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.

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

Scientists Discover How Loneliness Can Kill

Loneliness can increase the risk of premature death by 14 percent in older adults, according to a study published Monday that posits a physiological basis for the phenomenon.

The dangers of social isolation have long been known but its effects on the body have not been well understood, the researchers said in the work published in the Proceedings of the National Academy of Sciences/PNAS.

Led by University of Chicago psychologist John Cacioppo, the research team had previously identified a link between solitude and both a heightened expression of genes involved in inflammation and a diminution in the activity of other genes that play a role in the body’s antiviral responses.

The result is a weakened immune systems that makes a person who lives alone more vulnerable to illness. In their latest research, the researchers looked at leukocytes, white blood cells that the immune system uses to protect against bacteria and viruses.

They found the same shift in genetic expression in the white blood cells of people who lived alone and in social isolation.

They also found that loneliness predicted the gene behavior a year or more in advance and conversely that gene expression predicted loneliness measured a year or more later. (Source)

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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.    

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.

latimes.com
Brains of kidney donors seem built for generosity

As if giving a perfectly good kidney to a total stranger wasn’t enough of a distinction, it turns out that extreme altruists have bigger brains and are better than the rest of us at reading signs of distress in facial expressions.

From a very early age, I have known my mom’s wishes should anything ever happen to her: “Pull the plug if it comes to that. I don’t want any flowers – have people donate the money instead of wasting it on expensive arrangements. Donate everything that’s still usable.”

Last year, someone told me that she described me to friends as “one of the most Christlike people [she] knows.” I broke the news to her that I am actually agnostic, and she was stunned.

“How are you so good? How does your moral compass point in the right direction without Jesus and the church? How do you make the right decisions? How are you able to balance what you want and what others need?”

I always thought that I had just internalized all of the things that I had heard my mom say when I was growing up, but maybe there’s some biology in there, too. Nurture and nature. (As most things are.)

———————

I post about donating blood as often as I do, because it’s incredibly important. It’s also easy to post about, because it’s an active and repeated choice that I make. 

ANYWAY. This article reminded be that I’ve also been on the Be The Match marrow registry since 2007. I don’t think I have ever really mentioned it, because it’s something that you register for, and then you probably won’t ever hear about again. That said, it’s also incredibly important, and it’s very easy to do.

Join the Be The Match registry here.

[Peer-reviewed journal referenced in article here.]

Is using an electronic device before sleep bad for your health?

[The brain goes through a process of different levels of sleep throughout the night, and it has different physiological effects, some of which are still not completely understood. Image source: http://www.katkremp.com/wp-content/uploads/2015/03/Sleep-Cycle.jpg]

If you are reading this online close to or after your bedtime, I suggest you go to sleep and come back to this in the morning. A study published in Proceedings of the National Academy of Sciences (PNAS) shows that it may be beneficial to reduce reading from back-lit devices, like computers and smartphones, before sleep.

A quick word about the importance of sleep. Most of us are aware that sleep is important for a healthy brain function and physical health. Sleep promotes learning (i.e. you might be better off sleeping the night before a big exam) and repairing of heart and blood vessels, and controls of growth and development.

When it comes to sleep, both quantity and quality matter. Quantity-wise, if you are a teenager between ages 12-18, you need at least 8.5 hours of sleep. For adults over age 18, you need at least 7.5 hours of sleep. Even just losing 1 or 2 hours of sleep per night for several days can severely impair how you perform during the day.

The study done by PNAS found that reducing reading of backlit screens before bedtime increases the quality of sleep of its participant. This is particularly pertinent as a recent survey showed that nearly 90% of Americans use some type of electronic device at 2-3 nights per week within 1 hour before bedtime. Light, including that from electronic devices, is one of the major cues that influences the human circadian clock and may contribute to sleep deficiency.

The study showed that from subjects who read from an iPad before bedtime showed:

1. Nearly 50% reduction in plasma melatonin level. Melatonin is an important hormone in regulating the circadian rhythm. Circadian rhythm is the body’s internal clock that regulates when we sleep, when we wake, and indirectly controls when we are hungry.

2. Longer time to fall asleep. While this time was only 10 minutes, this can easily add up to large numbers after a long time. Also, subjects’ circadian clocks were delayed by more than 90 minutes the following day, which may compound the problem by causing individuals to fall asleep at a later time.

3. Significantly less rapid eye movement (REM) sleep. REM sleep is the phase of sleep that stimulates the brain regions responsible for learning. Scientists have found that individuals who have REM sleep after learning a new task have increased retention of what they have learned, versus those individuals who do not experience REM sleep.


4. Taking a longer time to feel “alert” the following morning. The researchers speculate that the negative effect is possibly due to short-wavelength blue light emitted from electronic devices, but further study needs to be done to confirm and elucidate the potentially long-term effects.


References

http://www.helpguide.org/articles/sleep/how-much-sleep-do-you-need.htm

http://www.pnas.org/content/112/4/1232.full.pdf

http://www.nhlbi.nih.gov/health/health-topics/topics/sdd/why



By Lee H., Discoverer

Edited by Peggy K. Editor.

Living with Oxygen

Earth’s atmosphere changes over time – the amount of oxygen has built up from virtually zero over billions of years. Living organisms have had to adapt to this changing atmosphere, developing mechanisms to cope with the presence of oxygen and the dangerous by-products of respiration known as reactive oxygen species (ROS), which can damage our cells. Proteins and enzymes are particularly susceptible to this oxidative damage, which can lead to many conditions including Alzheimer’s, cancer and heart failure. Studying the protein structural database has revealed that many protein structures contain the amino acids tyrosine and tryptophan. Researchers believe that these amino acids are being used to transport ROS away from the vulnerable sites of proteins. Pictured is SOD2, an antioxidant enzyme involved with respiration. The red, pink and blue chains represent different tyrosines and tryptophans. This finding gives insight into how cells adapt to protect against unwanted oxygen species.

Written by Helen Thomas

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pnas.org
Why are things the way they are? A case study in proteins

Note: This has been reposted from my personal blog.

I read the abstract for this science paper at work and I find the ideas really appealing (am I allowed to admit that I just read the abstract? I’m going to admit that I just read the abstract). In fairness, I didn’t read the whole thing because it involves some intense mathematical modeling, and I think the perspective is valuable regardless of what exactly the data looks like (and speaking of, wtf?).

Lynch and Hagner from Indiana University take on a really big question: why do proteins evolve the way they do? Their answer may sound surprising - essentially, their response is “no particular reason”.

To give some background, proteins are the molecular machines that power cells. They evolve - adapt to new environments, or gain a reproductive advantage over those of other cells - by slowly accumulating mutations, which come from the natural tendency for your DNA to accumulate errors as it is copied over and over again. A really important thing proteins do is interact with each other - to help each other out, to repress one another when appropriate, to communicate, to make new proteins, etc. And to interact, proteins have a physical interface where they meet, and mutations in the protein might disrupt that interface.

You may have learned in biology class that most mutations are harmful to your cells, but the truth is that most mutations have a negligible impact. Imagine if you got a mutation that made your arms one inch shorter. Is that mutation harmful? Maybe marginally, but how plausible is it that having tiny-arms will keep you from reproducing? It’s hard to imagine how such a slight change would get you killed or cause you to have fewer children - put differently, it’s unlikely that the tiny-arms gene will get weeded out of the gene pool. So if that’s the case, even though having tiny arms doesn’t make you more evolutionary fit, there’s a random chance that over time, that mutation (or other similarly neutral mutations) will spread simply because its impact is too small for evolutionary forces to take notice. This phenomenon - the spread of mutations that aren’t harmful or beneficial, but simply different and neutral - is called genetic drift, and it has been acknowledged since the late 1960’s.

Back to the paper. Often, for a given task in the cell, every species has a slightly different protein to do the job. The proteins that replicate your DNA are slightly different from the analogous protein in birds, in chimps, in frogs, in yeast, etc, even though they do the exact same thing. So the authors of the paper ask, why is nearly every protein for a given task unique? Is it because that protein has been finely tuned by evolution to be the perfect solution for the context of a human cell, and that being in a yeast cell will require a different solution? The authors say no, that by and large, such differences can be attributed to random chance. Because of drift, mutations will appear at the interface of two proteins. As long as that mutation doesn’t break the interaction past a certain threshhold - as long as the proteins can still do their job to let the cell survive - it will be tolerated. Next, the partner protein can mutate in a way that better accomodates the first mutation. Now another random mutation appears, and an accomodating mutation follows. This happens again and again until the protein interface has a completely new composition, but it still accomplishes the same task. Was the protein sculpted by the inexorable forces of evolution? Is it now more perfectly suited to the specific needs of its parent cell? No - it simply changed.

The paper is a refreshing rebuttal to the deterministic way people often talk about evolution - biological evolution, but also cultural evolution, technological evolution, etc. We tend to assume that things are the way they are for a good reason, that they have progressed over time towards an objective ‘good,’ but we gloss over that, much like proteins, humans and their institutions change over time simply because that’s what happens. It’s a liberating perspective, and acknowledging it is a call for more purposeful change.