Jul 14, 2020

Evolution after Chicxulub asteroid impact: Rapid response of life to end-cretaceous mass

The impact event that formed the Chicxulub crater (Yucatán Peninsula, México) caused the extinction of 75% of species on Earth 66 million years ago, including non-avian dinosaurs. One place that did not experience much extinction was the deep, as organisms living in the abyss made it through the mass extinction event with just some changes to community structure.

New evidence from International Ocean Discovery Program (IODP) Expedition 364 of trace fossils of burrowing organisms that lived in the seafloor of the Chicxulub Crater beginning a few years after the impact shows just how quick the recovery of the seafloor ecosystem was, with the establishment of a well-developed tiered community within  approximately 700,000 years after the event.

In April and May 2016, a team of international scientists drilled into the Chicxulub impact crater. This joint expedition, organized by the International Ocean Discovery Program (IODP) and International Continental Scientific Drilling Program (ICDP) recovered an extended syn- and post-impact set of rock cores, allowing study of the effects of the impact on life and its recovery after the mass extinction event. The end Cretaceous (K-Pg) event has been profusely studied and its effect on biota are relatively well-known. However, the effect of these changes on the macrobenthic community, the community of organisms living on and in the seafloor that do not leave body fossils, is poorly known.

The investigators concluded that the diversity and abundance of trace fossils responded primarily to variations in the flux of organic matter (i.e., food) sinking to the seafloor during the early Paleocene. Local and regional-scale effects of the K-Pg impact included earthquakes of magnitude 10-11, causing continental and marine landslides, tsunamis hundreds of meters in height that swept more than 300 km onshore, shock waves and air blasts, and the ignition of wildfires. Global phenomena included acid rain, injection of aerosols, dust, and soot into the atmosphere, brief intense cooling followed by slight warming, and destruction of the stratospheric ozone layer, followed by a longer-term greenhouse effect.

Mass extinction events have punctuated the past 500 million years of Earth's history, and studying them helps geoscientists understand how organisms respond to stress in their environment and how ecosystems recover from the loss of biodiversity. Although the K-Pg mass extinction was caused by an asteroid impact, previous ones were caused by slower processes, like massive volcanism, which caused ocean acidification and deoxygenation and had environmental effects that lasted millions of years.

By comparing the K-Pg record to earlier events like the end Permian mass extinction (the so-called "Great Dying" when 90% of life on Earth went extinct), geoscientists can determine how different environmental changes affect life. There are similar overall patterns of recovery after both events with distinct phases of stabilization and diversification, but with very different time frames. The initial recovery after the K-Pg, even at ground zero of the impact, lasted just a few years; this same phase lasted tens of thousands of years after the end Permian mass extinction. The overall recovery of seafloor burrowing organisms after the K-Pg took ~700,000 years, but it took several million years after the end Permian.

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Gigantic, red and full of spots

Among the Sun's most striking features are its sunspots, relatively darker areas compared to the rest of the surface, some of which are visible from Earth even without magnification. Numerous other stars, which like the Sun are in the prime of their lives, are also covered by spots. In red giants, on the other hand, which are in an advanced stage of stellar evolution, such spots were previously considered to be rare. The reason for this difference can be found deep in the interior of stars. In a dynamo process, the interplay of electrically conductive plasma currents and rotation generates a star's magnetic field that is then washed up to its surface. In some places, particularly strong magnetic fields prevent hot plasma from flowing upwards. These regions appear dark and constitute starspots.

"Rotation and convection are both crucial ingredients for the formation of surface magnetic fields and starspots," explains Dr. Federico Spada of MPS, co-author of the new study. "Stars with outer convective layers have the potential to generate surface magnetic fields via dynamo action, but only when the star rotates fast enough the magnetic activity becomes detectable," he adds. Until now, researchers had assumed that almost all red giants rotate rather slowly around their own axis. After all, stars expand dramatically when they develop into red giants towards the end of their lives. As a result their rotation slows down, like a figure skater doing a pirouette with his arms stretched out. The new study led by scientists from MPS and New Mexico State University (USA) now paints a different picture. About eight percent of the observed red giants rotate quickly enough for starspots to form.

The research team scoured the measurement data of about 4500 red giants recorded by NASA's Kepler space telescope from 2009 to 2013 for evidence of spots. Such spots reduce the amount of light that a star emits into space. Since they usually change only slightly over several months, they gradually rotate out of the telescope's field of view -- and then reappear after some time. This produces typical, regularly recurring brightness fluctuations.

In a second step, the scientists investigated the question why the spotted giants rotate so quickly. How do they muster the necessary energy? "To answer this question, we had to determine as many of the stars' properties as possible and then put together an overall picture," says Dr. Patrick Gaulme, lead author of the publication. At the Apache Point Observatory in New Mexico (USA), for example, the researchers studied how the wavelengths of starlight from some of the stars change over time. This allows conclusions about their exact movement. The team also looked at rapid fluctuations in brightness, which are superimposed on the slower ones caused by starspots. The faster fluctuations are the expression of pressure waves propagating through a star's interior to its surface. They contain information on many internal properties such as the star's mass and age.

The analysis revealed that approximately 15 percent of the spotted giants belong to close binary star systems, usually constituted of a red giant with a small and less massive companion. "In such systems, the rotational speeds of both stars synchronize over time until they rotate in unison like a pair of figure skaters," says Gaulme. The slower red giant thus gains momentum and spins faster than it would have without a companion star.

The other red giants with starspots, about 85 percent, are on their own -- and yet they rotate quickly. Those with a mass roughly equal to that of the Sun probably merged with another star or planet in the course of their evolution and thus gained speed. The somewhat heavier ones, whose masses are two to three times that of the Sun, look back on a different development. In the heyday of their lives before they became red giants, their internal structure prevented the creation of a global magnetic field that gradually carries particles away from the star. Unlike their magnetic counterparts, which therefore rotate slower and slower over time, their rotation has probably never slowed down significantly. Even as red giants, they still rotate almost as quickly as they did in their youth.

"In total, behind the common observational feature that some red giants have spots, we find three groups of rapidly rotating stars, each of which has a very different explanation. So it's no wonder that the phenomenon is more widespread than we previously thought," says Gaulme.

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Keeping innocent people out of jail using the science of perception

People wrongfully accused of a crime often wait years -- if ever -- to be exonerated. Many of these wrongfully accused cases stem from unreliable eyewitness testimony. Now, Salk scientists have identified a new way of presenting a lineup to an eyewitness that could improve the likelihood that the correct suspect is identified and reduce the number of innocent people sentenced to jail. Their report is published in Nature Communications on July 14, 2020.

"Misidentification by eyewitnesses is a long-standing problem in our society. Our new lineup method uncovers the structure of eyewitness memory, removes decision bias from the identification process, and quantifies performance of individual witnesses," says Salk Professor Thomas D. Albright, co-corresponding author of the study. "This study is a great example of using laboratory science to bring about criminal justice reform."

In the United States, nearly 70 percent of DNA exonerations are due to misidentifications by eyewitnesses, according to the Innocence Project. To overcome this societal problem, research has focused on factors that influence the likelihood that a witness will identify the correct person. One key factor is the way individuals are presented to the eyewitness during the lineup, according to Albright, who co-chaired a National Academy of Sciences committee to examine the validity of eyewitness identification. Albright, an expert in the fields of visual perception and recognition, taps into decades of research suggesting that people commonly misperceive visual events, and memories of those events are continuously augmented and deteriorate over time.

Currently, the two most common (or traditional) methods used by law enforcement are known as simultaneous and sequential lineups. In the simultaneous method the eyewitness views six photographs of individuals at the same time; in the sequential method the eyewitness views six photos, one at a time. The witness then either identifies a suspect or rejects the lineup if no face matches their memory of the crime scene.

The research team sought to create a new lineup method that would help estimate the strengths of memories for each face and eliminate unconscious biases that shape decisions without awareness.

"Traditional lineups just reveal the top choice -- the tip of the iceberg. But the cause of the witness's decision is ambiguous. It may reflect strong memory for the culprit, or it may mean that the witness was not very discerning," says Albright. "Our new procedure overcomes that ambiguity by revealing the strength of recognition memory for all lineup faces."

The scientists used a technique, called the method of paired comparisons, which works similar to how an optometrist gives an eye exam: Just like looking through pairs of lenses and stating which lens is clearer, the eyewitness is shown two photographs of individuals at a time and they choose the one that looks more similar to the person they remember from the crime scene. The procedure yields an estimate of the strength of recognition memory for each lineup face. Statistical analysis of these memory strengths then reveals the probability of correctly identifying the culprit.

"Our methods derive from a branch of science called sensory psychophysics," says Staff Scientist Sergei Gepshtein, first and co-corresponding author of the paper, who founded and directs the Collaboratory for Adaptive Sensory Technologies at Salk. "Psychophysical tools are designed to reveal how properties of the physical world are ordered -- or 'scaled' -- in the mind. Our approach allowed us to peek into the 'black box' and measure how lineup faces are organized in the witness's memory in terms of their similarity to the culprit."

The paired comparison method yields greater information about the identity of the culprit than previous methods. What is more, it offers an unprecedented quantitative index of certainty for individual eyewitnesses, which is what the judge and jury really need to know.

"The conduct of a lineup is just one application of our method," says Gepshtein. "Another application is selection of lineup 'fillers,' which are faces of people known to be innocent. The fillers should not be too similar or too dissimilar to the suspect. Because the new method reveals the perceived similarity of faces, it can be used to optimize the choice of lineup fillers."

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Vision scientists discover why people literally don't see eye to eye

We humans may not always see eye to eye on politics, religion, sports and other matters of debate. But at least we can agree on the location and size of objects in our physical surroundings. Or can we?

Not according to new research from the University of California, Berkeley, recently published in the Proceedings of the Royal Society B: Biological Sciences journal, that shows that our ability to pinpoint the exact location and size of things varies from one person to the next, and even within our own individual field of vision.

"We assume our perception is a perfect reflection of the physical world around us, but this study shows that each of us has a unique visual fingerprint," said study lead author Zixuan Wang, a UC Berkeley doctoral student in psychology.

The discovery by Wang and fellow researchers in UC Berkeley's Whitney Laboratory for Perception and Action has ramifications for the practices of medicine, technology, driving and sports, among other fields where accurate visual localization is critical.

For example, a driver who makes even a small miscalculation about the location of a pedestrian crossing the street can cause a catastrophe. Meanwhile, in sports, an error of visual judgment can lead to controversy, if not a fiercely disputed championship loss.

Take, for example, the 2004 U.S. Open quarterfinals, in which tennis icon Serena Williams lost to Jennifer Capriati after a series of questionable line calls. An umpire incorrectly overruled a line judge who called a backhand hit by Williams as in, resulting in an apology to Williams by the U.S. Tennis Association.

"Line judges need to rule on whether the ball is outside or inside the parameters. Even an error as small as half a degree of visual angle, equal to a sub-millimeter shift on the judge's retina, may influence the result of the whole match," said Wang, a die-hard tennis fan.

Researchers sought to understand if different people see objects in their surroundings exactly the same way. For example, when glancing at a coffee cup on a table, can two people agree on its exact position and whether its handle is big enough to grip? The result of a series of experiments suggest not, though there's an upside.

"We may reach for a coffee mug thousands of times in our life, and through practice we reach our target," Wang said. "That's the behavioral aspect of how we train ourselves to coordinate how we act in relation to what we see."

In the first task to test visual localization, study participants pinpointed on a computer screen the location of a circular target. In another experiment looking at variations of acuity within each person's field of vision, participants viewed two lines set a minimal distance apart and determined whether one line was located clockwise or counterclockwise to the other line.

And in an experiment measuring perception of size, participants viewed a series of arcs of varying lengths and were asked to estimate their lengths. Surprisingly, people perceived the exact same arcs to be bigger at some locations in the visual field and smaller at other locations.

Overall, the results showed remarkable variations in visual performance among the group and even within each individual's field of vision. The data were mapped to show each study participant's unique visual fingerprint of perceptual distortion.

"Though our study might suggest that the source of our visual deficiencies can originate from our brain, further investigations are needed to uncover the neural basis," said Wang.

"What's also important," she added, "is how we adapt to them and compensate for our errors."

Read more at Science Daily

Jul 13, 2020

Climate change will cause more extreme wet and dry seasons

The world can expect more rainfall as the climate changes, but it can also expect more water to evaporate, complicating efforts to manage reservoirs and irrigate crops in a growing world, according to a Clemson University researcher whose latest work has been published in the journal Nature Communications.

Ashok Mishra, who is the corresponding author on the new article, said that previous studies have focused mostly on how climate change will affect precipitation. But the key contribution of the new study is that it also examined the magnitude and variability of precipitation and evaporation and how much water will be available during the wettest and driest months of the year.

Researchers found that dry seasons will become drier, and wet seasons will become wetter, said Mishra, who is the Dean's Associate Professor in the Glenn Department of Civil Engineering.

Most of the Eastern United States, including all of South Carolina, has high precipitation that it is well distributed throughout the year, researchers found. The region and others like it can expect greater precipitation and evaporation in both wet and dry seasons, according to the study. The amount of water available will vary more widely than it does now, researchers found.

The greatest concern for such regions will be more flooding, Mishra said in an interview.

The regions that will be hardest hit by climate change are the ones that already get slammed with rain during wet seasons and struggle with drought during dry seasons, researchers found. They include much of India and its neighbors to the east, including Bangladesh and Myanmar, along with an inland swath of Brazil, two sections running east-west across Africa, and northern Australia, according to the study.

"The regions which already have more drought and flooding relative to other regions will further see an increase in these events," Mishra said.

As part of the study, researchers divided the world into nine land regions, or regimes. They looked at annual precipitation and how it fluctuates through the seasons for each region from 1971-2000.

Researchers then used that data to predict future water availability during each region's three wettest months and three driest months. They evaluated three scenarios based on multiple global climate models.

The best case scenario for relatively stable water availability during wet and dry seasons is that the global temperature will stabilize at 2 degrees Celsius over pre-industrial levels, according to the study.

But researchers also looked at what would happen if the temperature were to rise to 3.5 degrees Celsius or 5 degrees Celsius over pre-industrial levels by the end of the century.

The higher the temperature, the more variation in water availability, researchers found.

Mishra said that his message to the world is that water is a very important resource.

"The availability of this resource is an issue everybody is facing," he said. "We need to take precautions to optimally use how much water we have. As the climate changes and population increases, we should be preparing for the future by improving the technology to efficiently use water for crops."

Jesus M. de la Garza, chair of the Glenn Department of Civil Engineering, congratulated Mishra on publication of the research.

Read more at Science Daily

Genetic differences between global American Crocodile populations identified in DNA analysis

A genetic analysis of the American crocodile (Crocodylus acutus) has re-established our understanding of its population structure, aiding its conservation. The collaborative study spanning seven countries and led by the Wildlife Conservation Society and University of Bristol researchers is published in PLOS ONE.

The American crocodile is widespread across the American continent (from South Florida to Venezuela, across the Greater Antilles, and from Mexico to Ecuador). Successful due to its ability to thrive within brackish and saltwater environments. Efforts to conserve the crocodile species have existed since 1975 when their status was set to vulnerable on the IUCN (International Union for Conservation of Nature) red list. However, although conservation efforts have been put in place, the American crocodile faces further threats including habitat degradation due to coastal development.

Replenishing these populations requires understanding of population structures through genetic analysis, which can elaborate on the evolution of the species' distribution. Gaining more understanding on how a species has come to be distributed so widely and how populations can differentiate genetically, can inform regions how best to manage their populations.

The study reflected a regional collaborative effort, where DNA sampling occurred across seven countries including Venezuela, Jamaica and Cuba. There has been ongoing discussion on how these regional populations of C.acutus are similar. However, the study's results found that populations in Northern, Central and Southern America's and Great Antilles differed genetically. There were similarities found between Costa Rica and Jamaican populations. In Venezuela, they identified three new haplotypes, which are closely related genes that help scientists identify an origin of distribution.

Researchers believe that the mating with different species could have contributed to this distribution, also known as hybridisation. Crocodiles hybridise easily, contributing to their ability to survive since the prehistoric era. Additionally, in Florida genetic analysis showed there had been a case of unintentional translocation, where the species had been moved from a different location over time. This had been flagged by previous research, where crocodiles with haplotypes from Central and South America had been transported to Florida, most likely for the pet trade, and later escaped or released into the wild by owners.

By identifying these differences between regional populations of C. acutus, conservation efforts can establish population clusters which consider the populations as independent management units that may have different needs and focuses.

Natalia Rossi, Country Manager of the Cuba Program at the Wildlife Conservation Society and the study's co-author explains some of the challenges around taking samples from large crocodiles: "Our study involved several research teams across multiple sites and countries and often in difficult field conditions. For four years between May to July the team would record, mark and sample crocodile hatchings, and juvenile and adult crocodiles in Cuba's Birama Swamp, one of the study sites. It was not unusual for us to have to spend hours in the mangrove lakes waiting for one to appear, and when a crocodile was spotted the whole team would have to enter the water to help net it. While both exciting and rewarding work, it is also dangerous as the crocodiles are powerful and it involves lots of team co-ordination and trust to secure the crocodile to enable us to take samples."

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Drug that calms 'cytokine storm' associated with 45 percent lower risk of dying among COVID-19 patients on ventilators

Critically ill COVID-19 patients who received a single dose of a drug that calms an overreacting immune system were 45% less likely to die overall, and more likely to be out of the hospital or off a ventilator one month after treatment, compared with those who didn't receive the drug, according to a new study by a team from the University of Michigan.

The lower risk of death in patients who received intravenous tocilizumab happened despite the fact that they were also twice as likely to develop an additional infection, on top of the novel coronavirus.

The study is published in the peer-reviewed journal Clinical Infectious Diseases after being available as a preprint last month.

It suggests a benefit from timely and targeted efforts to calm the "cytokine storm" caused by the immune system's overreaction to the coronavirus. Tocilizumab, originally designed for rheumatoid arthritis, has already been used to calm such storms in patients receiving advanced immunotherapy treatment for cancer.

The researchers base their conclusions on a thorough look back at data from 154 critically ill patients treated at Michigan Medicine, U-M's academic medical center, during the first six weeks of the pandemic's arrival in Michigan from early March to late April. The analysis looked at patients' records through late May.

During that time, when little was known about what would help COVID-19 patients on ventilators, about half of the studied patients received tocilizumab and half did not. Most received it within the 24-hour period surrounding their intubation.

This created a natural opportunity for comparing the two groups' outcomes in an observational study, though clinical trials are still needed to truly see if the drug provides a benefit, the authors say.

Promising result

Lead author Emily Somers, Ph.D., Sc.M., an epidemiologist who has studied both rheumatologic and immunologic diseases, says the research team went into their analysis uncertain whether they would find a benefit, a risk, or no clear effect associated with tocilizumab in the patients with life-threatening COVID-19. But they knew it was a critically important question that they were uniquely positioned to answer at that point in the pandemic.

"One role of epidemiology is to rigorously evaluate real-world data on treatment effects, especially when evidence from clinical trials is not available. We kept trying to prove ourselves wrong as signals of benefit emerged in the data, both because of the immediate implications of these data, and in part because of concern about the supply of the medication for other patients," she says. "But the difference in mortality despite the increase in secondary infection is quite pronounced, even after accounting for many other factors."

Somers is an associate professor in the U-M Medical School's Department of Internal Medicine and member of the U-M Institute for Healthcare Policy and Innovation. She co-leads the COVID-19 Rapid Response Registry, which is supported by the Michigan Institute for Clinical and Health Research.

The paper's co-first author is Gregory Eschenauer, Pharm.D., a clinical pharmacist at Michigan Medicine and clinical associate professor at the U-M College of Pharmacy. He and senior author Jason Pogue, Pharm.D., are members of the Michigan Medicine Antimicrobial Stewardship Program.

The ASP group developed treatment guidelines provided to Michigan Medicine physicians in mid-March that identified tocilizumab as a potentially beneficial therapy for the most severely ill COVID-19 patients. Those guidelines also pointed out its risks and the lack of evidence for its use in COVID-19, and recommended a dose of 8 milligrams per kilogram.

This led some physicians to choose to use it, while others did not -- setting the stage inadvertently for a natural comparison.

More research needed

Pogue, clinical professor at the U-M College of Pharmacy and an infectious disease pharmacist at Michigan Medicine, notes that more robust data released in June from a large randomized controlled trial in the United Kingdom has led him to recommend the steroid dexamethasone as the first choice to treat critically ill COVID-19 patients.

"For a retrospective, single-center study, our data are robust. But at this time, due to the lack of randomized controlled trial data and the much higher cost, we recommend reserving tocilizumab for the treatment of select patients who decompensate while on or after receiving dexamethasone or in patients where the risks of adverse events from steroid therapy outweigh the potential benefits" says Pogue.

"Further studies of tocilizumab, which is more targeted than dexamethasone in addressing the hyperinflammatory process, could include combining these agents or comparing them head-to-head," he adds.

Pogue notes that a single dose of tocilizumab is roughly 100 times more expensive than a course of dexamethasone. He also notes that another drug that aims to treat cytokine storm by targeting the interleukin-6 (IL-6) receptor -- one called sarilumab -- appears to have failed to improve outcomes in a clinical trial in COVID-19 patients including those on ventilators.

Michigan Medicine had been participating in the sarilumab study at the time the patients in the current study were treated, but not all patients qualified because of the timing of their admission or issues around testing for COVID-19. The current study does not include any patients who received sarilumab.

If the evidence around IL-6 targeting bears out in further studies, the authors note that it will be important to select the dose and timing carefully, to address the cytokine storm without interfering with IL-6's other roles in activating the body's response to infections and its processes for repairing tissue.

More about the study

The majority of the patients were transferred to U-M from Detroit-area hospitals after diagnosis with COVID-19, and those who received tocilizumab were less likely overall to have been transferred while already on a ventilator.

By the end of the 28-day period after patients went on a ventilator, 18% of those who received tocilizumab had died, compared with 36% of those who had not. When adjusted for health characteristics, this represents a 45% reduction in mortality. Of those still in the hospital at the end of the study period, 82% of the tocilizumab patients had come off the ventilator, compared with 53% of those who didn't receive the drug.

In all, 54% of the tocilizumab patients developed a secondary infection, mostly ventilator associated pneumonia; 26% of those who didn't receive tocilizumab developed such infections. Such "superinfections" usually reduce the chance of survival for COVID-19 patients.

Hydroxychloroquine was included in the treatment guidelines for COVID-19 inpatients at Michigan Medicine for the first two and a half weeks of the study period, before being removed as evidence of its lack of benefit and risks emerged. In all, it was used in one-quarter of the patients who received tocilizumab and one-fifth of those who didn't. Similar percentages of the two patient groups received steroids, though none received dexamethasone.

The patients in the two groups were similar in most ways except for a slightly higher average age in the non-tocilizumab group, and lower rates of chronic obstructive pulmonary disease and chronic kidney disease among the tocilizumab patients.

Read more at Science Daily

Bird droppings carry risk of antibiotic resistance

Bird droppings may pose more health risks than people realize, according to Rice University environmental engineers who study antibiotic resistance.

Their study found high levels of genes that encode antibiotic resistance harbored by opportunistic pathogens in the droppings of common urban ducks, crows and gulls.

The study led by postdoctoral research associate Pingfeng Yu of Rice's Brown School of Engineering appears in the Elsevier journal Environmental Pollution. Yu is a member of the lab of civil and environmental engineer and co-author Pedro Alvarez.

Previous studies determined bird-carried antibiotic resistant genes (ARGs) and bacteria (ARBs) can be transferred to humans through swimming, contact with feces or impacted soil or inhalation of aerosolized fecal particles. Studies have also analyzed bird feces found near ARG hotspots like wastewater treatment plants and drainage from poultry farms.

But the Rice study digs deeper to quantify the abundance, diversity and seasonal persistence of ARGs.

"We still do not fully understand what factors exert selective pressure for the occurrence of ARGs in the gastrointestinal system of wild urban birds," Alvarez said. "Residual antibiotics that are incidentally assimilated during foraging is likely one of these factors, but further research is needed to discern the importance of other potential etiological factors, such as bird diet, age, gut microbiome structure and other stressors."

The team that included lead authors Huiru Zhao, a student at Nankai University in China, and Rice graduate student Ruonan Sun compared "freshly deposited" samples from each species found around Houston during the winter and summer months to samples from poultry and livestock known to carry some of the same mutations.

They found that ARGs in all of the species, regardless of season, encoded significant resistance to tetracycline, beta-lactam and sulfonamide antibiotics. The researchers were surprised to see the relatively high abundance of ARGs were comparable to those found in the fresh feces of poultry occasionally fed with antibiotics.

They also found intI1, an integron that facilitates rapid bacterial acquisition of antibiotic resistance, was five times more abundant in the birds than in farm animals.

"Our results indicate that urban wild birds are an overlooked but potentially important reservoir of antimicrobial resistance genes, although their significance as vectors for direct transmission of resistant infections is possible but improbable due to low frequency of human contact," Alvarez said.

The team also looked for ARGs in soil up to 1 inch deep around bird deposits and discovered they are "moderately persistent" in the environment, with half-lives of up to 11.1 days.

Of the three species, crows showed a significantly lower level of ARGs during the summer compared to ducks and gulls, they reported.

"That's probably due to differences in their ecological niches, foraging patterns and gut microbiome," Sun said. "Crows are omnivores and feed on abundant natural food with less anthropogenic contaminations in the summer. In addition, the composition of their gut microbiome impacts ARG dissemination and enrichment in vivo, and therefore influences ARG levels in the excreted bird feces."

The researchers found that opportunistic pathogens including bacteria that cause urinary tract infections, sepsis and respiratory infections were common in the feces of all of the birds, and another associated with food poisoning was detected in samples collected during the winter.

Winter feces, they wrote, contained more of the bad bacteria that may also harbor ARGs, possibly due to lower sunlight inactivation and differences in moisture levels and temperature.

Read more at Science Daily

Jul 12, 2020

Care for cats? So did people along the Silk Road more than 1,000 years ago

Person stroking kitten
Common domestic cats, as we know them today, might have accompanied Kazakh pastoralists as pets more than 1,000 years ago. This has been indicated by new analyses done on an almost complete cat skeleton found during an excavation along the former Silk Road in southern Kazakhstan. An international research team led by Martin Luther University Halle-Wittenberg (MLU), Korkyt-Ata Kyzylorda State University in Kazakhstan, the University of Tübingen and the Higher School of Economics in Russia has reconstructed the cat's life, revealing astonishing insights into the relationship between humans and pets at the time. The study will appear in the journal Scientific Reports.

The tomcat -- which was examined by a team led by Dr Ashleigh Haruda from the Central Natural Science Collections at MLU -- did not have an easy life. "The cat suffered several broken bones during its lifetime," says Haruda. And yet, based on a very conservative estimate, the animal had most likely made it past its first year of life. For Haruda and her colleagues, this is a clear indication that people had taken care of this cat.

During a research stay in Kazakhstan, the scientist examined the findings of an excavation in Dzhankent, an early medieval settlement in the south of the country which had been mainly populated by the Oghuz, a pastoralist Turkic tribe. There she discovered a very well-preserved skeleton of a cat. According to Haruda, this is quite rare because normally only individual bones of an animal are found during an excavation, which prevents any systematic conclusions from being drawn about the animal's life. The situation is different when it comes to humans since usually whole skeletons are found. "A human skeleton is like a biography of that person. The bones provide a great deal of information about how the person lived and what they experienced," says Haruda. In this case, however, the researchers got lucky: after its death, the tomcat was apparently buried and therefore the entire skull including its lower jaw, parts of its upper body, legs and four vertebrae had been preserved.

Haruda worked together with an international team of archaeologists and ancient DNA specialists. An examination of the tomcat's skeleton revealed astonishing details about its life. First, the team took 3D images and X-rays of its bones. "This cat suffered a number of fractures, but survived," says Haruda. Isotope analyses of bone samples also provided the team with information about the cat's diet. Compared to the dogs found during the excavation and to other cats from that time period, this tomcat's diet was very high in protein. "It must have been fed by humans since the animal had lost almost all its teeth towards the end of its life."

DNA analyses also proved that the animal was indeed likely to be a domestic cat of the Felis catus L. species and not a closely related wild steppe cat. According to Haruda, it is remarkable that cats were already being kept as pets in this region around the 8th century AD: "The Oghuz were people who only kept animals when they were essential to their lives. Dogs, for example, can watch over the herd. They had no obvious use for cats back then," explains the researcher. The fact that people at the time kept and cared for such "exotic" animals indicates a cultural change, which was thought to have occurred at a much later point in time in Central Asia. The region was thought to have been slow in making changes with respect to agriculture and animal husbandry.

The Dhzankent settlement, where the remains of the cat were found, was located along the Silk Road, an ancient network of important caravan routes that connected Central and East Asia with the Mediterranean region by land. According to Haruda, the find is also an indication of cultural exchange between the regions located along the Silk Road.

Read more at Science Daily

Scientists propose plan to determine if Planet Nine is a primordial black hole

Black hole abstract illustration
Scientists at Harvard University and the Black Hole Initiative (BHI) have developed a new method to find black holes in the outer solar system, and along with it, determine once-and-for-all the true nature of the hypothesized Planet Nine. The paper, accepted to The Astrophysical Journal Letters, highlights the ability of the future Legacy Survey of Space and Time (LSST) mission to observe accretion flares, the presence of which could prove or rule out Planet Nine as a black hole.

Dr. Avi Loeb, Frank B. Baird Jr. Professor of Science at Harvard, and Amir Siraj, a Harvard undergraduate student, have developed the new method to search for black holes in the outer solar system, based on flares that result from the disruption of intercepted comets. The study suggests that the LSST has the capability to find black holes by observing for accretion flares resulting from the impact of small Oort cloud objects.

"In the vicinity of a black hole, small bodies that approach it will melt as a result of heating from the background accretion of gas from the interstellar medium onto the black hole," said Siraj. "Once they melt, the small bodies are subject to tidal disruption by the black hole, followed by accretion from the tidally disrupted body onto the black hole." Loeb added, "Because black holes are intrinsically dark, the radiation that matter emits on its way to the mouth of the black hole is our only way to illuminate this dark environment."

Future searches for primordial black holes could be informed by the new calculation. "This method can detect or rule out trapped planet-mass black holes out to the edge of the Oort cloud, or about a hundred thousand astronomical units," said Siraj. "It could be capable of placing new limits on the fraction of dark matter contained in primordial black holes."

The upcoming LSST is expected to have the sensitivity required to detect accretion flares, while current technology isn't able to do so without guidance. "LSST has a wide field of view, covering the entire sky again and again, and searching for transient flares," said Loeb. "Other telescopes are good at pointing at a known target but we do not know exactly where to look for Planet Nine. We only know the broad region in which it may reside." Siraj added, "LSST's ability to survey the sky twice per week is extremely valuable. In addition, its unprecedented depth will allow for the detection of flares resulting from relatively small impactors, which are more frequent than large ones."

The new paper focuses on the famed Planet Nine as a prime first candidate for detection. The subject of much speculation, most theories suggest that Planet Nine is a previously undetected planet, but it may also flag the existence of a planet-mass black hole.

"Planet Nine is a compelling explanation for the observed clustering of some objects beyond the orbit of Neptune. If the existence of Planet Nine is confirmed through a direct electromagnetic search, it will be the first detection of a new planet in the solar system in two centuries, not counting Pluto, said Siraj, adding that a failure to detect light from Planet Nine -- or other recent models, such as the suggestion to send probes to measure gravitational influence -- would make the black hole model intriguing. "There has been a great deal of speculation concerning alternative explanations for the anomalous orbits observed in the outer solar system. One of the ideas put forth was the possibility that Planet Nine could be a grapefruit-sized black hole with a mass of five to ten times that of the Earth."

The focus on Planet Nine is based both in the unprecedented scientific significance that a hypothetical discovery of a planet-mass black hole in the solar system would hold as well as the continued interest in understanding what's out there. "The outskirts of the solar system is our backyard. Finding Planet Nine is like discovering a cousin living in the shed behind your home which you never knew about," said Loeb. "It immediately raises questions: why is it there? How did it obtain its properties? Did it shape the solar system history? Are there more like it?"

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