Friday, 31 January 2020

Brain's 'GPS system' toggles between present and possible future paths in real time

JANUARY 30, 2020, by University of California, San Francisco

Credit: CC0 Public Domain


Survival often depends on animals' ability to make split-second decisions that rely on imagining alternative futures: If I'm being chased by a hungry predator, do I zag left to get home safely or zig right to lead the predator away from my family? When two paths diverge in a yellow wood, which will lead me to breakfast and which will lead me to become breakfast? Both look really about the same, but imagination makes all the difference.

In a study of rats navigating a simple maze, neuroscientists at UC San Francisco have discovered how the brain may generate such imagined future scenarios. The work provides a new grounding for understanding not only how the brain makes decisions but also how imagination works more broadly, the researchers say.

"One of the brain's most amazing abilities is to imagine things that aren't right in front of it," said Loren Frank, Ph.D., a professor of physiology and Howard Hughes Medical Institute investigator in the UCSF Center for Integrative Neuroscience, co-director of the UCSF Kavli Institute for Fundamental Neuroscience, and member of the UCSF Weill Institute for Neurosciences. "Imagination is fundamental to decision-making, but so far neuroscience hasn't given a good explanation of how the brain generates imagined futures in real time to inform various kinds of everyday decisions—while keeping track of reality at the same time."

In the new study, published January 30, 2020, in Cell, Frank's team had rats explore an M-shaped maze, while recording the firing of neurons in the hippocampus called "place cells", which are traditionally thought to keep track of an animal's location—like a neural GPS system. But as the rats approached a fork in the maze, the researchers discovered that their place-cell activity began to switch back and forth extremely rapidly—at a rate of eight times per second—between representing the animal's current position and its two alternative future paths, as if to say: "Here I am—go left?—here I am—go right?"

The team also extended this finding to another type of imagined scenario. Apart from location, place cells have also been known to keep track of an animal's travel direction. The team found that place cells representing opposite travel directions could also switch back and forth extremely rapidly, as if to say, "I'm going this way, but I could also turn around and go the other way."

"The cells' fast switching between present and possible paths was unmistakable because it was so regular," said Kenneth Kay, Ph.D., a post-doctoral researcher at Columbia University who led the study as a graduate student in Frank's lab. "It was exciting to see because speed plus consistency is exactly what's needed in any number of real-world settings, for both animals and humans."

The place cells' oscillations between the present and possible futures didn't appear to be directly controlling rats' decisions about which path to choose, but did become stronger as the rats approached the decision point, Kay and colleagues found. This suggested to the researchers that the role of the hippocampus in decision-making might be to generate a "menu" of imagined scenarios for other parts of the brain that can associate these options with past experience of their value or potential danger, then make an appropriate decision based on the animal's current drives—hungry or thirsty, fearful or bold.

"We think this shows that the hippocampus is not just responsible for the recording the past and processing the present, but for imagining the future as well," Frank said. "This study is just a first step, but it opens new avenues for us to study how imagined scenarios are generated and evaluated in the brain as animals make decisions."

Study Suggests New Conception of Hippocampus as Source of Imagination

The hippocampus, a seahorse-shaped structure found on each side of the brain deep in the temporal lobes, is among the most intensively studied parts of the brain.

Hippocampal damage—whether by brain injury or in a disease such as Alzheimer's—robs people of the ability to form new memories, leading 20th century scientists to describe the hippocampus as the brain's memory center. In the 1970s, scientists identified hippocampal place cells, which spontaneously create maps of new environments as animals explore them, then store these maps for later use. This discovery, which was awarded the 2014 Nobel Prize in Physiology or Medicine, prompted scientists to recognize that the hippocampus is also a navigation center—responsible for, say, allowing an animal to find its way back to the place where it remembers eating those delicious blackberries last summer.

Along these lines, previous work by Frank and others has shown that place cell activity can replay an animal's recent movements or even anticipate where an animal may be headed next, but such activity had only been seen intermittently—typically when animals were resting or pausing during ongoing movement—as actively considering their next move.

The new Cell study is the first to show how hippocampal cells can represent different hypothetical scenarios consistently and systematically over time. Such a system could allow animals on the move to make extremely rapid decisions in the moment based on these imagined alternatives while also keeping track of the animal's present reality, the researchers say. It could even play a role in the brain's ability to generate hypothetical scenarios or thoughts more broadly.

"The regular switching between present and possible—or actual and imagined—looks like be a robust system for generating lots of ideas, not just for mechanically remembering or predicting," Kay said. "The hippocampus could be at the root of our ability to imagine."

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Oysters as catch of the day? Perhaps not, if ocean acidity keeps rising

JANUARY 30, 2020, by David Colgan, University of California, Los Angeles

Commercially important oysters are vulnerable to ocean acidification. Creative Commons

When it comes to carbon emissions, people tend to focus more on what happens in the atmosphere and on land. But about a quarter of carbon emissions dissolve into oceans, lowering the water's pH and causing ocean acidification.

That could affect what kind of seafood is on the menu in coming years. Species such as oysters and clams appear to be vulnerable to the change while others, including lobsters and crabs, are more resilient.

Robert Eagle, a UCLA expert on climate change and oceans, has explored the complex ways acidification affects marine life. Perhaps the biggest concern is that acidification interferes with the ability of organisms such as corals to form shells and skeletons—but it doesn't affect all shell-forming organisms in the same way. Some are unaffected or actually grow faster in more acidic waters, previous research showed. But why?

"These are complex and diverse biological organisms. Some of them are resilient or adapt in some way," Eagle said.

Species' ability to regulate internal pH may be a driving force, Eagle hypothesized in his latest paper, which is published in Science Advances. The research used materials from a previous experiment that set up tanks with various acidity levels to raise a range of organisms, including crabs, corals, oysters, urchins and shrimp. The tanks had various CO2 levels (which coincide with acidity) ranging from 400 to 2,850 parts per million—that is, from approximate current levels to an extreme but possible level within the next 100 years. Eagle analyzed the chemical composition of their shells using an isotope of boron that tracks with pH.

In some organisms, the hypothesis held up well. The ability of organisms to buffer internal pH closely reflected how they grew in response to changes in external pH. Species such as urchins and coral were able to regulate internal pH well and were not adversely affected except at the highest acidification levels. Others, including lobsters and blue crabs, were not only able to regulate pH, but also grew shells faster and larger when more CO2 was present.

However, some species, including commercially important oysters and other mollusks, fared poorly and had a hard time forming robust shells in acidic waters regardless of internal pH regulation. This could prove problematic for many eateries, raw bars and cocktail lounges that have these items on their menus.

The West Coast shellfish industry is worth an estimated $270 million a year and employs more than 3,000 people.

"Oysters are really important economically to fisheries on the West Coast," Eagle said. "They seem particularly susceptible to ocean acidification, so everyone is very worried about the future of the industry."

One positive takeaway was that many organisms appeared to be resilient or able to adapt to acidification, unless it gets too high or happens too fast, Eagle said.

But losing even a few species—or one species becoming too dominant—can have catastrophic effects on marine ecosystems. The purple sea urchin takeover of coastal waters along California, Oregon and Washington provides a good example.

"You had kelp forests that supported sea otters, fish and diverse marine invertebrates," Eagle said. "Kelp is a keystone species associated with well-balanced ecosystems." Urchin populations eat away at the roots of the kelp, decimating the forests.

Acidification is only one part of the story, of course. Corals were found to be relatively resilient to acidification, but hotter waters due to climate change cause bleaching events and the eventual death of reefs. And it is difficult to project how controlled experiments will play out in large populations where there are many other factors at play.

Still, the research could help fisheries, governments and conservation organizations target specific species as they grapple with the effects of ocean acidification.

Yi-Wei Liu, lead author of the paper and researcher with Academica Sinica in Taiwan, said greater attention is being paid to ocean acidification—but there is much more to learn and the stakes are high.

"This paper makes our understanding of how things could happen one step clearer," Liu said. "We know food webs are linked together. We saw effects across different levels of the food chain. If it crashes, the outcome could be really severe."


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Researchers combine X-rays and laser light to image sprays

JANUARY 30, 2020, by The Optical Society

Researchers from Lund University developed an imaging method that provides an unprecedented view of sprays such as the ones used for liquid fuel combustion. Pictured (from the left) are PhD student Kristoffer Svendsen, postdoctoral researcher Diego Guénot, group leader at the Division of Combustion Physics Edouard Berrocal, group leader at the Division of Atomic Physics Olle Lundh and PhD student Jonas Björklund Svensson. Credit: Edouard Berrocal, Lund University

Researchers have developed a new laser-based method that provides an unprecedented view of sprays such as the ones used for liquid fuel combustion in vehicle, ship and plane engines. The technique could provide new insights into these atomizing sprays, which are also used in a variety of industrial processes such as painting and producing food powders and drugs.

"We developed a new imaging method to better understand the transition from liquid to gas that occurs before fuel combustion," said research team leader Edouard Berrocal from the Division of Combustion Physics, Department of Physics at Lund University in Sweden. "This information could be used to develop smarter fuel injection strategies, better fuel-air mixing, more efficient combustion and, ultimately, reduce pollutant emissions from combustion devices typically used for transportation."

In Optica, The Optical Society's journal for high impact research, Berrocal and colleagues from the Department of Physics' Division of Atomic Physics describe a novel approach that combines x-rays and laser-induced fluorescence to observe and quantify atomizing spray phenomena that were not previously accessible. The fluorescence images provide details on the sprayed liquid's form, including its size and shape, while the X-ray radiographs quantify how the liquid is distributed.

"Usually, images of atomizing sprays are blurry and don't contain information about the spray's interior," said Diego Guénot, first author of the paper. "Our new imaging approach solves these problems and can even detect smaller amounts of liquid than have ever been detected before with x-rays."

Seeing into a spray

Sprays are very difficult to visualize with normal light because their thousands of small droplets scatter light in all directions. X-ray beams, however, are also absorbed, making it possible to measure the amount of liquid present by detecting the amount of X-ray radiation transmitted through the spray.

This type of analysis usually requires x-rays generated by large synchrotrons, which are available at only a few specialized facilities around the world. However, the researchers overcame this barrier by using a new table-top laser-plasma accelerator developed by Olle Lundh's team in the Division of Atomic Physics. It was designed to produce x-rays tailored for high-resolution and time-resolved X-ray imaging.

"Even though they are much smaller than a synchrotron, the new laser accelerators produce x-rays in the right energy range to be absorbed by liquids and can deliver it in femtosecond pulses that essentially freeze the spray motion for imaging," said Lundh. "Also, the X-ray flux is high enough to produce a good signal over a wide area."

In the laser-plasma accelerator, x-rays are generated by focusing an intense femtosecond laser pulse into a gas or a preformed plasma. The researchers also used these femtosecond laser pulses to perform two-photon fluorescence imaging. This fluorescence approach is often used in life science microscopy to provide high contrast images of submillimeter areas but has rarely been used to image sprays, which usually require an imaging area of a few square centimeters.

"Two-photon imaging of a relatively large area requires higher energy, ultrashort laser pulses," said Berrocal. "The fact that we used an intense femtosecond laser beam to generate x-rays meant we could simultaneously perform X-ray and two-photon fluorescence imaging. Performing these two imaging modalities at the same time with a relatively large viewed area has not been done before."

Getting a clear view
The researchers first tested the technique by generating x-rays and placing a spray in front of the X-ray camera. With the first image, it was immediately apparent that the spray could be clearly visualized. The researchers then modified the setup to add the two-photon fluorescence imaging. Using the combined technique to image water jets created by an automotive fuel injector produced a higher measurement sensitivity than has been achieved with the large synchrotron X-ray sources.
"This imaging approach will make studying sprays much easier for both academic and industry researchers because they will be able to perform studies, not only at the handful of synchrotron facilities, but also at various laser plasma accelerator laboratories over the world." explained Guénot.

The researchers plan to expand the technique to obtain 3-D images of sprays and study how they evolve over time. They also want to apply it to more challenging and realistic sprays such as biodiesel or ethanol direct-injection sprays as well as for spray systems used for gas turbines.

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Study provides first look at sperm microbiome using RNA sequencing

JANUARY 31, 2020, by Wayne State University


Credit: CC0 Public Domain

A new collaborative study published by a research team from the Wayne State University School of Medicine, the CReATe Fertility Centre and the University of Massachusetts Amherst provides the first in-depth look at the microbiome of human sperm utilizing RNA sequencing with sufficient sensitivity to identify contamination and pathogenic bacterial colonization.

"We show that non-targeted sequencing of human sperm RNA has the potential to provide a profile of micro-organisms (bacteria, viruses, archaea)," said Stephen Krawetz, Ph.D., associate director of the C.S. Mott Center for Human Growth and Development at WSU and the Charlotte B. Failing Professor of Fetal Therapy and Diagnosis in the Department of Obstetrics and Gynecology, and the Center for Molecular Medicine and Genetics. 
"This information was recovered from the data typically cast aside as part of routine nucleic acid sequencing. The enhanced sensitivity and specificity of the sequencing technology as compared to current approaches may prove useful as a diagnostic tool for microbial status as part of the routine assessment as we move toward personalized care."

The study, "What human sperm RNA-Seq tells us about the microbiome" published in the Journal of Assisted Reproduction and Genetics, sought to determine if human sperm RNA sequencing data could provide a sensitive method of detection of micro-organisms, including bacteria, viruses and archaea compared to current methods of targeted culturing. The researchers collected 85 semen samples, isolated the sperm RNA and subjected it to RNA sequencing.

Grace Swanson, Ph.D., a postdoctoral fellow working with Dr. Krawetz, discovered a sample with an abnormally high level of microbial sequences. After taking a closer look, the sample was found to contain a considerable amount of Streptococcus agalactiae bacteria. A leading cause of neonatal infection during pregnancy and post-delivery linked to significant mortality rates in premature births, this bacteria can also be life-threatening in adults, particularly the elderly.

The current method for testing the male reproductive tract microbiome relies on culturing samples. This, the study reported, can be limiting because the majority of pathogens cannot be cultured. The costs of RNA sequencing have dropped dramatically and continue to decrease, providing a more complete picture of the human biome.

"Given the recent increase and severity of Streptococcus (agalactiae) infection, as well as others in adults, neonates and newborns, non-targeted human sperm RNA sequencing data may, in addition to providing fertility status, prove useful as a diagnostic for microbial status," Dr. Krawetz said.

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Thursday, 30 January 2020

Scientists learn how plants manipulate their soil environment to assure a cheap, steady supply of nutrients

JANUARY 29, 2020, by Rice University

Rice University graduate student Ilenne Del Valle holds samples of soil with various concentrations of organic carbon and proteins produced by plants that regulate the acquisition of nutrients and pest control. Credit: Jeff Fitlow/Rice University

The next time you're thinking about whether to cook dinner or order a pizza for delivery, think of this: Plants have been doing pretty much the same thing for eons.

Researchers in Rice University's Systems, Synthetic and Physical Biology program detailed how plants have evolved to call for nutrients, using convenient bacteria as a delivery service.

Their open-access report in Science Advances looks at how plants read the local environment and, when necessary, make and release molecules called flavonoids. These molecules attract microbes that infect the plants and form nitrogen nodules—where food is generated—at their roots.

When nitrogen is present and available, plants don't need to order in. Their ability to sense the presence of a nearby slow-release nitrogen source, organic carbon, is the key.

"It's a gorgeous example of evolution: Plants change a couple of (oxygen/hydrogen) groups here and there in the flavonoid, and this allows them to use soil conditions to control which microbes they talk to," said Rice biogeochemist Caroline Masiello, a co-author of the study.

The Rice team, in collaboration with researchers at Cornell University, specifically analyzed how flavonoids mediate interactions between plants and microbes depending on the presence of abiotic (nonliving) carbon. Their experiments revealed, to their surprise, that an excess of dissolved—rather than solid—carbon in soil effectively quenches flavonoid signals.

Understanding how carbon in soil affects these signals may provide a way to engineer beneficial interactions between plants and microbes and to design effective soil amendments (additives that balance deficiencies in soil), according to the researchers. Plants use flavonoids as a defense mechanism against root pathogens and could manipulate the organic carbon they produce to interfere with signaling between microbes and other plants that compete for the same nutrients.

Overall, they showed that higher organic carbon levels in soil repressed flavonoid signals by up to 98%. In one set of experiments, interrupting the signals between legume plants and microbes sharply cut the formation of nitrogen nodules.

Rice graduate student Ilenne Del Valle began the study when she became interested in the subtle differences between the thousands of flavonoids and how they influence connections between plants and microbes in soil.

"We had studied how different soil amendments change how microbes communicate with one another," said Del Valle, co-lead author of the paper with former Cornell postdoctoral associate Tara Webster. "The next question was whether this was happening when the microbes communicate with plants.

"We knew that plants modulate symbiosis with microbes through flavonoid molecules," she said. "So we wanted to learn how flavonoids interact with soil amendments used for different purposes in agriculture."

         
Credit: Ilenne Del Valle/Rice University

Because she counts two Rice professors—Masiello and synthetic biologist Joff Silberg—as her advisers, she had access to tools from both disciplines to discover the mechanisms behind those subtleties.

"We came into this thinking there was going to be a big effect from biochar," Silberg said. "Biochar is charcoal made for agricultural amendment, and it is well-known to affect microbe-microbe signals. It has a lot of surface area, and flavonoids look sticky, too. People thought they would stick to the biochar.

"They didn't. Instead, we found that dissolved carbon moving through water in the soil was affecting signals," he said. "It was very different from all of our expectations."

The Rice and Cornell team set up experiments with soils from meadows, farms and forests and then mixed in three slightly different flavonoids: naringenin, quercetin and luteolin.

They found the most dramatic effects when dissolved carbons derived from plant matter or compost were present. Plants employ naringenin, a variant of the flavonoid that gives grapefruit its bitter taste, and luteolin, expressed by leaves and many vegetables, to call for microbial nitrogen fixation. These were most curtailed in their ability to find microbes. Quercetin, also found in foods like kale and red onions and used for defense against pests, did not suffer the same fate.

Masiello noted there's a cost for plants to connect with microbes in the soil.

"These relationships with symbionts are metabolically costly," she said. "Plants have to pay the microbes in photosynthesized sugar, and in exchange the microbes mine the soil for nutrients. Microbial symbionts can be really expensive subcontractors, sometimes taking a significant fraction of a plant's photosynthate.

"What Ilenne and Tara have shown is one mechanism through which plants can control whether they invest in expensive symbionts," she said. "Among a wide class of signaling compounds used by plants for many purposes, one specific signal related to nutrients is shut off by high soil organic matter, which is a slow-release source of nutrients. The plant signal that says 'come live with us' doesn't get through.

"This is good for plants because it means they don't waste photosynthate supporting microbial help they don't need. Ilenne and Tara have also shown that signals used for other purposes are slightly chemically modified so their transmission is not affected at the same rate."

The researchers checked flavonoid concentrations in soil with standard chromatography as well as unique fluorescent and gas biosensors, genetically modified microbes introduced in 2016 with the support of a Keck Foundation grant, which also backed the current project. The microbes release a gas when they sense a particular microbial interaction in opaque materials like soil.

"The gas sensor ended up being very useful in experiments that looked like tea, where we couldn't image fluorescent signals," Silberg said.

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Brain networks come online during adolescence to prepare teenagers for adult life

JANUARY 29, 2020, by Craig Brierley, University of Cambridge

Brain development during adolescence: red brain regions belong to the “conservative” pattern of adolescent development, while the blue brain regions belong to the “disruptive” pattern. Credit: Frantisek Vasa

New brain networks come 'online' during adolescence, allowing teenagers to develop more complex adult social skills, but potentially putting them at increased risk of mental illness, according to new research published in the Proceedings of the National Academy of Sciences (PNAS).

Adolescence is a time of major change in life, with increasing social and cognitive skills and independence, but also increased risk of mental illness. While it is clear that these changes in the mind must reflect developmental changes in the brain, it has been unclear how exactly the function of the human brain matures as people grow up from children to young adults.

A team based in the University of Cambridge and University College London has published a major new research study that helps us understand more clearly the development of the adolescent brain.

The study collected functional magnetic resonance imaging (fMRI) data on brain activity from 298 healthy young people, aged 14-25 years, each scanned on one to three occasions about six to 12 months apart. In each scanning session, the participants lay quietly in the scanner so that the researchers could analyse the pattern of connections between different brain regions while the brain was in a resting state.

The team discovered that the functional connectivity of the human brain—in other words, how different regions of the brain 'talk' to each other—changes in two main ways during adolescence.

The brain regions that are important for vision, movement, and other basic faculties were strongly connected at the age of 14 and became even more strongly connected by the age of 25. This was called a 'conservative' pattern of change, as areas of the brain that were rich in connections at the start of adolescence become even richer during the transition to adulthood.

However, the brain regions that are important for more advanced social skills, such as being able to imagine how someone else is thinking or feeling (so-called theory of mind), showed a very different pattern of change. In these regions, connections were redistributed over the course of adolescence: connections that were initially weak became stronger, and connections that were initially strong became weaker. This was called a 'disruptive' pattern of change, as areas that were poor in their connections became richer, and areas that were rich became poorer.

By comparing the fMRI results to other data on the brain, the researchers found that the network of regions that showed the disruptive pattern of change during adolescence had high levels of metabolic activity typically associated with active re-modelling of connections between nerve cells.

Dr. Petra Vértes, joint senior author of the paper and a Fellow of the mental health research charity MQ, said: "From the results of these brain scans, it appears that the acquisition of new, more adult skills during adolescence depends on the active, disruptive formation of new connections between brain regions, bringing new brain networks 'online' for the first time to deliver advanced social and other skills as people grow older."

Professor Ed Bullmore, joint senior author of the paper and head of the Department of Psychiatry at Cambridge, said: "We know that depression, anxiety and other mental health disorders often occur for the first time in adolescence—but we don't know why. These results show us that active re-modelling of brain networks is ongoing during the teenage years and deeper understanding of brain development could lead to deeper understanding of the causes of mental illness in young people."

Measuring functional connectivity in the brain presents particular challenges, as Dr. František Váša, who led the study as a Gates Cambridge Trust Ph.D. Scholar, and is now at King's College London, explained.

"Studying brain functional connectivity with fMRI is tricky as even the slightest head movement can corrupt the data—this is especially problematic when studying adolescent development as younger people find it harder to keep still during the scan," he said. "Here, we used three different approaches for removing signatures of head movement from the data, and obtained consistent results, which made us confident that our conclusions are not related to head movement, but to developmental changes in the adolescent brain."

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Gut reaction: How immunity ramps up against incoming threats

JANUARY 29, 2020, by Walter and Eliza Hall Institute

A new study has revealed how the gut's protective mechanisms ramp up significantly with food intake, and at times of the day when mealtimes are anticipated based on regular eating habits.Dr Cyril Seillet and Professor Gabrielle Belz from the Walter and Eliza Hall Institute in Melbourne, Australia, found that eating causes a hormone called VIP to be released, kickstarting the activity of immune cells in response to potentially incoming pathogens or 'bad' bacteria.The researchers also found that immunity increased at anticipated mealtimes indicating that maintaining regular eating patterns could be more important than previously thought. Credit: Walter and Eliza Hall Institute

A new study has revealed how the gut's protective mechanisms ramp up significantly with food intake, and at times of the day when mealtimes are anticipated based on regular eating habits.

Researchers from the Walter and Eliza Hall Institute found, in laboratory models, that eating sets off a hormonal 'chain reaction' in the gut.

Eating causes a hormone called VIP to kickstart the activity of immune cells in response to potentially incoming pathogens or 'bad' bacteria. The researchers also found that immunity increased at anticipated mealtimes indicating that maintaining regular eating patterns could be more important than previously thought.

With the rise in conditions associated with chronic inflammation in the gut, such as irritable bowel and Crohn's disease, a better understanding of the early protective mechanisms governing gut health could help researchers to develop prevention strategies against unwanted inflammation and disease.

The research, led by Professor Gabrielle Belz and Dr. Cyril Seillet from the Walter and Eliza Hall Institute, was published in the journal Nature Immunology.

Armed against invaders

So how does it work?

When food is consumed nerves in the intestine produce a hormone called vasoactive intestinal peptide (VIP) to 'switch on' a protective response in the gut.

Professor Belz said the team showed, for the first time, that food-induced activation of VIP in preclinical models was vital for a subset of immune cells called ILC3s to mount a protective response in the gut.

"Food intake 'switches on' VIP, which plays a critical role in alerting the gut's army of ILC3 immune cells. In response, ILC3s secrete interleukin-22 (IL-22), which swings into protective action to defend against pathogens and maintain tissue integrity."

"We also showed that a deficiency in VIP limits the production of IL-22, which in turn negatively impacts the immune system's ability to prevent unwanted inflammation," she said.

The researchers used advanced imaging techniques to identify the 'players' integral to protective immunity in the gut. Using a new imaging technique that makes tissue translucent, the researchers were able to capture high-resolution, 3-D images of how VIP and ILC3 immune cells interact to protect the gut. Results showed their close proximity which confirmed their interdependence.

Regular meals key to gut health

The researchers also showed that 'circadian clock' genes could enable the gut to ramp up immunity in anticipation of regular mealtimes.

Dr. Seillet said baseline gut immunity fluctuated throughout the day, based on circadian rhythms and an anticipatory response to regular eating patterns.

"We saw that gut immunity not only spikes with food intake. It also rises and falls due to inbuilt cellular machinery regulated by the circadian clock gene Bmal1, which appears to activate immune cells when eating is likely," Dr. Seillet said.

"While more work needs to be done to better understand this anticipatory mechanism, the results are very interesting and could help to explain why disruptions to circadian rhythms and regular eating patterns could increase chronic inflammation in the gut."

Protective effect
Dr. Seillet said a detailed knowledge about mechanisms for gut protection and tissue repair could be useful for preventing against early-stage gut inflammation, before full-blown disease occurred.

"The next steps of our research include gaining a molecular understanding of what properties of food are responsible for kickstarting the process of protective immunity," he said.

"For example, are there certain diets that drive a more protective response than others?"

The study was supported by the Victorian Government and the Australian National Health and Medical Research Council.

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Early North Americans may have been more diverse than previously suspected

JANUARY 29, 2020, by Jeff Grabmeier, The Ohio State University

Original position of the skeletal remains inside submerged cave of Muknal. Credit: Jerónimo Avilés

An analysis of four ancient skulls found in Mexico suggests that the first humans to settle in North America were more biologically diverse than scientists had previously believed.

The skulls were from individuals who lived 9,000 to 13,000 years ago, in the late Pleistocene and early Holocene eras.

These findings complicate the story accepted until now, based on ancient skeletons analyzed from South America, which suggested the first settlers in the Americas were very similar, said Mark Hubbe, co-lead author of the study and professor of anthropology at The Ohio State University.

"The first Americans were much more complex, much more diverse than we thought," Hubbe said.

"We have always talked about the settlement of the Americas as if North America and South America were the same. But they are different continents with different stories of how they were settled."

Hubbe led the work with Alejandro Terrazas Mata of the Universidad Nacional Autónoma de México in Mexico. Their work was published today (Jan. 29, 2020) in PLOS ONE.

Archaeologists discovered the four skulls between 2008 and 2015 in submerged caves in the state of Quintana Roo, Mexico. At the time the four people were living, the caves were above sea level.

The skulls were analyzed with a CT scan, which combines data from several X-rays to build a 3-D image of each skull.

The researchers analyzed the scans for specific landmarks on each skull and measured their positions on a 3-D grid. They then compared the position of the coordinates with skulls from reference populations from all over the world to determine which populations the skulls most resembled.

The oldest skull showed strong similarities to North American arctic populations, while the second-oldest skull was consistent with modern European populations. The third skull showed affinities with Asian and Native American groups and the fourth had affinities with arctic populations in addition to having some modern South American features.

These skulls are important because compared to South America, relatively few ancient skeletons have been found in North America, Hubbe said. Between 300 and 400 skeletons that are more than 8,000 years old have been found in South America, compared to fewer than 20 in North America.

"Not all the skulls we analyzed looked like the ones from South America. They are fairly distinct as far as the morphology," he said.

The results suggest that the initial populations that ventured from Asia into North America had a high level of biological diversity, Hubbe said. For whatever reason, that diversity was reduced as humans dispersed into South America.

"We always assumed that what was happening in South America was true in North America. Now we need to revise that.

"We need to stop talking about the settlement of the Americas. We should talk about the settlement of North America and the settlement of South America as very different."

Hubbe said the results also caution against trying to create overly simple narratives about human migration, especially in the Americas.

"Whatever we thought about the settlement of the Americas is probably not the whole story. We still have a lot to learn."

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Wednesday, 29 January 2020

Aireal view of Zagros

Ninth Heretic posted today Jan 29, 2020

 Heretic is a long time internet friend.  This vid is purely for visual enjoyment.

https://youtu.be/3T-aPHjwv8Y
ytube link , past into ytube open page, if you want a larger pic.  This is as big as blogger gets for vids.

Enjoy

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Mizzou Students 'Required' To Install Location-Traking App So College Can "Pinpoint" Them

by Tyler Durden, Tue, 01/28/2020 Authored by Blair Nelson and Jon Street via Campus Reform,

New students at the University of Missouri will be required to participate in a tracking program designed to measure and enforce class attendance, according to a new report from The Kansas City Star.

Despite privacy concerns, officials defended the decision as one to the benefit of students, as the school's athletics department has already been using the same app, SpotterEdu, to track certain student-athletes.

“A student will have to participate in this recording of attendance,” Jim Spain, vice provost for undergraduate studies at MU, said in a statement to The Kansas City Star.

Individual professors have to opt-in to using the app, but once they do, students in those professors' classes will not be able to opt-out.

SpotterEDU, developed by a former basketball coach, is designed to monitor a user’s attendance by "pinpoint[ing] students within a classroom until they leave, providing continuous, reliable and non-invasive attendance," according to the app's website. While the app ensures that students are in the classroom during class times, it claims it does not track students' locations anywhere else.

"We only care if students are in class during class; no GPS tracking means we can't locate them anywhere else," the app's website states.

However, the app is not incapable of tracking students' locations outside the classroom.

"From labs to auditoriums our technology can expand to cover any size of space accurately and precisely," the app's website adds.

In a statement to The Washington Post, SpotterEDU chief Rick Carter said that his company works with nearly 40 schools, including major schools such as Auburn, Central Florida, Indiana, and Missouri. Most schools only use SpotterEDU to track their student-athletes; however, many colleges are starting to use the app with their student bodies, like Missouri.

According to the Post, colleges use the data to ensure that student-athletes who are receiving scholarships are attending classes regularly. The program emails professors automatically if a student is not in a class, or shows up more than a few minutes late. Carter told the Post that professors can look specifically at attendance patterns for "students of color" or "out of state students" for retention purposes.

Some in academia, though, have reservations about colleges using this technology.

Indiana University assistant professor Kyle M. L. Jones told the Washington Post, “These administrators have made a justification for surveilling a student population because it serves their interests, in terms of the scholarships that come out of their budget, the reputation of their programs, the statistics for the school."

“What’s to say that the institution doesn’t change their eye of surveillance and start focusing on minority populations, or anyone else. [Students] should have all the rights, responsibilities and privileges that an adult has. So why do we treat them so differently?”Jones said.

Robby Pfeifer, a Virginia Commonwealth University student, echoed Jones' sentiment.

"We’re adults," he told the Washington Post.

"Do we really need to be tracked? Why is this necessary? How does this benefit us? And is it just going to keep progressing until we’re micromanaged every second of the day?”

“It embodies a very cynical view of education, that it’s something we need to enforce on students, almost against their will,” Erin Rose Glass, digital scholarship librarian at the University of California-San Diego, said, according to the Post.

“We’re reinforcing this sense of powerlessness...when we could be asking harder questions, like: Why are we creating institutions where students don’t want to show up?”

Sara Baker of the ACLU of Missouri told the Kansas City Star the group has "deep privacy concerns about this."

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Showbiz apes find peace through painting in Florida retirement

JANUARY 29, 2020, by Leila MacOr

Fifty-three chimpanzees and orangutans live in safety at the Center for Great Apes (CGA), a unique sanctuary in central Florida

One of them worked alongside Clint Eastwood, others acted in the remake of sci-fi classic "Planet of the Apes", while yet another was the darling favorite of Michael Jackson.

They are the 53 chimpanzees and orangutans who live in a unique sanctuary in central Florida.

All of these great apes were raised by humans and lack the basic survival skills to ever live in the wild. They do not know how to gather food, and the mothers would be incapable of caring for their offspring.

For that reason, they had no other place to go when Hollywood or scientific research labs had no more use for them, or when they grew too big and powerful for their celebrity owners to continue caring for them. The lucky ones make the final journey to this oasis, officially known as the Center for Great Apes (CGA) in Florida, in the southeastern US.

It is the only accredited orangutan sanctuary in the western hemisphere and one of only nine chimp sanctuaries in North America.

One of the more recent arrivals is 33-year-old orangutan Sandra, who joined the CGA community last November, after a court in Argentina declared her a "non-human person" with the right to liberty from a Buenos Aires zoo where she had been kept. After that historic legal finding, she was sent here to get over her depression.

Now she is the spoiled girl of Florida's most exclusive retirement community. "She plays a lot. She's doing really well," said Patti Ragan, who founded the center.

The 33-year-old orangutan Sandra joined the Florida retirement community after a court in Argentina declared her a 'non-human person' with the right to liberty from a Buenos Aires zoo

"She is meeting several orangutans right now. The one that I think she's most interested in is a male named Jethro," she said. "Pretty soon we're going to open the door so they can be in the same space. So we hope that goes well."

Another resident is Popi, a 48-year-old orangutan who was eight when she played the girlfriend of Clint Eastwood's simian sidekick in the movie "Every Which Way but Loose" and then again in the sequel "Any Which Way You Can".

She wounded up acting in Las Vegas until hidden camera footage showed she was being mistreated by her trainer.

Then there are the 23-year-old twin chimpanzees Jacob and Jonah, who appeared in the 2001 Tim Burton movie "Planet of the Apes", as well as Bubbles, once the adored baby chimp of Michael Jackson and now a hulking 37-year-old, the alpha male in his group.

Furthermore, there is Tango, an orangutan who for years served as the face of the orange beverage Tang.

"We have a lot of former entertainment great apes here," Ragan told AFP.

Not all of them are former Hollywood stars. Others were in circuses, research laboratories or were sold as exotic pets when they were still babies. Some wound up living in cramped cages or garages because they became more difficult to control when they grew up.

'Ape art' created by the orangutans and chimpanzees that live at the Center For Great Apes (CGA) is sold in a gift shop and at a silent auction in a fundraising event


Ape art

The CGA is located on 40 hectares (98 acres) of wooded land near Wauchula, surrounded by central Florida's orange groves.

The entrance to the sanctuary does not call attention to itself, with well-trodden dirt tracks snaking between the trees and connected by raised corridors along which the apes can move about.

In the clearings are the enclosures, like giant bird cages, full of plants, toys and things for the apes to climb on.

It is one of the few places in Florida to have been opened in secrecy, rather than with the usual fanfare of theme parks and tourist attractions. It is neither a zoo nor a park, does not accept visitors and does not promote itself.

Only donors can visit, and then only by invitation, and just a couple of times each year to get to know the apes. Even then, they are banned from posting pictures on social media.

"Their (the apes') well-being is priority," said Ragan.

The Center For Great Apes is located on 40 hectares (98 acres) of wooded land near Wauchula, surrounded by central Florida's orange groves

As a result, very few people even know the place exists, said Jeff Thomas, 76, who together with his wife Terrie were among a group of donors visiting the center during a recent auction of "ape art".

On tables arranged among the trees, the organizers had displayed paintings created by the chimps and orangutans, abstract and vibrant with color. On a paper to one side, the visitors write down their bids for the artwork.

"I'm very proud to know that this is a wonderful place for them," said Terrie Thomas, 60, her voice trembling slightly. "It makes me really emotional to talk about it because I really, truly love these animals. I think they're amazing."

The description of one painting by Jacob explains that the chimp "especially enjoys painting, and he usually likes to taste each bright color before he puts it on his canvas."

Supporting each animal costs around $23,000 per year, and together with other running costs, the sanctuary needs $1.8 million every year. It is financed solely by voluntary donations.

The foundation sprang up almost by chance. Patti Ragan was living in Miami and doing volunteer work at the city zoo when she was asked to look after a baby orangutan, due to experience she had gained in Borneo.

A year later, a baby chimp was added to her care, and in 1993, Ragan registered her sanctuary as a not-for-profit organization.

And the baby orangutan she was originally asked to look after is still with her, named Pongo, and now 29 years old.

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A Plague Of "Billions" Of Locusts Threatens To Create Horrific End-Times Famine Across Africa

by Tyler Durden, Wed, 01/29/2020

It can be difficult to imagine a plague of “billions” of locusts. After all, there are only about 7 billion people living on the entire planet.

Authored by Michael Snyder via The Economic Collapse blog,

Billions of locusts are eating everything in sight in east Africa right now, and every single day many more farms are being completely wiped out. Unfortunately, authorities are telling us that what we have seen so far is just the tip of the iceberg. In fact, if extreme measures are not implemented immediately, authorities are claiming that this locust plague could literally get “500 times” worse in a few months. But it is difficult to imagine conditions getting any worse than they are at this moment. Ravenous locust swarms that are “the size of cities” are consuming crops at a staggering pace, and this could potentially cause famine on the African continent that is unlike anything we have ever seen before.

But this is actually happening. Right now “billions of locusts” are absolutely devastating east Africa, and each one can eat “its own weight in food every day”…

Billions of locusts swarming through East Africa could prove disastrous for a region still reeling from drought and deadly floods, experts have warned, amid increasing calls for international help.

Dense clouds of the ravenous insects, each of which consumes its own weight in food every day, have spread from Ethiopia and Somalia into Kenya, in the region’s worse infestation in decades.

It would be hard to overstate what this is going to mean for the region. According to the FAO, this plague is an “unprecedented threat to food security and livelihoods in the Horn of Africa”…

The United Nation’s Food and Agriculture Organisation has described the situation as “extremely alarming,” representing an “unprecedented threat to food security and livelihoods in the Horn of Africa.”

We have seen starvation in Africa before. In fact, there was a time when our airwaves were filled with images of starving African children.

But if this plague continues to get even worse, the stage is being set for a famine that is far greater than anything that any of us have ever witnessed.

The density of some of these locust swarms is absolutely crazy. According to officials, a single locust swarm can have “up to 150 million locusts per square kilometer”…

“A typical desert locust swarm can contain up to 150 million locusts per square kilometer,” the East African regional body, the Intergovernmental Authority on Development, has said. “Swarms migrate with the wind and can cover 62 to 93 miles in a day. An average swarm can destroy as much food crops in a day as is sufficient to feed 2,500 people.”

And it is important to note that some of these swarms are many times that size.

In fact, one of the largest swarms in northeastern Kenya was measures to be “60 kilometers long by 40 kilometers wide”.

In other words, that swarm was far larger than any major city on the entire planet.

Spraying these locusts only has limited effectiveness, but it is one of the only things that can be done at this point.

Unfortunately, Kenya only has four planes currently flying, and the same goes for Ethiopia.

The UN is going to step in with 10 million dollars of additional funding, but that won’t really go too far…

The UN on Wednesday allocated $10 million for aerial spraying, with humanitarian chief Mark Lowcock saying families across the region “now face the prospect of watching as their crops are destroyed before their eyes.”

The truly frightening part of this story is that we are being told that the worst is yet to come.

If you can believe it, and I know that this sounds absolutely nuts, but UN officials are actually warning that this plague of locusts could get “500 times” larger when warmer weather arrives…

When rains arrive in March and bring new vegetation across much of the region, the numbers of the fast-breeding locusts could grow 500 times before drier weather in June curbs their spread, the United Nations says.

If what the UN is telling us is accurate, and I have no reason to believe that it isn’t, then Africa is facing a nightmare of almost unbelievable proportions. Yes, I keep warning that “the perfect storm” is here, but the scale of the plague that Africa is potentially facing is very hard to imagine.

With hundreds of billions of locusts potentially eating crops all across Africa, what will be left for people to eat?

Needless to say, many relief organizations are fearing the worst…

Save the Children’s Regional Director for East and Southern Africa, Ian Vale, said in a statement that their staff in Kenya are battling swarms so thick they can barely see through them.

“The impact on crops and pastureland will be severe. We are very concerned that this will place vulnerable children even closer to the brink of starvation,” he said.

Even before 2020 began, millions upon millions of Africans were dealing with “acute hunger”, and the outlook for the coming year was grim.

But now nobody has any idea how there will possibly be enough food for everyone.

1.2 billion people live in Africa. That is a lot of mouths to feed, and right now the locusts are stripping farm after farm completely bare.

I know that I have been writing about the coronavirus outbreak a lot in recent days, but this crisis could potentially kill far more people. We have reached a time when global events have really started to accelerate, and the months ahead promise to be quite challenging for all of us.


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Tuesday, 28 January 2020

Effects of contact between minority and majority groups more complex than once believed

JANUARY 27, 2020, by University of Massachusetts Amherst

added by CiC


For more than 50 years, social scientists and practitioners have suggested that having members of different groups interact with each other can be an effective tool for reducing prejudice. But emerging research points to a more complex and nuanced understanding of the effects of contact between groups, say Linda Tropp at the University of Massachusetts Amherst and Tabea Hässler, leader of a multi-national research team based at the University of Zurich, Switzerland.

As Tropp explains, studies from the last 10 to 15 years suggest that the positive effects of intergroup contact tend to be weaker among members of historically advantaged groups, such as white people and heterosexuals, compared to the effects typically observed among members of historically disadvantaged groups such as people of color and sexual minorities. There has also been growing concern that contact may effectively reduce prejudice between groups but do little to change existing social inequalities, she adds.

"With our research, we wanted to examine whether and how contact between groups might help to promote support for social change, in pursuit of greater social equality, while also testing whether the effects of contact might vary depending on status relations between the groups and how the relevant variables were measured," she explains. "So, we embarked on this multi-national study, which included researchers from more than twenty countries around the world, who gathered survey responses from 12,997 individuals across 69 countries."

The authors highlight that this comprehensive study "makes substantial advances in our understanding of the relation between intergroup contact and social change." Details appear in Nature Human Behaviour.

The researchers found robust evidence, Tropp says, that when members of historically advantaged groups engage in contact with disadvantaged groups, they are more likely to support social change to promote equality. In contrast, when members of historically disadvantaged groups have contact with advantaged groups, they are generally less likely to support social change to promote equality.

However, the researchers also point out an important exception: "Among both advantaged and disadvantaged groups, contact predicted greater willingness to work in solidarity to achieve greater social equality. Thus, this research may offer a new route to reach social cohesion and social change, such that social harmony would not come at the expense of social justice."

Tropp, Hässler and their colleagues say their results raise two important questions and directions for future research. First, they ask, "How can positive and intimate contact between groups occur without reducing disadvantaged group members' support for social change?" Second, "How can support for social change be increased among disadvantaged group members without requiring negative contact experiences?"

They suggest, "Possible answers to both questions may be that advantaged group members who engage in contact should openly acknowledge structural inequalities and express support for efforts by disadvantaged group members to reduce these inequalities," they conclude.

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Siberian Neanderthals were intrepid nomads

JANUARY 27, 2020, by University of Wollongong
https://phys.org/news/2020-01-siberian-neanderthals-intrepid-nomads.html


Chagyrskaya Cave in southern Siberia’s Altai Mountains. Credit: IAET

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A new study, published online today in the Proceedings of the National Academy of Sciences, reveals that Neanderthals made an intercontinental trek of more than 3000 km to reach Siberia's Altai Mountains, equipped with a distinctive toolkit used to kill and butcher bison and horses.

Neanderthals are our nearest evolutionary cousins and survived until around 40,000 years ago in western Europe. Their legacy lives on today in the DNA of all people with European or Asian ancestry.

Neanderthal fossils were first reported from the Altai Mountains—the easternmost outpost of their known geographic range—in 2007. Nestled in the foothills, Chagyrskaya Cave has yielded 74 Neanderthal fossils, more than any other site in the region, as well as almost 90,000 stone tools and numerous bone tools made by Neanderthals.

The multi-disciplinary team of researchers from Russia, Australia, Ukraine, Poland, Germany and Canada, including University of Wollongong geochronologist Professor Richard "Bert' Roberts, carried out detailed investigations of the site to discover new clues about the history of these Siberian Neanderthals.

Micoquian stone tool used as a meat knife by Neanderthals at Chagyrskaya Cave about 54,000 years ago. Credit: Alexander Fedorchenko


The 3.5 meter-thick cave deposits were first excavated in 2007. Dating of the sediments and the bones of butchered bison indicated that Neanderthals lived in the cave sometime between 59,000 and 49,000 years ago—shortly before modern humans first entered this region.

"The most surprising discovery was how closely the Chagyrskaya stone tools resemble Micoquian tools from archaeological sites in central and eastern Europe," project leader Dr. Kseniya Kolobova from the Russian Academy of Science's Institute of Archaeology and Ethnography in Novosibirsk said.

Using a variety of statistical tests, Dr. Kolobova and her team of archaeologists compared the distinctive stone tools found at Chagyrskaya Cave with those recovered from Micoquian sites in Europe and central Asia. They identified the region between the Crimea and the northern Caucasus as the likely ancestral homeland of the Chagyrskaya toolmakers.

"This part of eastern Europe is 3000 to 4000 kilometers from Chagyrskaya Cave, the equivalent of walking from Sydney to Perth or from New York to Los Angeles—a truly epic journey," co-author Professor Roberts from UOW's Centre for Archaeological Science said.

Analysis of animal and plant remains extracted from the Chagyrskaya Cave deposits showed that the Neanderthals were skilled at hunting bison and horses in the cold, dry and treeless environment, while microscopic study of the sediments yielded additional clues about the living conditions they had to endure.


Excavation of archaeological deposits in Chagyrskaya Cave. Credit: IAET


"Neanderthals were supremely adapted to life on steppe and tundra-steppe landscapes, and could have reached the Altai Mountains from eastern Europe by going around the Caspian Sea and then east along the steppe belt," co-author and geoarchaeologist Dr. Maciej Krajcarz from the Institute of Geological Sciences in the Polish Academy of Sciences said.

The new archaeological evidence indicates at least two separate migrations of Neanderthals into southern Siberia, and is independently supported by whole-genome studies of ancient DNA obtained from Neanderthal fossils.

The first migration occurred more than 100,000 years ago, blazing a trail to the nearby site of Denisova Cave—famous as the home of the enigmatic Denisovans, a sister group to Neanderthals, who also occupied the cave at times. A more recent migration event—originating in eastern Europe possibly about 60,000 years ago—led to the arrival of Neanderthals at Chagysrkaya Cave, armed with their distinctive Micoquian toolkit.

DNA studies confirm a link between Neanderthals living in Europe and at Chagyrskaya Cave after 100,000 years ago. Despite the geographic proximity of Chagyrskaya and Denisova Caves, the Chagyrskaya Neanderthal genome is more similar to those of European Neanderthals than it is to the 110,000 year-old Neanderthal from Denisova Cave.

"By combining these new insights from archaeology and genetics, we can start to piece together the intriguing story of the easternmost Neanderthals and the events that shaped the history of our ancient human relatives," Dr. Kolobova said.

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