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

Perceiving Is Believing


Do we really sing as well as we all think we do in the shower? Exactly how complex is Mel Taylor’s drumming in Wipeout? How we hear things is important not just for the field of music research, but also for the fields of psychology, neurology, and physics. There is a lot more to how we perceive sound than sound waves just hitting our ears. PLOS ONE recently published two research articles exploring music perception. One article focuses on how perceiving a sound as higher or lower in pitch—the frequency of a musical note relative to other notes—than another sound is influenced by different instruments and the listener’s musical training. The other explores rhythm, including musicians’ perception of rhythmic complexity.

Pitch is the frequency of a sound, commonly described using the words high or low. The quality of tone, or timbre, of an instrument, on the other hand, is less easy to define. Tone quality is often described using words like warm, bright, sharp, and rich, and can cover several frequencies. In the study presented in “The Effect of Instrumental Timbre on Interval Discrimination,” psychology researchers designed an experiment to determine if it is more difficult to perceive differences in musical pitch when played by different instruments. They also tested whether musicians are better at discriminating pitch than non-musicians (you can test yourself with this similar version) to see if musical training changes how people perceive pitch and tone.

The researchers compared the tones of different instruments, using flute, piano, and voice, along with pure tones, or independent frequencies not coming from any instrument. As you can see from the figure above, each instrument has a different frequency range, the pure tone being the most localized or uniformly “colored.” Study participants were given two choices, each choice with two pitches, and decided which set of pitches they thought were the most different from each other; sometimes they compared different instruments or tone qualities and sometimes, the same.

The researchers compared the participants’ answers and found that changes in tone quality influenced which set of pitches participants thought were the most different from each other. Evaluation of the different timbres showed that musicians were the most accurate at defining the pitch interval with pure tones, despite their training in generally instrumental tones. Non-musicians seemed to be the most accurate with both pure and piano tones, though the researchers noted this might be less reliable because non-musicians had a tendency to choose instrumental tones in general. Interestingly, both groups were faster at the pitch discrimination task when pure tones were used and musicians were better at the task than non-musicians. Everyone chose pitch intervals more accurately as the differences between the pitches became larger and more obvious.

Another group of researchers tested how we perceive syncopation, defined as rhythmic complexity, in their research presented in “Syncopation and the Score” by performing an experiment playing different rhythms to musicians.  They asked musicians to rank the degree of complexity of each rhythm.

The study was limited, with only ten participants, but in general, the rhythm patterns thought to be the most complex on paper were also perceived as the most complex when the participants listened to them. However, playing the same patterns in a different order sometimes caused listeners to think they were hearing something more or less syncopated. The authors suggest that a rhythm pattern’s perceived complexity depends upon the rhythm patterns played before and after it.

Both research studies highlight the intersection of music and music perception. We don’t need to be musicians to know that music can play tricks on our ears. It may be that some of us are less susceptible than others to these tricks, but even trained musicians can be fooled. Look here for more research on music perception.



Zarate JM, Ritson CR, Poeppel D (2013) The Effect of Instrumental Timbre on Interval Discrimination. PLoS ONE 8(9): e75410. doi:10.1371/journal.pone.0075410

Song C, Simpson AJR, Harte CA, Pearce MT, Sandler MB (2013) Syncopation and the Score. PLoS ONE 8(9): e74692. doi:10.1371/journal.pone.0074692

Image: Spectrograms of four tones – Figure 1A from Zarate JM, Ritson CR, Poeppel D (2013) The Effect of Instrumental Timbre on Interval Discrimination. PLoS ONE 8(9): e75410. doi:10.1371/journal.pone.0075410

Trapped in a Fig: The Perils and Payoffs of Pollination

Fresh figs

Pollinating insects are an industrious bunch, working tirelessly as they flit from blossom to blossom. But for insects like the short-lived, fig-pollinating wasp, the job of bringing fruit to fruition can be a dangerous business. According to a recent PLOS ONE study, some wasps can get trapped and die in the fig during pollination, when they enter to deposit their eggs. The researchers find that wasps of a certain size may take this risk into account when deciding which figs to approach.

Choosing which fig to pollinate is not like shopping at the supermarket, where items are placed in convenient, easy-to-reach places. Though the fig tree can produce fruit all year around?much like the availability of items in a supermarket?its flower is wrapped inside the fruit and only accessible via a small slit. Only pollinators of a certain size can enter these openings, and as the fruit ages, it may become increasingly difficult to get in and out.

In the study, the researchers sought to determine whether the fruit’s age had any correlation with successful entry, and whether the wasp’s size correlated with successful entry. To do this, they first selected fig trees whose fruit were just mature enough to attract pollinators. Then they selected and collected groups of fig-pollinating wasps and placed them in a sealed enclosure with the figs. After one day, they counted how many wasps were still alive and how many had died. They also checked to see how many wasps had successfully entered figs and how many had gotten stuck. Using the same selection process, the researchers ran an additional experiment using fig fruit of various ages.

Sid Mosdell

While not every wasp attempted to enter a fig during the experiment, those that did make the attempt met with various challenges based on their size and the age of the fruit. The researchers found that wasps attempting to enter older figs tended to take longer to reach the flower than wasps that tried  with younger figs. Their findings also indicated that the proportion of wasps that got trapped in the opening increased with fig age. In other words, the older the fruit was, the more likely a wasp would get stuck. The proportion of wasps that reached the flower decreased with fig age.

After measuring the size of the wasps’ heads, the researchers noted that wasps who couldn’t penetrate the fruit tended to have wider heads than other wasps. Wasps who made the attempt but got stuck and those that made it to the flower tended to have narrower heads than others.

The researchers hypothesize that the relationship between fig fruit age, wasp size, and successful entry indicates that a particular partnership has formed between this fruit and its pollinator. The small opening in the fruit may act as a sort of filter or barrier to encourage wasps to pollinate younger, more fertile fruit. Attempts to enter older fig fruit may reduce the number of wasp offspring and may even lead to death!

The next time you bite into a fig bar or wish for figgy pudding, take a moment to appreciate the intricate relationship between the wasp and this fruit. To learn more about this research, buzz over to the full study.


Citation: Liu C, Yang D-R, Compton SG, Peng Y-Q (2013) Larger Fig Wasps Are More Careful About Which Figs to Enter – With Good Reason. PLoS ONE 8(9): e74117. doi:10.1371/journal.pone.0074117

Image: Fresh figs by David Blaikie.

Image: Common Wasp by Sid Mosdell.

The RosettaCon 2012 Collection: Rosetta Developers Meet the Challenges in Macromodeling Head On

Rosetta2012 Collection ImageReproducibility continues to be one of the major challenges facing computational biologists today. Complicated experiments, massive data sets, scantily described protocols, and constantly evolving code can make experimental documentation and replication very difficult.  In addition, the need for specialized knowledge and access to large computational resources can create barriers when trying to design and model macromolecules.

Every year, the Rosetta developer community meets to discuss these challenges and advancements via Rosetta, a software suite that models and helps design macromolecules. In 2010, PLOS announced the RosettaCon2010 Collection, which made the latest research on protocols used to create macromolecular models available to all. Now, the PLOS ONE RosettaCon 2012 Collection continues to tackle issues related to use, reproducibility and documentation by highlighting new scientific developments within the Rosetta community.

The RosettaCon 2012 Collection comprises 14 articles detailing the scientific advancements made by developers that use Rosetta. In order to address reproducibility and documentation challenges, each article within this Collection includes an archive containing links to the exact version of the code used in the paper, all input data, links to external tools and example scripts.

This year’s Collection marks the tenth anniversary of RosettaCon and focuses on three long-term goals of the community: increase the usability of Rosetta, improve its current methods, and introduce completely new protocols.

Increasing the usability of Rosetta – Rosetta still requires specialized knowledge and large computational resources, but this collection features two articles describing advancements that make it easier for non-experts to use its applications. These articles introduce the Rosetta Online Server that Includes Everyone (ROSIE) workflow, which allows for rapid conversion of Rosetta applications into public web servers, and PyRosetta, a new graphical user interface (GUI) which allows users to run standard Rosetta design tasks.

Improving current prediction methods – Several articles describe improvements to Rosetta’s structure prediction capabilities and design methodologies. Some examples include improvements to loop conformational sampling, and a recently developed ray-casting (DARC) method for small molecule docking now enables virtual screening of large compound libraries.

Introducing new protocols – A number of articles featuring new procedures and applications that debuted at the conference are introduced in the Collection. Highlights include new methods for dealing with ligand docking, advancements to pre-refine scaffold proteins prior to computational design of functional sites, and new protocols to drive Rosetta de novo modeling.

The RosettaCon 2012 Collection continues to help serve the Rosetta community in an effort to ensure that newly developed protocols are as usable as more established workflows, are transparent, and are accurately documented even in an active development environment.

This post has been adapted from “The RosettaCon 2012 Special Collection: Code Writ on Water, Documentation Writ in Stone” which serves as a more in-depth overview of the new collection. To read all that this Collection has to offer, click here.

(Don’t) Watch that Mouth: Listen Up by Looking Away


A dish clatters to the floor, and you spin around to view the damage. A friend calls out from beyond your line of sight, and you turn toward the sound. We’re instinctively aware that looking at the source of a sound makes it easier to understand—except when your eyes trick your brain into hearing things.

In a phenomenon known as the McGurk illusion, the syllables you hear sound different if you simultaneously watch a person’s mouth moving in the shape of another syllable. Being aware of this audio-visual trick doesn’t stop your brain from falling for it over and over again, though watching subtitled movies can help a little.

Recently published PLOS ONE research shows that the illusion is caused by visual signals reaching the auditory cortex in the brain faster than the sounds processed by your ears. Researchers analyzed brain signals in the auditory cortex, the part of the brain that processes sound, when volunteers were given a combination of videos and sounds to watch and hear.

The sound clips were of the syllables “ba,” “ga,” “va,” and “tha,” but physical mouth movements in the concurrent video weren’t always the same. In some tests, movements in the video matched the spoken sound perfectly, but in others, the sounds were either completely mismatched, like watching a poorly dubbed movie, or just slightly mismatched. Listeners had no trouble identifying the sound they heard in the extreme case of an absolute mismatch, such as a video of “ba” paired with the sound of “tha”, and they did just as well when sound and video lined up perfectly.   However, when the mismatch was less obvious, such as “ba” with “va,” participants “heard” what they saw (va), and not what was played for them (ba).

When sounds and videos were perfectly matched or mismatched, participants’ brain activity corresponded to the auditory signals. But, when the mismatch wasn’t as obvious, activity in the auditory cortex increased in response to what participants saw, rather than what they heard. More simply, their brains ‘heard’ what they saw, not the sound that was played.

Understanding why the McGurk illusion occurs in the brain isn’t likely to change how we experience the effect (no really, try it for yourself), but the results take us a step closer to learning how we really hear voices in our heads.

Citation: Smith E, Duede S, Hanrahan S, Davis T, House P, et al. (2013) Seeing Is Believing: Neural Representations of Visual Stimuli in Human Auditory Cortex Correlate with Illusory Auditory Perceptions. PLoS ONE 8(9): e73148. doi:10.1371/journal.pone.0073148

Image: Dog looking at and listening to a phonograph, from Wikimedia Commons

A way with words: Data mining uncloaks authors’ stylistic flair


As any writer or wordsmith knows, searching for the right word can be a painful struggle. Here’s comforting news: word choice may be the key to understanding your stylistic flair.

New research in the field of text mining suggests that distinct writing styles are discernible by word selection and frequency. Even the use of common words, such as “you” and “say,” can help distinguish one writer from another. To learn more about style, the authors of a recent PLOS ONE paper turned to the famed lord of language, William Shakespeare.

The researchers assembled a pool of 168 plays written during the 16th and 17th centuries. After accounting for duplicates, 55,055 unique words were identified and then cross-referenced against the work of four writers from that time period: William Shakespeare, Ben Jonson, Thomas Middleton, and John Fletcher. The researchers counted how often these writers used words from the pool and ranked words by their frequency. Lists of twenty of the most-used and least-used words were then compiled for each writer and considered “markers” of their individual styles.

Fletcher, for one, frequently used the word “ye” in his plays, so a relatively high frequency of “ye” would be a strong marker of Fletcher’s particular writing style. Similarly, Middleton often used “that” in the demonstrative sense, and Jonson favored the word “or.” Shakespeare himself used “thou” the most frequently, and the word “all” the least.

In addition to looking at individual word use, the researchers analyzed specific works where the writer’s style changed significantly, such as in Middleton’s political satire “A Game at Chess,” which was notably different from his other works. They also compared word choice between writers. Their findings indicate that, unlike his contemporaries, Shakespeare’s style was marked more by his underuse of words rather than his overuse. Take, for example, Shakespeare’s use of “ye.” Unlike Fletcher, who used this word liberally, “ye” is one of Shakespeare’s least frequently used words.

Such analyses, the researchers suggest, may help with authorship controversies and disputes, but they can also address other concerns. In a post in The Conversation, the authors of this paper suggest that the mathematical method used to identify words as markers of style may also be helpful to identify biomarkers in medical research. In fact, the research team currently uses these methods to study cancer and the selection of therapeutic combinations, multiple sclerosis, and Alzheimer’s disease.


Citation: Marsden J, Budden D, Craig H, Moscato P (2013) Language Individuation and Marker Words: Shakespeare and His Maxwell’s Demon. PLoS ONE 8(6): e66813. doi:10.1371/journal.pone.0066813

Image: First Folio – Folger Shakespeare Library – DSC09660, Wikimedia Commons

Predicting Movie Box Office Success Using Wikipedia

Iron Man photo by HarshLight

It’s Friday evening and perhaps you’re planing to watch a movie, but will the new release you choose be a blockbuster or a lackluster flop? Well Wikipedia may help predict your choice’s success or failure in the box office, according to a recently published study.

In this study, researchers tracked activity on Wikipedia entries for 312 movies (released in 2010), including aspects like number of views, users, and edits; and compared this activity to the box office success of the movies in a computational model. They found a strong correlation between higher Wikipedia activity before a movie was released, and the box office success of the film.

The study could accurately predict the blockbuster success of movies like Iron Man 2, Shutter Island and Inception, but was unsuccessful with movies such as The Lottery and Animal Kingdom. The scientists attribute the lack of predictability to the amount of data provided for the different types of movies. According to the authors, their analysis can be used to provide reasonable predictions about a movie’s success as early as a month prior to its release.

The study is a foray into using “big data” generated from the social web to predict people’s reactions to a new product- in this case, a movie. Previous studies have used social data, such as tweets related to an event, to estimate public sentiment and reactions. Here, the authors use social data in advance of the ‘event’ to gauge public sentiment after the movie has launched. They conclude, “Our statistical approach, free of any language based or sentiment analysis, can be easily generalized to non-English speaking movie markets or even other kinds of products.”

CitationMestyán M, Yasseri T, Kertész J (2013) Early Prediction of Movie Box Office Success Based on Wikipedia Activity Big Data. PLoS ONE 8(8): e71226. doi:10.1371/journal.pone.0071226

Image Credit: Iron Man Tech by HarsLight

Lasting love? Research on Making and Breaking Romantic Relationships

4264611133_b9cfdd8566_zRomance 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


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


Crisis in the Late Bronze Age Triggered by Environmental Change


What does it take to topple a civilization, or a whole group of them? Over three thousand years ago, agriculture and trade-based societies flourished in the Eastern Mediterranean. Yet something fishy happened circa 1200 BC that brought these cultural and commercial centers to their knees—something that has left historians in the dark.

Correspondence from that time attributes the decline, at least partially, to invasions from a band of raiders, referred to as Sea Peoples. Other scholars studying this period point to natural disasters, such as earthquakes or drought. Research recently published in PLOS ONE reveals a more insidious culprit: Climate change may have fueled drought, the invasions, and eventually the collapse of these civilizations in what historians call the Late Bronze Age crisis.

To explore the environmental factors behind this crisis, the researchers took continuous core samples from modern-day Cyprus, at what is now called Larnaca Salt Lake, or Hala Sultan Tekke.


Core samples were analyzed for their pollen content and tested for the presence of dinoflagellates (pictured), a type of marine plankton. The researchers then studied the abundance and variety of plants represented by the ancient pollen and plotted fluctuations in the proportions of both between 1500 BC and 1500 AD. With similar data from nearby Syria, they reconstructed likely climate conditions in the region during the Late Bronze Age.

They found the abundance of marine plankton decreased around 1200 BC, suggesting the region was gradually becoming drier, as the lake lost its connection to the sea.  The pollen record reveals a shift towards plants that could handle drier weather, indicating a decrease in rainfall. Dwindling rain, the researchers suggest, may have made it difficult to maintain agricultural production and led to food shortages. These shortages might also have caused people to travel, migrate, or raid in search of more food.  This drought lasted three hundred years and coincides with the Sea People invasions.

It takes a lot to topple civilizations, and climate change has played its part in ending those in the Eastern Mediterranean during the Late Bronze Age. This evidence adds to the growing body of literature documenting the effects of climate change. This latest research adds a compelling chapter to the story of climate change, from which everyone can learn.


Citation: Kaniewski D, Van Campo E, Guiot J, Le Burel S, Otto T, et al. (2013) Environmental Roots of the Late Bronze Age Crisis. PLoS ONE 8(8): e71004. doi:10.1371/journal.pone.0071004


Keuninck (Coninck) Kerstiaen de – Fire of Troy, from Wikimedia

DINOFLAGELLATE, by fickleandfreckled

Young Cape Fur Seals Handle Heat with Built-in Air Conditioning

Dry Natal Cape Fur SealOne of the easiest ways to find relief from scorching summer heat is a quick dip in the water. Whether tiger, hippo, or seal, many animals also turn to the water to find relief. However, unlike their adult counterparts, newborn Cape fur seals can’t swim, and intense sun exposure poses a threat of overheating. Luckily, according to a recent PLOS ONE study, these seal pups may have built-in air conditioners, in the form of a furry natal coat, to keep them cool until they learn to stay afloat.

Cape fur seals live in the sunny climes of southern Africa, ranging from the north coast of Namibia, south to the Cape of Good Hope and northeast to Alogoa Bay. Temperatures in these regions can soar above 80° F, and adult seals rely on frequent swims to escape the Wet Cape Seal Pup Fursun. An adult spends half its life in the water, but pups are unable to swim until they’re at least 6 weeks old. At this age, coarse water repellent (read: swim-friendly) coats finally grow in to replace their “baby” fur.

Besides making fur seals extra cute and cuddly looking, fur coats may insulate seals from the harsh sun exposure that they are unable to escape from on land. To gain a better understanding of these unique insulating properties, researchers measured temperature daily in several spots on the baby seals, under varying environmental conditions: on the fur surface, within the fur, on the skin and in the rectum. They found that on the warmest days, at an ambient air temperature around 80° F, the pups’ fur measured a whopping 175° F on the surface; Temperature of Natal Cape Fur Sealthankfully, this temperature dropped as they measured fur closer to the skin. Within fur, the temperature was a slightly cooler 146° F, and the skin temperature was a more-normal 99.86° F. Internal body temperature remained relatively constant at 98.4° F, indicating that the temperature drastically changed within the fur layer to keep bodies cool. If  the seal pups got wet, however, the fur temperature reached 100° F and skin 84° F, showing a reduced ability of fur to insulate when wet. These results support the idea that the furry coat may be an adaptation that provides insulation against overheating during their first six weeks on land.

If you’re interested in reading more about how other animals keep cool, check out this post about African and Asian elephants.

Erdsack N, Dehnhardt G, Hanke W (2013) Coping with Heat: Function of The Natal Coat of Cape Fur Seal (Arctocephalus Pusillus Pusillus) Pups in Maintaining Core Body Temperature. PLoS ONE 8(8): e72081. doi:10.1371/journal.pone.0072081

Images: 10.1371/journal.pone.0072081

Coffee Plants Don’t Like It Hot

Guest blogger Atreyee Bhattacharya is a science correspondent and climate scientist, currently a research affiliate at the Department of Earth and Planetary Sciences, Harvard University. 

espressoLike most, I like my coffee black and piping hot. Coffee plants, however, may not be as fond of the heat.

When thinking about the impact of changing climate (increased droughts, wilder fluctuations in seasons) and increasing pest activity on food production—my thoughts tend toward crops such as rice, wheat, and corn. Not so much wine, chocolate, or coffee, though I probably consume more coffee throughout the day than I do these other staples.

However, two recent papers published in PLOS ONE deliver a double whammy to coffee, or more particularly the Coffea arabica plant, a species that today accounts for more than 70 percent of the world’s coffee. (Another, less common, variety is C. robusta, which has twice the caffeine content.)

In a 2011 study, Juiliana Jaramilo from the University of Hannover and her coauthors, Figure 2showed that warming air and land temperatures can change the distribution of the coffee berry borer Hypothenemus hampei in East African C. arabica producing regions.

The borer, a pest that attacks coffee beans, “causes losses exceeding US $500 million annually, and worldwide affects many of the more than 25 million rural households involved in coffee production” the study reports. A serious infestation can lower coffee production by more than three times!

Until about ten years ago, reports of H. hampei attacks on coffee plants growing above 1500 m (the preferred altitude of cultivated and naturally occurring C. arabica) were few and far between. But thanks to the 0.2-0.5 degrees Celsius temperature increase in coffee growing regions of East Africa, the pests are now found at higher altitude plantations as well.

As temperatures continue to rise as per projections from the  Intergovernmental Panel on Climate Change (IPCC), coffee borer infestations in this region are likely to spread  farther. Increasing temperatures will increase the number of H.hampei generations each year from 1-4.5 to 5-10 or more.

“These outcomes will have serious implications for C. arabica production and livelihoods in East Africa,” caution the authors, adding, “We suggest that the best way to adapt to a rise of temperatures in coffee plantations could be via the introduction of shade trees in sun grown plantations.”

Figure 3Though C. arabica plants do like to grow in the shade; another study indicates that this protection may still not be enough to combat the threat of warming temperatures. According to this research by Aaron Davis from the Royal Botanic Gardens in the United Kingdom, warming temperatures may make several localities within southwest Ethiopia and neighboring regions climatologically ill-suited to growing C. arabica.

“Based on known occurrences and ecological tolerances of Arabica, bioclimatic unsuitability would place populations in peril, leading to severe stress and a high risk of extinction,” write the researchers.

According to their estimates, the most favorable outcome of warming is a 65% decrease in areas with climate suitable for coffee plantations, and at worst, an almost 100% loss of these regions by 2080. In terms of available area for growing coffee, the most favorable outcome  is a 38% reduction in suitable space, and at worst a 90% reduction. Neighboring areas could fare even worse by as early as 2020.

Coffee is a 90-billion-dollar industry , but it is an industry that depends on long-term planning. The beans that we grind every morning today were planted about 7-10 years ago, and our morning brew a decade hence depends on today’s plantations.

Demand for coffee continues to rise in our ‘coffee culture’, and C. arabica still constitutes about 75-80% of the world’s coffee production. C. arabica is believed to be the first species of coffee to be cultivated, well over a thousand years ago. It epitomizes an incredible journey, and is one beverage that is certainly worth a second thought as rising temperatures threaten its existence.

Read these studies and more on the ecological impacts of climate change in the new PLOS Collection:

Citations:Jaramillo J, Muchugu E, Vega FE, Davis A, Borgemeister C, et al. (2011) Some Like It Hot: The Influence and Implications of Climate Change on Coffee Berry Borer (Hypothenemus hampei) and Coffee Production in East Africa. PLoS ONE 6(9): e24528. doi:10.1371/journal.pone.0024528

Davis AP, Gole TW, Baena S, Moat J (2012) The Impact of Climate Change on Indigenous Arabica Coffee (Coffea arabica): Predicting Future Trends and Identifying Priorities. PLoS ONE 7(11): e47981. doi:10.1371/journal.pone.0047981


Espresso by Richard Masoner on Flickr 

Distribution of the coffee berry borer (Hypothenemus hampei) in Eastern Africa under current climate. The EI values (0–100), indicates unsuitability of the location’s climate (0), and a ‘perfect’ climate for the given species (100). doi:10.1371/journal.pone.0024528.g001

Predicted and actual distribution of indigenous Arabica. Green dots show recorded data-points. Colored areas (yellow to red) show predicted distribution based on modeling. A context map is given in the top left hand corner. doi:10.1371/journal.pone.0047981.g001

Announcing the Ecological Impacts of Climate Change Collection

Ecoclimate change collection

Post authored by Collection Curator Ben Bond-Lamberty 

The ecological impacts of climate change are broad and diverse, and include alterations to species’ range limits, plant phenology and growth, carbon and nutrient cycling, as well as biodiversity and extinction risk. Recent PLOS articles have used a variety of experimental and observational approaches to examine these subjects.

Identifying at-risk regions, taxa, and species is a critical first step in adaptation and conservation efforts. A study by Mouillot et al. suggested that rare species are particularly important in conservation efforts, as rare species in diverse ecosystems are not replaceable by other species that fulfill the same ecological functions. At the same time, both rare and more common species experience the ecological impacts of climate change. Foden et al. combined biology and ecology to assess, on a global scale, the climate change vulnerability of birds, amphibians, and corals based on expert assessment and literature surveys. In a more regionally focused study, Gardali et al. assessed climate-change risk for California’s vulnerable bird species.

Birds were also the focus of two studies documenting how particular species can be ‘winners’ or ‘losers’ in a changing climate. Receding glaciers and thus increased breeding habitat have led to population increases for Adélie penguins in the southern Ross Sea. The outlook was more mixed for Pacific western grebes , which have shifted south, perhaps in response to changes in their forage fish prey. Further down the food chain, Suikkanen et al.  used thirty years of marine data to infer that climate change and eutrophication drove a trophic shift in Baltic Sea food webs.

Long-term data were also used to study how flowering dates have changed since the mid-19th century. In a study that received extensive media coverage, Ellwood et al. used flowering records initiated as early as 1852 to show that high spring temperatures in 2010 and 2012 resulted in the earliest flowering in recorded history in the eastern United States. The biological pathways through which temperature affects seasonal timing in endotherms were discussed by Caro et al. Two other widely-covered studies focused on coffee: predicting future trends and identifying priorities, and climate change impacts on this plant and one of its important pests. Both examine adaptation possibilities for managing coffee crops over the coming century.

Adaptation and vulnerability were central themes for Guest et al., who reported that corals under thermal stress showed lower bleaching susceptibility at locations that bleached a decade earlier, implying an adaptive or acclimatization response. The molecular mechanisms behind such thermal tolerance were explored by Bellantuono et al.

Finally, the ecological impacts of climate change affect our health, the urban environment, and the agricultural economy. Airborne pollen counts have been increasing across Europe, and Ziello et al. suggest that rising CO2 levels may be influencing this increase. In another study, Meineke et al. used an elegant combination of observation and manipulative experiments to show that urban warming was a key driver of insect pest outbreaks in the southeastern U.S. Rising temperatures are a significant driver for the expanding range of Asian tiger mosquitoes, known vectors for West Nile and other viral infections. Warming was also found to contribute to the decreasing quality of grassland for grazers such as bison and cattle, although the effects are often exerted via complex interactions with other factors.

The broad range of these papers emphasize not only the multi-faceted impacts of climate change on ecological and human systems, but also the breadth and depth of research on these subject being reported in the PLOS journals. These journals seem a particularly appropriate venue for the ‘citizen science’ and other long-term data used by many of these studies.

Collection Citation: Ecological Impacts of Climate Change Collection (2013)

Image Credit: (Clockwise from top) William Warby. Thomas Vignaud. PLOS Biology. 2011. 9(4). Colombi et al. PLOS ONE. 2013. Soto-Azat et al. PLOS ONE. 2013.

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Putting the brakes on blood clots

blood clots Helena de PuigWhether you get a paper cut or have a bad accident, our bodies respond  with a near-universal command: when bleeding, clot. Within seconds of skin being broken, a cascade of cells and proteins align at precise positions to hold the breach. They form a fine mesh to stop blood flow, identify offensive invaders (splinter or microbe?) and recruit cells to clean up the mess. The operation is swift, precise, and for minor injuries, leaves no trace.

For major wounds and during surgeries though, doctors must use anti-coagulant drugs to stop the clotting process and ensure a free flow of blood. However, once an anti-coagulant is used, the only way to reinitiate the process of clotting is to wait for the drug to run out.

Now, a laser-controlled gold switch could change that wait, as researchers have developed a way to switch blood clotting on and off with the flick of a nanoparticle switch. The switch relies on the ability of paired particles to release two different DNA molecules from their surface depending on the wavelength of laser light used to turn the switch on. When released, one piece of DNA binds to thrombin, a key protein in the clotting cascade, and blocks its activity, preventing coagulation. When the complementary DNA piece is released from the nanoparticle, it acts as an antidote, releasing thrombin to restore clotting.

Prior to this advance, there was no way to restore clotting after an anticoagulant was administered. As Kimberly Hamad-Schifferli, senior author on the study, explained in an MIT news release, “It’s like you have a light bulb, and you can turn it on with the switch just fine, but you can’t turn it off. You have to wait for it to burn out.”

The new method developed in this study could provide doctors and researchers with a more precise way to control where and when blood coagulates during surgery and healing. In the MIT news release, Luke Lee, a professor of bioengineering at the University of California at Berkeley (not an author on the study), elaborates, “It’s really a fascinating idea that you can control blood clotting not just one way but by having two different optical antennae to create two-way control. It’s an innovative and creative way to interface with biological systems.”

Citation: de Puig H, Cifuentes Rius A, Flemister D, Baxamusa SH, Hamad-Schifferli K (2013) Selective Light-Triggered Release of DNA from Gold Nanorods Switches Blood Clotting On and Off. PLoS ONE 8(7): e68511. doi:10.1371/journal.pone.0068511

Image: Red blood cells with gold nanorods (yellow dots) on their surfaces. The blue represents a fixing polymer. credit: Helena de Puig

Summertime Fun in the Sun

99-Bar Harbor

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.


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

Image:  99-Bar Harbor by Robert & Pam.

Resisting Antibiotics: Some Bacteria Get By With a Little Help From Their Friends


Antibiotic resistance is often in the news, as it threatens the effectiveness of one of the foundations of modern medicine. Usually, the concern is about resistance that is inherent to the bacteria, or else develops in bacteria through genetic changes. A paper published today in PLOS ONE suggests another possibility.

In “Chemical communication of antibiotic resistance by a highly resistant subpopulation of bacterial cells,” authors Omar El-Halfawy and Miguel Valvano reveal that some species of bacteria may help others in surviving an antibiotic attack. In addition, they were able to provide insight into the mechanics of how the bacteria perform this action.

The study began with an observation of the bacterial species Burkholderia cenopecia, which typically grows in the soil but can infect people who have cystic fibrosis and those with compromised immune systems. The authors noted that a subpopulation of the species was more resistant to the antibiotic polymyxin B than other bacteria of the species. In other words, these resistant bacteria were more likely to survive after treatment with polymyxin B, and levels of antibiotics that killed the less resistant bacteria did not harm this (more resistant) subpopulation.

When the authors grew the more-resistant B. cenopecia with another strain of bacteria called Pseudomonas aeruginosa (a disease-causing bacterium that can co-exist with B. cenopecia), the P. aeruginosa were much more resistant to the antibiotic than when they grew in isolation.

Why might the P. aeruginosa be more resistant when they were in the presence of B. cenopecia?

The authors suspected that the B. cenopecia were releasing something into their environment that interfered with the action of the antibiotic, making it less potent. Experiments revealed that the bacteria were indeed secreting two proteins associated with increased antibiotic resistance: putrescine (named for its putrid odor!) and Ycel, a protein whose function was previously unknown.

cartoon 3

The large amounts of secreted putrescine blocked the antibiotics’ binding to the surface of the bacteria, and could make both B. cenopecia and P.aeruginosa more resistant to polymyxin B when grown together.

Ycel, on the other hand, was able to bind to the antibiotic directly, presumably decreasing its potency. Ycel is predicted to bind amphiphilic molecules (such as detergents, which  are attracted to both water and oil). Consistent with this prediction, the authors showed that Ycel had a protective effect against amphiphilic antibiotics and less of an effect against others.

These results have implications for combating the growing problem of antibiotic resistance. If we could prevent bacteria from making putrescine or Ycel, antibiotic treatments might be more effective, helping us eventually outflank resistance.

Citations: El-Halfawy OM, Valvano MA (2013) Chemical Communication of Antibiotic Resistance by a Highly Resistant Subpopulation of Bacterial Cells. PLoSONE 8(7): e68874. doi:10.1371/journal.pone.0068874

Bragonzi A, Farulla I, Paroni M, Twomey KB, Pirone L, et al. (2012) Modelling Co-Infection of the Cystic Fibrosis Lung by Pseudomonas aeruginosa and Burkholderia cenocepacia Reveals Influences on Biofilm Formation and Host Response. PLoS ONE 7(12): e52330. doi:10.1371/journal.pone.0052330

Images: Pseudomonas aeruginosa doi:10.1371/journal.pone.0066257