Author Archives: Jyoti Madhusoodanan

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

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HMV

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

Plant Roots May Lie Beneath Namibian Fairy Circles

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fairy3Circles of barren land, ranging from one to several feet in diameter, appear and disappear spontaneously in Namibian grasslands. The origins of these ‘fairy circles’ remain obscure, and have been attributed to causes ranging from the fantastic (the poisonous breath of a subterranean dragon) to those backed by more evidence, such as the work of a soil termite. A recent PLOS ONE paper suggests another possibility: Patterns that emerge during normal plant growth. Author Michael Cramer elaborates on the results of this study:

How did you become interested in studying the Namibian fairy circles, and are similar circles seen elsewhere?

It would be hard not to be intrigued by these mysterious barren circles on the edge of the spectacular Namibian sand sea! These circles are also reminiscent of soil mounds in other places, for example mima mounds in the US, “heuweltjies” in South Africa and “campos de murundus” in South America that have primarily been ascribed to faunal activity. Like fairy circles, these mounds may, however, represent a distinct product of patterns formed by vegetation. My co-author, Nichole Barger, became intrigued by both these phenomena while I was on sabbatical in her lab.

Many other scientific ideas have been proposed to explain the occurrence of these circles. What’s missing from these explanations? 

Any explanation of fairy circles has to provide a plausible mechanism for regular spacing of these relatively large circles in the landscape. The most common explanation to date has been that termites cause the circles. While it is undoubtedly true that ants, termites and other fauna do occur in the circles and may play a role in maintenance of the circles, we suggest that inter-plant competition is the primary cause that drives circle formation. This places plant competition in focus as a possible mechanism for determining the shape, size and distribution of the circles.

What made you think the patterns could be formed by plant growth patterns themselves?

We stood on the shoulders of giants! Previous studies have alluded to vegetation patterning as a possible cause.  Other researchers have also produced computer models to predict fairy circle occurrence and found plant growth may play a role.  More generally, understanding of spatial patterns formed by plants and the realization that this emergent phenomenon is common in arid landscapes has increased recently. Several groups have produced mathematical models that explain the production of vegetation patterns (gaps, bands and spots) and show that increasing aridity can result in transition from one pattern to another.

fairy2How did you analyze the fairy circles?

We adopted two approaches. We used Google Earth to obtain images of sites across Namibia, analyzed these to determine circle morphological characteristics, and  then combined the images with environmental data to predict the distribution of fairy circles. We performed ground surveys to measure circle morphology and collect soil samples. Soils were sampled at various depths and regular intervals inside and outside the circles and analyzed for water and nutrient contents.

What did you find?

We found that we could predict, with 95% accuracy, the distribution of fairy circles based on just three variables. Rainfall strongly determined their distribution, and differences in rainfall from year to year may thus explain why circles dynamically appear and disappear in this landscape.  The patterns of moisture depletion across the circles are also consistent with plant roots foraging for water in the circle-soil. The size and density of the circles is inversely related to resource availability, indicating that bigger circles occur in drier areas and where soil nitrogen is lower.

Do the data in this study strengthen previous results or disprove any older explanations for the circles?

Our results corroborate previous results and extend them, but we have interpreted the results in a novel manner. Since our study was correlative, i.e: we correlated the occurrence of fairy circles with certain environmental conditions, it does not disprove existing hypotheses. Direct experiments that result in fairy circles being created or closing up are perhaps the only way  to prove or disprove any of these ideas.

fairy1Do these results have implications for other ecosystems? For example, could similar ecological conditions cause fairy circles to form in other grasslands around the world?

Circular grass rings do occur in many contexts. For example, Stipagrostis ciliata in the Negev and Muhlenbergia torreyi (ring muhly) in the US (e.g. New Mexico, Utah) form rings. The distinction is that these are much smaller (ca. < 1 – 2 m diameter) and less regularly spaced than fairy circles. Nevertheless, their origins may have some commonalities with fairy circles. The special circumstance that results in the spectacular Namibian fairy circles may be the fact that the soils are very sandy and homogenous.

More generally, the fairy circles represent an example of how patterns formed by growing plants can create heterogenous spaces in otherwise homogenous grassland. Differences in soil moisture or composition across the span of a fairy circle can provide habitat for both grasses and fauna that would otherwise not thrive in this arid environment.

 

Citation: Cramer MD, Barger NN (2013) Are Namibian “Fairy Circles” the Consequence of Self-Organizing Spatial Vegetation Patterning? PLoS ONE 8(8): e70876. doi:10.1371/journal.pone.0070876

Images: fairy circles by Vernon Swanepoel (top); images below from 10.1371/journal.pone.0070876

 

Coffee Plants Don’t Like It Hot

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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: http://www.ploscollections.org/ecoclimatechange

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

Images: 

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

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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) http://www.ploscollections.org/ecoclimatechange

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

This Collection is also available on Flipboard, please search “PLOS Collections” to subscribe.

 

Putting the brakes on blood clots

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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

Contextualizing the Hobbits

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LB1

18,000 years ago, the remote Indonesian island of Flores was home to a population of tiny humans. They stood only about 3.5 feet tall on their large feet, and their skulls housed unusually small brains approximately the size of a grapefruit. The identity of these ‘hobbits’ has been hotly debated for years: Were they modern humans suffering a disease, or a new species, Homo floresiensis?

Biological anthropologist Karen Baab first studied a model of LB1, the only skull recovered from the site, at the American Museum of Natural History in 2005. In a recently published PLOS ONE study, she and other researchers compare this specimen to a range of other modern human and extinct hominin skulls to get closer to settling the identity of Homo floresiensis, or ‘Flores man’.

The origins of ‘Flores man’ have been debated for quite a while now. What are the possible origins that are being discussed, and why the uncertainty?

The primary debate has centered on whether LB1 (and possibly the other individuals found on Flores) represents a new species that descended from an extinct species of the genus Homo or whether it is instead a pathological modern Homo sapiens, i.e the same species as us. If the Flores remains do in fact represent a distinct species, then the next question is whether they descended from Homo erectus, a species that may be our direct ancestor, or an even more primitive species. The latter scenario implies an otherwise undocumented migration out of Africa.

What makes it so hard to settle the argument one way or the other?

One of the difficulties in settling this particular argument is that most studies have focused on one or the other of these ideas and compared the Flores remains to either fossil hominins or to pathological modern humans, each using a different set of features. This makes it challenging to compare the alternative hypotheses side-by-side.

What kind of diseases might have caused modern humans to have features similar to these ‘hobbits’?

The three that have been discussed most prominently (and the three we looked at) are microcephaly, endemic hypothyroidism (“cretinism”) and Laron Syndrome. Microcephaly is not a disease per se, but rather a symptom of many different disorders. It refers to having an abnormally small brain and therefore skull. “Cretins” suffer from a lack of thyroid hormone before and after birth, which leads to stunted growth and possibly a slight decrease in skull size. Laron Syndrome individuals produce growth hormone, but their bodies do not properly recognize it, again leading to stunted growth and other developmental issues.

Only a few specimens of this hominin have been found, and there’s only one known skull, from the specimen named LB1. Are there reasons why these specimens have not been discovered elsewhere?

If Homo floresiensis descended from Homo erectus, then their closest relative lived just “next door” on the nearby island of Java. In this case, the unique features of the Homo floresiensis species probably evolved in the isolated island environment of Flores. If, however, the ancestor was a more primitive species, and Homo floresiensis didn’t branch off from H.erectus, it is possible that they might have migrated earlier than known, and we could still find older sites in mainland Asia containing this ancestral species.

Liang Bua cafe

You compared the morphology of the LB1 skull to many hominin ancestors and modern human populations from around the world. What were some of the most striking similarities and differences?

The LB1 skull is very distinct from the typical modern human’s, as it has a lower,  more elongated silhouette when viewed from the side, , greater width at the rear of the braincase, and a flatter frontal bone (the bone underlying the forehead) with a more pronounced brow ridge. Interestingly, these are some of the same features that distinguish archaic species like Homo erectus from modern humans.

Specimens of Laron Syndrome and “cretin” skulls from modern Homo sapiens presented large, round, globular braincases, which are very different from the smaller, lower and less rounded braincase of LB1. The microcephalic human skulls present a closer comparison to LB1, but still show clear distinctions from LB1 in much the same way that they differ from species like Homo erectus or Homo habilis.

Overall, the LB1 braincase is most similar in its overall shape to small-brained Homo erectus from Eurasia that are 1.8 million years old.

How does this analysis add to, or change, what we knew about Flores man? 

This analysis provides a unique opportunity to evaluate these evolutionary and pathological hypotheses side-by-side based on the same criterion – of cranial shape similarity. The results support a stronger affiliation of LB1 with fossil Homo than with any of the proposed pathologies. This study also offers an improvement over previous assessments of the microcephaly hypothesis by using a more extensive sample that better captures the variability in this disorder.

Do these results conclusively settle the discussion? What other possibilities still exist for the origins of H. floresiensis?

While very little in paleoanthropology is ever “settled,” I do think this study represents an important step forward in terms of putting the pathological hypotheses to rest. The question that remains to be answered definitively is which species of archaic Homo is the most likely ancestor of Homo floresiensis – Homo erectus or an earlier and more primitive species of Homo?

Citation: Baab KL, McNulty KP, Harvati K (2013) Homo floresiensis Contextualized: A Geometric Morphometric Comparative Analysis of Fossil and Pathological Human Samples. PLoS ONE 8(7): e69119. doi:10.1371/journal.pone.0069119

Images: Homo floresiensis by Ryan Somma, Cave where the remains of Homo Floresiensis where discovered in 2003, Liang Bua, Flores, Indonesia by Rosino

 

Malaria, tuberculosis caused death on the ancient Nile

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Nile

Southwest of Cairo, the Nile branches into a network of canals that feed Fayum, a fertile agricultural basin that was a center of civilization and royal pyramid-building for several centuries. The unusual geology responsible for Fayum’s rich terrain may have also led to the prevalence of malaria and tuberculosis in the region during these ancient times.

Ancient DNA (aDNA) from sixteen mummified heads recovered from the region reveals that at least four of these individuals suffered both these infections simultaneously. Many of the others showed signs of infection with either malaria or tuberculosis, as scientists report in a recent PLOS ONE study.

DNA extracted from muscle tissue samples was tested for the presence of two genes specific to Plasmodium falciparum, the malarial parasite, and another gene specific to Mycobacteria, which cause tuberculosis. Two samples tested positive for DNA specific to Plasmodium, one tested positive for the mycobacterial gene, and four individuals tested positive for DNA from both infectious agents, suggesting they suffered both infections together while alive. A previous study suggests that both malaria and tuberculosis were rampant in the Fayum region in the early 19th century, but the age of these mummified samples extends evidence of these diseases in Lower Egypt as far back as approximately 800 B.C.

The World Health Organization estimates that malaria is almost non-existent in the Fayum basin and the rest of Egypt now, but before its eradication, high levels of infection were seen in certain parts of the country, and were strongly linked to certain geological features. The lakes and canals that made the Fayum region so fertile also served as breeding grounds for the mosquito that carries the malarial parasite.

The heads tested here (all were missing bodies) were recovered from a village cemetery on the west bank of the lower Nile, and date from about 1064 BC to 300 AD, a period marked by an agricultural boom and dense crowding in the region, especially under the rule of the Ptolemies. These conditions may have increased the chances of tuberculosis incidence and spread of the disease. As the aDNA from these mummified heads attests, these living conditions and the unique irrigation of the Fayum basin likely created a harbor for both malaria and tuberculosis in ancient populations of this region.

Citation: Lalremruata A, Ball M, Bianucci R, Welte B, Nerlich AG, et al. (2013) Molecular Identification of Falciparum Malaria and Human Tuberculosis Co-Infections in Mummies from the Fayum Depression (Lower Egypt). PLoS ONE 8(4): e60307. doi:10.1371/journal.pone.0060307

Image: Sailing on the Nile by David Corcoran

Moms and babies respond to childbirth with different stress hormones

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stress

A quick internet search reveals that many women rank giving birth as one of the most painful human experiences. Though pain can be hard to quantify objectively, the physiological stress of childbirth is clinically assessed by measuring blood levels of the stress hormone cortisol.

Cortisol is currently used to estimate the stress experienced by both mother and child during the process of giving birth, but recently published PLOS ONE research suggests that a different stress hormone, corticosterone, may be a more accurate way to measure the stress experienced by healthy, full-term babies.

For their study, researchers tested fetal levels of cortisol and corticosterone in 265 samples of umbilical cord blood from healthy deliveries. Though the total levels of cortisol detected were higher than corticosterone levels, fetuses produced the latter at a greater rate in response to the stress of labor and delivery. Newborns secreted more corticosterone when a Caesarian section was performed due to complications during labor than they did after a normal C-section. Fetal corticosterone levels were also higher after passage through the birth canal. These differences were not seen in levels of cortisol production. Based on these data, the authors suggest that the full-term fetus is more likely to secrete corticosterone than cortisol in response to stress and hence, corticosterone may be a more accurate clinical biomarker to assess fetal stress.

Corticosterone isn’t unheard of in the adult world, as adults continue to make the hormone throughout our lives, though in a much smaller proportion relative to cortisol. When babies switch to producing more cortisol rather than corticosterone isn’t yet clear, but the developmental changes involved may help track or diagnose adrenal gland functions in newborns.

Citation: Wynne-Edwards KE, Edwards HE, Hancock TM (2013) The Human Fetus Preferentially Secretes Corticosterone, Rather than Cortisol, in Response to Intra-Partum Stressors. PLoS ONE 8(6): e63684. doi:10.1371/journal.pone.0063684

Image: stress by topgold

Hairy, Sticky Leg Pads are In: How Different Spiders Hunt

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Euophrys_L2_cryo__q17_bearb_color_composite

Spiders are everywhere (Arachnophobes, stop reading now). They’re among the most successful predators on earth today and colonize nearly every terrestrial habitat (that is, not just ceiling corners and under beds), and occasionally do so in numbers large enough to take over small islands. Spider silk may be strong enough to stop a speeding train and some webs, ten times stronger than Kevlar, can be large enough to cross rivers in tropical rainforests.

But more than half of today’s spider species don’t rely on webs or silk to capture their prey. Instead, these hunting spiders have evolved hairy adhesive pads on their legs to grab and hold struggling prey down, according to the results of a recently published PLOS ONE study. The adhesive pads, called scopulae, were commonly seen in many spider species but what wasn’t clear until now was whether they were found in all species, or more likely to occur in hunting spiders.

scopulaeIn this study, researchers used a phylogenetic analysis of spider family trees to correlate different species’ prey capture strategies with the presence or absence of adhesive pads on their legs. They found that the majority of spiders were either web builders or free-ranging hunters, and the latter were most often found to have adhesive hairs on their legs (Apart from these two, at least one rare variety may be mostly vegetarian). Nearly 83% of hunting spiders had adhesive bristles on their legs (compared with 1.1% of web-building varieties). Most of these hunters had either not developed silk-dependent strategies to capture prey, or abandoned web-building for hunting.

Spider Web on PlantWhy would so many spiders abandon an obviously successful way to catch prey? Web-building is a useful way to trap insects and some small mammals, but even to a spider, silk is expensive. Creating a web requires work, damages caused by prey or people need frequent repairs, and certain kinds of webs can require large amounts of silk to be effective. The classic orb-web (seen in the picture here) radically reduced these costs, which may be why the spiders that make these are particularly common. However, this new study reveals that hunting has proved at least as successful a strategy as web-building to more than half of today’s spiders.

Bristly scopulae on hunting spiders’ legs have played a big part in this, enabling spiders to grasp and hold on to struggling prey. The thin bristles on scopulae come in many shapes and forms, and also contribute to these spiders’ mad climbing skills. Read more about which spiders evolved these bristles or learn about other arachnid research published in PLOS ONE here.

 

Citations: Gregori? M, Agnarsson I, Blackledge TA, Kuntner M (2011) How Did the Spider Cross the River? Behavioral Adaptations for River-Bridging Webs in Caerostris darwini (Araneae: Araneidae). PLoS ONE 6(10): e26847. doi:10.1371/journal.pone.0026847

Rogers H, Hille Ris Lambers J, Miller R, Tewksbury JJ (2012) ‘Natural experiment’ Demonstrates Top-Down Control of Spiders by Birds on a Landscape Level. PLoS ONE 7(9): e43446. doi:10.1371/journal.pone.0043446

Wolff JO, Nentwig W, Gorb SN (2013) The Great Silk Alternative: Multiple Co-Evolution of Web Loss and Sticky Hairs in Spiders. PLoS ONE 8(5): e62682. doi:10.1371/journal.pone.0062682

Nyffeler M, Knörnschild M (2013) Bat Predation by Spiders. PLoS ONE 8(3): e58120. doi:10.1371/journal.pone.0058120

Images: Foot of the little jumping spider Euophrys frontalis, credit Jonas Wolff; varied shapes and sizes of bristles on scopulae from pone.0062682; spider web on plant by mikebaird

Opportunistic pathogens evolve mostly harmlessly in healthy humans

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Staphylococcus_aureus_VISA_2

Humans interact with bacteria almost every minute of our lives. Of the millions of these interactions, only a handful result in disease, and some bacteria only cause infections under certain conditions. In a recent PLOS ONE study, researchers probe these healthy human-bacterial relations  in one particularly notorious pathogen as it spends the majority of its time in our bodies, doing no harm.

Staphylococcus aureus can cause endocarditis, toxic shock syndrome and other diseases, killing approximately 1 in 100,000 infected people in the US each year. Strains like MRSA have also evolved to carry multiple antibiotic resistance genes, making infections extremely difficult to treat. If human-bacterial interactions are to be described as a ‘genetic arms race’, it may be tempting to cast S. aureus as an enemy that carries every available genetic weapon.

Yet despite a few sporadic skirmishes, the majority of our interactions remain peaceful, as these bacteria thrive in healthy human hosts.  In fact, about a third of healthy adults carry S. aureus in our noses at some point in our lives.  In the article, researchers analyzed the genetic changes in S. aureus carried in such hosts by sequencing the genomes of 130 strains of S. aureus from the nasal passages of 13 healthy adults, five of whom carried strains of MRSA (which is often harmless when carried nasally). Despite the arms race metaphors, they found that S. aureus strains in healthy hosts are not incessantly beefing up their genetic arsenal of antibiotic resistance or pathogenesis genes.

They found bacterial genomes were changed by processes of ‘micro-mutation’, i.e.: small bits of genetic material being added or removed, or changes in a single letter in the genetic code. Large insertions and deletions (macro-mutation) were also common, as were changes caused by bacteria-infecting viruses or small, independently moving rings of DNA called plasmids. Overall, the constant changes in S. aureus genomes were geared toward keeping bacterial genomes healthy by clearing erroneous or harmful mutations. Only on rare occasions did these bacteria acquire distinctive surface proteins or an enterotoxin that could alter their pathogenic potential. In addition, their research also analyzed changes in specific genes used to assess bacterial diversity and relatedness, and developed a new method to detect transmission of bacterial strains among human carriers. Read the full study to learn more about these interesting results.

Many of the changes identified in this study may not directly increase the virulence of disease-causing S. aureus. However, previous work by these researchers demonstrated that mutations arising in bacteria carried by healthy hosts may play an important role in tipping the balance between human health and disease. Here, the authors begin to paint a picture of what these mutations are and how they may occur.

Citation: Golubchik T, Batty EM, Miller RR, Farr H, Young BC, et al. (2013) Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage. PLoS ONE 8(5): e61319. doi:10.1371/journal.pone.0061319

Image: Scanning electron micrograph of S.aureus with increased resistance to vancomycin. Credit CDC/ Matthew J. Arduino, DRPH

 

Balancing nutrient diets determines how ecosystems age

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FranzGround young

From rainforests to rocky glaciers, the life of an ecosystem is rooted in the balance of nutrients in its soil. Shifting levels of soil nitrogen (N) and phosphorus (P) define how ecosystems evolve, and understanding the dynamics of these key nutrients can help ecologists identify crucial factors to help mitigate climate change.

A new model to understand N and P dynamics over different time scales was described in the PLOS ONE paper, “Nitrogen and Phosphorus Limitation over Long-term Ecosystem Development in Terrestrial Ecosystems”. Recently awarded the Ecological Society of America’s prize for an outstanding theoretical ecology paper, the study determines whether N or P are more likely to limit the productivity of ecosystems over short, intermediate and long timescales. Author Duncan Menge explains the background and results of their study:

How do N and P levels change with the age of an ecosystem like a rainforest?

A good question. Levels of both N and P are very low in very young ecosystems (which typically have rocky soils; see picture above), higher in intermediate-aged ecosystems (see picture), and often lower in old ecosystems.  How N levels change relative to P, though, is a trickier subject.  The best-studied sites show relatively low N in younger ecosystems and relatively high N in older ecosystems, but there are some places that show opposing trends.

Prior to your research, how did theoretical models assess the impact of these two nutrients on ecosystem dynamics?

Prior to our work there were a series of conceptual developments, which I will call “the classic model,” but there was no previous mathematical model of N and P dynamics during long-term ecosystem development.  The classic model states that ecosystems should progress from N deficiency in younger ecosystems to P deficiency in older ecosystems, as is seen on the best-studied sites.  According to the classic model, this happens because of the differences in where N and P come from.  P is present in most rocks, whereas N is not, so P inputs are largely controlled by the weathering of rocks.  Consequently, very young ecosystems have large P inputs, whereas very old ecosystems have small P inputs.  On the other hand, N comes primarily from rain, so N inputs don’t necessarily depend on ecosystem age.

Franz500yearsite_groundYour paper mentions that these models don’t account for several possible trajectories of ecosystem evolution. What was missing? 

There are a number of missing elements that jumped out as potentially important.  First, the input side of the story isn’t as simple as “P comes from rocks, N comes from rain.”  P also comes from dust that is blown in from upwind, whereas N can also come from organisms like soybean or alder that “fix” N from the air.  Second, N and P losses from ecosystems should be as important as inputs in determining N and P levels, but these weren’t the focus of the classic model.  These facts have been known for a long time in the scientific community, but no one had looked at what their implications might be for ecosystem development.

What was your new model and how did it cover these aspects?

Our model is novel for a couple of reasons.  First, we considered a broader set of N and P input and loss dynamics than the classic model, which made for a richer set of possible ecosystem trajectories.  Second, the type of mathematical analysis we did was unlike anything previous researchers had done in this particular field, and made it possible to pin down the types of conditions that might lead to different soil conditions.

What were some of the key data accounted for in your model that were overlooked in previous analyses?

Aside from the input and loss dynamics mentioned above, one piece of data we keyed in on was that microbes in the soil have an easier time accessing P than N in dead plant material.  Again, this “preferential P mineralization” is something that has been known for a long time, but we thought that the effects of this quirk might not be fully appreciated.

What were the main findings of your analyses?

In addition to the classic “N limitation to P limitation” path, our model shows that many other trajectories are feasible.  For example, if dust deposition is high and N-fixing organisms are abundant in young ecosystems (as they often are), an ecosystem might start out P limited and end N limited.  One of the more surprising findings was that the levels of N and P in soil organic matter (mostly dead plant material) don’t necessarily correspond to N versus P limitation in an intuitive way.

What are some of the practical applications of this model- for example, for developmental activities in rainforests, or human activities planned in other ecosystems?

Whether N or P has a greater effect in an ecosystem has important implications for many environmental issues. The most important application is enhancing our climate models.  Excess N can be transformed into a greenhouse gas, whereas P cannot.  So, a better understanding of nutrient levels will improve predictions about the extent of climate change.

Congratulations to the authors on receiving an ESA award for this outstanding research paper!

Citation: Menge DNL, Hedin LO, Pacala SW (2012) Nitrogen and Phosphorus Limitation over Long-Term Ecosystem Development in Terrestrial Ecosystems. PLoS ONE 7(8): e42045. doi:10.1371/journal.pone.0042045

Photos by Duncan Menge:

top: the rocky soil of a very young ecosystem, Franz Josef glacier in New Zealand.  The rainforests in the valley formed by the Franz Josef glacier are some of the best studied ecosystem development sites in the world.

below: a rainforest on 500 year old soil near the Franz Josef glacier.

Announcing the PLOS Text Mining Collection

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Text mining

Post authored by Casey M. Bergman, Lawrence E. Hunter, Andrey Rzhetsky

Text Mining is an interdisciplinary field combining techniques from linguistics, computer science and statistics to build tools that can efficiently retrieve and extract information from digital text. Over the last few decades, there has been increasing interest in text mining research because of the potential commercial and academic benefits this technology might enable. However, as with the promises of many new technologies, the benefits of text mining are still not clear to most academic researchers.

This situation is now poised to change for several reasons. First, the rate of growth of the scientific literature has now outstripped the ability of individuals to keep pace with new publications, even in a restricted field of study. Second, text-mining tools have steadily increased in accuracy and sophistication to the point where they are now suitable for widespread application. Finally, the rapid increase in availability of digital text in an Open Access format now permits text-mining tools to be applied more freely than ever before.

To acknowledge these changes and the growing body of work in the area of text mining research, today PLOS launches the Text Mining Collection, a compendium of major reviews and recent highlights published in the PLOS family of journals on the topic of text mining. As one of the major publishers of the Open Access scientific literature, it is perhaps no coincidence that research in text mining in PLOS journals is flourishing. As noted above, the widespread application and societal benefits of text mining is most easily achieved under an Open Access model of publishing, where the barriers to obtaining published articles are minimized and the ability to remix and redistribute data extracted from text is explicitly permitted. Furthermore, PLOS is one of the few publishers who is actively promoting text mining research by providing an open Application Programming Interface to mine their journal content.

Text Mining in PLOS

Over the years, PLOS has published several reviews, opinions, tutorials and dozens of primary research articles in this area in PLOS Biology, PLOS Computational Biology and, increasingly, PLOS ONE. Because of the large number of text mining papers in PLOS journals, we are only able to highlight a subset of these works in the first instance of the PLOS Text Mining Collection. These include major reviews and tutorials published over the last decade [1-6], plus a selection of research papers from the last two years [7-19] and three new papers arising from the call for papers for this collection [20-22].

The research papers included in the collection at launch provide important overviews of the field and reflect many exciting contemporary areas of research in text mining, such as:

  • methods to extract textual information from figures [7];
  • methods to cluster [8] and navigate [15] the burgeoning biomedical literature;
  • integration of text-mining tools into bioinformatics workflow systems [9];
  • use of text-mined data in the construction of biological networks [10];
  • application of text-mining tools to non-traditional textual sources such as electronic patient records [11] and social media [12];
  • generating links between the biomedical literature and genomic databases [13];
  • application of text-mining approaches in new areas such as the Environmental Sciences [14] and Humanities [16-17];
  • named entity recognition [18];
  • assisting the development of ontologies [19];
  • extraction of biomolecular interactions and events [20-21]; and
  • assisting database curation [22].

 Looking Forward

As this is a living collection, it is worth discussing two issues we hope to see addressed in articles that are added to the PLOS text mining collection in the future: scaling up and opening up. While application of text mining tools to abstracts of all biomedical papers in the MEDLINE database is increasingly common, there have been remarkably few efforts that have applied text mining to the entirety of the full text articles in a given domain, even in the biomedical sciences [4][23]. Therefore, we hope to see more text mining applications scaled up to use the full text of all Open Access articles. Scaling up will maximize the utility of text-mining technologies and the uptake by end users, but also demonstrate that demand for access to full text articles exists by the text mining and wider academic communities.

Likewise, we hope to see more text-mining software systems made freely or openly available in the future. As an example of the state of affairs in the field, only 25% of the research articles highlighted in the PLOS text mining collection at launch provide source code or executable software of any kind [13, 16, 19, 21]. The lack of availability of software or source code accompanying published research articles is, of course, not unique to the field of text mining. It is a general problem limiting progress and reproducibility in many fields of science, which authors, reviewers and editors have a duty to address. Making release of open source software the rule, rather than the exception, should further catalyze advances in text mining, as it has in other fields of computational research that have made extremely rapid progress in the last decades (such as genome bioinformatics).

By opening up the code base in text mining research, and deploying text-mining tools at scale on the rapidly growing corpus of full-text Open Access articles, we are confident this powerful technology will make good on its promise to catalyze scholarly endeavors in the digital age.

To view all the articles or read more about this collection, please visit: The PLOS Text Mining Collection (2013)

Citations:

1.   Dickman S (2003) Tough mining: the challenges of searching the scientific literature. PLoS biology 1: e48. doi:10.1371/journal.pbio.0000048.

2.   Rebholz-Schuhmann D, Kirsch H, Couto F (2005) Facts from Text—Is Text Mining Ready to Deliver? PLoS Biol 3: e65. doi:10.1371/journal.pbio.0030065.

3.   Cohen B, Hunter L (2008) Getting started in text mining. PLoS computational biology 4: e20. doi:10.1371/journal.pcbi.0040020.

4.   Bourne PE, Fink JL, Gerstein M (2008) Open access: taking full advantage of the content. PLoS computational biology 4: e1000037+. doi:10.1371/journal.pcbi.1000037.

5.   Rzhetsky A, Seringhaus M, Gerstein M (2009) Getting Started in Text Mining: Part Two. PLoS Comput Biol 5: e1000411. doi:10.1371/journal.pcbi.1000411.

6.   Rodriguez-Esteban R (2009) Biomedical Text Mining and Its Applications. PLoS Comput Biol 5: e1000597. doi:10.1371/journal.pcbi.1000597.

7.   Kim D, Yu H (2011) Figure text extraction in biomedical literature. PloS one 6: e15338. doi:10.1371/journal.pone.0015338.

8.   Boyack K, Newman D, Duhon R, Klavans R, Patek M, et al. (2011) Clustering More than Two Million Biomedical Publications: Comparing the Accuracies of Nine Text-Based Similarity Approaches. PLoS ONE 6: e18029. doi:10.1371/journal.pone.0018029.

9.   Kolluru B, Hawizy L, Murray-Rust P, Tsujii J, Ananiadou S (2011) Using workflows to explore and optimise named entity recognition for chemistry. PloS one 6: e20181. doi:10.1371/journal.pone.0020181.

10.       Hayasaka S, Hugenschmidt C, Laurienti P (2011) A network of genes, genetic disorders, and brain areas. PloS one 6: e20907. doi:10.1371/journal.pone.0020907.

11.       Roque F, Jensen P, Schmock H, Dalgaard M, Andreatta M, et al. (2011) Using electronic patient records to discover disease correlations and stratify patient cohorts. PLoS computational biology 7: e1002141. doi:10.1371/journal.pcbi.1002141.

12.       Salathé M, Khandelwal S (2011) Assessing Vaccination Sentiments with Online Social Media: Implications for Infectious Disease Dynamics and Control. PLoS Comput Biol 7: e1002199. doi:10.1371/journal.pcbi.1002199.

13.       Baran J, Gerner M, Haeussler M, Nenadic G, Bergman C (2011) pubmed2ensembl: a resource for mining the biological literature on genes. PloS one 6: e24716. doi:10.1371/journal.pone.0024716.

14.       Fisher R, Knowlton N, Brainard R, Caley J (2011) Differences among major taxa in the extent of ecological knowledge across four major ecosystems. PloS one 6: e26556. doi:10.1371/journal.pone.0026556.

15.       Hossain S, Gresock J, Edmonds Y, Helm R, Potts M, et al. (2012) Connecting the dots between PubMed abstracts. PloS one 7: e29509. doi:10.1371/journal.pone.0029509.

16.       Ebrahimpour M, Putni?š TJ, Berryman MJ, Allison A, Ng BW-H, et al. (2013) Automated authorship attribution using advanced signal classification techniques. PLoS ONE 8: e54998. doi:10.1371/journal.pone.0054998.

17.       Acerbi A, Lampos V, Garnett P, Bentley RA (2013) The Expression of Emotions in 20th Century Books. PLoS ONE 8: e59030. doi:10.1371/journal.pone.0059030.

18.       Groza T, Hunter J, Zankl A (2013) Mining Skeletal Phenotype Descriptions from Scientific Literature. PLoS ONE 8: e55656. doi:10.1371/journal.pone.0055656.

19.       Seltmann KC, Pénzes Z, Yoder MJ, Bertone MA, Deans AR (2013) Utilizing Descriptive Statements from the Biodiversity Heritage Library to Expand the Hymenoptera Anatomy Ontology. PLoS ONE 8: e55674. doi:10.1371/journal.pone.0055674.

20.       Van Landeghem S, Bjorne J, Wei C-H, Hakala K, Pyysal S, et al. (2013) Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization. PLOS ONE 8:  e55814. doi: 10.1371/journal.pone.0055814

21.       Liu H, Hunter L, Keselj V, Verspoor K (2013) Approximate Subgraph Matching-based Literature Mining for Biomedical Events and Relations. PLOS ONE 8: e60954. doi: 10.1371/journal.pone.0060954

22.       Davis A, Weigers T, Johnson R, Lay J, Lennon-Hopkins K, et al. (2013) Text mining effectively scores and ranks the literature for improving chemical-gene-disease curation at the Comparative Toxicogenomics Database. PLOS ONE 8: e58201. doi: 10.1371/journal.pone.0058201

23.       Bergman CM (2012) Why Are There So Few Efforts to Text Mine the Open Access Subset of PubMed Central? http://caseybergman.wordpress.com/2012/03/02/why-are-there-so-few-efforts-to-text-mine-the-open-access-subset-of-pubmed-central/.

 

 

Meet Vectidraco, a European pterosaur the size of a crow

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Fossil records show that pterosaurs of all sizes and shapes flew through the skies of China and Central Asia about 145 to 66 million years ago. A new species of small pterosaurs described in a PLOS ONE paper reveals that western Europe may have had a similar diversity of these ancient animals. Author Darren Naish discusses the importance of the new species, named Vectidraco.

How did you begin studying dinosaurs (or pterosaurs in particular)?

Most of my research is and has been based on the Lower Cretaceous fossils that come from the Isle of Wight and elsewhere  in southern England. The rocks here are famous for their dinosaurs, but fossil crocodilians, marine reptiles like plesiosaurs and rare pterosaurs are found here too. I’ve always been interested in pterosaurs and for several years have had a special research interest in a highly peculiar pterosaur group called the azhdarchoids – I’ve been working continuously on this group since 2007 or so and have been especially interested in their ecology, functional anatomy and evolutionary relationships. The finding of a new azhdarchoid in the Lower Cretaceous rocks of the Isle of Wight thus combined several of my special interests.

Where and how did you find the new fossil described in your study?

Most Cretaceous Isle of Wight fossils come from a rock unit termed the Wealden Supergroup. The new specimen – we’ve called it Vectidraco – is from a different, younger unit called the Atherfield Clay Formation, and as such it’s (so far as we know) only the second pterosaur reported from this unit.

I should say that the discovery of Vectidraco itself is interesting in that the find was made by a young girl, Daisy Morris (aged just 5 at the time!), while she was on holiday with her family. Daisy’s family wanted this fossil to be studied and cared for properly, so they did what I and many of my colleagues would say is “the right thing” and donated it to The Natural History Museum in London. So, we only know of Vectidraco thanks to Daisy: for this reason we named it in her honour. It’s full name is Vectidraco daisymorrisae.

What was previously known about this group of flying reptiles, the azhdarchoid pterosaurs?

So far as we know right now, azhdarchoids are unique to the Cretaceous period (that is, they were alive between about 145 and 66 million years ago) and all were toothless. They’re actually a pretty diverse group of pterosaurs, with some – like the tapejarids – being relatively small, withwingspans of about 3 feet or slightly less and others – namely the azhdarchids – being gigantic, withwingspans of more than 32 feet.

Tapejarids have short, deep snouts while azhdarchids have incredibly long, pointed jaws, and other kinds of azhdarchoid were intermediate between these two groups. Particularly good azhdarchoid fossils are known from South and North America and China, but their remains have been found right across Europe, Asia and Africa too.

Working out what azhdarchoids did when they were alive has been one of the great questions about the group, but it seems that they were mostly omnivores or carnivores that lived in terrestrial environments.

The paper describes the new fossil as “small-bodied”. How much larger are other known pterosaurs of this kind usually?

Azhdarchoids span a diversity of species that range from ‘small-bodied’ all the way up to gigantic. The biggest kinds –  like the famous Quetzalcoatlus from Texas – were something like 10 feettall at the shoulder and over 450 pounds heavy while small ones, and Vectidraco is one of them, had wingspans of just 30 inches or so and would have been similar in size to crows or gulls. I would say that Vectidraco belonged to an azhdarchoid group where small size was normal and widespread, with large and even giant size evolving in other azhdarchoid lineages.

How did you determine that the new fossil belonged to the same group as these other specimens?

Vectidraco is known only from its pelvis, but even with only a pelvis to go on, we could see several features of the new specimen that made it especially azhdarchoid-like, mostly to do with the weird anatomy of the big, T-shaped bony structure that projects upwards and backwards from the rear part of the pelvis. In an effort to better test the idea that Vectidraco is an azhdarchoid, we included it in a few different phylogenetic analyses and it came out as an azhdarchoid in these too. It also has several unique features, not seen in any other pterosaurs, and for these reasons we were able to name it as a new species.

How does this discovery change what we know about this group of pterosaurs?

We’ve known for a while that small-bodied azhdarchoids lived in western Europe during the Early Cretaceous: a new species called Europejara olcadesorum was described in PLOS ONE last year. Now we’ve found that Vectidraco lived in the same region during the same period, so we’re seeing a pattern: small-bodied azhdarchoids were living alongside longer-snouted, small-bodied pterosaurs and also alongside large, toothy kinds called ornithocheiroids.

This is essentially the same kind of pterosaur community that we  see in Chinese rocks of the same age – the great difference is that the Chinese fossils are relatively numerous, and frequently preserved as complete or near-complete skeletons. In fact, one of the things that we comment on in our paper is the fact that western Europe’s pterosaur assemblage looks far less rich than that of China due to differences in the way these fossils were preserved. Chinese pterosaur and small dinosaur fossils were buried rapidly by volcanic ash and hence preserved whole, while those of western Europe were usually broken apart on floodplains, extensively scavenged, and eventually preserved in fragmentary form.

The western European and Chinese assemblages might actually have contained similar sorts of species, but the conditions local to both places meant that their fossil records ended up being very different.

Read more about this exciting new fossil at Darren Naish’s own blog, Tetrapod Zoology.

Citation: Naish D, Simpson M, Dyke G (2013) A New Small-Bodied Azhdarchoid Pterosaur from the Lower Cretaceous of England and Its Implications for
Pterosaur Anatomy, Diversity and Phylogeny. PLoS ONE 8(3): e58451. doi:10.1371/journal.pone.0058451

Vullo R, Marugán-Lobón J, Kellner AWA, Buscalioni AD, Gomez B, et al. (2012) A New Crested Pterosaur from the Early Cretaceous of Spain: The First European Tapejarid (Pterodactyloidea: Azhdarchoidea). PLoS ONE 7(7): e38900. doi:10.1371/journal.pone.0038900

Images: Specimen and speculative reconstruction of Vectidraco from 10.1371/journal.pone.0058451, Life restoration of the head of Europejara from 10.1371/journal.pone.0038900

Marine microbes make musical waves

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Music may be the newest addition to a science communicator’s toolbox. A PLOS ONE paper published today describes an algorithm that represents terabytes of microbial and environmental data in tunes that sound remarkably like modern jazz.

“Microbial bebop”, as the authors describe it, is created using five years’ worth of consecutive measurements of ocean microbial life and environmental factors like temperature, dissolved salts and chlorophyll concentrations. These diverse, extensive data are only a subset of what scientists have been recording at the Western Channel Observatory since 1903.

As first author Larsen explained to the Wired blogs, “It’s my job to take complex data sets and find ways to represent that data in a way that makes the patterns accessible to human observations. There’s no way to look at 10,000 rows and hundreds of columns and intuit what’s going on.”

Each of the four compositions in the paper is derived from the same set of data, but highlights different relationships between the environmental conditions of the ocean and the microbes that live in these waters.

“There are certain parameters like sunlight, temperature or the concentration of phosphorus in the water that give a kind of structure to the data and determine the microbial populations. This structure provides us with an intuitive way to use music to describe a wide range of natural phenomena,” explains Larsen in an Argonne National Laboratories article.

Speaking to Living on Earth, Larsen describes how their music highlights the relationship between different kinds of data. “In most of the pieces that we have posted, the melody is derived from a numerical measurement, such that the lowest measure is the lowest note and the highest measure is the highest note. The other component is the chords. And the chords map to a different component of the data.”

As a result, the music generated from microbial abundance data played to chords generated from phosphorus concentration data will sound quite different from the same microbial data played to chords derived from temperature data.

“Songs themselves probably are never going to actively replace, you know, the bar graph for data analysis, but I think that this kind of translation of complex data into a very accessible format is an opportunity to lead people who probably aren’t highly aware of the importance of microbial ecology in the ocean, and give them a very appealing entry into this kind of data”, explained Larsen in the same interview with Living on Earth.

Though their primary intent was to create novel way to symbolize the interactions of microbes in the ocean, the study also suggests that microbial bebop may eventually have applications in crowd-sourcing solutions to complex environmental issues.

For further reading, a PLOS ONE paper in 2010 demonstrated that the metaphors used to explain a problem could have a powerful impact on people’s thoughts and decisions when designing solutions. Could re-phrasing complex environmental data in music lead to solutions we haven’t heard yet? As you ponder the question, listen to some microbial bebop!

Other media sources that also covered this research include LiveScience, gizmag and the PLOS blog Tooth and Claw

Citations:  Larsen P, Gilbert J (2013) Microbial Bebop: Creating Music from Complex Dynamics in Microbial Ecology. PLoS ONE 8(3): e58119. doi:10.1371/journal.pone.0058119

Thibodeau PH, Boroditsky L (2011) Metaphors We Think With: The Role of Metaphor in Reasoning. PLoS ONE 6(2): e16782. doi:10.1371/journal.pone.0016782

Image: sheet music by jamuraa on Flickr

 

A floral ‘map’ to nectar discourages bumblebee robbers

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In the business of survival, the bright colors of blooming flowers mark a serious transaction. Their nectar, color and fragrances are all designed to attract pollinators to come hither and transfer pollen to help plants reproduce but occasionally, these plans go awry. Some bees choose to avoid the pollen and tunnel into flowers to steal nectar instead. A study published in PLOS ONE last week explains how plants deter these robbers by providing them a map to reach nectar more quickly. Author Anne Leonard explains their results:

How did you become interested in studying floral guide patterns? 

I think many people are intrigued by the fact that bees see the patterns on flowers differently than we do. I was studying color learning in bumble bees, and as I looked through the literature I realized there were still many unanswered questions about how these patterns affect bees’ behavior. Living in Tucson, I started to photograph the dazzling variety of nectar guides on Sonoran desert wildflowers, slowing down many a hike in the process. Between all the reading and photography, I clearly had nectar guides on the brain.

Why do flowers have nectar guide patterns?

The patterns of nectar guides appear to be very attractive to many bee species. Bright colors, high color contrasts and star-like outlines could simply help a plant increase visits from pollinators. It’s even been suggested that these visual features might have evolved to mimic rewards, for example bright yellows and oranges might resemble protein-rich pollen to the insects. Secondly, plants that produce distinctive and memorable patterns might also benefit because they provide an identifying feature for pollinators to learn, remember, and return to.

Third, a nectar guide may reduce the overall time the bee spends on the flower. If bees are sensitive to the time costs associated with visiting different flowers, then they should prefer to visit flowers they can handle quickly. Finally, our research suggests a novel benefit: the pattern can reduce a bee’s tendency to rob nectar. In this case, the pattern benefits the plant by incentivizing the bee to access nectar “legitimately,” in a way that is most likely to transfer pollen.

Can you explain what nectar robbing refers to and what a ‘legitimate’ way of getting nectar looks like?

If you take a moment and imagine a bee visiting a trumpet-shaped flower like a morning glory, what you’re picturing is most likely what we call a “legitimate” visit. The bee lands on a  petal, and walks forward to probe down to the nectar located in the tube-like part of the flower. In the process, she is likely to pick up pollen or transfer pollen from her body to the flower. This exchange of nectar for pollen transfer forms the basis of the relationship between plant and bee. We refer to this type of nectar for pollen transfer via the floral opening as a “legitimate” visit, from the plant’s perspective.

In  a second type of visit,  the bee lands on the flower but instead of going the legitimate route, it  bites a hole in the side of the flower to access nectar, without necessarily depositing pollen or picking up new pollen. Because the plant has lost nectar to the bee without gaining pollen transfer, this type of visit is termed ‘nectar robbing’.

Why do bees indulge in ‘nectar robbing’? Is this behavior seen with other insects and birds?

Although observations of bees nectar robbing date back to at least the 18th century writings of Sprengel, we are still studying why bees do it. Some species, like carpenter bees, have a reputation as frequent robbers. Others like honey bees and the bumble bee species I study, Bombus impatiens, are better known as opportunistic nectar robbers. They’ll rob some plant species but not others; propensity to rob seems to also vary somewhat across individuals. Some studies show that bees may be more likely to rob if a previous visitor has already created the access hole. Likewise, our research suggests that if the flower doesn’t have a nectar guide pattern to direct the bee to the floral opening, they are more likely to stray and encounter an access hole left by a previous robber.

In your paper, you found that when a flower had a guide pattern, bees were less likely to rob nectar. How did you test the bees’ behavior?

We use an array of specially designed artificial flowers that my co-author Josh Brent spent many hours trouble-shooting. These flowers had nectar available in two different ways. The bee could either land on the top of the flower and access nectar “legitimately” from a small central well, or she could land on the underside of the flower, and “rob” nectar from a small well located on the side of the floral tube.

We kept bee colonies in the lab so they were naïve with respect to experience with real flowers. We let bees into the arena one at a time, and recorded their visits to the flowers on the array. Half the bees were given blue flowers with yellow star-shaped guides, and the other half saw only plain blue flowers with no patterns. We noted whether the bee robbed or visited each flower legitimately, and we were also able to measure how quickly she located the nectar after landing in each case.

We found that bees robbed less frequently when the flowers had nectar guides and also landed more quickly on flowers with guides than those without them. This suggests the bees indeed found the nectar guide more attractive to land upon than the plain flower top, and that the  guide helped them find nectar faster.

Does this discovery have applications for bee-keepers or horticulturists?

We’d need a few more of the pieces of the puzzle before claiming that our research on floral patterns might yield better honey or healthier honeybees, but our research suggests that the stripes and dots that provide color patterns pleasing to the human eye can also affect the way the bee interacts with the flower.

Typically, varieties of nursery plants are bred for human aesthetics. Given a choice, planting a variety with a dramatic nectar guide pattern might allow an observant gardener the satisfaction of seeing more pollen transferred by bees. On the other hand, those gardeners eager to see nectar robbing in action might select a relatively plain variety. The committed backyard scientist might be inspired to plant varieties with different types of patterns, sit back, and watch what happens. Of course, flowers of different plants can also differ in many other aspects that might affect a bee’s propensity to rob nectar (such as floral scent or nectar chemistry) and keep in mind that some may have UV patterns that the human eye can’t see.

Citation and images: Leonard AS, Brent J, Papaj DR, Dornhaus A (2013) Floral Nectar Guide Patterns Discourage Nectar Robbing by Bumble Bees. PLoS ONE 8(2): e55914. doi:10.1371/journal.pone.0055914