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One person's techno trash is a scientist's research tool

It's hard to study plant roots, but a plastic CD case makes it easier to observe a plant's underground activities

Cassie Freund

Ecology

Wake Forest University

Plant roots are complex and delicate structures that provide the aboveground stem and leaves with nutrients and water. Studying them can tell us a lot about a plant's survival strategy and its associations with soil fungi and bacteria. There's a lot going on beneath our feet that we just can't see.

And that's part of the problem: roots are very difficult to study because they are hidden below layers of soil. To measure and observe roots, plant biologists must either dig up the plant, an approach aptly referred to as "destructive sampling," or install a see-through chamber called a rhizotron. A rhizotron is kind of like an ant farm: it allows you to observe what is going on in the soil though a clear panel. But rhizotrons can be expensive and, depending on a scientist's research goals, not worth the effort it takes to construct them.

plants growing out of a CD case

CD case rhizotron

Steven Cassidy

Now, a group of biologists from the University of Pittsburgh have developed an inexpensive and simple mini-rhizotron from a now-defunct household object: a plastic CD case. Their method was published in April in Applications in Plant Sciences. The case itself is filled with soil, and the growing plants protrude from the hinge. Because plants can sense and grow in the direction of gravity, storing the CD cases at an angle forces the roots to grow up against the see-through sides of the cases, making them easy to see and measure without disturbing the plant.

This method only works for studying small plants — there is no CD case large enough to grow a tropical tree! But it's a clever method that fills a scientific need, and one that the authors hope will make root research accessible to teachers, ecologists, agricultural scientists, and other researchers no matter what financial resources they have available.

Iberian lynx eat more species of prey than previously thought

This big cat has recovered from the brink of extinction over the past 20 years

Luis Manuel Fernandez Porras

Conservation Biology

Canadian Organization for Tropical Education and Rainforest Conservation

Iberian lynx (Lynx pardinus) has been a paradigm of conservation efforts in Spain for decades. Between 2000 and 2019, its population increased from about 250 to 400 lynx, due to conservation initiatives such as translocation and reintroduction. Most of the studies on this species happened in southern Spain, where the Iberian lynx was considered a trophic super specialist, but there are populations in central Spain as well. Its decline has been attributed to the decline of its main prey species, the European rabbit. Now, research has challenged the traditional vision of the Iberian lynx as a trophic specialist. The lynx has a much wider diet than previously thought.

Within mammals, the study of large predator diets is mostly based on analyzing their scat (fecal matter) for undigested content such as hairs or feathers that hints at what the predator is eating. To do so, the first step is to find the scat and properly identify what species they belong to. In the case of Iberian Lynx, its scat is easily misidentified as belonging to European wildcats and red foxes. Therefore, in this study, genetic methods were necessary to properly identify the scat samples.

Researchers classified the content found in 46 scat samples into four different groups (small mammals, lagomorphs, birds, and ungulates) and calculated the proportion of each of them in the total. They compared these proportions between the central and southern lynx populations, and found that the former is better able to adapt to sub-par ecological conditions. They adopt a more generalist diet when there is an abundant variety of prey and a more specialist diet when there is low prey diversity.

Understanding the variables that determine the presence of a species in a specific habitat is vital to take informed decisions on wildlife management and to implement successful conservation actions. This finding sheds new light into the biology of an endangered and charismatic species of the Iberian fauna that can improve its recovery from the brink of extinction.

Marine sponges are coral reefs' great recyclers

Sponges eat the "marine snow" that falls from other organisms in the ocean

Sarah Heidmann

Fish ecology

University of the Virgin Islands

There are many threats to tropical coral reefs. For example, in addition to climate change, corals are susceptible to being smothered by sedimentation, and fishes are being extracted faster than they can reproduce. But these are not the only types of life on a reef.

Marine sponges, which are typically overlooked by recreational divers attracted to the colorful and active fish and to the corals that form massive bioengineered structures, play a key role in coral reef ecosystems through nutrient cycling. A paper recently published in the ISME Journal has determined the mechanism by which marine sponges consume and digest dissolved organic matter, or DOM. 

Just as dust in your home comes in part from dead skin, DOM  (sometimes called “marine snow”) is bits of carbon sloughed off of various ocean-dwelling organisms. Sponges filter these particles out of the water, using it as one of their main food sources while cleaning the water for more sensitive organisms like coral.

The predominant opinion used to be that DOM processing is performed by bacteria acting as symbionts, but this study found it also occurs in the cells of the sponge itself, with ratio of sponge versus symbiont processing varying across species and environments. This strategy of recycling has allowed sponges to exist for over 600 million years without large changes in their approach to life. 

Your antidepressants could affect color-changing shrimp

The jury is still out for the shrimp, but our medications do affect water-dwelling wildlife

Rafe Cotton

Marine Biology

The common sand shrimp, Crangon crangon, a small shrimp endemic to the northeast Atlantic, is capable of changing color to match its surroundings. This superpower is made possible by pigments in special organs embedded in their skin called chromatophores.

The effects that antidepressants have on wildlife is a growing research topic as more people take these drugs and secrete the leftover compounds into wastewater. These compounds then find their way into water bodies, like the ocean. They are so damaging due to their effect on the neurotransmitters, molecules important for movement, present in all animals.

A pair of researchers from the UK's University of Portsmouth designed an experiment to investigate the possible interaction between antidepressants and cryptic coloration in sand shrimp. They exposed adult shrimp to varying low levels of the antidepressant fluoxetine for three time intervals (1 hour, 1 day, or 1 week). Then, they altered the color of the substrate the shrimp were in from solid white to solid black and measured how dark their bodies became as the shrimps' chrompatophores gained or lost pigment. 

The results of the investigation were inconclusive. In two of the three studies the researchers saw a high degree of correlation between shrimp "darkness" and substrate color. But, there was no clear effect of fluoxetine exposure on this correlation. Although inconclusive, this investigation does draw attention to an important issue: how do the medications we take affect wildlife downstream?

Testing for lesser known antibodies produces a better COVID-19 test

Most antibody tests look for responses to SARS-CoV-2's spike protein, but more accurate results include antibodies against the virus's other proteins

Kialani Mackey

Biology

Occidental College

Before we can go back to a somewhat “normal” state, many scientists say we need widespread testing and contact tracing—but how effective is our current testing system? 

To determine if someone currently has COVID-19 we test for the presence of the virus. To determine if someone was previously infected, we test for the antibodies their body produced in response to the infection. These antibodies usually specifically target the COVID-19 spike protein—an appendage that helps the virus enter human cells. 

Many caution against the accuracy of COVID-19 tests as studies show a growing number of false negative results from infected individuals with milder symptoms. A paper published recently in Nature outlines that analyzing antibody responses to the lesser studied, nonstructural COVID-19 proteins—proteins of unknown function—answer this diagnostic problem.

These researchers measured levels of antibodies targeting various COVID-19 proteins in the blood of infected and uninfected individuals. Results showed that analyzing the combined antibody response to the presence of two specific nonstructural proteins, called ORF8 and ORF3b, produced results that were 73 percent more accurate than testing for all spike protein antibodies. 

ORF8 and ORF3b antibody levels were most constant across infected participants from 1 to over 30 days after the onset of symptoms. This suggests that, unlike the current spike protein antibody test, diagnostic tests looking at ORF8 and ORF3b antibodies are ideal for diagnosing individuals with current or past COVID-19 infections.  

COVID-19 testing previously ignored nonstructural SARS-CoV-2 protein antibodies. But now these have clear potential to replace current diagnostic targets. More accurate testing will allow for both the public and public health experts to better understand the spread of the virus so that they can work together to contain this destructive pandemic. 

Flash droughts are a new type of extreme weather event

Scientists are figuring out how to pinpoint the onset of a flash drought

Jack Hawley

Oceanography

Humboldt State University

You’ve heard of a flash flood, but what about a flash drought? Flash droughts are extreme weather events that occur rapidly, much like flash floods, and can have severe impacts on plants, animals, and people. Researchers at the National Center for Atmospheric Research in Boulder, Colorado in collaboration with Californian, Australian, and German universities have now proposed two methods to identify whether an area is suffering from a flash drought.

Currently, most drought monitoring is done on a monthly or weekly schedule. But flash droughts need monitoring methods for daily timescales. One potential variable that these researchers draw on is the Evaporative Demand Drought Index (EDDI), a measurement of how "thirsty" the atmosphere is in a certain location for a given period of time. They also propose using the US Drought Monitor (USDM). This system classifies areas by five categories that range from D0 (abnormally dry) through D4 (exceptional drought).

Using these metrics, the researchers came up with two scientific definitions for flash droughts: 

1) A 50% increase in Evaporative Demand Drought Index (EDDI) for two weeks, with the resulting high EEDI levels persisting for another two weeks

2) A two-category change in the USDM over two weeks that persists for another two weeks.

Both definitions come with their own caveats, but the researchers note that the first definition could be a good general definition for prediction and climate change research. Because the second definition uses the USDM, it is only relevant in the United States, and this definition would have to be tailored to existing drought monitoring systems for use in other countries.

These definitions are a good foundation for the next steps toward understanding flash droughts: Future research on the connectivity of soil moisture, land to atmosphere interactions, large scale atmospheric events, and the effects of a changing climate will be needed to characterize this new type of extreme weather event.

Eating a high-fat diet could change your brain for the worse

Research in mice shows how fatty foods alter the brain's response to healthy foods

Samuel J Walker

Neuroscience

Harvard Medical School and Beth Israel Deaconess Medical Center

Dieting is notoriously difficult. Thanks in part to evolution, we love foods that are high in calories. Not only that, but once we have experienced the kind of high-calorie foods that surround us in the modern world, more nutritionally-balanced foods become much less attractive. But why?

To understand how the brain makes dieting so difficult, and high-calorie foods so tempting, the authors of a recent study turned to mice, where they could record and manipulate the activity of specific neurons involved in energy balance and reward. They asked how exposing mice to high-calorie foods affected their consumption of, and neural responses to, regular foods.

When researchers gave the mice access to both high-fat (HFD) and standard (SD) diets, mice completely stopped eating the SD almost immediately, and preferred the HFD. They then removed the HFD, and saw that mice still ate very little SD, and so lost substantial weight. This devaluation of regular food was so strong that even fasting mice presented with an SD ate very little — they would only eat a lot if the HFD was available. Just experiencing the HFD for 24 hours was enough time to make the SD less tasty.

a cartoon of a mouse eating human foods

Suzanne Beaky 

To see how HFD exposure affects the brain’s response to food, the scientists recorded the activity of AgRP neurons, a population of neurons that is active during hunger and controls energy balance, and midbrain dopamine neurons, which release dopamine as a signal of reward. Exposure to the HFD greatly reduced the response of both groups of neurons to the SD: afterward, these neurons would only respond strongly to the HFD. Regular food became less rewarding, and less satiating, than high-calorie food.

Under normal conditions, AgRP neurons would only respond to food when a mouse is hungry. But after HFD withdrawal (mimicking dieting), the AgRP neurons became so sensitive to HFD that they would respond even if the mouse was not hungry. This could explain why when we diet, high-calorie foods are so hard to resist – these foods become rewarding even when we aren’t hungry.

This study suggests that exposure to a HFD alters the brain’s response to food so that only high-calorie foods are rewarding and satiating, while more nutritionally-balanced foods become less valuable. And, abstaining from high-fat foods might just make our brains' hunger centers responsive to these foods even when we’re not hungry, making it difficult to resist the urge to binge. Research on the circuits that regulate food intake will potentially lead to therapies that allow us to manipulate these biological urges and control the obesity epidemic.

Scientists identify a powerful anti-inflammatory compound in psychedelic drugs

The compound, called 2 C-H, reduces inflammation without mind-altering effects

Milena Marinković

Neurobiology

University of Exeter

People have long believed that using psychedelic drugs such as LSD, DMT, and psilocybin (from ''magic mushrooms") can help the body fight inflammation. Scientific support for this idea has emerged in the past couple decades, and newly published research goes further to show exactly which structural parts of these molecules are responsible for the anti-inflammatory effect.

Psychedelic drugs exert their profound effects on the mind by interacting with a serotonin receptor in the brain called 5HT-2A. This receptor can also be found in almost all other parts of the body, including immune-related structures like the spleen and white blood cells. The effects of serotonin made in immune cells are mainly pro-inflammatory, and its secretion can influence the progression of disorders like asthma and rheumatoid arthritis.

Like serotonin, psychedelic drugs can also activate the 5HT-2A receptor and reduce inflammation. This new study, which was published in ACS Pharmacology & Translational Science, shows what molecular structure is responsible for this effect. The researchers looked at rats with asthmatic symptoms to test 21 different compounds that activate the 5HT-2A receptor, and found that many of them were able to prevent and reverse inflammation in the lungs. They also discovered that the compound called 2C-H has the molecular structure that yields the fullest anti-inflammatory effects of the compounds they tested.

2C-H is structurally very similar to the popular psychedelic drug 2C-B (which is similar to ecstasy and MDMA), but it does not itself have any psychoactive effects. As such, 2C-H might open an exciting new venue in anti-inflammatory drug design: it is a powerful anti-inflammatory agent that won't get you high.

Keystone predators could help mitigate the effects of climate change

Sea otters keep Aleutian kelp forests healthy

Ashley Marranzino

Marine Biology

University of Rhode Island

Keystone species maintain order and uphold the balance in ecosystems. Scientists studying the shifting landscapes of Aleutian kelp forests suggest that keystone species may also help ecosystems cope with climate change. 

Sea otters are renowned keystone species — by preying upon kelp-eating sea urchins, sea otters regulate urchin populations and protect the entire kelp forest ecosystem. When fur traders depleted sea otter populations in the 18th and 19th centuries, sea urchins populations grew unchecked and decimated kelp forests. Kelp forests rebounded when sea otters were reintroduced, but sea otter populations are once again declining as the growing killer whale population — recovering from pre-industrial whaling — has added sea otters to their menu. In the absence of sea otters, sea urchin populations can once again flourish, jeopardizing kelp forest health. 

The slow-growing, calcareous red algal species (Clathromorphum nereostratum) that builds the Aleutian kelp forests managed to survive destruction when sea otters were initially wiped out because its hard skeleton deterred sea urchin predators. But climate change has made the algae susceptible to over-grazing as warming water speeds up sea urchin metabolism and ocean acidification weakens the algae’s protective skeleton. 

Aleutian kelp forests are rapidly declining due to combined effects from the restructuring of food webs and environmental changes. Based on models of sea otter abundance and sea urchin grazing rates on the red algae over the past 40 years, scientists suspect that kelp forest loss was initiated by the disappearance of sea otters and then worsened by environmental changes. If sea otters recovered, however, the researchers believe they would serve as a buffer — mitigating the detrimental effects of climate change on the kelp forest environment. It is possible that other keystone species could help lessen ecosystem changes in the face of rapidly changing environmental conditions. 

Daisy Shearer

Experimental Quantum Physics

University of Surrey

You may know that there are two classes of fundamental particles — fermions and bosons — underlying what we normally think of as matter. Neutrons, protons, and electrons are all fermions; photons are an example of bosons. Fermions repel each other, and bosons don't. These quantum statistics are well-known. But physicists have now observed particles that don’t fall under either category. 

Enter the anyon: a type of quasiparticle found in two dimensional systems which is neither a fermion or a boson that may be the key to the next stage of quantum technologies.

Although anyons have been theorized for many years now, evidence of such particles has only recently been observed experimentally. Anyons are of particular interest in the field of quantum computing as they are the building blocks of the topological quantum computer, which physicists believe would make a more stable version of the technology. But to bring such a machine out of the realm of theory and into reality, we first need to be able to create and control anyons.

In their experiment published in April in the journal Science, physicists developed a tiny particle collider to detect anyons. The device was made of a microscopic semiconductor. Inside this material system, electrons were confined in two dimensions. And in the presence of a large magnetic field, anyons arose. But here’s where things got a little tricky: because of the quantum mechanical nature of such a system, researchers needed to use sophisticated techniques, such as quantum tunneling, to guide, collide and detect the anyons.

They were able to study the quantum statistics of the system and see evidence of anyons in their experiment. They saw that the particles in their device did not display fermion-like or boson-like statistics, but instead something in between. Their results provide experimental evidence for the anyon-statistics previously predicted theoretically. 

This is the first step in a long journey to creating a physical topological quantum computer. Although likely to take decades, such a technology could revolutionize our society. But first, we need to learn a lot more about anyons to uncover their potential in quantum technology and beyond. 

Noisy, high-speed recreation disturbs sensitive wildlife

Camera traps in British Columbia show that mountain biking and ATVs affect wildlife more than hiking or horseback riding

I remember the first time I flipped through the images from a camera capturing the lives of wildlife without any humans around. After countless videos of grass blowing in the wind, there it was: A leopard, stalking a diminutive antelope called a dik dik through my experimental plots in the Kenyan savanna. I’ve been hooked ever since.

These glimpses into the animal world can help us navigate the needs of both wildlife and human recreation when designing protected areas. With people increasingly turning to the outdoors to socialize, exercise, and escape the 2020 news cycle, how might this be impacting wildlife and their habitat use? In a study published recently in Conservation Science and Practice, researchers used motion-triggered camera traps to examine how wildlife respond to human activity on the trails that bisect their habitat.

The researchers captured images of wildlife and humans in South Chilcotin Mountains Provincial Park in British Columbia. By strategically placing the cameras along trails, they identified 60 wildlife species. But the most common species recorded, by far, was humans.

Camera traps embed data such as the time and date on each photo. This lets the researchers calculate the time taken for a species to return after a human has passed through. 

Focusing on the 13 most frequent species — including coyotes, bears, moose, and wolves — the researchers found that all avoided humans on trails, but appeared to have a stronger aversion to mountain bikes and motorized vehicles than to hikers and horseback riders. In fact, and somewhat surprisingly, mountain bikes appeared to exhibit the strongest avoidance response in both moose and grizzlies.

By dissecting how species react to human activity, we can better incorporate this information into land-use planning and conservation efforts. Particularly sensitive species can be protected by limiting new trails in their habitat, or by restricting the most disturbing activities during sensitive periods (such as nesting season).

Researchers have reversed Parkinson's disease in mice

Infecting astrocytes with a virus made them develop into neurons

Ellie Tanimura

Neurobiology

Parkinson’s Disease is a movement disorder caused by the progressive loss of dopamine neurons in a brain-region called the substantia nigra (SN). Current treatments only relieve symptoms temporarily because they don't reverse what causes them: the loss of neurons. 

In a study recently published in Nature, researchers demonstrated that it is possible to reverse neuronal loss by converting astrocytes (helper brain cells) into neurons. They did so by injecting an astrocyte-targeting virus into the brains of mice. The simple virus suppressed the production of a protein called PTB, which blocks astrocytes from making neuronal proteins. 

With lower levels of PTB, these infected astrocytes could produce neuronal proteins, and became increasingly similar to neurons. Eventually, the former astrocytes were structurally and functionally indistinguishable from their neuronal counterparts! Following this conversion, researchers not only saw a significant restoration of dopamine neurons in the SN, but a full correction of movement symptoms in the mice. 

As bizarre as growing back a part of your brain sounds, the discovery of this new technique has transformed the idea of reversing Parkinson’s disease from a fantasy to a potential reality. 

Golden-collared manakins change choreography when the environment shifts

These bright yellow birds have elaborate courtship dances. Can they learn to do them differently?

Sukanya Ramani

Animal Behavior and Evolutionary Biology

Prayoga Education Research Centre

Males of many bird species perform elaborate courtship displays and dances that entice females into mating. This ritual acts as a precursor for females to choose males with “superior” characteristics, such as the ability to survive harsh environmental conditions, that she can ultimately pass on to her future offspring. 

Male golden collared manakins (Manacus vitellinus) are no exception — in fact, they have one of the most acrobatic courtship rituals among birds. They hop quickly from tree to tree in a consistent pattern within their display courts, a dance culminating in the final courtship element that is performed on a specific tree (the mating sapling) to win the chance to copulate with a nearby female. In a new paper published in Animal Behavior, scientists asked whether this consistent courtship behavior changes with a sudden change in the environment. In other words, do the birds adapt their dances when the layouts of their display courts change? 

The researchers first set out to measure different attributes of a courtship display, such as its duration and the speed of the courtship elements, from each of eight males. This was the pre-test phase. During the test phase, they placed a piece of bark on the mating sapling which was big enough so that the males wouldn’t be able to move it. They again measured the time taken for the courtship elements to be performed before the males perched onto an alternative mating sapling. They repeated the experiment at two different times each day for four consecutive days. Finally, in the post test phase, they removed the bark to see if the males came back to the original mating sapling or they continued using the alternative mating sapling. 

They found that the male manakins repeated a courtship element of the dance to buy time into choosing an alternative mating sapling, thereby showing behavioral flexibility. Some males went back to the original mating sapling in the post-test phase, and some alternated between the original and alternate saplings. Further research would help in showing why some males prefer going back to the original sapling while some prefer both, and what this meant for their mating success with their female audiences.

What will dexamethasone do to President Trump?

The cognitive and immunological effects of steroids face a test at a critical point in Trump's illness

Max G. Levy

Science and Health Journalism and Chemical Engineering

The president has had a life-threatening, infectious disease for over a week, and he and his doctors haven’t been very transparent about the timeline and course of his affliction. In lieu of detailed disclosures, reporters have to piece together his condition based on the treatments he’s been receiving. 

Trump was started off on an experimental therapeutic — an antibody cocktail — and then advanced to another — remdesivir. The other biomolecules coursing through Donald Trump's system (and this week's headlines) are corticosteroids, called dexamethasone.

You may have heard of cytokine storms, where the body's immune response to severe COVID-19 bombards healthy cells, making the illness worse. Trump has been given dexamethasone, an immuno-supressant that doctors prescribe to temper that effect. Unlike the other experimental treatments, dexamethasone is common and somewhat easy to access. However, it is rarely administered to a patient with a case as (self-)reportedly mild as Donald Trump’s.  In an interview with New York Magazine's Intelligencer, the co-author of a recent study testing dexamethasone elaborates:

James D. Walsh: Is there any reason to administer steroids to a patient who isn’t a severe case?
Bryan McVerry: I don’t think so. I don’t think that steroids are a preventive treatment in terms of progression of COVID-19 and if you look at the data from the recovery trial, which was the study published out of the U.K. in September, that was sort of the first steroid paper, a dexamethasone study, in patients with less severe disease, there was no clinical benefit, and potentially a trend towards worse clinical outcomes in patients who got it with milder disease. That didn’t reach statistical significance, but the odds ratio was headed in the wrong direction with the patients that they had recruited. I’m not sure you can draw any real conclusions from that except to say but there was no benefit — at least no trend towards benefit — on the population.

That lack of evidence is concerning as Trump heads into a critical point in the course of his illness. COVID-19 is known for being a bit of a roller coaster, with intermittent fevers, mysterious symptoms, and rapid declines. Abraar Karan, a physician with experience treating patients with COVID-19, told Monique Brouillette at Scientific American that some people have turned corners and left the hospital, only to  “come back feeling much sicker, with even worse oxygen levels and possibly other harm to the body’s organs.”

It is theoretically possible that the early steroid treatment may ward off a dangerous auto-inflammatory reaction. But beyond the inherent risks of immuno-supression, corticosteroids may also cause behavioral side effects in the President. Trump's cognitive and behavioral state has been a point of concern for years. Potent steroids such as dexamethasone are known to increase appetite, decrease restful sleep, and bring about heightened "maniacal" energy states.

As the nation enters the weekend, Speaker of the House Nancy Pelosi is rolling out a 25th amendment commission, Trump is boasting a miraculous recovery with a Fox News doctor, and the rest of us continue to wait and learn how biology will run its course. For better or worse, the side effects our president experiences may prove to have historical consequences. To my knowledge, “roid rage” has never been a factor in nuclear geopolitics. 

Female Barbary ground squirrels control their territory while males fly solo

New research uncovers the social lives of this African squirrel species

Jazmin Murphy

Ecology and Science Journalism

Since the 1980s, researchers have generally agreed that squirrels’ social structures are determined primarily by the females’ tendency to occupy a given territory. In a paper recently published in the Journal of Mammalogy, scientists took a closer look at the lives of Barbary ground squirrels to find out if they also exhibited this behavior. 

The researchers expected that, if the Barbary squirrels follow the behavioral patterns shown in other species of ground-dwelling squirrels in Africa, then the females would be “philopatric” (the ones who determine where the group lives) and males would be the dispersing sex, who must leave their family territories once they become adults to live alone or in all-male groups. 

Although the Barbary ground squirrel is native to Morocco and parts of Algeria, this study focused on an invasive population in the Canary Islands. The squirrels were live-trapped and marked for later identification, then released and observed through binoculars from morning to night. The relative stability of female and male groups was also measured by closely watching which individuals shared burrows each night, among other techniques that measured home range size and genetic relatedness. 

After spending about three breeding seasons with the squirrels, the research team had their answers. They concluded that the Barbary ground squirrels' social organization was just as they predicted. Interestingly, though, adult male and female squirrels share the same spaces during the day, but sleep separately at night.

In general, these squirrels were found to be far more gregarious (social) than initially thought, with surprising communal behavior from even lactating and nursing females. As the only living species in the genus Atlantoxerus — and an invasive one at that — the Barbary squirrel can now be better managed in areas where they are considered invasive and may endanger other wildlife. 

Working-class ants take the reins when the Indian jumping ant queen dies

This transition fundamentally changes their brains

Sree Rama Chaitanya

Molecular Biology

Instituto de Medicina Molecular

Social insect colonies, like those of ants and bees, are divided into castes based on distinct tasks such as reproduction, foraging, defense, and nest maintenance. Individuals belonging to different social castes show distinct molecular, physical, and behavior characters. These are usually established at the larval stage.    

But Indian jumping ants (Harpegnathos saltator) are unique. Unlike other ants, Indian jumping ants can switch castes when the reproductive queen dies. In these cases, about 70 percent of non-reproductive workers fight for dominance. Some successfully become reproductive queen-like ants, called gamergates, to ensure the continuation of the colony. This worker-gamergate transition incurs dramatic brain structural remodeling.

New research published in Science Advances has looked more closely at how the brains of gamergates compare to worker Indian jumping ants. By measuring gene expression changes in the brains of these ants at single-cell resolution, scientists discovered that the number of ensheathing glial cells — supportive neuronal cells essential to brain health and homeostasis — increases by 40 percent during the worker-gamergate transition. 

Not only that, when the scientists injured the brains of young Indian jumping ants (from stable or non-transitioning colonies) using needle punctures or antenna ablation, these same cells activated and expressed injury-responsive genes at a higher rate to cope with brain damage.

In ant colonies, reproductive queens live about ten times longer than workers, and gamergates about five times longer than workers. This study found that even older gamergates (~120 days in age) contained significantly more ensheathing glial cells than workers of the same age. (To put this into perspective, 120 days of Indian jumping ant life would translate to about 57 years on a human-age scale.) Older gamergates also expressed higher levels of injury-responsive genes after brain injury. Thus, scientists suggest that ensheathing glial cells protect gamergates from brain damage even in old age.

Yet, Indian jumping ants of all castes are genetically the same, so what makes them inherently distinct? The answer could be epigenetics: the inheritance of biological variation independent of the genetic sequence. Ants — and other social insects — provide a great example to study epigenetics and to explore the relative influence of nature and nurture on their lives.

Some people's immune systems control HIV infections without drugs

"Elite controllers" keep the deadly virus in check, and hide its DNA in a quiet section of the genome.

Hazel Walker

Immunology and Cell Biology

University of Cambridge

In what could be a world first, it appears that an HIV-1 patient may have completely eradicated their body of functional copies of the virus without requiring medical treatment. 

Researchers were studying a rare cohort of people known as "elite controllers," in which HIV-1 replication is suppressed by the immune system for many years. In order to better understand how this desirable control of the virus happens, researchers used advanced sequencing techniques to investigate the number of functional and non-functional copies of the virus and their location in the infected individual’s genomes. 

When compared with patients receiving the standard treatment of antiretroviral therapy, elite controllers had fewer viable copies of the virus in their genome. Furthermore, the viral DNA was stored in naturally inactive parts of the genome, rendering the virus mostly inert. 

The researchers also made another exciting finding: a patient known as "EC2" who had previously tested positive for HIV-1 appeared to have no functional copies of the virus despite analysis of over 1.5 billion of their cells. Provided viable virions are not lurking elsewhere, this could be the first instance of a natural cure.

Until now, cures came in the form of gruelling bone marrow transplants in the case of the "Berlin patient" and the "London patient" who simultaneously dealt with cancers. The Berlin patient, Timothy Ray Brown, was free from HIV for 13 years before he died in September of related leukemia.

This step forward in the understanding of elite controllers could help researchers developing therapies for the treatment of HIV-1, also highlighting that in some rare cases the immune system may be able to deal with the viral infection on its own.

Calculating the entropy of black holes helps solve fundamental questions about our universe

Physicists have shown that the Cardy limit can be used to calculate entropy

Marina David

Theoretical Physics

University of Michigan

Black holes are mysterious objects in space that physicists use as a tool to learn about gravity. On the experimental side, physicists use data from large telescopes to further understand how our universe works. On the theoretical side, the mathematics behind how black holes work have become our main guide towards a more fundamental interpretation of our universe.

Currently, physicists, including myself, are trying to explain the properties of black holes. This turns out to be quite a challenge! One way to tackle this is to use a principle that relates the gravitational theory of black holes to another physical theory called quantum field theory. This principle has become a dictionary of sorts, allowing us to translate ideas about black holes, such as entropy and temperature, between gravitational theory and quantum field theory. 

Recently, a group of scientists has predicted the entropy of black holes on the quantum side using a unique method, called the Cardy limit. The Cardy limit is a limit on the angular momentum of the black hole and corresponds to highly spinning black holes. No one has yet confirmed this method on the gravity side.

My collaborators and I have taken on this challenge to verify that the Cardy limit is valid on the gravity side and reproduces the expected entropy. It turns out this method works best when we zoom towards the event horizon of a black hole — a region of spacetime that acts a bit strange. If we get too close to the event horizon, nothing — not even light — can escape and we are destined to fall into the black hole! Yet, this region of spacetime along with the Cardy limit lead us to the same entropy and other properties of the black hole that were computed on the quantum side.

Our paper is one of many recent results that aim to solve the riddles behind black holes. It is a step towards getting closer to a full understanding our of universe.

Could we kill antibiotic-resistant bacteria by impaling them on nanowires?

Antibiotic-resistant bacteria have softer cell walls that leave them vulnerable

Sruthi Sanjeev Balakrishnan

Cell Biology

National Centre for Biological Sciences

In light of rising antimicrobial resistance, scientists have turned to metallic compounds to fight bacterial infections. By sculpting metallic compounds of silver, copper, and zinc into tiny spikes called nanowires, one can essentially stab the bacteria and and prevent them from growing. The design of nanowires was originally inspired by nature: cicadas and dragonflies have similar structures on their wings, helping them curb the spread of harmful bacteria.

Not all bacteria easily fall prey to nanowires, though. A recent study has found that, among Gram negative bacteria, antibiotic resistant and susceptible strains have different mechanical properties. The researchers used atomic force microscopy to determine the stiffness of a host of different types of bacteria. Across the board, they saw that antibiotic-susceptible bacteria were “tougher” and stiffer, able to withstand more poking and prodding. Antibiotic-resistant bacteria, on the other hand, were “softer" and thus more likely to be impaled by nanowires. But what is the reason for this difference?

Beta-lactams, the most widely used class of antibiotics, kill bacteria by preventing them from adding peptidoglycan, a key component for mechanical strength, to their cell walls. When the scientists looked at how strains resistant or susceptible to antibiotics made their cell walls, they found that the softer resistant strains make and use less peptidoglycan. This likely stems from generations of exposure to sub-lethal concentrations of beta-lactams, making the cell walls of antibiotic-resistant strains progressively thinner and softer.

Based on theoretical analysis, the researchers then crafted some nickel-cobalt-based nanowires of different tip diameters. They found that a tip diameter of 5 nanometers — about 20,000 times thinner than a human hair — penetrated the soft antibiotic-resistant bacteria best, but had little effect on the tough, antibiotic-susceptible bacteria. This is a promising development toward a potential solution to the pesky problem of antimicrobial resistance.

A glowing blue compound could help us understand the vibrant autumn leaves

Scientists are tracing what happens in plants when chlorophyll breaks down

Josseline Ramos-Figueroa

Chemistry

University of Saskatchewan

It’s this time of the year when those of us in northern temperate zones are spectators of a fascinating natural phenomenon – the appearance of autumn leaf colors.

The leaves start to change colors as they age, or senesce. During this period a cluster of enzymes in the leaves start chewing up their green pigment, called chlorophyll. As the leaves become less green, their red, yellow, and orange pigments (known as anthocyanins and carotenes) begin to shine. However, exactly how chlorophyll breakdown works is still only partially understood.

While autumn leaves are a great example of chlorophyll breakdown, evergreen plants (those that remain green all year long), vegetables, and fruits also experience chlorophyll decay. However, this happens only under special conditions such when fruit ripen or when evergreen plants are deprived of nutrients and water. 

Banana skin is one of the few fruits where chlorophyll degradation can be mapped under ultraviolet (UV) light. As bananas ripen, their skins lose their green color – a sign of chlorophyll breakdown – and form new pigments that fluoresce blue under the UV light. Scientists know that this new pigment, known as hypermodified fluorescent chlorophyll catabolite (hmFCC), is produced very briefly in most plants. Banana skins and grapevine leaves are known to produce hmFCCs for a longer period.

Recently scientists at Instituto de la Grasa, Spain analyzed devil’s ivy, an evergreen plant, in their quest to find signs of this fluorescent compound. They activated the aging process by starving the plant, and voila! Exposure to UV light produced the blue, fluorescent pigment hmFCC. The team also observed two other newly identified compounds that will provide more insights into the evergreen chlorophyll breakdown puzzle.

Although the actual benefit of producing this blue, fluorescent compound is still a mystery, scientists think that it could provide protection against radiation or function in communication between animals and plants.

Eating more fiber could help you handle stress better

Some dietary fibers are converted to fatty acids, which are linked to cortisol levels in your blood

Simon Spichak

Neuroscience

University College, Cork

The trillions of microbes in our guts connect the food we eat to the rest of our body, playing crucial roles in stress and health. Some dietary fibers in our food are digested by these microbes to generate signaling molecules.

Millions of people worldwide struggle from stress and associated burdens. A group of researchers from the Translational Research Center in Gastrointestinal Disorders in Belgium tested whether dietary fiber could modify our stress responses. These fibers are converted to signaling molecules called short-chain fatty acids (SCFAs), that may attenuate stress.

For one week, 66 healthy male subjects were given a pill containing the amount of fatty acids found in either 10 or 20 grams of fiber, or a placebo. Before they received their treatment or placebo, participants were stressed to get a baseline measurement.  To stress out these subjects, researchers used a common experimental paradigm that combined social and physical aspects of stress. Participants kept their hand submerged in cold water for two minutes, while being closely watched. They were told that their facial expressions were monitored. Afterwards, the researchers took blood samples to look at the stress hormone cortisol, as well as SCFAs at different points after the stress.

They discovered that the greater the dose of fatty acids a person received, the smaller the cortisol-stress response (meaning, that person had less cortisol in their blood in response to the stressful event), and the more SCFAs in their blood.

This study shows that eating more fiber could attenuate the acute stress response. Future studies on this topic could establish a dietary intervention that doctors could prescribe to lower high blood pressure associated with stress.

Lactose tolerance spread through Europe faster than previously thought

A new study traces the prevalence of a lactose-tolerance mutation through genetic analysis of Bronze Age bones

Rita Ponce

Evolutionary Biology

Polytechnic Institute of Setúbal

Most mammals stop being able to digest lactose — the main sugar in milk — past infancy. But an estimated 35 percent of the world's population retains lactose tolerance, or lactase persistence, past childhood. During infancy all mammals produce lactase, an enzyme that breaks lactose down into simpler sugars and allows its digestion, but around weaning time they stop producing it.

This lactase persistence is due to genetic mutations that keep bodies producing lactase well past childhood. There are several mutations known to have arisen independently in human populations the last 10,000 years. Today the trait is unevenly distributed in the world and can be more or less frequent in the populations depending on their ancestry. Previous studies have found that the evolution of lactase tolerance shows signs of positive selection — indicating it must have conferred an advantage to its bearers. 

A new study published in Current Biology using genetic analyses and bones from Bronze Age archeological sites dated from 5980 to 3200 years ago brings new information about the evolution of this trait.

Northern Europeans show a high frequency of a specific mutation, called rs4988235-A, that confers lactase tolerance. An international team led by Joachim Burger from Johannes Gutenberg University in Germany, studied gene variants from DNA extracted from bones of warriors found in the Tollense battlefield archeological site in Germany dated to 3200 years ago. The analysis revealed they belonged to Central/Northern European individuals. They also analyzed bones from an archeological site in Serbia dated 4100 to 3700 years before present, and from sites from the Eastern Europe Pontic-Caspian Steppe dating back 5980 to 3980 years.

Lactose tolerance in the Central/Northern European samples was low (7.1 percent), contrasting with present-day levels of 90 percent lactose tolerance in the same region, and it was also low in the South Eastern samples (4.6 percent). The trait was absent in the samples from the 37 individuals studied from the Eastern Europe steppes. This does not support an existing hypothesis that proposes that this mutation, rs4988235-A, originated at the Eastern European steppes. Although the sample sizes were small, the results indicate an big increase of lactose tolerance frequency in just the past 120 generations. 

What is the COVID-19 polyclonal antibody treatment that President Trump took?

It's a mix of different antibodies that target the virus slightly differently for a combined effect

Dan Samorodnitsky

Senior Editor

You may have heard that President Donald Trump is sick with COVID-19. He immediately received an experimental "polyclonal antibody" cocktail made by the large biopharma company Regeneron. This treatment has not yet been evaluated by the FDA. 

When our immune systems begin generating antibodies to a foreign object, they don't generate just one kind of antibody. They generate many, many different kinds, that have different structures and also target different individual pieces of the thing it's attacking (through a genetic mechanism unique to the immune system, immune cells can shuffle the genes that code for a "variable" region of an antibody like a deck of cards, generating antibodies of variable shape and targeting). So, in the case of SARS-CoV-2, our immune systems might generate one antibody that attacks the spike protein, while another antibody that attacks a part of the viral envelope. Or, they might generate multiple antibodies that all attack different parts of the spike protein. 

To create this antibody cocktail, Regeneron created "humanized" mice, which had immune systems more closely related to the human version than their natural mouse immune system. Sifting through antibodies from these mice after infection with SARS-CoV-2 and antibodies from humans who'd recovered from infection, they isolated two antibodies that targeted two different parts of the virus. 

It's called "polyclonal" because it's a mix of genetically distinct antibodies (with different targets). A collection of genetically identical antibodies that all attacked the same thing would be called "monoclonal." Whether this truly "polyclonal" or "two monoclonal antibodies mixed together" is a somewhat academic debate, in my mind.

The idea is that the antibodies shouldn't block each other out (imagine two people reaching for the same doorknob) and will hopefully have a combinatorial effect. The cocktail is still in trials but has some positive data

Scientists use 16 genes to distinguish between two types of lethal pancreatic cancer

This new subtyping method will head to clinical trials

Emily LaPlante

Computational Genomics

Baylor College of Medicine

Until recently people believed pancreatic ductal adenocarcinoma (PDAC), the most common and lethal pancreatic cancer, to be a single cancer type. In the last few years, subtypes of PDAC have been discovered, providing potential for treating each subtype as a different disease. This is important in PDAC as most patients don’t respond to current treatments.

Unfortunately, the PDAC subtyping methods were not useful in the clinic as they have been developed in a group dependent manner, where subtype is determined based on groups of samples. The addition or removal of a single sample to the overall group could change any other sample’s subtype.

One study set about to change that and develop a method to subtype a single patient. The researchers first determined they would try to create a single sample method to break patients into classical or basal-like subtypes, because classical patients respond better to therapy. Therefore, if doctors could tell if a patient was classical or basal-like, they could choose different treatment option.

Researchers created a system of gene pairs, where one first gene is present in classical patients, and the second gene is present in basal-like patients. Think of these pairs as light switches. Depending on which way the light switch points, a sample can be classified as one subtype or the other. With just 16 genes, they method is inexpensive and easily applied in a clinical setting.

Overall, researchers managed to create a clinically actionable subtyping system which has recently been adopted into the PanCAN Know Your Tumor Program and the Precision Promise clinical trial. The hope is that trials will be able to identify which patients will respond to their therapies as well as to create subtype specific therapies, similar to breast cancer where treatment is specialized by subtype.

100 million year old giant sperm discovered in a Cretaceous crustacean

New study uncovers ancient seed shrimp, and their ancient 'seed'

Amanda Rossillo

Evolutionary Anthropology

Duke University

Ostracods are tiny crustaceans that have existed for almost 500 million years. Also known as seed shrimp, these organisms are covered by a hard shell that tends to fossilize easily, allowing scientists to piece together a detailed picture of their exceptionally long history.

While hard parts of animals like bones and shells generally preserve well, softer components like organs and fluids are much more rare, making it difficult to learn about aspects of life that we can’t see. But a team of scientists recently uncovered a cache of ancient ostracods with many of these soft physical elements intact.

These ostracods were found in a village in Myanmar, nestled within a small chunk of amber estimated to be 100 million years old. Of the 39 ostracods present in the amber, 31 belong to a new species, which the team named Myanmarcypris hui.

To peer inside these tiny organisms without damaging them, the team left the ostracods inside the amber and X-rayed them at a high resolution. When they analyzed the images of an adult female M. hui, they found something shocking: coiled threads of sperm.

The previous record holder for oldest ostracod sperm was a 17 million year old individual from Australia, while the oldest sperm ever discovered was from a 50 million year old worm. But this 100 million year old sperm surpasses both records.

And this sperm isn’t just old — it's giant. The team found that when uncoiled, it would have been almost half as long as the animal itself. These megasperm would have had an advantage as they raced through the long coils to the female’s eggs, a strategy that is also found in fruit flies.

Finding such ancient, giant sperm shows just how successful this reproductive strategy has been over the last 100 million years. It also provides a snapshot of a singular moment deep in the past — one that occurred in a world that looked very different from our own, and is still occurring among ostracods today.

The immune systems of males and females respond to COVID-19 differently

Male patients had lower T cell responses, whereas female patients showed higher cytokines

Shelby Bradford

Immunology

West Virginia University

In a paper recently accepted in Nature, a team spanning several departments at Yale University and from Howard Hughes Medical Institute investigated differences in immune responses between men and women diagnosed with COVID-19. 

Different immune responses between males and females have been documented previously, but whether and how these immunological differences influence people's responses to COVID-19 have yet to be well-documented. Such distinctions may offer unique opportunities to better predict and monitor patient outcome and tailor therapeutic intervention. 

This team of researchers collected blood, nasal swab samples, saliva, urine, and stool from people recently admitted to the hospital who had tested positive for COVID-19. They determined the types and population sizes of specific immune cells, such as B cells, T cells, and monocytes in the samples. They also investigated the amount of molecules responsible for inflammation and cell recruitment, called cytokines and chemokines, respectively, detected in patient serum. These were compared between male and female patients as well as male and female health care workers, who served as non-infected controls. Finally, they evaluated how these factors were correlated the severity of each patient's COVID-19 symptoms.

They concluded that male patients developed lower T cell responses, specifically in a subset of T cell responsible for killing infected cells. Disease severity was greater over the course of infection in male patients who exhibited lower responses of this cell type. In female patients, disease severity was more determined by elevated inflammatory cytokines and chemokines. 

Furthermore, older males had worse disease outcomes, correlating with the less robust T cell responses in this population, while this trend did not hold true for females. 

This study provides important preliminary understandings of the difference of responses between males and females during COVID-19 infection. 

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