, we are able to estimate the severity of this novel coronavirus. Using a variety of data, and correcting for known biases, we estimate that approximately 1 percent of people infected with this virus will die as a result of that infection. Although this is lower than diseases such as Ebola or SARS, it is considerably higher than seasonal influenza."
Data painstakingly collected

In addition, the CFR estimates reported by individual countries in the coming months will vary depending on the sensitivity of those countries’ surveillance systems to detect cases of differing levels of severity, the clinical care offered to severely ill cases, and the method used to derive the estimate.

Dr Natsuko Imai , report co-author, explained: "Our team pieced together multiple sources of data to understand the potential health impact of the epidemic. These data have been painstakingly collected from hundreds of media reports and public health websites through a huge team effort. Everyone, from researchers, technical staff, and students have all pitched in to help with the response. What has also struck us is the openness and speed at which countries are publicly sharing information on these COVID-19 cases. This sharing of information between countries will be invaluable for the international response to this epidemic.”

Adapted from a press release from the MRC Centre for Global Infectious Disease Analysis


The full report is available here

Contacts and sources:
 by Kate Wighton, Dr Sabine L. van Elsland


Food Freshness Sensors Could Replace ‘Use-By’ Dates To Cut Food Waste

Imperial academics have developed low-cost, smartphone-linked, eco-friendly spoilage sensors for meat and fish packaging.

The researchers say the new sensors could help detect spoilage and reduce food waste for supermarkets and consumers.

One in three UK consumers throw away food solely because it reaches the use-by date, but sixty per cent (4.2 million tonnes) of the £12.5 billion-worth of food we throw away each year is safe to eat.

PEGS, incorporated into packaging, could soon detect spoilage gases in meat and fish
Photo of salmon fillets in packages
Credit:  Imperial College London

These new laboratory prototype sensors, developed at Imperial College London, cost two US cents each to make. Known as ‘paper-based electrical gas sensors’ (PEGS), they detect spoilage gases like ammonia and trimethylamine in meat and fish products.

The sensor data can be read by smartphones, so that people can hold their phone up to the packaging to see whether the food is safe to eat.

PEGS are made of carbon electrodes printed onto readily available cellulose paper.

Credit:  Imperial College London

Dr Firat Güder's team at Imperial’s Department of Bioengineering, made the sensors by printing carbon electrodes onto readily available cellulose paper.

The materials are biodegradable and nontoxic, so they don’t harm the environment and are safe to use in food packaging. The sensors are combined with ‘near field communication (NFC)’ tags – a series of microchips that can be read by nearby mobile devices.

During laboratory testing on packaged fish and chicken, PEGS picked up trace amounts of spoilage gases quickly and more accurately than existing sensors, at a fraction of their price.

The researchers say the sensors could also eventually replace the ‘use-by’ date – a less reliable indicator of freshness and edibility. Lower costs for retailers may also eventually lower the cost of food for consumers.

via GIPHY  Credit:  Imperial College London  

Dr Güder said: “Although they’re designed to keep us safe, use-by dates can lead to edible food being thrown away. In fact, use-by dates are not completely reliable in terms of safety as people often get sick from foodborne diseases due to poor storage, even when an item is within its use-by.

“Citizens want to be confident that their food is safe to eat, and to avoid throwing food away unnecessarily because they aren’t able to judge its safety. These sensors are cheap enough that we hope supermarkets could use them within three years.

“Our vision is to use PEGS in food packaging to reduce unnecessary food waste and the resulting plastic pollution.”

The research is published in ACS Sensors.

Consumers rely on use-by dates or even ‘sniff tests’ to see if their food is safe to eat, but there is currently no commercially viable, reliable alternative that provides objective feedback on food freshness and safety.

Although developed by food technologists over many years to ensure safety, use-by dates don’t take storage and processing conditions of specific food items into account. Thus, they can lead to safe and edible food being thrown away by shops and consumers. In addition, most of the food wasted is packaged in plastic, thus contributing to plastic pollution.

First author of the study Giandrin Barandun, also from Imperial’s Department of Bioengineering, said: “Use-by dates estimate when a perishable product might no longer be edible – but they don’t always reflect its actual freshness.

“Although the food industry – and consumers – are understandably cautious about shelf life, it’s time to embrace technology that could more accurately detect food edibility and reduce food waste and plastic pollution.”

Because PEGS work on high-value items like meat and fish, they could save money for shops and their customers, by reducing waste and by enabling shops to use targeted price reduction for specific items based on PEGS rather than use-by dates.

Current sensors
Credit: Shutterstock

Consumers rely on use-by dates or 'sniff tests'

Existing food spoilage sensors are either too expensive for common use (often comprising a quarter of overall packaging costs) or too difficult to interpret. Some types, like colour-changing sensors, could in fact increase food waste as consumers might interpret even the slightest colour change as ‘bad food’.

  • PEGS aim to address both these issues. As well as being cheaper to produce and easier to interpret with electrical readings, the authors found that PEGS overcome many of the disadvantages of current gas sensors:
  • They function effectively at nearly 100 per cent humidity, where most sensors struggle above 90 per cent.
  • They work at room temperature and do not need to be heated, so they consume very low amounts of energy.
  • They're sensitive only to the gases involved in food spoilage, where other sensors can be triggered by non-spoilage gases.

What’s next?

The researchers used ballpoint pens and robotic cutters to create the sensors. Dr Güder said: “We believe our very simple technique could easily be scaled up to produce PEGS on a mass scale by using existing high-volume printing methods such as screen printing and roll-to-roll printing.”

The authors hope that PEGS could have applications beyond food processing, like sensing chemicals in agriculture, air quality, and detecting disease markers in breath like those involved in kidney disease. However, before they can be applied beyond their current use, the researchers will address how sensitive PEGS are to lower humidity.

They are also developing an array of PEGS in which each sensor detects a different chemical. Using this technique, the array will give unique signals for different gases and/or changing humidity, which would make the technology applicable to a wider variety of food types.

This work was funded by the Engineering and Physical Sciences Research Council (EPSRC).

Contacts and sources:
Caroline Brogan
Imperial College London

Publication: "Cellulose fibers enable near zero-cost electrical sensing of water-soluble gases” by Giandrin Barandun, Matteo Soprani, Sina Naficy, Max Grell, Michael Kasimatis, Kwan Lun Chiu, Andrea Ponzoni, and Firat Guder, published 5 June 2019 in ACS Sensors.

Planet Twice Earth's Size Could Have The Right Conditions For Life

Astronomers have found an exoplanet more than twice the size of Earth to be potentially habitable, opening the search for life to planets significantly larger than Earth but smaller than Neptune.

Artist's impression of K2-18b

Credit: Amanda Smith

A team from the University of Cambridge used the mass, radius, and atmospheric data of the exoplanet K2-18b and determined that it’s possible for the planet to host liquid water at habitable conditions beneath its hydrogen-rich atmosphere. The results are reported in The Astrophysical Journal Letters.

The exoplanet K2-18b, 124 light-years away, is 2.6 times the radius and 8.6 times the mass of Earth, and orbits its star within the habitable zone, where temperatures could allow liquid water to exist. The planet was the subject of significant media coverage in the autumn of 2019, as two different teams reported detection of water vapour in its hydrogen-rich atmosphere. However, the extent of the atmosphere and the conditions of the interior underneath remained unknown.

“Water vapour has been detected in the atmospheres of a number of exoplanets but, even if the planet is in the habitable zone, that doesn’t necessarily mean there are habitable conditions on the surface,” said Dr Nikku Madhusudhan from Cambridge’s Institute of Astronomy, who led the new research. “To establish the prospects for habitability, it is important to obtain a unified understanding of the interior and atmospheric conditions on the planet – in particular, whether liquid water can exist beneath the atmosphere.”

Given the large size of K2-18b, it has been suggested that it would be more like a smaller version of Neptune than a larger version of Earth. A ‘mini-Neptune’ is expected to have a significant hydrogen ‘envelope’ surrounding a layer of high-pressure water, with an inner core of rock and iron. If the hydrogen envelope is too thick, the temperature and pressure at the surface of the water layer beneath would be far too great to support life.

Now, Madhusudhan and his team have shown that despite the size of K2-18b, its hydrogen envelope is not necessarily too thick and the water layer could have the right conditions to support life. They used the existing observations of the atmosphere, as well as the mass and radius, to determine the composition and structure of both the atmosphere and interior using detailed numerical models and statistical methods to explain the data.

The researchers confirmed the atmosphere to be hydrogen-rich with a significant amount of water vapour. They also found that levels of other chemicals such as methane and ammonia were lower than expected for such an atmosphere. Whether these levels can be attributed to biological processes remains to be seen.

The team then used the atmospheric properties as boundary conditions for models of the planetary interior. They explored a wide range of models that could explain the atmospheric properties as well as the mass and radius of the planet. This allowed them to obtain the range of possible conditions in the interior, including the extent of the hydrogen envelope and the temperatures and pressures in the water layer.

“We wanted to know the thickness of the hydrogen envelope – how deep the hydrogen goes,” said co-author Matthew Nixon, a PhD student at the Institute of Astronomy. “While this is a question with multiple solutions, we’ve shown that you don’t need much hydrogen to explain all the observations together.”

The researchers found that the maximum extent of the hydrogen envelope allowed by the data is around 6% of the planet’s mass, though most of the solutions require much less. The minimum amount of hydrogen is about one-millionth by mass, similar to the mass fraction of the Earth’s atmosphere. In particular, a number of scenarios allow for an ocean world, with liquid water below the atmosphere at pressures and temperatures similar to those found in Earth’s oceans.

This study opens the search for habitable conditions and bio-signatures outside the solar system to exoplanets that are significantly larger than Earth, beyond Earth-like exoplanets. Additionally, planets such as K2-18b are more accessible to atmospheric observations with current and future observational facilities. The atmospheric constraints obtained in this study can be refined using future observations with large facilities such as the upcoming James Webb Space Telescope.

Contacts and sources:
Sarah Collins
University of Cambridge

Publication: ‘ The interior and atmosphere of the habitable-zone exoplanet K2-18b.’ Nikku Madhusudhan et al. The Astrophysical Journal Letters (2020). DOI: 10.3847/2041-8213/ab7229

Animal AI: ‘Wearable for Pets’ and People Developed

Imperial College London researchers have invented a new health tracking sensor for pets and people that monitors vital signs through fur or clothing.

The new type of sensor, which can detect vital signs like heart and breathing rates through fur and up to four layers of clothing, could help make everyday wearables for pets and livestock a reality.

They could help owners keep track of their pets’ health, and help vets monitor animals during surgery without the need for shaving.

They could even help improve the work of sniffer dogs used to detect bombs and missing persons.

In people, they could provide a new way to measure vital signs that can provide measurements over clothing without direct contact with the skin.

Lead author Dr Firat Guder, of Imperial’s Department of Bioengineering, said: “Wearables are expected to play a major role in monitoring health and detecting diseases early. Our stretchy, flexible invention heralds a whole new type of sensor that can track the health of animals and humans alike over fur or clothing.”

The research on this new class of sensors is published today in Advanced Functional Materials.

Bomb sniffing dog with the sensor and its results

 Diagram: Guder Research Group/Imperial College London

"Watery, squishy stethoscope"

The sensor works like a watery, squishy stethoscope, filling any gaps between it and its subject so no air bubbles are present to dampen the sound.Yasin CoturDepartment of Bioengineering

Unlike in humans, for whom there are many fitness tracking devices, there aren’t currently many ‘wearable’ options for pets and other animals. The researchers suggest that one reason for this is that current trackers cannot monitor vital signs through fur.

The new Imperial-developed device is made of a silicone-water composite material which houses a microphone that picks up sound waves, like a watery, squishy stethoscope. It is flexible and stretchy enough that it tightly moulds to the shape of the fur, clothing, or body part it is placed on, squeezing out any sound-sucking air bubbles and preventing them from re-forming.

First author Yasin Cotur, also of Imperial’s Department of Bioengineering, said: “The sensor works like a watery, squishy stethoscope, filling any gaps between it and its subject so no air bubbles are present to dampen the sound.”

The sound is converted to a digital signal which is then transmitted to a nearby portable computer so that people can track an animal’s physiology in real-time.

When the researchers tested their device on five humans and one dog, they found that it works through up to four layers of clothes, and that the sensor works best when the clothing or fur sits right up against the skin.

The making of the sensor, using silicone, water, microphone, and a mold.
 Diagram: Guder Research Group/Imperial College London

Dogs with jobs

As well as health tracking, the researchers say the sensors could help turn findings from sniffer dogs into measurable data.

Sniffer dogs are trained to exhibit behaviours like sitting or barking when they detect a target object such as an explosive device or person stuck inside rubble following an earthquake.

When dogs ‘alert’ to target objects, such as bombs, their heart and breathing rates increase because they are excited to be rewarded for correctly identifying their target.

Dogs can be trained to sniff out bombs, drugs, and cadavers

Credit: Shutterstock

However, ‘alerting’ behaviour can be difficult to quantitatively measure.

The researchers say their new sensor could establish baselines of normal heart and breathing rates from which to quantify the level of excitement for each dog. This would be measured by how much their vital signs diverge from the norm.

By measuring how excited the dogs are, an inbuilt algorithm might even be able to tell the strength of the dog’s reaction to the smell it detects and work out how ‘sure’ the dog is of finding the desired object.

Animal AI

The sensors have been tested only on dogs and humans so far, but the researchers will next try to adapt them for use on other types of pets, as well as horses and livestock.

Yasin said: “The next step is to validate our system further with animals, primarily focusing on sniffer dogs and then horses and livestock later on.”

They are also integrating motion sensors to the system so they can track animals’ movements in real time. The software could use an artificial intelligent algorithm to indicate when pets are standing, sitting, or lying, as well as which direction they are facing and how their vital signs diverge from the norm. This could hook up to a smartphone app that will tell owners how, and where, their pets are in real time.

We might soon be able to track dogs' health as we do our own
Credit: Shutterstock 

The research was funded by the Imperial Institute for Security Science and Technology Champions Fund, Engineering and Physical Sciences Research Council, and Wellcome Trust.

Stretchable Composite Acoustic Transducer for Wearable Monitoring of Vital Signs” by Yasin Cotur, Michael Kasimatis, Matti Kaisti, Selin Olenik, Charis Georgiou, and Firat Güder, published 25 February in Advanced Functional Materials.

Contacts and sources:
Caroline Brogan, Madeleine Stone
Imperial College London

Publication: Stretchable Composite Acoustic Transducer for Wearable Monitoring of Vital Signs. Yasin Cotur, Michael Kasimatis, Matti Kaisti, Selin Olenik, Charis Georgiou, Firat Güder. Advanced Functional Materials, 2020; 1910288 DOI: 10.1002/adfm.201910288

How Resident Microbes Restructure Body Chemistry

The makeup of our microbiomes — the unique communities of bacteria, viruses and other microbes that live in and on us — have been linked, with varying degrees of evidence, to everything from inflammatory bowel disease to athletic performance.

As much as 70 percent of the molecules in a mouse are determined by the microbes that live within the animal. But exactly how could such tiny organisms have such immense influences on a person?

University of California San Diego researchers have created the first-ever map of all the molecules in every organ of a mouse and the ways in which they are modified by microbes. In one surprising example, they discovered that microbes control the structure of bile acids in both mice and people.

This is the entire molecular map of the mice used in this project. Each small circle represents a molecule. They are connected together based on their chemical similarities. The circles are colored by whether they were found in germ-free (sterile) mice or normal mice with microbiomes. Pink = shared, Green = found only in mice with microbiomes, Blue = found only in sterile mice.

Credit: University of California San Diego

The study, published February 26, 2020 in Nature, was led by Pieter Dorrestein, PhD, professor and director of the Collaborative Mass Spectrometry Innovation Center in the Skaggs School of Pharmacy and Pharmaceutical Sciences at UC San Diego, and Robert Quinn, PhD, assistant professor at Michigan State University.

When you change the structure of molecules, such as bile acids, you could change how cells talk to one another and which genes are turned “on” or “off” at a given time, Dorrestein said. And that might have huge consequences for body function and the development of disease.

“We hear a lot about how our own human genes influence our health and behaviors, so it may come as a shock to think that we could have molecules in the body that look and act the way they do not because of our genes, but because of another living organism,” Dorrestein said.
Mapping molecules and microbes in mice

The team compared germ-free (sterile) mice and mice with normal microbes. They used a laboratory technique called mass spectrometry to characterize the non-living molecules in every mouse organ. They identified as many molecules as possible by comparing them to reference structures in the GNPS database, a crowdsourced mass spectrometry repository developed by Dorrestein and collaborators. They also determined which living microbes co-locate with these molecules by sequencing a specific genetic region that acts as a barcode for bacterial types.

In total, they analyzed 768 samples from 96 sites of 29 different organs from four germ-free mice and four mice with normal microbes. The result was a map of all of the molecules found throughout the body of a normal mouse with microbes, and a map of molecules throughout a mouse without microbes.

A comparison of the maps revealed that as much as 70 percent of a mouse’s gut chemistry is determined by its gut microbiome. Even in distant organs, such as the uterus or the brain, approximately 20 percent of molecules were different in the mice with gut microbes.
Bacteria modify bile acids

After constructing these maps, the researchers homed in on one particular family of molecules that appeared to be significantly different when microbes were present: bile acids. Bile acids are primarily produced by the mouse or human liver, and they help digest fats and oils. They can also carry messages throughout the body.

The team discovered bile acids with previously unknown structures in mice with normal microbiomes, but not in germ-free mice. It’s long been known that host liver enzymes add amino acids to bile acids, specifically the amino acids glycine and taurine. But in mice with normal microbiomes, the team found that bacteria are tagging bile acids with other amino acids — phenylalanine, tyrosine and leucine.

“More than 42,000 research papers have been published about bile acids over the course of 170 years,” Quinn said. “And yet these modifications had been overlooked.”
Influence on human health

Curious if the same types of microbe-modified bile acids are found in humans, the researchers used a tool they created, the Mass Spectrometry Search Tool (MASST), to search 1,004 public datasets of samples analyzed with mass spectrometry. They also analyzed by mass spectrometry approximately 3,000 fecal samples submitted to the American Gut Project, a large citizen science effort based at UC San Diego School of Medicine.

Here’s what they found: The unique microbial-modified bile acids the researchers saw in mice were also present in up to 25.3 percent of all human samples in the datasets. These novel bile acids were more abundant in infants and patients with inflammatory bowel disease or cystic fibrosis.

One way bile acids can deliver messages from the gut to other parts of the body is through specific gut receptors called farnesoid X receptors. Bile acids bind and activate the receptors, which then inhibit genes responsible for making more bile acids. The receptors also help regulate liver triglyceride levels and fluid regulation in the intestines, making them important in liver disease and possibly obesity. Several drugs are currently being developed to treat liver disease by activating farnesoid X receptors.

Sure enough, in mice and human cells grown in the lab, Dorrestein, Quinn and team found that the newly discovered, microbe-modified bile acids strongly stimulate farnesoid X receptors, reducing expression of genes responsible for bile acid production in the liver.

The study raises many questions about the role microbes might play in driving liver and other diseases, and in influencing the activity of therapeutics, such as drugs that target farnesoid X receptors.

“This study provides a clear example of how microbes can influence the expression of human genes,” Dorrestein said. “What we still don’t know is the downstream consequences this could have, or how we might be able to intervene to improve human health.”

Additional study co-authors include: Alexey V. Melnik, Alison Vrbanac, Kathryn A. Patras, Mitchell Christy, Zsolt Bodai, Pedro Belda-Ferre, Anupriya Tripathi, Lawton K. Chung, Melissa Quinn, Greg Humphrey, Morgan Panitchpakdi, Kelly Weldon, Alexander Aksenov, Ricardo da Silva, Robert Bussell, Andrew T. Nelson, Mingxun Wang, Eric Leszczynski, Fernando Vargas, Julia M. Gauglitz, Michael J. Meehan, Emily Gentry, Alexis C. Komor, Orit Poulsen, Brigid S. Boland, John T. Chang, William J. Sandborn, Meerana Lim, Kyung E. Rhee, David Ferguson, Manuela Raffatellu, Gabriel G. Haddad, Dionicio Siegel, Victor Nizet, Rob Knight, UC San Diego; Ting Fu, Michael Downes, Ryan D. Welch, Salk Institute for Biological Studies; Julian Avila-Pacheco, Clary Clish, Ramnik J. Xavier, Hera Vlamakis, Broad Institute of MIT and Harvard; Sena Bae, Harvard University; Himel Mallick, Eric A. Franzosa, Jason Lloyd-Price, Curtis Huttenhower, Broad Institute and Harvard University; Taren Thron, Sarkis K. Mazmanian, California Institute of Technology; Timothy D. Arthur, UC San Diego and Broad Institute; Neha Garg, Georgia Institute of Technology and Emory-Children’s Cystic Fibrosis Center; Julie C. Lumeng, University of Michigan; Barbara I. Kazmierczak, Ruchi Jain, Marie Egan, Yale School of Medicine; and Ronald M. Evans, Howard Hughes Medical Institute, Salk Institute.

This research was funded, in part, by the National Institutes of Health (5U01AI124316-03, 1R03CA211211-01, 1R01HL116235 U54DE023798, R24DK110499, GMS10RR029121, R01HD084163, 1KL2TR001444, T15LM011271, DK057978, HL105278, HL088093, ES010337, DK057978, HL105278, HL088093, CA014195, P42ES010337), American Heart Association (grant 13EIA14660045), Howard Hughes Medical Institute, March of Dimes Chair in Molecular and Developmental Biology at the Salk Institute, Samuel Waxman Cancer Research Foundation, Hewitt Medical Foundation, UC San Diego Center for Microbiome Innovation, National Health and Medical Research Council of Australia Project grants (grant 1087297), Leona M. and Harry B. Helmsley Charitable Trust (grant 2017PG-MED001), SWCRF Investigator Award, Ipsen/Biomeasure, Salk Alumni Fellowship, Crohn’s & Colitis Foundation Visiting IBD Research Fellowship, Stand Up to Cancer-Cancer Research UK-Lustgarten Foundation Pancreatic Cancer Dream Team (grant SU2C-AACR-DT-20-16).


Contacts and sources:
Heather Buschman, Ph.D.
University of California - San Diego
Publication: Global chemical effects of the microbiome include new bile-acid conjugations. Robert A. Quinn, Alexey V. Melnik, Alison Vrbanac, Ting Fu, Kathryn A. Patras, Mitchell P. Christy, Zsolt Bodai, Pedro Belda-Ferre, Anupriya Tripathi, Lawton K. Chung, Michael Downes, Ryan D. Welch, Melissa Quinn, Greg Humphrey, Morgan Panitchpakdi, Kelly C. Weldon, Alexander Aksenov, Ricardo da Silva, Julian Avila-Pacheco, Clary Clish, Sena Bae, Himel Mallick, Eric A. Franzosa, Jason Lloyd-Price, Robert Bussell, Taren Thron, Andrew T. Nelson, Mingxun Wang, Eric Leszczynski, Fernando Vargas, Julia M. Gauglitz, Michael J. Meehan, Emily Gentry, Timothy D. Arthur, Alexis C. Komor, Orit Poulsen, Brigid S. Boland, John T. Chang, William J. Sandborn, Meerana Lim, Neha Garg, Julie C. Lumeng, Ramnik J. Xavier, Barbara I. Kazmierczak, Ruchi Jain, Marie Egan, Kyung E. Rhee, David Ferguson, Manuela Raffatellu, Hera Vlamakis, Gabriel G. Haddad, Dionicio Siegel, Curtis Huttenhower, Sarkis K. Mazmanian, Ronald M. Evans, Victor Nizet, Rob Knight, Pieter C. Dorrestein. Nature, 2020; DOI: 10.1038/s41586-020-2047-9

Methane Emitted Via Human Fossil Fuel Use ‘Vastly Underestimated’

Rochester researchers in Greenland drill for ice cores, which contain air bubbles with small quantities of ancient air trapped inside. By measuring the carbon-14 isotope in air from more than 200 years ago, the researchers found that scientists have been vastly overestimating the amount of fossil methane emitted by natural sources, and have therefore been underestimating the amount of methane humans are emitting into the atmosphere via fossil fuels. 
two researchers at a ice core drill in Greenland.
Photo credit Xavier Faïn / University of Grenoble Alpes

Methane is a powerful greenhouse gas and large contributor to global warming. Methane emissions to the atmosphere have increased by approximately 150 percent over the past three centuries, but it has been difficult for researchers to determine exactly where these emissions originate; heat-trapping gases like methane can be emitted naturally, as well as from human activity.

University of Rochester researchers Benjamin Hmiel, a postdoctoral associate in the lab of Vasilii Petrenko, a professor of earth and environmental sciences, and their collaborators, measured methane levels in ancient air samples and found that scientists have been vastly underestimating the amount of methane humans are emitting into the atmosphere via fossil fuels. In a paper published in Nature, the researchers indicate that reducing fossil fuel use is a key target in curbing climate change.

“Placing stricter methane emission regulations on the fossil fuel industry will have the potential to reduce future global warming to a larger extent than previously thought,” Hmiel says.
Two types of methane

Methane is the second largest anthropogenic—originating from human activity—contributor to global warming, after carbon dioxide. But, compared to carbon dioxide, as well as other heat-trapping gases, methane has a relatively short shelf-life; it lasts an average of only nine years in the atmosphere, while carbon dioxide, for instance, can persist in the atmosphere for about a century. That makes methane an especially suitable target for curbing emission levels in a short time frame.

“If we stopped emitting all carbon dioxide today, high carbon dioxide levels in the atmosphere would still persist for a long time,” Hmiel says. “Methane is important to study because if we make changes to our current methane emissions, it’s going to reflect more quickly.”

Methane emitted into the atmosphere can be sorted into two categories, based on its signature of carbon-14, a rare radioactive isotope. There is fossil methane, which has been sequestered for millions of years in ancient hydrocarbon deposits and no longer contains carbon-14 because the isotope has decayed; and there is biological methane, which is in contact with plants and wildlife on the planet’s surface and does contain carbon-14. Biological methane can be released naturally from sources such as wetlands or via anthropogenic sources such as landfills, rice fields, and livestock. Fossil methane, which is the focus of Hmiel’s study, can be emitted via natural geologic seeps or as a result of humans extracting and using fossil fuels including oil, gas, and coal.

Methane emitted into the atmosphere can be sorted into two categories–fossil or biological–based on its signature of the isotope carbon-14. Biological methane can be released naturally from sources such as wetlands or via anthropogenic sources such as landfills, rice fields, and livestock. Fossil methane can be emitted via natural geologic seeps or as a result of humans extracting and using fossil fuels.

 Credit: University of Rochester illustration / Michael Osadciw

Scientists are able to accurately quantify the total amount of methane emitted to the atmosphere each year, but it is difficult to break down this total into its individual components: Which portions originate from fossil sources and which are biological? How much methane is released naturally and how much is released by human activity?

“As a scientific community we’ve been struggling to understand exactly how much methane we as humans are emitting into the atmosphere,” says Petrenko, a coauthor of the study. “We know that the fossil fuel component is one of our biggest component emissions, but it has been challenging to pin that down because in today’s atmosphere, the natural and anthropogenic components of the fossil emissions look the same, isotopically.”
Turning to the past

In order to more accurately separate the natural and anthropogenic components, Hmiel and his colleagues turned to the past, by drilling and collecting ice cores from Greenland. The ice core samples act like time capsules: they contain air bubbles with small quantities of ancient air trapped inside. The researchers use a melting chamber to extract the ancient air from the bubbles and then study its chemical composition.

Hmiel’s research expands on previous research conducted by Petrenko, but is focused on measuring the composition of air from the early 18th century—before the start of the Industrial Revolution—to the present day. Humans did not begin using fossil fuels in significant amounts until the mid-19th century. Measuring emission levels before this time period allows researchers to identify the natural emissions absent the emissions from fossil fuels that are present in today’s atmosphere. There is no evidence to suggest natural fossil methane emissions can vary over the course of a few centuries.

By measuring the carbon-14 isotopes in air from more than 200 years ago, the researchers found that almost all of the methane emitted to the atmosphere was biological in nature until about 1870. That’s when the fossil component began to rise rapidly. The timing coincides with a sharp increase in the use of fossil fuels.

The levels of naturally released fossil methane are about 10 times lower than previous research reported. Given the total fossil emissions measured in the atmosphere today, Hmiel and his colleagues deduce that the manmade fossil component is higher than expected—25-40 percent higher, they found.
Climate change implications

The data has important implications for climate research: if anthropogenic methane emissions make up a larger part of the total, reducing emissions from human activities like fossil fuel extraction and use will have a greater impact on curbing future global warming than scientists previously thought.

To Hmiel, that’s actually good news. “I don’t want to get too hopeless on this because my data does have a positive implication: most of the methane emissions are anthropogenic, so we have more control. If we can reduce our emissions, it’s going to have more of an impact.”

This study was supported by the US National Science Foundation and the David and Lucille Packard Foundation and is a recent example of Rochester’s initiatives to better understand the global methane budget. Scientists from Rochester’s Department of Earth and Environmental Sciences have conducted field research in Antarctica, Greenland, the Great Lakes, and Earth’s oceans, and have used machine learning and climate models to advance an understanding of the potent greenhouse gas methane and the ways it affects global warming and climate change.

Contacts and sources:
Lindsey Valich
University of Rochester

Publication: Preindustrial 14CH4 indicates greater anthropogenic fossil CH4 emissions. Benjamin Hmiel, V. V. Petrenko, M. N. Dyonisius, C. Buizert, A. M. Smith, P. F. Place, C. Harth, R. Beaudette, Q. Hua, B. Yang, I. Vimont, S. E. Michel, J. P. Severinghaus, D. Etheridge, T. Bromley, J. Schmitt, X. Faïn, R. F. Weiss, E. Dlugokencky. Nature, 2020; 578 (7795): 409 DOI: 10.1038/s41586-020-1991-8

Surviving the Toba Super-Eruption 74,000 Years Ago

New archaeological work supports the hypothesis that human populations were present in India by 80,000 years ago and that they survived one of the largest volcanic eruptions in the last two million years

Remains of the Toba volcano eruption seen in satellite image of Lake Toba
File:Toba overview.jpg
Credit: NASA / Wikimedia Commons

In a study published in Nature Communications, researchers from the Department of Archeology at the Max Planck Institute for Human History, together with international partners, provide evidence that before and after the super eruption of the Toba volcano in India 74,000 years ago, users of Middle Paleolithic stone tools in India were present. The results support the assumption that Homo sapiens had reached South Asia even before the great waves of expansion of humans 60,000 years ago and that human population groups survived climatic and ecological changes there.

The Toba super eruption on the island of Sumatra, Indonesia, was one of the most violent volcanic events of the past two million years, about 5,000 times larger than the eruption of Mount St. Helen in the 1980s. This eruption occurred 74,000 years ago. Long-standing theories claim that it caused a "volcanic winter" of six to ten years that led to a 1,000-year cooling of the earth's surface and major catastrophes, including the decimation of Asian hominin and mammalian populations and the almost complete eradication of our own Species. The few surviving Homo sapiens are said to have survived in Africa through the development of sophisticated social, symbolic and economic strategies. These strategies, so the assumption

Field research in southern India conducted by some of the authors of this study in 2007 questioned these theories and sparked major debates in archeology, genetics, and geosciences on the timing of modern humans' spread beyond Africa and the effects of the Toba Super Eruption on climate and the environment. The current study continues this debate and provides evidence that Homo sapiens was present in Asia earlier and that the Toba supereruption was less apocalyptic than previously thought.

The Toba volcano eruption and human evolution

The current study reports on a unique, 80,000-year stratigraphic record from the archaeological site of Dhaba in the Middle Son Valley in northern India. Middle Paleolithic stone tools found in Dhaba provide strong evidence that there were human populations using tools in India before and after the Toba eruption 74,000 years ago. Professor JN Pal, senior researcher at the University of Allahabad in India, notes that "although the Toba ash in the Son Valley was first identified in the 1980s, we have had no relevant archaeological evidence so far, so the archaeological finds from Dhaba to fill a large gap in time. "

View over the Middle Son valley in the north of India from the archaeological site Dhaba. The archaeological excavation can be seen on the left side of the picture.

Credit: © Christina Neudorf

Professor Chris Clarkson of the University of Queensland, lead author of the study, added: "The stone tools used in Dhaba are similar to the tool sets used at the same time by Homo sapiens were used in Africa. The fact that these tool sets neither disappeared at the time of the Toba super outbreak, nor changed significantly shortly afterwards, indicates that the human population survived the so-called catastrophe and continued to create tools for changing their environment. "This new archaeological evidence underpins fossil fuels Evidence suggests that humans emigrated from Africa earlier than 60,000 years ago and spread across Eurasia, and it is in line with genetic evidence that humans crossed archaic hominin species like the Neanderthals more than 60,000 years ago ,

Stone tools from the Dhaba archaeological site. They were found in the layer that corresponds to the eruption of the Toba volcano. The molds typical of the Middle Paleolithic are shown here.

Credit: © Chris Clarkson

Toba, climate change and human resilience

Although the Toba super eruption was a gigantic event, only a few climatologists and geoscientists continue to represent the previously formulated scenario of a "volcanic winter". This suggests that the cooling of the earth was less serious and that the Toba eruption may not have caused the subsequent cold period. Recent archaeological research in Asia, including the findings reported by this study, does not support the belief that the hominin populations died out due to the Toba Super Outbreak.

Instead, archaeological evidence suggests that the human population in the region survived and coped with one of the most violent volcanic events in human history. This proves that small groups of hunters and gatherers were able to adapt to environmental changes. Nevertheless, the population groups that lived in the region around Dhaba more than 74,000 years ago do not seem to have contributed significantly to the gene pool of today's population groups. It is likely that these hunters and gatherers faced a number of challenges for their long-term survival, including the dramatic environmental changes that followed over the millennia.

Contacts and sources:
Michael PetragliaMax Planck Institute for Human History

Publication:  Human occupation of northern India spans the Toba super-eruption ~ 74,000 years ago
Chris Clarkson, Clair Harris, Bo Li, Christina M. Neudorf, Richard G. Roberts, Christine Lane, Kasih Norman, Jagannath Pal, Sacha Jones, Ceri Shipton, Jinu Koshy, MC Gupta, DP Mishra, AK Dubey, Nicole Boivin, and Michael Petraglia

Nature Communications

Unique Non-Oxygen Breathing Animal Discovered

Researchers at Tel Aviv University (TAU) have discovered a non-oxygen breathing animal. The unexpected finding changes one of science’s assumptions about the animal world.

A study on the finding was published on February 25 in PNAS by TAU researchers led by Prof. Dorothee Huchon of the School of Zoology at TAU's Faculty of Life Sciences and Steinhardt Museum of Natural History.

TEM image of H. salminicola mitochondrion-related organelle with few cristae.
Credit: TAU

The tiny, less than 10-celled parasite Henneguya salminicola lives in salmon muscle. As it evolved, the animal, which is a myxozoan relative of jellyfish and corals, gave up breathing and consuming oxygen to produce energy.

"Aerobic respiration was thought to be ubiquitous in animals, but now we confirmed that this is not the case," Prof. Huchon explains. "Our discovery shows that evolution can go in strange directions. Aerobic respiration is a major source of energy, and yet we found an animal that gave up this critical pathway."

Some other organisms like fungi, amoebas or ciliate lineages in anaerobic environments have lost the ability to breathe over time. The new study demonstrates that the same can happen to an animal — possibly because the parasite happens to live in an anaerobic environment.

Its genome was sequenced, along with those of other myxozoan fish parasites, as part of research supported by the U.S.-Israel Binational Science Foundation and conducted with Prof. Paulyn Cartwright of the University of Kansas, and Prof. Jerri Bartholomew and Dr. Stephen Atkinson of Oregon State University.

The parasite's anaerobic nature was an accidental discovery. While assembling the Henneguya genome, Prof. Huchon found that it did not include a mitochondrial genome. The mitochondria is the powerhouse of the cell where oxygen is captured to make energy, so its absence indicated that the animal was not breathing oxygen.

Until the new discovery, there was debate regarding the possibility that organisms belonging to the animal kingdom could survive in anaerobic environments. The assumption that all animals are breathing oxygen was based, among other things, on the fact that animals are multicellular, highly developed organisms, which first appeared on Earth when oxygen levels rose.

"It's not yet clear to us how the parasite generates energy," Prof. Huchon says. "It may be drawing it from the surrounding fish cells, or it may have a different type of respiration such as oxygen-free breathing, which typically characterizes anaerobic non-animal organisms."

According to Prof. Huchon, the discovery bears enormous significance for evolutionary research.

"It is generally thought that during evolution, organisms become more and more complex, and that simple single-celled or few-celled organisms are the ancestors of complex organisms," she concludes. "But here, right before us, is an animal whose evolutionary process is the opposite. Living in an oxygen-free environment, it has shed unnecessary genes responsible for aerobic respiration and become an even simpler organism."

See the publication at the PNAS web site here.

Contacts and sources: American Friends of Tel Aviv University
Tel Aviv University

Publication: A cnidarian parasite of salmon (Myxozoa: Henneguya) lacks a mitochondrial genome Dayana Yahalomi, Stephen D. Atkinson, Moran Neuhof, E. Sally Chang, Hervé Philippe, Paulyn Cartwright, Jerri L. Bartholomew, Dorothée Huchon.. Proceedings of the National Academy of Sciences, 2020; 201909907 DOI: 10.1073/pnas.1909907117

Tuesday, February 25, 2020

It's Snowing: First Quantifiable Observation of Cloud Seeding

Two University of Wyoming researchers contributed to a paper that demonstrated, for the first time, direct observation of cloud seeding using radar and gauges to quantify the snowfall. Traditionally, cloud seeding -- used to increase winter snowpack -- has been evaluated using precipitation gauges and target/control statistics that led mostly to inconclusive results.
Credit: Tom Koerner/USFWS

The research, dubbed SNOWIE (Seeded and Natural Orographic Wintertime Clouds -- the Idaho Experiment), took place Jan. 7-March 17, 2017, within and near the Payette Basin, located approximately 50 miles north of Boise, Idaho. The research was in concert with Boise-based Idaho Power Co., which provides a good share of its electrical power through hydroelectric dams.

Footage from a drone shows one of the Doppler on Wheels radars deployed on a mountaintop during the SNOWIE experiment during January 2017. Between snowstorms, crews were busy digging out and maintaining the radar site in preparation for the next storm. 
Credit: Joshua Aikins Video

“This looks at how much snow falls out of seeded clouds at certain locations. That’s what’s in this paper,” says Jeff French, an assistant professor in UW’s Department of Atmospheric Science and fourth author of the paper. “We want to see if we can apply what we learned over a number of cases over an entire winter.”

The paper, titled “Quantifying Snowfall from Orographic Cloud Seeding,” appears in the Feb. 24 (today’s) issue of the Proceedings of the National Academy of Sciences (PNAS), one of the world’s most prestigious multidisciplinary scientific journals, with coverage spanning the biological, physical and social sciences.

The paper is a follow-up to a previous PNAS paper, by the same research team, titled “Precipitation Formation from Orographic Cloud Seeding,” which was published in January 2018. That paper focused on what happens in the clouds when silver iodide is released into the clouds. In the case of the SNOWIE Project, the silver iodide was released by a second aircraft funded through Idaho Power Co., while the UW King Air took measurements to understand the impact of the silver iodide, French says.

Katja Friedrich, an associate professor and associate chair of atmospheric and oceanic sciences at the University of Colorado-Boulder, was the newest paper’s lead author. Bart Geerts, a UW professor and department head of atmospheric science, was sixth author on the paper. Other contributors were from the University of Illinois at Urbana-Champaign, the National Center for Atmospheric Research (NCAR) and Idaho Power Co.

Throughout the western U.S. and other semiarid mountainous regions across the globe, water supplies are fed primarily through snowpack melt. Growing populations place higher demand on water, while warmer winters and earlier spring reduce water supplies. Water managers see cloud seeding as a potential way to increase winter snowfall.

“We tracked the seeding plumes from the time we put the silver iodide into the cloud until it generated snow that actually fell onto the ground,” Friedrich says.

French credits modern technology, citing the use of ground-based radar, radar on UW’s King Air research aircraft and multiple passes over a target mountain range near Boise, with making the detailed cloud-seeding observations happen. Despite numerous experiments spanning several decades, no direct, unambiguous observation of this process existed prior to SNOWIE, he says.

Over the years, research of cloud seeding “has been clouded,” so to speak, Geerts adds. He says it was difficult to separate natural snowfall and what amount was actually produced through cloud seeding. However, this study was able to provide quantifiable snowfall.

“Natural snowfall was negligible. That really allowed us to isolate snow added through cloud seeding,” Geerts says. “However, we are still in the dark where there is lots of natural snowfall.”

Following a brief airborne seeding period Jan. 19, 2017, snow fell from the seeded clouds for about 67 minutes, dusting roughly 900 square miles of land in about one-tenth of a millimeter of snow, based on the team’s calculations. In all, that cloud-seeding event and two more later that month produced a total of about 235 Olympic-sized swimming pools’ worth of water.

Other observations where snow from cloud seeding was measured took place Jan. 20 and Jan. 31 of that year.

In all, the UW King Air made 24 research flights or intense observation periods (IOPs) lasting 4-6 hours each during SNOWIE. Of those IOPs, cloud seeding occurred during 21 of the flights. During the last three flights, Idaho Power had to suspend cloud seeding because there was so much snow in the mountains already.

While a good deal of research took place aboard the King Air, much of it also occurred on the ground. Numerical modeling of precipitation measurements was conducted using the supercomputer, nicknamed Cheyenne, at the NCAR-Wyoming Supercomputing Center. The numerical models simulated clouds and snow precipitation -- created in natural storms and with cloud seeding -- over the Payette Basin near Boise. The numerical models also allow researchers to study future storm events where measurements have not been obtained in the field.

While the 24 cloud-seeding flights by King Air was a good start, Geerts says, in an ideal world, even more flights are necessary to learn more about cloud seeding in other regions of the country.

Friedrich adds that the research is an important first step toward better understanding just how efficient cloud seeding can be at creating those winter wonderlands.

“Everyone you talk to will say, even if you can generate a little bit more snow, that helps us in the long run,” she says.

French says the team has applied for a new National Science Foundation grant to continue analyzing cloud-seeding data collected from the remaining research flights during 2017.

“We will look at areas where natural snowfall occurs,” French says. “We’ll take what we learned and see if we can quantify how much snow was produced through silver iodide in areas already receiving snow.

“When we get done with the next three years, we’d like to go out and make similar-type measurements in Wyoming, Colorado or Utah, where clouds may have different characteristics,” French adds. “We can broaden the types of clouds we can sample.”

Contacts and sources:
University of Wyoming
Publication: Quantifying snowfall from orographic cloud seeding. Katja Friedrich, Kyoko Ikeda, Sarah A. Tessendorf, Jeffrey R. French, Robert M. Rauber, Bart Geerts, Lulin Xue, Roy M. Rasmussen, Derek R. Blestrud, Melvin L. Kunkel, Nicholas Dawson, and Shaun Parkinson. PNAS, 2020 DOI: 10.1073/pnas.1917204117