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Lab Notes

Short stories and links shared by the scientists in our community

Simon Spichak

Neuroscience

As we age, our brain becomes more vulnerable to different diseases. Parkinson’s disease is one such debilitating disorder. It affects more than 10 million people worldwide. Men are 1.5 times more likely than women to develop it. Most people with Parkinson’s disease develop it when they are around 60 years old, when the motor cells in their brains begin to die off, leading to a loss of motor control.

This brain cell death is caused by clumping of alpha-synuclein (α-syn) proteins. We know that α-syn is found in the region of the neuron that sends packages of neurochemical signals, which are called vesicles. But we don’t know what this protein does in a healthy brain. This might hold a clue to why α-syn begins clumping. 

A new study in Nature Communications provides more context into their function. Scientists used artificial cell membranes to mimic the vesicles sent out by cells. By adding α-syn to these vesicles, they found that it sticks like glue to the inside of the vesicle and keeps these tiny packages of neurochemicals at their origins until the cell is ready to send them out. This might explain how one abnormally clumping α-syn protein can spread and build up inside of neurons in people with Parkinson’s disease. This very basic scientific finding could lead to better treatments for the disease in the future.

Green bridges in Germany are keeping a growing gray wolf population — and their prey — safe

Road accidents account for over 75 percent of all known wolf mortality in Germany

Three clusters of neurons control zebrafish decision-making and movement

New research sheds light on how our neurons guide our behavior

Simone Lackner

Neuroscience

Laboratório de Instrumentação e Física Experimental de Partículas

New research describes how the inflammation characteristic of multiple sclerosis affects neurons

Inflammation destroys the junctions between neurons, slowing information transfer

Bhargavi Murthy

Neuroscience

Max Planck Institute of Psychiatry

Despite a mistaken mathematical proof, you do only need four colors to make a good map

Alfred Kempe’s 1879 proof of the Four Color Theorem contained a mistake. Nearly a century, later his work was vindicated

Rebecca Lea Morris

Mathematics

Mathematicians are human, just like the rest of us, which means that they sometimes make mistakes. As their work is read by other mathematicians, both during peer review and after publication, we might expect errors to be quickly spotted and addressed. But a fatal mistake in Alfred Kempe’s 1879 “proof” of the Four Color Theorem remained unnoticed for over a decade.  The error was finally uncovered by Percy Heawood in 1890. 

The Four Color Theorem states that for any map of contiguous countries drawn on a plane only four colors are needed to ensure that adjacent countries are given different colors. In the heart of his “proof,” Kempe had to consider a number of different cases of possible map configurations.  To tackle these cases, he invented a new mathematical tool called Kempe chains. However Heawood discovered that Kempe’s treatment of one of these cases didn’t work and presented an example to show how his reasoning failed.

Heawood’s discovery did not mean that all was lost, though. First, Heawood showed that Kempe’s work was enough to establish a weaker result called the Five Color Theorem which says that only five colors are needed to color a map in the required way.  Second, although Kempe’s proof was flawed, the Four Color Theorem was true. It was first proved successfully, though somewhat controversially, using a computer by Kenneth Appel and Wolfgang Haken nearly a century later in 1976. And Kempe’s ideas played a significant role in their work. So while Kempe made a mistake in his “proof,” it still contained valuable mathematics.

Summits of underwater mountains are prime real estate for fish

Seamounts in Papua New Guinea have nearly twice the biodiversity as nearby shallow reefs

Sarah Heidmann

Fish Ecology

University of the Virgin Islands

Imagine yourself underwater with hundreds of fish schooling and swirling around you. What does that place look like?

Chances are, you imagined yourself on a tropical coral reef, the well-known, fish-friendly habitat often found in movies and vacation daydreams.

Think instead of being high atop an underwater mountain called a seamount. Despite their small habitat area and isolation from land, it turns out seamounts can host high numbers and diversity of fish species compared to nearby reefs, according to a recent study in Papua New Guinea published in the journal Coral Reefs. The researchers found that submerged pinnacles had 3.7 times the average fish abundance and nearly twice the biodiversity as nearby shallow reefs. This is a particularly important finding as coral reefs near the shores are vulnerable to pollution, fishing, and other ecological problems.

So the next time you think of schooling fish, imagine them atop an underwater mountain oasis!

Antioxidant found in green tea protects “the guardian of the genome”

New research identifies a molecular mechanism for green tea’s anti-cancer effects

Yuning Wang

Biochemistry and Structural Biology

University of Western Ontario

Green tea has long been believed to have a variety of health benefits. One of the most important benefits is the preventive and treatment effects against cancer, which are mainly attributed to polyphenolic compounds, such as epigallocatechin-3-gallate (EGCG), a powerful natural antioxidant found in green tea. 

The anti-cancer effect of EGCG has been extensively demonstrated in epidemiological, cell culture, and animal studies, as well as in clinical trials. However there has been limited success in clarifying how this anti-cancer effect works at the molecular level, raising uncertainty about green tea’s value in cancer therapy.

The uncertainty was eased by a recent study, where scientists identified and validated a direct interaction between EGCG in green tea and the tumor suppressor protein p53, also known as “the guardian of the genome.” This interaction prevents p53 from degradation, meaning that EGCG has a protective effect for the tumor suppressor protein, which in turn guards cells against cancer. This work provides molecular insights into the mechanisms for EGCG’s anti-cancer activity and serves as strong evidence for the extraordinary benefit of consuming green tea. 

Derek Smith

University of Michigan

Methane is an important greenhouse gas in Earth’s atmosphere. Methane accumulates in oxygenated, surface freshwaters with high amounts of cyanobacteria. Cyanobacteria are photosynthetic bacteria, that grow using the same light-dependent, oxygen-producing process that plants use. However, the exact methane source in these environments are unknown, and many researchers believed that methanogenic archaea that live in anaerobic “pockets” or attached to cyanobacteria may be responsible for the methane produced in these waters.  

A recent study tested if cyanobacteria directly contribute to global methane budgets. The researchers grew 13 different kinds of cyanobacteria from various environments in the laboratory and fed them heavy carbon (“Carbon-13”). The heavy carbon was then incorporated into the cyanobacteria biomass, “labelling” the compounds that the cyanobacteria produced by making them heavier than usual. The researchers saw that methane was labelled with heavy carbon, even in cultures in which the cyanobacterium was the only organism present, which shows that cyanobacteria directly produce methane.

Because cyanobacteria blooms are expected to increase with global climate change, and methane is a potent greenhouse gas, the observation that cyanobacteria directly produce methane suggests that cyanobacteria blooms may be a previously unrecognized positive feedback loop on global climate change. However, the controls on methane production by cyanobacteria in the environment and the contribution of cyanobacteria to global methane budgets are still poorly understood.

Tiny, wearable generator charges itself using body heat

Get ready to wear green energy on your wrist

Megan Otto

Writer

Our experiences help us judge how well we will learn new things

New research disentangles the effects of experience and belief on metamemory

Daniel Ribeiro

Neuroscience

University of Coimbra

Kids can tell if you’re smiling under your mask

Study finds that a mask has the same impact as sunglasses on a child’s ability to perceive the wearer’s emotions

Jayati Sharma

Genetics and Epidemiology

Johns Hopkins University

Wallet, keys, phone, mask. Mask-wearing, a core and useful intervention to combat the raging pandemic, has become a daily habit for most people. It’s also, however, raised concerns around kids’ ability to understand emotions and social clues when surrounded by masked adults.

Psychologists at the University of Wisconsin-Madison explored this question of how well kids can identify anger, sadness, and fear among mask-wearers in a study of 81 US children aged seven to 13 years old published in PLoS ONE. Study participants made inferences about the emotions being conveyed in facial configurations of digital simulations of three types of faces: uncovered, wearing sunglasses, or wearing surgical masks.

Though children were best able to identify emotions in uncovered images 66 percent of the time, children were still able to successfully draw emotional inferences from facial configurations of mask wearers. This accuracy was also no more impaired by mask wearing than it was by sunglass wearing, with kids identifying emotions around 27 percent correctly in both cases.

Children’s resilience, already supported by strong evidence in this study, is likely to be increased in real-world settings, where additional clues like vocal inflection and body language clue kids into what emotions to expect from others. The study suggest that kids are well able to adapt to mask-wearing without impediments to their growth and development.

Feeling down or bored? Watching a nature documentary can help!

COVID-19 is making travel impossible, but Netflix-based nature could help your mood

Rita Ponce

Evolutionary Biology

Polytechnic Institute of Setúbal

Taking a stroll in the park can make us feel good. But, what about watching a movie about it? Although there is evidence that contact with nature improves our wellbeing, unfortunately not everyone can access the outdoors. Could virtual nature experiences be a solution?

A team of researchers from the University of Exeter and the University of Surrey set out to test whether exposure to virtual nature could improve one’s mood and alleviate boredom. First, the participants (96 adult volunteers) performed a boredom-inducing task, watching a four minute video where a man talked in a monotone voice about his office work. Afterward, they were exposed to virtual nature by watching five minutes of a documentary about coral reefs on either a high-definition 2D television, a 360º virtual reality video on a headset, or an interactive computer-generated virtual reality experience similar to the video versions on a headset with hand-held controllers. The researchers assessed the participants’ moods and feelings before and after their contacts with virtual nature.

All three types of virtual exposure to nature reduced negative feelings, had a positive effect in the mood and increased feelings of connectedness to nature. While all settings were equally good at reducing bad feelings, the interactive virtual reality inspired the greatest positive feelings. 

The researchers point out, their results can be a first step to prepare for further analysis in “real” boring settings, such as hospitals or care homes. And, as many of us are facing lockdowns, we may keep in mind that nature documentaries can be a good companion — fancy virtual reality headset not required.

New help for allergies could be on the way

Researchers have identified the cells that trigger uncomfortable allergic responses

Hazel Walker

Immunology and Cell Biology

University of Cambridge

A new tweak to an old model explains the existence of primordial black holes

Black holes formed in the early universe could be linked to dark matter

Briley Lewis

Astronomy and Astrophysics

University of California, Los Angeles

Dark matter makes up almost 30% of our universe, yet we still aren’t sure exactly what it is. One suggestion is that dark matter is made up of primordial black holes (PBHs), black holes formed in the very early universe. 

Usually, we think of black holes as forming from the deaths of the largest stars — but these PBHs had to be created before stars existed in the universe. A new model from researchers at UCLA shows a way that PBHs could have formed so that they explain all the dark matter observed in the universe.

This model builds on the Standard Model of particle physics, which describes how different particles and forces are related to each other, by adding only one additional term to its equations. In the early universe, particles coalesced together into massive halos, which could possibly collapse to make PBHs. The problem, though, is that in order for these halos to collapse, they’d need to get rid of some of their energy. This updated model describes a way for halos to radiate away that energy, meaning PBHs are, indeed, possible.

The model suggests that if PBHs are small, they could be abundant enough to explain all the mass of dark matter we see. If PBHs are large, they might not be able to explain all of dark matter, but they could still explain a fraction of it and even be detected by LIGO, the Laser Interferometer Gravitational Wave Observatory — meaning we could someday have concrete evidence for them.

Disclaimer: This research is by one of the author’s colleagues.

An accidental experiment discovered new cells in cat brains and led to a Nobel Prize

Cats looking at dots inside a tent revealed the different eye cells that process movement and light

Julia A Licholai

Neurobiology

Brown University

A trio of imaging techniques brings new insight into how neurons work

Researchers found evidence that refuted previous scientific beliefs

Laura McCormick

Cell Biology

University of North Carolina - Chapel Hill

Defective ribosomes leave proteins to build up in our cells

New research on fruit flies illustrates what happens when ribosomes go awry

Joyce Yu

Cell Biology and Developmental Biology

The Francis Crick Institute

Science and philosophy can, and should, coexist

MC Hammer’s recent tweet has sparked a conversation about the complementary nature of these two fields

Rebecca Lea Morris

Mathematics

Researchers develop a new tool to quantify self-care during COVID-19

We’ve all probably heard the term self care. What does it really mean?

Emma Okumura

Life Sciences

McGill University

The Perseverance rover sends back the first photos and sounds from Mars

The rover’s landing was captured in an incredible video

Briley Lewis

Astronomy and Astrophysics

University of California, Los Angeles

Having trouble sleeping? Look to the moon for answers

New research shows that our circadian rhythms are guided by the moon as well as the sun

Anna Wernick

Neuroscience

University College London

Female scorpions pay a steep cost when they shed their tails for survival

Many species shed limbs and tails to escape sticky situations

Prayan Pokharel

Entomology

University of Hohenheim

There are many organisms such as spiders, lizards, and even starfishes (and many more) who voluntarily shed or detach a body part, also known as autotomy. They do so for several reasons. For example, autotomy is an escape strategy (for instance, if a leg is trapped between two rocks). It can also be a distraction for predators — an amputated tail wriggles, and makes a predator look one way while the tail shedder runs the other. Sometimes organisms self-amputate wounded limbs. 

In a nutshell, autotomy enhances survival. However, it may also impose some costs.

Recently, scientists tested if this survival strategy incurs any reproductive costs in a scorpion species, Ananteris balzani. The scorpion sheds its tail permanently, causing the loss of the anus and a lifelong inability to poop. Male scorpions also use their tails during mating. 

However, the researchers showed that tail loss has no effect on male mating success when compared to males with a tail. Remarkably, a tail-less female had less of babies than females with tails. This interesting finding suggests that the negative effect of “taillessness” is sex-dependent, and in these scorpions it is the females that pay the cost.

Texas weather has a disproportionate financial impact on marginalized families

Electricity companies can charge some consumers more for the same electricity

Coral larvae swim more slowly in dim light

Their search for the right light intensity and color could set them up for success later in life

Raj Rajeshwar Malinda

Cell Biology and Developmental Biology

Natural light is thought to be one of essential environmental factors dictating the ways animals live their lives. In aquatic animals, like coral larvae, the intensity and color of the light can be a crucial factor associated with swimming and moving behavior.

A new research study by a team of Japanese researchers, published in Scientific Reports, has explained how Acropora tenuis (a common reef coral) larvae move through the deep sea in response to the light intensity and color. 

Coral larvae are the free-moving life stage of corals, and they build colonies of the things that we think of as reef corals. The researchers found that these coral larvae swim slower in deeper water where there is less light, and that blue light is a particularly important cue for swimming. This is remarkable, since larvae lack eyes, yet they can still sense light intensity and color. The researchers suggest that this behavior could help the larvae locate habitat with the bright and blue wavelengths of light they need as adults. 

This behavioral phenomenon in coral larvae provides a more fundamental understanding of the early phases of larval settlement coral reefs in the natural environment.

The range of microbes in your sourdough starter affect its smell and rise

Getting bored of pandemic-baking? Maybe you need different microbes!

Adam Fortais

Physics

McMaster University

In what is perhaps the most “2020” study, a group of researchers from the United States and Denmark (with the help of community scientist-bakers across the globe) have studied the biodiversity contained within 500 sourdough starters. Their research was recently published in the journal eLife

The researchers collected 500 sourdough starters. These came mainly from the United States and Europe, but also included contributions from New Zealand, Thailand, and Australia. 

All 500 sourdough samples were DNA-sequenced to determine their microbial makeup. They then took 40 samples that represented the range of diversity and tested them for aroma profiling, chemical analysis, and rising speed. They discovered that an until-now overlooked component of microbial diversity, acetic acid bacteria, play a significant role in sourdough’s aroma and rising speed.

As an observational study, the results do not give us a master recipe for exactly which microbes create which bread characteristics. But the study does show that the types of microbes in a sourdough started affects how it rises, smells, and bakes. If you are still pandemic-baking, rest assured that there is plenty more fun to be had in determining the exact role of the microbes found in sourdough.