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Monkeys and apes in Africa and Asia are also susceptible to SARS-CoV-2

New research compared the configurations of the ACE2 protein in 29 non-human primates

Brittany Kenyon-Flatt

Biological Anthropology

North Carolina State University

While scientists continue to study the effect of SARS-CoV-2 on humans, less work has focused on how susceptible other primates are to the virus. 

New research explored the likelihood that our primate relatives are susceptible to SARS-CoV-2 infection. The SARS-CoV-2 virus binds to a cellular receptor protein, the ACE2 protein. ACE2 resides on the surface of cells throughout the human body. When SARS-CoV-2 binds to ACE2, it overtakes the cell’s protein mechanisms, makes copies of itself, and the infection begins. 

This new research studied the characteristics of the ACE2 protein in 29 primate species, as well as four non-primate species for comparison. The researchers found that catarrhines, a group of monkeys and apes that live in Africa and Asia, are likely to be susceptible to a SARS-CoV-2 infection because their ACE2 proteins are similar to ours. This is supported by findings that biomedical populations of catarrhines, specifically rhesus monkeys, long-tailed macaques, and vervet monkeys have become infected with SARS-CoV-2 and expressed COVID-19-like symptoms

The platyrrhines (monkeys that live in the Americas) and  strepsirrhines (lemurs, lorises, and tarsiers) are generally less susceptible to contracting the disease. 

These results are important for our understanding of the novel coronavirus and for primate conservation during the COVID-19 pandemic. The endangered status of many non-human primates means that contracting the virus could be disastrous. For example, there are about 1000 mountain gorillas alive today and should that population become infected with SARS-CoV-2, the effect would be devastating. 

A protein variant inherited from Neanderthals protects people from severe COVID-19

The protein in question activates enzymes in our cells that degrade RNA

Anna Wernick

Neuroscience

University College London

A phenomenon that has underpinned the COVID-19 pandemic is the range in severity of symptoms. While millions have tragically lost their lives, many people are asymptomatic. Although COVID-19 symptoms can vary by age, gender and ethnicity, these factors alone do not explain this disparity.

Scientists have been investigating this in the hope of identifying an effective way to treat severe COVID-19. Using different methods of investigation, two pre-prints have reported that a protein called OAS1 influences COVID-19 outcomes. The studies, which have not yet undergone peer review, describe a protective variant in OAS1 that is inherited from Neanderthals.

OAS1 activates enzymes in our cells that are responsible for RNA degradation. SARS-CoV-2, the virus responsible for COVID-19, is an RNA virus, and therefore this protein could potentially serve as part of the immune response against it. The same variant was found to be protective against SARS-CoV, the virus responsible for the 2002-2004 SARS outbreak.

Different people have different forms of proteins due to genetic variation. The Neanderthal variant of OAS1 has greater anti-viral activity than other isoforms. The variant was introduced into the European population via gene flow between Neanderthals and the ancestors of present-day humans. Neanderthal ancestry makes up 1.5-2.1% DNA in people outside of Africa, and many of these genes have been selected for over time.

This is not the first instance of Neanderthal variants influencing COVID-19 outcomes. A study published in Nature in September 2020 detailed a stretch of DNA on chromosome 3, identical to the Neanderthal genome, that tripled the risk of developing severe COVID-19. 

Scientists create an 'atlas' of fruit fly brain development

This map will shed light on how other animals' brains develop, too

Joyce Yu

Cell Biology and Developmental Biology

The Francis Crick Institute

Why do scientists study the fruit fly brain? Although the fly brain is much simpler compared to a human brain, it is still capable of performing complex tasks, like navigation, memory, and color detection. 

A brain is made up of different types of neurons, which have to be connected correctly to carry out tasks. These physical connections in the fruit fly brain were recently mapped in 3D. Scientists used machine learning algorithms to analyze ultrathin brain slices imaged under an electron microscope, and identified over 25,000 neurons and 20 million connections.

Now, a recent Nature study has added another dimension to this brain map. Scientists identified which genes are turned on or off in specific neurons over the course of fly development, from early pupae to adult, during which critical neuronal connections are made. 

One interesting discovery from this new ‘developmental atlas’ is that certain neurons die before the fly becomes an adult, possibly because they are only needed for establishing connections of other neurons. Moreover, a new type of cell was identified which is similar to a type of neuron found in humans that is essential for brain development.

Having a clearer picture of how gene activities allow neurons to connect with one another in the fly brain will also benefit researchers working on the vertebrate brain. Importantly, the resources generated from this study pave the way towards a better understanding of developmental disorders that originate from improper neuronal connections.

The Moderna mRNA vaccine works against newly emerged COVID-19 mutants

Mutants like B.1.1.7 and B.1.351 carrying changes in the virus spike protein appear to help the virus spread, but not to evade currently available vaccines

Dan Samorodnitsky

Senior Editor

COVID-19 variants have been emerging all over the world since the pandemic started. Some mutants arising in the last few months are spreading faster than the SARS-CoV-2 virus seemed capable of previously. Understandably, this has caused concern that the vaccines from Pfizer, Moderna, AstraZeneca, and other biopharma companies that will hopefully bring the pandemic under control won't be as effective. 

The B.1.1.7 variant, which was detected in England in September 2020, carries a handful of different mutations, eight of which appear in the spike protein that allows the virus to attach to cells. One mutation, called N501Y, attracts a lot of attention because it sits at the interface between the spike protein and the cell about to be infected. 

The amino acid asparagine

The amino acid asparagine

On top of that, the N501Y mutation itself — where the amino acid asparagine (in biochemical nomenclature simply called "N") at position 501 changed to tyrosine (called "Y") — is a rather significant change in terms of chemistry and size, because tyrosine has a bulky ring of carbons that asparagine lacks. Large rings like tyrosine's can change how areas of the protein around it are shaped. This mutation appears in other SARS-CoV-2 lineages as well. Another mutation in the spike protein, E484K present in the lineage B.1.351 that was first detected in South Africa in October 2020, is not as treatable with monoclonal antibodies. 

The amino acid tyrosine

The amino acid tyrosine

These changes in the spike protein appear to strengthen the link between the virus and a cell. Since both the already-being-distributed Pfizer and Moderna vaccines target the spike protein, do these mutations alter their efficacy?  

Scientists at Moderna and the NIH re-visited serum drawn from either non-human primates vaccinated with Moderna's mRNA-1273 vaccine or humans from vaccine's phase 1 clinical trial. They tested whether that serum could still effectively neutralize different SARS-CoV-2 mutants in comparison to earlier lineages, using non-infectious engineered viruses that had the genetic characteristics of the SARS-CoV-2 virus. They published their results in a preprint on bioRxiv this morning.

The B.1.1.7 virus had little-to-no ability to evade the immune response from vaccinated humans or non-human primates. However, the B.1.351 virus was more difficult to neutralize, requiring about 2 to 10 times more serum than the "original" SARS-CoV-2 virus. 

However, all viruses and mutations tested were neutralized in these experiments — none of them escaped, it just took more of the immune response in the serum to do it. This mirrors the success of the Pfizer vaccine, which uses similar mRNA technology to Moderna's and is effective against the B.1.1.7 mutant.

Cellar spiders use chemical cues to identify each other's webs

This ability comes in handy for stealing a rival's hunting spot

Margaret Swift

Ecology

Duke University

The last time you walked through a sticky spider web, you might have brushed it off in annoyance. Building these webs, though, is no small feat. It requires precious time and energy that could be spent eating or mating, so spiders are quite picky about where they string their silk.

If you’re a spider, better real estate means better hunting; it’s all about location, location, location. Stealing someone else’s web in a prime spot might pay off, but only if you’re confident you’re much bigger than your opponent. Web-building spiders, however, have notoriously poor eyesight. So, how do they size up their rivals?

Like human noses, spiders’ hairy legs can pick up chemical cues from their environment. Researchers from Miami University of Ohio found that one species of cellar spider, Pholcus manueli, can tell a web builder’s size by smelling chemicals left on the silk. And, this sizing-up ability might give P. manueli an edge on a closely-related competitor, the long-bodied cellar spider (Pholcus phalangioides). While both are considered invasive, P. manueli is challenging its longbodied counterpart's century-long dominance in the midwestern United States.

To determine how the species differ in their chemical sensitivity, the team first had a set of “builder” spiders from both species construct webs, then traded the builder out for another, “focal” spider. They measured each spider’s size and recorded how quickly the focal spider invaded the builder’s web. To ensure the spiders’ reactions were due to chemicals signals and not simply web design or structure, researchers repeated their experiment, adding an ethanol “web washing” control step before introducing focal spiders.

They found that P. phalangioides invaded webs faster than P. manueli no matter the size of the builder. P. manueli were flexible in their strategy, though, invading webs made by larger spiders more cautiously. Because this behavior disappeared after the web wash, the researchers concluded that P. manueli was definitely exploiting chemical clues.

What does this mean for upstart P. manueli? Despite P. phalangioides’ more aggressive approach, by picking their battles carefully, P. manueli just might win the war.

Bacillus bacteria can keep fruits and vegetables free of Listeria

Some bacteria make us sick, and others keep our food safe to eat

Madeline Barron

Microbiology

University of Michigan

While eating fruits and veggies is a healthy thing to do, if they’re crawling with the bacterium Listeria monocytogenes (Lm), they may do more harm than good.

Lm contamination of fresh produce can stem from soil, water, and animals, among other sources (in the US, Listeria outbreaks have been traced to cantaloupe melons, Enoki mushrooms, and bean sprouts). The effects of Lm infection, or “listeriosis”, range diarrhea and fever to brain and bloodstream infections.

While proper handling or avoidance of high-risk foods is one way to prevent listeriosis, another is to use biological control tactics to limit Lm growth on food in the first place. 

Biological control involves reducing populations of one organism, often insect pests or invasive weeds, by introducing a natural predator. To this end, a recent study in Applied and Environmental Microbiology sought to identify bacteria capable of limiting Lm colonization and persistence on produce, specifically cantaloupe melons. 

The scientists isolated bacteria from various types of produce, ranging from alfalfa to grapes. They then tested the ability of each of 8,736 isolates to inhibit Lm growth in the laboratory. Of seven highly effective isolates, one called Bacillus amyloliquefaciens ALB65 (BaA) was the best inhibitor.

BaA was able to grow and persist on cantaloupe melon rinds and, importantly, did not inhibit plant growth or fruit production — in fact, cantaloupes colonized by BaA grew twice as fast as cantaloupes without it. Excitingly, BaA significantly reduced Lm growth on whole cantaloupes in the greenhouse, and completely inhibited growth at post-harvest refrigerator conditions (this is key, as Lm can survive cold temperatures, making it difficult to control). 

While the researchers did not determine exactly how BaA inhibits Lm, they did identify genes in BaA’s genome that likely encode compounds known to limit growth of other bacterial species; these compounds may be responsible for the observed effects on Lm. This study points to a novel, effective biological control agent for reducing Lm growth on cantaloupes, with potential applications for other produce types as well.

Fatigue is an understudied consequence of hearing loss

Over 30 percent of people over age 65 experience hearing loss

Adriel John Orena

Language acquisition

University of British Columbia

It is easy to take our senses, like hearing, for granted – but over one-third of people over 65 experience some degree of hearing loss, either due to degenerative effects of aging or accumulative exposure to loud noises.

When we think about the consequences of hearing loss, we might immediately think about how it would make communication with family and friends more difficult, or how we would miss the sounds of music in songs and films. But the detrimental effects of hearing loss go beyond reduced access to sounds.  

In a review published in Ear and Hearing, researchers investigated an understudied consequence of hearing loss: fatigue. Certainly, one could imagine that the constant effort of trying to understand what others are saying may eventually take a toll on our brains.

After scouring through studies on hearing loss and fatigue, researchers found overwhelming evidence that hearing loss does, in fact, result in increased fatigue. There is also some evidence that obtaining a hearing device – such as a hearing aid or a cochlear implant – may relieve some of this fatigue, but researchers are quick to point out that more research on this topic is needed.

One limitation of current studies is that what we know today about this topic is based on subjective measures, such as questionnaires, and that each person might experience or describe fatigue differently. Future research could integrate more objective measures, such as behavioral or physiological measures, to provide stronger evidence about the link between hearing loss and fatigue. Despite these limitations, the current review is important for addressing the needs of people with hearing loss and for promoting continued research on this topic.

Aerosols from urban emissions can, literally, make it rain

Atmospheric model of a Houston storm shows emissions increase rainfall intensity and occurrence

Krystal Vasquez

Atmospheric Chemistry

California Institute of Technology

Though humanity hasn’t discovered how to control the weather, we certainly can influence it. Land use changes and air pollutants have both been shown to influence weather and climate. In cities, the urban heat island effect can alter both where and how much precipitation falls. Likewise, aerosols emitted from power plants, oil refineries, and other sources cause atmospheric changes that result in more intense storms. 

Many studies focus on the effects of urban land cover and air pollution individually, but fewer focus on how these two processes work together. To what extent do they affect weather events like rain? This question is especially important Houston, Texas, which is not only one of the largest cities in the US by area, but also produces high amounts of aerosol particles due to its many oil refineries. 

A new study published in Atmospheric Chemistry and Physics sought to understand how Houston’s landscape and aerosol emissions impact its rainstorms. To do this, researchers ran four simulations of a storm that occurred in the region in June 2013. Each simulation toggled aerosol pollution on or off, or replaced the Houston urban area with croplands and pastures similar to those that are present outside the city. 

Using these models, researchers determined that Houston’s aerosol pollution caused storms to produce 30 percent more peak rainfall and made intense rain eventsq five times more likely. Furthermore, when this aerosol pollution occurred within the city of Houston, the two processes amplified each other, creating even more rainfall and further increasing the probability of experiencing higher intensity storms. 

While this study looked at Houston specifically, its results have much broader impacts. Studies like this give us a better idea on how storms will be impacted as cities continue to expand to accommodate our growing urban population. In addition, this research helps weather forecasters more accurately predict when hazardous weather will occur. This can, in turn, save lives and limit the destruction these natural events often cause. 

Octopuses sometimes punch fish out of spite

The mysterious behavior appears related to collaborative hunting and hints at complex emotions

Simon Spichak

Neuroscience

University College, Cork

Octopuses are fascinating models for understanding the evolution of complex behaviors. Two-thirds of their brain cells are spread out inside their arms, meaning that each one can operate independently. The cephalopods change their texture and shape at will — an effective trick for hunting prey or hiding from predators. Octopus also cooperate with other predatory fish when they hunt. New research reveals that the inner-workings of this interspecies collaboration is not without surprises. 

Many different species exhibit collaborative behavior in nature. Groupers and reef fish often hunt with octopuses to cover more gorund. They understand gestures from other fish which helps the group capture prey. Now for the first time, researchers captured footage of octopuses punching fish. Sometimes, seemingly, for no apparent reason.

Researchers studying cooperative hunting events filmed these interactions off the coast of Egypt. While observing different Octopus cyanea collaboratively hunting, they noticed these punches. Specifically, the octopus would aim at a fish and strike them with an explosive motion. These punches targeted different species of fish, suggesting this behavior serves an important function. 

When an octopus punches a fish, it exerts a small amount of energy while hindering an individual fish's hunt. The fish then might lose their position within the hunt, may lose out on a prey opportunity or might even be kicked out of the group. The octopus clearly has the better end of this bargain, allowing it to control which individuals it hunts with. The researchers observed cases where the octopus would quickly grab the prey after punching a fish. Curiously though, sometimes it did not gain any immediate advantage from these punches. 

The authors hypothesize that in these cases, the octopus might be punching out of spite to punish a hunting partner that cheated in the past. Alternatively, this aggression might serve to deter fish from non-collaborative behavior. This behavior may stem from complex cognitive or emotional pathways. This research provides another indication that the octopus brain, though drastically different than ours, is capable of complex behavior and cognition.

Did humans ever hibernate to survive harsh winters?

Fossil evidence from Spain suggests early humans may have hibernated for up to four months at a time

Anna Wernick

Neuroscience

University College London

Just like the American black bear and the European hedgehog, early humans may have hibernated to endure severe winter months.

Animals hibernate to survive cold weather and reduced food access by decreasing their metabolic rate and body temperature for months at a time. Accustomed to our modern-day central heating and abundance of supermarkets, the prospect of human hibernation seems like science fiction. However, 430,000 years ago, Earth experienced a period of extreme glaciation — otherwise known as the Ice Age. New research from scientists in Spain suggests evidence that these brutally cold times may have led to hibernation.

Animal hibernation causes high levels of the hormone parathyroid in the blood. This chemical damages bones, leaving long-lasting tell-tale signs. In this study, paleontologists examined human specimens for hyperparathyroidism from the Sima de los Huesos cave — Spanish for "pit of bones." The burial site is home to over 7,500 human fossils, from 29 individuals, between 300,000 and 600,000 years old — making it the largest and oldest collection of human remains to date.

The team studied the bones using a combination of microscopy and CT scans — the same as those used in hospitals. They discovered a plethora of lesions and bone damage indicative of disorders such as rickets, Chronic Kidney Disease — Mineral and Bone Disorder (CKD-MBD) and hyperparathyroidism. The authors propose that these diseases were caused by poor toleration to hibernation.

They argue that these ancestors may have hibernated for up to four months at a time. This strategy was imperative for survival during frigid and food-scarce periods, such as the extreme glaciation 430,000 years ago where these individuals lived.

While this discovery is certainly exciting, it is not entirely conclusive. Fossil experts will likely continue gathering more research to determine whether early humans really did hibernate, or not.

Even megalodon babies needed nurseries to survive

To look back into shark evolutionary history, paleontologists analyzed the fossilized teeth of these ancient predators

Sara Zlotnik

Ecology & Evolutionary Biology

University of Florida

For around 20 million years, gigantic sharks called megalodons roamed the oceans across the globe, eating whales, porpoises, and even other sharks. But while megalodons are known for being the prehistoric ocean's apex predator as adults, they first had to survive their vulnerable juvenile stage. A recent study suggests that young megalodons spent their early years in relatively safe and secluded coastal regions known as shark nurseries. According to the study authors, these nurseries may have played a key role in shark evolution.

Paleontologists compared the size of megalodon teeth from eight sites known as well as one newly discovered fossil-rich site in Spain. Of these locations, five were determined to be likely megalodon nurseries due to the prevalence of newborn and juvenile-sized teeth in comparison to the number of adult teeth. These five nurseries varied dramatically in age, with some dating back nearly 16 million years, while others were only three to four million years old. The researchers concluded that the megalodons’ reliance on nurseries must have been a stable characteristic throughout their long existence on earth.

As with many modern-day sharks, megalodons likely benefitted from nurseries due to their extremely slow rate of development. Some paleontologists estimate that they may have taken over 25 years for megalodons to reach their final adult size. If juveniles lacked a safe place to live, they could easily have been eaten by the same animals that their larger relatives considered prey.

The discovery of these megalodon nurseries suggests that this strategy for juvenile protection may have been one reason why this species survived for so many millions of years. On the flip side, the widespread loss of coastal habitats due to climatic changes likely caused a spike in mortality of juvenile megalodons and may have been a critical factor driving the extinction of this iconic species.

Algae keep nitrogen savings to help them survive nutrient-poor ocean waters

Guanine, one of the four bases of DNA, also keeps algae's nitrogen sources rich

Rashi Ranjan

Computational Biology

University of Pittsburgh

For microalgae, the microscopic organisms photosynthesizing in the ocean, nitrogen is crucial in regulating metabolism. When nitrogen levels dip, their cells don't divide efficiently and they can't photosynthesize as well as when nitrogen is not limited. So how do microalgae continue to thrive even though the majority of oceanic surface waters are nitrogen-deficient?

In a recent paper published in PNAS, researchers found that the ability of microalgae to persist in both nitrogen-poor and nitrogen-fluctuating environments is thanks to the nucleic acid guanine. Guanine is the "G" in DNA, and is also a nitrogen-containing metabolite used for all kinds of cellular purposes. It is widely available in nature from sources such as decomposing fish tissues and scales.  

This new research found that diverse microalgae, including freshwater and marine algae as well as those present in reef-building corals, all contain long-term nitrogen reserves in the form of crystalline guanine. 

Using fluorescence and transmission electron microscopy, researchers found that for one marine single-celled alga Amphidinium carterae, the storage capacity for crystalline guanine was enough to support nitrogen requirements for several new generations. By using guanine as a storage form for nitrogen, microalgae can protect themselves from the potential harms of nitrogen shortage. 

Biologists find the world’s southernmost tree on a wind-battered island in Chile

Wind, and not temperature, is the biggest determinant of where it lives (and where it does not)

Cassie Freund

Ecology

Wake Forest University

At the beginning of 2019, a group of 14 researchers led by biologist Brian Buma from the University of Colorado-Denver, made the days-long journey to Isla Hornos in the Cape Horn archipelago, near the tip of southern Chile. Their goal? To lay eyes on the southernmost tree in the world.

Their trip was not simply another expedition documenting life at the world’s extremes: the data they collected is important in understanding what environmental factors limit plant life on earth. Their findings have recently been published in the journal Ecography.

The expedition team surveyed trees across Isla Hornos, a craggy island just nine square miles in size. Their approach to surveying its plant life was similar to methods used by forest ecologists around the world: they identified and measured trees, and took wood cores from them to determine their ages. But in contrast to tropical forests, which can have well over 500 species of tree per hectare, just three types of tree can be found on Isla Hornos. And, because the wind that whips across the island is so strong, the trees there grow horizontally instead of vertically. 

Most of the island was treeless, so the researchers found picking out the southernmost tree to be fairly easy. This record-holder is a 42-year-old Magellan’s beech tree (Nothofagus betuloides). It is just 57 centimeters tall – a little above knee-height – but stretches two meters horizontally. The wood core data told them that this tree was much younger than the trees in the more forested areas, which were over 100 years old.

From the wealth of data they collected during their expedition, the researchers concluded that at these southernmost reaches of the planet, trees are limited more by wind exposure than by temperature. This is unlike other treelines around the world. But similar to other trees, those on Isla Hornos will change as Earth’s climate does. The island is already one of the windiest places in the world, with wind speeds topping 72 kilometers per hour (~45 mph). 

Isla Hornos is projected to get even windier with climate change. If that happens, someday the world’s southernmost tree might not quite be so far south — the record-holding Magellan beech will die and the treeline's edge could contract to the north, where there is protection from other trees. And, given that the National Geographic staff writer that accompanied the research team, Craig Welch, noted that they “hiked and camped through gales that knocked us down,” I wonder if biologists will even be able to get there to see it.     

Scientists discover a gene for scarless skin regeneration

This gene is active in newborn mice and gets turned off as they age

Sree Rama Chaitanya

Molecular Biology

Instituto de Medicina Molecular

Our skin rapidly heals our wounds to prevent exposure from infectious microorganisms, but it comes with a price – scars. For example, the hair follicles – the foundations of hair growth in the skin – do not develop completely after serious wounds, leaving visible marks. 

Surprisingly, human fetal skin can regenerate without scars, but we somehow lose this power as we age. Now, scientists found a gene expressed by a specific cell type in the deeper layers in the skin of newborns that supports scar-free regeneration after wounds.

To identify the cell types and molecular factors that guide scar-free skin regeneration, scientists looked at changes in gene expression in the skin of newborn and older mice at single-cell resolution (because mice skin is structurally similar to us). They found different kinds of cells in their analysis. One cell type called fibroblasts caught their eye; these cells are known to support the wound healing process. Although fibroblasts were present in both newborns and older mice, scientists found that fibroblasts from newborns could support the regeneration of hair follicles during the wound healing process. Therefore, they figured that newborns have a special type of fibroblasts that can support scar-free skin regeneration.

They were able to pinpoint the changes in the way genes worked in these special fibroblasts, and a gene called Lef1 stood out. Then, they genetically manipulated older mice to specifically turn on Lef1 levels in the skin fibroblasts. Now backed by the Lef1, fibroblasts of the older skin were able to form hair follicles. Also, the skin regenerated at the wounded area without scars. 

Scientists suggest that Lef1 could relay external cellular signals during early development (like in fetuses). Hence, they are now trying to understand what exactly Lef1 is doing in the fibroblasts. They openly shared the genomic data in an interactive website and hope to “develop clinically tractable solutions that promote the regeneration of adult tissue.

Tasmanian devils are changing their behavior to avoid giving each other cancer

Devil facial tumor disease has proved disastrous for these animals

Anna Wernick

Neuroscience

University College London

Tasmanian devils, native to the island of Tasmania, are the world's largest carnivorous marsupial. These nocturnal animals are voracious eaters and have gained a reputation for their aggressive nature. This has been the downfall of this species: devil facial tumor disease (DFTD) is a transmissible cancer that is spread between devils via biting. Consequently, DFTD has caused disastrous local population losses of over 90 percent.

DFTD tumors develop around the head and face and are mostly fatal within a year. As the tumor grows, the solitary animal has difficulty catching prey and feeding. How DFTD affects devil social interactions over the course of the disease, however, has never been studied before. A research team has now tracked affected individuals over time to learn more about the social aspects of DFTD.

Over a six-month period, including the mating and non-mating season, the team monitored the social interactions of 22 Tasmanian devils and their disease progression. The group fitted 12 female and 10 male devils with tracking collars, which emitted different signals when in close proximity to other collared devils. The animals were recaptured each month to monitor their disease status and identify any newly infected individuals.

At the beginning of the study, three devils presented with DFTD tumors, and over the course of the six months, seven more developed symptoms. The researchers discovered that Tasmanian devils afflicted with the transmissible cancer were less likely to interact with others, particularly during the mating season. As their tumor sizes and infection loads increased, their probability of interaction dramatically declined.

This antisocial behavior may be a mechanism adopted by diseased devils to promote the survival of their species — an act of altruism that could prevent their extinction.

Gut bacteria helped mice fight off pesky pneumonia

Pneumonia strains are becoming antibiotic-resistant, so we need to find new ways of treating infections

Madeline Barron

Microbiology

University of Michigan

Pneumonia, a bacterial infection of the lungs, is a prominent health threat worldwide. True to its name, the bacterium Klebsiella pneumoniae is a key cause of pneumonia, particularly in healthcare settings. Unfortunately, a number of K. pneumoniae strains are multi-drug resistant, which limits the repertoire of antibiotics capable of treating infection. Discovering therapeutics to combat these feisty microbes is a pressing need. 

Where should we look for such therapies? A recent study suggests the gut microbiota might be a good place to start. 

Scientists found that mice whose gut microbiota were depleted by antibiotics developed more severe K. pneumoniae infection compared to mice with an intact microbial community. Interestingly, alveolar macrophages (a type of immune cell that resides in the lung and “eats” microbial invaders) isolated from antibiotic-treated mice were less able to engulf and eliminate K. pneumoniae cells. These results suggest the gut microbiota play a role in K. pneumoniae lung clearance. The question is, how? 

As gut bacteria go about the business of living, they release small molecules, called metabolites, that circulate throughout the body and interact with our cells to keep us healthy. The scientists observed decreases in several microbiota-derived metabolites in the guts of antibiotic-treated mice. 

Klebsiella pneumoniae

National Institute of Allergy and Infectious Diseases (NIAID)

Interestingly, if mice were fed these metabolites prior to K. pneumoniae infection, they developed fewer bacteria in their lungs and less severe disease. Furthermore, the metabolites increased the ability of alveolar macrophages to consume K. pneumoniae and increased cell activity involved in bacterial clearance, thus supporting the idea that these compounds help macrophages fight K. pneumoniae infection. 

These exciting observations provide a basis for developing gut microbiota-associated therapies to prevent or treat pneumonia. More broadly, they add to the mounting body of evidence that gut microbes do important work both inside and outside their intestinal home. 

Smoke pollution disrupts the flight of painted lady butterflies

The longer the butterflies are exposed to smoke, the slower they fly

Adithi Ramakrishnan

Developmental Neuroscience

College of William and Mary

Human-driven fires are used to clear land and remove leftover crop residue at the end of a harvest. These fires, though useful, have a cost: they release smoke containing small inhalable particles that harm nearby living things

 A recent study found evidence that high smoke levels can negatively affect the flight patterns of butterflies. The researchers had a group of adult painted lady butterflies fly in a controlled environment filled either with clean or smoky air. They then burned incense sticks to release smoke similar to what might come out of a human-driven fire after a harvest. The researchers measured the butterflies’ flight distance, speed, and flight times in the clean and polluted conditions.

a painted lady butterfly on lavender

A painted lady butterfly

By Isiwal/Wikimedia Commons/CC BY-SA 4.0

The butterflies flying in smoky conditions had a shorter flight distance and slower flight speed. The longer the butterflies were exposed to the smoke, the worse their flight became. The researchers suggested that tiny particles from the smoke may have attached to the butterflies’ wings, making them fly slower.  

A butterfly’s ability to fly is not only important to keeping it alive, but also in maintaining the survival of the ecosystem around it. Butterflies that fly slower or shorter distances due to smoke pollution could be worse at migrating to new areas or pollinating surrounding flowers. This study was the first to examine how smoke pollution affects butterfly flight, revealing how a helpful tool for humans can have dangerous consequences for the surrounding wildlife.

Pug-nosed tree frogs have figured out how to stay safe while attracting mates

Male frogs "sing" to attract females, but this also alerts predators to their location

Margaret Swift

Ecology

Duke University

In a sequence of sounds, our ears pay the most attention to the first, and our brains assume all sounds in the sequence come from the same location. This is what's known as the precedence effect, and it biases animal hearing. When male frogs "sing" to attract mates, they also broadcast their locations to eavesdropping predators, and animal behaviorists have long been interested in the balance of risk versus reward in male mating displays. 

But male pug-nosed tree frogs have developed a trick to stay safe without sacrificing their mating chances: they chorus in unison. These males have a unique opportunity because — for some, currently unknown reason — female pug-nosed tree frogs aren’t subject to the precedence effect. Singing in unison can therefore overwhelm predators’ senses without confusing their prospective mates.

To study this risk versus reward, a trio of researchers compared the preferences of female pug-nosed frogs to those of two eavesdropping predators (midges and bats) and a related species (túngara frogs) whose males do not chorus. For each experiment, researchers positioned two speakers far from the target animal (for the bats, speakers were baited with fish to sweeten the deal). Male pug-nosed frog calls were piped in through the speakers asynchronously: either the left or the right speaker would play the call first, with the other following shortly after. If a target moved towards one of the speakers, the researchers interpreted that as it “preferring” that speaker over the other, evidence of the precedence effect.

Researchers found that túngara, bats, and midges all preferred the first-call speaker; therefore, predators and related frogs do experience the precedence effect. Female pug-nosed frogs, however, did not show any speaker preference. It is clear that males are taking advantage of this lack of preference. This suggests that, having removed any advantage for singing first, the male frogs would rather not tip off predators to their individual locations.

Why, then, would any male start the chorus? Well, someone has to lead  —  and the biological urge to reproduce is strong.

Massive Science Year in Review: 2020 edition

A glimpse into the inner workings of our digital media company over the past year

Nadja Oertelt

Co-founder and CEO, Massive Science

2020 was transformative in violent and destructive ways - the pandemic has taken a huge social, medical, cultural, and financial toll on us collectively as a species. As of the writing of this note, COVID-19 has caused the deaths of 1.62 million people, including over 300,000 Americans. Our pandemic coverage has attempted to make simple the complexity of this moment, crystalizing expertise from bioethicists, biochemists, immunologists, virologists, bioengineers, epidemiologists, geneticists, healthcare practitioners, and global health specialists.

That said, we did not abandon our bread-and-butter scientific reporting. Ninety percent of our published stories were about research and stories across the sciences and engineering and that paid off in terms of traffic. We had about 2.7M pageviews in 2020, up 65 percent from 1.6M in 2019. COVID-19 coverage overwhelmed many readers in 2020, and we found our non-pandemic articles were welcomed by readers awash in hot-takes by writers without scientific expertise.

Unlike many other science news outlets that saw outsized growth driven entirely by pandemic coverage, our growth has been organic across all of our topics and channels — around 11 percent of our pageviews in 2020 came from COVID-19 coverage. This growth bodes well for us in a shifting science news landscape in the coming years, as climate change drives more of the big news cycles.

We've done our best to stay value-aligned, creating equitable structures for our team and our community of scientist writers. We also make our values transparent to our audiences. The values we stated as the national uprising for Black liberation erupted in the summer of 2020 are still values we fight for in our work as a news media organization. The disparate impact of COVID-19 on BIPOC communities is stark and brutal and we will continue to highlight the violence that research can perpetuate when carelessly designed, implemented, and funded.

In addition to leading Massive Science, I started working at the media organization Science Friday in February of 2020, and shortly after my co-founder Allan Lasser began working at the content management system (CMS) company TakeShape. Massive runs on the TakeShape CMS, and Science Friday's audio products and radio program are mission-aligned with the work that Massive does. We've found that working within these organizations has been helpful in pushing Massive to grow in new directions.

We hope in the next two years to find a home for Massive that is more permanent. The options for Massive are infinite, and it will be our goal to find a safe and equitable place for Massive to continue to grow as an editorial science community and platform.

Just a few of our accomplishments in 2020...

  • We continued in our second year of financial sustainability. We grew our revenue 225 percent from 2019 to 2020, while our expenses grew 20 percent. This is an amazing feat for our small team!
  • On Jan 1 2020 we had 1860 scientists in our community of science communicators, and we jumped to 2520 by Dec 2020.
  • We had a 20 percent annual increase in our newsletter subscribers from 19k to 22k.
  • We published 543 articles and notes, syndicated 34 stories, and built and strengthened our syndication partnerships with Slate, Salon, Smithsonian Magazine, Inverse, The Wire, ASBMB Today, The Biota Project, Truthout, High Country News, and more.
  • We shipped 194 packages to our shop customers. We have customers in over 36 states and 6 countries.
  • We completed a video co-production with the US National Human Genome Research Institute on the human pangenome.

Editorial in 2020

Communicating science during the pandemic has been an interesting challenge for scientists, news media outlets, and journalists. Thankfully, we had spent three years preparing for this moment. One of our first editors, Dr. Ashely Juavinett, summed the challenge up nicely:

Massive broke its previous monthly traffic record in May 2020. We haven't been able to consistently clear 300,000 monthly pageviews yet, but in comparison to 2019, monthly traffic has remained higher and more constant.

2020 easily broke our yearly traffic record set in 2019. The higher traffic also came with a 12 percent increase in the average time readers spend on a page, from 3:03 in 2019 to 3:25 in 2020, with long-form article time-on-page clocking in at 4:11. We're happy with the increase — two minutes is considered the start of the "good" time-on-page range, so increasing at a healthy rate here is wonderful.

Massive's bread-and-butter is always basic science, but 2020 was the year we started doing more explainer articles, specifically focused on trending science news. For instance, in July, months ahead of most outlets, we published a piece explaining what exactly an mRNA vaccine is, and what its pros and cons are. In preparation for the winter holidays, we published a series of explainers on evolution and climate change (a two-parter), that we figured would be fodder for family arguments.

In the past, we've experimented with theme weeks, but we tried a theme month this year and had a lot more success. In the second half of 2020, we started publishing many more interviews than we have in the past. These include one-offs (like this interview with neuroscientist Yewande Pearse about life extension) and series of interviews, like our collaboration with Science Friday on conversations with prominent women scientists. Massive also kept up with the evolving intersection of politics and science. This includes publishing anonymously-written articles from Black scientists as well as immigrant scientists facing deportation.

The most popular articles were, predictably, articles that explained rumors about COVID or put the pandemic in a different light. Five of the 10 most popular articles of the year were about COVID — one explained how the virus initially spread, one debunked a conspiracy theory about the virus's origins, and the #1 most popular article put social distancing behavior in a new light.

A Huge Thanks

None of what we do at Massive would have been possible without the support of the community of scientists who work with us and write with us. None of it would have been possible without the support of our partners, supporters and collaborators. And none of it would happen without the dedication of our community, editorial, and infrastructure teams! They are amazing people and I am so proud of what we've done.

I hope this has given you a sense of what Massive is all about, and how we dealt with the ups and downs of 2020. We're really excited about 2021 and hope you'll stick with us. If you ever have questions or feedback about Massive, please email me directly at nadja@massivesci.com.

Onwards to 2021 with the lessons of 2020 close at hand...

Researchers uncover gut bacteria that can break down cholesterol

Treating high cholesterol by manipulating the gut microbiome could prevent cardiovascular disease

Raj Rajeshwar Malinda

Cell Biology and Developmental Biology

You have probably read that high cholesterol can cause health problems, especially heart disease. Generally, a person's diet has been shown to have a direct impact on their cholesterol levels. Recently, involvement of the gut microbiome has also been reported to regulate our cholesterol levels.

Now, researchers at MIT and Harvard University have uncovered one way that some gut bacteria can influence cholesterol. They found a group of bacteria that can produce a compound called ismA, which breaks down cholesterol. They found that people with these bacteria had lower cholesterol levels in their blood and fecal samples than people who lacked bacteria that can manufacture ismA.

This finding may enable scientists to make new medications to manipulate cholesterol levels, or to treat people with high cholesterol with prebiotics to spur the growth of these cholesterol-digesting bacteria. 

Succinate is the key to muscle communication during exercise

A new study examines the complex molecular signaling that happens in your muscles when you move

Sree Rama Chaitanya

Molecular Biology

Instituto de Medicina Molecular

Do you know that our muscle tissue is not made exclusively of muscle cells, but different kinds of cells? These cells communicate with each other by sending chemical signals. This communication is important for normal muscle movement and post-workout recovery. But, until now, no one really understood what the chemical signals that allowed the cells to communicate were.

In an article published in the journal Cell, scientists investigated the signals that kick start muscle changes after exercise in humans and mice. 

They found that succinate, a metabolite released by the muscle cells' mitochondria, triggers the communication network. During exercise, a mildly acidic environment is temporarily generated in the muscle cells. This acidic environment activates succinate, which is then transported out of the muscle cells as a messenger. 

Then scientists found that another protein (known as MCT1) acts as a portal in the muscle cell wall to channel succinate out of the muscle cells. But this protein portal is selective, and only allows activated succinate to pass through. 

In the same way that an antenna receives a signal only when tuned to a particular frequency, cells also need the right receiving proteins (called receptors) to catch the signals. The receptor for succinate, researchers discovered, is not produced by the muscle cells, but by the neighboring cells that support muscle growth and adaptation. Once succinate attaches to the receptor, the signal is complete, which further orchestrates action by many other genes and proteins to support muscle growth and adaptation after exercise.

Our memories of shared experiences have unique neural signatures

New neuroscience research shows why you do not remember an event the same way as other people who attended do

Kelly Cotton

Cognitive Psychology

City University of New York

Think of the last party you attended. While other people at the same party likely have similar memories of the festivities, your specific perception and memories of the event are unique to you. 

Most neuroimaging research looks at group-level patterns of brain activity – which areas of most participants' brains light up when they do a certain task or think a certain thought. But recent research published in Nature Communications took a more personalized approach, investigating whether patterns of brain activity elicited while imagining common experiences can distinguish individual people. 

Participants were instructed to “vividly imagine themselves in the scenario” (such as driving a car, attending a party, or cooking a meal) and describe the imagined experience. The researchers then created custom models for each participant based on their verbal descriptions and non-linguistic elements (such as sensory, motor, and emotional characteristics) of the experiences. They found that an individual’s personalized model better predicted their neural activity than other participants’ models, suggesting that neuroimaging can be used to detect and predict individual differences in our memory for common experiences. 

While this study focused on healthy older adults, future research may be able to use this method to personalize diagnoses and treatments for disorders related to memory and imagery deficits, such as Alzheimer’s disease and depression. The findings more generally underscore the importance of individual differences – that our unique experiences of common events are what make us individuals, down to the neural level.

Scientists uncover how sunflowers that live nearby each other maintain genetic diversity

Large study shows that enormous "haplotypes" account for the enduring variation

Max Barnhart

Plant Biology

University of Georgia

Everywhere we look, we find plants that seem to be perfectly fit for their environment. This is due to a process known as local adaptation. Some species of plant are found in many different environments, and so different individuals from the same species develop characteristics to better suit them within their environment. Groups of these individuals with special characteristics are called ecotypes.

Sometimes the environment can change drastically over short distances and we can find many different ecotypes of the same plant species living in close proximity. Surprisingly, even though these ecotypes are likely interbreeding, they manage to maintain their differences. How is this possible?

In a great collaborative effort, an international research team sought to answer this question using some of the most prolific and resourceful plant species of them all: sunflowers.

The researchers collected samples from 151 different sunflower populations across North America. These represented three different species, each with multiple ecotypes. They then sequenced the genomes of over 1,500 individual sunflowers from these 151 populations to uncover the genetic mysteries underlying ecotypic differentiation in sunflowers.

One of the specific traits that varies between sunflower ecotypes they investigated was flowering time. Some ecotypes flower early to avoid the heat of the summer while others flower later because they live in cooler conditions. The consortium conducted a genome-wide association study to find out where the genes controlling flowering time, along with the genes controlling over 90 other traits, are located on the sunflower genome.

The researchers discovered that the genes controlling flowering in the early flowering ecotype were completely absent from the late flowering ecotype. And, overall, each sunflower ecotype had unique, non-recombining regions of the genome that contained genes contributing to local adaption. 

These “massive haplotypes” aren't exchanged during interbreeding because they simply don’t exist in the other ecotypes. This explains why sunflower ecotypes can coexist in close proximity, but also raises further questions about how the new species within the sunflower family might develop.

Shrinking habitat means fewer sleeping spots for Northern pig-tailed macaques

These monkeys are adapting their behavior as forests change

Anna Nordseth

Ecology

Duke University

Where you sleep is important. If you’re like me, you like to sleep where you’re safe, comfortable, and with a full stomach. Northern pigtailed macaques (Macaca leonina), found in southeast Asia, have a similar checklist when choosing trees to sleep in: they have to balance avoiding predators, staying close to food, and keeping warm. 

Northern pigtail macaques sleep in large groups of up to 80 individuals. To avoid being spotted by predators at night, macaques and other canopy-dwelling primates will choose big, tall sleeping trees. And, to save energy looking for food, primates will sleep close to valuable fruit resources.  

What happens though, when the forest is fragmented, and has fewer good trees to sleep in? A recent study published in the International Journal of Primatology showed that macaques in Thailand's Sakaerat Biosphere Reserve are less likely to reuse sleeping trees in degraded habitat than in more pristine forest. But they are still systematic in their sleep site selection, choosing taller trees with more branches that are close to food resources. 

Northern pigtail macaques are listed as vulnerable on the IUCN Red List and their habitat continues to shrink. Understanding how these macaques respond to habitat changes is necessary for their conservation. The study authors suggest that macaques’ flexibility in choosing sleep sites is a good sign for the species’ resilience. 

Fish need to socialize for their brains to develop

Zebrafish held in isolation show social avoidance behavior that other fish don't

Simone Lackner

Neuroscience

Laboratório de Instrumentação e Física Experimental de Partículas

Since COVID-19 is ruling our daily routines, we recognize more than ever how important interpersonal relationships are for well-being, productivity, and mental health. Humans and other social species such as monkeys, rodents, and even fish have an innate need for interactions with others. However, it is still not fully understood how early-life social isolation shapes brain development. 

A team of scientists at the Champalimaud Center for the Unknown in Portugal studied one-week old larval zebrafish raised in isolation and found that early-life social isolation has an impact on the strength of social avoidance reactions and that the lateral line organ — a system of organs in aquatic vertebrates that detect movement in surrounding water — plays a crucial role in shaping them.

Larval zebrafish don’t swim continuously but make discrete movements called swim bouts. These swim bouts can be combined into complex behaviors, such as hunting, escaping, and social interactions. Scientists use high-speed video tracking to automatically detect those swim bouts and can classify them into different swim types. This allows detailed dissection of behavioral phenotypes for comparison between individuals or experimental groups.

Analyzing the differences in swimming behavior between group- or isolation-raised larvae, the scientists found that isolation-raised larvae display enhanced social avoidance. This behavior is independent of the visual system; blind fish behave similar to seeing fish. Mimicking swimming neighbors with local water vibrations is sufficient to induce this enhanced reaction and suggest a role of the mechanosensory system. The scientists used pharmacology to damage the lateral line mechanosensory organ and discovered that this reduced the social avoidance behavior of isolation-raised larvae.

One-week old larval zebrafish are not considered social yet, as they do not display social attraction behavior. The observation that one-week old isolation-raised larvae display strong avoidance reactions to water vibrations and swimming neighbors around them suggests that early-life social isolation has a strong impact on the development of the sensory system and marks the fishes behavior much earlier than previously thought.

New study shows how using machine learning in healthcare worsens inequality

Predictive models lack the necessary context to interpret the data they are given

Shannon Casey

Biology and Medicine

Healthcare providers have to make a lot of decisions when it comes to providing the best patient care, and in some cases, algorithms are used to help with this clinical decision-making process. However, the fairness of such tools is not a guarantee.

As a physician assistant, using algorithms to help guide clinical decision-making has been a frequent occurrence. For example, I’ve used a tool called the Pooled Cohort Equations to estimate a patient’s risk of atherosclerotic cardiovascular disease in a 10-year period. If a patient’s risk exceeds a certain cutoff, statin therapy is recommended. But it is imperative that clinicians understand the limitations of such algorithms.

In a new pre-print posted on arXiv, researchers from Stanford University characterized the trade-offs between a predictive model’s fairness and its performance. Using 25 combinations of datasets, clinical outcomes, and demographic attributes (such as race, ethnicity, gender, sex, or age), they set up a series of predictive models. The models included specific fairness criteria that were adjusted to be more or less strict, and they quantified the effect this had on the model’s performance.

The researchers concluded that there were concerning limitations regarding algorithmic fairness in healthcare. Moreover, they noted that constraining a predictive model in order to achieve fairness was “insufficient for, and may actively work against, the goal of promoting health equity.”

This is partly because predictive models lack the context of how systemic factors lead to health disparities, such as how bias and historical inequalities affect the data going into the models. Furthermore, these factors may also play a role in the intervention triggered by the model’s prediction. Due to this complexity, the researchers suggested that it might be necessary “to abstain from algorithm-aided decision making entirely.”

The use of machine learning in healthcare could potentially worsen health disparities. Therefore, it is necessary for researchers developing healthcare-related predictive models to actively engage in participatory design practices to address the biases currently present in healthcare.

More Lab Notes →