bluuebunny/crossref_metadata_2025 huggingface dataset:
The improved oxidation resistance of Si-doped SmCo7 nanocrystalline magnet
Authors: Liu Lili , Jiang Chengbao
Published: June 2011

A drastic improvement in oxidation resistance of SmCo7 nanocrystalline magnet was achieved by alloying silicon at 500 °C. The maximum energy product (BH)max loss of SmCo6.1Si0.9 nanocrystalline magnet was about 5.6% after oxidation at 500 °C for 500 h, which was significantly less than 52.1% of SmCo7 nanocrystalline magnet. A general mode was proposed to predict the (BH)max loss as a function of oxidation time at 500 °C. The formation of SiO2 oxide in the internal oxidation layer plays an important role in reducing the oxidation rate and oxygen diffusion coefficient, which leads to the enhancement of inherent oxidation resistance of SmCo6.1Si0.9 nanocrystalline magnet.
Acceptor deactivation in individual silicon nanowires: From thick to ultrathin
Authors: Ou Xin , Geyer Nadine , Kögler Reinhard , Werner Peter , Skorupa Wolfgang
Published: June 2011

We investigate the doping behavior in the ultrathin part of individual free standing spicular or conic silicon nanowires (NWs) by measuring the local resistivity of the NWs using scanning spreading resistance microscopy. The NWs are boron-doped and the doping efficiency is found to dramatically decrease as the NW diameter is below 25 nm. Our experimental results reveal the dependence of the acceptor deactivation on the diameter of the NW cross section. The deactivation mechanism is discussed by comparing the experimental data with theoretical models considering the dopant deactivation induced by carrier traps at the Si/SiO2 interface and due to the dielectric mismatch.
Differential ultra low noise amplifier for low frequency noise measurements
Authors: Scandurra Graziella , Cannatà Gianluca , Ciofi Carmine
Published: June 2011

Almost all low noise voltage preamplifier suitable for application in the field of Low Frequency Noise Measurements (either commercially available or proposed in the literature) are single ended input amplifiers. This means that one end of the measuring port of the Device Under Test (DUT) must be connected to common ground. This may be a severe limitation in many interesting measurement configurations, such as the case in which Kelvin connections to the DUT must be employed. In this paper we propose a simple design of a fully differential input ultra low noise amplifier with noise performances, in term of equivalent input voltage noise, comparable to those of the best single ended input amplifiers for low frequency noise measurements reported in the literature. Indeed, the amplifier we propose is characterized by a voltage gain of 80 dB, in the bandwidth from a few tens of mHz up to a few kHz, and by an equivalent input voltage noise as low as 14 nV/√Hz (100 mHz), 2 nV/√Hz (1 Hz), 1.2 nV/√Hz (10 Hz) and 1 nV/√Hz (1 kHz). Such an amplifier can also be employed as a single ended input amplifier by simply shorting to ground one of the two differential input ports.
Size-controlled growth of ZnO nanowires by catalyst-free high-pressure pulsed laser deposition and their optical properties
Authors: Liu W. Z. , Xu H. Y. , Wang L. , Li X. H. , Liu Y. C.
Published: June 2011

Single crystalline ZnO nanowires were fabricated on Si (100) substrates by catalyst-free high-pressure pulsed laser deposition. It is found that the nanowires start to form when the substrate temperature and growth pressure exceed the critical values of 700 oC and 700 Pa, and their size strongly depends on these growth conditions. That is, the aspect ratio of the nanowires decreases with increasing temperature or decreasing pressure. Such a size dependence on growth conditions was discussed in terms of surface migration and scattering of ablated atoms. Room-temperature photoluminescence spectrum of ZnO nanowires shows a dominant near-band-edge emission peak at 3.28 eV and a visible emission band centered at 2.39 eV. Temperature-dependent photoluminescence studies reveal that the former consists of the acceptor-bound exciton and free exciton emissions; while the latter varies in intensity with the aspect ratio of the nanowires and is attributed to the surface-mediated deep level emission.
Performance of passive integrated transponders (PIT tags) as a marking system for common brushtail possums Trichosurus vulpecula - a cautionary tale.
Authors: Eymann J. , Webley L.S. , Cooper D. W. , Herbert C. A.
Published: June 2011

Passive integrated transponders (PIT tags) have been used to mark many vertebrates and in this study 196 Trichosurus vulpecula were fitted with a Trovan ID-100 PIT tag when first captured for DNA studies using tissue samples from the ear pinnae. Not all individuals were recaptured but evidence based on a hole, scar or tear in the ear, presumably form previous tissue sampling, suggested 17 PIT tag failures. In 6 individuals a PIT tag was palpable under the skin at the place of insertion. In 3 animals the PIT tag malfunctioned after 5-16 months despite working on previous recaptures. Of the 17 suspected malfunctions, 13 could be verified as recaptured individuals through genotypic matching. The remaining 4 suspected failures could not be matched genotypically and were considered to be newly trapped. A back-up mehtod, such as tattooing or genetic tagging, should be considered.
Experimental study and modelling of inorganic Cd2+ speciation in natural waters
Authors: Foti Claudia , Lando Gabriele , Millero Frank J. , Sammartano Silvio
Published: June 2011

Environmental contextCadmium(II) is considered as one of the most dangerous pollutants in natural waters. We performed a complete study on the interactions of cadmium(II) with inorganic components of natural waters, by using new experiments and some literature data. The body of results can be considered an improvement in modelling the inorganic speciation of cadmium(II) in natural waters.
AbstractAn analysis of literature data together with new potentiometric and voltammetric studies on the interaction between Cd2+ and the common environmental inorganic ligands, such as OH–, Cl–, F–, CO32– and SO42–, was reported at t = 25°C. New formation constant values for CdCl+, CdCl20, CdCl(OH)0, CdSO40, CdCO30 and CdF+ species at different ionic strengths (0.1 ≤ I ≤ 1 mol L–1) were determined. The cumulative seawater ligand capacity was evaluated by using a model in which synthetic seawater is expressed as a single salt BA, where the major cations (Na+, K+, Ca2+ and Mg2+) are represented by a single cation Bz+ and the anions (Cl– and SO42–) by a single anion Az– (|z| = 1.117). The formation of CdA0.883+ and CdA(OH)0.117– species was proposed and formation constants are reported at different salinities (5 ≤ S ≤ 45). The ionic strength dependence of the stability constants was studied by means of Pitzer and SIT (Specific ion Interaction Theory) equations.
Nutrition and physical activity guidance for women in the pre- and post-natal period: a continuing education needs assessment in primary health care
Authors: Hughes Roger , Maher Judith , Baillie Elizabeth , Shelton Doug
Published: June 2011

The study objective was to assess primary health care (PHC) providers’ exposure to women in the pre- and post-natal period, current nutrition and physical activity guidance practices, confidence and perceived needs for continuing education relevant to nutrition and physical activity guidance in the peri-natal period. A self-administered cross-sectional questionnaire survey amongst a purposively recruited sample of 226 local primary health care providers evenly distributed across general practice, community nursing, pharmacist and pharmacy assistant worker groups. The questionnaire contained 106 items about primary health care providers’ exposure to women in the pre- and post-natal life-stage, their current nutrition and physical activity guidance practices, confidence and perceived needs for continuing education relevant to nutrition and physical activity guidance in the peri-natal period. Results indicate that PHC providers across general practice, community nursing and pharmacy service settings are frequently accessed by women during this life-stage, and regularly and variably provide guidance on nutrition and physical activity, and report different continuing education needs. Continuing education interventions need to be tailored to match the needs of each PHC group. Pharmacy-based staff are a priority for PHC continuing education about nutrition and physical activity if the potential of the community-based pharmacy as a primary health setting is to be realised.
Improving the professional support for parents of young infants
Authors: Eronen Ritva , Calabretto Helen , Pincombe Jan
Published: June 2011

The objective of this study was to discuss ideas for improving child health services on the basis of findings of an observational study that was designed to explore the role of child health nurses in supporting parents during the first 6 months following the birth of an infant. As part of a larger study in a child health service in urban Australia, surveys were used to collect data from two independent samples of both parents and nurses at an 8-month interval. Data were condensed using factor analysis; regression analyses were used to determine which aspects of care were most important for the parents, and importance–performance analysis was used to determine which aspects of care needed improvement. While the majority of parents valued support from child health nurses, a need for improvement was identified in empowering parents to make their own decisions, discussing emotional issues with parents, providing continuity of care and giving consistent advice. Organisations should value and provide support for child health nurses in their invisible, non-quantifiable work of supporting families. The structure of child health services should also provide child health nurses continuity of care with the families they support.
Laminar differences in gamma and alpha coherence in the ventral stream
Authors: Buffalo Elizabeth A. , Fries Pascal , Landman Rogier , Buschman Timothy J. , Desimone Robert
Published: June 2011

Attention to a stimulus enhances both neuronal responses and gamma frequency synchrony in visual area V4, both of which should increase the impact of attended information on downstream neurons. To determine whether gamma synchrony is common throughout the ventral stream, we recorded from neurons in the superficial and deep layers of V1, V2, and V4 in two rhesus monkeys. We found an unexpected striking difference in gamma synchrony in the superficial vs. deep layers. In all three areas, spike-field coherence in the gamma (40–60 Hz) frequency range was largely confined to the superficial layers, whereas the deep layers showed maximal coherence at low frequencies (6–16 Hz), which included the alpha range. In the superficial layers of V2 and V4, gamma synchrony was enhanced by attention, whereas in the deep layers, alpha synchrony was reduced by attention. Unlike these major differences in synchrony, attentional effects on firing rates and noise correlation did not differ substantially between the superficial and deep layers. The results suggest that synchrony plays very different roles in feedback and feedforward projections.
Neurotrophin-mediated dendrite-to-nucleus signaling revealed by microfluidic compartmentalization of dendrites
Authors: Cohen Michael S. , Orth Carlos Bas , Kim Hyung Joon , Jeon Noo Li , Jaffrey Samie R.
Published: June 2011

Signaling from dendritic synapses to the nucleus regulates important aspects of neuronal function, including synaptic plasticity. The neurotrophin brain-derived neurotrophic factor (BDNF) can induce long-lasting strengthening of synapses in vivo and this effect is dependent on transcription. However, the mechanism of signaling to the nucleus is not well understood. Here we describe a microfluidic culture device to investigate dendrite-to-nucleus signaling. Using these microfluidic devices, we demonstrate that BDNF can act directly on dendrites to elicit an anterograde signal that induces transcription of the immediate early genes,
Arc
and
c-Fos
. Induction of Arc is dependent on dendrite- and cell body-derived calcium, whereas induction of c-Fos is calcium-independent. In contrast to retrograde neurotrophin-mediated axon-to-nucleus signaling, which is MEK5-dependent, BDNF-mediated anterograde dendrite-to-nucleus signaling is dependent on MEK1/2. Intriguingly, the activity of TrkB, the BDNF receptor, is required in the cell body for the induction of Arc and c-Fos mediated by dendritically applied BDNF. These results are consistent with the involvement of a signaling endosome-like pathway that conveys BDNF signals from the dendrite to the nucleus.
Slow protein evolutionary rates are dictated by surface–core association
Authors: Tóth-Petróczy Ágnes , Tawfik Dan S.
Published: June 2011

Why do certain proteins evolve much slower than others? We compared not only rates per protein, but also rates per position within individual proteins. For ∼90% of proteins, the distribution of positional rates exhibits three peaks: a peak of slow evolving residues, with average log
2
[normalized rate], log
2
μ, of ca. −2, corresponding primarily to core residues; a peak of fast evolving residues (log
2
μ ∼ 0.5) largely corresponding to surface residues; and a very fast peak (log
2
μ ∼ 2) associated with disordered segments. However, a unique fraction of proteins that evolve very slowly exhibit not only a negligible fast peak, but also a peak with a log
2
μ ∼ −4, rather than the standard core peak of −2. Thus, a “freeze” of a protein's surface seems to stop core evolution as well. We also observed a much higher fraction of substitutions in potentially interacting residues than expected by chance, including substitutions in pairs of contacting surface-core residues. Overall, the data suggest that accumulation of surface substitutions enables the acceptance of substitutions in core positions. The underlying reason for slow evolution might therefore be a highly constrained surface due to protein–protein interactions or the need to prevent misfolding or aggregation. If the surface is inaccessible to substitutions, so becomes the core, thus resulting in very slow overall rates.
Glycogen synthase kinase 3β-dependent Snail degradation directs hepatocyte proliferation in normal liver regeneration
Authors: Sekiya Sayaka , Suzuki Atsushi
Published: June 2011

Liver regeneration proceeds under the well-orchestrated control of multiple transcription factors that lead hepatocytes to reenter the cell cycle, proliferate, and renew quiescence. Here, we found an important role of the zinc-finger transcription factor Snail in liver regeneration. Snail was typically expressed in quiescent adult hepatocytes, but was rapidly degraded when the liver needed to regenerate itself. Decreased levels of Snail induced DNA synthesis in hepatocytes through up-regulation of cell cycle-related proteins. Snail degradation was dependent on phosphorylation by glycogen synthase kinase (GSK)-3β, whose quantity and activity were immediately increased after loss of liver mass or hepatic injury. Inactivation of GSK-3β resulted in suppression of Snail degradation and DNA synthesis in hepatocytes, leading to impaired liver growth during regeneration. This GSK-3β–dependent Snail degradation occurred as a result of cytokine, growth factor, and bile acid signals that are known to drive liver regeneration. Thus, GSK-3β–dependent Snail degradation acts as a fundamental cue for the initiation of hepatocyte proliferation in liver regeneration.
Household and community poverty, biomass use, and air pollution in Accra, Ghana
Authors: Zhou Zheng , Dionisio Kathie L. , Arku Raphael E. , Quaye Audrey , Hughes Allison F. , Vallarino Jose , Spengler John D. , Hill Allan , Agyei-Mensah Samuel , Ezzati Majid
Published: June 2011

Many urban households in developing countries use biomass fuels for cooking. The proportion of household biomass use varies among neighborhoods, and is generally higher in low socioeconomic status (SES) communities. Little is known of how household air pollution varies by SES and how it is affected by biomass fuels and traffic sources in developing country cities. In four neighborhoods in Accra, Ghana, we collected and analyzed geo-referenced data on household and community particulate matter (PM) pollution, SES, fuel use for domestic and small-commercial cooking, housing characteristics, and distance to major roads. Cooking area PM was lowest in the high-SES neighborhood, with geometric means of 25 (95% confidence interval, 21–29) and 28 (23–33) μg/m
3
for fine and coarse PM (PM
2.5
and PM
2.5–10
), respectively; it was highest in two low-SES slums, with geometric means reaching 71 (62–80) and 131 (114–150) μg/m
3
for fine and coarse PM. After adjustment for other factors, living in a community where all households use biomass fuels would be associated with 1.5- to 2.7-times PM levels in models with and without adjustment for ambient PM. Community biomass use had a stronger association with household PM than household's own fuel choice in crude and adjusted estimates. Lack of regular physical access to clean fuels is an obstacle to fuel switching in low-income neighborhoods and should be addressed through equitable energy infrastructure.
Evolution of restraint in a structured rock–paper–scissors community
Authors: Nahum Joshua R. , Harding Brittany N. , Kerr Benjamin
Published: June 2011

It is not immediately clear how costly behavior that benefits others evolves by natural selection. By saving on inherent costs, individuals that do not contribute socially have a selective advantage over altruists if both types receive equal benefits. Restrained consumption of a common resource is a form of altruism. The cost of this kind of prudent behavior is that restrained individuals give up resources to less-restrained individuals. The benefit of restraint is that better resource management may prolong the persistence of the group. One way to dodge the problem of defection is for altruists to interact disproportionately with other altruists. With limited dispersal, restrained individuals persist because of interaction with like types, whereas it is the unrestrained individuals that must face the negative long-term consequences of their rapacity. Here, we study the evolution of restraint in a community of three competitors exhibiting a nontransitive (rock–paper–scissors) relationship. The nontransitivity ensures a form of negative feedback, whereby improvement in growth of one competitor has the counterintuitive consequence of lowering the density of that improved player. This negative feedback generates detrimental long-term consequences for unrestrained growth. Using both computer simulations and evolution experiments with a nontransitive community of
Escherichia coli
, we find that restrained growth can evolve under conditions of limited dispersal in which negative feedback is present. This research, thus, highlights a set of ecological conditions sufficient for the evolution of one form of altruism.
Expanded social fitness and Hamilton's rule for kin, kith, and kind
Authors: Queller David C.
Published: June 2011

Inclusive fitness theory has a combination of simplicity, generality, and accuracy that has made it an extremely successful way of thinking about and modeling effects on kin. However, there are types of social interactions that, although covered, are not illuminated. Here, I expand the inclusive fitness approach and the corresponding neighbor-modulated approach to specify two other kinds of social selection. Kind selection, which includes greenbeards and many nonadditive games, is where selection depends on an actor's trait having different effects on others depending on whether they share the trait. Kith selection includes social effects that do not require either kin or kind, such as mutualism and manipulation. It involves social effects of a trait that affect a partner, with feedback to the actor's fitness. I derive expanded versions of Hamilton's rule for kith and kind selection, generalizing Hamilton's insight that we can model social selection through a sum of fitness effects, each multiplied by an appropriate association coefficient. Kinship is, thus, only one of the important types of association, but all can be incorporated within an expanded inclusive fitness.
Molecular evolutionary analyses of insect societies
Authors: Fischman Brielle J. , Woodard S. Hollis , Robinson Gene E.
Published: June 2011

The social insects live in extraordinarily complex and cohesive societies, where many individuals sacrifice their personal reproduction to become helpers in the colony. Identifying adaptive molecular changes involved in eusocial evolution in insects is important for understanding the mechanisms underlying transitions from solitary to social living, as well as the maintenance and elaboration of social life. Here, we review recent advances made in this area of research in several insect groups: the ants, bees, wasps, and termites. Drawing from whole-genome comparisons, candidate gene approaches, and a genome-scale comparative analysis of protein-coding sequence, we highlight novel insights gained for five major biological processes: chemical signaling, brain development and function, immunity, reproduction, and metabolism and nutrition. Lastly, we make comparisons across these diverse approaches and social insect lineages and discuss potential common themes of eusocial evolution, as well as challenges and prospects for future research in the field.
Spatiotemporal environmental variation, risk aversion, and the evolution of cooperative breeding as a bet-hedging strategy
Authors: Rubenstein Dustin R.
Published: June 2011

In cooperatively breeding systems in which some individuals delay reproduction to help raise others’ offspring, environmental variation in space and time influences individual reproductive strategies as well as interspecific patterns of sociality. Although most environmental explanations for cooperative breeding emphasize the mean fitness gains of living socially, the fittest individuals are not always those that produce on average the highest number of offspring. At times, variance in fecundity can influence fitness as much as mean fecundity, particularly in small populations like those of cooperative breeders. Cooperative breeding behavior could therefore be a risk-averse strategy to maximize fitness by reducing environmentally induced fecundity variance. Such a within-generation bet-hedging hypothesis for social evolution predicts that (
i
) variance in reproductive success should be related to environmental variation, (
ii
) variance in reproductive success should be related to the potential for cooperation in a group, and (
iii
) the potential for cooperation should be related to environmental variation. Using data from a 10-y study of cooperatively breeding superb starlings (
Lamprotornis superbus
) living in a temporally and spatially variable savanna ecosystem, I found that variance in reproductive success declined with increasing environmental quality (temporal variation), increasing territory quality (spatial variation), and increasing group size (potential for cooperation), which is itself related to environmental variation. To understand the adaptive value of cooperative breeding behavior in variable environments, researchers must consider both mean and environmentally induced variance in fecundity. Determining how spatiotemporal environmental variation drives risk-averse strategies may provide insights into the evolution of complex social behavior.
Evolutionary transitions in bacterial symbiosis
Authors: Sachs Joel L. , Skophammer Ryan G. , Regus John U.
Published: June 2011

Diverse bacterial lineages form beneficial infections with eukaryotic hosts. The origins, evolution, and breakdown of these mutualisms represent important evolutionary transitions. To examine these key events, we synthesize data from diverse interactions between bacteria and eukaryote hosts. Five evolutionary transitions are investigated, including the origins of bacterial associations with eukaryotes, the origins and subsequent stable maintenance of bacterial mutualism with hosts, the capture of beneficial symbionts via the evolution of strict vertical transmission within host lineages, and the evolutionary breakdown of bacterial mutualism. Each of these transitions has occurred many times in the history of bacterial–eukaryote symbiosis. We investigate these evolutionary events across the bacterial domain and also among a focal set of well studied bacterial mutualist lineages. Subsequently, we generate a framework for examining evolutionary transitions in bacterial symbiosis and test hypotheses about the selective, ecological, and genomic forces that shape these events.
Diffusion model for one-choice reaction-time tasks and the cognitive effects of sleep deprivation
Authors: Ratcliff Roger , Van Dongen Hans P. A.
Published: June 2011

One-choice reaction-time (RT) tasks are used in many domains, including assessments of motor vehicle driving and assessments of the cognitive/behavioral consequences of sleep deprivation. In such tasks, subjects are asked to respond when they detect the onset of a stimulus; the dependent variable is RT. We present a cognitive model for one-choice RT tasks that uses a one-boundary diffusion process to represent the accumulation of stimulus information. When the accumulated evidence reaches a decision criterion, a response is initiated. This model is distinct in accounting for the RT distributions observed for one-choice RT tasks, which can have long tails that have not been accurately captured by earlier cognitive modeling approaches. We show that the model explains performance on a brightness-detection task (a “simple RT task”) and on a psychomotor vigilance test. The latter is used extensively to examine the clinical and behavioral effects of sleep deprivation. For the brightness-detection task, the model explains the behavior of RT distributions as a function of brightness. For the psychomotor vigilance test, it accounts for lapses in performance under conditions of sleep deprivation and for changes in the shapes of RT distributions over the course of sleep deprivation. The model also successfully maps the rate of accumulation of stimulus information onto independently derived predictions of alertness. The model is a unified, mechanistic account of one-choice RT under conditions of sleep deprivation.
Reduction-oxidation poise regulates the sign of phototaxis in
Chlamydomonas reinhardtii
Authors: Wakabayashi Ken-ichi , Misawa Yuka , Mochiji Shota , Kamiya Ritsu
Published: June 2011

In many phototrophic microorganisms and plants, chloroplasts change their positions relative to the incident light to achieve optimal photosynthesis. In the case of motile green algae, cells change their swimming direction by switching between positive and negative phototaxis, i.e., swimming toward or away from the light source, depending on environmental and internal conditions. However, little is known about the molecular signals that determine the phototactic direction. Using the green alga
Chlamydomonas reinhardtii
, we found that cellular reduction-oxidation (redox) poise plays a key role: Cells always exhibited positive phototaxis after treatment with reactive oxygen species (ROS) and always displayed negative phototaxis after treatment with ROS quenchers. The redox-dependent switching of the sign of phototaxis may contribute in turn to the maintenance of cellular redox homeostasis.
Functional motor recovery from brain ischemic insult by carbon nanotube-mediated siRNA silencing
Authors: Al-Jamal Khuloud T. , Gherardini Lisa , Bardi Giuseppe , Nunes Antonio , Guo Chang , Bussy Cyrill , Herrero M. Antonia , Bianco Alberto , Prato Maurizio , Kostarelos Kostas , Pizzorusso Tommaso
Published: June 2011

Stroke is the second cause of death worldwide with ischemic stroke accounting for 80% of all stroke insults. Caspase-3 activation contributes to brain tissue loss and downstream biochemical events that lead to programmed cell death after traumatic brain injury. Alleviation of symptoms following ischemic neuronal injury can be potentially achieved by either genetic disruption or pharmacological inhibition of caspases. Here, we studied whether silencing of Caspase-3 using carbon nanotube-mediated in vivo RNA interference (RNAi) could offer a therapeutic opportunity against stroke. Effective delivery of siRNA directly to the CNS has been shown to normalize phenotypes in animal models of several neurological diseases. It is shown here that peri-lesional stereotactic administration of a Caspase-3 siRNA (siCas 3) delivered by functionalized carbon nanotubes (f-CNT) reduced neurodegeneration and promoted functional preservation before and after focal ischemic damage of the rodent motor cortex using an endothelin-1 induced stroke model. These observations illustrate the opportunity offered by carbon nanotube-mediated siRNA delivery and gene silencing of neuronal tissue applicable to a variety of different neuropathological conditions where intervention at well localized brain foci may offer therapeutic and functional benefits.
Acute hepatitis A virus infection is associated with a limited type I interferon response and persistence of intrahepatic viral RNA
Authors: Lanford Robert E. , Feng Zongdi , Chavez Deborah , Guerra Bernadette , Brasky Kathleen M. , Zhou Yan , Yamane Daisuke , Perelson Alan S. , Walker Christopher M. , Lemon Stanley M.
Published: June 2011

Hepatitis A virus (HAV) is an hepatotropic human picornavirus that is associated only with acute infection. Its pathogenesis is not well understood because there are few studies in animal models using modern methodologies. We characterized HAV infections in three chimpanzees, quantifying viral RNA by quantitative RT-PCR and examining critical aspects of the innate immune response including intrahepatic IFN-stimulated gene expression. We compared these infection profiles with similar studies of chimpanzees infected with hepatitis C virus (HCV), an hepatotropic flavivirus that frequently causes persistent infection. Surprisingly, HAV-infected animals exhibited very limited induction of type I IFN-stimulated genes in the liver compared with chimpanzees with acute resolving HCV infection, despite similar levels of viremia and 100-fold greater quantities of viral RNA in the liver. Minimal IFN-stimulated gene 15 and IFIT1 responses peaked 1–2 wk after HAV challenge and then subsided despite continuing high hepatic viral RNA. An acute inflammatory response at 3–4 wk correlated with the appearance of virus-specific antibodies and apoptosis and proliferation of hepatocytes. Despite this, HAV RNA persisted in the liver for months, remaining present long after clearance from serum and feces and revealing dramatic differences in the kinetics of clearance in the three compartments. Viral RNA was detected in the liver for significantly longer (35 to >48 wk) than HCV RNA in animals with acute resolving HCV infection (10–20 wk). Collectively, these findings indicate that HAV is far stealthier than HCV early in the course of acute resolving infection. HAV infections represent a distinctly different paradigm in virus–host interactions within the liver.
Selfish genetic elements, genetic conflict, and evolutionary innovation
Authors: Werren John H.
Published: June 2011

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible “evolutionary functions” of SGEs.
Evolution of cooperation and control of cheating in a social microbe
Authors: Strassmann Joan E. , Queller David C.
Published: June 2011

Much of what we know about the evolution of altruism comes from animals. Here, we show that studying a microbe has yielded unique insights, particularly in understanding how social cheaters are controlled. The social stage of
Dictylostelium discoideum
occurs when the amoebae run out of their bacterial prey and aggregate into a multicellular, motile slug. This slug forms a fruiting body in which about a fifth of cells die to form a stalk that supports the remaining cells as they form hardy dispersal-ready spores. Because this social stage forms from aggregation, it is analogous to a social group, or a chimeric multicellular organism, and is vulnerable to internal conflict. Advances in cell labeling, microscopy, single-gene knockouts, and genomics, as well as the results of decades of study of
D. discoideum
as a model for development, allow us to explore the genetic basis of social contests and control of cheaters in unprecedented detail. Cheaters are limited from exploiting other clones by high relatedness, kin discrimination, pleiotropy, noble resistance, and lottery-like role assignment. The active nature of these limits is reflected in the elevated rates of change in social genes compared with nonsocial genes. Despite control of cheaters, some conflict is still expressed in chimeras, with slower movement of slugs, slightly decreased investment in stalk compared with spore cells, and differential contributions to stalk and spores.
D. discoideum
is rapidly becoming a model system of choice for molecular studies of social evolution.
Gas uptake and chemical aging of semisolid organic aerosol particles
Authors: Shiraiwa Manabu , Ammann Markus , Koop Thomas , Pöschl Ulrich
Published: June 2011

Organic substances can adopt an amorphous solid or semisolid state, influencing the rate of heterogeneous reactions and multiphase processes in atmospheric aerosols. Here we demonstrate how molecular diffusion in the condensed phase affects the gas uptake and chemical transformation of semisolid organic particles. Flow tube experiments show that the ozone uptake and oxidative aging of amorphous protein is kinetically limited by bulk diffusion. The reactive gas uptake exhibits a pronounced increase with relative humidity, which can be explained by a decrease of viscosity and increase of diffusivity due to hygroscopic water uptake transforming the amorphous organic matrix from a glassy to a semisolid state (moisture-induced phase transition). The reaction rate depends on the condensed phase diffusion coefficients of both the oxidant and the organic reactant molecules, which can be described by a kinetic multilayer flux model but not by the traditional resistor model approach of multiphase chemistry. The chemical lifetime of reactive compounds in atmospheric particles can increase from seconds to days as the rate of diffusion in semisolid phases can decrease by multiple orders of magnitude in response to low temperature or low relative humidity. The findings demonstrate that the occurrence and properties of amorphous semisolid phases challenge traditional views and require advanced formalisms for the description of organic particle formation and transformation in atmospheric models of aerosol effects on air quality, public health, and climate.
Structure of
Trypanosoma brucei
flagellum accounts for its bihelical motion
Authors: Koyfman Alexey Y. , Schmid Michael F. , Gheiratmand Ladan , Fu Caroline J. , Khant Htet A. , Huang Dandan , He Cynthia Y. , Chiu Wah
Published: June 2011

Trypanosoma brucei
is a parasitic protozoan that causes African sleeping sickness. It contains a flagellum required for locomotion and viability. In addition to a microtubular axoneme, the flagellum contains a crystalline paraflagellar rod (PFR) and connecting proteins. We show here, by cryoelectron tomography, the structure of the flagellum in three bending states. The PFR lattice in straight flagella repeats every 56 nm along the length of the axoneme, matching the spacing of the connecting proteins. During flagellar bending, the PFR crystallographic unit cell lengths remain constant while the interaxial angles vary, similar to a jackscrew. The axoneme drives the expansion and compression of the PFR lattice. We propose that the PFR modifies the in-plane axoneme motion to produce the characteristic trypanosome bihelical motility as captured by high-speed light microscope videography.
Measuring single-cell density
Authors: Grover William H. , Bryan Andrea K. , Diez-Silva Monica , Suresh Subra , Higgins John M. , Manalis Scott R.
Published: June 2011

We have used a microfluidic mass sensor to measure the density of single living cells. By weighing each cell in two fluids of different densities, our technique measures the single-cell mass, volume, and density of approximately 500 cells per hour with a density precision of 0.001 g mL
-1
. We observe that the intrinsic cell-to-cell variation in density is nearly 100-fold smaller than the mass or volume variation. As a result, we can measure changes in cell density indicative of cellular processes that would be otherwise undetectable by mass or volume measurements. Here, we demonstrate this with four examples: identifying
Plasmodium falciparum
malaria-infected erythrocytes in a culture, distinguishing transfused blood cells from a patient’s own blood, identifying irreversibly sickled cells in a sickle cell patient, and identifying leukemia cells in the early stages of responding to a drug treatment. These demonstrations suggest that the ability to measure single-cell density will provide valuable insights into cell state for a wide range of biological processes.
Designing super selectivity in multivalent nano-particle binding
Authors: Martinez-Veracoechea Francisco J. , Frenkel Daan
Published: June 2011

A key challenge in nano-science is to design ligand-coated nano-particles that can bind selectively to surfaces that display the cognate receptors above a threshold (surface) concentration. Nano-particles that bind monovalently to a target surface do not discriminate sharply between surfaces with high and low receptor coverage. In contrast, “multivalent” nano-particles that can bind to a larger number of ligands simultaneously, display regimes of “super selectivity” where the fraction of bound particles varies sharply with the receptor concentration. We present numerical simulations that show that multivalent nano-particles can be designed such that they approach the “on-off” binding behavior ideal for receptor-concentration selective targeting. We propose a simple analytical model that accounts for the super selective behavior of multivalent nano-particles. The model shows that the super selectivity is due to the fact that the number of distinct ligand-receptor binding arrangements increases in a highly nonlinear way with receptor coverage. Somewhat counterintuitively, our study shows that selectivity can be improved by making the individual ligand-receptor bonds weaker. We propose a simple rule of thumb to predict the conditions under which super selectivity can be achieved. We validate our model predictions against the Monte Carlo simulations.
Functional genome analysis of
Bifidobacterium breve
UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor
Authors: O'Connell Motherway Mary , Zomer Aldert , Leahy Sinead C. , Reunanen Justus , Bottacini Francesca , Claesson Marcus J. , O'Brien Frances , Flynn Kiera , Casey Patrick G. , Moreno Munoz Jose Antonio , Kearney Breda , Houston Aileen M. , O'Mahony Caitlin , Higgins Des G. , Shanahan Fergus , Palva Airi , de Vos Willem M. , Fitzgerald Gerald F. , Ventura Marco , O'Toole Paul W. , van Sinderen Douwe
Published: June 2011

Development of the human gut microbiota commences at birth, with bifidobacteria being among the first colonizers of the sterile newborn gastrointestinal tract. To date, the genetic basis of
Bifidobacterium
colonization and persistence remains poorly understood. Transcriptome analysis of the
Bifidobacterium breve
UCC2003 2.42-Mb genome in a murine colonization model revealed differential expression of a type IVb tight adherence (Tad) pilus-encoding gene cluster designated “

tad
2003

.” Mutational analysis demonstrated that the

tad
2003

gene cluster is essential for efficient in vivo murine gut colonization, and immunogold transmission electron microscopy confirmed the presence of Tad pili at the poles of
B. breve
UCC2003 cells. Conservation of the Tad pilus-encoding locus among other
B. breve
strains and among sequenced
Bifidobacterium
genomes supports the notion of a ubiquitous pili-mediated host colonization and persistence mechanism for bifidobacteria.
Centralized sanctioning and legitimate authority promote cooperation in humans
Authors: Baldassarri Delia , Grossman Guy
Published: June 2011

Social sanctioning is widely considered a successful strategy to promote cooperation among humans. In situations in which individual and collective interests are at odds, incentives to free-ride induce individuals to refrain from contributing to public goods provision. Experimental evidence from public goods games shows that when endowed with sanctioning powers, conditional cooperators can discipline defectors, thus leading to greater levels of cooperation. However, extant evidence is based on peer punishment institutions, whereas in complex societies, systems of control are often centralized: for instance, we do not sanction our neighbors for driving too fast, the police do. Here we show the effect of centralized sanctioning and legitimate authority on cooperation. We designed an adaptation of the public goods game in which sanctioning power is given to a single monitor, and we experimentally manipulated the process by which the monitor is chosen. To increase the external validity of the study, we conducted lab-in-the-field experiments involving 1,543 Ugandan farmers from 50 producer cooperatives. This research provides evidence of the effectiveness of centralized sanctioning and demonstrates the causal effect of legitimacy on cooperation: participants are more responsive to the authority of an elected monitor than a randomly chosen monitor. Our essay contributes to the literature on the evolution of cooperation by introducing the idea of role differentiation. In complex societies, cooperative behavior is not only sustained by mechanisms of selection and reciprocity among peers, but also by the legitimacy that certain actors derive from their position in the social hierarchy.
Dispatched mediates Hedgehog basolateral release to form the long-range morphogenetic gradient in the
Drosophila
wing disk epithelium
Authors: Callejo Ainhoa , Bilioni Aphrodite , Mollica Emanuela , Gorfinkiel Nicole , Andrés Germán , Ibáñez Carmen , Torroja Carlos , Doglio Laura , Sierra Javier , Guerrero Isabel
Published: June 2011

Hedgehog (Hh) moves from the producing cells to regulate the growth and development of distant cells in a variety of tissues. Here, we have investigated the mechanism of Hh release from the producing cells to form a morphogenetic gradient in the
Drosophila
wing imaginal disk epithelium. We describe that Hh reaches both apical and basolateral plasma membranes, but the apical Hh is subsequently internalized in the producing cells and routed to the basolateral surface, where Hh is released to form a long-range gradient. Functional analysis of the 12-transmembrane protein Dispatched, the glypican Dally-like (Dlp) protein, and the Ig-like and FNNIII domains of protein Interference Hh (Ihog) revealed that Dispatched could be involved in the regulation of vesicular trafficking necessary for basolateral release of Hh, Dlp, and Ihog. We also show that Dlp is needed in Hh-producing cells to allow for Hh release and that Ihog, which has been previously described as an Hh coreceptor, anchors Hh to the basolateral part of the disk epithelium.
Adjuvanticity of the oil-in-water emulsion MF59 is independent of Nlrp3 inflammasome but requires the adaptor protein MyD88
Authors: Seubert Anja , Calabro Samuele , Santini Laura , Galli Barbara , Genovese Alessia , Valentini Sara , Aprea Susanna , Colaprico Annalisa , D'Oro Ugo , Giuliani Marzia M. , Pallaoro Michele , Pizza Mariagrazia , O'Hagan Derek T. , Wack Andreas , Rappuoli Rino , De Gregorio Ennio
Published: June 2011

Oil-in-water emulsions have been successfully used to increase the efficacy, immunogenicity, and cross-protection of human vaccines; however, their mechanism of action is still largely unknown. Nlrp3 inflammasome has been previously associated to the activity of alum, another adjuvant broadly used in human vaccines, and MyD88 adaptor protein is required for the adjuvanticity of most Toll-like receptor agonists. We compared the contribution of Nlrp3 and MyD88 to the adjuvanticity of alum, the oil-in-water emulsion MF59, and complete Freund's adjuvant in mice using a three-component vaccine against serogroup B
Neisseria meningitidis
(rMenB). Although the basal antibody responses to the nonadjuvanted rMenB vaccine were largely dependent on Nlrp3, the high-level antibody responses induced by alum, MF59, or complete Freund's adjuvant did not require Nlrp3. Surprisingly, we found that MF59 requires MyD88 to enhance bactericidal antibody responses to the rMenB vaccine. Because MF59 did not activate any of the Toll-like receptors in vitro, we propose that MF59 requires MyD88 for a Toll-like receptor-independent signaling pathway.
Pannexin 3 functions as an ER Ca2+ channel, hemichannel, and gap junction to promote osteoblast differentiation
Authors: Ishikawa Masaki , Iwamoto Tsutomu , Nakamura Takashi , Doyle Andrew , Fukumoto Satoshi , Yamada Yoshihiko
Published: June 2011

The pannexin proteins represent a new gap junction family. However, the cellular functions of pannexins remain largely unknown. Here, we demonstrate that pannexin 3 (Panx3) promotes differentiation of osteoblasts and ex vivo growth of metatarsals. Panx3 expression was induced during osteogenic differentiation of C2C12 cells and primary calvarial cells, and suppression of this endogenous expression inhibited differentiation. Panx3 functioned as a unique Ca2+ channel in the endoplasmic reticulum (ER), which was activated by purinergic receptor/phosphoinositide 3-kinase (PI3K)/Akt signaling, followed by activation of calmodulin signaling for differentiation. Panx3 also formed hemichannels that allowed release of ATP into the extracellular space and activation of purinergic receptors with the subsequent activation of PI3K–Akt signaling. Panx3 also formed gap junctions and propagated Ca2+ waves between cells. Blocking the Panx3 Ca2+ channel and gap junction activities inhibited osteoblast differentiation. Thus, Panx3 appears to be a new regulator that promotes osteoblast differentiation by functioning as an ER Ca2+ channel and a hemichannel, and by forming gap junctions.