A Blog Around The Clock

There is lots of cool new stuff in PLoS Biology this week. Take a look:
Conspicuous Chameleons is a synopsis/summary of this article:
Selection for Social Signalling Drives the Evolution of Chameleon Colour Change:

The ability to change colour has evolved in numerous vertebrate and invertebrate groups, the most well-known of which are chameleons and cephalopods (octopuses and their relatives). There is great variation among species, however, in the apparent capacity for colour change, ranging from limited changes in brightness to dramatic changes in hue. What drives the evolution of this remarkable strategy? We addressed this question by using a combination of field-based behavioural trials in which we quantified colour change, models of colour perception, and our knowledge of phylogenetic relationships for 21 distinct lineages of southern African dwarf chameleons. We show that evolutionary changes in the capacity for colour change are consistently associated with the use of social signals that are highly conspicuous to the visual system of chameleons. Moreover, capacity for colour change is unrelated to variation in the environmental backgrounds that chameleons must match in order to be camouflaged. Overall, our results suggest that the evolution of the ability to exhibit striking changes in colour evolved as a strategy to facilitate social signalling and not, as popularly believed, camouflage.

There are types of pain that naked mole-rats do not feel – Selective Inflammatory Pain Insensitivity in the African Naked Mole-Rat (Heterocephalus glaber):

Chemicals such as capsaicin and acid are considered noxious because they cause irritation and pain when applied to the skin. Acid is, for example, a very noxious stimulus and can cause intense pain. Indeed, acid is both noxious and painful to all animals including amphibians and fish. Here we describe a member of the rodent family, the African naked mole-rat (Heterocephalus glaber), that is behaviorally completely oblivious to capsaicin and acid. Tissue injury and inflammation increase sensitivity to normally non painful stimuli, a phenomenon called hyperalgesia. Here we show that the naked mole-rat does not experience hyperalgesia to painful thermal stimuli after inflammation. To our knowledge, no other mammal has so far been described that is selectively insensitive to chemical pain or that lacks thermal hyperalgesia. Naked mole-rats live in very large subterranean social groups and are remarkably tolerant to low-oxygen and high-carbon dioxide conditions. We hypothesize that naked mole-rats are selectively pain insensitive partly because of selection pressure arising from the extremity of their normal habitat.

The Evolution of Quorum Sensing in Bacterial Biofilms:

Bacteria are increasingly recognized as highly interactive organisms with complex social lives, which are critical to their capacity to cause disease. In particular, many species inhabit dense, surface-bound communities, termed biofilms, within which they communicate and respond to local cell density through a process known as quorum sensing. Enormous effort has been devoted to understanding the genetics and biochemistry of biofilm formation and quorum sensing, but how and why they evolve remain virtually unexplored. Many bacteria use quorum sensing to regulate the secretion of sticky extracellular slime, an integral feature of biofilm life. Intriguingly, however, some pathogenic species turn on slime production at high cell density, whereas others turn it off. Using an individual-based model of biofilm growth, we investigated why different species use quorum sensing to control slime production in opposite ways. The secret underlying this variation appears to reside in the nature of infections. Turning slime on at high cell density can allow one strain to suffocate another when competition is intense, as occurs in long-lived chronic infections. Meanwhile, turning slime secretion off at high cell density can benefit a strain causing an acute infection by allowing rapid growth before departing the host.

Riders of a Modern-Day Ark:

Amphibians may not seem the hardiest of creatures, but they have roamed Earth for 360 million years–a span including at least two major Ice Ages and four warming, interglacial periods. Yet their ability to evolve in concert with an ever-changing environment may not be enough to survive a world now dominated by human activity. Over 1,800 amphibian species, one-third of all known species, are threatened with extinction, according to the Global Amphibian Assessment [1]. Countless other, yet-undescribed, species may never have their place on Earth documented. Of all amphibians–toads, salamanders, newts, and caecilians–the frog’s prevalence renders it at greatest risk.

EDGE Amphibians: World’s Weirdest Creatures Just Got Weirder:

A gigantic, ancient relative of the newt, a drawing-pin sized frog, a limbless, tentacled amphibian and a blind see-through salamander have all made it onto a list of the world’s weirdest and most endangered creatures.

Scientists Look At Those In Evolutionary Race Who Don’t Make It ‘Out Of The Gate’:

In the race of evolution, scientists until now have only looked at winners and losers. Now, they’ve come up with a way to look at the contenders who never made it out of the gate. It’s the organisms — in this case lizards — that die early in life, before scientists can even assess what they might bring to the reproduction game, and that have gone uncounted in the effort to quantify genetic fitness. This group has been dubbed the “invisible fraction.” Andrew McAdam, assistant professor of fisheries and wildlife and zoology at Michigan State University, has co-authored a paper in the Jan. 23 Proceedings of the Royal Society which brings that elusive fraction to light.

World’s Aging Population To Defuse War On Terrorism:

Changing demographic trends will impact the future of international relations, according to the latest issue of Public Policy & Aging Report (PP&AR). Several hotbed areas in the world that offer the motive and opportunity for political violence are due to stabilize by the year 2030.

How Much You’re Willing To Pay Depends On What You Were Just Doing:

Your shopping buddy turns to you and asks, “Which one of these would you get?” Or, you’re talking with your spouse about which candidate you’d like to vote for before switching on the nightly news. Turns out simply being asked to make a choice– especially if you’re in a hurry or have something on your mind — will make you like the next thing you see more, says a new study from the Journal of Consumer Research. The researchers found that asking people to choose among things primed them to think about positive attributes — and caused them to be in a positive frame of mind when evaluating the next item they saw.

Extinct Marsupial Lion Tops African Lion In Fight To Death:

Pound for pound, Australia’s extinct marsupial lion (Thylacoleo carnifex) would have made mince meat of today’s African lion (Panthera leo) had the two big hyper-carnivores ever squared off in a fight to the death, according to an Australian scientist.

Secret Of Scottish Sheep Evolution Discovered:

Researchers from the University of Sheffield, as part of an international team, have discovered the secret of why dark sheep on a remote Scottish Island are mysteriously declining, seemingly contradicting Darwin’s evolutionary theory. Dr Jacob Gratten and Dr Jon Slate, from the University’s Department of Animal and Plant Sciences, led the team, which found that the gene responsible for dark coat colour is linked to other genes that reduce an animal’s fitness.

Friday – time to take a look at the new articles in PLoS Computational Biology, Genetics and Pathogens – check them all out, but here are a couple of picks:
Exploration of Small RNAs:

There is substantial interest in noncoding RNAs (ncRNAs), which play an essential role in complex biological systems without encoding for proteins. Only a limited number of ncRNAs, such as ribosomal RNA (rRNA) and transfer RNA (tRNA), have previously been characterized in any depth. Recent studies revealed many novel ncRNAs, covering a wide range of sizes [1]. RNA molecules have several functions including catalytic activity and ability to act as a structural component. Of these functions, the ability to specify a nucleic acid sequence is superior compared to proteins. A common way in which ncRNA contributes to biological processes is through the ribonucleoprotein (RNP) complex, where its role is to guide recognition of nucleic acid target sequences relying upon sequence complementarity [2]. Small RNA molecules are widely utilized in this type of machinery, and are involved in important biological processes [3]. Exploration of novel small RNA species and their functions attracts substantial interest. The advent of recent technologies to profile cellular RNAs, such as high-throughput sequencing and microarray, coupled with computational analysis, has contributed to rapid progress in this field. Here, we review the recently discovered small RNA species and their pathways in a view of conservations and differences between higher eukaryotes. We also summarize recent exploration efforts of novel small RNAs based on devised technologies to provide a perspective for the future.

Why is Real-World Visual Object Recognition Hard?:

The ease with which we recognize visual objects belies the computational difficulty of this feat. At the core of this challenge is image variation–any given object can cast an infinite number of different images onto the retina, depending on the object’s position, size, orientation, pose, lighting, etc. Recent computational models have sought to match humans’ remarkable visual abilities, and, using large databases of “natural” images, have shown apparently impressive progress. Here we show that caution is warranted. In particular, we found that a very simple neuroscience “toy” model, capable only of extracting trivial regularities from a set of images, is able to outperform most state-of-the-art object recognition systems on a standard “natural” test of object recognition. At the same time, we found that this same toy model is easily defeated by a simple recognition test that we generated to better span the range of image variation observed in the real world. Together these results suggest that current “natural” tests are inadequate for judging success or driving forward progress. In addition to tempering claims of success in the machine vision literature, these results point the way forward and call for renewed focus on image variation as a central challenge in object recognition.

Getting Started in Text Mining:

Text mining is the use of automated methods for exploiting the enormous amount of knowledge available in the biomedical literature. There are at least as many motivations for doing text mining work as there are types of bioscientists. Model organism database curators have been heavy participants in the development of the field due to their need to process large numbers of publications in order to populate the many data fields for every gene in their species of interest. Bench scientists have built biomedical text mining applications to aid in the development of tools for interpreting the output of high-throughput assays and to improve searches of sequence databases (see [1] for a review). Bioscientists of every stripe have built applications to deal with the dual issues of the double-exponential growth in the scientific literature over the past few years and of the unique issues in searching PubMed/MEDLINE for genomics-related publications. A surprising phenomenon can be noted in the recent history of biomedical text mining: although several systems have been built and deployed in the past few years–Chilibot, Textpresso, and PreBIND (see Text S1 for these and most other citations), for example–the ones that are seeing high usage rates and are making productive contributions to the working lives of bioscientists have been built not by text mining specialists, but by bioscientists. We speculate on why this might be so below.

Seismic Images Show Dinosaur-killing Meteor Made Bigger Splash:

The most detailed three-dimensional seismic images yet of the Chicxulub crater, a mostly submerged and buried impact crater on the Mexico coast, may modify a theory explaining the extinction of 70 percent of life on Earth 65 million years ago.

Jacky Dragons Are Born When The Temperature Is Right For Their Sex:

An Iowa State University researcher spent four years in Australia studying reptiles. Dan Warner, a researcher in the ecology, evolution and organismal biology department, has been working with the jacky dragon, a lizard found in Australia, to discover if egg incubation temperature and sex affects the viability of the lizards.

Adaptive Functional Evolution Of Leptin In Cold-adaptive Pika Family:

Researchers at the Northwest Institute of Plateau Biology, Chinese Academy of Sciences have put forward the viewpoint for the first time that adaptive functional evolution may occur in the leptin protein of the pika (Ochotona) family, a typical cold-adaptive mammal. They speculated that the cold, rather than hypoxia, may be the primary environmental factor that drives the adaptive evolution of pika leptin.

Forests Could Benefit When Fall Color Comes Late:

Do those fall colors seem to show up later and later–if at all? Scientists say we can blame increasing amounts of carbon dioxide in the atmosphere for prolonging the growing season of the trees. And that may actually be good news for forestry industries.

Changing Fashions Govern Mating Success In Lark Buntings, Study Finds:

A study of how female lark buntings choose their mates, published in Science, adds a surprising new twist to the evolutionary theory of sexual selection. Researchers at the University of California, Santa Cruz, discovered that female lark buntings show strong preferences for certain traits in the males, but those preferences change from year to year.

There is a lot of new stuff published this week in PLoS Biology, PLoS Medicine, PLoS Neglected Tropical Diseases and PLoS ONE.
Molecular Studies in Treponema pallidum Evolution: Toward Clarity? is an Expert Commentary on last week’s (widely reported) study On the Origin of the Treponematoses: A Phylogenetic Approach (the paper that suggests that Columbus brought syphilis from the New World back to Europe).
Looking at the 33 new articles on PLoS ONE, here are a few titles I found intriguing:
Seasonal Changes in Mood and Behavior Are Linked to Metabolic Syndrome:

Obesity is a major public health problem worldwide. Metabolic syndrome is a risk factor to the cardiovascular diseases. It has been reported that disruptions of the circadian clockwork are associated with and may predispose to metabolic syndrome. 8028 individuals attended a nationwide health examination survey in Finland. Data were collected with a face-to-face interview at home and during an individual health status examination. The waist circumference, height, weight and blood pressure were measured and samples were taken for laboratory tests. Participants were assessed using the ATP-III criteria for metabolic syndrome and with the Seasonal Pattern Assessment Questionnaire for their seasonal changes in mood and behavior. Seasonal changes in weight in particular were a risk factor of metabolic syndrome, after controlling for a number of known risk and potential confounding factors. Metabolic syndrome is associated with high global scores on the seasonal changes in mood and behavior, and with those in weight in particular. Assessment of these changes may serve as a useful indicator of metabolic syndrome, because of easy assessment. Abnormalities in the circadian clockwork which links seasonal fluctuations to metabolic cycles may predispose to seasonal changes in weight and to metabolic syndrome.

Natural Selection and Adaptive Evolution of Leptin in the Ochotona Family Driven by the Cold Environmental Stress:

Environmental stress can accelerate the evolutionary rate of specific stress-response proteins and create new functions specialized for different environments, enhancing an organism’s fitness to stressful environments. Pikas (order Lagomorpha), endemic, non-hibernating mammals in the modern Holarctic Region, live in cold regions at either high altitudes or high latitudes and have a maximum distribution of species diversification confined to the Qinghai-Tibet Plateau. Variations in energy metabolism are remarkable for them living in cold environments. Leptin, an adipocyte-derived hormone, plays important roles in energy homeostasis. To examine the extent of leptin variations within the Ochotona family, we cloned the entire coding sequence of pika leptin from 6 species in two regions (Qinghai-Tibet Plateau and Inner Mongolia steppe in China) and the leptin sequences of plateau pikas (O. curzonia) from different altitudes on Qinghai-Tibet Plateau. We carried out both DNA and amino acid sequence analyses in molecular evolution and compared modeled spatial structures. Our results show that positive selection (PS) acts on pika leptin, while nine PS sites located within the functionally significant segment 85-119 of leptin and one unique motif appeared only in pika lineages-the ATP synthase α and β subunit signature site. To reveal the environmental factors affecting sequence evolution of pika leptin, relative rate test was performed in pikas from different altitudes. Stepwise multiple regression shows that temperature is significantly and negatively correlated with the rates of non-synonymous substitution (Ka) and amino acid substitution (Aa), whereas altitude does not significantly affect synonymous substitution (Ks), Ka and Aa. Our findings support the viewpoint that adaptive evolution may occur in pika leptin, which may play important roles in pikas’ ecological adaptation to extreme environmental stress. We speculate that cold, and probably not hypoxia, may be the primary environmental factor for driving adaptive evolution of pika leptin.

Mammalian Cells Change Volume during Mitosis:

Using single cell-imaging methods we have found that the volume of adherent cells grown in culture decreases as the cells rounds when it enters mitosis. A minimal volume is reached at metaphase. Rapid volume recovery initiates before abscission as cells make the transition from metaphase to cytokinesis. These volume changes are simultaneous with the rapid surface area decrease and recovery observed in mitotic cells.

A Technique for Characterizing the Development of Rhythms in Bird Song:

The developmental trajectory of nervous system dynamics shows hierarchical structure on time scales spanning ten orders of magnitude from milliseconds to years. Analyzing and characterizing this structure poses significant signal processing challenges. In the context of birdsong development, we have previously proposed that an effective way to do this is to use the dynamic spectrum or spectrogram, a classical signal processing tool, computed at multiple time scales in a nested fashion. Temporal structure on the millisecond timescale is normally captured using a short time Fourier analysis, and structure on the second timescale using song spectrograms. Here we use the dynamic spectrum on time series of song features to study the development of rhythm in juvenile zebra finch. The method is able to detect rhythmic structure in juvenile song in contrast to previous characterizations of such song as unstructured. We show that the method can be used to examine song development, the accuracy with which rhythm is imitated, and the variability of rhythms across different renditions of a song. We hope that this technique will provide a standard, automated method for measuring and characterizing song rhythm.

The Epidemics of Donations: Logistic Growth and Power-Laws:

This paper demonstrates that collective social dynamics resulting from individual donations can be well described by an epidemic model. It captures the herding behavior in donations as a non-local interaction between individual via a time-dependent mean field representing the mass media. Our study is based on the statistical analysis of a unique dataset obtained before and after the tsunami disaster of 2004. We find a power-law behavior for the distributions of donations with similar exponents for different countries. Even more remarkably, we show that these exponents are the same before and after the tsunami, which accounts for some kind of universal behavior in donations independent of the actual event. We further show that the time-dependent change of both the number and the total amount of donations after the tsunami follows a logistic growth equation. As a new element, a time-dependent scaling factor appears in this equation which accounts for the growing lack of public interest after the disaster. The results of the model are underpinned by the data analysis and thus also allow for a quantification of the media influence.

Deconstructing Insight: EEG Correlates of Insightful Problem Solving:

Cognitive insight phenomenon lies at the core of numerous discoveries. Behavioral research indicates four salient features of insightful problem solving: (i) mental impasse, followed by (ii) restructuring of the problem representation, which leads to (iii) a deeper understanding of the problem, and finally culminates in (iv) an “Aha!” feeling of suddenness and obviousness of the solution. However, until now no efforts have been made to investigate the neural mechanisms of these constituent features of insight in a unified framework. In an electroencephalographic study using verbal remote associate problems, we identified neural correlates of these four features of insightful problem solving. Hints were provided for unsolved problems or after mental impasse. Subjective ratings of the restructuring process and the feeling of suddenness were obtained on trial-by-trial basis. A negative correlation was found between these two ratings indicating that sudden insightful solutions, where restructuring is a key feature, involve automatic, subconscious recombination of information. Electroencephalogram signals were analyzed in the space×time×frequency domain with a nonparametric cluster randomization test. First, we found strong gamma band responses at parieto-occipital regions which we interpreted as (i) an adjustment of selective attention (leading to a mental impasse or to a correct solution depending on the gamma band power level) and (ii) encoding and retrieval processes for the emergence of spontaneous new solutions. Secondly, we observed an increased upper alpha band response in right temporal regions (suggesting active suppression of weakly activated solution relevant information) for initially unsuccessful trials that after hint presentation led to a correct solution. Finally, for trials with high restructuring, decreased alpha power (suggesting greater cortical excitation) was observed in right prefrontal area. Our results provide a first account of cognitive insight by dissociating its constituent components and potential neural correlates.

The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples:

Viruses are the most abundant biological entities on our planet. Interactions between viruses and their hosts impact several important biological processes in the world’s oceans such as horizontal gene transfer, microbial diversity and biogeochemical cycling. Interrogation of microbial metagenomic sequence data collected as part of the Sorcerer II Global Ocean Expedition (GOS) revealed a high abundance of viral sequences, representing approximately 3% of the total predicted proteins. Cluster analyses of the viral sequences revealed hundreds to thousands of viral genes encoding various metabolic and cellular functions. Quantitative analyses of viral genes of host origin performed on the viral fraction of aquatic samples confirmed the viral nature of these sequences and suggested that significant portions of aquatic viral communities behave as reservoirs of such genetic material. Distributional and phylogenetic analyses of these host-derived viral sequences also suggested that viral acquisition of environmentally relevant genes of host origin is a more abundant and widespread phenomenon than previously appreciated. The predominant viral sequences identified within microbial fractions originated from tailed bacteriophages and exhibited varying global distributions according to viral family. Recruitment of GOS viral sequence fragments against 27 complete aquatic viral genomes revealed that only one reference bacteriophage genome was highly abundant and was closely related, but not identical, to the cyanomyovirus P-SSM4. The co-distribution across all sampling sites of P-SSM4-like sequences with the dominant ecotype of its host, Prochlorococcus supports the classification of the viral sequences as P-SSM4-like and suggests that this virus may influence the abundance, distribution and diversity of one of the most dominant components of picophytoplankton in oligotrophic oceans. In summary, the abundance and broad geographical distribution of viral sequences within microbial fractions, the prevalence of genes among viral sequences that encode microbial physiological function and their distinct phylogenetic distribution lend strong support to the notion that viral-mediated gene acquisition is a common and ongoing mechanism for generating microbial diversity in the marine environment.

What Happens in Between? Human Oscillatory Brain Activity Related to Crossmodal Spatial Cueing:

Previous studies investigated the effects of crossmodal spatial attention by comparing the responses to validly versus invalidly cued target stimuli. Dynamics of cortical rhythms in the time interval between cue and target might contribute to cue effects on performance. Here, we studied the influence of spatial attention on ongoing oscillatory brain activity in the interval between cue and target onset. In a first experiment, subjects underwent periods of tactile stimulation (cue) followed by visual stimulation (target) in a spatial cueing task as well as tactile stimulation as a control. In a second experiment, cue validity was modified to be 50%, 75%, or else 25%, to separate effects of exogenous shifts of attention caused by tactile stimuli from that of endogenous shifts. Tactile stimuli produced: 1) a stronger lateralization of the sensorimotor beta-rhythm rebound (15-22 Hz) after tactile stimuli serving as cues versus not serving as cues; 2) a suppression of the occipital alpha-rhythm (7-13 Hz) appearing only in the cueing task (this suppression was stronger contralateral to the endogenously attended side and was predictive of behavioral success); 3) an increase of prefrontal gamma-activity (25-35 Hz) specifically in the cueing task. We measured cue-related modulations of cortical rhythms which may accompany crossmodal spatial attention, expectation or decision, and therefore contribute to cue validity effects. The clearly lateralized alpha suppression after tactile cues in our data indicates its dependence on endogenous rather than exogenous shifts of visuo-spatial attention following a cue independent of its modality.