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Researchin' with urchins

Take a look inside the lab of a sea urchin researcher

Purple sea urchins are eating all the kelp in California. But in Pittsburgh, hundreds of miles from the ocean, we order them in the mail.

They arrive wrapped in wet newspaper with pieces of seaweed to snack on. We keep them in tanks, next to some sea star buddies, and study how they grow skeletons. When we're done, we bleach them (the university considers them a biohazard) and save them as extremely fragile decorations.

Be cautious about misleading coronavirus news. Here's how to spot what's accurate and what's dodgy

Incorrect reports spread like wildfire during events like these, so be prepared

Bhavya Singh

Microbiology

McMaster University

In light of the recent coronavirus outbreak, new developments have been popping up every few minutes, especially on social media. However, everyone should be aware of misleading news and false reporting. While some claims are comically outlandish, such as the one about Bill Gates supposedly creating the coronavirus, other claims that misreport the coronavirus death toll or official WHO statements are more dangerous.  

Here are a few things to keep in mind during this outbreak:

  1. Get your news straight from the source, such as your local and federal  health organizations. This includes the WHO or the CDC.
  2. If a website is making a claim that you can't quite wrap your head around — check their sources! If they are citing an older version of their own article, that's a pretty big red flag.
  3. Be critical of the information you see, and always cross-check the consistency of facts by looking for the same information on different news platforms. 
  4. The good old "correlation vs causation" rule. Yes, there is a video out there that shows someone eating a cooked bat. And yes, coronaviruses are known to infect bats. Does that mean that this video shows an example of an incident that caused a coronavirus infection? Not necessarily. 

For more ways to dodge fake news, here is another great article by from Harvard University. 

Also, remember, if you're feeling panicky about coronavirus, it's not nearly as worrisome as regular, old-fashioned influenza, which we live with every day. 

Whales molt, and scientists are trying to work out how

Researchers examined tissues from bowhead whales

Stephanie Zimmer

Cell Biology

Emory University

Did you know that whales molt? They exfoliate by rubbing against rocks every spring. New research shows that whale molting has an underlying molecular process which may involve structures called desmosomes.

Desmosomes form between cells in the outermost layer of skin and are one of several factors that allow skin to be a flexible fortress, capable of defending the body and repairing wounds. 

But these spots of glue do more than hold our skin together. They also hold together pumping heart tissue, and they keep the lining of our guts, kidneys, and various other internal organs intact, too. 

Unlike glue which hardens, the desmosome is dynamic. It assembles, changes shape, or disassembles in response to various cues, including during cell differentiation, injury and wound healing. The desmosome is actually a complex formed by thousands of copies of five different proteins, which are intricately organized into discrete spots lining adjacent cells.

Most desmosome studies to date have focused on human and mice, but these structures are necessary for just about any organism that has skin. Without desmosomes, skin would break and blister very easily, giving foreign bodies easier access, as is the case in people with genetic diseases caused by mutations in the genes that encode the desmosome proteins.

bowhead whale

A bowhead whale spyhops off the coast of western Sea of Okhotsk.

By Olga Shpak at Wikimedia Commons

This new research on whale molting mechanisms suggests that desmosome loss can also be functional. Researchers took tissue samples from bowhead whales (Balaena mysticetus) across three different sub-groups: molting adults (spring), non-molting adults (fall), and molting juveniles (spring). Next, they used a technique called immunohistochemistry to test for the presence of two desmosome proteins: desmoglein and desmocollin. The levels of these proteins have been previously shown to regulate desmosome assembly and adhesion.

The researchers found that there were season-dependent decreases in the levels of desmocollin, consistent with skin shedding. For example, in all spring-caught molting adults, there were reduced desmosome proteins in their oral cavity.

This study suggests that skin shedding in mammals, whether it's a result of normal molting or is the result of injury or disease, involves desmosome function. As for bowhead whales, more work is needed to understand the mechanism, and to determine if these changes in desmosome protein expression occur in other organisms with annual molts.

Researchers develop an app for tracking trade of endangered fish

Say "cheese!" for Napoleon wrasse conservation

Ashley Marranzino

Marine Biology

University of Rhode Island

The Napoleon, or humphead, wrasse (Cheilinus undulatus), is a giant and ornately decorated reef fish which can grow over 6 feet long and live for over 30 years. Unfortunately, these rare fish are a coveted delicacy in live fish markets throughout Asia, and the high volume at which they are traded has landed them a spot on the CITES endangered species list. 

To keep them from going extinct, stricter regulations must be implemented and enforced surrounding the collection and trade of Napoleon wrasses. Unfortunately, fish trading networks are complicated, and it can be difficult to track where fish come from and if they are being sold legally.

While all fish imported to major markets may be inspected, those within the live fish trade cannot easily be tagged or marked, making it difficult to track these fish from the point of capture through to their final sale point. But a pair of researchers from the University of Hong Kong decided to try a new technique in lieu of a physical fish barcode: facial recognition software. Napoleon wrasses have complex facial patterns that the researchers hoped could be used as a unique identifier for individuals.

First, they had to test if the facial markings were unique and variable enough between fish to reliably identify individuals, and that they did not change over time. Then to ensure that the identification system was feasible, researchers developed and tested an app used to compare pictures of Napoleon wrasses at fish markets to those in a database of previously identified fish. And it worked – this study served as a proof-of-concept that facial recognition software could reliably identify endangered Napoleon wrasses sold in live fish markets. 

Although not currently used on a large scale, there is real potential that the software and app developed could improve the monitoring and enforcement of legal endangered species trading. This approach could also apply to other animals that have distinct, readily identifiable markings.    

Puffins captured on film using sticks as a tool to scratch themselves

It's the first observation of seabirds using tools

Carly Scott

Evolutionary Biology

University of Texas at Austin

Zoologists have captured footage of puffins performing an unexpected behavior: using a wooden stick to scratch a difficult-to-reach itch. Analysis of animal behavior is important for understanding both evolution in the broad sense but also the evolutionary history of humans. One behavior humans excel at is tool use and understanding the origins of this behavior also gives us insight into what it means to be "us." Although tool use has been documented in some other species — like for food extraction in apes and crows — this is the first time body-care tool use has been recorded in seabirds. The researchers found two independent instances of puffins using a stick for body care in locations more than 1,700 km apart. 

This indicates a higher cognitive function in the seabirds than previously thought, and begs the question whether all puffins have this ability or if it arose in certain puffins only as an adaptation to the environment.  Above all else, this finding emphasizes that tool-use may be more widespread than formerly believed and a better understanding its origins may require the inclusion of additional, understudied taxa. 

My brother has 4% Neanderthal DNA. What does that actually mean?

Neanderthals are an extinct relative of Homo Sapiens, having died out around 40,000 years ago

Kristen Vogt Veggeberg

Science Education

University of Illinois at Chicago

Like a lot of Americans, my brother decided to fork over some cash and have his DNA analyzed to see his ancestry via 23andMe. The usual information popped up — some German ancestry, some Scandinvian, but then a strange name and number...4% Neanderthal.

Neanderthals are an extinct relative of Homo Sapiens, having died out around 40,000 years ago. They’re not exactly roaming the streets of Stuttgart like some of the other Vogts I’m related to. But, surely there are some applicable traits that we share, right? After all, my brothers and I often joked about our physical anomalies while growing up — we have large rib cages and shoulders, wide nostrils, and can handle brutal cold temperatures, which are all traits of what scientists such as Joshua Akey have attributed to Neanderthals

What this DNA does define, according to The Scientist, is that my modern human ancestors bred with Neanderthals roughly 50,000 to 55,000 years ago. A variety of scientists working on genome sequences have come up with different concepts as to why humans mated with their closely related cousins, and the effects it has on their far-flung descendants, such as my family. One of them is the effect on skin, as well as fatty tissue beneath, as Neanderthals survived in brutally cold environments thousands of years ago. Finally, a study mentions that some of these genomes may relate to psychiatric disorders that are prevalent in some human populations, which I myself happen to have.

Nothing much outside of interesting facts as they come, but I do find it funny when certain individuals glorify blond, blue-eyed, fair-skinned individuals like myself and my brothers. They have no idea that we’re not fully human. Maybe we should take them back to our caves and teach them how to get along, Neanderthal and human alike.

Solitary confinement is bad for the heart too

A new study shows that a third of individuals in solitary confinement are more likely to have heart attacks and strokes

Solitary confinement does little to rehabilitate inmates, is extremely expensive (where the average per-cell cost is $75,000), and exacerbates health problems — yet the American prison system is over-reliant on solitary confinement. In fact, a 2018 report found that, 61,000 individuals were being held in solitary confinement across the US. While the living conditions in such units are known to be associated with adverse health outcomes, we still don't understand the lifetime cardiovascular burden (i.e. the direct and indirect costs) associated with solitary confinement.

To explore the health consequences of solitary confinement, Brie Willams and her colleagues compared the lifetime cardiovascular health burden from solitary confinement, relative to those of inmates who were not held in isolation.

heart organ model anatomy

Hypertension refers to abnormally high blood pressure.

By jesse orrico on Unsplash 

The researchers first looked into public data from a 2015 lawsuit. This data contained descriptions of hypertension diagnoses among two groups of men: individuals in the first group who were held in a prison’s solitary confinement “supermax” units (the “Supermax Unit Group”), while individuals in the second group were housed in regular, less-isolating maximum security units (the “Less Isolated Group”). Both groups’ levels of loneliness were measured with the UCLA Loneliness Scale.

The researchers then used the Cardiovascular Disease Policy Model to estimate and compare the lifetime burden of cardiovascular problems for both groups, while accounting for potential factors, such as socioeconomic factors, which may affect comparisons. Medical costs associated with the cardiovascular disease burden were also estimated using California’s health costs, and these estimates were then deflated to the U.S. national average costs.

The study found that the hypertension rates were 31% higher in the SuperMax Unit Group than those in less-isolated units. In addition, about a third of the SuperMax Unit Group were more likely to experience heart attacks, strokes, and higher scores of loneliness.

In fact, the authors point out that if their findings were applied to simply 25,000 individuals held in “supermax” solitary confinement units, this alone would result in $155 million in additional future healthcare costs — and would likely still be an underestimate as there is a widespread use of solitary confinement beyond “supermax” units.

These findings call for a reform in American prisons. Evidence already shows that solitary confinement is counter-productive — this is one more study which points to the health consequences of solitary confinement.

Specialized nerves let squid tentacles strike with lightning speed

Squid have different types of nerves in appendages with different functions

Dori Grijseels

Neuroscience

University of Sussex

Contrary to octopuses, which only have arms, squid have both arms and tentacles. You can distinguish between the two by looking at the tips: tentacles have a bulb at the end, called a club, but arms do not. Additionally, the tentacles are extendable while arms aren’t, reflecting the difference in function between the two. Squid use the tentacles to strike at their prey and reel them in, at which point the arms take over and subdue the prey.

Squid have arms AND tentacles. Here, the tentacles are the whiter appendages with the clubs at the end.

prilfish via Flickr

Squid can extend their tentacles in 20-40ms, which is about 10 times faster than a blink. This is especially impressive, since they don’t use any spring-like mechanisms. They only use their powerful muscles for this, which are arranged in a special criss-cross pattern. However, their muscles aren't the only things with special adaptations. 

On 3 January, William Gilly from the Hopkins Marine Station and his colleagues published a study where they studied the nerves that drive these muscles. The most striking difference they found between the nerves that innervate the arms and those that innervate the tentacles, is that only the latter could produce action potentials. Action potentials are extremely fast electrical events where the inside of a nerve cell temporarily becomes more positive than outside the cell. This may cause the release of neurotransmitters, which in turn causes the muscle to move.  

Action potentials are widely used in vertebrates, but invertebrates, including the squid, often use graded potentials. This means that rather than a fast electrical event, there are gradual changes of the electrical charge. And this is the type of communication that the nerves in the arms of the squid use.

By using the quick action potentials for the tentacles, the squid can perform rapid strikes to catch their prey. The arms don’t need to move as quickly, so no action potentials are needed to move those. This is how squid not only evolved the muscles in their limbs, but also the nerves, to optimize each type of limb for its own specific job.

How many things can scientists name -Seq? Let us count the ways

From lettuce to cat poop to human cells, we're ready to sequence it all

Farah Qaiser

Molecular Genetics

University of Toronto

In the past decade, scientists have been slowly sequencing everything — and yes, I mean everything. Scientists have sequenced romaine lettuce to detect food-borne pathogen outbreaks, increasing numbers of people across the world to address under-representation in genomics, and even kitty poop to better understand the cat microbiome.

But in the midst of all these sequencing studies, what sticks out to me the most is how often scientists find a way to use the word -Seq when naming new methods. Here, Seq is short for sequencing, and is often used to name experiments which involve high-throughput sequencing.

So here's a list of the many ways scientists have managed to incorporate the word -Seq when naming new methods. It certainly isn't comprehensive, and doesn't include every -Seq method out there, but here it is anyway.

Here are (some of) the ways you can sequence DNA

scientific instrument

 The Oxford Nanopore MinION is a pocket-sized DNA sequencer  — just in case you want to sequence on the go.

Oxford Nanopore Technologies

There are so many different aspects of biology to consider today when it comes to sequencing DNA. Are you interested in learning what DNA interacts with? Try using ChIP-Seq to explore protein-DNA interactions, or if you want to get more specific, use MAINE-Seq to find DNA bound by histone proteins.

Interested in the regulatory regions of the genome? There's also FAIRE-Seq to identify regulatory regions in the human genome, and 4C-Seq to characterize how DNA is physically organized around regulatory elements. Or perhaps you're interested in whether DNA is methylated or not? If so, you can take your pick between BS-Seq, BisChIP-Seq, Methyl-Seq and so many more.

Want to look at RNA? There's a -Seq for that, too

The first step to building a protein in your cells is to transcribe DNA into RNA (ribonucleic acid). Scientists can map RNA using RNA-Seq, but that's not all. Check out RIP-Seq to find out where RNA-protein complexes are, dsRNA-seq to investigate double-stranded RNA molecules, and structure-Seq to find secondary RNA structures across the genome. There's even single-cell RNA sequencing (scRNA-seq) if you want to look at individual cells, which was hailed as Science's Breakthrough Of The Year in 2018. Fun fact: scRNA-seq was originally called mRNA-Seq, but perhaps that name wasn't catchy enough.

cartoon of the chemical structure of RNA

Sponk on Wikimedia Commons

Don't forget about CRISPR!

Scientists can use the CRISPR/Cas system to edit genes, but it doesn't always work out effectively. So why not use GUIDE-Seq to identify all the double-stranded breaks introduced by CRISPR/Cas enzymes? Or Digenome-Seq to capture off-target CRISPR effects in human cells? Or perhaps CIRCLE-Seq to capture off-target effects in vitro? Or...okay, I'll stop now. But there are so many more -Seq methods out there as the scope of sequencing continues to expand.

But let's face it: I also carry out DNA sequencing to better understand complex neurological disorders. If I ever developed a method, I'd try to find a way to fit -Seq in too when naming it. How else would you know that sequencing was involved?

Why did blue whales get so big when their prey is teeny tiny?

When the food source is abundant, animals with bigger mouths can consume more calories.

Marie Claire Chelini

Evolutionary Biology

University of Nebraska – Lincoln

When we think of large animals, whales immediately come to mind. Whales come in all sizes, though. Why aren’t dolphins and orcas (which are technically toothed whales) as large as blue whales? And how come blue whales, the largest of all animals, survive on the tiniest of prey items, such as krill? A new study published in Science explores these questions.

Amanda Slater via Flickr

Being so large could help whales dive deeper and for longer, which could be good for finding large prey. Yet, for toothed whales, such as sperm whales and porpoises, such large prey is rare and hard to find. This means that, although larger toothed whales can dive deeper, their prey/dive ratio is smaller than that of smaller whales. For baleen, filtering whales, however, the story is different. There is plenty of krill in the ocean. One of the main constraints to eating, for baleen whales, is to open their mouths wide enough to swallow massive amounts of krill-containing water. And guess who has bigger mouths? Bigger baleen whales.

For baleen whales, feeding efficiency increases with mouth size, which in turn increases with large body sizes. Huge baleen whales can swallow more calories per dive than their smaller cousins. Why aren’t blue whales even bigger, then? Scientists think that it is probably due to seasonal shortages in krill density. During dry spells, fat energy storages would probably not be enough to sustain an even bigger whale. 

For toothed whales, on the other hand, being very large is not really an advantage, since there are very few large prey to be found in the ocean. It’s more energetically advantageous for these toothed predators to be medium size and eat medium size prey, than to dive long and deep searching for an elusive large meal. 

Go to bed: sleep deprivation changes how you experience pain

New research highlights the role of the nucleus accumbens in how sleep-deprived individuals respond to pain

Kamila Kourbanova

Neuroscience and Molecular Biology

Johns Hopkins University

We have all felt the sensation of pain. And we are also all familiar with sleep, a necessary bodily process, has cognitive and physiological functions. While sleep is behaviorally regulated, research shows that poor sleep can actually tamper with our brain's processing of pain. Using fMRI imaging, scientists have now visualized the amplification of the pain signal in the somatosensory cortex of sleep deprived individuals. 

The somatosensory cortex is the area of the brain that registers pain stimuli, meaning it tells us where the pain sensation we feel is coming from. Then, the pain signal moves into the insula, the part of the brain which integrates all incoming signals and creates our conscious perception of pain. Following that, the signal is sent along to the nucleus accumbens (NAcc) which plays a major role in decision-making, reward, and pain evaluation. 


The study, published last year in the Journal of Neuroscience, found that the activity of the NAcc in sleep deprived individuals is altered: compared to the pain response in people who aren't sleep-deprived, the NAcc dulls incoming pain signals, increases pain-relief seeking behavior and affects decision-making. 

A previous study highlighted the increase of opioid consumption in burn patients after just one night of interrupted sleep, which reinforces the idea that sleep and our sensations of pain are closely linked. While research strongly supports the idea that sleep deprivation does increase pain, but exactly how our brains process the interplay of sleep and pain is still being investigated. For instance, the NAcc has broad connectivity with many regions of the brain including the prefrontal cortex, anterior cingulate cortex, and the amygdala (just to name a few). Future research should tease apart the question of “What’s more important: the amount of sleep we get or the quality of sleep?” 

But in the meantime, consider counting sheep an aid to resetting our bodies and our brains. 

Scientists, beware of the consequences of routine practices in your lab!

The harmless practice of using parafilm to seal agar petri dishes containing the model organism, C. elegans, actually impacts larval development

Matthew Vandermeulen

Biology

University at Buffalo

What if some of your common practices in the lab were actually having a significant effect on your results...and you just didn’t know about it? Recently, a group of researchers from Utica College found that the practice of using parafilm to seal agar petri dishes containing the model organism, Caenorhabditis elegans, actually has a significant effect on its early development.

C. elegans is a nematode and a well-established model organism which is often used to model various aspects of development. This organism is often grown on Nematode Growth Media (NGM) agar in a petri dish.

Image of the model worm C. elegans

Meet Caenorhabditis elegans — a common model organism used in biological sciences.

NGM can sometimes dry out or become contaminated by microbes, so to prevent this, researchers often wrap up the petri dish with parafilm, the way you wrap up food containers with plastic wrap in the kitchen. This practice has been used for a long time, however, it has never been fully explored to see if it actually affects nematode development. In this study, researchers tackled this very question and investigated whether wrapping NGM agar plates with parafilm had an effect on larval growth and development.

In their study, the researchers found that both the larval growth rate and length change after 48 hours were significantly increased when the NGM agar plates were wrapped with parafilm. 

Researchers also found reduced variability in growth among parafilm-wrapped replicates in this study. This echoes findings of a previous study which looked at the effects of parafilm on the model plant, Arabidopsis thaliana. Overall, this suggests that parafilm helps to create a standardized condition for measuring responses in model organisms.

Any researcher that uses parafilm as common practice with their organism should be aware of these possible effects and take the time to identify if this practice of wrapping up has any influence on their results. And in addition, perhaps there are other types of common practices out there that can affect results...that we just don’t know about yet. 

I chased lemurs around Madagascar to help stave off their extinction

Planting fruiting trees is a vital component of reforestation and conservation efforts

Jake Krauss

Wildlife Conservation

Rice University

A lemur, a primate cousin that evolved separately on the island of Madagascar, leaps above me through the rainforest canopy. Ninety percent of the lemurs on this island off the east coast of Africa are in danger of extinction. I am studying the Milne Edward’s sifaka, an endangered species of lemur in Ranomafana National Park. I am following these lemurs around to better understand their diet and behavior, research which hasn't been updated in over a decade but is very important for this species' conservation.

I’m a senior student at Rice University collecting data for my honor’s thesis. I received a grant from my school to go to Madagascar to conduct this research. 

I run through the forest after the lemurs, taking observations of their behavior every three minutes, following the protocol for past studies. During my time here I am following six different groups of lemurs, three in degraded forests and three in pristine forests. The group I'm following today, which occupies the disturbed forest, consists of two adults females and two juveniles. They run out of sight down a steep ravine. One false step, and I slide down the muddy slope on my butt. Desperate for every piece of data, I pick myself up and keep running to maintain pace with the lemur I’m focused on. She’s a mother, and a green-eyed baby pokes her head out below mom's belly. She nibbles on some young leaves, a common food item in this degraded forest.

As compared to the pristine forest, there are less vines and more tall trees with fruits and seeds. So far, my observations mirror the finding of previous research that lemurs eat more fruits and seeds in degraded forests because these foods are relatively more available. This research shows the importance of having these food items available for the sifaka lemurs to eat and reinforces the approach taken by reforestation efforts elsewhere on the island: tree species that yield abundant seeds and fruits should be prioritized.

I will return to the US after my time with the lemurs and publish these results. Hopefully, this will aid conservation managers in informing reforestation efforts to provide food for the endangered Milne Edwards’s sifaka lemurs.

Hermit crabs are using old bottle caps and plastic as shells — and it's killing them slowly

Around 570,000 crabs become entrapped in debris each year on the Henderson and Cocos (Keeling) islands

Dori Grijseels

Neuroscience

University of Sussex

Unlike many other crustaceans, hermit crabs don’t have their own hard shell to protect them. Instead they find an empty shell, often left behind by a sea snail, to climb in. However, hermit crabs are not particular about their shell: in fact, an artist convinced hermit crabs to use 3D printed shelters in the shape of famous cities. 

Because of this, we might expect that hermit crabs are quick to adapt to increasing amounts of plastic on their beaches. Indeed, crabs have been found using old bottle caps and other plastic objects as shelters. But a new study by Jennifer Lavers from the University of Tasmania shows that this plastic is in fact incredibly damaging to hermit crab populations. 

The major danger for the crabs is plastic bottles that wash up on shore. If these bottles don’t have a cap or have a hole of some sort, the hermit crabs may climb in them. However, they often can’t climb out again and get stuck without food and water, causing them to die after about a week. 

note: Dori (lab note author) gave permission to use this

Hermit crabs as seen in Okinawa.

Dori Grijseels (2019)

This is the start of a chain reaction. Hermit crabs rely on their shells to survive, and good shells are hard to come by. If a crab dies, it releases a special odor that other crabs can detect. They will climb into the bottle in search of the shell of the dead crab, but get stuck themselves. This was probably the cause of the single bottle with 526 hermit crabs stuck in it that the researchers found. They estimated the total number of hermit crabs that got stuck in bottles on the Cocos (Keeling) Islands and Henderson Island was about 507,000 and 62,000 respectively. 

We often hear about the damage plastics cause in our oceans, but this research shows that the effects are not limited to marine environments. Many terrestrial animals are also endangered by the plastics that accumulate on beaches. If we don’t reduce the amount of plastics that end up in the ocean, we could risk extinction of these species.

Shi En Kim

Molecular Engineering and Materials Science

University of Chicago

You’ve probably heard of the Google Glass (and its demise), but there are more vision-based wearables in development, including smart contact lenses. Smart contact lenses are not yet available on the market, partly because they face additional technical challenges. Most people might overlook the inconvenience of wearing spectacles, but we probably won’t see eye-to-eye on the matter of placing an electronic device directly on our eyeballs. 

Recently, a group of South Korean researchers demonstrated that their latest smart contact lens design is indeed feasible, going as far as to demonstrate for the first time that their prototype can be worn safely by humans.

It seems so — it is made from hybrid nanomaterials encased in a soft, stretchable polymer. The lens can be elongated up to 1/3 more than its original dimensions, repeatedly too.

Is the lens safe? Check — it operates at low voltages and maintains a stable temperature far below body temperatures. 

Is it convenient to use? Why, yes — it can be wirelessly charged to full power in four minutes. The researchers claim that their smart contact lens are the first that can be operated continuously, thanks to a built-in supercapacitor. The supercapacitor stores a large amount of charge per unit volume and releases it, allowing for continuous function.

How is this contact lens “smart”? Well, it blinks. So far, its only function is for an embedded LED to turn on and off. 

Nevertheless, this research has cleared the major technical hurdles. Now, it behooves the rest of society to ask why we should want smart contact lenses. 

Previous attempts by major companies have had outlooks far from eye-catching. Google Contact Lens was conceived in 2014 for monitoring glucose levels in tears, but the project has been discontinued because of measurement inaccuracies. Samsung has filed several patents to develop smart contact lenses for augmented reality, but a concrete product remains nowhere near market-ready. If we blindly chase after the bandwagon, then smart contact lenses might suffer the same fate as the Google Glass

Here's how earthquakes rocked Puerto Rico into another emergency

Multiple events shook Puerto Rico's southern coast

Michele Cooke

Geosciences

University of Massachusetts Amherst

The moderate earthquake in Puerto Rico makes January 5th's 5.8 a foreshock (Ed: a tremor that occurs before a larger event, the mainshock). There have been several earthquakes over the past few days along the southern coast of Puerto Rico.

The map below is from the IRIS interactive view, showing earthquakes since Saturday with depth in color (purple = <33 km) and size denotes magnitude. The east circle represents the largest event, which is not quite co-located with the other events.

A map of seismic events around Puerto Rico that occurred in January 2020.

Michele Cooke

The focal mechanism shows normal slip event with some strike-slip (Ed: one kind of motion involved in an earthquake, where plates are moving horizontally relative to each other) and the expected seafloor displacement triggered a tsunami warning, which was cancelled.

Anthony Lomax

The following image from Wikipedia views Puerto Rico from the northeast showing the Puerto Rico trench to the north of the island and the less active Muertos Trough to the south of the PR.  The recent shallow normal-strike-slip slip seismicity is likely related to the deeper Muertos trough. Like other islands in the northern Caribbean, strain within Puerto Rico is partitioned with off-shore subduction zones and on-shore strike-slip systems.

Puerto Rico from the northeast showing the Puerto Rico trench to the north of the island and the less active Muertos Trough to the south of Puerto Rico.

You've probably seen the reports coming out of Puerto Rico of widespread damage from shaking. The soft first story of many buildings have collapsed. When you think "soft first story," think of vertical posts to support the house so you can park underneath. When the ground shakes, these posts are very unstable. 

We will likely learn of more damages and fatalities with time. I hope that the federal government acts quickly to support our fellow citizens in crisis in and not repeat mistakes made after Hurricane Maria.

Coral reef bacteria are being killed off by human activity

Microbes could provide important clues about the health of coral reefs

Janani Hariharan

Soil Science

Cornell University

Across the globe, coral reefs are in trouble. One of the biggest challenges we face today is figuring out how to save them. Like any good doctor, we need an efficient and reliable way to determine how sick or healthy different coral reefs are. A team of researchers from the USA, Mexico and Cuba wonder if reef microbial ecology might be the answer. 

Photo by Francesco Ungaro on Unsplash

To understand how the microbial community differs between different types of reefs, the team sampled water from different coral reefs on the coasts of Florida and Cuba. Jardines de la Reina in Cuba, a reef that has been largely protected from human activity, had the richest microbial community. This area was especially rich in bacteria that can perform photosynthesis and cycle nitrogen, thus increasing productivity in the region. 

In contrast, the site that had been most impacted by human activity, the Florida Keys, had a smaller and more variable microbial community. Disturbances like overfishing, coastal development and nutrient run-off in the Keys seem to have produced a small but competitive group of microbial residents. Studies like these can help us understand how human activity can disturb the microbial communities of coral reefs.

Previously used metrics like coral coverage and algal coverage did not vary significantly between these reef systems, indicating that these might not be the best metrics to measure coral reef health. Perhaps it's time to let the microbes speak and tell us the true story of coral reef health. 

Nanoparticles could one day store your vaccination record in your skin

Quantum dots successfully provide in-skin vaccination record (in rats)

Satarupa Bhaduri

Cell Biology

University of California, San Diego

Vaccines save 2-3 million lives around the world annually. However, 1.5 million deaths from vaccine-preventable diseases still occur each year. Although many factors may lead to undervaccination, one important factor is the inability to accurately determine whether an individual has previously received a given vaccine, especially in developing countries where many people may not have vaccination records

Several alternatives to the traditional paper records have been proposed, including smartphone-based databases, fingerprinting and communication chips. However, these expensive options have not yet become prevalent due to difficulty in implementation. 

In a recent study published in the journal Science Translational Medicine, a group of researchers, including scientists from MIT and the Chinese Academy of Sciences, has come up with a cheap and easy-to-implement solution. They have designed a system to administer and detect very small nanoscale particles called quantum dots. The quantum dots are administered along with the vaccine and remain in the skin, serving as a vaccination record. 

First, the researchers had to synthesize the quantum dots, which are very small crystals, in the range of 2-10 nanometers. These particles are widely used in biomedical imaging, photovoltaic cells, and some TV screen displays. Scientists selected one type of quantum dot (called S10C5H) for its structural and functional stability under simulated sunlight. The quantum dots were then encapsulated in micro-sized capsules made of a special polymer. These encapsulated particles wrapped in pigmented human skin showed stability upon exposure to simulated sunlight up to an equivalent time of 5 years. The encapsulated polymers were packed in microneedles that were designed to dissolve in the skin.

A pair of black and white rats

A pair of black and white rats

Jason Snyder on Wikimedia Commons

The researchers subsequently treated rats with these dissolvable microneedles containing the polio vaccine and quantum dots (as the record of vaccine administration). No significant unaccounted tissue damage or toxicity was observed in the rats. The quantum dots could be visualized only under special LED lights in the near-infrared region (like the waves emitted by remote control), so they are invisible to the naked eye. For imaging purposes, researchers designed special lenses and imaging software for a Google Nexus 5X smartphone. Scientists found that the record-keeping quantum dots remained visible under near-infrared light for at least nine months. Furthermore, the dots did not seem to negatively impact the effectiveness of the vaccine: animals had antibody levels that were considered high enough to protect them from the disease.

For effective usage in the real world, clinical studies assessing biocompatibility and potential toxicity of the encapsulated dots will have to be done on humans. Overall, this study opens new and exciting possibilities for medical data storage, which could prove very valuable in eliminating vaccine-preventable diseases. 

DNA barcodes help identify fish eggs and inform conservation

Determining where fish spawn could help us protect these crucial habitats and bolster declining fish populations

Makenzie Burrows

Marine Science

University of South Florida

Fish are economically and ecologically important in the Gulf of Mexico, yet their stocks are decreasing due to overfishing. One major way that we can help protect fish is to protect the habitats where they reproduce. But in order to do that, we first have to find out where they reproduce. One way to find these spawning habitats is by using floating fish eggs.

Nicole Seiden

Before setting up projects focused on reef fishes, like grouper and snapper, we needed to know if eggs from shallow water fishes stay in the shallows or if the eggs move into deeper waters as they float.

Fish eggs can be found in most surface waters, making them easy to collect with a plankton net. However, these eggs are usually clear balls the size of the tip of a pencil, making them difficult to visually identify down to species level. To solve this problem, we use a laboratory method called DNA barcoding. DNA barcoding allows us to look at the genetic material of each fish egg to figure out which species it belongs to. Each species has a unique DNA signature, just like how each product at a grocery store has its own unique barcode.

Using DNA barcoding, we found that most shallow water fish eggs stay in shallow waters. This information will help us plan future fish egg collections to help inform fisheries managers where and how much these shallow water species are spawning. 

Photons pop in and out of existence to transfer heat

It isn't heat conduction, convection, or radiation

Katherine McCormick

Quantum Physics

University of Washington

When we learn about heat transfer in school, we learn there are three types: conduction, convection, and radiation. But scientists have finally observed a fourth type of heat transfer, and it's all thanks to quantum mechanics.

One main principle of quantum mechanics is so-called zero-point energy, or vacuum fluctuations. This means that, even at a temperature of absolute zero, a system will still have some amount of energy. This causes all sorts of bizarre phenomena, like particles randomly popping in and out of existence near a black hole, or, in this case, photons popping in and out of existence between two plates of metal. Known as the Casimir effect, these short-lived, "virtual" photons can transfer energy from one of the metal plates to the other.

The scientists observed the effect in this new experiment by making the metal plates out of a deform-able material that can vibrate like the head of a drum. Each of these drumheads were tethered to blocks at different temperatures. Heat from the blocks caused the atoms in the plates to jiggle faster, making them vibrate. But because the blocks were at different temperatures, the two drumheads vibrated with different amounts of energy. When they were brought close enough together, the scientists saw that the Casimir photons took energy from the hotter drumhead and transported it across the vacuum to the cooler one, until the two were in thermal equilibrium. 

Overall, the influence of quantum mechanics on everyday human experiences like temperature is a hot research area, and I personally find it pretty cool!

Ice Bucket Challenge donations have helped fund promising ALS clinical trials, especially for "fast progressors"

There are currently only four drugs approved to help treat amyotrophic lateral sclerosis (ALS)

Monica Javidnia

Neuroscience

University of Rochester

Promising results from a Phase 2 clinical trial show AMX0035 (Amylyx Pharmaceuticals), a combination of sodium phenylbutyrate and tauroursodeoxycholic acid, may slow disease progression in individuals with amyotrophic lateral sclerosis (ALS). The news comes days after the passing of Pete Frates who championed the ‘Ice Bucket Challenge’, raising global awareness of the devastating disease and over $200 million for research and advocacy efforts. The trial, known as CENTAUR (Combination of Phenylbutyrate and Tauroursodeoxycholic Acid), was funded in part by Ice Bucket Challenge donations.

ALS affects approximately 16,000 people across the United States, and only four drugs are currently approved to help treat the disease. In ALS, a loss of nerve cells that control movement (motor neurons) leads to progressive muscle weakness. As the disease progresses, people with ALS experience difficulty with movement, speaking, eating, and breathing, and may require interventions such as a tracheostomy to prevent respiratory failure.

The CENTAUR clinical trial found that research participants taking AMX0035 had a significant reduction in disease progression compared to placebo, as measured by the ALS Functional Rating Scale. Notably, enrollment criteria for the study selected 'fast progressors' — a subtype of participants believed to be more likely to show an effect (if there is one) during a trial — by studying a database of over 10,000 people with ALS. In an interview with Neurology Live, study principal investigator Dr. Sabrina Paganoni stated, "These patients are not biologically different from other people with ALS; this was basically a statistical strategy to increase our power to see a treatment effect with a relatively smaller trial." Participants are being invited to enroll in an open-label extension study, providing everyone with access to the study drug and an extended follow-up period. 

Prior research studies have found that sodium phenylbutyrate improved outcomes in an ALS mouse model and provided neuroprotection, while tauroursodeoxycholic acid reduced endoplasmic reticulum stress and prevented neurotoxicity. Both tauroursodeoxycholic acid and sodium phenylbutyrate were each individually tested in people with ALS, but there was no larger-scale follow-up of the compounds until now. Amylyx Pharmaceuticals found the combination reduced cell death, prompting the current trials in ALS as well as Alzheimer’s disease.

Being exposed to reactive oxygen helps worms live longer lives

Worms exposed to reactive oxygen species early in life actually lived about 18% longer than their unexposed counterparts

Satarupa Bhaduri

Cell Biology

University of California, San Diego

The most widely accepted theory of ageing is that reactive atoms or molecules of oxygen, referred to collectively as reactive oxygen species (ROS), damage molecules like lipids, DNA and proteins. Accumulation of ROS has been implicated in many age-related diseases, including chronic obstructive pulmonary disease, chronic kidney disease, neurodegenerative diseases, and cancer.   

In a recent study published in Nature, a team of scientists from the University of Michigan and the Chinese Academy of Sciences have discovered that roundworms (Caenorhabditis elegans) exposed to high levels of ROS in the early stages of their development are more resistant to oxidative damage, and this allows them to live longer. Roundworms are powerful biological model organisms as most of their genes have functional counterparts in humans. So, this could illuminate how to mediate the effects of aging in humans, as well.

The group studied two different groups of roundworms who experienced different ROS levels during early development, allowing them to categorize the worms as being in one of two states: oxidative (stressed) and reduced (normal). Both groups of worms went on to have similar ROS levels to each other in early adult stages. However, by late adulthood (day 7 in worms), they saw that the oxidized group had significantly lower ROS levels than the reduced group, and they were living about 18% longer. 

The researchers also looked at gene expression patterns in the two groups of worms to determine the molecular mechanism of the stress resistance. They found a major difference in the way that proteins called histones function. Histones package and order DNA. An enzyme called H3K4me3, which alters the chemical structure on the surface of the DNA, was found to be reduced in the worms that had been part of the oxidated group early on. This modification acted as a form of memory for the cells and led to increased stress resistance in later life. 

This study establishes how early-life events alters DNA expression throughout an organism's life and ultimately leads to stress resistance and increased lifespan. One next step is to look for evidence that similar mechanisms play a role in human aging. This important study might eventually lead to improved treatments for age related degenerative diseases.

Not surprisingly, science still has a huge racism and sexism problem

All STEM fields have this problem, with physics having particularly large gaps

Vanessa Vieites

Psychology

Florida International University

Stereotypes about others’ gender and race can influence the way we perceive and judge them. Such biases have been shown to affect employers’ hiring decisions, even when evaluating “fake” but identical resumes. A 2019 study examines how intersecting stereotypes about gender and race influence professors’ perceptions of fictitious post-doctoral candidates applying for positions in different STEM departments at universities. 

In science, as the study shows, there is still a tendency to view women as less competent and hireable than comparable men, but fields that are more male-dominated (i.e., physics) appear to be more discriminating than those that are more gender-balanced (i.e., biology). Meanwhile, Black and Latinx PhDs, especially those who are women, tend to be viewed as less competent or hireable than comparable White and Asian PhDs. 

We’ve known there to be racism and sexism in the academy for a long time, but what is unique about this study is that the authors took an intersectional approach to their analyses. For instance, instead of just looking at the effects of race (i.e., black vs white applicants) or gender (i.e., men vs women) on professors’ ratings of applicants’ hireability, likability, and competence, the authors made sure to analyze the effects of intersecting identities (i.e., Black/Latinx/Asian women, Black/Latinx/Asian men in comparison to white men/women) on such outcomes. Their results highlight how understanding the underrepresentation of women and racial minorities in STEM requires examining how racial and gender biases intersect.

What I found most interesting about the study’s findings is that even though physics and biology are both STEM fields, the discrimination against women was found more so in physics, where women are severely underrepresented compared to biology (Women earn a little more than half of doctorate degrees in biology but only one-fifth of the doctorate degrees in physics). Similarly, the study also found that Asian applicants were not discriminated against compared to black and Latinx candidates, which further supports the point about representation in STEM fields making a difference in how job candidates of different groups are perceived and rated for those jobs.

These findings raise some important questions and implications about gender and racial discrimination in STEM. Would women be more accepted in currently male-dominated professions if those professions were more gender-balanced? Do women and some racial minorities appear "out of place" in physics because they are underrepresented in that field as it stands, thus leading to hiring biases? Are women relatively accepted in the life sciences because such fields have become more “feminized” over the years and, thus, are perceived as “easier” to excel at? 

We need better volcano forecasts to prevent tragedies like New Zealand's Whakaari explosion

Researchers are working on modeling eruptions to prevent loss of life when volcanoes explode

Two weeks ago, Te Puia O Whakaari Island, off the coast of Aotearoa (New Zealand), erupted, killing at least 16 people. The volcanic alert level for the island was raised to Level 2 in November, suggesting the volcano may be entering a state of increased volcanic activity. But what does a Level 2 mean? And is it even possible to forecast when a volcano can erupt?

Raising the volcano to a Level 2 indicates changes in volcanic parameters (like seismic activity). Levels 1 and 2 relate to volcanic unrest, while levels 3-5 indicate current eruptions. GeoNet, a hazard monitoring program of Aotearoa, indicates that eruptions can occur at any level on the scale, and sometimes no eruptions occur even after alert levels are raised. After the island was raised to a Level 2, an eruption likelihood was calculated on December 2nd, estimating an 8 to 14% chance of an eruption in the following 4 week period. The eruption occurred 7 days later on December 9th.

Photo by Farrah Fuerst on Unsplash

A sub-discipline of volcanology research is centered around improving forecasts of when volcanic eruptions may occur. While strides are being made in this area of research, not all volcanic eruptions are the same, and some are harder to forecast than others. Monitoring around active volcanoes is used to forecast if an eruption is possible in the near future. Parameters such as seismic activity, flow of electrical current through rock, deformation of the ground around the volcano, and changes in the gas emitted from volcanoes (such as an increase in sulfur dioxide) may all be a precursors to an eruption and are often part of a monitoring program. However, changes in these parameters may occur without an eruption, and sometimes eruptions may even occur without any notable changes in those parameters.

The Whakaari eruption was a steam-based eruption, among the hardest to monitor. Shane Cronin, a Professor at the University of Auckland, explains that in these types of systems, water is trapped in rock pores, and any changes in the system may cause a sudden expansion of the water into steam, leading to catastrophic eruptions.

The likelihood of continued eruptions of Whakaari are steadily decreasing, but these events beg the question of what can be done to assure safety of those who live near and travel to active and dormant volcanoes. Massey University volcanologist Associate Professor Gert Lube and others were recently awarded a million New Zealand dollar grant to test volcanic eruptions and flows, similar to those that occurred in Whakaari, using computer simulations. They hope their research will help more effectively assess risks associated with volcanoes like Whakaari.

Could radiation in deep space fry astronauts' brains?

New research in mice suggests that long-term low-dose radiation impairs learning and memory

Thiago Arzua

Neuroscience

Medical College of Wisconsin

Even though it happened half a century ago, the Moon landing remains one of the most ambitious space exploration projects ever. The future, however, holds even more exciting and longer flights. It takes about a week to get to the moon and back, depending on the route. But the much-talked-about trip to Mars would take us, at a minimum, 8 months — one way. During those months, aspiring interplanetary settlers would be exposed to a constant dose of radiation, without the protection usually afforded by Earth’s magnetic field. 

We are still unsure about the impact that this radiation exposure could have on  astronauts’ bodies. New research done by a group led by Charles Limoli, a radiation oncologist at the University of California, Irvine, suggests that chronic, low dose radiation can lead to severe impairments in learning and memory, as well as distress behaviors — at least in mice.

In this study, the scientists exposed mice to radiation at a rate of 1 milligray per day for 6 months — a relatively low dose that is comparable to what a deep-space astronaut would encounter. After this exposure, the scientists examined the hippocampus of the mice, the area of the brain responsible for the formation of memories. There they found differences in the electrical activity between the exposed mice and the control group. Exposed mice also had reduced synaptic plasticity — the ability for neurons to make new connections, which is an important component of learning.  Scientists also  conducted tests to measure both cognition and anxiety. These tests showed that the mice exposed to radiation performed worse in learning and memory tests and displayed increased anxiety-like behaviors.

Mars shot from the Curiosity Rover

NASA Goddard Space Flight Center via Flickr

So what does this mean for future Mars missions?

In the original paper, researchers write that this “radiation environment in space will not deter our efforts to travel to Mars.” This is exactly the type of research needed if we are serious about a settlement on the red planet. While we do not have immediate answers to the radiation problem, understanding how it affects brain function is a start. In space travel, and in science in general, there are known unknowns and unknown unknowns. The more unknowns we are able to study here on Earth, the better the chances of humans setting foot on another planet in the foreseeable future.

Good news: Canadian Arctic seals have not been eating plastics

Publishing null results helps us understand where wildlife is safe from plastic ingestion

Farah Qaiser

Molecular Genetics

University of Toronto

Plastics are everywhere. It isn't just humans who are ingesting microplastics on a daily basis, but animals too, such as sea turtles and albatrosses. Plastics can even be found in remote locations, including a high-altitude lake in the Pyrenees mountains in southern France. This increase in plastic pollution prompted researchers to ask: how prevalent is marine plastic pollution, and to what extent is it impacting Arctic wildlife?

But there's good news here for once: a new study out in the Marine Pollution Bulletin found no sign of plastics in the stomachs of 142 seals found in the eastern Canadian Arctic.

Madelaine Bourdages

Seals are an important member of the Arctic marine ecosystem, and act as a vital source of nutrition, cultural and economic value in northern communities. Any plastic ingestion would impact not only the seals, but their surrounding ecosystem and communities too. To investigate whether seals were ingesting and accumulating plastics, researchers collaborated with Inuit hunters to examine the stomach contents of 142 seals found in Arviat, Naujaat, Sanikiluaq, and Iqaluit between 2007 and 2019. 

Together, the Inuit hunters and researchers characterized the seals; they  determined age, examined tissue pathology, and used sieves to collect plastics >425 μm in size (that's about the size of the period at the end of this sentence!) in the stomach contents for 135 ringed seals (Phoca hispida), six bearded seals (Erignathus barbatus) and one harbour seal (Phoca vitulina).

The study found no accumulation of large plastics in the seals examined. Instead, krill or small fish were found in the seal stomachs, with a few containing parasitic roundworms. Around 30 seal stomachs were empty (consistent with other studies), and for 10 stomachs, the contents could not be identified as they were partially digested.

Seal stomach contents.

Madelaine Bourdages

It's worth noting that there may have been microplastics smaller than 425 μm in the seal stomachs. These microplastics wouldn't have been picked up by the sieves, but they also are likely too small to be retained and would have passed straight through the seals' stomachs.

The lead author, Madelaine Bourdages, is a graduate student at Carleton University. Bourdages commented that the results were somewhat surprising given the increase in plastic pollution in the environment, but points out that since “the majority of the seal stomachs contained euphausiids [krill] and fish, [this] suggests that the seals we looked at were likely feeding somewhere in the middle of the water column, and could have potentially been less exposed to larger plastics that typically either float or sink.”

Interestingly, this study is one of the few to report zero plastic ingestion; others include no plastic ingestion found in 134 silver hakes (Merluccius bilinearis) on the Newfoundland south coast, and in Antarctic fur seal scat and albatross stomachs from three islands in the Indian and South Atlantic Oceans. Reporting null results like this study is important — not only to establish a baseline to monitor marine plastic pollution in this particular region, but to better understand where plastic ingestion is and isn't happening.

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