Robofish: How Color and Tail Wagging Helped Bring a Robot Fish to “Life”

Figure 1

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.

pone.0077589 Figure 2

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.

pone.0077589 Figure 4

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

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Biking the Distance… In 30 Minutes or Less: The Impact of Cost and Location on Urban Bike Share Systems

Citi Bike

Those of us who commute to the PLOS San Francisco office have noticed the emergence of bike share stations cropping up along the San Francisco Bay and on the city’s main drag. And we’re not alone here in San Francisco: the picture above is from the New York City Department of Transportation’s bike share. Around the world, bike share systems, which aim to make bicycles available on a short-term basis to anyone, have experienced massive growth as cities work to decrease gas emissions and encourage people to stay active. However, not everyone is ready to forgo the convenience of four wheels for two just yet. To understand why more people haven’t made the switch from cars to bike share systems, the author of a recently published PLOS ONE paper delved into possible factors affecting our willingness to don a helmet and cycle the distance.

Using publically available data from Washington DC and Boston, Dr. Jurdak, an Australian researcher, conducted a series of statistical analyses designed to examine the impact of bike share system pricing and neighborhood layout on potential bikers. It turns out cost is a major factor for commuters and tourists alike, but distance is not. Although analyses showed a bias towards shorter trips with a tendency towards a peak of 6 minutes—averaging 13 minutes per trip—a sharp drop off occurred in the likelihood of trips right around 30 minutes.

Why the decline at around 30 minutes? In both Boston and Washington DC, trips under 30 minutes incurred no additional cost in the bike share pricing system. Registered users of the bike share, typically commuters, must pay an initial registration fee but have a grace period for all trips completed in less than 30 minutes. Trips extending beyond 30 minutes, however, incur additional fees. In other words, public bicyclers are looking to maximize the distance biked and time spent without incurring any additional cost. Researchers have labeled this as ‘cost sensitivity.’

Statistical analyses also demonstrated the same cost sensitivity in casual users, or those who do not have a monthly or annual membership, and who likely use the bike share system for tourism. However, instead of noting a decline in the likelihood of trips around 30 minutes, Dr. Jurdak found a decline for casual users at around 60 minutes (another price point).

On the other hand, despite sensitivity to cost, bikers appeared less dissuaded from bike trips based on neighborhood layout. Although stations in Boston were on average much closer to other nearby stations than in Washington DC, in general, the trip distribution for both cities was remarkably similar. Perhaps not surprisingly, the most popular routes taken in both Boston and Washington DC were relatively flat.

To encourage more people to cut the car usage and grab a rental bike, Dr. Jurdak recommends that cities consider incentivizing their constituents with what they care about: cost. Modified prices for bike rental during peak hours may decrease car traffic on congested roads; an extension of grace periods for biking difficult topology, like up a steep San Francisco hill, might encourage us to bike even though the clock is ticking to 30 minutes and an incurred rise in price. As cities look to evolve public transportation systems and increase responsible urban mobility, and as city dwellers look for cost-effective ways to get around, bike share programs continue to offer healthy solutions for all, even at 30 minutes or less.

For more on the effects bike share systems are having around the world, check out another recent PLOS ONE paper and the researchers’ blog post on bike webs, visualizations of bike share schemes.


Jurdak R (2013) The Impact of Cost and Network Topology on Urban Mobility: A Study of Public Bicycle Usage in 2 U.S. Cities. PLoS ONE 8(11): e79396. doi:10.1371/journal.pone.0079396

Image 1: Citi Bike Launch by New York City Department of Transportation

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Ant-Mimicking Spider Relies on a “Double-Deception” Strategy to Fool Different Audiences

From snakes that look like they have two heads to color-shifting chameleons, deception is at the heart of many animals’ survival strategies.  Both visual and chemical predator deterrence are well-documented phenomena in the animal world, but new research on ant-mimicking spiders, published in PLOS ONE, may be the first documented case of a species that uses visual deception to elude one group of predators, and chemical deception to escape another.

Ant mimicry, or myrmecomorphy, is a tactic used by numerous spider species, and with good reason, since many predators steer clear of preying on ants due to their aggressive tendencies and often unpleasant taste. Ant-mimicking spiders can have body shapes that closely resemble those of ants, as well as colored patches that look like ant eyes.  Combine these characteristics with behaviors such as waving their front legs in the air to resemble probing ant antennae, and these spiders can successfully convince predators to look elsewhere for their next meal.  The jumping spider Peckhamia picata is one such ant mimic whose visual signals are an effective deterrent for visually focused predators, such as other species of jumping spiders.  The picture below shows a jumping spider on the left and the ant it imitates on the right.

1 Ant mimic and predators

The PLOS ONE study shows that the ant-mimicking spider can also elude predators that rely heavily on chemical signals to identify their prey.  In the current study, the spiders successfully eluded spider-hunting mud-dauber wasps (pictured below), and received significantly less aggression from the ants they mimic than other non-mimicking jumping spiders. The researchers presented wasps with a choice between freshly killed ant-mimicking and non-mimicking spiders. In all of the trials conducted, the wasps probed both types of spiders with their antennae, but every time a wasp chose to sting and capture a spider (seven out of eight times), it chose the non-mimicking spider.The researchers also staged encounters between Camponotus ants and live ant-mimicking and non-mimicking spiders.  After probing them with their antennae, the ants were significantly less likely to bite the ant-mimicking spiders than non-mimicking ones.  These results demonstrate that the jumping spider has a remarkably effective ability to deceive potential predators who focus on chemical cues when selecting prey.

2 wasp

The researchers point out that the spider is not a chemical mimic of the ant species it emulates. Insects rely heavily on hydrocarbons secreted from their cuticles (the hard outer covering of invertebrates) to identify and signal one another. It turns out that ant-mimicking spiders have very low levels of these molecules, only a small fraction of the amount found in non-mimicking spiders and the ants themselves. While further research is required to fully explain the jumping spider’s chemical mechanism for predator evasion, a likely explanation is that the low level of these chemicals does not register as significant to a probing ant or wasp, and the chemical evasion is accomplished in this way.

This study may be the first to describe an animal using a “double-deception” strategy:  visual tricks and a deceptive chemical signature, both intended for different audiences.  The authors hypothesize that this kind of chemical deception is likely widespread among other visual mimics in the animal kingdom.

Related links:

Video of a ramblin’ ant-mimicking jumping spider (great music)

Spiders gather in groups to impersonate ants

Citation: Uma D, Durkee C, Herzner G, Weiss M (2013) Double Deception: Ant-Mimicking Spiders Elude Both Visually- and Chemically-Oriented Predators. PLoS ONE 8(11): e79660. doi:10.1371/journal.pone.0079660

Images:  Images come from Figure 1 of the manuscript

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Picked Clean: Neanderthals’ Use of Toothpicks to Fight Toothache


The toothpick —an often unnoticed tool for post-meal rituals and appetizer stability—has played a greater role in our ancestors’ health and comfort than many would imagine. In a world before dentists, Neanderthals and modern humans may have taken oral hygiene into their own hands using the only tools they had readily available: little bits of nature they found surrounding them.

Researchers from Spain have presented evidence in PLOS ONE that Neanderthals may have used small sticks or blades of grass not only to remove fragments of food from between their teeth, but also to lessen the pain caused by periodontal disease, a form of gum disease. While multiple human and Neanderthal remains have been found showing possible evidence of toothpick use, the authors propose that the combined evidence of toothpick use and gum disease suggests that Neanderthals were perhaps practicing an early form of dental care.

The samples in the image above show an adult’s upper jaw with three teeth left intact found at the Cova Foradà cave site in Valencia, Spain, amidst animal remains and tools dated to the Mousterian era (300,000-30,000 years ago). The adult teeth, believed to belong to an individual between 35-45 years old, show heavy wear on the top surface and exposed roots, the possible result of a lifetime’s consumption of fibrous and abrasive foods like meats and grains. There are no signs of cavities in the remaining teeth, though decayed bone and the porous surface texture of the left side of the jaw indicate the presence of gum disease.

Two distinct grooves are present on the sides of the existing premolar and molar above the crown of the tooth. These grooves may have been caused by consistent dragging of a tool across the side of the tooth. The existence of these marks above the gum line indicates heavy dental wear and disease. Here, the gums had receded and left the base of the tooth unprotected. With the roots exposed, it would be easy for leftover debris from meals to get stuck and put pressure on already inflamed gums. The use of a foreign object pushed between the teeth would remove any particles lodged in this sensitive area. Without the extra burden of invasive food detritus, force on the gums would be reduced and irritation and pain would decrease.

Over the last few years, studies have shown that Neanderthals may have been capable of complex behaviors and emotions, may have used a sophisticated language, were more often right-handed than left, and were generally not the inferior cousins some thought they were. As this study shows, they may have practiced dental care as well. So, the next time you’re heading out of your favorite restaurant, take a good look at that bowl of toothpicks at the front: the contents could very well be evidence of one of our oldest habits.

Check out more coverage of this article in National Geographic and Archaeology magazine.

UPDATE: This post has been updated to reflect that the research in this study may suggest that Neanderthals used a toothpick like tool to relieve dental pain, though it is not possible to make definite claims.

Citation: Lozano M, Subirà ME, Aparicio J, Lorenzo C, Gómez-Merino G (2013) Toothpicking and Periodontal Disease in a Neanderthal Specimen from Cova Foradà Site (Valencia, Spain). PLOS ONE 8(10): e76852. doi:10.1371/journal.pone.0076852

Image Credit: Image from Figure 2 of the manuscript

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A Rat’s Journey Through Virtual Reality

Virtual EnvironmentFew ideas excite the imagination more than virtual reality. We humans use virtual reality for training, entertaining, and even education, but we can also use it to study human and animal behavior. Adaptive behavior, or the ability to adjust to new situations, is influenced by what we see, hear, and experience in our environment; unfortunately, for this reason, it is difficult to isolate the possible stimuli that affect it. The authors of this recently published PLOS ONE paper developed a virtual reality environment to try to isolate and measure the impact of visual and sound cues on rats navigating through a virtual space.

The virtual reality navigation test is based on an experiment called the Morris Water Maze, a standard lab test where a rat swims through water using visual cues on the walls to Virtual Reality Rat Harnessnavigate. The virtual version uses a 14 square-foot room with visual cues projected on each wall and sounds from 4 sides (pictured above). The rat is at the center of the room, wearing a harness (pictured on the right) on a spherical treadmill placed on a three-foot circular table.

Before beginning the navigation tasks, researchers trained nine male rats to move in virtual reality. The rat started from one of 4 random start locations, facing the wall (see video below). The northeast quadrant of the space was designated as the ‘reward zone,’ indicated by a white dot. Upon entry to this zone, the rat was rewarded with sugar water (if only all video games worked this way).

After training, the researchers tested each rat’s ability to navigate to the reward zone using one of three cues: audiovisual, visual, or auditory. Once the rat found the reward zone, a 2-second blackout period was initiated, and then the rat was ‘moved’ back to one of the 4 random start locations. The video below shows the visual cue test.

Scientists found that rats can learn to navigate to an unmarked location based on visual cues—with a moderate amount of training. However, the rats were unable to use the auditory cues to navigate to the reward zone, and instead moved in circles to try to locate it.

Although the rat’s harness may look a little funny, it is a relatively noninvasive test, and since the animal is not in water, like in the Morris Water Maze test, it is easier to combine this test with tools to measure neural and physical variables in the task. Additionally, the virtual maze may contribute to new methodology evaluating the underlying factors in adaptive behavior, specifically because no other cues besides the audiovisual, visual, and auditory defined the spatial location of reward, something that is difficult to achieve in the real world. Despite humans not yet understanding what virtual reality means to us, we can already use it to better understand animal learning and behavior.

Citation: Cushman JD, Aharoni DB, Willers B, Ravassard P, Kees A, et al. (2013) Multisensory Control of Multimodal Behavior: Do the Legs Know What the Tongue Is Doing? PLoS ONE 8(11): e80465. doi:10.1371/journal.pone.0080465

Image 1: doi:10.1371/journal.pone.0080465

Image 2: doi:10.1371/journal.pone.0080465

Video 1: doi:10.1371/journal.pone.0080465

Video 2: doi:10.1371/journal.pone.0080465

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Spotlight on PLOS ONE’s Neuromapping and Therapeutics Collection

Collection image.pcol.v02.i17.g001Launched in 2010, the Neuromapping and Therapeutics Collection is a unique collaboration between PLOS ONE and the Society for Brain Mapping and Therapeutics. The Neuromapping and Therapeutics Collection provides a forum for interdisciplinary research aimed at translation of knowledge across a number of fields such as neurosurgery, neurology, psychiatry, radiology, neuroscience, neuroengineering, and healthcare and policy issues that affect the treatment delivery and usage of related devices, drugs, and technologies. The Collection is open to submissions on these topics from any researcher—so far, 24 research papers have been published as part of this Collection.

We spoke to Dr. Allyson Rosen, one of the members of the Society for Brain Mapping and Therapeutics who helps coordinate the Neuromapping and Therapeutics Collection, to discuss the latest news and research in this area, and the new submissions to the collection they’re hoping to see in the next few months:

What’s exciting in Neuromapping and Therapeutics at the moment?

CollectionSBMT-BMF-Logo for blog


It is exciting to see how creative scientists and clinicians are at solving important clinical problems by combining diverse techniques in innovative ways. We see our collection as a home for cross-disciplinary work that might not “fit” in traditional journals. For example, we have published MR methods to enable effective brain infusions and work that exploits computer-aided design for cranial reconstructions. There are invasive and non-invasive techniques for stimulating selective brain regions and creating focal lesions, such as transcranial magnetic stimulation, transcranial Doppler technology, and X-ray microplanar beam technology. There are also innovative analysis techniques that exploit powerful computational methods that were previously unavailable.

What are the implications of President Obama’s commitment to Human Brain Mapping research?

Given the high-profile nature of the Brain Mapping Initiative and the state of the US economy, we have advocated that there be some clinical implications to the announcement. We believe that this approach will ensure continued public support at a time of great need and uncertainty.

Are there any specific research areas where you’d like to see more submissions to the Collection?

We are proud of the work we’ve received and deeply impressed with the broad array of papers submitted so far. This is a testament to the creativity of our contributors, and we welcome their diversity. We particularly welcome work presented at the international meeting of the Society for Brain Mapping and Therapeutics that occurs in the spring of each year.

Why do you think it’s important to publish this kind of research in an open access journal such as PLOS ONE?

Our society is committed to being inclusive and welcoming any profession that seeks to improve the health and wellbeing of patients with brain disorders. An open access journal enables easier promotion of work we feel is important and encourages sharing among diverse disciplines. Often, truly cutting-edge work is so far ahead of its time that there is not yet an appreciation for its importance. Often, clinical problems are seen as practical but not necessarily novel. We appreciate the mission of PLOS ONE as upholding strong scientific integrity and not as triaging work based on arbitrary decisions regarding importance.

To read more about this Collection, including new research papers like, “Verifying three-dimensional skull model reconstruction using cranial index of symmetryandUnique anti-glioblastoma activities of Hypericin are at the crossroad of biochemical and epigenetic events and culminate in Tumor Cell Differentiation,” click here.

Come visit us at SFN 2013.

Both the Society for Brain Mapping and Therapeutics and PLOS ONE will be attending SFN 2013 – please drop by booth #136 to say hello and learn more about the Collection. For instructions on how to submit to the Collection, please visit the Collection page and download the submission document.

If you have any questions about this Collection, or any other PLOS Collections, please email

Image credit for Collection cover: Alka Joshi

Image Credit: Society for Brain Mapping & Therapeutics

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Public Health Links, Lost in Translation


PLOS is at SpotOn London (#solo13) again this year, taking part in workshops and panels on science communication tools, policy, and outreach. On Friday November 8, I’ll be joined by three PLOS authors and two independent science journalists for a science outreach workshop titled Public Health Links, Lost in Translation. With our moderator, science journalist Suzi Gage (@soozaphone) of the Sifting the Evidence blog on The Guardian, we will address weak links in the science communication “food chain” that contribute to falling vaccination rates, mainly in the UK, Europe, and the US.

For this session, I will be speaking as Editorial Director of PLOS ONE, the world’s largest scientific journal. But the debate around vaccination began before PLOS existed and it has gone on longer than I’ve been involved in science communication. Coming as I do from a background of ‘peddling the evidence,’ it disturbs me when I see evidence ignored in favour of quackery. But I also bring a personal perspective to this issue. As with climate change, it frustrates me that my own actions are not enough to safeguard my children against a threat to their health and safety. Although no vaccine is perfect, every time my children play with others who are intentionally un-vaccinated their risk of contracting preventable contagious diseases increases.

So it seems to me that the aim of this workshop will be to use our combined perspectives – and those of the science community members present – to discuss how we strengthen the links between evidence-based science and the public on vaccines. We aren’t the first and certainly won’t be the last meeting of scientists and science writers to take on this issue, but that doesn’t let us off the hook and excuse us for not trying.

Good and Bad News

The news on vaccines in the UK is not all bad. By summer of 2013, ninety per cent of two-year-old children had received their first dose of the MMR (measles-mumps-rubella) vaccine – the highest level for 13 years according to the Health Protection Agency. This uptake in MMR vaccinations has been a public reaction to widely-reported measles outbreaks in Europe and the UK – suggesting an appropriate public response to highly visible evidence. However, present MMR uptake is still short of the 95% rate that would establish a sufficient level for herd immunity, which would stop the spread of the disease in the community.

The Legacy of MMR

All of us continue to pay the price for the broken public trust that came from the Andrew Wakefield-MMR debacle of the mid-90s. Strong distrust concerning vaccine safety exists not only in rich and middle income countries, but also on the front lines of the Global Polio Eradication Initiative, as my colleagues at PLOS Medicine have covered in depth.

The link between this widespread distrust and falling vaccination rates are clearly established:

New vaccinations for diseases such as HPV, and new approaches to old ones, e.g. targeting different populations to avert new outbreaks of influenza or shingles, increase the challenges for public health practitioners and advocates.

A More Honest System

In many ways, I don’t blame the public for being mistrustful of scientific research – the scientific community and mainstream media make it very hard for people to know what to believe. As Editorial Director of a large journal, I see the entire spectrum of misinterpretation of data. I see original datasets being over-interpreted by authors, in order to get published in top journals. I see journalists taking these papers and adding yet another layer of spin in order to sell them to the public. I see newspaper editors pushing the most shocking articles to the front pages to ensure maximum impact. It’s little wonder that the public are mistrustful.

At PLOS ONE, we are trying to deal with these challenges by encouraging honest reporting of data. By removing the question of ‘novelty’ and ‘impact’ from our review process, we aim to get authors to state simply what they’ve discovered without feeling they have to dress it up in layers of over-interpretation. That drug you’ve discovered kills some cells in a petri dish. Great! Is it a cure for cancer? No. So don’t say it is – we’ll still publish your paper!

We are also very careful about what we release to the press, and how the message is put out. Clearly we can’t stop journalists misinterpreting our papers, but we can at least give the science we publish a decent chance of being reported correctly.

Finally, we track press and blog coverage and add it to the comments of the papers. Combined with our Article-level Metrics, which display a whole array of reactions to the paper and usage statistics, readers can see whether high activity on a paper is a result of heavy media attention, or whether it’s from interest from other researchers.

Certainly the papers most covered in the press are among those that receive the most views, so if we are to affect public attitudes on vaccines or any other highly-charged public health or science issue, we are as dependent on the excellent work of our authors as we are on our colleagues in new and old media. Panelists at this Friday’s SpotOn London 13 workshop represent this wide spectrum. With each bio below, I’ve included some of the research or science writing that will inform our discussion.

Marc Baguelin PhD (@marcbaguelin) is a mathematical modeler working in the Immunisation department at the Health Protection Agency and at the London School of Hygiene and Tropical Medicine on models of influenza transmission, immunization, and control. Marc’s research has been published in the journals Vaccine, Biostatistics, and Emerging Infectious Disease. His latest study, Assessing Optimal Target Populations for Influenza Vaccination Programmes: An Evidence Synthesis and Modelling Study, published in PLOS Medicine, resulted in a change of UK health policy with an extension of the influenza vaccination programme to 2-16 year old children.

Tammy Boyce, PhD (@tamboyce) holds an honorary lecturing post with the Centre for Infection Prevention and Management, Imperial College London, Hammersmith Hospital, London, and was a Research Fellow in Health, Risk, Science and Communication at the Cardiff School of Journalism.  Tammy’s research has been published in Nature Reviews Immunology, and the British Journal of Healthcare Management. She was one of the first to examine public reception of media coverage and the impact the style of reporting has on public opinion and vaccination decisions. From this research, Tammy published the book Health, Risk and News: The MMR Vaccine and the Media (with Peter Lang, 2007). Her latest research article in PLOS ONE examines the role of the school nurse in addressing inequities in HPV vaccine uptake in the UK.

Stephan Lewandowsky PhD (@STWorg) is a cognitive scientist in the School of Experimental Psychology, University of Bristol, UK. His research, published in Nature Climate Change, Journal of Experimental Psychology, and Cognitive Psychology, examines peoples’ memory and decision making with particular emphasis on how people respond to corrections of misinformation. His latest PLOS ONE research article, The Role of Conspiracist Ideation and Worldviews in Predicting Rejection of Science,. studies how conspiracist thinking affects public attitudes towards scientific issues; as Hilda Bastain blogged: a “strong consensus around science can be seen as evidence that ‘they’re all in cahoots’… with vaccination, say, presenting yet more facts or another study could paradoxically confirm their rejection of science.”

Beth Skwarecki (@BethSkw) is an independent science journalist specializing in public health issues who writes for AAAS Science News, and DoubleXScience and blogs on the PLOS BLOGS Network. Recent posts have covered the HPV vaccine’s “image problem” and the role of Twitter in spreading misinformation on the 2009 H1N1 pandemic.

Please add your thoughts and suggest questions for our panel by tweeting to the hashtag #solo13links. You can watch the live stream of the discussion at:

Here is the entire Spot On London 2013 program, FYI. Keep in mind all sessions will be live streamed with the archives kept online thereafter for your viewing.

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Yersinia pestis, Ghost of Plagues Past

Skeleton Blog2

Who’s afraid of the big bad plague? Bet you the owners of the bones above were. This Halloween, we’re highlighting the work of researchers who tested (extremely carefully) for the presence of the pathogen Yersinia (Y.) pestis (a.k.a., the “Bubonic Plague”) in human skeletal remains from three sites in Germany and Switzerland.  Thought to be victims of the Black Death, these individuals died alongside an estimated 75-200 million other Europeans affected by this outbreak of the plague, which diminished Europe’s population during the 14th century by one third.

The specialized protocol the researchers used in this study was carefully created to be in line with modern plague diagnostic procedures and to address the unique challenge of working with ancient DNA (aDNA), which varies in quality from sample to sample and is easily contaminated with modern DNA. Contamination is common and can be hard to identify, often resulting from poor handling practices at excavation or during preparatory procedures. The researchers  did their best to avoid the possibility by thoroughly cleaning the surfaces of the bones and teeth that samples were drawn from, and using multiple controls to highlight any points of contamination from the laboratory that occurred during the experiments. At a time when the results from testing of aDNA samples can be highly contested, a validated  DNA replication process was used to ensure authenticity of the tests and to prevent misinterpretation of the results by the scientific community.

Bones and teeth from 29 individuals, ranging from 300-600 years old, were collected from sites in Manching-Pichl and Brandenburg in Germany and Basel, Switzerland and housed at the State Collection for Anthropology and Palaeoanatomy  in Munich. Selected samples were then moved to newly constructed labs at the ArcheoBio Center of the Ludwig Maximilian University  Munich for preparation and aDNA extraction. Researchers followed a strict protocol to prevent any sample contamination at this stage. The new facility contains three air-locked and pressurized rooms, each meant to provide a contamination-free workplace for processing aDNA samples for replication. Before admittance to the three-room complex, staff were required to shower, wash their hair, and enter a gowning room to replace their freshly laundered clothes with two pairs of gloves, a hairnet, hooded overalls, and a screened facemask. A second gowning room required the addition of another set of hooded overalls. Scientists then moved through the rooms sequentially, preparing the aDNA samples and negative controls (meant to test for contamination in the replication process) for analysis.

Once preparatory procedures were complete, sealed tubes containing the negative controls and aDNA were transferred to the Bundeswehr Institute of Microbiology for the addition of positive controls (tubes containing DNA from Y. pestis), DNA replication and analysis. Of the 29 samples tested, seven contained fragments of a Y. pestis gene after an initial round of replication, and four additional samples tested positive for Y. pestis after further rounds of testing.

Although the skeletons above are not, Y. pestis is still alive and well in parts of the world. Now called the “Modern Plague” to differentiate it from previous plagues caused by the same pathogen, such as Justinian’s plague and the Black Death, the disease affects 1,000-3,000 people per year. Modern treatments have thankfully limited the number of deaths that result from these cases, leaving us less likely to end up in the ground after getting sick, like these poor individuals. Nevertheless, research on the presence of the pathogen in ancient samples remains crucial for our continued understanding of how this disease affected our population in the past.

So, in case you need a scary costume idea for tonight’s festivities, why not draw some inspiration from our friends above? A skeletal Black Death victim and a masked, double-overalled plague researcher sound like great costume ideas to us.

Happy Halloween from PLOS ONE!

Citation: Seifert L, Harbeck M, Thomas A, Hoke N, Zöller L, et al. (2013) Strategy for Sensitive and Specific Detection of Yersinia pestis in Skeletons of the Black Death Pandemic. PLoS ONE 8(9): e75742. doi:10.1371/journal.pone.0075742

Image Credit: Courtesy of the authors and the Bavarian State Department of Historical Monuments

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The New PLOS ONE Collection on “Sauropod Gigantism – A Cross-Disciplinary Approach”

Sauropod-Collection-600x600 (3) (2)The exceptional gigantism of sauropod dinosaurs has long been recognized as an important stage in the evolution of vertebrates, the presence of which raises questions as to why no other land-based lineage has ever reached this size, how these dinosaurs functioned as living animals, and how they were able to maintain stable populations over distinct geological periods.

We are pleased to announce the publication of a PLOS Collection featuring new research on the complex Evolutionary Cascade Theory that attempts to answer  these questions and  explain how the unique gigantism of sauropod dinosaurs was possible. The fourteen papers that make up the collection address sauropod gigantism from a number of varied disciplinary viewpoints, including ecology, engineering, functional morphology, animal nutrition, evolutionary biology, and paleontology.

Sauropod dinosaurs were the largest terrestrial animals to roam the earth, exceeding all other land-dwelling vertebrates in both mean and maximal body size. While convergently evolving many features seen in large terrestrial mammals, such as upright, columnar limbs and barrel-shaped trunks, sauropods evolved some unique features, such as the extremely long necks and diminutive heads they are famous for. Dr Martin Sander, Professor of Paleontology at Universität Bonn and coordinating author for this series of 14 papers, said of the collection:

“This new collection brings together the latest research on the biology of sauropod dinosaurs, the largest animals to ever walk on Earth. Having been extinct for 65 million years, reconstructing sauropod biology represents a particular challenge. Using a wide array of scientific expertise, often from seemingly unlikely fields, has led to some amazing insights. For example, principles of soil mechanics have been used to ‘weigh a dinosaur’ based on its trackways, whilst the latest in computer modeling can make a dinosaur walk again.

The ultimate question underlying this research is how sauropods were able to evolve their uniquely gigantic body size. The wide-ranging disciplines covered in the collection means that there is a -broad, multi-disciplinary audience for the research, as well as general interest in dinosaurs; therefore, we felt that it was essential to publish such a volume in a leading open-access journal such as PLOS ONE to ensure the widest possible dissemination of our work.”

Readers are able to download “Sauropod Gigantism: A Cross-Disciplinary Approach” not only as a PDF but also as an ebook (.mobi and .epub formats) from the collection page. It will also be available on Flipboard (search “PLOS Collections”).

Image credits:
Collection Image: Kent A. Stevens, University of Oregon

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Moonlit Rendezvous: The Box Jellyfish’s Monthly Meet-up in Waikiki

Box Jellyfish

When you think about tropical paradise, Hawaii is often at the top of the list. Waikiki is one of the most iconic Hawaiian beaches on Oahu and is a popular swimming and surfing spot. However, it is also a popular stop for the box jellyfish, one of the most venomous animals in the world. Once a month, about 8 to 12 days after the full moon, the shallow waters of Waikiki beach are temporarily flooded with box jellyfish. They are not coming in for a mai tai under the waning moon; rather, scientists believe that jellyfish reproduce in these waters. This monthly influx creates a hazard to swimmers due to the jellyfish’s painful—and even lethal—stings.

The environmental factors that affect these influxes are not well understood, and learning more about them may help us predict and mitigate the risk that box jellyfish pose to swimmers. Several scientists from Hawaiian institutions published the first long-term (14-year) assessment of the environmental conditions that potentially correlate with box jellyfish population changes in the North Pacific Sub-tropical Gyre.

The researchers surveyed a 400-m section of Waikiki beach during the days jellyfish were present. They counted more than 66,000 jellyfish over 14 years and compared the data to 3 measures of how the climate changes over time, called climate indices; 13 physical and biological variables, such as sea surface temperature and plankton; and seven weather measurements, including wind speed, air temperature, and rainfall.

They confirmed that box jellyfish arrive at Waikiki monthly after each full moon and stay for 2- 4 days. They counted on average 400 jellyfish each month, but the range was quite wide at 5-2,365 individuals. Rather than seeing a net population change over 14 years, researchers observed approximately 4-year periods of increased population count followed by 4-year periods of decreased population count, which coincided with fluctuations in three main environmental factors: oceanic changes in salinity and nutrient availability, called the North Pacific Gyre Oscillation, small organisms’ ability to access nutrients, called primary production, and abundance of small zooplankton.

The researchers suggest that the relationship between environmental fluctuations and jellyfish population changes at Waikiki may result from changes in the availability of food for jellyfish in the ocean around Hawaii, brought about by the North Pacific Gyre Oscillation. During an increase in nutrient availability, phytoplankton populations also increase, meaning more food for jellyfish, allowing them to grow faster and increase their rate of reproduction.

Previous studies have shown that jellyfish populations change due to human-caused disturbances, but this is one of the first long-term studies showing that large-scale climate patterns may also impact box jellyfish populations. Understanding long-term climate and oceanic trends and their effects on jellyfish populations may provide information to develop strategies for avoiding mass stinging events and beach closures at Waikiki and other popular recreation sites in the Pacific.


Citation: Chiaverano LM, Holland BS, Crow GL, Blair L, Yanagihara AA (2013) Long-Term Fluctuations in Circalunar Beach Aggregations of the Box Jellyfish Alatina moseri in Hawaii, with Links to Environmental Variability. PLoS ONE 8(10): e77039. doi:10.1371/journal.pone.0077039

Image Credit: Jellyfish by James Brennan Molokai Hawaii

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