The post Supporting Hepatitis Awareness with Open Access Hepatitis Research appeared first on EveryONE.
Category Archives: Internet/Blogging
If at First You Don’t Succeed, Sit Back and Listen
The Science of Snakeskin: Black Velvety Viper Scales May be Self-Cleaning
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
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)
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
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)
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
The post The Science of Snakeskin: Black Velvety Viper Scales May be Self-Cleaning appeared first on EveryONE.
A Year in Review: 2013 PLOS ONE Papers in the Media
Image Credit: Yutaka Tsutano
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
Image credit: PLOS ONE article
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?
Image credit: PLOS ONE article
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
Image credit: PLOS ONE article
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 story.
4. Wrapped up in a Book
Image credit: moriza
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
Image credit: PLOS ONE article
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?
Image credit: PLOS ONE article
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
Image credit: PLOS ONE article
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?
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…
Image credit: Denis Defreyne
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 their fear of cats. The story received coverage from several news outlets, including a CNN segment by Charlie Rose, BBC, National Geographic Phenomena, and Nature.
11. Just in Time for the Movie: Jurassic Park is Fake
Image credit: Wikipedia
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
Image credit: PLOS ONE article
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
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?
Image credit: PLOS ONE article
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
Image credit: PLOS ONE article
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!
The post A Year in Review: 2013 PLOS ONE Papers in the Media appeared first on EveryONE.
New Year, New Species
Rock lizards, pigment producing fungus, eagle rays, ant garden parasites, and Antarctic sea anemones: new species are discovered all the time and there are likely still millions that we simply haven’t yet discovered or assessed. Species are identified by researchers using a range of criteria including DNA, appearance, and habitat. PLOS ONE typically publishes several new species articles every month, and below we are pleased to help introduce five that were discovered in 2013.
Thought previously to consist of only three species, this group of lizards are now seven distinct species. They appear very similar to one another, making it difficult to tell which characteristics define different species, and which are just variations present in the same species. They also have a variety of habitats, from trees to rocky outcrops, and the genus is widespread. Iranian, German, and Portuguese scientists used genetic variation and habitat to help describe four new species of Iranian rock lizards, Darevskia caspica, D. Kamii, D. kopetdaghica, and D. schaekeli. These techniques, in addition to analysis of the the lizards’ physical features, as in the photo of the four new species’ heads at the top of this page, helped to identify them definitively.
Found in soil, indoor environments, and fruit, Talaromyces atroroseus produces a red pigment that might be good for manufacturing purposes, especially in food. Some other species of this type of fungus produce red pigments, but they are not always as useful because they can also produce toxins. T. atroroseus produces a stable red pigment with no known toxins, making it safer for human use, according to the Dutch and Danish researchers who identified it.
Fish, like rays and sharks, are at high risk for extinction as a group, but as rare as they are, they can be plentiful enough in some locations to make them undesirable to locals. The discovery of the Naru eagle ray, Aetobatus narutobiei, splits a previously defined species, A. flagellum, that, due to its shellfish-eating habits, is considered a pest and culled in southern Japan. The discovery by Australian and Japanese scientists that this species is actually two species prompted the authors to encourage a reassessment of the conservation status of the rays.
Fungal parasites in ant gardens
In the Brazilian rainforest of Minas Gerais, leafcutter ants cultivate fungus, their primary source of food, on harvested leaf clippings. But scientists from Brazil, United Kingdom, and The Netherlands have discovered that their food source is threatened by four newly identified mycoparasites, Escovopsis lentecrescens, E. microspora, E. moellieri, and Escovopsioides nivea. The parasites grow like weeds in the ants’ gardens, crowding out more desirable fungus used for food. Unfortunately for the ants, researchers expect there are many similar unidentified species yet to be discovered.
Living on the previously undocumented ecosystem of the underside of the Ross Ice Shelf in Antarctica, American researchers discovered the first species of sea anemone known to live in ice, Edwardsiella andrillae. Fields of anemone were discovered using a scientist-driven remote-controlled submersible. The anemone burrows and lives within the ice and dangles a tentacle into the water beneath, almost as if it is dipping a toe in the water to test the chilly temperature.
Look here to read more about new species.
Citations
Ahmadzadeh F, Flecks M, Carretero MA, Mozaffari O, Böhme W, et al. (2013) Cryptic Speciation Patterns in Iranian Rock Lizards Uncovered by Integrative Taxonomy. PLoS ONE 8(12): e80563. doi:10.1371/journal.pone.0080563
Frisvad JC, Yilmaz N, Thrane U, Rasmussen KB, Houbraken J, et al. (2013)Talaromyces atroroseus, a New Species Efficiently Producing Industrially Relevant Red Pigments. PLoS ONE 8(12): e84102. doi:10.1371/journal.pone.0084102
White WT, Furumitsu K, Yamaguchi A (2013) A New Species of Eagle RayAetobatus narutobiei from the Northwest Pacific: An Example of the Critical Role Taxonomy Plays in Fisheries and Ecological Sciences. PLoS ONE 8(12): e83785. doi:10.1371/journal.pone.0083785
Augustin JO, Groenewald JZ, Nascimento RJ, Mizubuti ESG, Barreto RW, et al. (2013) Yet More “Weeds” in the Garden: Fungal Novelties from Nests of Leaf-Cutting Ants. PLoS ONE 8(12): e82265. doi:10.1371/journal.pone.0082265
Daly M, Rack F, Zook R (2013) Edwardsiella andrillae, a New Species of Sea Anemone from Antarctic Ice. PLoS ONE 8(12): e83476. doi:10.1371/journal.pone.0083476
Figures are all from their respective articles.
The post New Year, New Species appeared first on EveryONE.
PLOS ONE at AGU 2013
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.
I’ll Have What He’s Having: Dogs Eavesdrop on Human Interactions
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.
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.
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!
Robofish: How Color and Tail Wagging Helped Bring a Robot Fish to “Life”
In an age of 3D printing and bionic limbs, distinctions between the manmade and the natural can sometimes blur. Take, for example, the case of the robotic fish depicted above (part A). This little guy is modeled after Notemigonus crysoleucas (image, part B), also known as the golden shiner, and in a recent PLOS ONE study, researchers put it to the test: can a robotic fish influence the behavior of a real fish, and if so, what characteristics enable the robotic fish to do so? According to the researchers at Polytechnic Institute of New York University, answers may depend on the robot fish’s color and the frequency with which it waggles its tail.
To find out more, the authors commissioned the making of two robot fish for this study: one gray and one red. While both physically modeled the golden shiner in many respects, only the gray robot fish was painted to mimic its real-life counterpart. Other than color, the two robots were identical: both consisted of three rigid parts, connected on hinges, and sported silicone tail fins.
As illustrated above, one robot fish was placed in a water tunnel with a real fish during each trial. The real fish was free to swim in the tunnel while the robot fish “swam,” or waggled its tail fin, in the center of the apparatus. The robotic fish’s tail waggled at various frequencies, ranging from 0 Hz to 4 Hz, as webcams tracked the real fish’s movements. The middle of the tunnel was designated the “focal region” to indicate where fish and robot interaction was likely to occur. The researchers further divided the region behind the fish into four parts, explaining that the robot fish’s tail wagging was likely to affect the water flow, and thus the real fish’s behavior, in this area.
After reviewing the webcam footage, they found that neither factor (color, tail wagging frequency) working alone had a significant impact on the real fish’s swimming behavior. However, when the gray robot wagged its tail at 3 Hz, the real fish spent a significantly longer time swimming in the center of the tunnel, preferring to spend most of its time swimming right behind the robot. When this happened, the wake created by the robot’s tail wagging could allow the real fish to reduce its energy expenditure while swimming.
What’s so special about wagging your tail fin at 3 Hz, you ask? The researchers ascertained through preliminary research that when golden shiners swim, their tails waggle at 3.32 Hz. In addition, the gray robot’s coloring may have been more attractive to the golden shiner than the red robot’s, as it may have elicited a likeness-related social response in the real shiner. This suggestion is in line with other robot work in comparable fish species.
In other words, the robot fish exerted the most influence—or was the most convincing to the real fish—when its coloring and movements closely corresponded to the coloring and movements of a real fish. Go figure!
If you are interested in learning more, visit our website and see what others had to say.
Citation: Polverino G, Phamduy P, Porfiri M (2013) Fish and Robots Swimming Together in a Water Tunnel: Robot Color and Tail-Beat Frequency Influence Fish Behavior. PLoS ONE 8(10): e77589. doi:10.1371/journal.pone.0077589
Image 1: Figure 1 from the paper
Image 2: Figure 2 from the paper
Image 3: Figure 4 from the paper
Can You Image That? Imaging a Cell and Its Proteins Together
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.
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).
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.
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.
Citation: 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
Image Credits: All images from the article
Editorial Highlight: Reporting Standards at PLOS ONE
Most readers are by now familiar with the core principle behind PLOS ONE: to publish all papers that are scientifically and technically sound, regardless of their perceived impact or importance. Another publication criterion that has received far less attention until recently is our commitment to the quality and completeness of reporting.
PLOS ONE considers reporting quality to be of importance in two main areas: first in relation to completeness of authors’ descriptions of study methods and results, and second in assuring readers of the ethical basis underlying the work. The rationale for ensuring high standards of reporting and ethical oversight is aligned with our core mission to facilitate the re-use of open-access research; if studies aren’t reported appropriately, or don’t have the necessary ethical oversight, it is much more difficult for others to replicate the work or incorporate the data as part of a larger study.
The natural follow-up question might be: how do we as a journal maintain these standards? Here, we’d like to outline briefly our standards, the reasons for them, and the process for ensuring that authors adhere to them. By doing this, we hope to shed light on some of our internal processes, both for the journal’s community, as well as for interested readers that appreciate sound, well-done science as much as we do.
PLOS ONE is a large, international, open-access scientific journal that considers all manuscripts reporting the results of primary scientific research. Day to day, the journal receives many types of studies, including experimental and observational work on animal and human populations, as well as a range of computational and theoretical work. These are submitted by researchers around the world who are not necessarily bound by common standards of reporting or ethical oversight.
As an international journal, however, PLOS ONE has a responsibility to establish and maintain consistent and high standards for publication. Therefore, we require that authors assure us on submission of appropriate ethical review and approval for experimental work involving animals and human participants; relevant permissions for field studies or observational work; and adherence to appropriate discipline-specific guidelines for the reporting of taxonomic, paleontological, or archaeological specimens. In some areas, there are also more prescriptive guidelines to ensure the full description of study methods and results—including CONSORT for reporting randomized clinical trials and PRISMA for reporting systematic reviews in relation to human participants—and we provide links to many more in our manuscript guidelines.
How do journal staff check for these standards when we receive so many submissions each day? At PLOS ONE, we’ve found that the most effective way to ensure papers meet our requirements is to perform a series of checks at submission. This ensures that by the time articles are assigned to Academic Editors for detailed review, crucial information about ethical oversight and study conduct will be available for their consideration. By screening papers before the formal peer-review process, we provide support to our Editorial Board and reviewers, who volunteer their time and offer an invaluable service to the journal and the scientific community as a whole. Equipping our Academic Editors with additional, important details when they agree to handle a manuscript allows them to focus their specialized expertise where it is most valued: on the scientific and technical quality of the paper.
That said, we consider our Academic Editors as partners in our goal of maintaining high standards for reporting, research ethics, and integrity. We ask our Editorial Board members for advice in difficult situations, and greatly appreciate the expert input that they provide. In certain situations we seek the advice of additional experts in reporting or ethics to provide oversight on specific papers, and are currently setting up dedicated advisory boards to assist us. We also consult Editorial Board members when developing new internal policies, or when robust community guidelines (such as CONSORT for randomized clinical trials or the proposed ARRIVE for experimental animal research) are not yet available for specific study types.
We appreciate the support of PLOS ONE authors, editors, and reviewers in helping us maintain the highest standards possible.
Posted on behalf of the in-house editors at PLOS ONE:
Associate Editors Gina Alvino, Sarah Bangs, Meghan Byrne, Christna Chap, Michelle Dohm, Matt Hodgkinson, Anna Schmidt, and Elizabeth Silva; Senior Editors Eric Martens and Emma Veitch; Consulting Editors Catriona MacCallum and Iratxe Puebla; and Editorial Director Damian Pattinson
US Government Shutdown: Possible Effects at PLOS ONE
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 voluntary—and much appreciated—but 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
Lasting love? Research on Making and Breaking Romantic Relationships
Romance is in the air. Vacation getaways, cool breezes, and warm nights can set the scene for a good, old fashioned ‘summer fling.’ In celebration of love and the summer, here is some romance-centric science to round out the season:
As the saying goes, beauty is in the eye of the beholder; however, researchers have found beauty may also be in the face of the beholder. In a recent study, researchers discovered that we prefer partners who most resemble ourselves! The authors recruited over 20 couples and morphed each partner’s face in different ways: a morph with a prototypical female, one with a prototypical male, and a morph blending the participants’ faces with that of their mates. Using a ranking system, they found that participants clearly preferred their partner’s face when it resembled their own over all other facial morphs. This research provides insight into what may attract us to our summer flings, but how about their longevity?
Conflict resolution is key to the stability of adult relationships; however, we have little understanding of how conflict resolution affects teen relationships. In a study published this spring, researchers sought to discover if successfully resolving conflicts predicts whether a teen relationship will last. The authors interviewed 80 teenage couples and observed each of them during a confrontation. They then followed up with the couples over the next four years. During this analysis, the researchers discovered that adolescents who successfully resolved conflicts were not more likely to stay together then the couples who struggled through conflict resolution. Factors such as peer-groups, personality changes, and other causes may be more likely to influence the success of an adolescent relationship.
But what becomes of adult couples who can’t resolve conflicts? Researchers found that the quality of a person’s romantic relationship may predict the likelihood of depression. The authors analyzed survey data, including a ten-year follow-up, from nearly five thousand adults. The initial analysis outlined the quality of social and romantic relationships, assessing the individual’s social support and strain. In the follow-up survey, the researchers analyzed the quality of a participant’s relationship with their partners, family, and friends to assess social stress or support. Through this analysis, they found that strained romantic relationships increased the risk for depression more than stressed friendships or family relationships.
From physical preference, to conflict resolution, to depression, these research articles give us a glimpse of what shapes our romantic choices. For more PLOS ONE articles on the topic of love, visit our website
Citations:
Laeng B, Vermeer O, Sulutvedt U (2013) Is Beauty in the Face of the Beholder? PLoS ONE 8(7): e68395. doi:10.1371/journal.pone.0068395
Ha T, Overbeek G, Lichtwarck-Aschoff A, Engels RCME (2013) Do Conflict Resolution and Recovery Predict the Survival of Adolescents’ Romantic Relationships? PLoS ONE 8(4): e61871. doi:10.1371/journal.pone.0061871
Teo AR, Choi H, Valenstein M (2013) Social Relationships and Depression: Ten-Year Follow-Up from a Nationally Representative Study. PLoS ONE 8(4): e62396. doi:10.1371/journal.pone.0062396
Image: Lovers embracing on the beach at sundown / sunset on Morro Strand State Beach by Mike Baird
The Poop Will Tell Us: Do Elephants and Rhinos Compete for Food?
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.
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
Summertime Fun in the Sun
We are well into the summer months so discard those winter doldrums and get active! To help you get in the mood, we’ve assembled a variety of outdoorsy studies from around the world:
With the advent of digital cameras and camera phones, we have all become amateur photographers. Picturesque peaks and beautiful beaches can be captured with the press of a button, tagged, and shared with others instantly via social media. Researchers, like the ones in a recent PLOS ONE study, can now use this user-generated data—these geo-tagged photographs—to find striking vistas and examine how they correlate with environmental factors, such as soil carbon and farming. These researchers used photos of Cornwall, England, uploaded to Panaramio and plotted them on a map to see where users were taking pictures. Photographs that were clustered together indicated that the area was valued for its aesthetic or visual beauty. As you might think, most clusters were found in beaches and sparsely populated coastal towns. Their findings also suggest that agricultural areas were negatively correlated with aesthetic value.
When looking for your next vacation destination, find somewhere picturesque with clean water. In the US, researchers have studied the effect that water quality may have on recreational activities in the Puget Sound. To do so, they used data from the Washington State Parks to determine how many people entered, camped, or moored in the Puget Sound, starting from the late 1980s to the present day. They then plotted this against fluctuations in Enterococcus, a type of bacteria associated with urinary tract infections and meningitis, in the water. Their findings indicate that an increase of Enterococcus corresponded to a recorded decrease in visitation rates.
Feel like getting involved in the scientific process? You can spend your summer taking part in the citizen science movement and enjoy the great outdoors at the same time. Your contributions may help someone with their research! For example, take this recent PLOS ONE study that uses observational data collected by a Turkish ornithological society. The researchers took recorded sightings of 29 songbird species and combined it with climate data (rainfall and temperature) to develop a model predicting how songbirds may be affected by climate change. The model helped them predict the birds’ distribution in 2020, 2050, and 2080.
Fun can also be found closer to home. For those of you with little ones, there is research to indicate that children’s sedentary behavior can be reduced using a few simple methods. The researchers of this study suggest decreasing the amount of time parents watch TV on the weekend, and instead recommend participating in boys’ sports and encouraging girls to play outside. Their suggestions are based on data collected from participants’ accelerometers over the course of a year. Learn more about this study here.
Citations:
Casalegno S, Inger R, DeSilvey C, Gaston KJ (2013) Spatial Covariance between Aesthetic Value & Other Ecosystem Services. PLoS ONE 8(6): e68437. doi:10.1371/journal.pone.0068437
Kreitler J, Papenfus M, Byrd K, Labiosa W (2013) Interacting Coastal Based Ecosystem Services: Recreation and Water Quality in Puget Sound, WA. PLoS ONE 8(2): e56670. doi:10.1371/journal.pone.0056670
Abolafya M, Onmu? O, ?ekercio?lu ÇH, Bilgin R (2013) Using Citizen Science Data to Model the Distributions of Common Songbirds of Turkey Under Different Global Climatic Change Scenarios. PLoS ONE 8(7): e68037. doi:10.1371/journal.pone.0068037
Atkin AJ, Corder K, Ekelund U, Wijndaele K, Griffin SJ, et al. (2013) Determinants of Change in Children’s Sedentary Time. PLoS ONE 8(6): e67627. doi:10.1371/journal.pone.0067627
https://en.wikipedia.org/wiki/Enterococcus
Image: 99-Bar Harbor by Robert & Pam.
Unlikely Critters Found in Avocado Orchards
Wildlife isn’t always restricted to wild spaces.
Avocado orchards and other agricultural landscapes also buzz with species that forage and reproduce in these spaces. Birds and herbivores are able to find food and shelter in these cultivated areas, but what about carnivores? In a study published this week in PLOS ONE, researchers at the University of Washington have discovered that mammalian carnivores also occupy avocado orchards in southern California.
The authors used motion-activated cameras to observe animals in orchards and in adjacent wild lands in Santa Barbara and Ventura. Avocado orchards were of particular interest due to their location near native vegetation.
Through their investigation, the researchers detected more carnivores in the avocado orchards than in neighboring wild land sites. At least 7 out of the 11 native carnivores in the area were spotted roaming the orchards, including coyotes, gray foxes and bobcats.
Having delicious avocados handy may explain why some omnivores such as bears and raccoons are present in the area, however, little is known about why animals like bobcats and mountain lions might leave their wild habitat for cultivated land. One possibility is that the orchards provide water and fruits for herbivores, and an increased herbivore population could translate to more prey for the carnivores. The orchards may also serve as shelter, offering forest cover similar to oak woodlands in the area.
These native species cannot always persist in protected reserves, so it is important to learn how cultivated lands can serve their lifestyle and behaviors. The carnivores may not be searching for the perfect guacamole ingredient; however there is no doubt that the avocado orchards are serving as a habitat for a wide range of species.
Citation: Nogeire TM, Davis FW, Duggan JM, Crooks KR, Boydston EE (2013) Carnivore Use of Avocado Orchards across an Agricultural-Wildland Gradient. PLoS ONE 8(7): e68025. doi:10.1371/journal.pone.0068025
Image 1: doi:10.1371/journal.pone.0068025
Image 2: Image on Flickr by Graeme Churchard