Author: Michelle Dohm

The Science of Snakeskin: Black Velvety Viper Scales May be Self-Cleaning

West African Gaboon Viper

West African Gaboon viper

Whether you love them or hate them, snakes have long captivated our interest and imagination. They’ve spurred countless stories and fears, some of which may have even affected the course of human evolutionary history. We must admit, there is something a little other-worldly about their legless bodies, willingness to swallow and digest animals much bigger than them, and fangs and potentially fatal (or therapeutic?) venomous bites.

Not least of all, their scaly skin is quite mesmerizing and often laden with intricate and beautifully geometric patterns just perfect for camouflaging, regardless of whether they live high up in a tree, deep in murky waters, or on the forest floor. Snakeskin was the focus of recent research by the authors of this PLOS ONE study who sought to determine whether it has any special properties less obvious to the naked eye.

Please meet the West African Gaboon viper, Bitis gabonica rhinoceros (pictured above). Native to the rainforests and woodlands of West Africa, these large, white-brown-and-black snakes can be identified by large nasal horns and a single black triangle beneath each eye—nevermind that, because they also lay claim to titles for the longest fangs and most venom volume produced per bite. The pattern of their skin is intricate and excellent for camouflage, and the black sections have a particularly velvety appearance. These eye-catching characteristics intrigued zoology and biomechanics researchers from Germany, who decided to take a closer look.

In a previously published paper, the authors analyzed the Gaboon viper’s skin surface texture by using scanning electron microscopy (SEM), as well as its optical abilities by shining light on the snakeskin in different ways to see how it’s reflected, scattered, or transmitted. They found that only the black sections contained leaf-like microstructures streaked with what they call “nanoridges” on the snake scales, a pattern that has not been observed before on snakeskin. What’s more, the black skin reflects less than 11% of light shone on it—a lot less than other snakes—regardless of the angle of light applied. The authors concluded from the previous study that both of these factors may contribute to the viper’s velvet-like, ultra-black skin appearance.

Scanning electron microscopy (SEM) of viper scales

Scanning electron microscopy (SEM) of viper scales

In their most recent PLOS ONE paper titled “Non-Contaminating Camouflage: Multifunctional Skin Microornamentation in the West African Gaboon Viper (Bitis rhinoceros),” the authors conducted wettability and contamination tests in hopes of further characterizing the viper skin’s properties, particularly when comparing the pale and black regions.

To test the wettability of the viper scales, the authors sprayed droplets of water, an iodide-containing compound (diiodomethane), and ethylene glycol on the different scale types shown above, on both a live and dead snake, and then measured the contact angle—the angle at which a liquid droplet meets a solid surface. This angle lets us know how water-friendly a surface is; in other words, the higher the contact angle, the less water-friendly the surface.

Contact angle (A) and snake skin with water droplet on light and dark areas (B)

Contact angle (A) and snake skin with water droplet on light and dark areas (B)

As you can see in the graph above, the contact angle was different depending on the liquid applied and the type of scale; in particular, the contact angle on the black scales was significantly higher than the others, in a category that the authors refer to as “outstanding superhydrophobicity,” or really, really, really water-repelling. This type of water-repelling has been seen in geckos, but not snakes.

Water droplet appearance on live snake skin

Water droplet appearance on live snake skin

The authors then took some of the snake carcass and dusted it with a sticky powder in a contamination chamber, after which they generated a fog for 30 minutes and took pictures.

Skin before dusting (A), skin under black light after dusting (B), skin under black light after fogging (C), section of SEM, showing light and dark skin (D)

Skin before dusting (A), skin under black light after dusting (B), skin under black light after fogging (C), section of SEM, showing light and dark skin (D)

After 30 minutes of fogging, the black areas were mostly free of the dusting powder, while the pale areas were still completely covered with dust. The powder itself was also water-repelling, and so the authors showed that despite this, the powder rolled off with the water rather than sticking to the black areas of snake skin. Therefore, as suggested by the authors, this could be a rather remarkable self-cleaning ability. The authors suspect that the “nanoridges,” or ridges arranged in parallel in the black regions, may allow liquid runoff better than on the paler areas of the snake.

How does this texture variation help the snake, you ask? The authors posit that all these properties basically contribute to a better form of camouflage. If the snake were completely covered in one color, it may stand out against a background of mixed colors (or “disruptive coloration”), like that of a forest floor. If the black regions have fairly different properties from the paler regions, mud, water, or other substances would rub off in these areas and continue to provide the light-dark color contrast and variation in light reflectivity that helps the snake do what it does best: slither around and blend in unnoticed.

Citations

Spinner M, Kovalev A, Gorb SN, Westhoff G (2013) Snake velvet black: Hierarchical micro- and nanostructure enhances dark colouration in Bitis rhinoceros. Scientific Reports 3: 1846. doi:10.1038/srep01846

Spinner M, Gorb SN, Balmert A, Bleckmann H, Westhoff G (2014) Non-Contaminating Camouflage: Multifunctional Skin Microornamentation in the West African Gaboon Viper (Bitis rhinoceros). PLoS ONE 9(3): e91087. doi:10.1371/journal.pone.0091087

Images

First image, public domain with credit to TimVickers

Remaining images from the PLOS ONE paper

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A Year in Review: 2013 PLOS ONE Papers in the Media

 

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Tired of year-end lists? We know you’ve got room for at least one more. 2013 was a great year for PLOS ONE media coverage: We had over 5,000 news stories on over 1450 published articles.

The PLOS ONE press team poured tirelessly over the list to whittle down the papers that stood out the most. In celebration of the New Year, we’d like to share some of these titles with you.

Zipping back to January 2013 and moving forward from there, here they are:

 

1. Flowers Flowering Faster (Sooner)

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In “Record-Breaking Early Flowering in the Eastern United States,” US researchers used 161 years of historical reports—initiated by Henry David Thoreau and Aldo Leopold in 1935—to track spring flowering times. They discovered that exceptionally warm spring temperatures in Massachusetts and Wisconsin in 2010 and 2012 may have resulted in the earliest recorded spring in the eastern United States. Furthermore, scientists indicate that these advanced flowering times could be predicted based on the historical data. This research received media attention from the The New York Times, National Geographic, and NPR.

 

2. Lend an Ear?

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US scientists 3D-printed a human ear using collagen hydrogels (a network of polymers that form a gel with water) derived from cow cartilage in the lab. They shared their results in “High-Fidelity Tissue Engineering of Patient-Specific Auricles for Reconstruction of Pediatric Microtia and Other Auricular Deformities.” The authors suggest that this advancement may be a significant first step toward creating patient-specific tissue implants for those who require ear prosthesis. Popular Science, Discovery News, and NPR covered this research.

 

3. Central African Elephants in Big Trouble

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African forest elephant populations may have declined by an alarming 62% in the last decade, according to the study “Devastating Decline of Forest Elephants in Central Africa.” The authors suggest that this dramatic drop is largely due to continuing illegal ivory trade and inadequate efforts to put a stop to it. ScienceNow, TIME, Slate, Smithsonian, and many others covered this article.

 

4. Wrapped up in a Book

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For everyone who enjoys a good page-turner, researchers in the study “The Expression of Emotions in 20th Century Books” indicate that recent British and American books have fewer emotional “mood” words than they did in the earlier half of the 20th century. What’s more, the study’s authors provide evidence that American authors express more emotion than British authors, and that newer American books use more words conveying fear than older ones. This research was covered by the The New York Times Arts Beat, Jezebel, our EveryONE blog, and Nature.

 

5. Gaming for All Ages

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In the article “A Randomized Controlled Trial of Cognitive Training Using a Visual Speed of Processing Intervention in Middle Aged and Older Adults,” researchers from multiple institutions in Iowa discovered that when middle-aged and older adults played video games, they scored better on cognitive function tests. The authors hope that these results might help us slow cognitive decline in older individuals. This paper was covered by the The Wall Street Journal, Nature, and The Telegraph.

 

6. Seafood Watch for Arctic Foxes?

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In another saddening story of declining wild animal populations, researchers studying the “Correlates between Feeding Ecology and Mercury Levels in Historical and Modern Arctic Foxes (Vulpes lagopus)” found that mercury levels in seafood may be the culprit. They emphasize that overall direct exposure to toxic materials may not be as important as the feeding ecology and opportunities of predators, like the arctic fox, that have a very marine-based diet, which may contain these toxic substances. This research received media attention from Wired UK, Scientific American, and The Guardian.

 

7. Cancer in Neandertals

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At least one Neandertal 120,000 years ago had a benign bone tumor in a rib, according to researchers in the study “Fibrous Dysplasia in a 120,000+ Year Old Neandertal from Krapina, Croatia.” The authors note, however, that they cannot comment on any health effects or the overall health condition of the individual without further evidence. This article received media attention from sources including the BBC, The New York Times, ScienceNOW, and Gizmodo.

 

8. Who Needs Rows of Teeth When You’ve Got a Tail to Slap Sardines?

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Image credit: PLOS ONE article

Thresher Sharks Use Tail-Slaps as a Hunting Strategy” contains the first video evidence of long-tailed sharks tail-slapping to stun their sardine prey. The authors suggest that this method may be effective when hunting prey that swim in schools. A Scientific American podcast, National Geographic’s Phenomena blogs, and NBC News were some of the media outlets that covered this research.

 

9. Contagious Yawning in Dogs and Chimps

Video credit: PLOS ONE article

Yawning animals were the focus of more than one PLOS ONE article in 2013. In one study, “Familiarity Bias and Physiological Responses in Contagious Yawning by Dogs Support Link to Empathy,” Japanese researchers found that dogs yawn more often in response to their owners’ yawns rather than a stranger’s, and received media coverage from The Guardian, CBS News, and The Telegraph. The authors of another research article “Chimpanzees Show a Developmental Increase in Susceptibility to Contagious Yawning: A Test of the Effect of Ontogeny and Emotional Closeness on Yawn Contagion” showed that chimpanzees appear to develop a contagion for yawning as they get older, just as humans do, and this article received media attention from The New York Times Science Takes, Los Angeles Times, and Scientific American Blogs.

 

10. What, the Cat? Oh, He’s Harml…

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Our favorite parasite Toxoplasma gondii strikes again. Mice are normally terrified of cats, and rightly so, but Berkeley researchers (including a PLOS founder Mike Eisen) in “Mice Infected with Low-Virulence Strains of Toxoplasma gondii Lose Their Innate Aversion to Cat Urine, Even after Extensive Parasite Clearance” show that mouse exposure to the parasite, carried in cat feces, may alter the mouse’s brain, causing the mouse to permanently lose its fear of cats. The story received coverage from several news outlets, including a CNN segment by Charlie Rose, and coverage by BBC, National Geographic Phenomena, and Nature.

 

11. Just in Time for the Movie: Jurassic Park is Fake

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Sorry in advance for the disheartening news: Jurassic Park will likely remain a work of fiction. In “Absence of Ancient DNA in Sub-Fossil Insect Inclusions Preserved in ‘Anthropocene’ Colombian Copal,” UK researchers were unable to find any evidence of ancient DNA in specimens of prehistoric insects fossilized in hardened tree sap. Conveniently, the article published right when the newest Jurassic Park film series was announced, and was covered by San Francisco Chronicle, The Telegraph, The Conversation, and others.

 

12. Not Now, Honey – The Pressure Just Dropped

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Insects avoid sex when a drop in atmospheric pressure occurs, which usually precedes rain, according to researchers in the study “Weather Forecasting by Insects: Modified Sexual Behaviour in Response to Atmospheric Pressure Changes.” Injury from rain can be deadly for some insect species, so the authors suggest that the insects modified their behavior to enhance survival (good choice!). The article has received attention from nearly 20 news outlets, including Nature, Los Angeles Times, Scientific American, and ScienceNOW.

 

13. Dinos with Squishy Joints and Tiny Arms

 

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Image credit: PLOS ONE article

Dinosaurs were a popular item in PLOS ONE in 2013, especially with the launch of PLOS ONE’s New Sauropod Gigantism Collection. The most popular article was a simulation of how the largest dinosaur, the Argentinosaurus, might have walked in “March of the Titans: The Locomotor Capabilities of Sauropod Dinosaurs,” which was covered in Washington Post and The Guardian. Another group of researchers showed that squishy joints were a major factor in the massiveness of saurischian dinosaurs in “What Lies Beneath: Sub-Articular Long Bone Shape Scaling in Eutherian Mammals and Saurischian Dinosaurs Suggests Different Locomotor Adaptations for Gigantism.” The article was covered by Gizmodo, Inside Science, and Discovery. Finally, a new super-predator larger than T. rex lived 80 million years ago and was described in “Tyrant Dinosaur Evolution Tracks the Rise and Fall of Late Cretaceous Oceans” and covered by BBC, Nature, and Discovery.

 

14. Huh?

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The title of this next study says it all: “Is “Huh?” a Universal Word? Conversational Infrastructure and the Convergent Evolution of Linguistic Items.” The authors of this article suggest that it is, and that at least ten countries use a variation of this word to verbally express confusion. The article was featured in NPR, The New York Times, and LA Times.

 

15. Little Red Riding Hood: The Evolution of a Folk Tale

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Little Red Riding Hood has very deep roots, as the authors of “The Phylogeny of Little Red Riding Hood” show in their article. It has made its way across China to Europe and back again, but where did it begin? The authors indicate that phylogenetic methods (like the branched chart above) may be a new way to analyze cultural relationships among folk tales and oral narratives. This article received coverage in ScienceNOW, National Geographic, and Nature.

Thank you to all of our Academic Editors, reviewers, and authors for making these articles a reality. Needless to say, PLOS ONE staff cannot wait to see what lies ahead in 2014!

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PLOS ONE at AGU 2013

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PLOS ONE is excited to participate in the American Geophysical Union’s (AGU) Fall Meeting 2013, held this week in San Francisco’s Moscone Center. Conveniently, Moscone is just down the street from our San Francisco office, so several members of PLOS staff will be in attendance and available to chat with you about the journal. We’re looking forward to meeting both current and potential Academic Editors, reviewers, and of course authors! Please stop by Booth #301 to say hello.

Last week was a very geophysics-oriented one for us, with both the publication of Hansen et al.’s work “Assessing “Dangerous Climate Change”: Required Reduction of Carbon Emissions to Protect Young People, Future Generations and Nature” and with the announcement of our call for papers in a new collection entitled “Responding to Climate Change.” What’s more exciting is that James Hansen will be in attendance at AGU and will be giving a talk today (December 10th) on this topic, in support of taking significant, active measures to reduce fossil fuel emissions.

Last year, at AGU 2012, we were a little bit of an unfamiliar face to many. This year, we hope to continue our conversation with the physical sciences community about our commitment to open access and the publication of sound scientific research in all areas of science and medicine, including geoscience, space science, chemistry, and physics.

After AGU, look out for the PLOS booth again in just a few days at the American Society for Cell Biology!

Image Credit: Detailed view of Arctic Sea Ice in 2007, from NASA Visible Earth.

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I’ll Have What He’s Having: Dogs Eavesdrop on Human Interactions

dogs_begging

In the spirit of Thanksgiving and sharing a warm meal with loved ones, we’d like to take a moment to give some social credit to our loving, faithful, and clever furry friends. Researchers have been investigating the question of whether animals can eavesdrop—or listen in on third-party interactions—for some time, and evidence of potential eavesdropping has been identified in dogs and other mammals, fish, and birds.

Dogs are especially good candidates for studying eavesdropping because they are social animals and have been domesticated, so they are accustomed to interacting with humans day-in and day-out. Most dog owners know how well their dogs can “read” them, and some might argue that their dogs can do this better than other people they know. Researchers have also confirmed that dogs can recognize human emotions, facial expressions, and friendliness versus hostility, the latter even in strangers.

In a more nuanced form of social interaction, dogs have been shown to prefer certain people over others depending on the outcome of third-party interactions. To further investigate how dogs respond to interactions among people, the authors of this recently published PLOS ONE article asked whether dogs can develop a preference for or against givers, or “donors,” in a “begging” interaction between people.

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The study recruited 72 dogs of various breeds and sizes and put them in a testing environment that either resembled a home or a dog care facility. While the dog watched from across the room, two human assistants acted as “donors” (females, pictured above) who offered food to a “beggar” (male, above), and the beggar either reacted positively or negatively to the offered food. The extent of the reaction was controlled to try to determine which social cues the dog was picking up on: gesture + verbal (GV), gesture only (G), or verbal (V) only.

In the GV group positive scenario, the beggar received a yummy corn flake, ate it, and said “So tasty!”; in the negative scenario, the beggar said “So ugly!” gave the corn flake back, and then turned his back. The G and V groups differed in that they isolated the gesture and verbal components, respectively. After the beggar left, the dog was released and had 10 seconds to decide between the donors, who did not signal the dog in any way. Dogs that did not make a choice were removed from the analysis.

As the results below show, dogs were more likely to choose the donor who received a positive reaction; the authors also noted that the dogs tended to watch or gaze at the donor who received a positive reaction longer than the donor who received a negative reaction. However, the authors state that both gesture and verbal cues (the GV group) were required to show a reliable difference among the groups.

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Although these results alone are not conclusive, as it is difficult to control for all the variables affecting these scenarios (e.g., the authors note that dogs chose randomly if the donors switched places), the authors suggest that the dogs may have attributed a “reputation” to the donor based on the beggar’s reaction, where both gesture and verbal cues were required for the dog to make this association.

While not the same as a scientific experiment, it might be fun to “test” your dog in various eavesdropping scenarios, especially in relation to available food* on the Thanksgiving table.

Happy Thanksgiving from PLOS ONE!

Citation: Freidin E, Putrino N, D’Orazio M, Bentosela M (2013) Dogs’ Eavesdropping from People’s Reactions in Third Party Interactions. PLoS ONE 8(11): e79198. doi:10.1371/journal.pone.0079198

Image Credits: Figure 1 by carterse, Figures 2 and 3 from the article

*food safe for pets to eat, of course!

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Can You Image That? Imaging a Cell and Its Proteins Together

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Observing the world around us is a natural human instinct, and exploring the realm of the tiny and beautiful is especially captivating for scientists and the public alike. The business of building and testing new microscopes, and developing new methods of microscopy, is rapidly changing and evolving over time. As early as 1914, scientists started documenting the history of the microscope.

Thankfully, rather than drawing out what we see through the lens onto a piece of paper, there are now advanced forms of microscopy, like electron microscopy, that allow scientists to scan a substance—with an electron beam—to sample its topography, or surface shape, and produce wonderfully detailed images that also contain tremendous amounts of data. In a separate form of microscopy called fluorescence microscopy, fluorescent proteins—proteins in the cell engineered to have a fluorescent tag—and intracellular proteins fused to a fluorescent protein can be imaged because they emit light in response to certain wavelengths of light coming from the microscope.

In a continuous effort to “see what’s going on a bit better,” Howard Hughes Medical Institute researchers published an article in PLOS ONE today detailing improvements of their relatively new form of 3D super-resolution microscopy. It combines what they call PhotoActivated Localization Microscopy, or PALM (a type of fluorescence microscopy), with electron microscopy (EM), and lets us have a look at organelles, like mitochondria, and the location of nearby proteins, right in the same cell at roughly the same time.

For instance, if we know a specific protein attaches directly to DNA in a specific organelle, PALM allows us to see precisely the nanometer-scale location of this protein, when it is fused to a fluorescent protein. EM on the other hand, allows us to see the overall structure of the organelle, and so combining these to see both at the same time is extremely useful to cell biologists studying structure and function.

In their study design, PALM needs to be performed before EM (see image of sample preparation and setup below), and then the two images are overlaid by correlating the area of fluorescence, seen during fluorescence microscopy, to the area of the cell structure seen during electron microscopy. The overlaid image is the final result, and the goals of the researchers in this improvement study were to optimize the image resolution and the number of useable fluorescent dyes, speed up the protocol, and simplify the equipment involved by moving it from 3D (very difficult, less accessible) to 2D (easier, common in research institutions), in hopes of making this technique accessible to cell biologists.

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In this and the previous work, the researchers describe how they combined the two forms of microscopy to achieve the results they were looking for. All forms of microscopy have limitations, especially when it comes to the limits of the optics and sample preparation, and in this case, scientists overcame a barrier between optimizing the available fluorescence and also optimizing the quality of the EM images that were produced.

As you might imagine, the better the overall image quality is, the better biologists can use the image information to help understand the structure and function of biological components, such as organelles and proteins. Additionally, though the cells used in this study were frozen and prepared, there is a possibility that live cells could be directly imaged using this technique.

Though explaining and understanding the method are a little complicated, the pictures make it all worth it—and the scientists would agree. Below are example image sets. The first set is of an image containing mitochondria, or the powerhouse of the cell, and a protein that localizes in its DNA.

The first image in the set shows the result of PALM, the second contains the EM, and the third is the alignment of the two images (and M is for mitochondria).

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And here’s a second set, with imaging of a whole cell by traditional confocal microscopy (A), followed by a similar sequence as above (B-D) for a nucleus and the location of a fluorescent dye that adheres to actin (protein) filaments.

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The researchers also managed to perform imaging using two colors (title image), demonstrating the versatility of the technique. Check out the full details and image set here, as well as other recent studies involving new imaging techniques here, here, and here.

Citations:

Gaietta GM, Giepmans BNG, Deerinck TJ, Smith WB, Ngan L, Llopis J, Adams SR, Tsien RY, and Ellisman MH (2006) Golgi twins in late mitosis revealed by genetically encoded tags for live cell imaging and correlated electron microscopy. PNAS 103(47) doi:10.1073/pnas.0608509103

Kopek BG, Shtengel G, Grimm JB, Clayton DA, Hess HF (2013) Correlative Photoactivated Localization and Scanning Electron Microscopy. PLoS ONE 8(10): e77209. doi:10.1371/journal.pone.0077209

Kopek BG, Shtengel G, Xu CS, Hess HF (2012) Correlative Photoactivated Localization and Scanning Electron Microscopy. PNAS Early Edition. doi:10.1073/pnas.1121558109

Image Credits: All images from the PLOS ONE article doi:10.1371/journal.pone.0077209

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US Government Shutdown: Possible Effects at PLOS ONE

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Effective as of midnight, October 1st, 2013, the US government is closed for business, which means that all nonessential US federal services and agencies have stopped operating until further notice. Please note that anyone affiliated with a US federal agency may not be working. Below is our understanding of the details and implications for PLOS ONE services. (Any of you who are affiliated with a US government agency, and who may have more accurate information to offer, please do comment.)

Those who work for US federal agencies will not go to work, and we have been informed that some may not access or use email. Therefore, PLOS ONE reviewers and editors employed by or affiliated with the US government may or may not be available to handle manuscripts. The work these folks do for us is voluntaryand much appreciatedbut these services may be directly associated with their US government employment.

We kindly ask all PLOS ONE authors to please be aware that they may experience delays in manuscript handling due to these closures. Editors and reviewers who have already agreed to evaluate a manuscript may not be reachable at this time. We will do our best to keep everyone abreast of the status of their manuscripts, but please feel free to email us with questions or concerns (plosone@plos.org).

A non-exhaustive list of affected agencies is as follows: CDC, DOD, DOE (and all national labs), DOI, EPA, FDA, HHS, NASA, NCBI, NCI, NHGRI, NIH (all institutes, which may affect those at hospitals), NIMH, NIOSH, NIST, NOAA, NSF, USDA, USFS, and USGS.

We apologize for the inconvenience, and hope that all government services will resume shortly.

Image Credit: Photo by saratogajean

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DNA Funtime: How to Stretch DNA and Put It Anywhere You Want (sort of)

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Ever since the days of Watson and Crick—and Franklin, but we won’t get into that right now—we’ve known that double-stranded DNA’s favorite shape is that of a helix. DNA also comes single-stranded and as a random coil, but regardless, as a type of strand, it stands to reason that if tension could somehow be applied to it, it could be elongated or “stretched.”

Why mess with the shape of DNA strands, single, double, random, or otherwise? Actually, when stretched out in all its glory, scientists hope that they may be able to do many things: map patterns in the DNA sequence, characterize chromosomal abnormalities, and possibly even directly read the genetic or epigenetic information right off its back…bone.

Stretching DNA is very tricky, as you might imagine, and requires fairly complicated (and slow) techniques that often create limitations. Particularly, once you’ve stretched the DNA, you’d like to set it down on a surface somewhere to have a look at it. To do this, scientists often need to use a liquid or solid “carrier,” like a pH-controlled solution, to get the DNA in contact with the depositing surface. However, problems can arise if the surface is fragile or otherwise incompatible with the carrier.

In an epic race to try to stretch DNA the fastest, cheapest, and best, scientists have been wracking their brains to come up with new ways in which this can be done. One of these is illustrated in a recently published PLOS ONE study, titled “Molecular Threading: Mechanical Extraction, Stretching and Placement of DNA Molecules from a Liquid-Air Interface,” where Harvard researchers developed a new method of stretching DNA that allows the strands to be deposited on many types of surfaces in a precise manner.

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The authors call this technique molecular threading, and the method is as follows: stick a special-coated glass microneedle into a DNA-containing droplet of solution, pull it out, and suspend the DNA segment in air until you are ready to put it down on the dry surface below (illustrated in the figure above and the video here).  This works because when you are pulling the DNA out of the droplet, there is an air-liquid interface between the droplet and the air that has the ever-so-convenient property known as surface tension. In a desperate fight to keep the droplet’s shape, the droplet molecules “hold on” to the pulled DNA molecule and create a restoring force that allows the molecule to be suspended in air. As the needle is lowered to the surface, the DNA molecule makes contact with it, and the substrate has enough weak forces to overcome the surface tension, so the DNA sticks to it. And, because threading stretches DNA in air rather than in liquid, the extended thread can be placed onto water-soluble, dry, or fragile surfaces. Voilà!

The researchers gadgeted out the apparatus so that they could monitor this high-throughput process in real-time, take pictures, introduce alternate positioning and angling, and make very precise needle movements. In addition, they made efforts to prevent droplet evaporation and make the straightest DNA strands that they could. The scientists took a look at their handiwork by introducing a fluorescent dye to the DNA and imaging the threads with both fluorescence and electron microscopy; the results of the fluorescence imaging can be seen as bright green lines (individual DNA strands!) in the image below.

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As with any technique, there are caveats and limitations, including the occasional multi-thread extraction and missing thread, but all in all, the authors believe that this technique produces cleaner, straighter, and more reproducible strands than other techniques, like molecular combing, and it also allows them to deposit more molecules closer together. Of course, more work is needed to improve the set up and understand exactly what is going on during stretching.

If you are interested in geeking out further on this topic, please check out the awesome instrument and method pics in the article here.

Citation: Payne AC, Andregg M, Kemmish K, Hamalainen M, Bowell C, et al. (2013) Molecular Threading: Mechanical Extraction, Stretching and Placement of DNA Molecules from a Liquid-Air Interface. PLoS ONE 8(7): e69058. doi:10.1371/journal.pone.0069058

Image and Video Credits: Figure 1, Figure 2, and Video S1 from the article

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The Poop Will Tell Us: Do Elephants and Rhinos Compete for Food?

Africa

A recent study of the two animals in Addo Elephant National Park, called “Shift in Black Rhinoceros Diet in the Presence of Elephant: Evidence for Competition?” suggests the answer is yes.

Scientists interested in helping endangered species like the African elephant and the black rhinoceros would like to know whether these animals compete for resources in the wild, as such food contests could impact the population and health of both species. Unfortunately, our favorite rough-skinned big guys have IUCN statuses of vulnerable and critically endangered, respectively, so competition for food between them may present a bit of an ecological puzzle.

To gain evidence of food competition, researchers from Australia and the Centre for African Conservation Ecology took a close look at elephant and rhino poop (no, seriously) across different seasons to identify the types of plants each herbivore  was eating. Poop collecting was performed at times of the year when rhinos and elephants ate in the same region, and then again when only rhinos grazed in the area (in the absence of elephants). Variations in the plant types found in the feces were counted as indicators of dietary differences.

While it’s been shown that the presence of elephants can help some herbivores with habitat and food access, limited studies have been conducted on how the elephants’ foraging behavior may affect that of specifically megaherbivores. The authors state that there is clear evidence that elephants hog and monopolize food, a behavior that they suspected would affect the diets of other large herbivores. Indeed, the results of this study revealed that resource use was clearly separated by season, and rhinos munched on different grasses depending on whether or not the elephants were present. Without elephants around, rhinos ate more diverse plants, like woody shrubs and succulents, but in their presence, rhinos restrained themselves and consumed more grasses. This may not seem like a big deal, but rhinos are known to be strict browsers (read: picky about their food choices), so this dietary difference discovery was surprising to researchers.

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The authors go on to suggest that elephants living at high population densities in certain regions may significantly affect the foraging opportunities of other grazers, and these close living quarters may have long-term effects on the overall fitness of the other animals. These behaviors may have particularly important consequences in smaller or fenced-in wildlife parks, where populations tend to grow at the same time that food availability goes down.

Citation: Landman M, Schoeman DS, Kerley GIH (2013) Shift in Black Rhinoceros Diet in the Presence of Elephant: Evidence for Competition? PLoS ONE 8(7): e69771. doi:10.1371/journal.pone.0069771

Image Credits: African wildlife photo by Chris Eason (Mister E); plot from article

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It’s for the birds: Citizen science reveals shift in winter bird homes

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Just in time for summer solstice (the longest day of the year!), we bring you the heartwarming tale of a study that analyzed data collected about our feathery friends in the middle of winter. The Audobon Christmas Bird Count, a yearly bird census originating back in 1900, is conducted by bird-loving volunteers all over the Western Hemisphere who spot birds and record their sightings. It is also an example of what some call “citizen” or “crowd-sourced” science, and a newly published PLOS ONE article demonstrates how this scientific data, collected by the general public, can help researchers assess the conservation needs of an at-risk migratory bird, the western grebe.

Canadian researchers wanted to take a closer look at the bird population patterns of the grebe, a marine water bird that had recently been showing a worrying trend of drastic population declines in its winter home, ranging from the Pacific coast to California. In “Citizen Science Reveals an Extensive Shift in the Winter Distribution of Migratory Western Grebes,” researchers modeled a whoppin’ 36 years of collected bird count data from 163 “circles,” or designated diameters of land, mounting to a total of 2.5 million grebe observations.

So, what did they—and we, in this case—find? Thanks to decades of data collected by birdwatchers (1975-2010), researchers were able to show that western grebe populations along the northern Pacific coastal region decreased by about 95% over 36 years, but increased by over 300% in coastal California. Similar trends were observed for related bird species, suggesting that the winter habitat of the grebe has shifted south by ~ 900 km, to California, between 1980 and 2010.

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This is much better news than finding a concerning population decline that might prompt time-consuming and expensive conservation efforts. The researchers state that they aren’t yet sure of the reasons for this shift, but they suspect that the types of fish prey the grebes feed on may have also shifted in abundance between the two locations. All in all, this study demonstrates that wildlife data gathered by the general public (in any season, really) can result in meaningful, published scientific research that is useful to ecologists and conservationists alike.

Citation: Wilson S, Anderson EM, Wilson ASG, Bertram DF, Arcese P (2013) Citizen Science Reveals an Extensive Shift in the Winter Distribution of Migratory Western Grebes. PLoS ONE 8(6): e65408. doi:10.1371/journal.pone.0065408

Image Credits: Grebe photo by Mike Baird; map photo from article

 

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Sharing was Caring for Ancient Humans and Their Prehistoric Pups

huskies_1While the tale of how man’s best friend came to be (i.e., domestication) is still slowly unfolding, a recently published study in PLOS ONE may provide a little context—or justification?—for dog lovers everywhere. It turns out that even thousands of years ago, humans loved to share food with, play with, and dress up their furry friends.

In the study titled “Burying Dogs in Ancient Cis-Baikal, Siberia: Temporal Trends and Relationships with Human Diet and Subsistence Practices,” biologists, anthropologists, and archaeologists joined forces to investigate the nature of the ancient human-dog relationship by analyzing previously excavated canid remains worldwide, with a large portion of specimens in modern-day Eastern Siberia, Russia. The authors performed genetic analysis and skull comparisons to establish that the canid specimens were most likely dogs, not wolves, which was an unsurprising but important distinction when investigating the human-canine bond. The canid skulls from the Cis-Baikal region most closely resembled large Siberian huskies, or sled dogs. Radiocarbon dating from previous studies also provided information regarding the dates of death and other contextual information at the burial sites.

The researchers found that the dogs buried in Siberia, many during the Early Neolithic period 7,000-8,000 years ago, were only found at burial sites shared with foraging humans. Dogs were found buried in resting positions, or immediately next to humans at these sites, and their graves often included various items or tools seemingly meant for the dogs. One dog in particular was adorned with a red deer tooth necklace around its neck and deer remnants by its side, and another was buried with what appears to be a pebble or toy in its mouth.

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By analyzing the carbon and nitrogen in human and dog specimens in this region, the researchers were able to determine similarities in human and dog diets, both of which were rich in fish. This finding may be somewhat surprising because one might assume that dogs helped humans hunt terrestrial game, and would consequently be less likely found among humans that ate primarily fish.

The authors speculate that dogs were considered spiritually similar to humans, and were therefore buried at the same time in the same graves. The nature of the burials and the similarities in diet also point toward an intimate and personal relationship, both emotional and social, between humans and their dogs—one that involved sharing food and giving dogs the same burial rites as the humans they lived among. Ancient dogs weren’t just work animals or hunters, the authors suggest, but important companion animals and friends as well.

Citation: Losey RJ, Garvie-Lok S, Leonard JA, Katzenberg MA, Germonpré M, et al. (2013) Burying Dogs in Ancient Cis-Baikal, Siberia: Temporal Trends and Relationships with Human Diet and Subsistence Practices. PLoS ONE 8(5): e63740. doi:10.1371/journal.pone.0063740

Image Credits: Losey RJ, Garvie-Lok S, Leonard JA, Katzenberg MA, Germonpré M, et al. (2013) Burying Dogs in Ancient Cis-Baikal, Siberia: Temporal Trends and Relationships with Human Diet and Subsistence Practices. PLoS ONE 8(5): e63740. doi:10.1371/journal.pone.0063740

Siberian husky photo by Pixel Spit

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