Public Library of Science - PLoS ONE Blog

The Neuroscience of Things That Make You Go "Ew!"

Rebecca Walton — Mon, 18 Aug 2008 12:04:22 -0700

Paul Sereno’s paper wasn’t – by any means – the only PLoS ONE paper published last week to have been covered by the press and by bloggers.

Reporting in PLoS ONE on August 13, Matt Finer, of Save America's Forests, and colleagues at Duke University and Land Is Life tracked hydrocarbon exploration projects across the western Amazon and generated a detailed map of oil and gas activities across the region, which, the researchers found, overlaps considerably with the latest biodiversity maps for amphibians, birds and mammals. Unlike the eastern Brazilian Amazon, the western region is still largely intact but large reserves of oil and gas lie below the landscape of the latter and growing global demand is leading to increased exploration and development in the region. There were news stories on the study in The Guardian, New Scientist and The Associated Press and it was blogged by Daily Kos, The Intersection and DigitalJournal.com.

Another study raising environmental issues – this one by Alex Pyron and colleagues at The City University of New York – outlined the potential effects of climate change on Burmese python populations in the United States. The PLoS ONE study found that, contrary to previous research, the pythons were unlikely to spread beyond the Floridian everglades in which they make their homes. The researchers used records on the distribution of pythons in their native range along with high resolution global climate databases to predict the potential extent of the python’s distribution in the U.S. and model the possible effects of global warming on the snakes. The results suggest that the pythons are restricted to the vicinity of the Everglades in extreme south Florida. The study was featured on Live Science and was also picked up on some of the wires.

As an ophidiophobic, reading Pyron’s article and some of the news stories (especially those with accompanying images) made me feel a little uneasy. In their article published in PLoS ONE last week, Mbemba Jabbi at the National Institutes of Mental Health, along with colleagues at the University Medical Center Groningen, shed some light on how reading a book or watching a film can invoke in us the same emotions as if we were experiencing the events ourselves. Focusing on the emotion of disgust, the researchers used an fMRI scanner to measure the participants’ brain activity while they: had drops of an unpleasant, bitter liquid placed on their tongue; watched a video of “disgusting” behaviour; and read a passage of disgusting text. They found that the same areas of the brain – the anterior insula and adjacent frontal operculum – were activated both when the participants tasted the liquid and when they watched the video and read the passage. The article was covered by New Scientist (although, note the disclaimer – “Warning: this story contains a paragraph of disgusting text” at the top of the story), Wired, PsychCentral and Discount Thoughts.

Finally, researchers led by Daniel Perez at the University of Maryland studied the H9N2 strain of the influenza virus, publishing their findings in a paper entitled, Replication and Transmission of H9N2 Influenza Viruses in Ferrets: Evaluation of Pandemic Potential. The scientists used ferrets (whose biology is very close to humans when it comes to flu) to characterise the mechanism of replication and transmission of recent avian H9N2 viruses and, according to the paper, the results suggest that, “the establishment and prevalence of H9N2 viruses in poultry pose a significant threat for humans.” There were news stories about the study in Reuters, AFP, Science News and Discover Magazine.

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Digging into the "Green Desert" of Niger's Holocene Past

Rebecca Walton — Mon, 18 Aug 2008 11:47:14 -0700

After the massive media buzz surrounding the last paper published in PLoS ONE by Paul Sereno, in which he and colleagues described the anatomy and behaviour of Nigersaurus taqueti (dubbed “the Mesozoic cow” by the press), you can imagine that we were quite excited to receive another paper from the University of Chicago Palaeontologist and National Geographic Explorer-in-Residence.

Sereno and his team had originally been on a dinosaur-hunting expedition in the Ténéré Desert in Niger (which is where the Nigersaurus fossil was discovered) when they happened on a large, Stone Age graveyard. In the new PLoS ONE article, Lakeside Cemeteries in the Sahara: 5000 Years of Holocene Population and Environmental Change, the researchers outline the findings from a series of new archaeological sites at Gobero, dating from the Holocene and preserving the earliest Saharan cemetery from around 9500 years ago, as well as burials from two separate periods of occupation spanning more than 5000 years. Arid conditions forced the initial occupants to abandon the area a little over 8000 years ago but with the return of more humid conditions, around 6600 years ago, the region was repopulated by a more gracile people who left behind elaborate grave goods, including animal bone and ivory ornaments, many of which are pictured in the paper.

One of the graves contained the skeleton of a small Tenerian woman facing the skeletons of two small children (a photograph of this by Mike Hettwer, captioned Stone Age Embrace, has been widely used alongside many of the news stories on the article). Samples from the grave contained pollen clusters, suggesting the individuals had been laid to rest on a bed of flowers.

Some of the accompanying images are part of the published paper (and so can be reused in line with the terms of the Creative Commons Attribution License); other images, along with more information about the expedition can be found on the Project Exploration website (Project Exploration being a nonprofit science education organization that makes science accessible to the public—especially minority youth and girls—through personalized experiences with scientists and science). Any users registered on the PLoS ONE site can, of course, post notes and comments and rate the paper online.

Understandably, the article received huge amounts of coverage in the media and in the blogosphere (despite “Bigfoot”’s efforts to steal the spotlight). As well as making the front page of Slashdot, the story was the top Associated Press science story on Thursday (it was also one of the overall top stories), it was in Yahoo science news’s most viewed list on Friday, and in the New York Times most-emailed list. There were several hundred news stories on Google News, so here are a few highlights of the coverage (see also Knight Science Journalism Tracker and A Blog Around the Clock):

News:

New York Times – Graves Found From Sahara’s Green Period
Washington Post – Excavations Show a Lush Life in the Sahara
Los Angeles Times – Archaeologists get a glimpse of life in a Sahara Eden
Reuters – Stone Age graveyard shows Sahara was once green
National Geographic – Ancient Cemetery Found; Brings "Green Sahara" to Life
Scientific American – Paleontology's Indiana Jones
New Scientist – Stone Age mass graves reveal green Sahara
Nature News – Back when the desert was green

Blogs:

Wired – Saharan Snapshot of Stone Age Life
Pharyngula – I Wish I Was a Paleontologist
Greg Laden’s Blog – Stone Age Graveyard Reveals Lifestyles of a Green Sahara
Stones, Bones ‘n’ Things – Paleontology Meets Archaeology
Anthropology.net – The Kiffian & Tenerean Occupation Of Gobero, Niger: Perhaps The Largest Collection Of Early-Mid Holocene People In Africa
Metafilter – Lost Tribes of the Green Sahara

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ONE journal, two birthdays

Liz Allen — Fri, 1 Aug 2008 10:32:43 -0700

The English Monarch has two birthdays – their real date of birth is celebrated in private with family and friends and the official date (which could historically be moved should their real birthday fall at a time of year when the weather was inclement) which is celebrated in public through the Trooping of the Colour Ceremony and a fly-past over Buckingham Palace in London.

PLoS ONE also celebrates twice (but far less grandly) – first there’s the date we opened our doors for submissions, 4 August 2006 (the date of our conception) and then there’s the date we launched (our birth), 20th December 2006.

Within less than 3 weeks of opening our doors we had received 70 manuscripts which represented far more papers flowing far faster than we’d ever experienced before. Now, two years later, we receive approximately 350 submissions per month. Not surprisingly, the PLoS team has grown since then to cope with the increased workload.

Two folks who deserve special mention for being there at the start and still being on board now - they are Bex Walton and Lindsay King.

Two years on, the person who still sums up our publishing philosophy well is the author of the first paper accepted for PLoS ONE, Andrej Romanovsky of St. Joseph's Hospital, Phoenix, Arizona, USA. He said "A traditional publisher uses complex rules to determine who, when, how, and at what price will be allowed to see your results. You can continue supporting this system ... or you can submit your next paper to PLoS”.

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Happy, er, conception-day?

from A Blog Around The Clock on Mon, 2008-08-04 04:55

Two years ago on this day, PLoS ONE opened for submissions (and surprisingly many manuscripts - 70 - got submitted immediatelly)....

Tyrannosaurus Re-examined

Rebecca Walton — Fri, 1 Aug 2008 08:38:54 -0700

This week saw the publication of another dinosaur study in PLoS ONE. In the article, entitled, Dinosaurian Soft Tissues Interpreted as Bacterial Biofilms, Thomas Kaye, at the Burke Museum of Natural History, and colleagues reported that material recovered from dissolved dinosaur bones by palaeontologists in 2005 (and believed to be dinosaurian soft tissue) may actually have been slimy biofilm created by bacteria that coated the voids once occupied by blood vessels and cells.

This study has already generated a large number of news articles and blog posts, including the following: New Scientist (T. rex 'tissue' may just be bacterial scum), Scientific American (Presumed dinosaur flesh may just be bacterial sludge), National Geographic (Dinosaur Slime Sparks Debate Over Soft-Tissue Finds), USA Today (New study has a bone to pick about dinosaur soft tissue), Aetiology (Dinosaur soft tissue--just bacterial biofilm?) and Pharyngula (Tyrannosaur morsels).

Several comments have already been posted on the published article and you can join in the discussion once you have created an account on the PLoS ONE publication website.

On the topic of biofilm, Carsten Matz’s paper, Marine Biofilm Bacteria Evade Eukaryotic Predation by Targeted Chemical Defense, published last week also picked up some coverage in the Washington Post (Social Lives of Bacteria May Yield Benefits for Humans) and Chemistry World (Biofilms deploy chemical weapons).

Also on a watery theme was Natalia Ospina-Álvarez and Francesc Piferrer’s paper on the potential effects of climate change on sex determination in fish. In vertebrates with separate sexes, sex determination can be genotypic (GSD) or temperature-dependent (TSD). The Spanish researchers used field and laboratory data to critically analyze the presence of TSD in the 59 species of fish where this type of sex determining mechanism had been postulated and found that increasing temperatures invariably resulted in highly male-biased sex ratios and that even small changes of just 1-2°C can significantly alter the sex ratio from 1:1 (males:females) up to 3:1 in both freshwater and marine species. Time Magazine covered the article (Global Warming's Fish-Sex Effect) and the story has also been Dugg several times.

Danish palaeontologist Per Christiansen compared the evolution of skull and mandible shape both in modern cats and in (the now extinct) sabercats; Greg Laden has posted a nice write-up of the study on his blog and there also posts on The Dragon’s Tales and on Counter Minds.

Finally, here is a quick round-up of some of coverage of several papers published in PLoS ONE on July 23^rd: Does Pathogen Spillover from Commercially Reared Bumble Bees Threaten Wild Pollinators? (New Scientist, Reuters, Greg Laden’s blog); Sample Size and Precision in NIH Peer Review (The Scientist, Mike the Mad Biologist); and Changes in Gray Matter Induced by Learning—Revisited (Mind Hacks).

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Natural and Synthetic Vision - call for papers - deadline extended to 9.15.08

Liz Allen — Mon, 28 Jul 2008 12:53:08 -0700

We're seeking more articles in the field of Natural and Synthetic Vision (an area in which we have already published 40+ papers, you can see them listed below). At the current time we are especially interested in articles that will be of interest to those who are implementing Synthetic Vision Systems.

We would like to expand our coverage of this area by announcing the publication of a Special Collection that emphasizes electronic and computational image processing, including machine learning in vision. We look forward to publishing your research.

Special Collection—submit by September 15th

PLoS ONE would like to receive your work so that we may consider it for inclusion in the collection. Since we pride ourselves on fast publication, for all articles submitted by September 15th, 2008, we will strive to get a first decision back to the authors by October 15th, 2008. Allowing a month for any revisions and resubmissions, we will then aim to publish the Special Collection in late Autumn 2008.

The Academic Editors leading this call for papers include Andreas G. Andreou (Johns Hopkins University), Eugenio Culurciello (Yale University), Yann Lecun (New York University), and Teresa Serrano-Gotarredona (Microelectronics Institute of Seville). The following three articles have been chosen by these Academic Editors to showcase the quality and breadth of our coverage in this area:
* Visual Coding in Locust Photoreceptors by Olivier Faivre and Mikko Juusola.
* Neural Decision Boundaries for Maximal Information Transmission by Tatyana Sharpee and William Bialek.
* Integration across Time Determines Path Deviation Discrimination for Moving Objects by David Whitaker, Dennis M. Levi, and Graeme J. Kennedy.

I interviewed the corresponding author of the paper entitled Visual Coding in Locust Photoreceptors listed above about why he and his co-author chose PLoS ONE, their experiences publishing with us and where their work is heading now.

Q. Why did you choose PLoS ONE to publish your work?
A. We chose to publish in PLoS ONE because the publication process is fast and authors are given great freedom for deciding the layout of the article and choosing the way they present they data. The fact that there was no size restriction, for the text or the number of (colour) figures was an appreciable bonus. Furthermore, we strongly support the open-source policy of PLoS ONE.
Q. What was your publishing experience like and would you do it again? A. The publication process went well, and was overall pretty fast. We especially appreciated that 2 out of 3 referees decided to reveal their identities. We would certainly do it again and recommend our colleagues to publish in PLoS ONE.

Why are Natural and Synthetic Vision researchers like these already publishing in PLoS ONE? Because it is:
* Open Access—freely and immediately available to everyone online. * Fast—papers that pass peer review are rapidly published.
* Peer-Reviewed—for technical soundness and scientific rigor.
* Interactive—tools for rating, commenting on, and discussing research with an online scientific community.
* Funder-Compliant—everything we publish is automatically deposited in PubMed Central.

Here are the papers that we've already published in this field categorized for your convenience.
Neuronal Mechanisms for Vision
Visual Coding in Locust Photoreceptors Olivier Faivre, Mikko Jussola (2008)
Ganglion Cell Adaptability: Does the Coupling of Horizontal Cells Play a Role? Dedek K, Pandarinath C, Alam NM, Wellershaus K, Schubert T, Willecke K, Prusky GT, Weller R, Nirenberg S (2008)
High-Pass Filtering of Input Signals by the Ih Current in a Non-Spiking Neuron, the Retinal Rod Bipolar Cell Cangiano L, Gargini C, Della Santina L, Demontis GC, Cervetto L (2007)
A Novel Interhemispheric Interaction: Modulation of Neuronal Cooperativity in the Visual Areas Carmeli C, Lopez-Aguado L, Schmidt, KE, De Feo O, Innocenti GM (2007)
A Functional Architecture of Optic Flow in the Inferior Parietal Lobule of the Behaving Monkey Raffi M, Siegel RM (2007)

Network Properties and Modeling
Effects of Active Conductance Distribution over Dendrites on the Synaptic Integration in an Identified Nonspiking Interneuron Takashima A, Takahata M (2008)
On How Network Architecture Determines the Dominant Patterns of Spontaneous Neural Activity Galen RF (2008)
Long-Term Activity-Dependent Plasticity of Action Potential Propagation Delay and Amplitude in Cortical Networks Bakkum DJ, Chao ZC, Potter SM (2008)
Network ‘Small-World-Ness’: A Quantitative Method for Determining Canonical Network Equivalence Humphries MD, Gurney K (2008)
Calmodulin Activation by Calcium Transients in the Postsynaptic Density of Dendritic Spines Keller DX, Franks KM, Bartol TM, Sejnowski TJ (2008)
Spike Timing Dependent Plasticity Finds the Start of Repeating Patterns in Continuous Spike Trains Masquelier T, Guyonneau R, Thorpe SJ (2008)
Information and Discriminability as Measures of Reliability of Sensory Coding Grewe J, Weckstrom M, Egelhaaf M & Warzecha A-K (2007) Cellular and Network Contributions to Excitability of Layer 5 Neocortical Pyramidal Neurons in the Rat Bar-Yehuda D, Korngreen A (2007)
Identification and Classification of Hubs in Brain Networks Sporns O, Honey CJ, Kotter R (2007)
Development of Neural Circuitry for Precise Temporal Sequences through Spontaneous Activity, Axon Remodeling, and Synaptic Plasticity Jun JK, Jin DZ (2007)
Synaptic Transmission and Plasticity in an Active Cortical Network Reig R, Sanchez-vives MV (2007)
Neural Decision Boundaries for Maximal Information Transmission Sharpee T, Bialek W (2007)
On the Dynamics of the Spontaneous Activity in Neuronal Networks Mazzoni A, Broccard FD, Garcia-Perez E, Bonifazi P, Ruaro ME, Torre V (2007)
Subspace Projection Approaches to Classification and Visualization of Neural Network-Level Encoding Patterns Osan R, Zhu L, Shoham S, Tsien JZ (2007)
Spike Timing and Reliability in Cortical Pyramidal Neurons: Effects of EPSC Kinetics, Input Synchronization and Background Noise on Spike Timing Rodroguez-Molina VM, Aertsen A, Heck DH (2007)

Visual Psychophysics and Perception
Visual Learning in Multiple-Object Tracking Makovski T, Vázquez GA, Jiang YV (2008)
Spatial and Temporal Dynamics of Attentional Guidance during Inefficient Visual Search Zenon A, Ben Hamed S, Duhamel J-R, Olivier E (2008)
Saccadic Eye Movements Minimize the Consequences of Motor Noise van Beers RJ (2008)
Integration across Time Determines Path Deviation Discrimination for Moving Objects Whitaker D, Levi DM, Kennedy GJ (2008)
Are There Multiple Visual Short-Term Memory Stores? Sligte IG, Scholte HS, Lamme, VAF (2008)
Crayfish Recognize the Faces of Fight Opponents Van der Velden J, Zheng Y, Patullo BW, Macmillan DL (2008)
Self-Consistent Estimation of Mislocated Fixations during Reading Engbert R, Nuthmann A (2008)
Benefits of Stimulus Congruency for Multisensory Facilitation of Visual Learning Sandkuhler S, Bhattacharya J (2008)
Multi-Timescale Perceptual History Resolves Visual Ambiguity Brascamp JW, Knapen THJ, Kanai R, Noest AJ, van Ee R, van den Berg AV (2008)
The Role of Temporally Coarse Form Processing during Binocular Rivalry van Boxtel JJA, Alais D, Erkelens CJ, van Ee R (2008)
Visual Feedback Is Not Necessary for the Learning of Novel Dynamics Franklin DW, So U, Burdet E, Kawato M (2007)
The Effect of Real-World Personal Familiarity on the Speed of Face Information Processing Balas B, Cox D, Conwell E (2007)
Illusory Stimuli Can Be Used to Identify Retinal Blind Spots Crossland MD, Dakin SC, Bex PJ (2007)
Cross-Modal Object Recognition Is Viewpoint-Independent Lacey S, Peters A, Sathian K (2007)
Retinal Encoding of Ultrabrief Shape Recognition Cues Greene E (2007)
Stimulus Motion Propels Traveling Waves in Binocular Rivalry Knapen T, van Ee R, Blake R (2007)
Parts, Wholes, and Context in Reading: A Triple Dissociation Pelli DG, Tillman KA (2007)
Changing Human Visual Field Organization from Early Visual to Extra-Occipital Cortex Jack AI, Patel GH, Astafiev SV, Snyder AZ, Akbudak E, Shulman GL, Corbetta M (2007)
Onset Rivalry: Brief Presentation Isolates an Early Independent Phase of Perceptual Competition Carter O, Cavanaugh P (2007)
Spatio-Temporal Interpolation Is Accomplished by Binocular Form and Motion Mechanisms Kandil FI, Lappe M (2007)
High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes Fahlgren N, Howell M, Kasschau K, Chapman E, Sullivan C, Cumbie J, Givan S, Law T, Grant S, Dang J, Carrington J (2007)
Perceptual Learning of Motion Leads to Faster Flicker Perception Seitz AR, Nanez JE Sr, Holloway SR, Watanabe T (2006)

We look forward to publishing your research.

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Natural and Synthetic Vision - call for papers

from 2007 on Mon, 2008-07-28 19:11

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The Birds and the 'Bots

Rebecca Walton — Mon, 14 Jul 2008 03:50:48 -0700

Some of the topics presented in the news coverage of several papers published in PLoS ONE last week included birds, music and artificial intelligence.

Coen Elemans and colleagues at the University of Pennsylvania and the University of Utah studied the European starling and the zebra finch and found that these songbirds control their songs with the fastest-contracting muscle type yet described. These superfast muscles are previously known only from the sound-producing organs of rattlesnakes, several fish and the ringdove but the new study suggests they may be more common than once thought. The study was covered in the New York Times (Learning From a Muddy Muscle Master), National Geographic (Fastest Known Muscles Found in Songbirds' Throats), The Telegraph (Songbirds have superfast muscles) and The Independent (Songbirds develop super muscles for dawn chorus), among other places.

Birds were also the subject of a study entitled, Birds Reveal their Personality when Singing, by Garamszegi and colleagues. The researchers used bird song as a model to investigate whether behavioural traits involved in sexual advertisement can serve as good indicators of personality in wild animals. They found that the females preferred males who sang close to the ground, which may involve a higher predation risk, because it offers less concealment and puts males in a conspicuous position from the predators’ eye. Only prime quality individuals can cope with such costs of exposed singing, while cheaters will be eliminated by predators. The study was picked up by CBS News (Bold male bird gets the girl: study) and blogged by GrrlScientist (Singing the Praises of Mr Personality).

“Most musical, most melancholy bird,” said Samuel Taylor Coleridge of the nightingale but whether birdsong can affect us in the same way as a beautiful sonata played by a human musician is another matter. Stefan Koelsch at the University of Sussex, meanwhile, investigated whether people respond in the same ways to computerised music – particularly to unexpected chord changes – as they do to music played by humans. The researchers recorded the electrical brain responses and skin conductance responses of the participants and found that while the original, human music elicited brain activity in the listeners and caused them to sweat, the modified music generated little response. The authors suggest that the brain is therefore more likely to look for musical meaning when the music was played by a pianist. Perhaps the computerised music in the study wasn’t quite as poignant as HAL’s rendition of Daisy in 2001: A Space Odyssey.

The best headline of the week must surely be The Chronicle of Higher Education for its article on the study: Don't Cry For Me, R2D2. Other coverage included stories in The Telegraph (Sweaty music find could help develop new treatments), The Guardian (Music that brings a tear to the eye), Wired (Study: Computer Musicians Ain't Got No Soul) and PsychCentral (Computer Music Not As Calming).

Finally, a study by Sören Krach and colleagues investigated how the increase of human-likeness of interaction partners modulates the participants’ brain activity. In this study, participants were playing an easy computer game (the prisoners’ dilemma game) against four different game partners: a regular computer notebook, a functionally designed Lego-robot, the anthropomorphic robot BARTHOC Jr. and a human. The fMRI study found that the more human-like the opponent, the more engaged the cortical regions associated with mental state attribution of the participants and the more the participants enjoyed the interaction. The study was blogged by io9 (Proof that the Brain Cannot Distinguish Between Human and Humanoid) and in the Chronicle of Higher Education (Our Brains Attribute Human Qualities to Humanoid Machines).

53 other papers were published in PLoS ONE last week (including an article by Laurie Graham and colleagues, which was covered by The Economist) and can all be read, rated and discussed on the journal website.

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Express yourself through PLoS ONE

Liz Allen — Mon, 7 Jul 2008 09:37:06 -0700

Every month, PLoS ONE takes a different scientific field and focuses on what we’ve published from each. We then reach out to these communities to show them the benefits of publishing with us with the goal of encouraging more of them to do so.

So far this year we’ve covered Ecology and Evolutionary Biology, Cell Signaling (our number one most published topic), Avian Research and now it’s July we’re going to reach out to the Gene Expression folks (our second most published subject).

Since our launch, we’ve published over 140 articles in the field of Gene Expression and the paper with the most unique page views from Google Analytics is Promoter-Wide Hypermethylation of the Ribosomal RNA Gene Promoter in the Suicide Brain by Patrick O. McGowan et al.

We reached out to the corresponding authors on the paper, Gustavo Turecki and Moshe Szy, to find out more about why the group chose to publish their work in PLoS ONE, what their experience of publishing with us was like and where their research has headed subsequently.

Here’s what Moshe said about why the group to chose PLoS ONE to publish their research. “Our data was provocative and new, truly different from the common wisdom. We wanted a journal that will look at our data as it is and judge the quality of the data rather than be biased against our hypothesis. Unfortunately opinionated dogmas dominate much of the field and from what I read about PLoS ONE I felt that it would be different. In addition, we thought that an online free-to-read publication would provide the widest exposure of our results”.

As to their experiences of publishing with us, I am pleased to report that they were not disappointed. “The review process was tough and critical but honest and unbiased and the comments of the referees guided us as to how to revise the manuscript. We feel that the manuscript was truly strengthened by the comments of the referees”. Finally, on looking forwards from this piece of research, Moshe said “This paper was the first evidence for Epigenetic marks of suicide in the brain of humans and suggested that early childhood events might be behind this. Epigenetics could serve as an interface between the social environment and our genome and could explain the effects of early social exposure on our health and behavior. Seeing these differential methylation patterns in the brains of suicide victims is consistent with this hypothesis. We are interested in further exploring the possibility that epigenetic processes mediate between adverse social environments and the genome. We are studying live subjects and different human cohorts”.

Other top performing papers in the Gene Expression category include miRNA Profiling of Naïve, Effector and Memory CD8 T Cells in number two slot and then in slots three through five Identification of Novel High-Frequency DNA Methylation Changes in Breast Cancer; Identification of Key Processes Underlying Cancer Phenotypes Using Biologic Pathway Analysis; Meta-Analysis in Genome-Wide Association Datasets : Strategies and Application in Parkinson Disease.

The Gene Expression Community is already publishing in PLoS ONE and we welcome more submissions from them and researchers in every scientific field who want fast publication times and the widest reach for their research through open access.

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Gene Expression in PLoS ONE

from A Blog Around The Clock on Mon, 2008-07-07 20:13

As you probably know by now, we have monthly themes in PLoS ONE. This month, the topic is Gene Expression, where there are more than 140 articles already, mainly looking at genome-wide expression and epigenetics. Of course, we want more....

Rhapsody in Green

Rebecca Walton — Fri, 4 Jul 2008 08:25:40 -0700

If you have visited the PLoS ONE homepage this week, you may have noticed the rather quirky juxtaposition in the Recently Published block of a paper on the effect of a broccoli-rich diet on prostate gene expression with an article on the acoustic properties of classical and modern violins. Indeed, these two articles generated the most news coverage of the 63 papers published in PLoS ONE on July 2.

In the first of these, entitled, Broccoli Consumption Interacts with GSTM1 to Perturb Oncogenic Signalling Pathways in the Prostate, Richard Mithen and colleagues report the results of a study on changes in gene expression in the prostate gland of volunteers as they participated in a dietary intervention study, involving broccoli-rich or pea-rich diets. The authors are based in Norwich (just up the road from the UK office in Cambridge), and so there were quite a few articles in the UK press (as well as from further afield), ranging from the Norwich Evening News to the BBC News, as well as The Telegraph (Broccoli reduces risk of prostate cancer), The Guardian (Broccoli 'could help fight cancer'), Reuters (Study shows how broccoli fights cancer) and The Age (Broccoli 'reduces risk of prostate cancer'). Mithen was also interviewed about the study by BBC News 24.

The coverage of Berend Stoel’s article, A Comparison of Wood Density between Classical Cremonese and Modern Violins, was no less extensive. Stoel, a researcher at the Leiden University Medical Center, teamed up with an American luthier, Terry Borman, to try to determine why it is that certain classical violins, such as those made by Antonio Stradivari and Giuseppe Guarneri Del Gesu, have set the standards in terms of sound and acoustics, which modern luthiers often try to emulate. The researchers used computed tomography scans to compare five classical violins with eight modern violins. Although the median densities of the modern and the antique violins were similar, the density difference between wood grains of early and late growth was significantly smaller in the classical Cremonese violins compared with modern violins, and the authors suggest this may contribute to the superior sound production of classical Cremonese violins.

Some of the stories on the study have included: BBC News (Wood density key to violin sound), The Telegraph (Secret of Stradivarius violins' superiority uncovered), The Independent (Solved: the mystery of why Stradivarius violins are best), Nature (Acoustics: Fiddling the numbers) and Reuters (Wood density holds key to Stradivarius sweet sound). I am also hopeful that the question “what does a luthier make?” will come up now in the pub quiz some of the Cambridge-based PLoS staff often attend.

Sunny Jun and colleagues at Stanford may have found a way of predicting a woman's chances of becoming pregnant after IVF treatment by assessing an embryo’s quality, as well as recording the woman’s hormone levels; this is reported in an article entitled, Defining Human Embryo Phenotypes by Cohort-Specific Prognostic Factors. “We envision that dissection of human embryo phenotypes and their corresponding molecular correlates is not only a necessary step towards improving the treatment of clinical infertility,” said the corresponding author, Mylene Yao, “but will also contribute significantly to research efforts in the hESC field.” The article was featured in The Guardian (Fertility: Doctors find test to predict chances of IVF success), Time (Predicting In Vitro Success) and Reuters (New method may help predict IVF success: study), and on BBC Radio 4.

Several other papers also enjoyed some media coverage – a paper on the potential benefits of relaxation by Dusek and colleagues was picked up by Newsweek (Train Your Mind, Change Your DNA) and El Mundo (Los genes también 'se relajan'), while French researchers made the front page of Le Monde (En France, les hépatites B et C font entre 4 000 et 5 000 morts par an) and Gratwicke and colleagues were featured in Journal Watch (Extinction in pieces).

Jake Snaddon’s article on children’s perceptions of rainforest biodiversity was featured in Wired, even if the writer, Brandom Keim, described “the study as a well-meaning but hopelessly academic analysis” (not that this is a bad thing)! The Cambridge-based researchers had young children draw pictures of a rainforest, as part of a museum competition, and found that while the children were shown to have a sophisticated understanding of the biodiversity of the rainforest ecosystem, they tended to overemphasise the numbers of charismatic megafauna at the expense of (arguably) “less cute” annelids and social insects, which the authors felt may be a reflection of the number of articles in the news about the plight of mammals, reptiles and birds, as well as the possibility that the children thought they might stand a better chance of winning the competition if they drew more prettier animals.

The other 56 papers published this week are, of course, ready and waiting to be read, rated and discussed online on the PLoS ONE website.

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Going to San Francisco? Finding Flowers for Your Hair May Get Tougher

Rebecca Walton — Fri, 27 Jun 2008 08:42:44 -0700

Those who follow the advice of Scott McKenzie by wearing flowers in their hair when visiting the Bay Area may find it increasingly difficult to find native Californian flora over the coming years.

Scott Loarie and colleagues discovered that two-thirds of the state's endemic plants could suffer more than an 80 percent reduction in geographic range by the end of the century, thanks to the effects of global climate change. In their study, Climate Change and the Future of California's Endemic Flora, published in PLoS ONE on June 25^th, the researchers warn that because native species not found outside the state make up nearly half of all California's native plants, a changing climate will have a major impact on the state's unparalleled plant diversity. The article prompted an Associated Press story, which has been widely syndicated, along with the following news and blog coverage:

Los Angeles Times – Climate change threatens two-thirds of California's unique plants, study says (see also a beautiful slideshow of images of the flora that could be in danger)
San Francisco Chronicle – Grim look at state's plant life
Reuters – Climate change to create "plant refugees"
Science News – Move It or Lose It
The Great Beyond – Californian plants can’t take the heat

A second article on climate change was published in PLoS ONE this week (Climate Extremes Promote Fatal Co-Infections during Canine Distemper Epidemics in African Lions by first author Linda Munson and senior author Craig Packer). The researchers studied the effects of extreme weather conditions, worsened by global climate change, on the spread of infectious diseases. They found that the increased frequency of droughts and floods expected with global warming, can create conditions in which diseases that are tolerated one at a time may converge and cause mass die-offs of livestock or wildlife as the normal host-pathogen relationships are altered, causing a “perfect storm” of multiple infectious outbreaks that could trigger epidemics with catastrophic mortality. Some of the news coverage of the article includes:

Reuters – Floods and droughts make mild diseases deadly
National Geographic – Major Lion Die-Offs Linked to Climate Change
Discover Magazine – Lion Die-Off Shows How Climate Change Can Cause Epidemics

Finally, in an article entitled, Increased Avian Diversity Is Associated with Lower Incidence of Human West Nile Infection: Observation of the Dilution Effect, John Swaddle and colleagues found an interesting example of how biodiversity can reduce the disease incidence in humans, namely that areas that have a more diverse bird population show much lower incidences of West Nile virus infection in the human population. West Nile develops rapidly in bird populations, and then can be passed to humans or other animals through a vector mechanism, often a mosquito. The article was featured on the Discovery Channel (More Bird Species Means Fewer West Nile Cases) and the blog 10,000 Birds (Bird Biodiversity Good for Humans Too).

You can, of course, read, rate and discuss the other 51 papers published in PLoS ONE on June 25th by visiting the journal publication site.

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Avian Journal Club in PLoS ONE!

Bora Zivkovic — Wed, 25 Jun 2008 08:36:14 -0700

As part of the monthly focus on birds, there is a new Journal Club in PLoS ONE this week.

Dr.Elizabeth Adkins Regan from Cornell and her postdoc Dr Joanna Rutkowska from Jagiellonian University have already posted their first comments on the paper by Keith Sockman (here at UNC): Ovulation Order Mediates a Trade-Off between Pre-Hatching and Post-Hatching Viability in an Altricial Bird.

Please join in the discussion!

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