A Blog Around The Clock

There are 54 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 week – you go and look for your own favourites:
Tropical Mosquito Assemblages Demonstrate ‘Textbook’ Annual Cycles:

Annual biological rhythms are often depicted as predictably cyclic, but quantitative evaluations are few and rarely both cyclic and constant among years. In the monsoon tropics, the intense seasonality of rainfall frequently drives fluctuations in the populations of short-lived aquatic organisms. However, it is unclear how predictably assemblage composition will fluctuate because the intensity, onset and cessation of the wet season varies greatly among years. Adult mosquitoes were sampled using EVS suction traps baited with carbon dioxide around swamplands adjacent to the city of Darwin in northern Australia. Eleven sites were sampled weekly for five years, and one site weekly for 24 years, the sample of c. 1.4 million mosquitoes yielding 63 species. Mosquito abundance, species richness and diversity fluctuated seasonally, species richness being highly predictable. Ordination of assemblage composition demonstrated striking annual cycles that varied little from year to year. The mosquito assemblage was temporally structured by a succession of species peaks in abundance. Ordination provided strong visual representation of annual rhythms in assemblage composition and the means to evaluate variability among years. Because most mosquitoes breed in shallow freshwater which fluctuates with rainfall, we did not anticipate such repeatability; we conclude that mosquito assemblage composition appears adapted to predictable elements of the rainfall.

RNA-Interference Knockdown of Drosophila Pigment Dispersing Factor in Neuronal Subsets: The Anatomical Basis of a Neuropeptide’s Circadian Functions:

In animals, neuropeptide signaling is an important component of circadian timekeeping. The neuropeptide pigment dispersing factor (PDF) is required for several aspects of circadian activity rhythms in Drosophila. Here we investigate the anatomical basis for PDF’s various circadian functions by targeted PDF RNA-interference in specific classes of Drosophila neuron. We demonstrate that PDF is required in the ventro-lateral neurons (vLNs) of the central brain and not in the abdominal ganglion for normal activity rhythms. Differential knockdown of PDF in the large or small vLNs indicates that PDF from the small vLNs is likely responsible for the maintenance of free-running activity rhythms and that PDF is not required in the large vLNs for normal behavior. PDF’s role in setting the period of free-running activity rhythms and the proper timing of evening activity under light:dark cycles emanates from both subtypes of vLN, since PDF in either class of vLN was sufficient for these aspects of behavior. These results reveal the neuroanatomical basis PDF’s various circadian functions and refine our understanding of the clock neuron circuitry of Drosophila.

Whole Genome Duplications and a ‘Function’ for Junk DNA? Facts and Hypotheses:

The lack of correlation between genome size and organismal complexity is understood in terms of the massive presence of repetitive and non-coding DNA. This non-coding subgenome has long been called “junk” DNA. However, it might have important functions. Generation of junk DNA depends on proliferation of selfish DNA elements and on local or global DNA duplication followed by genic non-fonctionalization. Evidence from genomic analyses and experimental data indicates that Whole Genome Duplications (WGD) are often followed by a return to the diploid state, through DNA deletions and intra/interchromosomal rearrangements. We use simple theoretical models and simulations to explore how a WGD accompanied by sequence deletions might affect the dosage balance often required among several gene products involved in regulatory processes. We find that potential genomic deletions leading to changes in nuclear and cell volume might potentially perturb gene dosage balance. The potentially negative impact of DNA deletions can be buffered if deleted genic DNA is, at least temporarily, replaced by repetitive DNA so that the nuclear/cell volume remains compatible with normal living. Thus, we speculate that retention of non-functionalized non-coding DNA, and replacement of deleted DNA through proliferation of selfish elements, might help avoid dosage imbalances in cycles of polyploidization and diploidization, which are particularly frequent in plants.

Consistent Paternity Skew through Ontogeny in Peron’s Tree Frog (Litoria peronii):

A large number of studies in postcopulatory sexual selection use paternity success as a proxy for fertilization success. However, selective mortality during embryonic development can lead to skews in paternity in situations of polyandry and sperm competition. Thus, when assessment of paternity fails to incorporate mortality skews during early ontogeny, this may interfere with correct interpretation of results and subsequent evolutionary inference. In a previous series of in vitro sperm competition experiments with amphibians (Litoria peronii), we showed skewed paternity patterns towards males more genetically similar to the female. Here we use in vitro fertilizations and sperm competition trials to test if this pattern of paternity of fully developed tadpoles reflects patterns of paternity at fertilization and if paternity skews changes during embryonic development. We show that there is no selective mortality through ontogeny and that patterns of paternity of hatched tadpoles reflects success of competing males in sperm competition at fertilization. While this study shows that previous inferences of fertilization success from paternity data are valid for this species, rigorous testing of these assumptions is required to ensure that differential embryonic mortality does not confound estimations of true fertilization success.

Synchrotron X-Ray Visualisation of Ice Formation in Insects during Lethal and Non-Lethal Freezing:

Although the biochemical correlates of freeze tolerance in insects are becoming well-known, the process of ice formation in vivo is subject to speculation. We used synchrotron x-rays to directly visualise real-time ice formation at 3.3 Hz in intact insects. We observed freezing in diapausing 3rd instar larvae of Chymomyza amoena (Diptera: Drosophilidae), which survive freezing if it occurs above −14°C, and non-diapausing 3rd instar larvae of C. amoena and Drosophila melanogaster (Diptera: Drosophilidae), neither of which survive freezing. Freezing was readily observed in all larvae, and on one occasion the gut was seen to freeze separately from the haemocoel. There were no apparent qualitative differences in ice formation between freeze tolerant and non-freeze tolerant larvae. The time to complete freezing was positively related to temperature of nucleation (supercooling point, SCP), and SCP declined with decreasing body size, although this relationship was less strong in diapausing C. amoena. Nucleation generally occurred at a contact point with the thermocouple or chamber wall in non-diapausing larvae, but at random in diapausing larvae, suggesting that the latter have some control over ice nucleation. There were no apparent differences between freeze tolerant and non-freeze tolerant larvae in tracheal displacement or distension of the body during freezing, although there was markedly more distension in D. melanogaster than in C. amoena regardless of diapause state. We conclude that although control of ice nucleation appears to be important in freeze tolerant individuals, the physical ice formation process itself does not differ among larvae that can and cannot survive freezing. This suggests that a focus on cellular and biochemical mechanisms is appropriate and may reveal the primary adaptations allowing freeze tolerance in insects.

High and Far: Biases in the Location of Protected Areas:

About an eighth of the earth’s land surface is in protected areas (hereafter “PAs”), most created during the 20th century. Natural landscapes are critical for species persistence and PAs can play a major role in conservation and in climate policy. Such contributions may be harder than expected to implement if new PAs are constrained to the same kinds of locations that PAs currently occupy. Quantitatively extending the perception that PAs occupy “rock and ice”, we show that across 147 nations PA networks are biased towards places that are unlikely to face land conversion pressures even in the absence of protection. We test each country’s PA network for bias in elevation, slope, distances to roads and cities, and suitability for agriculture. Further, within each country’s set of PAs, we also ask if the level of protection is biased in these ways. We find that the significant majority of national PA networks are biased to higher elevations, steeper slopes and greater distances to roads and cities. Also, within a country, PAs with higher protection status are more biased than are the PAs with lower protection statuses. In sum, PAs are biased towards where they can least prevent land conversion (even if they offer perfect protection). These globally comprehensive results extend findings from nation-level analyses. They imply that siting rules such as the Convention on Biological Diversity’s 2010 Target [to protect 10% of all ecoregions] might raise PA impacts if applied at the country level. In light of the potential for global carbon-based payments for avoided deforestation or REDD, these results suggest that attention to threat could improve outcomes from the creation and management of PAs.

Sexually Transmitted Infections among HIV-1-Discordant Couples:

More new HIV-1 infections occur within stable HIV-1-discordant couples than in any other group in Africa, and sexually transmitted infections (STIs) may increase transmission risk among discordant couples, accounting for a large proportion of new HIV-1 infections. Understanding correlates of STIs among discordant couples will aid in optimizing interventions to prevent HIV-1 transmission in these couples. HIV-1-discordant couples in which HIV-1-infected partners were HSV-2-seropositive were tested for syphilis, chlamydia, gonorrhea, and trichomoniasis, and HIV-1-uninfected partners were tested for HSV-2. We assessed sociodemographic, behavioral, and biological correlates of a current STI. Of 416 couples enrolled, 16% were affected by a treatable STI, and among these both partners were infected in 17% of couples. A treatable STI was found in 46 (11%) females and 30 (7%) males. The most prevalent infections were trichomoniasis (5.9%) and syphilis (2.6%). Participants were 5.9-fold more likely to have an STI if their partner had an STI (P<0.01), and STIs were more common among those reporting any unprotected sex (OR = 2.43; P<0.01) and those with low education (OR = 3.00; P<0.01). Among HIV-1-uninfected participants with an HSV-2-seropositive partner, females were significantly more likely to be HSV-2-seropositive than males (78% versus 50%, P<0.01). Treatable STIs were common among HIV-1-discordant couples and the majority of couples affected by an STI were discordant for the STI, with relatively high HSV-2 discordance. Awareness of STI correlates and treatment of both partners may reduce HIV-1 transmission.

Chaperonin Contributes to Cold Hardiness of the Onion Maggot Delia antiqua through Repression of Depolymerization of Actin at Low Temperatures:

Winter-diapause and cold-acclimated non-diapause pupae of the onion maggot, Delia antiqua (Diptera: Anthomyiidae), show strong cold hardiness. To obtain insights into the mechanisms involved in the enhancement of cold hardiness, we investigated the expression patterns of genes encoding subunits of chaperonin (CCT) and the morphology of actin, a substrate of CCT, at low temperatures. Quantitative real-time PCR analyses showed the mRNA levels of CCT subunits in pupal tissues to be highly correlated with the cold hardiness of the pupae. While actin in the Malpighian tubules of non-cold-hardy pupae showed extensive depolymerization after a cold treatment, actin in the same tissue of cold-hardy pupae was not depolymerized. Damage to cell membranes became apparent after the depolymerization of actin. Moreover, administration of Latrunculin B, an inhibitor of actin polymerization, to the larvae markedly decreased the cold hardiness of the pupae obtained. These findings suggest that CCT contributes to the cold hardiness of D. antiqua through the repression of depolymerization of actin at low temperatures.

Tension at the Surface: Which Phase Is More Important, Liquid or Vapor?:

Tension at the surface is a most fundamental physicochemical property of a liquid surface. The concept of surface tension has widespread implications in numerous natural, engineering and biomedical processes. Research to date has been largely focused on the liquid side; little attention has been paid to the vapor–the other side of the surface, despite over 100 years of study. However, the question remains as to whether the vapor plays any role, and to what extent it affects the surface tension of the liquid. Here we show a systematic study of the effect of vapor on the surface tension and in particular, a surprising observation that the vapor, not the liquid, plays a dominant role in determining the surface tension of a range of common volatile organic solutions. This is in stark contrast to results of common surfactants where the concentration in the liquid plays the major role. We further confirmed our results with a modified adsorption isotherm and molecular dynamics simulations, where highly structured, hydrogen bonded networks, and in particular a solute depletion layer just beneath the Gibbs dividing surface, were revealed.

Molecular Characterization of Pneumococcal Isolates from Pets and Laboratory Animals:

Between 1986 and 2008 Streptococcus pneumoniae was isolated from 41 pets/zoo animals (guinea pigs (n = 17), cats (n = 12), horses (n = 4), dogs (n = 3), dolphins (n = 2), rat (n = 2), gorilla (n = 1)) treated in medical veterinary laboratories and zoos, and 44 laboratory animals (mastomys (multimammate mice; n = 32), mice (n = 6), rats (n = 4), guinea pigs (n = 2)) during routine health monitoring in an animal facility. S. pneumoniae was isolated from nose, lung and respiratory tract, eye, ear and other sites. Carriage of the same isolate of S. pneumoniae over a period of up to 22 weeks was shown for four mastomys. Forty-one animals showed disease symptoms. Pneumococcal isolates were characterized by optochin sensitivity, bile solubility, DNA hybridization, pneumolysin PCR, serotyping and multilocus sequence typing. Eighteen of the 32 mastomys isolates (56%) were optochin resistant, all other isolates were optochin susceptible. All mastomys isolates were serotype 14, all guinea pig isolates serotype 19F, all horse isolates serotype 3. Rats had serotypes 14 or 19A, mice 33A or 33F. Dolphins had serotype 23F, the gorilla serotype 14. Cats and dogs had many different serotypes. Four isolates were resistant to macrolides, three isolates also to clindamycin and tetracyclin. Mastomys isolates were sequence type (ST) 15 (serotype 14), an ST/serotype combination commonly found in human isolates. Cats, dogs, pet rats, gorilla and dolphins showed various human ST/serotype combinations. Lab rats and lab mice showed single locus variants (SLV) of human STs, in human ST/serotype combinations. All guinea pig isolates showed the same completely new combination of known alleles. The horse isolates showed an unknown allele combination and three new alleles. The isolates found in mastomys, mice, rats, cats, dogs, gorilla and dolphins are most likely identical to human pneumococcal isolates. Isolates from guinea pigs and horses appear to be specialized clones for these animals. Our data redraw attention to the fact that pneumococci are not strictly human pathogens. Pet animals that live in close contact to humans, especially children, can be infected by human isolates and also carriage of even resistant isolates is a realistic possibility.

The Extraction of Depth Structure from Shading and Texture in the Macaque Brain:

We used contrast-agent enhanced functional magnetic resonance imaging (fMRI) in the alert monkey to map the cortical regions involved in the extraction of 3D shape from the monocular static cues, texture and shading. As in the parallel human imaging study [1], we contrasted the 3D condition to several 2D control conditions. The extraction of 3D shape from texture (3D SfT) involves both ventral and parietal regions, in addition to early visual areas. Strongest activation was observed in CIP, with decreasing strength towards the anterior part of the intraparietal sulcus (IPS). In the ventral stream 3D SfT sensitivity was observed in a ventral portion of TEO. The extraction of 3D shape from shading (3D SfS) involved predominantly ventral regions, such as V4 and a dorsal potion of TEO. These results are similar to those obtained earlier in human subjects and indicate that the extraction of 3D shape from texture is performed in both ventral and dorsal regions for both species, as are the motion and disparity cues, whereas shading is mainly processed in the ventral stream.

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, 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:
White Shark Offshore Habitat: A Behavioral and Environmental Characterization of the Eastern Pacific Shared Offshore Foraging Area:

Although much is known about the behavior of white sharks in coastal regions, very little is known about their vertical movements offshore in the eastern Pacific where they spend up to five months. We provide the first detailed description of the offshore habitat use of white sharks in the eastern North Pacific. This study uses 2-min data from four recovered pop-up satellite archival tags deployed at Guadalupe Island (2002 and 2005). Deployments ranged from 5.4 to 8.2 months. Two predominant vertical patterns were described. The first was a bimodal vertical pattern with time spent at the surface and at depth, which was observed while traveling. The second was a repetitive oscillatory diving mode displayed by sharks in the Shared Offshore Foraging Area (SOFA). For all four datasets the average maximum daily dive depths ranged from 442.5 to 492.8 m and were typically associated with dissolved oxygen concentrations of above 1.7 ml L−1. Although infrequent, occasional dives to near 1000 m with a minimum temperature of 3.9°C and a minimum O2 level of 0.3 ml L−1 were observed. Recovered pop-up satellite tags from Guadalupe Island white sharks advance our understanding of the vertical habitat use of white sharks while offshore. The bimodal vertical pattern during traveling is most likely related to geolocation. The oscillatory dive pattern is likely associated with foraging. While feeding is not documented, foraging is likely occurring in association with the deep scattering layer. Diving depths were not limited by temperature but were constrained by O2 levels below approximately 1.5 ml L−1. While oxygen may limit the extent of sharks’ vertical movements, it will also impact prey distribution. Consequently, the shallow oxygen minimum zone in the SOFA may act to concentrate prey, thus enhancing foraging opportunities in these oligotrophic waters.

A Wireless Brain-Machine Interface for Real-Time Speech Synthesis:

Brain-machine interfaces (BMIs) involving electrodes implanted into the human cerebral cortex have recently been developed in an attempt to restore function to profoundly paralyzed individuals. Current BMIs for restoring communication can provide important capabilities via a typing process, but unfortunately they are only capable of slow communication rates. In the current study we use a novel approach to speech restoration in which we decode continuous auditory parameters for a real-time speech synthesizer from neuronal activity in motor cortex during attempted speech. Neural signals recorded by a Neurotrophic Electrode implanted in a speech-related region of the left precentral gyrus of a human volunteer suffering from locked-in syndrome, characterized by near-total paralysis with spared cognition, were transmitted wirelessly across the scalp and used to drive a speech synthesizer. A Kalman filter-based decoder translated the neural signals generated during attempted speech into continuous parameters for controlling a synthesizer that provided immediate (within 50 ms) auditory feedback of the decoded sound. Accuracy of the volunteer’s vowel productions with the synthesizer improved quickly with practice, with a 25% improvement in average hit rate (from 45% to 70%) and 46% decrease in average endpoint error from the first to the last block of a three-vowel task. Our results support the feasibility of neural prostheses that may have the potential to provide near-conversational synthetic speech output for individuals with severely impaired speech motor control. They also provide an initial glimpse into the functional properties of neurons in speech motor cortical areas.

Sub-Optimal Allocation of Time in Sequential Movements:

The allocation of limited resources such as time or energy is a core problem that organisms face when planning complex actions. Most previous research concerning planning of movement has focused on the planning of single, isolated movements. Here we investigated the allocation of time in a pointing task where human subjects attempted to touch two targets in a specified order to earn monetary rewards. Subjects were required to complete both movements within a limited time but could freely allocate the available time between the movements. The time constraint presents an allocation problem to the subjects: the more time spent on one movement, the less time is available for the other. In different conditions we assigned different rewards to the two tokens. How the subject allocated time between movements affected their expected gain on each trial. We also varied the angle between the first and second movements and the length of the second movement. Based on our results, we developed and tested a model of speed-accuracy tradeoff for sequential movements. Using this model we could predict the time allocation that would maximize the expected gain of each subject in each experimental condition. We compared human performance with predicted optimal performance. We found that all subjects allocated time sub-optimally, spending more time than they should on the first movement even when the reward of the second target was five times larger than the first. We conclude that the movement planning system fails to maximize expected reward in planning sequences of as few as two movements and discuss possible interpretations drawn from economic theory.

Using Association Mapping in Teosinte to Investigate the Function of Maize Selection-Candidate Genes:

Large-scale screens of the maize genome identified 48 genes that show the putative signature of artificial selection during maize domestication or improvement. These selection-candidate genes may act as quantitative trait loci (QTL) that control the phenotypic differences between maize and its progenitor, teosinte. The selection-candidate genes appear to be located closer in the genome to domestication QTL than expected by chance. As a step toward defining the traits controlled by these genes, we performed phenotype-genotype association mapping in teosinte for 32 of the 48 plus three other selection-candidate genes. Our analyses assayed 32 phenotypic traits, many of which were altered during maize domestication or improvement. We observed several significant associations between SNPs in the selection-candidate genes and trait variation in teosinte. These included two associations that surpassed the Bonferroni correction and five instances where a gene significantly associated with the same trait in both of our association mapping panels. Despite these significant associations, when compared as a group the selection-candidate genes performed no better than randomly chosen genes. Our results suggest association analyses can be helpful for identifying traits under the control of selection-candidate genes. Indeed, we present evidence for new functions for several selection-candidate genes. However, with the current set of selection-candidate genes and our association mapping strategy, we found very few significant associations overall and no more than we would have found with randomly chosen genes. We discuss possible reasons that a large number of significant genotype-phenotype associations were not discovered.

Unconsciously Perceived Fear in Peripheral Vision Alerts the Limbic System: A MEG Study:

In ecological situations, threatening stimuli often come out from the peripheral vision. Such aggressive messages must trigger rapid attention to the periphery to allow a fast and adapted motor reaction. Several clues converge to hypothesize that peripheral danger presentation can trigger off a fast arousal network potentially independent of the consciousness spot. In the present MEG study, spatio-temporal dynamics of the neural processing of danger related stimuli were explored as a function of the stimuli position in the visual field. Fearful and neutral faces were briefly presented in the central or peripheral visual field, and were followed by target faces stimuli. An event-related beamformer source analysis model was applied in three time windows following the first face presentations: 80 to 130 ms, 140 to 190 ms, and 210 to 260 ms. The frontal lobe and the right internal temporal lobe part, including the amygdala, reacted as soon as 80 ms of latency to fear occurring in the peripheral vision. For central presentation, fearful faces evoked the classical neuronal activity along the occipito-temporal visual pathway between 140 and 190 ms. Thus, the high spatio-temporal resolution of MEG allowed disclosing a fast response of a network involving medial temporal and frontal structures in the processing of fear related stimuli occurring unconsciously in the peripheral visual field. Whereas centrally presented stimuli are precisely processed by the ventral occipito-temporal cortex, the related-to-danger stimuli appearing in the peripheral visual field are more efficient to produce a fast automatic alert response possibly conveyed by subcortical structures.

The Severity of Pandemic H1N1 Influenza in the United States, from April to July 2009: A Bayesian Analysis:

Accurate measures of the severity of pandemic (H1N1) 2009 influenza (pH1N1) are needed to assess the likely impact of an anticipated resurgence in the autumn in the Northern Hemisphere. Severity has been difficult to measure because jurisdictions with large numbers of deaths and other severe outcomes have had too many cases to assess the total number with confidence. Also, detection of severe cases may be more likely, resulting in overestimation of the severity of an average case. We sought to estimate the probabilities that symptomatic infection would lead to hospitalization, ICU admission, and death by combining data from multiple sources. We used complementary data from two US cities: Milwaukee attempted to identify cases of medically attended infection whether or not they required hospitalization, while New York City focused on the identification of hospitalizations, intensive care admission or mechanical ventilation (hereafter, ICU), and deaths. New York data were used to estimate numerators for ICU and death, and two sources of data–medically attended cases in Milwaukee or self-reported influenza-like illness (ILI) in New York–were used to estimate ratios of symptomatic cases to hospitalizations. Combining these data with estimates of the fraction detected for each level of severity, we estimated the proportion of symptomatic patients who died (symptomatic case-fatality ratio, sCFR), required ICU (sCIR), and required hospitalization (sCHR), overall and by age category. Evidence, prior information, and associated uncertainty were analyzed in a Bayesian evidence synthesis framework. Using medically attended cases and estimates of the proportion of symptomatic cases medically attended, we estimated an sCFR of 0.048% (95% credible interval [CI] 0.026%-0.096%), sCIR of 0.239% (0.134%-0.458%), and sCHR of 1.44% (0.83%-2.64%). Using self-reported ILI, we obtained estimates approximately 7-9× lower. sCFR and sCIR appear to be highest in persons aged 18 y and older, and lowest in children aged 5-17 y. sCHR appears to be lowest in persons aged 5-17; our data were too sparse to allow us to determine the group in which it was the highest. These estimates suggest that an autumn-winter pandemic wave of pH1N1 with comparable severity per case could lead to a number of deaths in the range from considerably below that associated with seasonal influenza to slightly higher, but with the greatest impact in children aged 0-4 and adults 18-64. These estimates of impact depend on assumptions about total incidence of infection and would be larger if incidence of symptomatic infection were higher or shifted toward adults, if viral virulence increased, or if suboptimal treatment resulted from stress on the health care system; numbers would decrease if the total proportion of the population symptomatically infected were lower than assumed.

Differing Prevalence and Diversity of Bacterial Species in Fetal Membranes from Very Preterm and Term Labor:

Intrauterine infection may play a role in preterm delivery due to spontaneous preterm labor (PTL) and preterm prolonged rupture of membranes (PPROM). Because bacteria previously associated with preterm delivery are often difficult to culture, a molecular biology approach was used to identify bacterial DNA in placenta and fetal membranes. We used broad-range 16S rDNA PCR and species-specific, real-time assays to amplify bacterial DNA from fetal membranes and placenta. 74 women were recruited to the following groups: PPROM <32 weeks (n = 26; 11 caesarean); PTL with intact membranes <32 weeks (n = 19; all vaginal birth); indicated preterm delivery <32 weeks (n = 8; all caesarean); term (n = 21; 11 caesarean). 50% (5/10) of term vaginal deliveries were positive for bacterial DNA. However, little spread was observed through tissues and species diversity was restricted. Minimal bacteria were detected in term elective section or indicated preterm deliveries. Bacterial prevalence was significantly increased in samples from PTL with intact membranes [89% (17/19) versus 50% (5/10) in term vaginal delivery p = 0.03] and PPROM (CS) [55% (6/11) versus 0% (0/11) in term elective CS, p = 0.01]. In addition, bacterial spread and diversity was greater in the preterm groups with 68% (13/19) PTL group having 3 or more positive samples and over 60% (12/19) showing two or more bacterial species (versus 20% (2/10) in term vaginal deliveries). Blood monocytes from women with PTL with intact membranes and PPROM who were 16S bacterial positive showed greater level of immune paresis (p = 0.03). A positive PCR result was associated with histological chorioamnionitis in preterm deliveries. Bacteria are found in both preterm and term fetal membranes. A greater spread and diversity of bacterial species were found in tissues of women who had very preterm births. It is unclear to what extent the greater bacterial prevalence observed in all vaginal delivery groups reflects bacterial contamination or colonization of membranes during labor. Bacteria positive preterm tissues are associated with histological chorioamnionitis and a pronounced maternal immune paresis.

Reappraising Sexual Coevolution and the Sex Roles:

The history of evolutionary biology illustrates how theory shapes what we see and don’t see in nature. Over the past 30 years, theoretical reappraisals in two areas of evolutionary research–sexual coevolution and the sex roles–have challenged longstanding ideas and yielded rich harvests of startling observations. This process continues apace.

A Cost of Sexual Attractiveness to High-Fitness Females:

In many species, females are frequently subject to harassing courtship from males attempting to mate with them. These persistent male behaviors can result in females incurring substantial direct fitness costs. We set out to examine how these costs may influence adaptive potential in a species that also exhibits male mate choice, i.e., a preference by males for females exhibiting certain traits. We found that harmful courtship behaviors were directed predominantly towards females of greater reproductive potential (and away from females of lesser potential), resulting in a reduction in the variation of lifetime reproductive successes among females in the population. This change in distribution of realized fitnesses represents a previously unappreciated consequence of sexual conflict-adaptive male mate preference can slow the rate of accumulation of beneficial mutations and speed the rate of accumulation of harmful mutations, thereby creating a “sexual conflict adaptive load” within a species.

Molecular Mechanism for Human Sperm Chemotaxis Mediated by Progesterone:

Sperm chemotaxis is a chemical guiding mechanism that may orient spermatozoa to the egg surface. A picomolar concentration gradient of Progesterone (P), the main steroidal component secreted by the cumulus cells that surround the egg, attracts human spermatozoa. In order to elucidate the molecular mechanism of sperm chemotaxis mediated by P, we combine the application of different strategies: pharmacological inhibition of signaling molecules, measurements of the concentrations of second messengers and activation of the chemotactic signaling. Our data implicate a number of classic signal transduction pathways in the response and provide a model for the sequence of events, where the tmAC-cAMP-PKA pathway is activated first, followed by protein tyrosine phosphorylation (equatorial band and flagellum) and calcium mobilization (through IP3R and SOC channels), whereas the sGC-cGMP-PKG cascade, is activated later. These events lead to sperm orientation towards the source of the chemoattractant. The finding proposes a molecular mechanism which contributes to the understanding of the signal transduction pathway that takes place in a physiological process as chemotaxis.

There are 21 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 week – you go and look for your own favourites:
Comparison of Trunk Activity during Gait Initiation and Walking in Humans:

To understand the role of trunk muscles in maintenance of dynamic postural equilibrium we investigate trunk movements during gait initiation and walking, performing trunk kinematics analysis, Erector spinae muscle (ES) recordings and dynamic analysis. ES muscle expressed a metachronal descending pattern of activity during walking and gait initiation. In the frontal and horizontal planes, lateroflexion and rotation occur before in the upper trunk and after in the lower trunk. Comparison of ES muscle EMGs and trunk kinematics showed that trunk muscle activity precedes corresponding kinematics activity, indicating that the ES drive trunk movement during locomotion and thereby allowing a better pelvis mobilization. EMG data showed that ES activity anticipates propulsive phases in walking with a repetitive pattern, suggesting a programmed control by a central pattern generator. Our findings also suggest that the programs for gait initiation and walking overlap with the latter beginning before the first has ended.

The Impact of the Wenchuan Earthquake on Birth Outcomes:

Earthquakes and other catastrophic events frequently occurring worldwide can be considered as outliers and cause a growing and urgent need to improve our understanding of the negative effects imposed by such disasters. Earthquakes can intensively impact the birth outcomes upon psychological and morphological development of the unborn children, albeit detailed characteristics remain obscure. We utilized the birth records at Du Jiang Yan and Peng Zhou counties to investigate the birth outcomes as a consequence of a major earthquake occurred in Wenchuan, China on May 12, 2008. Totally 13,003 of neonates were recorded, with 6638 and 6365 for pre- and post- earthquake, respectively. Significant low birthweight, high ratio of low birthweight, and low Apgar scores of post-earthquake group were observed. In contrast, the sex ratio at birth, birth length and length of gestation did not show statistical differences. The overall ratio of birth-defect in the post-earthquake (1.18%) is statistically high than that of pre-earthquake (0.99%), especially for those in the first trimester on earthquake day (1.47%). The birth-defect spectrum was dramatically altered after earthquake, with the markedly increased occurrences of ear malformations. The ratio of preterm birth post-earthquake (7.41%) is significant increased than that of pre-earthquake (5.63%). For the birth outcomes of twins, significant differences of the ratio of twins, birth weight, ratio of low birthweight and birth-defect rate were observed after earthquake. A hospital-based study of birth outcomes impacted by the Wenchuan earthquake shows that the earthquake was associated with significant effects on birth outcomes, indicating it is a major monitor for long-term pregnant outcomes.

Does Haplodiploidy Purge Inbreeding Depression in Rotifer Populations?:

Inbreeding depression is an important evolutionary factor, particularly when new habitats are colonized by few individuals. Then, inbreeding depression by drift could favour the establishment of later immigrants because their hybrid offspring would enjoy higher fitness. Rotifers are the only major zooplanktonic group where information on inbreeding depression is still critically scarce, despite the fact that in cyclical parthenogenetic rotifers males are haploid and could purge deleterious recessive alleles, thereby decreasing inbreeding depression. We studied the effects of inbreeding in two populations of the cyclical parthenogenetic rotifer Brachionus plicatilis. For each population, we compared both the parental fertilization proportion and F1 fitness components from intraclonal (selfed) and interclonal (outcrossed) crosses. The parental fertilization proportion was similar for both types of crosses, suggesting that there is no mechanism to avoid selfing. In the F1 generation of both populations, we found evidence of inbreeding depression for the fitness components associated with asexual reproduction; whereas inbreeding depression was only found for one of the two sexual reproduction fitness components measured. Our results show that rotifers, like other major zooplanktonic groups, can be affected by inbreeding depression in different stages of their life cycle. These results suggest that haplodiploidy does not purge efficiently deleterious recessive alleles. The inbreeding depression detected here has important implications when a rotifer population is founded and intraclonal crossing is likely to occur. Thus, during the foundation of new populations inbreeding depression may provide opportunities for new immigrants, increasing gene flow between populations, and affecting genetic differentiation.

Alternation of Sound Location Induces Visual Motion Perception of a Static Object:

Audition provides important cues with regard to stimulus motion although vision may provide the most salient information. It has been reported that a sound of fixed intensity tends to be judged as decreasing in intensity after adaptation to looming visual stimuli or as increasing in intensity after adaptation to receding visual stimuli. This audiovisual interaction in motion aftereffects indicates that there are multimodal contributions to motion perception at early levels of sensory processing. However, there has been no report that sounds can induce the perception of visual motion. A visual stimulus blinking at a fixed location was perceived to be moving laterally when the flash onset was synchronized to an alternating left-right sound source. This illusory visual motion was strengthened with an increasing retinal eccentricity (2.5 deg to 20 deg) and occurred more frequently when the onsets of the audio and visual stimuli were synchronized. We clearly demonstrated that the alternation of sound location induces illusory visual motion when vision cannot provide accurate spatial information. The present findings strongly suggest that the neural representations of auditory and visual motion processing can bias each other, which yields the best estimates of external events in a complementary manner.

Seasonal Differences of Gene Expression Profiles in Song Sparrow (Melospiza melodia) Hypothalamus in Relation to Territorial Aggression:

Male song sparrows (Melospiza melodia) are territorial year-round; however, neuroendocrine responses to simulated territorial intrusion (STI) differ between breeding (spring) and non-breeding seasons (autumn). In spring, exposure to STI leads to increases in luteinizing hormone and testosterone, but not in autumn. These observations suggest that there are fundamental differences in the mechanisms driving neuroendocrine responses to STI between seasons. Microarrays, spotted with EST cDNA clones of zebra finch, were used to explore gene expression profiles in the hypothalamus after territorial aggression in two different seasons. Free-living territorial male song sparrows were exposed to either conspecific or heterospecific (control) males in an STI in spring and autumn. Behavioral data were recorded, whole hypothalami were collected, and microarray hybridizations were performed. Quantitative PCR was performed for validation. Our results show 262 cDNAs were differentially expressed between spring and autumn in the control birds. There were 173 cDNAs significantly affected by STI in autumn; however, only 67 were significantly affected by STI in spring. There were 88 cDNAs that showed significant interactions in both season and STI. Results suggest that STI drives differential genomic responses in the hypothalamus in the spring vs. autumn. The number of cDNAs differentially expressed in relation to season was greater than in relation to social interactions, suggesting major underlying seasonal effects in the hypothalamus which may determine the differential response upon social interaction. Functional pathway analyses implicated genes that regulate thyroid hormone action and neuroplasticity as targets of this neuroendocrine regulation.

Accelerated Evolution of the Prdm9 Speciation Gene across Diverse Metazoan Taxa:

Speciation, the process by which one species splits into two, involves reproductive barriers between previously interbreeding populations. The question of how speciation occurs has rightly occupied the attention of biologists since before Darwin’s “On the Origin of Species.” Studies of recently diverged species have revealed the presence of hybrid sterility genes (colloquially referred to as “speciation genes”), alleles of which are associated with sterility of interspecies hybrids. Mouse Prdm9 is the only known such gene in vertebrate animals. Here we report that the Prdm9 protein has evolved extremely rapidly in its DNA-binding domain, comprising an array of “zinc fingers.” This suggests that hybrid sterility may arise from a mismatch between the DNA-binding specificity of Prdm9 and rapidly evolving DNA. We propose that Prdm9 binds to satellite-DNA repeats evolving rapidly within and between different species. Prdm9 evolution is unusual because other hybrid sterility genes appear only to evolve rapidly in isolated bursts, whereas Prdm9 has evolved rapidly over 700 million years, in many rodent species, diverse primates and other metazoans. This leads to the tantalizing possibility that Prdm9 may have served as a “speciation gene” on other occasions in metazoan evolution, a possibility that will now need to be investigated.

Temporal Control of Immediate Early Gene Induction by Light:

The light-gated cation channel channelrhodopsin-2 (ChR2) is a powerful tool for the optical induction of action potentials in neurons. Mutations of the cysteine 128 (C128) residue have been shown to greatly extend the lifetime of the conducting state of ChR2. However, until now, only subthreshold depolarizations have been reported from C128 mutants. Here we report the induction of long high-frequency spike trains by brief light pulses in ChR2(C128A)-transfected pyramidal cells in hippocampal slice culture. ChR2(C128A)-mediated spike bursts triggered expression of the immediate early gene c-fos in pyramidal neurons. Robust and cell-specific expression of c-Fos protein was detected after a single blue light pulse and depended on action potential firing, but not on synaptic activity. However, photocurrents diminished upon repeated stimulation and limited the number of action potential bursts that could be elicited. We conclude that the C128A mutant is not suitable for chronic stimulation of neurons, but very useful for light-controlled induction of immediate early genes. This property of ChR2(C128A) could be harnessed to control the expression of proteins under control of the c-fos promoter with precise timing and single cell specificity.

Spike-Based Reinforcement Learning in Continuous State and Action Space: When Policy Gradient Methods Fail:

Changes of synaptic connections between neurons are thought to be the physiological basis of learning. These changes can be gated by neuromodulators that encode the presence of reward. We study a family of reward-modulated synaptic learning rules for spiking neurons on a learning task in continuous space inspired by the Morris Water maze. The synaptic update rule modifies the release probability of synaptic transmission and depends on the timing of presynaptic spike arrival, postsynaptic action potentials, as well as the membrane potential of the postsynaptic neuron. The family of learning rules includes an optimal rule derived from policy gradient methods as well as reward modulated Hebbian learning. The synaptic update rule is implemented in a population of spiking neurons using a network architecture that combines feedforward input with lateral connections. Actions are represented by a population of hypothetical action cells with strong mexican-hat connectivity and are read out at theta frequency. We show that in this architecture, a standard policy gradient rule fails to solve the Morris watermaze task, whereas a variant with a Hebbian bias can learn the task within 20 trials, consistent with experiments. This result does not depend on implementation details such as the size of the neuronal populations. Our theoretical approach shows how learning new behaviors can be linked to reward-modulated plasticity at the level of single synapses and makes predictions about the voltage and spike-timing dependence of synaptic plasticity and the influence of neuromodulators such as dopamine. It is an important step towards connecting formal theories of reinforcement learning with neuronal and synaptic properties.

There are 14 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 week – you go and look for your own favourites:
A Biological Rationale for Musical Scales:

Scales are collections of tones that divide octaves into specific intervals used to create music. Since humans can distinguish about 240 different pitches over an octave in the mid-range of hearing [1], in principle a very large number of tone combinations could have been used for this purpose. Nonetheless, compositions in Western classical, folk and popular music as well as in many other musical traditions are based on a relatively small number of scales that typically comprise only five to seven tones [2]-[6]. Why humans employ only a few of the enormous number of possible tone combinations to create music is not known. Here we show that the component intervals of the most widely used scales throughout history and across cultures are those with the greatest overall spectral similarity to a harmonic series. These findings suggest that humans prefer tone combinations that reflect the spectral characteristics of conspecific vocalizations. The analysis also highlights the spectral similarity among the scales used by different cultures.

An Auditory Illusion of Infinite Tempo Change Based on Multiple Temporal Levels:

Humans and a few select insect and reptile species synchronise inter-individual behaviour without any time lag by predicting the time of future events rather than reacting to them. This is evident in music performance, dance, and drill. Although repetition of equal time intervals (i.e. isochrony) is the central principle for such prediction, this simple information is used in a flexible and complex way that accommodates both multiples, subdivisions, and gradual changes of intervals. The scope of this flexibility remains largely uncharted, and the underlying mechanisms are a matter for speculation. Here I report an auditory illusion that highlights some aspects of this behaviour and that provides a powerful tool for its future study. A sound pattern is described that affords multiple alternative and concurrent rates of recurrence (temporal levels). An algorithm that systematically controls time intervals and the relative loudness among these levels creates an illusion that the perceived rate speeds up or slows down infinitely. Human participants synchronised hand movements with their perceived rate of events, and exhibited a change in their movement rate that was several times larger than the physical change in the sound pattern. The illusion demonstrates the duality between the external signal and the internal predictive process, such that people’s tendency to follow their own subjective pulse overrides the overall properties of the stimulus pattern. Furthermore, accurate synchronisation with sounds separated by more than 8 s demonstrate that multiple temporal levels are employed for facilitating temporal organisation and integration by the human brain. A number of applications of the illusion and the stimulus pattern are suggested.

Early Assessment of Anxiety and Behavioral Response to Novel Swine-Origin Influenza A(H1N1):

Since late April, 2009, a novel influenza virus A (H1N1), generally referred to as the “swine flu,” has spread around the globe and infected hundreds of thousands of people. During the first few days after the initial outbreak in Mexico, extensive media coverage together with a high degree of uncertainty about the transmissibility and mortality rate associated with the virus caused widespread concern in the population. The spread of an infectious disease can be strongly influenced by behavioral changes (e.g., social distancing) during the early phase of an epidemic, but data on risk perception and behavioral response to a novel virus is usually collected with a substantial delay or after an epidemic has run its course. Here, we report the results from an online survey that gathered data (n = 6,249) about risk perception of the Influenza A(H1N1) outbreak during the first few days of widespread media coverage (April 28 – May 5, 2009). We find that after an initially high level of concern, levels of anxiety waned along with the perception of the virus as an immediate threat. Overall, our data provide evidence that emotional status mediates behavioral response. Intriguingly, principal component analysis revealed strong clustering of anxiety about swine flu, bird flu and terrorism. All three of these threats receive a great deal of media attention and their fundamental uncertainty is likely to generate an inordinate amount of fear vis-a-vis their actual threat. Our results suggest that respondents’ behavior varies in predictable ways. Of particular interest, we find that affective variables, such as self-reported anxiety over the epidemic, mediate the likelihood that respondents will engage in protective behavior. Understanding how protective behavior such as social distancing varies and the specific factors that mediate it may help with the design of epidemic control strategies.

There are 31 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 week – you go and look for your own favourites:
High-Pitched Notes during Vocal Contests Signal Genetic Diversity in Ocellated Antbirds:

Animals use honest signals to assess the quality of competitors during aggressive interactions. Current theory predicts that honest signals should be costly to produce and thus reveal some aspects of the phenotypic or genetic quality of the sender. In songbirds, research indicates that biomechanical constraints make the production of some acoustic features costly. Furthermore, recent studies have found that vocal features are related to genetic diversity. We linked these two lines of research by evaluating if constrained acoustic features reveal male genetic diversity during aggressive interactions in ocellated antbirds (Phaenostictus mcleannani). We recorded the aggressive vocalizations of radiotagged males at La Selva Biological Station in Costa Rica, and found significant variation in the highest frequency produced among individuals. Moreover, we detected a negative relationship between the frequency of the highest pitched note and vocalization duration, suggesting that high pitched notes might constrain the duration of vocalizations through biomechanical and/or energetic limitations. When we experimentally exposed wild radiotagged males to simulated acoustic challenges, the birds increased the pitch of their vocalization. We also found that individuals with higher genetic diversity (as measured by zygosity across 9 microsatellite loci) produced notes of higher pitch during aggressive interactions. Overall, our results suggest that the ability to produce high pitched notes is an honest indicator of male genetic diversity in male-male aggressive interactions.

Associative Learning during Early Adulthood Enhances Later Memory Retention in Honeybees:

Cognitive experiences during the early stages of life play an important role in shaping the future behavior in mammals but also in insects, in which precocious learning can directly modify behaviors later in life depending on both the timing and the rearing environment. However, whether olfactory associative learning acquired early in the adult stage of insects affect memorizing of new learning events has not been studied yet. Groups of adult honeybee workers that experienced an odor paired with a sucrose solution 5 to 8 days or 9 to 12 days after emergence were previously exposed to (i) a rewarded experience through the offering of scented food, or (ii) a non-rewarded experience with a pure volatile compound in the rearing environment. Early rewarded experiences (either at 1-4 or 5-8 days of adult age) enhanced retention performance in 9-12-day-conditioned bees when they were tested at 17 days of age. The highest retention levels at this age, which could not be improved with prior rewarded experiences, were found for memories established at 5-8 days of adult age. Associative memories acquired at 9-12 days of age showed a weak effect on retention for some pure pre-exposed volatile compounds; whereas the sole exposure of an odor at any younger age did not promote long-term effects on learning performance. The associative learning events that occurred a few days after adult emergence improved memorizing in middle-aged bees. In addition, both the timing and the nature of early sensory inputs interact to enhance retention of new learning events acquired later in life, an important matter in the social life of honeybees.

How Many Genetic Variants Remain to Be Discovered?:

A great majority of genetic markers discovered in recent genome-wide association studies have small effect sizes, and they explain only a small fraction of the genetic contribution to the diseases. How many more variants can we expect to discover and what study sizes are needed? We derive the connection between the cumulative risk of the SNP variants to the latent genetic risk model and heritability of the disease. We determine the sample size required for case-control studies in order to achieve a certain expected number of discoveries in a collection of most significant SNPs. Assuming similar allele frequencies and effect sizes of the currently validated SNPs, complex phenotypes such as type-2 diabetes would need approximately 800 variants to explain its 40% heritability. Much smaller numbers of variants are needed if we assume rare-variants but higher penetrance models. We estimate that up to 50,000 cases and an equal number of controls are needed to discover 800 common low-penetrant variants among the top 5000 SNPs. Under common and rare low-penetrance models, the very large studies required to discover the numerous variants are probably at the limit of practical feasibility. Under rare-variant with medium- to high-penetrance models (odds-ratios between 1.6 and 4.0), studies comparable in size to many existing studies are adequate provided the genotyping technology can interrogate more and rarer variants.

Fulfilling the Promise of Personalized Medicine? Systematic Review and Field Synopsis of Pharmacogenetic Studies:

Studies of the genetic basis of drug response could help clarify mechanisms of drug action/metabolism, and facilitate development of genotype-based predictive tests of efficacy or toxicity (pharmacogenetics). We conducted a systematic review and field synopsis of pharmacogenetic studies to quantify the scope and quality of available evidence in this field in order to inform future research. Original research articles were identified in Medline, reference lists from 24 meta-analyses/systematic reviews/review articles and U.S. Food and Drug Administration website of approved pharmacogenetic tests. We included any study in which either intended or adverse response to drug therapy was examined in relation to genetic variation in the germline or cancer cells in humans. Study characteristics and data reported in abstracts were recorded. We further analysed full text from a random 10% subset of articles spanning the different subclasses of study. From 102,264 Medline hits and 1,641 articles from other sources, we identified 1,668 primary research articles (1987 to 2007, inclusive). A high proportion of remaining articles were reviews/commentaries (ratio of reviews to primary research approximately 25:1). The majority of studies (81.8%) were set in Europe and North America focussing on cancer, cardiovascular disease and neurology/psychiatry. There was predominantly a candidate gene approach using common alleles, which despite small sample sizes (median 93 [IQR 40-222]) with no trend to an increase over time, generated a high proportion (74.5%) of nominally significant (p<0.05) reported associations suggesting the possibility of significance-chasing bias. Despite 136 examples of gene/drug interventions being the subject of ≥4 studies, only 31 meta-analyses were identified. The majority (69.4%) of end-points were continuous and likely surrogate rather than hard (binary) clinical end-points. The high expectation but limited translation of pharmacogenetic research thus far may be explained by the preponderance of reviews over primary research, small sample sizes, a mainly candidate gene approach, surrogate markers, an excess of nominally positive to truly positive associations and paucity of meta-analyses. Recommendations based on these findings should inform future study design to help realise the goal of personalised medicines.