Category Archives: Uncategorized

Good night. Tomorrow is another week….
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It’s still weekend, right?
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Teaching tomorrow, The Monti in the evening, a busy weekend, so read these until Monday:
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Busy (but good) day today, more tomorrow, some links to keep you busy till then:
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A few for now, more posts by me soon, I promise:
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Shana tova!!!
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Just a few to get you going for the day…
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Linky goodness for today:
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Something to keep you busy today:
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An incredibly productive Labor Day:
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There should be something for everyone:
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Long weekend in the USA, thus plenty of time to read:
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Intently watching #solo10 hashtag on Twitter….join me, or read these links instead:
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Lotsa kewl stuff today:
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Lots of good stuff today!!!
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To get your day started:
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Lots of great stuff today – here is a sampling:
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I am back, after a 10-hr drive from NJ to NC, and preparing Grand Round for tomorrow morning. In the meantime, read these:

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What’s Your STEM? and What do science bloggers blog about? My study of the Wikio Top 100

Why was a bear following an anteater through Peru’s mountains?

Goat breath causes aphids to drop to the ground

Does it matter to your P.I. what you did this weekend?

Kangaroo testicle? Chefs in Serbia say, ‘Yes!’ (Related: Offal is Good)

Obama Signs Sweeping Student Loan Reform Bill Into Law

Still far from home, but you can read these in the meantime:
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While I am gone, you can read these:
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Here, while I’m gone to a wedding, a few links for you:
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Wealth of great stuff today!

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It is nice to know that this new blog is already getting some traffic from searches. Some are good, some are…interesting. And some are…wow! Here is a sampling of some of the recent ones….
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From here

Sorry for missing in action. Lots of new articles in various PLoS journals yesterday and today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

A Sinister Bias for Calling Fouls in Soccer:

Distinguishing between a fair and unfair tackle in soccer can be difficult. For referees, choosing to call a foul often requires a decision despite some level of ambiguity. We were interested in whether a well documented perceptual-motor bias associated with reading direction influenced foul judgments. Prior studies have shown that readers of left-to-right languages tend to think of prototypical events as unfolding concordantly, from left-to-right in space. It follows that events moving from right-to-left should be perceived as atypical and relatively debased. In an experiment using a go/no-go task and photographs taken from real games, participants made more foul calls for pictures depicting left-moving events compared to pictures depicting right-moving events. These data suggest that two referees watching the same play from distinct vantage points may be differentially predisposed to call a foul.

Intergenomic Arms Races: Detection of a Nuclear Rescue Gene of Male-Killing in a Ladybird:

Normally, in sexually reproducing organisms, the sex ratio (ratio of males to females) is 1:1. However, examples are known where this is not the case and there are more females than males in a population. Extreme bias in sex ratio can lead to females failing to find a mate. We studied Cheilomenes sexmaculata, a ladybird species that has females that produce more female than male offspring. In aphid-eating ladybirds, this phenomenon has been widely reported and is known to be due to the presence of bacteria that live inside the mother and are passed via her eggs to her offspring. In eggs destined to become male, the bacteria kill the embryo by some unknown mechanism. This is known as male-killing. Female offspring develop normally. Evolutionary theory predicts that in such systems, the genome of the host can fight back if a variant arises that stops the bacteria killing male offspring. In C. sexmaculata we found females that carried the male-killer but the sex ratio of their offspring depended on the male that they mated with. We carried out breeding tests to show that some ladybirds had a version of a gene that rescued the male offspring from the pathological effects of the male-killer.

Herbivory on Temperate Rainforest Seedlings in Sun and Shade: Resistance, Tolerance and Habitat Distribution:

Differential herbivory and/or differential plant resistance or tolerance in sun and shade environments may influence plant distribution along the light gradient. Embothrium coccineum is one of the few light-demanding tree species in the temperate rainforest of southern South America, and seedlings are frequently attacked by insects and snails. Herbivory may contribute to the exclusion of E. coccineum from the shade if 1) herbivory pressure is greater in the shade, which in turn can result from shade plants being less resistant or from habitat preferences of herbivores, and/or 2) consequences of damage are more detrimental in the shade, i.e., shade plants are less tolerant. We tested this in a field study with naturally established seedlings in treefall gaps (sun) and forest understory (shade) in a temperate rainforest of southern Chile. Seedlings growing in the sun sustained nearly 40% more herbivore damage and displayed half of the specific leaf area than those growing in the shade. A palatability test showed that a generalist snail consumed ten times more leaf area when fed on shade leaves compared to sun leaves, i.e., plant resistance was greater in sun-grown seedlings. Herbivore abundance (total biomass) was two-fold greater in treefall gaps compared to the forest understory. Undamaged seedlings survived better and showed a slightly higher growth rate in the sun. Whereas simulated herbivory in the shade decreased seedling survival and growth by 34% and 19%, respectively, damaged and undamaged seedlings showed similar survival and growth in the sun. Leaf tissue lost to herbivores in the shade appears to be too expensive to replace under the limiting light conditions of forest understory. Following evaluations of herbivore abundance and plant resistance and tolerance in contrasting light environments, we have shown how herbivory on a light-demanding tree species may contribute to its exclusion from shade sites. Thus, in the shaded forest understory, where the seedlings of some tree species are close to their physiological tolerance limit, herbivory could play an important role in plant establishment.

Can Bacteria Evolve Resistance to Quorum Sensing Disruption?:

Traditional treatment of bacterial infections relies heavily on the use of antibacterial compounds that either kill bacteria (bactericidal) or inhibit their growth (bacteriostatic). Typically, the targets for the main conventional antibiotics are essential cellular processes such as bacterial cell wall biosynthesis, bacterial protein synthesis, and bacterial DNA replication and repair. However, resistance to these drugs arises and spreads very rapidly, even to such an extent that bacteria have been identified that are simultaneously resistant to all available antibiotics [1]. The increasing occurrence of resistant bacteria gradually renders antibiotics ineffective in treating infections and has enormous human and economic consequences worldwide. As a result, the identification of novel drug targets and the development of novel therapeutics constitute an important area of current scientific research. An alternative to killing or inhibiting growth of pathogenic bacteria is the specific attenuation of bacterial virulence, which can be attained by targeting key regulatory systems that mediate the expression of virulence factors. One of the target regulatory systems is quorum sensing (QS), or bacterial cell-to-cell communication. QS is a mechanism of gene regulation in which bacteria coordinate the expression of certain genes in response to the presence or absence of small signal molecules (Figure 1).

Making the Invisible Visible: Verbal but Not Visual Cues Enhance Visual Detection:

Can hearing a word change what one sees? Although visual sensitivity is known to be enhanced by attending to the location of the target, perceptual enhancements of following cues to the identity of an object have been difficult to find. Here, we show that perceptual sensitivity is enhanced by verbal, but not visual cues. Participants completed an object detection task in which they made an object-presence or -absence decision to briefly-presented letters. Hearing the letter name prior to the detection task increased perceptual sensitivity (d′). A visual cue in the form of a preview of the to-be-detected letter did not. Follow-up experiments found that the auditory cuing effect was specific to validly cued stimuli. The magnitude of the cuing effect positively correlated with an individual measure of vividness of mental imagery; introducing uncertainty into the position of the stimulus did not reduce the magnitude of the cuing effect, but eliminated the correlation with mental imagery. Hearing a word made otherwise invisible objects visible. Interestingly, seeing a preview of the target stimulus did not similarly enhance detection of the target. These results are compatible with an account in which auditory verbal labels modulate lower-level visual processing. The findings show that a verbal cue in the form of hearing a word can influence even the most elementary visual processing and inform our understanding of how language affects perception.

Promoter Complexity and Tissue-Specific Expression of Stress Response Components in Mytilus galloprovincialis, a Sessile Marine Invertebrate Species:

Adaptation of sessile animals, such as molluscs, to stress is achieved by a number of molecular mechanisms, few of which are clearly understood. Insights from this research can provide clues about stress tolerance both for sessile and mobile organisms. The Mediterranean mussel, of the genus Mytilus, is a model organism for the study of stress at the molecular level, with sufficient gene structure and function data available. We have thus investigated a key stress response gene, Hsp90, and in particular its upstream region, using a combination of sequence and expression analysis approaches. We demonstrate that this region, responsible for the regulation of heat shock-associated gene expression, exhibits an unparalleled structural and functional complexity compared to other model organisms, as well as subtle gene expression patterns across multiple tissues. These results form the basis upon which the heat shock response can be used as a molecular biosensor for environmental monitoring in the future.

Vitamin C: Intravenous Use by Complementary and Alternative Medicine Practitioners and Adverse Effects:

Anecdotal information and case reports suggest that intravenously administered vitamin C is used by Complementary and Alternate Medicine (CAM) practitioners. The scale of such use in the U.S. and associated side effects are unknown. We surveyed attendees at annual CAM Conferences in 2006 and 2008, and determined sales of intravenous vitamin C by major U.S. manufacturers/distributors. We also queried practitioners for side effects, compiled published cases, and analyzed FDA’s Adverse Events Database. Of 199 survey respondents (out of 550), 172 practitioners administered IV vitamin C to 11,233 patients in 2006 and 8876 patients in 2008. Average dose was 28 grams every 4 days, with 22 total treatments per patient. Estimated yearly doses used (as 25g/50ml vials) were 318,539 in 2006 and 354,647 in 2008. Manufacturers’ yearly sales were 750,000 and 855,000 vials, respectively. Common reasons for treatment included infection, cancer, and fatigue. Of 9,328 patients for whom data is available, 101 had side effects, mostly minor, including lethargy/fatigue in 59 patients, change in mental status in 21 patients and vein irritation/phlebitis in 6 patients. Publications documented serious adverse events, including 2 deaths in patients known to be at risk for IV vitamin C. Due to confounding causes, the FDA Adverse Events Database was uninformative. Total numbers of patients treated in the US with high dose vitamin C cannot be accurately estimated from this study. High dose IV vitamin C is in unexpectedly wide use by CAM practitioners. Other than the known complications of IV vitamin C in those with renal impairment or glucose 6 phosphate dehydrogenase deficiency, high dose intravenous vitamin C appears to be remarkably safe. Physicians should inquire about IV vitamin C use in patients with cancer, chronic, untreatable, or intractable conditions and be observant of unexpected harm, drug interactions, or benefit.

A Threshold Equation for Action Potential Initiation:

Neurons communicate primarily with stereotypical electrical impulses, action potentials, which are fired when a threshold level of excitation is reached. This threshold varies between cells and over time as a function of previous stimulations, which has major functional implications on the integrative properties of neurons. Ionic channels are thought to play a central role in this modulation but the precise relationship between their properties and the threshold is unclear. We examined this relationship in biophysical models and derived a formula which quantifies the contribution of various mechanisms. The originality of our approach is that it provides an instantaneous time-varying value for the threshold, which applies to the highly fluctuating regimes characterizing neurons in vivo. In particular, two known ionic mechanisms were found to make the threshold adapt to the membrane potential, thus providing the cell with a form of gain control.

Uncertainty Compensation in Human Attention: Evidence from Response Times and Fixation Durations:

Uncertainty and predictability have remained at the center of the study of human attention. Yet, studies have only examined whether response times (RT) or fixations were longer or shorter under levels of stimulus uncertainty. To date, no study has examined patterns of stimuli and responses through a unifying framework of uncertainty. We asked 29 college students to generate repeated responses to a continuous series of visual stimuli presented on a computer monitor. Subjects produced these responses by pressing on a keypad as soon a target was detected (regardless of position) while the durations of their visual fixations were recorded. We manipulated the level of stimulus uncertainty in space and time by changing the number of potential stimulus locations and time intervals between stimulus presentations. To allow the analyses to be conducted using uncertainty as common description of stimulus and response we calculated the entropy of the RT and fixation durations. We tested the hypothesis of uncertainty compensation across space and time by fitting the RT and fixation duration entropy values to a quadratic surface. The quadratic surface accounted for 80% of the variance in the entropy values of both RT and fixation durations. RT entropy increased as a function of spatial and temporal uncertainty of the stimulus, alongside a symmetric, compensatory decrease in the entropy of fixation durations as the level of spatial and temporal uncertainty of the stimuli was increased. Our results demonstrate that greater uncertainty in the stimulus leads to greater uncertainty in the response, and that the effects of spatial and temporal uncertainties are compensatory. We also observed compensatory relationship across the entropies of fixation duration and RT, suggesting that a more predictable visual search strategy leads to more uncertain response patterns and vice versa.

A Comprehensive Phylogenetic Analysis of the Scleractinia (Cnidaria, Anthozoa) Based on Mitochondrial CO1 Sequence Data:

Classical morphological taxonomy places the approximately 1400 recognized species of Scleractinia (hard corals) into 27 families, but many aspects of coral evolution remain unclear despite the application of molecular phylogenetic methods. In part, this may be a consequence of such studies focusing on the reef-building (shallow water and zooxanthellate) Scleractinia, and largely ignoring the large number of deep-sea species. To better understand broad patterns of coral evolution, we generated molecular data for a broad and representative range of deep sea scleractinians collected off New Caledonia and Australia during the last decade, and conducted the most comprehensive molecular phylogenetic analysis to date of the order Scleractinia. Partial (595 bp) sequences of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene were determined for 65 deep-sea (azooxanthellate) scleractinians and 11 shallow-water species. These new data were aligned with 158 published sequences, generating a 234 taxon dataset representing 25 of the 27 currently recognized scleractinian families. There was a striking discrepancy between the taxonomic validity of coral families consisting predominantly of deep-sea or shallow-water species. Most families composed predominantly of deep-sea azooxanthellate species were monophyletic in both maximum likelihood and Bayesian analyses but, by contrast (and consistent with previous studies), most families composed predominantly of shallow-water zooxanthellate taxa were polyphyletic, although Acroporidae, Poritidae, Pocilloporidae, and Fungiidae were exceptions to this general pattern. One factor contributing to this inconsistency may be the greater environmental stability of deep-sea environments, effectively removing taxonomic “noise” contributed by phenotypic plasticity. Our phylogenetic analyses imply that the most basal extant scleractinians are azooxanthellate solitary corals from deep-water, their divergence predating that of the robust and complex corals. Deep-sea corals are likely to be critical to understanding anthozoan evolution and the origins of the Scleractinia.

A man who has been in danger, When he comes out of it forgets his fears, And sometimes he forgets his promises.
– Euripides

I am collecting all the blog and media coverage on this wiki page, but redundancy is always a good idea in the digital realm, so the links are also now posted here, under the fold:
Update: the wiki page has reached its limit of number of links per page, so I am only updating this post from now on, adding freshest posts I can find on top. Please let me know if I missed yours.
Also, read the interviews with ScienceOnline2010 participants

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Not much to say myself, I just find the diversity of opinions in posts and comments fascinating:
Dr.Isis: Careful, Girls! That’s Too Much Power!
Arikia: Gendered Color Dichotomies-R-Us
PZ: The powerlessness of pink
Cori Kesler: My Droid is Pink
Mareserinitatis: Pink
Chad: Does Pinkification Fool Anybody?

Deadline is December 1st at midnight EST!
That is roughly 37 hours to go.
The submissions for OpenLab 2009 to date are under the fold. On December 2nd, I’ll put them all above the fold for all to see all the submissions. And then SciCurious and a large gang of judges will start sorting them all out and judging them until only 50 essays, one poem and one cartoon remain.
Please use the submission form to add more of your and other people’s posts (remember that we are looking for original poems, art, cartoons and comics, as well as essays). Realize that nobody knows your archives as well as you do – there is nothing wrong about submitting your own (about half of the entries, each year, are submitted by authors, and that is just fine).
Make sure that the submitted posts are possible (and relatively easy) to convert into print. Posts that rely too much on video, audio, color photographs, copyrighted images, or multitudes of links just won’t do.
Also check first if a post is already on the list. Submitting duplicates makes our job more difficult.
You can buy the 2006, 2007 and 2008 editions at Lulu.com.
The 2009 book should be published in time for ScienceOnline2010 if possible (but we will not undermine quality for the sake of speed, so the date is approximate).

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Here are the submissions for OpenLab 2009 to date. As we have surpassed 470 entries, all of them, as well as the “submit” buttons and codes and the bookmarklet, are under the fold. You can buy the 2006, 2007 and 2008 editions at Lulu.com. Please use the submission form to add more of your and other people’s posts (remember that we are looking for original poems, art, cartoons and comics, as well as essays):

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Read about it on TechCrunch, FriendFeed, FriendFeed blog and Facebook.

Carnival of Evolution #13 is up on FYI: Science!
Festival of the Trees #37 is up on TGAW
Four Stone Hearth #70 is up on Afarensis
114th Meeting of the Skeptics’ Circle is up on Homologous Legs
Grand Rounds Vol. 5 No. 41 are up at Edwin Leap
Carnival of the Green #186 is up on Conserve Plastic Bags
Friday Ark #249 is up on Modulator

Trying to see if uploading audio works – feel free to ignore:

VN520001.WMA –

In any case, try over here.

…in embedding FriendFeed conversations in a blog post:

Here are some titles, from all seven PLoS journals, that caught my attention this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are 23 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the day – you go and look for your own favourites:
The Emergence of Predators in Early Life: There was No Garden of Eden:

Eukaryote cells are suggested to arise somewhere between 0.85~2.7 billion years ago. However, in the present world of unicellular organisms, cells that derive their food and metabolic energy from larger cells engulfing smaller cells (phagocytosis) are almost exclusively eukaryotic. Combining these propositions, that eukaryotes were the first phagocytotic predators and that they arose only 0.85~2.7 billion years ago, leads to an unexpected prediction of a long period (~1-3 billion years) with no phagocytotes – a veritable Garden of Eden. We test whether such a long period is reasonable by simulating a population of very simple unicellular organisms – given only basic physical, biological and ecological principles. Under a wide range of initial conditions, cellular specialization occurs early in evolution; we find a range of cell types from small specialized primary producers to larger opportunistic or specialized predators. Both strategies, specialized smaller cells and phagocytotic larger cells are apparently fundamental biological strategies that are expected to arise early in cellular evolution. Such early predators could have been ‘prokaryotes’, but if the earliest cells on the eukaryote lineage were predators then this explains most of their characteristic features.

Effects of Global Warming on Ancient Mammalian Communities and Their Environments:

Current global warming affects the composition and dynamics of mammalian communities and can increase extinction risk; however, long-term effects of warming on mammals are less understood. Dietary reconstructions inferred from stable isotopes of fossil herbivorous mammalian tooth enamel document environmental and climatic changes in ancient ecosystems, including C3/C4 transitions and relative seasonality. Here, we use stable carbon and oxygen isotopes preserved in fossil teeth to document the magnitude of mammalian dietary shifts and ancient floral change during geologically documented glacial and interglacial periods during the Pliocene (~1.9 million years ago) and Pleistocene (~1.3 million years ago) in Florida. Stable isotope data demonstrate increased aridity, increased C4 grass consumption, inter-faunal dietary partitioning, increased isotopic niche breadth of mixed feeders, niche partitioning of phylogenetically similar taxa, and differences in relative seasonality with warming. Our data show that global warming resulted in dramatic vegetation and dietary changes even at lower latitudes (~28°N). Our results also question the use of models that predict the long term decline and extinction of species based on the assumption that niches are conserved over time. These findings have immediate relevance to clarifying possible biotic responses to current global warming in modern ecosystems.

Coping with Commitment: Projected Thermal Stress on Coral Reefs under Different Future Scenarios:

Periods of anomalously warm ocean temperatures can lead to mass coral bleaching. Past studies have concluded that anthropogenic climate change may rapidly increase the frequency of these thermal stress events, leading to declines in coral cover, shifts in the composition of corals and other reef-dwelling organisms, and stress on the human populations who depend on coral reef ecosystems for food, income and shoreline protection. The ability of greenhouse gas mitigation to alter the near-term forecast for coral reefs is limited by the time lag between greenhouse gas emissions and the physical climate response. This study uses observed sea surface temperatures and the results of global climate model forced with five different future emissions scenarios to evaluate the “committed warming” for coral reefs worldwide. The results show that the physical warming commitment from current accumulation of greenhouse gases in the atmosphere could cause over half of the world’s coral reefs to experience harmfully frequent (p≥0.2 year−1) thermal stress by 2080. An additional “societal” warming commitment, caused by the time required to shift from a business-as-usual emissions trajectory to a 550 ppm CO2 stabilization trajectory, may cause over 80% of the world’s coral reefs to experience harmfully frequent events by 2030. Thermal adaptation of 1.5°C would delay the thermal stress forecast by 50-80 years. The results suggest that adaptation – via biological mechanisms, coral community shifts and/or management interventions – could provide time to change the trajectory of greenhouse gas emissions and possibly avoid the recurrence of harmfully frequent events at the majority (97%) of the world’s coral reefs this century. Without any thermal adaptation, atmospheric CO2 concentrations may need to be stabilized below current levels to avoid the degradation of coral reef ecosystems from frequent thermal stress events.

The Alliance Hypothesis for Human Friendship:

Exploration of the cognitive systems underlying human friendship will be advanced by identifying the evolved functions these systems perform. Here we propose that human friendship is caused, in part, by cognitive mechanisms designed to assemble support groups for potential conflicts. We use game theory to identify computations about friends that can increase performance in multi-agent conflicts. This analysis suggests that people would benefit from: 1) ranking friends, 2) hiding friend-ranking, and 3) ranking friends according to their own position in partners’ rankings. These possible tactics motivate the hypotheses that people possess egocentric and allocentric representations of the social world, that people are motivated to conceal this information, and that egocentric friend-ranking is determined by allocentric representations of partners’ friend-rankings (more than others’ traits). We report results from three studies that confirm predictions derived from the alliance hypothesis. Our main empirical finding, replicated in three studies, was that people’s rankings of their ten closest friends were predicted by their own perceived rank among their partners’ other friends. This relationship remained strong after controlling for a variety of factors such as perceived similarity, familiarity, and benefits. Our results suggest that the alliance hypothesis merits further attention as a candidate explanation for human friendship.

Trophic Garnishes: Cat-Rat Interactions in an Urban Environment:

Community interactions can produce complex dynamics with counterintuitive responses. Synanthropic community members are of increasing practical interest for their effects on biodiversity and public health. Most studies incorporating introduced species have been performed on islands where they may pose a risk to the native fauna. Few have examined their interactions in urban environments where they represent the majority of species. We characterized house cat (Felis catus) predation on wild Norway rats (Rattus norvegicus), and its population effects in an urban area as a model system. Three aspects of predation likely to influence population dynamics were examined; the stratum of the prey population killed by predators, the intensity of the predation, and the size of the predator population. Predation pressure was estimated from the sizes of the rat and cat populations, and the characteristics of rats killed in 20 alleys. Short and long term responses of rat population to perturbations were examined by removal trapping. Perturbations removed an average of 56% of the rats/alley but had no negative long-term impact on the size of the rat population (49.6±12.5 rats/alley and 123.8±42.2 rats/alley over two years). The sizes of the cat population during two years (3.5 animals/alley and 2.7 animals/alley) also were unaffected by rat population perturbations. Predation by cats occurred in 9/20 alleys. Predated rats were predominantly juveniles and significantly smaller (144.6 g±17.8 g) than the trapped rats (385.0 g±135.6 g). Cats rarely preyed on the larger, older portion of the rat population. The rat population appears resilient to perturbation from even substantial population reduction using targeted removal. In this area there is a relatively low population density of cats and they only occasionally prey on the rat population. This occasional predation primarily removes the juvenile proportion of the rat population. The top predator in this urban ecosystem appears to have little impact on the size of the prey population, and similarly, reduction in rat populations doesn’t impact the size of the cat population. However, the selected targeting of small rats may locally influence the size structure of the population which may have consequences for patterns of pathogen transmission.

Explaining the Evolution of Warning Coloration: Secreted Secondary Defence Chemicals May Facilitate the Evolution of Visual Aposematic Signals:

Several pathways have been postulated to explain the evolution of warning coloration, which is a perplexing phenomenon. Many of these attempt to circumvent the problem of naïve predators by inferring kin selection or neophobia. Through a stochastic model, we show that a secreted secondary defence chemical can provide selective pressure, on the individual level, towards developing warning coloration. Our fundamental assumption is that increased conspicuousness will result in longer assessment periods and divergence from the predators’ searching image, thus reducing the probability of a predator making mistakes. We conclude that strong olfactory signaling by means of chemical secretions can lead to the evolution of warning coloration.

Paleo-Immunology: Evidence Consistent with Insertion of a Primordial Herpes Virus-Like Element in the Origins of Acquired Immunity:

The RAG encoded proteins, RAG-1 and RAG-2 regulate site-specific recombination events in somatic immune B- and T-lymphocytes to generate the acquired immune repertoire. Catalytic activities of the RAG proteins are related to the recombinase functions of a pre-existing mobile DNA element in the DDE recombinase/RNAse H family, sometimes termed the “RAG transposon”. Novel to this work is the suggestion that the DDE recombinase responsible for the origins of acquired immunity was encoded by a primordial herpes virus, rather than a “RAG transposon.” A subsequent “arms race” between immunity to herpes infection and the immune system obscured primary amino acid similarities between herpes and immune system proteins but preserved regulatory, structural and functional similarities between the respective recombinase proteins. In support of this hypothesis, evidence is reviewed from previous published data that a modern herpes virus protein family with properties of a viral recombinase is co-regulated with both RAG-1 and RAG-2 by closely linked cis-acting co-regulatory sequences. Structural and functional similarity is also reviewed between the putative herpes recombinase and both DDE site of the RAG-1 protein and another DDE/RNAse H family nuclease, the Argonaute protein component of RISC (RNA induced silencing complex). A “co-regulatory” model of the origins of V(D)J recombination and the acquired immune system can account for the observed linked genomic structure of RAG-1 and RAG-2 in non-vertebrate organisms such as the sea urchin that lack an acquired immune system and V(D)J recombination. Initially the regulated expression of a viral recombinase in immune cells may have been positively selected by its ability to stimulate innate immunity to herpes virus infection rather than V(D)J recombination Unlike the “RAG-transposon” hypothesis, the proposed model can be readily tested by comparative functional analysis of herpes virus replication and V(D)J recombination.

Virtual Partner Interaction (VPI): Exploring Novel Behaviors via Coordination Dynamics:

Inspired by the dynamic clamp of cellular neuroscience, this paper introduces VPI–Virtual Partner Interaction–a coupled dynamical system for studying real time interaction between a human and a machine. In this proof of concept study, human subjects coordinate hand movements with a virtual partner, an avatar of a hand whose movements are driven by a computerized version of the Haken-Kelso-Bunz (HKB) equations that have been shown to govern basic forms of human coordination. As a surrogate system for human social coordination, VPI allows one to examine regions of the parameter space not typically explored during live interactions. A number of novel behaviors never previously observed are uncovered and accounted for. Having its basis in an empirically derived theory of human coordination, VPI offers a principled approach to human-machine interaction and opens up new ways to understand how humans interact with human-like machines including identification of underlying neural mechanisms.

Usually on Thursday nights I take a look at all seven PLoS journals to see what strikes my fancy. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

Continue reading →

There are 23 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Does Sleep Really Influence Face Recognition Memory?:

Mounting evidence implicates sleep in the consolidation of various kinds of memories. We investigated the effect of sleep on memory for face identity, a declarative form of memory that is indispensable for nearly all social interaction. In the acquisition phase, observers viewed faces that they were required to remember over a variable retention period (0-36 hours). In the test phase, observers viewed intermixed old and new faces and judged seeing each before. Participants were classified according to acquisition and test times into seven groups. Memory strength (d′) and response bias (c) were evaluated. Substantial time spent awake (12 hours or more) during the retention period impaired face recognition memory evaluated at test, whereas sleep per se during the retention period did little to enhance the memory. Wakefulness during retention also led to a tightening of the decision criterion. Our findings suggest that sleep passively and transiently shelters face recognition memory from waking interference (exposure) but does not actively aid in its long-term consolidation.

Diurnally Entrained Anticipatory Behavior in Archaea:

By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. Significantly, the diurnally entrained transcription was observed under constant darkness after removal of the LD stimulus (free-running rhythms). The memory of diurnal entrainment was also associated with the synchronization of oxic and anoxic physiologies to the LD cycle. Our results suggest that under nutrient limited conditions halophilic archaea take advantage of the causal influence of sunlight (via temperature) on O2 diffusivity in a closed hypersaline environment to streamline their physiology and operate oxically during nighttime and anoxically during daytime.

Hippocampal Lesions Impair Rapid Learning of a Continuous Spatial Alternation Task:

The hippocampus is essential for the formation of memories for events, but the specific features of hippocampal neural activity that support memory formation are not yet understood. The ideal experiment to explore this issue would be to monitor changes in hippocampal neural coding throughout the entire learning process, as subjects acquire and use new episodic memories to guide behavior. Unfortunately, it is not clear whether established hippocampally-dependent learning paradigms are suitable for this kind of experiment. The goal of this study was to determine whether learning of the W-track continuous alternation task depends on the hippocampal formation. We tested six rats with NMDA lesions of the hippocampal formation and four sham-operated controls. Compared to controls, rats with hippocampal lesions made a significantly higher proportion of errors and took significantly longer to reach learning criterion. The effect of hippocampal lesion was not due to a deficit in locomotion or motivation, because rats with hippocampal lesions ran well on a linear track for food reward. Rats with hippocampal lesions also exhibited a pattern of perseverative errors during early task experience suggestive of an inability to suppress behaviors learned during pretraining on a linear track. Our findings establish the W-track continuous alternation task as a hippocampally-dependent learning paradigm which may be useful for identifying changes in the neural representation of spatial sequences and reward contingencies as rats learn and apply new task rules.

Genetic Structure of Europeans: A View from the North-East:

Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (λ) (ranging from 1.00 to 4.21), fixation index (Fst) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population), a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS).

Quantifying the Risk of Localised Animal Movement Bans for Foot-and-Mouth Disease:

The maintenance of disease-free status from Foot-and-Mouth Disease is of significant socio-economic importance to countries such as the UK. The imposition of bans on the movement of susceptible livestock following the discovery of an outbreak is deemed necessary to prevent the spread of what is a highly contagious disease, but has a significant economic impact on the agricultural community in itself. Here we consider the risk of applying movement restrictions only in localised zones around outbreaks in order to help evaluate how quickly nation-wide restrictions could be lifted after notification. We show, with reference to the 2001 and 2007 UK outbreaks, that it would be practical to implement such a policy provided the basic reproduction ratio of known infected premises can be estimated. It is ultimately up to policy makers and stakeholders to determine the acceptable level of risk, involving a cost benefit analysis of the potential outcomes, but quantifying the risk of spread from different sized zones is a prerequisite for this. The approach outlined is relevant to the determination of control zones and vaccination policies and has the potential to be applied to future outbreaks of other diseases.

Reduced Population Control of an Insect Pest in Managed Willow Monocultures:

There is a general belief that insect outbreak risk is higher in plant monocultures than in natural and more diverse habitats, although empirical studies investigating this relationship are lacking. In this study, using density data collected over seven years at 40 study sites, we compare the temporal population variability of the leaf beetle Phratora vulgatissima between willow plantations and natural willow habitats. The study was conducted in 1999-2005. The density of adult P. vulgatissima was estimated in the spring every year by a knock-down sampling technique. We used two measures of population variability, CV and PV, to compare temporal variations in leaf beetle density between plantation and natural habitat. Relationships between density and variability were also analyzed to discern potential underlying processes behind stability in the two systems. The results showed that the leaf beetle P. vulgatissima had a greater temporal population variability and outbreak risk in willow plantations than in natural willow habitats. We hypothesize that the greater population stability observed in the natural habitat was due to two separate processes operating at different levels of beetle density. First, stable low population equilibrium can be achieved by the relatively high density of generalist predators observed in natural stands. Second, stable equilibrium can also be imposed at higher beetle density due to competition, which occurs through depletion of resources (plant foliage) in the natural habitat. In willow plantations, competition is reduced mainly because plants grow close enough for beetle larvae to move to another plant when foliage is consumed. To our knowledge, this is the first empirical study confirming that insect pest outbreak risk is higher in monocultures. The study suggests that comparative studies of insect population dynamics in different habitats may improve our ability to predict insect pest outbreaks and could facilitate the development of sustainable pest control in managed systems.

Endocrine Activity of Extraembryonic Membranes Extends beyond Placental Amniotes:

During development, all amniotes (mammals, reptiles, and birds) form extraembryonic membranes, which regulate gas and water exchange, remove metabolic wastes, provide shock absorption, and transfer maternally derived nutrients. In viviparous (live-bearing) amniotes, both extraembryonic membranes and maternal uterine tissues contribute to the placenta, an endocrine organ that synthesizes, transports, and metabolizes hormones essential for development. Historically, endocrine properties of the placenta have been viewed as an innovation of placental amniotes. However, an endocrine role of extraembryonic membranes has not been investigated in oviparous (egg-laying) amniotes despite similarities in their basic structure, function, and shared evolutionary ancestry. In this study, we ask whether the oviparous chorioallantoic membrane (CAM) of chicken (Gallus gallus) has the capability to synthesize and receive signaling of progesterone, a major placental steroid hormone. We quantified mRNA expression of key steroidogenic enzymes involved in progesterone synthesis and found that 3β-hydroxysteroid dehydrogenase, which converts pregnenolone to progesterone exhibited a 464 fold increase in the CAM from day 8 to day 18 of embryonic development (F5, 68 = 89.282, p<0.0001). To further investigate progesterone synthesis, we performed explant culture and found that the CAM synthesizes progesterone in vitro in the presence of a steroid precursor. Finally, we quantified mRNA expression and performed protein immunolocalization of the progesterone receptor in the CAM. Collectively, our data indicate that the chick CAM is steroidogenic and has the capability to both synthesize progesterone and receive progesterone signaling. These findings represent a paradigm shift in evolutionary reproductive biology by suggesting that endocrine activity of extraembryonic membranes is not a novel characteristic of placental amniotes. Rather, we hypothesize that these membranes may share an additional unifying characteristic, steroidogenesis, across amniotes at large.

Cyanogenesis of Wild Lima Bean (Phaseolus lunatus L.) Is an Efficient Direct Defence in Nature:

In natural systems plants face a plethora of antagonists and thus have evolved multiple defence strategies. Lima bean (Phaseolus lunatus L.) is a model plant for studies of inducible indirect anti-herbivore defences including the production of volatile organic compounds (VOCs) and extrafloral nectar (EFN). In contrast, studies on direct chemical defence mechanisms as crucial components of lima beans’ defence syndrome under natural conditions are nonexistent. In this study, we focus on the cyanogenic potential (HCNp; concentration of cyanogenic glycosides) as a crucial parameter determining lima beans’ cyanogenesis, i.e. the release of toxic hydrogen cyanide from preformed precursors. Quantitative variability of cyanogenesis in a natural population of wild lima bean in Mexico was significantly correlated with missing leaf area. Since existing correlations do not by necessity mean causal associations, the function of cyanogenesis as efficient plant defence was subsequently analysed in feeding trials. We used natural chrysomelid herbivores and clonal lima beans with known cyanogenic features produced from field-grown mother plants. We show that in addition to extensively investigated indirect defences, cyanogenesis has to be considered as an important direct defensive trait affecting lima beans’ overall defence in nature. Our results indicate the general importance of analysing ‘multiple defence syndromes’ rather than single defence mechanisms in future functional analyses of plant defences.

There are 16 new articles in PLoS ONE today (as well as 13 last night and 5 on Friday night). As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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The 2008 anthology was noted in the American Scientist’s Bookshelf yesterday!
Here are the 2009 submissions to date and, below them, codes for Submission buttons. Please use the submission form to add more of your and other people’s posts:
A Blog Around The Clock: Circadian Rhythm of Aggression in Crayfish
A Blog Around The Clock: Co-Researching spaces for Freelance Scientists?
A Blog Around The Clock: The Shock Value of Science Blogs
A Blog Around The Clock: Defining the Journalism vs. Blogging Debate, with a Science Reporting angle
a k8, a cat, a mission: Moms asking for help
a k8, a cat, a mission: What does good mentorship look like?
a k8, a cat, a mission: Praise and Appreciation
a k8, a cat, a mission: Proximate mechanisms
a k8, a cat, a mission: The lives of women in science
All my faults are stress-related: Scientiae: surviving getting shaked and baked
Biochemical Soul: Darwin and the Heart of Evolution
Birds and Science: Caged budgerigars and invasive parakeets
Birds and Science: How do huge bird colonies synchronize?
Birds and Science: Fight and coordination in bird duets
Brontossauros em meu Jardim: Navigation is required*: the incredible case of the desert ant
Coyote Crossing: Spermophilus
Expression Patterns: A Squishy Topic
Expression Patterns: Mr. Darwin, you make me blush
Highly Allochthonous: Is the Earth’s magnetic field about to flip?
The Intersection: Singled Out
Island of Doubt: Sea level rise a red herring?
Living the Scientific Life: Genetic Compatibility Drives Choice of Mates and Sex of Chicks in Gouldian Finches, Erythrura gouldiae
Living the Scientific Life: Let’s Give Three Bronx Cheers for Bumblebees!
The MacGuffin: Topiramate Does Not Treat Alcohol Dependnece: Part 1
Made With Molecules: Hey Baby, what’s your AVPR1A like?
Mad Scientist, Junior: Pretty Pictures That Toaster Takes
Malaria, Bedbugs, Sea Lice, and Sunsets: An Interesting Patch of Quicksand
Masks of Eris: Mathematics instruction as a fish
Mind the Gap: In which I ponder economies of scale
Mind the Gap: In which I tend a strange garden
Mind the Gap: In which I ramp up
Mind the Gap: In which I muster a hypothesis
Mind the Gap: In which I continue to suspend disbelief
Mind the Gap: In which the data back up our habitual suspicions
Mind the Gap: In which I wade through the fringes of textbook fact
Mind the Gap: In which I dally with both sides
Mind the Gap: In which I am given weird treasures
Neurophilosophy: Amnesia in the movies
Neurophilosophy: Brain & behaviour of dinosaurs
Neurophilosophy: Voluntary amputation and extra phantom limbs
Neurotopia: The Value of Stupidity: are we doing it right?
Neurotopia: Why I’m a Scientist
Neurotopia: Korsakoff’s Psychic Disorder in Conjunction with Peripheral Neuritis
Observations of a Nerd: How big things relate to sex, stress and testosterone
Observations of a Nerd: Why I am not a Darwinist, but we should celebrate Darwin Day
Observations of a Nerd: Darwin’s Degenerates – Evolution’s Finest
Pharyngula: A brief moment in the magnificent history of mankind
Prerogative of Harlots: He Blinded Me With Science
The Primate Diaries: The Nature of Partisan Politics
Reciprocal Space: This is not good enough
The Scientist: On the nature of faith: Part 1
The Scientist: On the last days
The Scientist: On the passing of reprints
The Scientist: On saying goodbye
The Scientist: Ontology
The Scientist: Ontology #2
The Scientist: On winding down
The Scientist: On the weekend
The Scientist: On small victories
The Scientist: On the nature of networking: reprise
The Scientist: Grey Council
The Scientist: On interfaces
The Scientist: Coincidental Chemistry
The Scientist: On the Future
The Scientist: The year of living dangerously–Part 1
The Scientist: The year of living dangerously–Part 2
The Scientist: The year of living dangerously–Finale
The Scientist: What I want to do when I grow up
The Scientist: Inspiration
The Scientist: In which I watch the Watchmen, and land a new job
The Scientist: Ongoing
Skulls in the Stars: Michael Faraday, grand unified theorist? (1851)
Song for jasmine: Charles Darwin’s first theory of evolution
Stripped Science: The right pairing (comic strip)
Suppertime Sonnets: In Which I Celebrate A Certain Member of the Lycaenidae Family (poem)
Ways.org: The journal scope in focus — putting scholarly communication in context
White Coat Underground: Journeys
Why Science: Beautiful and essential
xkcd: Correlation (cartoon)
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There are 19 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Phase Shifting Capacity of the Circadian Pacemaker Determined by the SCN Neuronal Network Organization:

In mammals, a major circadian pacemaker that drives daily rhythms is located in the suprachiasmatic nuclei (SCN), at the base of the hypothalamus. The SCN receive direct light input via the retino-hypothalamic tract. Light during the early night induces phase delays of circadian rhythms while during the late night it leads to phase advances. The effects of light on the circadian system are strongly dependent on the photoperiod to which animals are exposed. An explanation for this phenomenon is currently lacking. We recorded running wheel activity in C57 mice and observed large amplitude phase shifts in short photoperiods and small shifts in long photoperiods. We investigated whether these different light responses under short and long days are expressed within the SCN by electrophysiological recordings of electrical impulse frequency in SCN slices. Application of N-methyl-D-aspartate (NMDA) induced sustained increments in electrical activity that were not significantly different in the slices from long and short photoperiods. These responses led to large phase shifts in slices from short days and small phase shifts in slices from long days. An analysis of neuronal subpopulation activity revealed that in short days the amplitude of the rhythm was larger than in long days. The data indicate that the photoperiodic dependent phase responses are intrinsic to the SCN. In contrast to earlier predictions from limit cycle theory, we observed large phase shifting responses in high amplitude rhythms in slices from short days, and small shifts in low amplitude rhythms in slices from long days. We conclude that the photoperiodic dependent phase responses are determined by the SCN and propose that synchronization among SCN neurons enhances the phase shifting capacity of the circadian system.

A Specialized Odor Memory Buffer in Primary Olfactory Cortex:

The neural substrates of olfactory working memory are unknown. We addressed the questions of whether olfactory working memory involves a verbal representation of the odor, or a sensory image of the odor, or both, and the location of the neural substrates of these processes. We used functional magnetic resonance imaging to measure activity in the brains of subjects who were remembering either nameable or unnameable odorants. We found a double dissociation whereby remembering nameable odorants was reflected in sustained activity in prefrontal language areas, and remembering unnameable odorants was reflected in sustained activity in primary olfactory cortex. These findings suggest a novel dedicated mechanism in primary olfactory cortex, where odor information is maintained in temporary storage to subserve ongoing tasks.

A Fast Na+/Ca2+-Based Action Potential in a Marine Diatom:

Electrical impulses in animals play essential roles in co-ordinating an array of physiological functions including movement, secretion, environmental sensing and development. Underpinning many of these electrical signals is a fast Na+-based action potential that has been fully characterised only in cells associated with the neuromuscular systems of multicellular animals. Such rapid action potentials are thought to have evolved with the first metazoans, with cnidarians being the earliest representatives. The present study demonstrates that a unicellular protist, the marine diatom Odontella sinensis, can also generate a fast Na+/Ca2+ based action potential that has remarkably similar biophysical and pharmacological properties to invertebrates and vertebrate cardiac and skeletal muscle cells. The kinetic, ionic and pharmacological properties of the rapid diatom action potential were examined using single electrode current and voltage clamp techniques. Overall, the characteristics of the fast diatom currents most closely resemble those of vertebrate and invertebrate muscle Na+/Ca2+ currents. This is the first demonstration of voltage-activated Na+ channels and the capacity to generate fast Na+-based action potentials in a unicellular photosynthetic organism. The biophysical and pharmacological characteristics together with the presence of a voltage activated Na+/Ca2+ channel homologue in the recently sequenced genome of the diatom Thalassiosira pseudonana, provides direct evidence supporting the hypothesis that this rapid signalling mechanism arose in ancestral unicellular eukaryotes and has been retained in at least two phylogenetically distant lineages of eukaryotes; opisthokonts and the stramenopiles. The functional role of the fast animal-like action potential in diatoms remains to be elucidated but is likely involved in rapid environmental sensing of these widespread and successful marine protists.

Psychological Typhoon Eye in the 2008 Wenchuan Earthquake:

On May 12, 2008, an earthquake measuring 8.0 on the Richter scale jolted Wenchuan, China, leading to 69,227 deaths and 374,643 injured, with 17,923 listed as missing as of Sept. 25, 2008, and shook the whole nation. We assessed the devastating effects on people’s post-earthquake concern about safety and health. From June 4 to July 15, 2008, we surveyed a convenience sample of 2,262 adults on their post-earthquake concern about safety and health. Residents in non-devastated areas (Fujian and Hunan Provinces, and Beijing) and devastated areas (Sichuan and Gansu Provinces) responded to a questionnaire of 5 questions regarding safety measures, epidemic disease, medical workers, psychological workers, and medication. The ANOVAs showed a significant effect of residential devastation level on the estimated number of safety measures needed, the estimated probability of the outbreak of an epidemic, and the estimated number of medical and psychological workers needed (Ps<0.001). The post-earthquake concern decreased significantly as the level of residential devastation increased. Because of the similarity with the meteorological phenomenon of the eye of a typhoon, we dubbed these findings a "Psychological Typhoon Eye": the closer to the center of the devastated areas, the less the concern about safety and health a resident felt. Contrary to common perception and ripple effect that the impact of an unfortunate event decays gradually as ripples spread outward from a center, a "Psychological Typhoon Eye" effect was observed where the post-earthquake concern was at its lowest level in the extremely devastated areas. The resultant findings may have implications for Chinese governmental strategies for putting "psychological comfort" into effect.

There are 26 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Mating First, Mating More: Biological Market Fluctuation in a Wild Prosimian:

In biology, economics, and politics, distributive power is the key for understanding asymmetrical relationships and it can be obtained by force (dominance) or trading (leverage). Whenever males cannot use force, they largely depend on females for breeding opportunities and the balance of power tilts in favour of females. Thus, males are expected not only to compete within their sex-class but also to exchange services with the opposite sex. Does this mating market, described for humans and apes, apply also to prosimians, the most ancestral primate group? To answer the question, we studied a scent-oriented and gregarious lemur, Propithecus verreauxi (sifaka), showing female dominance, promiscuous mating, and seasonal breeding. We collected 57 copulations involving 8 males and 4 females in the wild (Berenty Reserve, South Madagascar), and data (all occurrences) on grooming, aggressions, and marking behaviour. We performed the analyses via exact Spearman and matrix correlations. Male mating priority rank correlated with the frequency of male countermarking over female scents but not with the proportion of fights won by males over females. Thus, males competed in an olfactory tournament more than in an arena of aggressive encounters. The copulation frequency correlated neither with the proportion of fights won by males nor with the frequency of male countermarking on female scents. Male-to-female grooming correlated with female-to-male grooming only during premating. Instead, in the mating period male-to-female grooming correlated with the copulation frequency. In short, the biological market underwent seasonal fluctuations, since males bargained grooming for sex in the mating days and grooming for itself in the premating period. Top scent-releasers gained mating priority (they mated first) and top groomers ensured a higher number of renewed copulations (they mated more). In conclusion, males maximize their reproduction probability by adopting a double tactic and by following market fluctuations.

A Parsimonious Approach to Modeling Animal Movement Data:

Animal tracking is a growing field in ecology and previous work has shown that simple speed filtering of tracking data is not sufficient and that improvement of tracking location estimates are possible. To date, this has required methods that are complicated and often time-consuming (state-space models), resulting in limited application of this technique and the potential for analysis errors due to poor understanding of the fundamental framework behind the approach. We describe and test an alternative and intuitive approach consisting of bootstrapping random walks biased by forward particles. The model uses recorded data accuracy estimates, and can assimilate other sources of data such as sea-surface temperature, bathymetry and/or physical boundaries. We tested our model using ARGOS and geolocation tracks of elephant seals that also carried GPS tags in addition to PTTs, enabling true validation. Among pinnipeds, elephant seals are extreme divers that spend little time at the surface, which considerably impact the quality of both ARGOS and light-based geolocation tracks. Despite such low overall quality tracks, our model provided location estimates within 4.0, 5.5 and 12.0 km of true location 50% of the time, and within 9, 10.5 and 20.0 km 90% of the time, for above, equal or below average elephant seal ARGOS track qualities, respectively. With geolocation data, 50% of errors were less than 104.8 km (<0.94°), and 90% were less than 199.8 km (<1.80°). Larger errors were due to lack of sea-surface temperature gradients. In addition we show that our model is flexible enough to solve the obstacle avoidance problem by assimilating high resolution coastline data. This reduced the number of invalid on-land location by almost an order of magnitude. The method is intuitive, flexible and efficient, promising extensive utilization in future research.

Ant Queen Egg-Marking Signals: Matching Deceptive Laboratory Simplicity with Natural Complexity:

Experiments under controlled laboratory conditions can produce decisive evidence for testing biological hypotheses, provided they are representative of the more complex natural conditions. However, whether this requirement is fulfilled is seldom tested explicitly. Here we provide a lab/field comparison to investigate the identity of an egg-marking signal of ant queens. Our study was based on ant workers resolving conflict over male production by destroying each other’s eggs, but leaving queen eggs unharmed. For this, the workers need a proximate cue to discriminate between the two egg types. Earlier correlative evidence indicated that, in the ant Pachycondyla inversa, the hydrocarbon 3,11-dimethylheptacosane (3,11-diMeC27) is more abundant on the surface of queen-laid eggs. We first tested the hypothesis that 3,11-diMeC27 functions as a queen egg-marking pheromone using laboratory-maintained colonies. We treated worker-laid eggs with synthetic 3,11-diMeC27 and found that they were significantly more accepted than sham-treated worker-laid eggs. However, we repeated the experiment with freshly collected field colonies and observed no effect of treating worker-laid eggs with 3,11-diMeC27, showing that this compound by itself is not the natural queen egg-marking pheromone. We subsequently investigated the overall differences of entire chemical profiles of eggs, and found that queen-laid eggs in field colonies are more distinct from worker-laid eggs than in lab colonies, have more variation in profiles, and have an excess of longer-chain hydrocarbons. Our results suggest that queen egg-marking signals are significantly affected by transfer to the laboratory, and that this change is possibly connected to reduced queen fertility as predicted by honest signaling theory. This change is reflected in the worker egg policing response under field and laboratory conditions.

Intron Evolution: Testing Hypotheses of Intron Evolution Using the Phylogenomics of Tetraspanins:

Although large scale informatics studies on introns can be useful in making broad inferences concerning patterns of intron gain and loss, more specific questions about intron evolution at a finer scale can be addressed using a gene family where structure and function are well known. Genome wide surveys of tetraspanins from a broad array of organisms with fully sequenced genomes are an excellent means to understand specifics of intron evolution. Our approach incorporated several new fully sequenced genomes that cover the major lineages of the animal kingdom as well as plants, protists and fungi. The analysis of exon/intron gene structure in such an evolutionary broad set of genomes allowed us to identify ancestral intron structure in tetraspanins throughout the eukaryotic tree of life. We performed a phylogenomic analysis of the intron/exon structure of the tetraspanin protein family. In addition, to the already characterized tetraspanin introns numbered 1 through 6 found in animals, three additional ancient, phase 0 introns we call 4a, 4b and 4c were found. These three novel introns in combination with the ancestral introns 1 to 6, define three basic tetraspanin gene structures which have been conserved throughout the animal kingdom. Our phylogenomic approach also allows the estimation of the time at which the introns of the 33 human tetraspanin paralogs appeared, which in many cases coincides with the concomitant acquisition of new introns. On the other hand, we observed that new introns (introns other than 1-6, 4a, b and c) were not randomly inserted into the tetraspanin gene structure. The region of tetraspanin genes corresponding to the small extracellular loop (SEL) accounts for only 10.5% of the total sequence length but had 46% of the new animal intron insertions. Our results indicate that tests of intron evolution are strengthened by the phylogenomic approach with specific gene families like tetraspanins. These tests add to our understanding of genomic innovation coupled to major evolutionary divergence events, functional constraints and the timing of the appearance of evolutionary novelty.

Insect-Specific microRNA Involved in the Development of the Silkworm Bombyx mori:

MicroRNAs (miRNAs) are endogenous non-coding genes that participate in post-transcription regulation by either degrading mRNA or blocking its translation. It is considered to be very important in regulating insect development and metamorphosis. We conducted a large-scale screening for miRNA genes in the silkworm Bombyx mori using sequence-by-synthesis (SBS) deep sequencing of mixed RNAs from egg, larval, pupal, and adult stages. Of 2,227,930 SBS tags, 1,144,485 ranged from 17 to 25 nt, corresponding to 256,604 unique tags. Among these non-redundant tags, 95,184 were matched to the silkworm genome. We identified 3,750 miRNA candidate genes using a computational pipeline combining RNAfold and TripletSVM algorithms. We confirmed 354 miRNA genes using miRNA microarrays and then performed expression profile analysis on these miRNAs for all developmental stages. While 106 miRNAs were expressed in all stages, 248 miRNAs were egg- and pupa-specific, suggesting that insect miRNAs play a significant role in embryogenesis and metamorphosis. We selected eight miRNAs for quantitative RT-PCR analysis; six of these were consistent with our microarray results. In addition, we searched for orthologous miRNA genes in mammals, a nematode, and other insects and found that most silkworm miRNAs are conserved in insects, whereas only a small number of silkworm miRNAs has orthologs in mammals and the nematode. These results suggest that there are many miRNAs unique to insects.

Most people are mirrors, reflecting the moods and emotions of the times; few are windows, bringing light to bear on the dark corners where troubles fester. The whole purpose of education is to turn mirrors into windows.
– Sydney J. Harris