PNAS

Dolphins, incredibly, have a unique naming system for each other, encoded in their “language of echolocation”. PNAS (a real journal, stop snickering) published the study in their August 6 issue.

We’ve known that dolphins have underground societies for a while now (where do you think Atlantis came from) but finally, my party-trick fact of dolphins talking about each other behind their backs IS ACTUALLY BELIEVABLE.

theconversation.com
Red, yellow, pink and green: How the world's languages name the rainbow
New research investigates how people sequentially add new color terms to languages over time – and the results hold surprises about assumptions linguists have made for 40 years.
By Claire Bowern

Claire Bowern has a new paper about how people add words for different colours to their languages, and she’s written up an accessible version of it for The Conversation. Excerpt: 

Color words vary a lot across the world. Most languages have between two and 11 basic color words. English, for example, has the full set of eight basic colors: black, white, red, green, yellow, blue, pink, gray, brown, orange and purple. In a 1999 survey by linguists Paul Kay and Luisa Maffi, languages were roughly equally distributed between the basic color categories that they tracked.

In languages with fewer terms than this – such as the Alaskan language Yup'ik with its five terms – the range of a word expands. For example, for languages without a separate word for “orange,” hues that we’d call “orange” in English might be named by the same color that English speakers would call “red” or “yellow.” We can think of these terms as a system that together cover the visible spectrum, but where individual terms are centered on various parts of that spectrum.

Does that mean that speakers of languages with fewer words for colors see less color? No, just as English speakers can see the difference between the “blue” of the sky and the “blue” of an M&M. Moreover, if language words limited our perception of color, words wouldn’t be able to change; speakers would not be able to add new distinctions.

My colleague Hannah Haynie and I were interested in how color terms might change over time, and in particular, in how color terms might change as a system. That is, do the words change independently, or does change in one word trigger a change in others? In our research, recently published in the journal PNAS, we used a computer modeling technique more common in biology than linguistics to investigate typical patterns and rates of color term change. Contrary to previous assumptions, what we found suggests that color words aren’t unique in how they evolve in language.

Read the whole thing.

Here’s a worksheet from the World Colour Survey of 1976-78, if you’re wondering how colour terms are collected in the first place. And here’s a long read about the history of researching colour typology, to put this new study into some context.

Blindsight is an incredibly interesting phenomenon

Some people are cortically blind - their eyes still work fine, but the part of the brain that processes the visual information from the eyes is damaged, and so they cannot see. Cortically blind patients will have different blind spots and different severities of blindness depending on the extent and location of the brain damage. Interestingly, some of these patients are able to respond to visual stimuli that they are adamant they do not see. For example, if a researcher presents a screen with red stripes on it to the blind visual field of the patient, and asks an individual with blindsight what they see, their typical response would be - “Nothing”. However, if the individual is forced to answer - they would “guess” red stripes. Past studies have shown that blindsight individuals guess with much higher than chance odds - with around 90% accuracy in some studies. 

What is even more remarkable is that this also seems to apply to obstacle avoidance. In a past study (Striemer, Chapman & Goodale, 2009) they tested a man with a blind left visual field, and a sighted right visual field. The task they gave him was rather simple - reach from a start button to a target strip with his hand. However, he had to wear special glasses that briefly covered his eyes, so as to allow researchers to place obstacles in between the start button and the target strip. The glasses then allowed researchers to test his blind visual field and sighted visual field separately, but only allowing one eye to see at at time.

As expected - when obstacles were placed in his sighted visual field, he performed the same as normal controls. However - he was also sensitive to the position of obstacles in his blind visual field! He never reported seeing any of the obstacles placed in his blind visual field, but he did not collide with any of them either.

Read the original paper

Watch a video of a blindsight patient avoiding obstacles while walking

(Just for your info - this blog post was inspired from a lecture given by Gregor Thut, from the Psychology Department at the University of Glasgow, 2012). 

West Nile virus is devastating bird populations

West Nile virus is crippling North American bird populations, killing millions of birds across the continent and affecting species year after year, according to new research partially funded by NSF. The research – which included scientists from UCLA, Colorado State University and Washington University – reveals that bird populations have suffered from West Nile far more than previously thought.

The discovery shows the harm infectious diseases can bring, and offers insights into the effects of future outbreaks. It was published this week in the scientific journal PNAS.

Keep reading

Bonobos’ attention attracted by emotions
via ScienceDaily, March 16, 2016

Bonobos – just like humans – pay more attention to pictures that show other members of their species displaying emotional behaviour than to neutral scenes. Leiden researcher Dr Mariska Kret made this discovery while conducting research at Apenheul Primate Park.

Social grooming, sex and yawning

Unlike humans, however, bonobos prefer to look at positive behaviours: social grooming, sex and yawning. Bonobos, with chimpanzees, are the closest living relatives of humans. Research on their emotional behaviour can therefore also give insight into how emotions have developed in humans, says Kret. However, this type of research in bonobos is still quite rare. Together with colleagues from the University of Amsterdam and Apenheul, Kret is now publishing her findings in the journal Proceedings of the National Academy of Sciences (PNAS).
(continue reading)

Journal Reference:

Mariska E. Kret, Linda Jaasma, Thomas Bionda, Jasper G. Wijnen. Bonobos (Pan paniscus) show an attentional bias toward conspecifics’ emotions. Proceedings of the National Academy of Sciences, 2016; 201522060 DOI:10.1073/pnas.1522060113 (x)

Friction controls viral DNA ejection

Bacteriophages are viruses which infect bacteria, many of which contain double-stranded genomes packed down to almost crystalline densities. The inherent pressure this creates is exploited to “eject” the DNA into the now-infected bacterial cell.

The figure above shows 3 runs of a Monte Carlo molecular modelling simulation, which provided evidence that the topology and organisation of DNA inside the viral capsid is key to determining control and timescale of this ejection.

Even with similar osmotic pressure pushing out the DNA, we find that spatially ordered DNA spools have a much lower effective friction than disordered entangled states. Such spools are only found when the tendency of nearby DNA strands to align locally is accounted for.

This topological or conformational friction also depends on DNA knot type in the packing geometry and slows down or arrests the ejection of twist knots and very complex knots. We also find that the family of (2, 2k+1) torus knots unravel gradually by simplifying their topology in a stepwise fashion.

Finally, an analysis of DNA trajectories inside the capsid shows that the knots formed throughout the ejection process mirror those found in gel electrophoresis experiments for viral DNA molecules extracted from the capsids.


I’ve posted about the relationship between DNA knot linking number and electrophoretic mobility (abovein a previous post, however the type of structure modelled here is entirely new to me.

Cholesteric structures were named after the well-known molecule which can make up as much as half (50 mol%) of the lipid membrane in eukaryotic cells. Some cholesterol derivatives generate the liquid crystalline “cholesteric phase”, which is in fact a chiral nematic phaseits colour changing with temperature.

DNA-cholesteric interactions have nothing to do with cholesterol, but rather the “cholesteric” phase DNA enters at high densities. The crystal forms a helix (on top of the DNA helix, in turn subject to helical supercoiling) and is therefore chiral (“left- or right-handed”).


» Check out the Simple View on a Complex Matter series from the optics/photonics society SPIE.

Furthermore, the crystal is organised in layers, with no positional ordering between them, but a director axis for each layer, which varies periodically in nature.

To better understand the impact that DNA spatial arrangement has on its ejection kinetics we consider the ordering effects of local DNA–DNA interactions. We concentrate in particular on the known tendency of contacting dsDNA strands to align at a small angle with respect to each other (regardless of the 3′–5′ orientation in each of the strands).

Increasing evidence shows that this cholesteric interaction is not only important for the formation of cholesteric phases in concentrated solutions of DNA but can favor the spool-like DNA arrangements of viral DNA inside small capsids. Moreover it can control the complexity of DNA self-entanglement in the form of knots. It is useful here to recall that DNA knots have been already reported for some bacteriophages, although it is not yet clear how virus-specific effects (such as the genome anchoring to the capsid) may affect knot type and abundance.

The authors suggest this biophysical mechanism has been unexplored for too long, their results hinting at an explanation for observations of variable and as yet unpredictable ejection speeds, dormancy and “occasional major pauses during genome delivery”.

analagous to the unraveling of a neatly coiled anchor line once the anchor is thrown overboard

In most of these cases we find that the genome forms a spool which can be released by pulling out the end at the exit pore, without propagating disturbances to the rest of the chain which reptates inside the capsid.

In the main figure (top), the DNA-cholesteric interactions were considered for runs and B, and neglected in C, leading to a disordered, entangled DNA conformation inside the virtual capsid. A and B differ in their absence and presence of an initial lag phase, respectively. The rainbow colour scheme gives a simple indication of position along the DNA and (for clarity, not in the actual model) the rendered size of the beads was decreased systematically going from the red to the blue end.

The cholesteric interaction… is known to deeply affect the conformational organization of the phage genome at various scales. Indeed, at the local level it promotes the collinearity of contacting strands, whereas globally it affects the presence and complexity of physical knots in the packaged DNA.

Could this be a way for a virus to ensure its DNA is present and correct before ejection? The authors make no comment on the biological implications of this novel form of genome regulation, but the bias created for torus knots (imagine wrapping DNA around a bagel) over twist knots (linking together two ends of a twisted loop) must surely have consequences for which levels and types of topoisomerase for example will lead to successfully ejected DNA.

Moreover, given the dependence of these effects observed with ionic strength, as well as the importance on liquid crystal structure of local temperature and entropic changes, a capsid’s changing structure and permeability to ions could have knock-on effects to the ejection process — could this mean potentially unforeseen modes of blocking infection?

⌘ Marenduzzo et al (2013) Topological friction strongly affects viral DNA ejectionPNAS, 110(50) 20081-6

2

Researchers have discovered that Jökulsárgljúfur, a 28-kilometer long, 100-meter deep canyon in Northeast Iceland, was created by just a few days of catastrophic flooding, separated by thousands of years.

The study published in PNAS concludes that the extreme floods occurred 9,000 years ago, 5,000 years ago and 2,000 years ago and lasted only a few days each. They were triggered by the volcanoes beneath Iceland’s ice sheet. Eruptions from these volcanoes would have released vast amounts of water from glaciers.

Theses flooding events were so powerful that they tore up the bedrock and formed the canyon’s walls. These eruptions also pushed three of Iceland’s waterfalls, including Dettifoss -Europe’s most powerful waterfall-  upstream by as much as 2km, retreating at a startling rate of hundreds of metres within days.

From here and there

Fairy Circles in the Outback

Whimsically classified as fairy circles, these strange hexagonal patches of land never over-lap and can only truly be appreciated with an aerial view. Resembling the same pattern as honeycomb, they can be found in the millions along a 1,800km (more than 1,000 miles) long area of South Africa extending from Angola south toward the Northwestern Cape province. Most of them, however, are located in the Namib desert. Individually they appear as rings of tall grass enclosing barren centers of red earth, which can measure between 2m (7ft) and 20m (65ft) in diameter.

Keep reading

Cover Photo — September 18, 2007, 104 (38)

“Mountain bluebird (Sialia currucoides, male) in flight. Aggressive and dispersive behavior in western bluebird males enabled the species to recolonize its historical range across the northwestern United States over the past 30 years, at the expense of mountain bluebirds. Once western bluebird colonies were reestablished, natural selection quickly reduced aggression. See the article by Duckworth and Badyaev on pages 15017–15022. Photo courtesy of Alex Badyaev”.

Showing parents graphic pictures of children infected with measles improves their anti-vaccine attitude.

http://bit.ly/1KPePOG

Vaccination rates have recently declined, leading to a resurgence in preventable infections, like measles. Efforts to counter anti-vaccine attitudes have largely failed, and in some cases, have entrenched anti-vaxxer’s views even further. Now, a team of scientists from the USA have shown success by showing parents graphic pictures of infected children, or letting them read messages from the parents of infected children.

Image credit: CDC​

news.nationalgeographic.com
Deep-sea Trawling Has “Devastating” Impact, Study Finds

Deep-sea trawling threatens the seafloor’s health and diversity, suggests a Mediterranean canyon study.

An important article was just published in the Proceedings of the National Academy of Sciences.  The study compares areas where deep sea trawling has occurred with areas that have escaped the practice.  The results show very significant changes, including a huge decrease in species diversity at the base of the food chain.  If you choose to consume seafood, make sure and be very conscious about your choices.  You can print off a pocket guide or download the app from the Monterey Bay Aquarium, which will tell you (based on where you live) the most sustainable seafood choices you can make.  I would argue the most sustainable, personal choice you can make is to limit or forgo consumption of fish all together.    

Code cracked for infections by major group of viruses including common cold and polio

Researchers have cracked a code that governs infections by a major group of viruses including the common cold and polio. Until now, scientists had not noticed the code, which had been hidden in plain sight in the sequence of the ribonucleic acid (RNA) that makes up this type of viral genome.

But a paper published in the Proceedings of the National Academy of Sciences (PNAS) Early Edition by a group from the University of Leeds and University of York unlocks its meaning and demonstrates that jamming the code can disrupt virus assembly. Stopping a virus assembling can stop it functioning and therefore prevent disease.

Professor Peter Stockley, Professor of Biological Chemistry in the University of Leeds’ Faculty of Biological Sciences, who led the study, said: “If you think of this as molecular warfare, these are the encrypted signals that allow a virus to deploy itself effectively.”

“Now, for this whole class of viruses, we have found the ‘Enigma machine’ – the coding system that was hiding these signals from us. We have shown that not only can we read these messages but we can jam them and stop the virus’ deployment.”

Single-stranded RNA viruses are the simplest type of virus and were probably one of the earliest to evolve. However, they are still among the most potent and damaging of infectious pathogens.

read more

gizmodo.com
Indestructible Water Bears Have a Genome That Is Seriously Weird
Water bears, known to scientists as tardigrades, are famously adorable microscopic creatures who can survive anything: freezing, total dehydration, radiation bombardment, and even the vacuum of deep space. Now scientists have sequenced a tardigrade genome, and are very surprised by the results.
By Annalee Newitz

Water bears, known to scientists as tardigrades, are famously adorable microscopic creatures who can survive anything: freezing, total dehydration, radiation bombardment, and even the vacuum of deep space.  Now scientists have sequenced a tardigrade genome, and are very surprised by the results.

Yesterday a group of researchers led by University of North Carolina at Chapel Hill biologist Thomas Boothby published their analysis of the tardigrade genome in the Proceedings of the National Academy of Sciences.  What they found was that 17.5% of the tardigrade genome actually comes from other organisms, including plants, fungi, bacteria, and viruses.  These genes entered tardigrade DNA in a process known as horizontal gene transfer, which is quite common among single-celled organisms but rare among animals.  The closest comparison with the tardigrade is a microscopic form of plankton called a rotifer, which has about 9% of its DNA from other organisms.

The researchers reached the 17.5% number by isolating non-animal genes in the tardigrade sequence, and then comparing those non-animal genes with those of other sequenced organisms.  About 17.5% of tardigrade genes closely resembled genes from non-animal organisms like plants and bacteria.  This is the first time scientists have ever found an animal with 1/6 of its genome coming from non-animal sources.

Biologist Bob Goldstein, who worked with Boothby on the paper, told Gizmodo via email that they can’t be sure of the exact species that donated DNA to the tardigrade, partly because some of the species’ genomes may not have been sequenced yet.

The real question is, how did the tardigrade become such a genetic hodgepodge?  Boothby and his colleagues speculate that it has to do with the animal’s response to stress.  Tardigrades live in wet moss, and one of the common forms of peril they must endure is desiccation, or drying out.  When tardigrades are desiccated, their DNA breaks into pieces.  Any organisms around them will also suffer the same fate.  But when water returns to the tardigrade’s environment, they re-hydrate and return to life.  As they re-hydrate, their cell walls become porous and leaky, and fragments of DNA from the desiccated organisms around them can flow inside and merge with the animal’s rejuvenating DNA.

Tardigrades: Nature’s Doomsday?

Read the full scientific paper at PNAS.

bbc.com
Dinosaurs 'in decline' 50 million years before asteroid strike
The dinosaurs were already in decline 50 million years before the asteroid strike that finally wiped them out, a study suggests.

The dinosaurs were already in decline 50 million years before the asteroid strike that finally wiped them out, a study suggests.

The new assessment adds further fuel to a debate on how dinosaurs were doing when a 10km-wide space rock slammed into Earth 66 million years ago.

A team suggests the creatures were in long-term decline because they could not cope with the ways Earth was changing.

The study appears in PNAS journal.

Researchers analysed the fossil remains of dinosaurs from the point they emerged 231 million years ago up to the point they went extinct.

To begin with, new species evolved at an explosive rate. But things started to slow about 160 million years ago, leading to a decline in the number of species which commences at about 120 million years ago.

Dr Manabu Sakamoto, a palaeontologist from the University of Reading, who led the research, said: “We were not expecting this result.”

“Even though they were wiped out ultimately by the impact of the asteroid, they were actually already on their way out around 50 million years before the asteroid hit.”

Continue Reading.

How Our Brains Store Recent Memories, Cell by Single Cell
Findings may shed light on how to treat neurological conditions like Alzheimer’s and epilepsy

Confirming what neurocomputational theorists have long suspected, researchers at the Dignity Health Barrow Neurological Institute in Phoenix, Ariz. and University of California, San Diego School of Medicine report that the human brain locks down episodic memories in the hippocampus, committing each recollection to a distinct, distributed fraction of individual cells.

The findings, published in the June 16 Early Edition of PNAS, further illuminate the neural basis of human memory and may, ultimately, shed light on new treatments for diseases and conditions that adversely affect it, such as Alzheimer’s disease and epilepsy.

“To really understand how the brain represents memory, we must understand how memory is represented by the fundamental computational units of the brain – single neurons – and their networks,” said Peter N. Steinmetz, MD, PhD, program director of neuroengineering at Barrow and senior author of the study. “Knowing the mechanism of memory storage and retrieval is a critical step in understanding how to better treat the dementing illnesses affecting our growing elderly population.”

Steinmetz, with first author John T. Wixted, PhD, Distinguished Professor of Psychology, Larry R. Squire, PhD, professor in the departments of neurosciences, psychiatry and psychology, both at UC San Diego, and colleagues, assessed nine patients with epilepsy whose brains had been implanted with electrodes to monitor seizures. The monitoring recorded activity at the level of single neurons.

The patients memorized a list of words on a computer screen, then viewed a second, longer list that contained those words and others. They were asked to identify words they had seen earlier, and to indicate how well they remembered them. The observed difference in the cell-firing activity between words seen on the first list and those not on the list clearly indicated that cells in the hippocampus were representing the patients’ memories of the words.

The researchers found that recently viewed words were stored in a distributed fashion throughout the hippocampus, with a small fraction of cells, about 2 percent, responding to any one word and a small fraction of words, about 3 percent, producing a strong change in firing in these cells.

“Intuitively, one might expect to find that any neuron that responds to one item from the list would also respond to the other items from the list, but our results did not look anything like that. The amazing thing about these counterintuitive findings is that they could not be more in line with what influential neurocomputational theorists long ago predicted must be true,” said Wixted.

Although only a small fraction of cells coded recent memory for any one word, the scientists said the absolute number of cells coding memory for each word was large nonetheless – on the order of hundreds of thousands at least. Thus, the loss of any one cell, they noted, would have a negligible impact on a person’s ability to remember specific words recently seen.

Ultimately, the scientists said their goal is to fully understand how the human brain forms and represents memories of places and things in everyday life, which cells are involved and how those cells are affected by illness and disease. The researchers will next attempt to determine whether similar coding is involved in memories of pictures of people and landmarks and how hippocampal cells representing memory are impacted in patients with more severe forms of epilepsy.

Pictured: Human neuron showing actin formation in response to stimulation. Michael A. Colicos, UC San Diego