Ecosystems worldwide are disrupted by lack of large wild herbivores—except in Africa

Biological research has repeatedly demonstrated that the relationship between the producer and the consumer is governed by a scaling law. An international research team has now looked into whether this law of nature can be reproduced in the relationship between the production of plants in an area and the number of large herbivores that graze on them. The study reveals that Africa is the only continent where the scaling law holds true.

June 2021 saw the start of the United Nations Decade on Ecosystem Restoration. A total of 115 countries have committed themselves to restoring up to a billion hectares of nature worldwide.

According to a group of researchers from Aarhus University and the University of Sussex, one of biggest challenges will be restoring the historical and prehistoric grazing of large mammals. What level of restoration should we aim for? How many large herbivores will we need? And how are we going to co-exist with these large animals?

The researchers examined the current low densities of large herbivores in a scientific article in the Journal of Applied Ecology. In the article, they calculated a baseline for large animals based on the ratio between producer and consumer, i.e. plants and herbivores, in nature reserves in Africa.

They stress that this relationship between producers and consumers applies across ecosystems and biomes implying a close correlation between the biomass produced and the biomass of dependent consumers.

However, after investigating the density of large herbivores in  nature reserves throughout the world, the researchers were only able to find such a close correlation on one continent: Africa. On the other continents, they found strong indications of impoverished fauna, even in protected natural areas.

African ecosystems have species-rich mammal fauna and a large biomass of big herbivores that are significantly linked to plant productivity. But we can't find this pattern on other continents, and in general the large herbivore biomass is much lower than we would expect considering the level of productivity.

In the article, the researchers argue that large herbivores are still being displaced, hunted and eradicated, and that there is a widespread perception, even among game managers, that there are plenty of herbivores in the wild, perhaps even too many. This perception is not supported by the new study.

On the contrary, efforts to decrease populations of large herbivores can reflect a shifting baseline.

Bringing back big animals is crucial to restoring self-sustaining ecosystems and conserving biodiversity, but it is not going to be easy. Large animals are troublesome, because they damage crops, disrupt traffic and generally just get in the way. It will require political commitment and careful physical planning, including fenced reserves.

Camilla Fløjgaard et al, Exploring a natural baseline for large‐herbivore biomass in ecological restoration, Journal of Applied Ecology (2021). DOI: 10.1111/1365-2664.14047

https://phys.org/news/2021-11-ecosystems-worldwide-disrupted-lack-l...

Using microbes to make carbon-neutral fuel

Researchers  have discovered a new way to train microbes to make a readily usable biofuel.

A team of biologists and engineers modified a microbe called Rhodopseudomonas palustris TIE-1 (TIE-1) so that it can produce a biofuel using only three renewable and naturally abundant source ingredients: carbon dioxide, solar panel-generated electricity and light.

The resulting biofuel, n-butanol, is an authentically carbon-neutral fuel alternative that can be used in blends with diesel or gasoline. The results are reported Nov. 3 in the journal Communications Biology.

 n-Butanol production by Rhodopseudomonas palustris TIE-1, Communications Biology (2021). DOI: 10.1038/s42003-021-02781-z

https://techxplore.com/news/2021-11-microbes-carbon-neutral-fuel.ht...

The Twisted Paths of Perception

These patterned pavements make pedestrians watch their step

The King Pedro IV Square in Lisbon, Portugal, better known as the Rossio, regales visitors with a delightful exemplar of the traditional pavement called calçada portuguesa. Originally cobbled in 1848, the dizzying light and dark undulations symbolize the sea voyages of Portuguese navigators and predate 20th-century designs by Op Art creators such as Victor Vasarely and Bridget Riley, while inducing similar perceptions of flowing motion. But does the vibrant pattern stand in the way of safety?

A recent study from the University of Bristol in England asked participants how walking on floors patterned with visual illusions affected their discomfort levels and feeling of instability. Neuropsychologist Ute Leonards, who led the study, first considered the potential negative impact of such illusory patterns on walking during a visit to the iconic street of La Rambla in Barcelona, Spain. “I had noticed the 3-D effect of the floor patterns and wanted to add them to my collection,” she recalls. As Leonards photographed the waves in the paving design, an older gentleman approached her. “He said that he didn’t like the floor at all, as he wasn’t sure when his feet would actually hit the ground and how high he should lift his feet not to trip . . . he walked [as if] afraid that there might be black ice.”

Part1 

Back in the laboratory, Leonards and her collaborators investigated the effects of four illusory patterns on people’s walking experience. Two of the designs, consisting of black-and-white alternating “furrows and ridges” modeled after the undulating pattern in Rossio Square, looked three-dimensional despite being printed on flat surfaces. More than half of the walkers found such designs aversive or uncomfortable to tread on, affecting their stability and even occasionally inducing fear of falling. The discomfort may lie in the mismatch between the sensory and physical characteristics of the walking environment. In nature, surfaces that look bumpy are generally bumpy, but this was not the case for the floor patterns examined in the study—a concern that may extend to a number of human-built environments.

This article was originally published with the title "The Twisted Paths of Perception" in SA Mind 32, 6, 33-34 (November 2021)

doi:10.1038/scientificamericanmind1121-33

https://www.scientificamerican.com/article/the-twisted-paths-of-per...

Part 2

Vascular disease in COVID-19 is not caused by viral infection of blood vessels

Researchers identify bird and reptile 'microchromosomes' once thought to be dust specks on a microscope slide

 Scientists have discovered that tiny 'microchromosomes' in birds and reptiles, initially thought to be specks of dust on the microscope slide, are linked to a spineless animal ancestor that lived 684 million years ago. They prove to be the building blocks of all animal genomes, but underwent "dizzying rearrangement" in mammals, including humans.

A team of researchers made the discovery by lining up the DNA sequence of microchromosomes that huddle together in the cells of birds and reptiles.

When these little microchromosomes were first seen under the microscope, scientists thought they were just specks of dust among the larger bird chromosomes, but they are actually proper chromosomes.

Using advanced DNA sequencing technology, scientists can at last sequence microchromosomes end-to-end.

Researchers lined up these sequences from birds, turtles, snakes and lizards, platypus and humans and compared them. Astonishingly, the microchromosomes were the same across all bird and reptile species. Even more astonishingly, they were the same as the tiny chromosomes of Amphioxus—a little fish-like animal with no backbone that last shared a common ancestor with vertebrates 684 million years ago.

 In marsupial and placental mammals these ancient genetic remnants are split up into little patches on our big, supposedly normal, chromosomes. The exception is the platypus genome, in which the microchomosomes have all fused together into a few large blocks that reflect our oldest mammal ancestor.  the findings highlight the need to rethink how we view the human genome.

Microchromosomes form a compartment in the cell that might help the genes work together.

Rather than being 'normal,' chromosomes of humans and other mammals were puffed up with lots of 'junk DNA' and scrambled in many different ways. The new knowledge helps explain why there is such a large range of mammals with vastly different genomes inhabiting every corner of our planet. 

https://researchnews.cc/news/9809/Researchers-identify-bird-and-rep...

https://theconversation.com/specks-of-dust-on-the-microscope-slide-...

Part1

https://www.karger.com/Article/Abstract/63018

https://www.pnas.org/content/118/45/e2112494118

https://www.pnas.org/content/118/45/e2112494118

part2

Antibiotic resistance outwitted by supercomputers

 Scientists may have made a giant leap in fighting the biggest threat to human health by using supercomputing to keep pace with the impressive ability of diseases to evolve.

A new study by an international team tackled the problem of antibiotic resistance by redesigning existing antibiotics to overcome bacterial resistance mechanisms.

About 700,000 people are estimated to die every year because of antibiotic resistant bacteria, and that number is expected to rise to millions.

Without effective antibiotics, life expectancy is predicted to drop by 20 years.

The race has been on for many years to develop new antibiotics to fight disease faster than a disease can evolve.

Computers have been used in drug design for decades, but this is the first study to use a multi-pronged computer-guided strategy to make a new antibiotic from an existing one which bacteria have outwitted.

The research was published in PNAS.

Antibiotics are one of the pillars of modern medicine and antibiotic resistance is one of the biggest threats to human health. There's an urgent need to develop new ways of fighting ever-evolving bacteria. It's only a matter of time until bacteria develop counterstrategies against our counterstrategies and become resistant to the new antibiotic, so we will have to keep on studying bacterial resistance mechanisms and develop new derivatives accordingly.

The hope of this new work lies in showing that the resistance mechanisms of bacteria can be addressed in a systematic way, allowing science to continually fight back with a computational evolution of new antibiotics.

Researchers developed a strategy to simulate many aspects of a redesigned antibiotic at the same time, including how soluble it is, how effective it is at entering into the bacteria, and how efficient it is at blocking their protein production.

The computational work outlined in the research was done in a matter of weeks on one of the top supercomputers in Europe, but it took the international team several years to verify experimentally that their approach was indeed correct.

Using a computational approach makes the development of new antibiotic derivatives faster and cheaper, and predicting whether a chemical compound is going to be active before it is synthesized also avoids chemical waste. This is an extremely empowering technology.

https://www.port.ac.uk/news-events-and-blogs/news/antibiotic-resist...

https://researchnews.cc/news/9807/Antibiotic-resistance-outwitted-b...

A fungus that uses chemicals to trick male flies into mating with infected dead females

A combined team of researchers from the University of Copenhagen and the Swedish University of Agricultural Sciences reports that a certain fungus uses chemicals to trick male flies into mating with infected dead females. They have written a paper describing their findings and have posted it on the bioXiv preprint server.

Prior research has shown that some types of fungus can give insect victims what has become known as summit disease, in which a victim's nervous system is infected and the unwilling creature begins climbing to the highest vantage point possible. Once there, the wings are spread wide and the victim begins spewing spores. In this new effort, the researchers have found a fungus that takes summit disease one step further by having its female victims also emit chemicals that sexually attract males.

In studying the fungus Entomophthora muscae, the researchers found that it was capable of infecting other insects, primarily house flies, with summit disease. Airborne spores land on a female victim and penetrate her skin. Soon, they invade her entire body, including her nervous system and brain. Chemicals produced by the spores incite the female to begin climbing until she reaches the highest possible point, such as a leaf on a tree. Then, she opens her wings and dies. Meanwhile, the fungus covers her body with little spore-filled cannons. At some point, a male happens by, and when he touches her body, the cannons fire, filling the air with spores, ready to infect others in the vicinity.

Part 1

In their lab, the researchers captured a host of infected and non-infected flies. Males were given a choice of mating with either an infected or non-infected female, and more often than not, chose the one that was infected. This suggested that the fungus was doing something to make the infected female more attractive to the male even though she was dead. In studying the dead females, the researchers found instances of unusual volatile compounds, including some chemicals called sesquiterpenes, which are not normally associated with house flies but have been found to sexually attract many types of insects, including house flies.

The vast little library inside your cells

The human genome can be thought of as a massive library, containing over 20,000 different "instruction manuals": your genes. For example, there are genes which contain information to build a brain cell, a skin cell, a white blood cell, and so on. There are even genes that contain information about regulating the genome itself—like books that explain how to organize a library. The ability to regulate gene expression—in other words, the cell's ability to turn various constellations of genes on or off—is the basis of why different cells (such as a muscle cell or a brain cell) have different forms and functions.
In a cellular nucleus, there is over six feet of genetic material packed into a space 50 times smaller than the width of a human hair. How is the "library" in the nucleus organized? When a cell needs to regulate certain genes, how does the cellular machinery find the right ones amongst 20,000 others?
A new study uses a powerful new tool that can peer into the world of the cell's genetic material (DNA and RNA) in order to find answers to these questions.

Part1

A research  team found that molecules of non-coding RNA are responsible for establishing "compartments" within the nucleus and shepherding in key molecules to precise regions in the genome. Noncoding RNA are molecules that do not encode for proteins, and instead have an array of functions that are often still mysterious to biologists. In the library analogy, non-coding RNA molecules act as the "shelves" that organize different groups of genes and the machinery that interacts with them.

Understanding how genetic material is organized spatially is a crucial part of understanding the basic workings of life. Dysfunction within the nucleus is a hallmark of many diseases, including cancer, neurodegenerative disorders, and others.

The research was made possible by a powerful tool developed in the Guttman laboratory that enables detailed views of the RNA world, called RD-SPRITE (RNA and DNA Split-Pool Recognition of Interactions by Tag Extension). In essence, RD-SPRITE works by tagging molecules of RNA and DNA with miniscule unique barcodes based on their locations; analyzing the barcodes can then tell you which molecules were at which positions within the cell.

 Sofia A. Quinodoz et al, RNA promotes the formation of spatial compartments in the nucleus, Cell (2021). DOI: 10.1016/j.cell.2021.10.014

https://phys.org/news/2021-11-vast-library-cells.html?utm_source=nw...

Part2

Lightning Strikes Carve a Deadly Signature Deep Inside The Bones, Scientists Discover

When a body is struck by lightning, a lot of different things happen. For those who do not survive the ordeal, a range of physical evidence is left on their bodies that can identify the cause of death: damage to the skin, including sometimes burn marks, as well as trauma to various organs.

But what if all the tissue decomposes? From the standpoint of forensic scientists who may only have bones to work with, does lightning leave any discernible trace behind on a skeleton?

According to a new study, yes it does.

In previous experiments, Bacci and fellow researchers identified these unique markers in animal bones, noting "extensive micro-fracturing and fragmentation of the bone matrix" in pig bones subjected to high impulse current, simulating the electrical jolt of a lightning bolt.

In that study, the same kind of micro-fracturing was also seen in the bones of a wild giraffe that was killed by a lightning strike, but it remained unclear whether human skeletons exposed to lightning-levels of current would reveal the same gruesome signature.

With the aid of cadavers donated to science, we now have our answer, with the researchers observing similar patterns of micro-fracturing in human bone subjected to the current application, and of a kind that's distinct from purely thermally induced changes to bone (such as bones burnt in a fire).

"[The lightning damage] takes the form of cracks which radiate out from the center of bone cells, or which jump irregularly between clusters of cells. The pattern of trauma is identical even though the micro-structure of human bone is different from animal bone.

Part 1

Another expected differentiator affecting micro-fracture propagation in human skeletons is bone density, which decreases with age after people reach about 40 years of age, and which might be susceptible to greater amounts of lightning-induced fracturing due to bones being more brittle.

According to the researchers, a two-fold mechanism explains why the micro-fractures in bones form the way they do.

"Firstly, the current itself produces a high-pressure shock wave when traveling through the bone," members of the research team explain in an article written for The Conversation.

"Lightning specialists term this barotrauma: the passage of electrical energy literally blows bone cells apart."

The second mechanism is an example of the piezoelectric effect, affecting how bone behaves when it's in an electric field.

"Collagen, the organic part of bone, is arranged as fibers or fibrils," the researchers explain.

"These fibrils rearrange themselves when a current is applied, causing stress to build up in the mineralized and crystallized component of bone, in turn leading to deformation and cracking."

For forensic pathologists, the discovery of the micro-fracture patterns could indeed be a "smoking gun", indicating the probable cause of death in mysterious fatalities where no other evidence remains.

For the rest of us, if we want to avoid sustaining these microscopic ruptures ourselves, it's best to stay inside whenever the weather looks like it could turn deadly.

After all, even if lightning (almost) never strikes twice, it often only needs once.

The findings are reported in Forensic Science International: Synergy.

https://www.sciencealert.com/lightning-strikes-carve-a-deadly-signa...

part 2

**

How bacteria can clean up oil spills too 

Bacteria are often painted as our adversaries, but when it comes to oil spills, toxic chemicals, and radioactive waste, they could be what save us from ourselves.

Dr. Kamal Ranadive’s 104th BirthdayToday’s (google's) Doodle celebrates Indian cell biologist Dr. Kamal Ranadive, who is best known for her groundbreaking cancer research and devotion to creating a more equitable society through science and education.

Why Arthritis Keeps Flaring Up in The Same Joints

According to new research conducted on mice, this could be because our immune system keeps a record of these past afflictions, creating a personalized disease pattern in each individual. Understanding more about how and why this happens could open up new opportunities for treating the disorder.

This latest study zooms in on the T cells in mice's bodies, white blood cells that are key to the immune system. In particular, the T cells in the synovium – the tissue lining the inside of the capsule around each joint – appear to hold a memory of previous RA problems.

Overwhelmingly, flares occur in a previously involved joint. The study shows that  these T cells anchor themselves in the joints and stick around indefinitely after the flare is over, waiting for another trigger. If you delete these cells, arthritis flares stop.

This was demonstrated through two mouse models using chemical triggers to cause joint inflammation and one mouse model using a genetic trigger to generate the same effect: The researchers removed a protein that blocked the pro-inflammatory cytokine IL-1.

These triggers caused T cells to rally other cells to the immunity cause, leading to arthritis flare-ups in specific joints in the mice. When these T cells were taken out, additional inflammation was prevented. These T cells don't move between joints and take up "long-term residency" where they are, the researchers say, ready to be reactivated again.

The approach taken here was actually inspired by skin studies. T cells with a form of memory are known to reside in the skin, leading to repeating patterns in skin problems such as psoriasis. It also happens with reactions to nickel in jewelry or wristwatches.

The research team thinks that other types of autoimmune arthritis could work in the same way, which could lead to better treatments and approaches to these issues. The next step is to confirm that the same process happens in humans and find out ways to target it.

https://www.cell.com/cell-reports/fulltext/S2211-1247(21)01372-3

https://www.sciencealert.com/immune-system-memory-might-explain-why...

Why teapots always drip

The "teapot effect" has been threatening spotless white tablecloths for ages: if a liquid is poured out of a teapot too slowly, then the flow of liquid sometimes does not detach itself from the teapot, finding its way into the cup, but dribbles down at the outside of the teapot.

This phenomenon has been studied scientifically for decades—now a research team  has succeeded in describing the "teapot effect" completely and in detail with an elaborate theoretical analysis and numerous experiments: An interplay of different forces keeps a tiny amount of liquid directly at the edge, and this is sufficient to redirect the flow of liquid under certain conditions.

The "teapot effect" was first described by Markus Reiner in 1956.

So rheology is the science of flow behavior. Again and again, scientists have tried to explain this effect precisely. Although this is a very common and seemingly simple effect, it is remarkably difficult to explain it exactly within the framework of fluid mechanics. 

The sharp edge on the underside of the teapot beak plays the most important role: a drop forms, the area directly below the edge always remains wet. The size of this drop depends on the speed at which the liquid flows out of the teapot. If the speed is lower than a critical threshold, this drop can direct the entire flow around the edge and dribbles down on the outside wall of the teapot.

Researchers  have now succeeded for the first time in providing a complete theoretical explanation of why this drop forms and why the underside of the edge always remains wetted. 

 The mathematics behind it is complicated—it is an interplay of inertia, viscous and capillary forces. The inertial force ensures that the fluid tends to maintain its original direction, while the capillary forces slow the fluid down right at the beak. The interaction of these forces is the basis of the teapot effect. However, the capillary forces ensure that the effect only starts at a very specific contact angle between the wall and the liquid surface. The smaller this angle is or the more hydrophilic (i.e. wettable) the material of the teapot is, the more the detachment of the liquid from the teapot is slowed down.

Interestingly, the strength of gravity in relation to the other forces that occur does not play a decisive role. Gravity merely determines the direction in which the jet is directed, but its strength is not decisive for the teapot effect. The teapot effect would therefore also be observed when drinking tea on a moon base, but not on a space station with no gravity at all.

B. Scheichl et al, Developed liquid film passing a smoothed and wedge-shaped trailing edge: small-scale analysis and the 'teapot effect' at large Reynolds numbers, Journal of Fluid Mechanics (2021). DOI: 10.1017/jfm.2021.612

https://phys.org/news/2021-11-teapots.html?utm_source=nwletter&...

We don’t ‘believe in’ Newton’s laws. We trust them and accepted them because there is genuine evidence that they work.

Newton's laws of motion are three laws of classical mechanics that describe the relationship between the motion of an object and the forces acting on it. These laws can be paraphrased as follows (1):

Law 1. A body continues in its state of rest, or in uniform motion in a straight line, unless acted upon by a force.

Law 2. A body acted upon by a force moves in such a manner that the time rate of change of momentum equals the force.

Law 3. If two bodies exert forces on each other, these forces are equal in magnitude and opposite in direction.

Newton's laws were verified by experiment and observation for over 200 years, and they are excellent approximations at the scales and speeds of everyday life. 

1. https://en.wikipedia.org/wiki/Newton%27s_laws_of_motion

How are epilepsy and autism linked?

Epilepsy and autism spectrum disorders, or ASD, show a remarkable degree of comorbidity and may share pathological mechanisms. Questions that have bogged down scientists about these disorders include: Does autism lead to an increase in epilepsy? Or does epilepsy alter the brain circuit, which then leads to autism?

One hypothesis is that during brain development, inhibitory neurons,  which regulate brain rhythms, develop in an abnormal manner. If this is true, then how the brain circuit gets set up is abnormal, which may lead to both autism and epilepsy. 

unlike excitatory neurons that lead to a forward propagation of information, inhibitory neurons work like a brake by suppressing and sculpting the activity of downstream neurons.

The researchers generated mice with a global mutation in all cells that prevented the inhibitory neurons from migrating to their normal location in mature brain circuits. Not surprisingly, they found a reduction in inhibitory currents in the hippocampus, a region of the brain known for memory function. Notably, the mutant mice showed behavioral traits associated with ASD and were more prone to seizures.

Results of the study suggest that a common underlying defect in circuit formation could contribute to both ASD and epilepsy.

Carol Eisenberg et al, Reduced hippocampal inhibition and enhanced autism-epilepsy comorbidity in mice lacking neuropilin 2, Translational Psychiatry (2021). DOI: 10.1038/s41398-021-01655-6

https://medicalxpress.com/news/2021-11-epilepsy-autism-linked.html?...

Modified silk cloth keeps skin cooler than cotton

A team of researchers has developed a modified textile that can keep skin cooler than materials made of cotton. In their paper published in the journal Nature Nanotechnology, the group describes their approach to developing garments that are cooler when worn in outdoor conditions.

The researchers noted that silk does a good job of reflecting sunlight in the mid-infrared range, which suggests it could be suitable as a cooling garment material. But because it is made by spiders, it contains a protein component that tends to absorb ultraviolet radiation, making the material and its wearer grow hotter under direct sunlight.

To make the silk material UV reflective, the researchers dipped a standard piece of silk fabric into a liquid solution containing highly refractive inorganic oxide nanoparticles. These adhered to the silk fabric, allowing it to become evenly saturated throughout the material. They allowed the fabric to dry and then tested it to see if the addition of the nanoparticles made the material more UV reflective. They found that under peak sunlight conditions, the temperature under the material was approximately 3.5 degrees Celsius cooler than the ambient air temperature. Next, they placed the material on a patch of simulated skin and found the skin temperature was approximately 8 degrees Celsius cooler than the same type of simulated skin without the material covering. They also found that it kept the artificial skin approximately 12.5 degrees Celsius cooler than standard cotton material. Further testing showed that the material was able to reflect approximately 95% of sunlight, preventing it from passing through to the skin underneath.

Bin Zhu et al, Subambient daytime radiative cooling textile based on nanoprocessed silk, Nature Nanotechnology (2021). DOI: 10.1038/s41565-021-00987-0

https://phys.org/news/2021-11-silk-skin-cooler-cotton.html?utm_sour...

White-tailed deer found to be huge reservoir of coronavirus infection

New research from the US has shown that white-tailed deer are being infected with SARS-CoV-2, the virus that causes COVID-19 in humans. Antibodies were found in 40% of deer that were tested from January to March 2021 across Michigan, Pennsylvania, Illinois and New York state. A second unpublished study has detected the virus in 80% of deer sampled in Iowa between November 2020 and January 2021.

Such high levels of infection led the researchers to conclude that deer are actively transmitting the virus to one another. The scientists also identified different SARS-CoV-2 variants, suggesting there have been many human-to-deer infections.

The large numbers of white-tailed deer in North America and the fact that they often live close to people provide several opportunities for the disease to move between the two species. This can include wildlife management operations, field research, recreation, tourism and hunting. In fact, hunters are likely to be one of the most obvious sources of potential reinfection as they regularly handle dead animals. It has also been suggested that water sources contaminated with SARS-CoV-2 might provide a pathway for transmission, although this has yet to be proved.

Human-to-deer and deer-to-deer transmission are believed to be driving the rapid spread of the disease within white-tailed deer populations across the US. This is particularly apparent during the early months of 2021 when COVID infections were spiking in the human population. Previous studies have shown that SARS-CoV-2 can be passed from humans to domestic and captive animals including cats, dogs, zoo animals and, most notably, farmed mink. But, until now, the disease had not been shown to spread in wildlife species.

There is the possibility that viral mutation in a reservoir host, such as white-tailed deer, could lead to new variants of the disease. These variants may lead to greater infection rates, increased virulence (severity of symptoms) and prove more effective at evading the human immune system. Likewise, any reinfection from wildlife reservoirs could also complicate our long-term efforts to fight and suppress the disease.

https://www.pnas.org/content/118/47/e2114828118

https://www.biorxiv.org/content/10.1101/2021.10.31.466677v1

https://theconversation.com/white-tailed-deer-found-to-be-huge-rese...

Humans are guilty of breaking an oceanic law of nature: study

A new international study has examined the distribution of biomass across all life in the oceans, from bacteria to whales. Their quantification of human impact reveals a fundamental alteration to one of life's largest scale patterns.

Scientists have used advances in ocean observation and large meta-analyses to show that human impacts have already had major consequences for the larger oceanic species, and have dramatically changed one of life's largest scale patterns—a pattern encompassing the entire ocean's biodiversity, from bacteria to whales.

Early samples of marine plankton biomass from 50 years ago led researchers to hypothesize that roughly equal amounts of biomass occur at all sizes. For example, although bacteria are 23 orders of magnitude smaller than a blue whale, they are also 23 orders of magnitude more abundant. This size-spectrum hypothesis has since remained unchallenged, even though it was never verified globally from bacteria to whales. The authors of the study, published in the journal Science Advances, sought to test this hypothesis on a global scale for the first time. They used historical reconstructions and marine ecosystem models to estimate biomass before industrial scale fishing got underway (pre-1850) and compared this data to the present-day.

One of the biggest challenges to comparing organisms spanning bacteria to whales is the enormous differences in scale.

The ratio of their masses is equivalent to that between a human being and the entire Earth. Researchers estimated organisms at the small end of the scale from more than 200,000 water samples collected globally, but larger marine life required completely different methods.

Their approach focused on 12 major groups of aquatic life over roughly 33,000 grid points of the ocean. Evaluating the pre-industrial ocean conditions (pre-1850) largely confirmed the original hypothesis: There is a remarkably constant biomass across size classes.

Researchers were amazed to see that each order of magnitude size class contains approximately 1 gigaton of biomass globally.

While bacteria are over-represented in the cold, dark regions of the ocean, the largest whales are relatively rare, thus highlighting exceptions from the original hypothesis.

In contrast with an even biomass spectrum in the pre-1850 ocean, an investigation of the spectrum at present revealed human impacts on ocean biomass through a new lens. While fishing and whaling only account for less than 3 percent of human food consumption, their effect on the biomass spectrum is devastating: large fish and marine mammals such as dolphins have experienced a biomass loss of 2 Gt (60% reduction), with the largest whales suffering an unsettling almost 90% decimation. The authors estimate that these losses already outpace potentialbiomass losses even under extreme climate change scenarios.

Humans have impacted the ocean in a more dramatic fashion than merely capturing fish. It seems that we have broken the size spectrum—one of the largest power law distributions known in nature.  These results provide a new quantitative perspective on the extent to which anthropogenic activities have altered life at the global scale. 

Ian A. Hatton et al, The global ocean size spectrum from bacteria to whales, Science Advances (2021). DOI: 10.1126/sciadv.abh3732

https://phys.org/news/2021-11-humans-guilty-oceanic-law-nature.html

Nuclear radiation used to transmit digital data wirelessly

Engineers have successfully transferred digitally encoded information wirelessly using nuclear radiation instead of conventional technology.

Radio waves and mobile phone signals relies on electromagnetic radiation for communication but in a new development, engineers from Lancaster University in the UK, working with the Jožef Stefan Institute in Slovenia, transferred digitally encoded information using "fast neutrons" instead.

The researchers measured the spontaneous emission of fast neutrons from californium-252, a radioactive isotope produced in nuclear reactors.

Modulated emissions were measured using a detector and recorded on a laptop.

Several examples of information, i.e., a word, the alphabet and a random number selected blindly, were encoded serially into the modulation of the neutron field and the output decoded on a laptop which recovered the encoded information on screen.

A double-blind test was performed in which a number derived from a random number generator was encoded without prior knowledge of those uploading it, and then transmitted and decoded. 

All transmission tests attempted proved to be 100% successful.

Malcolm J. Joyce et al, Wireless information transfer with fast neutrons, Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment (2021). DOI: 10.1016/j.nima.2021.165946

https://phys.org/news/2021-11-nuclear-transmit-digital-wirelessly.html

Bioengineers find new way heart valves grow – and go wrong

We're Doing Mindfulness Wrong, Psychologists Say

What does mindfulness mean to you? Is it about being aware of what comes your way without distraction? Or is it engaging with life's challenges without judgement, and responding as required?

A new meta-analysis of almost 150 studies has found that most of us understand that mindfulness is about both being aware and engaging with whatever comes our way. Unfortunately, we're much worse at putting this 'engaging' part into action.

Scientific understanding of mindfulness goes beyond mere stress-relief and requires a willingness to engage with stressors. It is, in fact, the engagement with stressors that ultimately results in stress relief. More specifically, mindfulness includes two main dimensions: awareness and acceptance.

Mindfulness derives from Buddhist traditions, and has become used in Western settings since the 1970s as part of psychiatry and psychology. It has been shown to help reduce depression, stress, anxiety, and even drug addiction, and is regularly recommended as a coping mechanism as part of therapy. 

In terms of regular people's understanding of mindfulness, we're really good at the 'awareness' part, the researchers say – where we take stock of what's around us, and any potential issues coming our way.

But the team found that we then tend to use mindfulness as a passive endorsement of the experience: the mindfulness equivalent of a shrug emoji. 

What we should do to get the full benefits of mindfulness is engage with our experiences, finding solutions and responses to our environment – something that the researchers found that we're aware of, but we just don't do.

"These modern applications of mindfulness have recently faced substantial criticism. Scholars suggest that popular definitions cast mindfulness as a 'quick fix' for suffering rather than a longitudinal practice of re-orienting, re-framing, and engaging with daily experience," the team writes in their paper.

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The team looked at 145 datasets, in total covering 41,966 participants who did the Five Facet Mindfulness Questionnaire. The five facets are observing, describing, acting with awareness, non-judging inner experience and non-reactivity to inner experience.

What the team found was that there was little 'convergence' across these facets across participants in non-clinical settings. Put simply, we're not embracing the whole package.

Researchers found that people seem to conceptually understand that mindfulness involves engagement, the general public is not walking the talk. Our results suggest that laypeople may understand what awareness is, but the next step of acceptance may not be well understood – limiting potential for engaging with problems.

https://www.sciencedirect.com/science/article/abs/pii/S027273582100...

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Protein-based COVID vaccines

Some people can’t get current COVID-19 vaccines for health reasons, but protein-based vaccines offer hope that they might soon be immunized. To elicit a protective immune response, these shots deliver proteins, along with immunity-stimulating adjuvants, directly to a person’s cells, rather than sending in a fragment of genetic code that the cells must read to synthesize the proteins themselves. After months of quality-control setbacks and manufacturing delays, the protein-based jab from US biotechnology firm Novavax has just received its first emergency-use authorization, in Indonesia. Meanwhile, Clover Biopharmaceuticals, based in China, and Biological E in India are on track to file for authorization in various countries in the coming weeks and months.

https://mcusercontent.com/2c6057c528fdc6f73fa196d9d/images/eadad212..." alt="Protein vaccines 101: An infographic that shows how COVID-19 protein-based vaccines are made, and how the body reacts to them."/>

Giant Study Identifies The Best Time to Fall Asleep to Lower Risk of Heart Problems

While the link between sleep and a healthy heart is well established, researchers are still sussing out the details. A new study suggests there might even be an optimal time, within our 24-hour body clock, for falling asleep.

Of course, the reasons for not obtaining the right sleep, whether it's the best amount or right timing are not always within our control. So anyone struggling with their sleep should seek medical advice and focus on whatever they need to do that works for them – as dictating a specific bedtime may be counterproductive for some.

But for the rest of us it may be helpful to know that falling asleep between 10-11 pm seems to hit the sweet spot for a healthy cardiovascular system.

The body has a 24-hour internal clock, called circadian rhythm, that helps regulate physical and mental functioning. While we cannot conclude causation from our study, the results suggest that early or late bedtimes may be more likely to disrupt the body clock, with adverse consequences for cardiovascular health.

The team found falling asleep after midnight or before 10 pm both was associated with around a 25 percent increase in risk of cardiovascular disease, compared to falling asleep between 10-11 pm. This increase in risk dropped to 12 percent for those who fell asleep between 11-12 pm.

"The riskiest time was after midnight, potentially because it may reduce the likelihood of seeing morning light, which resets the body clock.

This trend remained when taking into account age, gender, sleep duration, being an early bird or night owl, smoking status, weight, diabetes, blood pressure, cholesterol level, and socioeconomic status. It was also more pronounced for women, but the researchers aren't yet sure why.

https://academic.oup.com/ehjdh/advance-article/doi/10.1093/ehjdh/zt...

https://www.sciencealert.com/huge-accelerometer-study-suggests-the-...

Sustainable, biodegradable, vegan glitter

Glitter is a bane of modern living. But beyond its general annoyance factor, it's also made of toxic and unsustainable materials, and contributes to plastic pollution.

Now, researchers from the University of Cambridge have found a way to make sustainable, non-toxic, vegan, and biodegradable glitter from cellulose—the main building block of cell walls in plants, fruits and vegetables—and that's just as sparkly as the original.

The glitter is made from cellulose nanocrystals, which can bend light in such a way to create vivid colors through a process called structural color. The same phenomenon produces some of the brightest colors in nature—such as those of butterfly wings and peacock feathers—and results in hues which do not fade, even after a century.

Using self-assembly techniques which allow the cellulose to produce intensely-colored films, the researchers say their materials could be used to replace the plastic glitter particles and tiny mineral effect pigments which are widely used in cosmetics.

The films of cellulose nanocrystals prepared by the team can be made at scale using roll-to-roll processes like those used to make paper from wood pulp, and this is the first time these materials have been fabricated at industrial scale. The results are reported in the journal Nature Materials.

Silvia Vignolini, Large-scale fabrication of structurally coloured cellulose nanocrystal films and effect pigments, Nature Materials (2021). DOI: 10.1038/s41563-021-01135-8. www.nature.com/articles/s41563-021-01135-8

https://phys.org/news/2021-11-sustainable-biodegradable-vegan-glitt...

'Dancing molecules' successfully repair severe spinal cord injuries in mice

Researchers have developed a new injectable therapy that harnesses "dancing molecules" to reverse paralysis and repair tissue after severe spinal cord injuries.

In a new study, researchers administered a single injection to tissues surrounding the spinal cords of paralyzed mice. Just four weeks later, the animals regained the ability to walk.

The research will be published in the Nov. 12 issue of the journal Science.

By sending bioactive signals to trigger cells to repair and regenerate, the breakthrough therapy dramatically improved severely injured spinal cords in five key ways: (1) The severed extensions of neurons, called axons, regenerated; (2) scar tissue, which can create a physical barrier to regeneration and repair, significantly diminished; (3) myelin, the insulating layer of axons that is important in transmitting electrical signals efficiently, reformed around cells; (4) functional blood vessels formed to deliver nutrients to cells at the injury site; and (5) more motor neurons survived.

After the therapy performs its function, the materials biodegrade into nutrients for the cells within 12 weeks and then completely disappear from the body without noticeable side effects. This is the first study in which researchers controlled the collective motion of molecules through changes in chemical structure to increase a therapeutic's efficacy.

The secret behind Stupp's new breakthrough therapeutic is tuning the motion of molecules, so they can find and properly engage constantly moving cellular receptors. Injected as a liquid, the therapy immediately gels into a complex network of nanofibers that mimic the extracellular matrix of the spinal cord. By matching the matrix's structure, mimicking the motion of biological molecules and incorporating signals for receptors, the synthetic materials are able to communicate with cells.

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Once connected to the receptors, the moving molecules trigger two cascading signals, both of which are critical to spinal cord repair. One signal prompts the long tails of neurons in the spinal cord, called axons, to regenerate. Similar to electrical cables, axons send signals between the brain and the rest of the body. Severing or damaging axons can result in the loss of feeling in the body or even paralysis. Repairing axons, on the other hand, increases communication between the body and brain.

The second signal helps neurons survive after injury because it causes other cell types to proliferate, promoting the regrowth of lost blood vessels that feed neurons and critical cells for tissue repair. The therapy also induces myelin to rebuild around axons and reduces glial scarring, which acts as a physical barrier that prevents the spinal cord from healing.

The signals used in the study mimic the natural proteins that are needed to induce the desired biological responses. While the new therapy could be used to prevent paralysis after major trauma (automobile accidents, falls, sports accidents and gunshot wounds) as well as from diseases, researchers think the underlying discovery—that "supramolecular motion" is a key factor in bioactivity—can be applied to other therapies and targets.

Zaida Alvarez et al, Bioactive Scaffolds with Enhanced Supramolecular Motion Promote Recovery from Spinal Cord Injury, Science (2021). DOI: 10.1126/science.abh3602. www.science.org/doi/10.1126/science.abh3602

https://medicalxpress.com/news/2021-11-molecules-successfully-sever...

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Scientists appeal for immediate climate action at COP26

More than 200 scientists told the COP26 summit Thursday to take immediate action to halt global warming, warning in an open letter that some climate change impacts were "irreversible" for generations.

The central task of the Glasgow meeting is to implement the Paris Agreement, with its goal of limiting temperature rise to between 1.5 and 2 degrees Celsius above pre-industrial levels.

But as negotiations enter their final days, commitments made so far could still lead to "catastrophic" warming of as much as 2.7C by 2100, according to the UN.

"We, climate scientists, stress that immediate, strong, rapid, sustained and large-scale actions are necessary," to keep warming within the Paris target, said the letter, signed by researchers across the world.

In August, a bombshell "code red" report from the world's top climate science body, the Intergovernmental Panel on Climate Change (IPCC), warned that Earth's average temperature will hit the 1.5C threshold around 2030, a decade earlier than projected only three years ago.

To keep from overshooting that temperature target the IPCC says emissions must fall 45 percent this decade.

Thursday's open letter, signed by some of the IPCC's report authors, calls on delegates in Glasgow to "fully acknowledge" the scientific evidence they have compiled of the severe threats posed by climate change.

"Cumulative greenhouse gas emissions to date already commit our planet to key changes of the climate system affecting human society and marine and terrestrial ecosystems, some of which are irreversible for generations to come," said the letter.

https://phys.org/news/2021-11-scientists-appeal-climate-action-cop2...

Second instance of canine coronavirus found in a person

 A University of Florida research team is helping to build the case that coronaviruses move between animals and people at a more frequent rate than previously understood. Earlier this year, the team reported the first known instance of a coronavirus common in pigs to have "spilled over" into people. Spillovers refer to events where a virus that is adapted to a certain kind of host—say, a dog, or pig—acquires features that allow it to infect an entirely different species of host, such as a person. In their newest work, the team retrospectively uncovered an instance where a coronavirus known from dogs, called a canine coronavirus, infected at least one person visiting Haiti in early 2017. The infected person had a mild illness with fever and fatigue. The new work published in Clinical Infectious Diseases on Oct. 28,2021. In an unusual twist, the virus was determined to closely match a canine coronavirus reported earlier in 2021.

Study Finds Fish Rubbing Up Against Their Predators — Sharks. Researchers suggest this behaviour plays a greater ecological role than previously known

There's a Strange Difference Between Human Brains And Those of Other Mammals

When it comes to the world of mammals, humans tend to stand out a fair bit.

While many animals share some aspects of our intelligence, they don't take it to the same level we have. But pinning down why we're more cognitively advanced on a neurological level has been tricky; to date, studies have found no significant differences between the brains of mammals. Now, we finally have a lead.

A team of researchers from the Massachusetts Institute of Technology (MIT) has found that, compared to other mammals, human brains have a much lower number of the neuronal channels that allow the flow of ions such as calcium, potassium, and sodium.

This flow produces the electrical impulses that allow neurons to communicate with each other; having fewer of them could mean that the human brain can operate more efficiently, diverting resources to more complex cognitive functions.

One of their findings concerned dendrites, the branching structures at the tips of nerve cells through which the brain's electrical impulses are received via ion channels. From here, the dendrite generates what we call an action potential, which transfers the signal onwards.

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When comparing the brains of the two species, the researchers found that the human dendrites had a marked lower density of these ion channels compared to rat dendrites. This was worth investigating further.

The new research has been expanded to include 10 species: shrew, mouse, gerbil, rat, ferret, guinea pig, rabbit, marmoset, macaque and, of course, human, using samples of tissue excised from epilepsy patients during brain surgery.

An analysis of the physical structure of these brains revealed that ion channel density increases with neuron size, with one notable exception: the human brain.

This, the researchers concluded, was to maintain ion channel density across a range of brain sizes; so, although the shrew had a higher number of neurons than the rabbit or the macaque in a given volume of brain, the density of ion channels in that volume was consistent.

"This building plan is consistent across nine different mammalian species. What it looks like the cortex is trying to do is keep the numbers of ion channels per unit volume the same across all the species. This means that for a given volume of cortex, the energetic cost is the same, at least for ion channels.

The exceptionally low ion channel density in the human brain was glaring, when compared with all the other brains.

All the comparison animals were significantly smaller than humans, of course, so it may be worth testing the samples of even larger animals. However, the macaque is often used in research as a model for the human brain.

The researchers suspect an evolutionary trade-off is possible for humans – this is when a biological system loses or diminishes a trait for an optimization elsewhere.

For example, it takes energy to pump ions through dendrites. By minimizing ion channel density, the human brain may have been able to deploy the energy savings elsewhere – perhaps in more complex synaptic connections, or more rapid action potentials.

"If the brain can save energy by reducing the density of ion channels, it can spend that energy on other neuronal or circuit processes

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Researchers think that humans have evolved out of this building plan that was previously restricting the size of cortex, and they figured out a way to become more energetically efficient, so you spend less ATP [energy molecules] per volume compared to other species."

This finding reveals, the researchers said, an intriguing avenue for further investigation. In future research, the team hopes to explore the evolutionary pressures that might have led to this difference, and isolate where, exactly, that extra brain energy is going.

The research has been published in Nature.

https://www.nature.com/articles/s41586-021-04072-3

https://www.sciencealert.com/we-ve-just-found-a-fascinating-differe...

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Part 3

The Matilda effect is a bias against acknowledging the achievements of those women scientists whose work is attributed to their male colleagues. This effect was first described by suffragist and abolitionist Matilda Joslyn Gage (1826–98) in her essay, "Woman as Inventor" (first published as a tract in 1870 and in the North American Review in 1883). The term "Matilda effect" was coined in 1993 by science historian Margaret W. Rossiter. Rossiter provides several examples of this effect. Trotula (Trota of Salerno), a 12th-century Italian woman physician, wrote books which, after her death, were attributed to male authors. Nineteenth- and twentieth-century cases illustrating the Matilda effect include those of Nettie Stevens, Lise Meitner, Marietta Blau, Rosalind Franklin, and Jocelyn Bell Burnell. The Matilda effect was compared to the Matthew effect, whereby an eminent scientist often gets more credit than a comparatively unknown researcher, even if their work is shared or similar.

https://en.wikipedia.org/wiki/Matilda_effect

Introduced birds are not replacing roles of human-caused extinct species: study

Human-caused bird extinctions are driving losses of functional diversity on islands worldwide, and the gaps they leave behind are not being filled by introduced (alien) species, finds a new study.

The study, published in Science Advances, shows how human impacts such as habitat destruction and climate change are impoverishing ecosystems, even on islands where alien birds actually outnumber the species that have gone extinct.

Humans have drastically changed bird communities, not only by driving animals to extinction but also by introducing species into new habitats across the globe. There has been some debate as to whether introduced species might replace the roles of the extinct species, thus maintaining functional diversity within the ecosystem; here, researchers found that is unfortunately not the case.

 Valuable functions that may be lost with bird extinctions can include pollination and seed dispersal, which can have cascading harmful effects on other species.

Some groups of birds have been particularly successful at establishing outside their natural areas—for example, many species of parrot and starling. Because of this, islands are becoming more homogeneous as the same kind of birds are established everywhere.

These new  findings add to evidence that conservation efforts should be focused on preserving functionally distinct threatened species, to stem the tide of harmful losses to biodiversity that are driven by human actions. Huge numbers of species are being driven to extinction by human-driven effects such as habitat loss and climate change, so it is vital that we act now to reduce our negative impact on global biodiversity.

 Ferran Sayol, Loss of functional diversity through anthropogenic extinctions of island birds is not offset by biotic invasions, Science Advances (2021). DOI: 10.1126/sciadv.abj5790. www.science.org/doi/10.1126/sciadv.abj5790

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For this study, the researchers compiled an exhaustive list of all bird species that have been present in nine different archipelagos* before and after human-caused extinctions occurred. This covered 1,302 bird species, including 265 globally or locally extinct, and 355 established introductions from 143 separate species. In addition, the scientists visited different museum collections, including the Natural History Museum, to measure several morphological traits in skin or skeleton specimens. With this data, the researchers were able to quantify the trait diversity before and after bird extinctions, and identify the ecological niches extinct birds once filled.

The research team found that before human arrival, island bird communities were more morphologically diverse than they are today. Their findings show how human-driven extinctions have disproportionally affected some types of birds (for example, larger birds and flightless birds are more likely to go extinct), leading to the loss of certain ecological roles.

The researchers also found that different archipelagos are becoming more and more similar in terms of trait diversity as native birds go extinct and the same kind of alien species are being newly established in many places.

https://phys.org/news/2021-11-birds-roles-human-caused-extinct-spec...

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Researchers discover link between dietary fat and the spread of cancer

A new study uncovers how palmitic acid alters the cancer genome, increasing the likelihood the cancer will spread. Researchers have started developing therapies that interrupt this process and say a clinical trial could start in the next couple of years.
Metastasis—or the spread—of cancer remains the main cause of death in cancer patients and the vast majority of people with metastatic cancer can only be treated, but not cured. Fatty acids are the building blocks of fat in our body and the food we eat. Metastasis is promoted by fatty acids in our diet, but it has been unclear how this works and whether all fatty acids contribute to metastasis.
Newly published findings reveal that one such fatty acid commonly found in palm oil, called palmitic acid, promotes metastasis in oral carcinomas and melanoma skin cancer in mice. Other fatty acids called oleic acid and linoleic acid—omega-9 and omega-6 fats found in foods such as olive oil and flaxseeds—did not show the same effect. Neither of the fatty acids tested increased the risk of developing cancer in the first place.
The research found that when palmitic acid was supplemented into the diet of mice, it not only contributed to metastasis, but also exerts long-term effects on the genome. Cancer cells that had only been exposed to palmitic acid in the diet for a short period of time remained highly metastatic even when the palmitic acid had been removed from the diet.
The researchers discovered that this "memory" is caused by epigenetic changes—changes to how our genes function. The epigenetic changes alter the function of metastatic cancer cells and allow them to form a neural network around the tumor to communicate with cells in their immediate environment and to spread more easily. By understanding the nature of this communication, the researchers uncovered a way to block it and are now in the process of planning a clinical trial to stop metastasis in different types of cancer.

Salvador Benitah, Dietary palmitic acid promotes a prometastatic memory via Schwann cells, Nature (2021). DOI: 10.1038/s41586-021-04075-0. www.nature.com/articles/s41586-021-04075-0

https://researchnews.cc/news/9975/Researchers-discover-link-between...

New research helps explain the genetic basis for why we look the way we do

 Which genes control the defining features that make us look as we do? And how do they make it happen?

In 1990, University of California San Diego biologist William McGinnis conducted a seminal experiment that helped scientists unravel how high-level control genes called Hox genes shape our appearance features. The "McGinnis experiment" helped pave the way for understanding the role of Hox genes in determining the uniform appearances of species, from humans to chimpanzees to flies.

McGinnis, a professor emeritus of Cell and Developmental Biology and former dean of the Division of Biological Sciences, helped discover a defining DNA region that he termed the "homeobox," a sequence within genes that directs anatomical development. Since the now-famous McGinnis experiment, evolutionary and developmental biologists have pondered how these highly influential Hox genes determine the identities of different body regions.

More than three decades later, a study published in Science Advances and led by Ankush Auradkar, a UC San Diego postdoctoral scholar mentored by coauthor McGinnis and study senior author Ethan Bier, helps answer questions about how Hox genes function.

The now-textbook McGinnis experiment tested whether the proteins produced by a human or mouse Hox gene could function in flies. Following in these footsteps, the new study leveraged modern CRISPR gene editing to investigate whether all aspects of Hox gene function, which consists of both protein coding and control regions, could be replaced in a common laboratory fruit fly (Drosophila melanogaster) with its counterpart from a rarer Hawaiian cousin (Drosophila mimica), which has a very different face.

1. Ankush Auradkar, Emily A. Bulger, Sushil Devkota, William McGinnis, Ethan Bier. Dissecting the evolutionary role of the Hox gene proboscipedia in Drosophila mouthpart diversification by full locus replacement. Science Advances, 2021; 7 (46) DOI: 10.1126/sciadv.abk1003

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The gene in question, proboscipedia, would plainly reveal itself since it directs the formation of strikingly different mouth parts—smooth and spongy in D. mel but more grill-like (resembling the face of the alien in Predator science fiction films) in D. mim.

Study coauthor Emily Bulger first collected the notoriously difficult-to-breed D. mim samples from Hawai'i Volcanoes National Park, along with the only native fruit (Sapindus saponaria—Hawaiian soapberry) that the insects are known to eat, in order to establish a temporary colony in Bier's laboratory. Auradkar then collaborated with coauthor Sushil Devkota to decipher the genome sequence of the D. mim proboscipedia gene, which was nearly 44,000 bases long. The researchers then deleted the D. mel proboscipedia gene and replaced it with the D. mim version of the same.

As McGinnis had predicted, the new results revealed that the graceful facial structure of D. mel emerged as the "winner" over the rough features of D. mim. One trait of D. mim, however, did surface during the experiment: Sensory organs called maxillary palps that stick out from the face in D. mel instead ran parallel to feeding mouthparts as they do in D. mim. Auradkar used sophisticated genetic tools to determine the basis for this difference and tracked it down to a change in the pattern by which the proboscipedia gene is activated (control region changes).

The experiment's results help answer longstanding questions about whether Hox genes function as "master" regulatory genes that dictate different body parts in organisms. Or, as McGinnis proposed, whether Hox genes instead provide abstract positional codes and serve as scaffolds for downstream genes that best benefit the organism. Other than the maxillary palps, the new results demonstrated that McGinnis' scaffolding idea proved to be the case.

McGinnis says that beyond the implications for evolutionary biology, the results could help explain developmental issues rooted in fundamental human genetic processes.

"These fly studies provide a window into deep evolutionary time and inform us about the mechanisms by which body plans change during evolution," said Bier. "These insights may lead to a better of understanding of processes tied to congenital birth defects in humans. With the advent of powerful new CRISPR-based genome editing systems for human therapy on the horizon, new strategies might be formulated to mitigate some of the effects of these often debilitating conditions."

https://researchnews.cc/news/9981/New-research-helps-explain-the-ge...

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Achieving razor-sharp vision in the metaverse

Researchers may have unlocked function of mysterious structure found on neurons

 For 30 years, mysterious clusters of proteins found on the cell body of neurons in the hippocampus, a part of the brain, both intrigued and baffled James Trimmer.

Now, the distinguished professor of physiology and membrane biology at the UC Davis School of Medicine may finally have an answer. In a new study published in PNAS, Trimmer and his colleagues reveal these protein clusters are calcium signaling "hotspots" in the neuron that play a crucial role in activating gene transcription.

Transcription allows portions of the neuron's DNA to be "transcribed" into strands of RNA that are then used to create the proteins needed by the cell.

Structures found in many animals
Trimmer's lab studies the enigmatic clusters in mice, but they exist in invertebrates and all vertebrates—including humans. Trimmer estimates that there can be 50 to 100 of these large clusters on a single neuron.

He and his colleagues knew that the clusters are formed by a protein that passes potassium ions through membranes (a potassium channel). They also knew these clusters contain a particular type of calcium channel. Calcium channels allow calcium to enter cells, where it triggers a variety of physiological responses depending on the type of cell.

"The presence of these clusters in neurons is highly conserved," Trimmer said. Highly conserved features are relatively unchanged through evolutionary timescales, suggesting they have an important functional property in these very different types of animals.

The hippocampus, one region of the brain where the clusters are found on neurons, plays a major role in learning and memory. Researchers knew that disruption to these clusters—for example, from genetic mutations in the potassium channel—results in severe neurological disorders. But it was not clear why.

"We have known the function of other types of ion channel clusters, for example those at synapses, for a long time. However, there was no known role that these much larger structures on the cell body played in the physiology of the neuron," Trimmer said.

Experiment flooded calcium channels with 'decoys'
The experiment that revealed the function of the neuronal clusters was designed by Nicholas C. Vierra, a postdoctoral researcher in Trimmer's lab and lead author for the study.

"We developed an approach that let us uncouple the calcium channel from the potassium channel clusters in neurons. A key finding was that this treatment blocked calcium-triggered gene expression. This suggests that the calcium channel-potassium channel partnership at these clusters is important for neuronal function," Vierra said.

For their experiment, the researchers essentially "tricked" the calcium channels at these clusters by flooding the neurons with decoy potassium channel fragments. When the calcium channels grabbed onto the decoys instead of the real potassium channels, they fell away from the clusters.

As a result, the process known as excitation-transcription coupling, which links changes in neuronal electrical activity to changes in gene expression, was inactivated.

"There are a lot of different calcium channels, but the particular type of calcium channel found at these clusters is necessary for converting changes in electrical activity to changes in gene expression," Trimmer said. "We found that if you interfere with the calcium-signaling proteins located at these unusual clusters, you basically eliminate excitation-transcription coupling, which is critical for learning, memory, and other forms of neuronal plasticity."

Trimmer and Vierra hope their findings will open new avenues of research.

"A lot of research has focused on calcium signaling in dendrites—the sites where neurons receive signals from other neurons. Calcium signaling in the cell body of neurons has received less attention," said Vierra. "Now we understand much more about the significance of signaling at these specific sites on the cell body of the neuron."

"We are only at the beginning of understanding the significance of this signaling, but these new results may provide information that could shape new research into its role in brain function, and perhaps eventually into the development of new classes of therapeutics," said Trimmer.

Additional authors on the study include Samantha C. O'Dwyer, Collin Matsumoto and L. Fernando Santana, Department of Physiology and Membrane Biology, UC Davis School of Medicine.

https://researchnews.cc/news/9979/Researchers-may-have-unlocked-fun...

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Microbiomes: It's who you are that matters most

Every mammal hosts a hidden community of other organisms—the microbiome. Their intestines teem with complex microbial populations that are critical for nutrition, fighting disease and degrading harmful toxins. Throughout their lives, mammals are exposed to countless microbes through their food and environment, but only a small subset take up permanent residence in the host. Although scientists agree that diet, geography and evolutionary history structure the microbiome, the relative influence of each factor is a mystery. No rigorous study has investigated all three at once in wild mammal populations. Until now.

A team of University of Utah biologists analyzed the bacteria in the gut microbiome of woodrats (Neotoma species), a group of closely related herbivorous rodents abundant in the southwestern United States. The animals offered a unique opportunity to test how diet, geography and evolutionary history influence microbiome structure. The many woodrat species are morphologically similar, but populations live in a variety of habitats and have distinct diets. Woodrats are famous for eating extremely toxic plants and do so with support from specialized gut bacteria.

Woodrats are amazing—they have incredibly diverse diets. Individuals from the same species eat different foods at different locations, so it creates a natural experiment. It's hard to say what's driving their different microbiomes—is it what they're eating? Is it where they're living? Or is it who they are?

The researchers used DNA barcoding techniques to characterize the diet and gut bacteria of seven woodrat species from 25 populations at 19 locations across the southwestern U.S. The biologists then brought the rodents into captivity, fed them a diet of rabbit chow for one month and then resampled their microbiome. The results show that in both wild and captive individuals, evolutionary history was the biggest predictor of microbiome structure—more than diet and geography.

Microbiome stability and structure is governed by host phylogeny over diet and geography in woodrats (Neotoma spp.), Proceedings of the National Academy of Sciences (2021). DOI: 10.1073/pnas.2108787118.

https://phys.org/news/2021-11-woodrat-microbiomes.html?utm_source=n...

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