Compositional heterogeneity may limit the usefulness of some commercial naphthenic acids for toxicity assays

Naphthenic acids are considered variously as monocarboxylic acids fitting the formula C(n)H(2n+z)O(2) (where z is a zero or negative even integer), as only alicyclic (i.e. non-aromatic) monocarboxylic acids fitting this formula (z≤0), or simply as those carboxylic acids occurring in petroleum products or crude oils that have been formed through biodegradation of hydrocarbons. Such acids are known constituents of the process-affected water associated with some expanding oil sands industries, of some immature and biodegraded crude oils, of produced water discharges from oil production platforms and are used as biocides and as components in the manufacture of steel radial tyres. As a result of these potential vectors of the acids into the environment, various naphthenic acid mixtures which are available commercially have been used for a range of toxicity studies. However, as some manufacturers make clear, but which is not often emphasised in the toxicity studies, a range of different quality naphthenic acids is produced commercially. It has been suggested previously, and we showed recently and elucidate further herein, that such commercial mixtures therefore sometimes contain toxic components other than carboxylic acids. For example, we identify herein by two-dimensional comprehensive gas chromatography-mass spectrometry, a range of C(0-6) alkylphenols in a batch of commercial naphthenic acids. Since these compounds are known toxicants, the contribution of such non-carboxylic acids, if any, to the toxicity attributed previously to the acids, should also be considered. This will be reflected in the concentrations and effective toxicities of such components. In order to establish the toxicity of the acids per se, assays of pure synthetic carboxylic acids of the type now known to be present in naphthenic acids from petroleum or oil sands may be more appropriate than tests of the toxicity of largely unknown, heterogeneous, mixtures.

Interactions between CCM and N2 fixation in Trichodesmium

In view of the current increase in atmospheric pCO(2) and concomitant changes in the marine environment, it is crucial to assess, understand, and predict future responses of ecologically relevant phytoplankton species. The diazotrophic cyanobacterium Trichodesmium erythraeum was found to respond strongly to elevated pCO(2) by increasing growth, production rates, and N(2) fixation. The magnitude of these CO(2) effects exceeds those previously seen in other phytoplankton, raising the question about the underlying mechanisms. Here, we review recent publications on metabolic pathways of Trichodesmium from a gene transcription level to the protein activities and energy fluxes. Diurnal patterns of nitrogenase activity change markedly with CO(2) availability, causing higher diel N(2) fixation rates under elevated pCO(2). The observed responses to elevated pCO(2) could not be attributed to enhanced energy generation via gross photosynthesis, although there are indications for CO(2)-dependent changes in ATP/NADPH + H(+) production. The CO(2) concentrating mechanism (CCM) in Trichodesmium is primarily based on HCO(3)(-) uptake. Although only little CO(2) uptake was detected, the NDH complex seems to play a crucial role in internal cycling of inorganic carbon, especially under elevated pCO(2). Affinities for inorganic carbon change over the day, closely following the pattern in N(2) fixation, and generally decrease with increasing pCO(2). This down-regulation of CCM activity and the simultaneously enhanced N(2) fixation point to a shift in energy allocation from carbon acquisition to N(2) fixation under elevated pCO(2) levels. A strong light modulation of CO(2) effects further corroborates the role of energy fluxes as a key to understand the responses of Trichodesmium.

Analysis of osteoarthritis in a mouse model of the progeroid human DNA repair syndrome trichothiodystrophy

The increasing average age in developed societies is paralleled by an increase in the prevalence of many age-related diseases such as osteoarthritis (OA), which is characterized by deformation of the joint due to cartilage damage and increased turnover of subchondral bone. Consequently, deficiency in DNA repair, often associated with premature aging, may lead to increased pathology of these two tissues. To examine this possibility, we analyzed the bone and cartilage phenotype of male and female knee joints derived from 52- to 104-week-old WT C57Bl/6 and trichothiodystrophy (TTD) mice, who carry a defect in the nucleotide excision repair pathway and display many features of premature aging. Using micro-CT, we found bone loss in all groups of 104-week-old compared to 52-week-old mice. Cartilage damage was mild to moderate in all mice. Surprisingly, female TTD mice had less cartilage damage, proteoglycan depletion, and osteophytosis compared to WT controls. OA severity in males did not significantly differ between genotypes, although TTD males had less osteophytosis. These results indicate that in premature aging TTD mice age-related changes in cartilage were not more severe compared to WT mice, in striking contrast with bone and many other tissues. This segmental aging character may be explained by a difference in vasculature and thereby oxygen load in cartilage and bone. Alternatively, a difference in impact of an anti-aging response, previously found to be triggered by accumulation of DNA damage, might help explain why female mice were protected from cartilage damage. These findings underline the exceptional segmental nature of progeroid conditions and provide an explanation for pro- and anti-aging features occurring in the same individual.

The ectopic expression of a pectin methyl esterase inhibitor increases pectin methyl esterification and limits fungal diseases in wheat

Cell wall pectin methyl esterification can influence plant resistance because highly methyl-esterified pectin can be less susceptible to the hydrolysis by pectic enzymes such as fungal endopolygalacturonases (PG). Pectin is secreted into the cell wall in a highly methyl-esterified form and, here, is de-methyl esterified by pectin methyl esterase (PME). The activity of PME is controlled by specific protein inhibitors called PMEI; consequently, an increased inhibition of PME by PMEI might modify the pectin methyl esterification. In order to test the possibility of improving wheat resistance by modifying the methyl esterification of pectin cell wall, we have produced durum wheat transgenic lines expressing the PMEI from Actinidia chinensis (AcPMEI). The expression of AcPMEI endows wheat with a reduced endogenous PME activity, and transgenic lines expressing a high level of the inhibitor showed a significant increase in the degree of methyl esterification. These lines showed a significant reduction of disease symptoms caused by the fungal pathogens Bipolaris sorokiniana or Fusarium graminearum. This increased resistance was related to the impaired ability of these fungal pathogens to grow on methyl-esterified pectin and to a reduced activity of the fungal PG to hydrolyze methyl-esterified pectin. In addition to their importance for wheat improvement, these results highlight the primary role of pectin despite its low content in the wheat cell wall.

Quantitative analysis of shape and volume changes in activated thrombocytes in real time by single-shot spatial light modulator-based differential interference contrast imaging

We suggest to use a combination of optical tweezers and single-image quantitative differential interference contrast (DIC) emulated by a spatial light modulator (SLM) to study physiological shape changes in thrombocytes after activation and demonstrate the effectiveness of this system for the given task. A specially designed phase mask displayed at the SLM enables quantitative phase calculation from only a single recording. The optical tweezers stabilize trapped thrombocytes for long-time monitoring of changes in the optical thickness profile of thrombocytes during activation by adenosine diphosphate (ADP).

Prospective assessment of prostate cancer aggressiveness using 3-T diffusion-weighted magnetic resonance imaging-guided biopsies versus a systematic 10-core transrectal ultrasound prostate biopsy cohort

BACKGROUND

Accurate pretreatment assessment of prostate cancer (PCa) aggressiveness is important in decision making. Gleason grade is a critical predictor of the aggressiveness of PCa. Transrectal ultrasound-guided biopsies (TRUSBxs) show substantial undergrading of Gleason grades found after radical prostatectomy (RP). Diffusion-weighted magnetic resonance imaging (MRI) has been shown to be a biomarker of tumour aggressiveness.

OBJECTIVE

To improve pretreatment assessment of PCa aggressiveness, this study prospectively evaluated MRI-guided prostate biopsies (MR-GBs) of abnormalities determined on diffusion-weighted imaging (DWI) apparent diffusion coefficient (ADC) maps. The results were compared with a 10-core TRUSBx cohort. RP findings served as the gold standard.

DESIGN, SETTING, AND PARTICIPANTS

A 10-core TRUSBx (n=64) or MR-GB (n=34) was used for PCa diagnosis before RP in 98 patients.

MEASUREMENTS

Using multiparametric 3-T MRI: T2-weighted, dynamic contrast-enhanced imaging, and DWI were performed to identify tumour-suspicious regions in patients with a negative TRUSBx. The regions with the highest restriction on ADC maps within the suspicions regions were used to direct MR-GB. A 10-core TRUSBx was used in a matched cohort. Following RP, the highest Gleason grades (HGGs) in biopsies and RP specimens were identified. Biopsy and RP Gleason grade results were evaluated using chi-square analysis.

RESULTS AND LIMITATIONS

No significant differences on RP were observed for proportions of patients having a HGG of 3 (35% vs 28%; p=0.50), 4 (32% vs 41%; p=0.51), and 5 (32% vs 31%; p=0.61) for the MR-GB and TRUSBx cohort, respectively. MR-GB showed an exact performance with RP for overall HGG: 88% (30 of 34); for TRUS-GB it was 55% (35 of 64; p=0.001). In the MR-GB cohort, an exact performance with HGG 3 was 100% (12 of 12); for HGG 4, 91% (10 of 11); and for HGG 5, 73% (8 of 11). The corresponding performance rates for TRUSBx were 94% (17 of 18; p=0.41), 46% (12 of 26; p=0.02), and 30% (6 of 20; p=0.01), respectively.

CONCLUSIONS

This study shows prospectively that DWI-directed MR-GBs significantly improve pretreatment risk stratification by obtaining biopsies that are representative of true Gleason grade.

Nonlinear charge transport in redox molecular junctions: a Marcus perspective

Redox molecular junctions are molecular conduction junctions that involve more than one oxidation state of the molecular bridge. This property is derived from the ability of the molecule to transiently localize transmitting electrons, implying relatively weak molecule-leads coupling and, in many cases, the validity of the Marcus theory of electron transfer. Here we study the implications of this property on the nonlinear transport properties of such junctions. We obtain an analytical solution of the integral equations that describe molecular conduction in the Marcus kinetic regime and use it in different physical limits to predict some important features of nonlinear transport in metal-molecule-metal junctions. In particular, conduction, rectification, and negative differential resistance can be obtained in different regimes of interplay between two different conduction channels associated with different localization properties of the excess molecular charge, without specific assumptions about the electronic structure of the molecular bridge. The predicted behaviors show temperature dependences typically observed in the experiment. The validity of the proposed model and ways to test its predictions and implement the implied control strategies are discussed.

On the lack of consensus over the meaning of openness: an empirical study

This study set out to explore the views and motivations of those involved in a number of recent and current advocacy efforts (such as open science, computational provenance, and reproducible research) aimed at making science and scientific artifacts accessible to a wider audience. Using a exploratory approach, the study tested whether a consensus exists among advocates of these initiatives about the key concepts, exploring the meanings that scientists attach to the various mechanisms for sharing their work, and the social context in which this takes place. The study used a purposive sampling strategy to target scientists who have been active participants in these advocacy efforts, and an open-ended questionnaire to collect detailed opinions on the topics of reproducibility, credibility, scooping, data sharing, results sharing, and the effectiveness of the peer review process. We found evidence of a lack of agreement on the meaning of key terminology, and a lack of consensus on some of the broader goals of these advocacy efforts. These results can be explained through a closer examination of the divergent goals and approaches adopted by different advocacy efforts. We suggest that the scientific community could benefit from a broader discussion of what it means to make scientific research more accessible and how this might best be achieved.

Vitamin A supplementation at birth might prime the response to subsequent vitamin A supplements in girls. Three year follow-up of a randomized trial

Objectives

Within a randomised trial of neonatal vitamin A supplementation (VAS) in Guinea-Bissau, neonatal VAS did not affect overall infant mortality. We conducted a post-hoc analysis to test the hypothesis that neonatal VAS primes the response to subsequent vitamin A.

Methods

All trial children were offered VAS after follow-up ended at 1 year of age (FU-VAS). We compared mortality between 1 and 3 years of age according to initial randomization to neonatal VAS or placebo in Cox-regression models; we expected that children randomized to neonatal VAS compared with those randomized to placebo would have lower mortality after reception of FU-VAS.

Results

Of 4345 infants enrolled in the original trial, 3646 lived in the study area at 1 year of age and 2958 received FU-VAS. Between 1 and 3 years of age, 112 children died. After FU-VAS, neonatal VAS was associated with lower mortality than placebo: Mortality Rate Ratio (MRR) = 0.54 (95%CI: 0.31–0.94). The effect was more pronounced in girls (MRR = 0.37 (0.16–0.89)) than boys (MRR = 0.73 (0.35–1.51)). The beneficial effect of neonatal VAS may have been particularly strong for girls who received both VAS in a campaign and FU-VAS (MRR = 0.15 (0.03–0.67)). Among children who had not received FU-VAS, mortality in the second and third year of life did not differ according to reception of neonatal VAS or placebo. Hence, in the second and third year of life the effect of neonatal VAS versus placebo was different in girls who had or had not received FU-VAS (p for homogeneity = 0.01).

Conclusions

The present results suggest that neonatal VAS primes the response in girls such that they get a beneficial effect after a subsequent dose of VAS.

Trial Registration

Clinicaltrials.gov NCT00168597

Sucrose utilization in budding yeast as a model for the origin of undifferentiated multicellularity

We use the budding yeast, Saccharomyces cerevisiae, to investigate one model for the initial emergence of multicellularity: the formation of multicellular aggregates as a result of incomplete cell separation. We combine simulations with experiments to show how the use of secreted public goods favors the formation of multicellular aggregates. Yeast cells can cooperate by secreting invertase, an enzyme that digests sucrose into monosaccharides, and many wild isolates are multicellular because cell walls remain attached to each other after the cells divide. We manipulate invertase secretion and cell attachment, and show that multicellular clumps have two advantages over single cells: they grow under conditions where single cells cannot and they compete better against cheaters, cells that do not make invertase. We propose that the prior use of public goods led to selection for the incomplete cell separation that first produced multicellularity.

The evolution of multicellularity is one of the major steps in the history of life and has occurred many times independently. Despite this, we do not understand how and why single-celled organisms first joined together to form multicellular clumps of cells. Here, we show that clumps of cells can cooperate, using secreted enzymes, to collect food from the environment. In nature, the budding yeast Saccharomyces cerevisiae grows as multicellular clumps and secretes invertase, an enzyme that breaks down sucrose into smaller sugars (glucose and fructose) that cells can import. We genetically manipulate both clumping and secretion to show that multicellular clumps of cells can grow when sucrose is scarce, whereas single cells cannot. In addition, we find that clumps of cells have an advantage when competing against “cheating” cells that import sugars but do not make invertase. Since the evolution of secreted enzymes predates the origin of multicellularity, we argue that the social benefits conferred by secreted enzymes were the driving force for the evolution of cell clumps that were the first, primitive form of multicellular life.

Ultrasound-mediated optical tomography: a review of current methods

Ultrasound-mediated optical tomography (UOT) is a hybrid technique that is able to combine the high penetration depth and high spatial resolution of ultrasound imaging to overcome the limits imposed by optical scattering for deep tissue optical sensing and imaging. It has been proposed as a method to detect blood concentrations, oxygenation and metabolism at depth in tissue for the detection of vascularized tumours or the presence of absorbing or scattering contrast agents. In this paper, the basic principles of the method are outlined and methods for simulating the UOT signal are described. The main detection methods are then summarized with a discussion of the advantages and disadvantages of each. The recent focus on increasing the weak UOT signal through the use of the acoustic radiation force is explained, together with a summary of our results showing sensitivity to the mechanical shear stiffness and optical absorption properties of tissue-mimicking phantoms.

Bacteriophages as vehicles of the resistome in cystic fibrosis

Environmental microbial communities and human microbiota represent a huge reservoir of mobilizable genes, the 'mobilome', including a pool of genes encoding antimicrobial resistance, the 'resistome'. Whole-genome sequencing of bacterial genomes from cystic fibrosis (CF) patients has demonstrated that bacteriophages contribute significantly to bacterial genome alterations, and metagenomic analysis of respiratory tract DNA viral communities has revealed the presence of genes encoding antimicrobial resistance in bacteriophages of CF patients. CF airways should now be considered as the site of complex microbiota, where bacteriophages are vehicles for the adaptation of bacteria to this specific environment and for the emergence and selection of multidrug-resistant bacteria with chimeric repertoires. As phages are already known to be mobilized during chronic infection of the lungs of patients with CF, it seems particularly important to improve the understanding of the mechanisms of phage induction to prevent the spread of virulence and/or antimicrobial resistance determinants within the CF population as well as in the community. Such a modern point of view may be a seminal reflection for clinical practice in the future since current antimicrobial therapy guidelines in the context of CF may lead to the emergence of genes encoding antimicrobial resistance.

Recruitment of the major vault protein by InlK: a Listeria monocytogenes strategy to avoid autophagy

L. monocytogenes is a facultative intracellular bacterium responsible for listeriosis. It is able to invade, survive and replicate in phagocytic and non-phagocytic cells. The infectious process at the cellular level has been extensively studied and many virulence factors have been identified. Yet, the role of InlK, a member of the internalin family specific to L. monocytogenes, remains unknown. Here, we first show using deletion analysis and in vivo infection, that InlK is a bona fide virulence factor, poorly expressed in vitro and well expressed in vivo, and that it is anchored to the bacterial surface by sortase A. We then demonstrate by a yeast two hybrid screen using InlK as a bait, validated by pulldown experiments and immunofluorescence analysis that intracytosolic bacteria via an interaction with the protein InlK interact with the Major Vault Protein (MVP), the main component of cytoplasmic ribonucleoproteic particules named vaults. Although vaults have been implicated in several cellular processes, their role has remained elusive. Our analysis demonstrates that MVP recruitment disguises intracytosolic bacteria from autophagic recognition, leading to an increased survival rate of InlK over-expressing bacteria compared to InlK(-) bacteria. Together these results reveal that MVP is hijacked by L. monocytogenes in order to counteract the autophagy process, a finding that could have major implications in deciphering the cellular role of vault particles.

Adsorption and reduction of glutathione disulfide on α-Al2O3 nanoparticles: experiments and modeling

Glutathione disulfide (GSSG; γ-GluCysGly disulfide) was used as a physiologically relevant model molecule to investigate the fundamental adsorption mechanisms of polypeptides onto α-alumina nanoparticles. Its adsorption/desorption behavior was studied by enzymatic quantification of the bound GSSG combined with zeta potential measurements of the particles. The adsorption of GSSG to alumina nanoparticles was rapid, was prevented by alkaline pH, was reversed by increasing ionic strength, and followed a nearly ideal Langmuir isotherm with a standard Gibbs adsorption energy of -34.7 kJ/mol. Molecular dynamics simulations suggest that only one of the two glutathionyl moieties contained in GSSG binds stably to the nanoparticle surface. This was confirmed experimentally by the release of GSH from the bound GSSG upon reducing its disulfide bond with dithiothreitol. Our data indicate that electrostatic interactions via the carboxylate groups of one of the two glutathionyl moieties of GSSG are predominantly responsible for the binding of GSSG to the alumina surface. The results and conclusions presented here can provide a base for further experimental and modeling studies on the interactions of biomolecules with ceramic materials.

Leptin administration to overweight and obese subjects for 6 months increases free leptin concentrations but does not alter circulating hormones of the thyroid and IGF axes during weight loss induced by a mild hypocaloric diet

OBJECTIVE

Short-term energy deprivation reduces leptin concentrations and alters the levels of circulating hormones of the hypothalamic-pituitary-peripheral axis in lean subjects. Whether the reduction in leptin concentration during long-term weight loss in obese individuals is linked to the same neuroendocrine changes seen in lean, leptin-sensitive subjects remains to be fully clarified.

METHODS

In this study, 24 overweight and obese adults (16 women and eight men; body mass index (BMI): 27.5-38.0 kg/m(2)) were prescribed a hypocaloric diet (-500 kcal/day) and were randomized to receive recombinant methionyl leptin (n=18, metreleptin, 10 mg/day self-injected s.c.) or placebo (n=6, same volume and time as metreleptin) for 6 months.

RESULTS

Metreleptin administration did not affect weight loss beyond that induced by hypocaloric diet alone (P for interaction=0.341) but increased the serum concentrations of total leptin by six- to eight-fold (P<0.001) and led to the generation of anti-leptin antibodies. Despite free leptin concentration (P for interaction=0.041) increasing from 9±1 ng/ml at baseline to 43±15 and 36±12 ng/ml at 3 and 6 months, respectively, changes in circulating hormones of the thyroid and IGF axes at 3 and 6 months were not significantly different in the placebo- and metreleptin-treated groups.

CONCLUSIONS

Leptin does not likely mediate changes in neuroendocrine function in response to weight loss induced by a mild hypocaloric diet in overweight and obese subjects.

The relation between reproductive value and genetic contribution

What determines the genetic contribution that an individual makes to future generations? With biparental reproduction, each individual leaves a "pedigree" of descendants, determined by the biparental relationships in the population. The pedigree of an individual constrains the lines of descent of each of its genes. An individual's reproductive value is the expected number of copies of each of its genes that is passed on to distant generations conditional on its pedigree. For the simplest model of biparental reproduction (analogous to the Wright-Fisher model), an individual's reproductive value is determined within ∼10 generations, independent of population size. Partial selfing and subdivision do not greatly slow this convergence. Our central result is that the probability that a gene will survive is proportional to the reproductive value of the individual that carries it and that, conditional on survival, after a few tens of generations, the distribution of the number of surviving copies is the same for all individuals, whatever their reproductive value. These results can be generalized to the joint distribution of surviving blocks of the ancestral genome. Selection on unlinked loci in the genetic background may greatly increase the variance in reproductive value, but the above results nevertheless still hold. The almost linear relationship between survival probability and reproductive value also holds for weakly favored alleles. Thus, the influence of the complex pedigree of descendants on an individual's genetic contribution to the population can be summarized through a single number: its reproductive value.

What differs in visual recognition of handwritten vs. printed letters? An fMRI study

In models of letter recognition, handwritten letters are considered as a particular font exemplar, not qualitatively different in their processing from printed letters. Yet, some data suggest that recognizing handwritten letters might rely on distinct processes, possibly related to motor knowledge. We applied functional magnetic resonance imaging to compare the neural correlates of perceiving handwritten letters vs. standard printed letters. Statistical analysis circumscribed to frontal brain regions involved in hand-movement triggering and execution showed that processing of handwritten letters is supported by a stronger activation of the left primary motor cortex and the supplementary motor area. At the whole-brain level, additional differences between handwritten and printed letters were observed in the right superior frontal, middle occipital, and parahippocampal gyri, and in the left inferior precentral and the fusiform gyri. The results are suggested to indicate embodiment of the visual perception of handwritten letters.

The telomerase activator TA-65 elongates short telomeres and increases health span of adult/old mice without increasing cancer incidence

Here, we show that a small-molecule activator of telomerase (TA-65) purified from the root of Astragalus membranaceus is capable of increasing average telomere length and decreasing the percentage of critically short telomeres and of DNA damage in haploinsufficient mouse embryonic fibroblasts (MEFs) that harbor critically short telomeres and a single copy of the telomerase RNA Terc gene (G3 Terc(+/-) MEFs). Importantly, TA-65 does not cause telomere elongation or rescue DNA damage in similarly treated telomerase-deficient G3 Terc(-/-) littermate MEFs. These results indicate that TA-65 treatment results in telomerase-dependent elongation of short telomeres and rescue of associated DNA damage, thus demonstrating that TA-65 mechanism of action is through the telomerase pathway. In addition, we demonstrate that TA-65 is capable of increasing mouse telomerase reverse transcriptase levels in some mouse tissues and elongating critically short telomeres when supplemented as part of a standard diet in mice. Finally, TA-65 dietary supplementation in female mice leads to an improvement of certain health-span indicators including glucose tolerance, osteoporosis and skin fitness, without significantly increasing global cancer incidence.

Ptf1a/Rbpj complex inhibits ganglion cell fate and drives the specification of all horizontal cell subtypes in the chick retina

During development, progenitor cells of the retina give rise to six principal classes of neurons and the Müller glial cells found within the adult retina. The pancreas transcription factor 1 subunit a (Ptf1a) encodes a basic-helix-loop-helix transcription factor necessary for the specification of horizontal cells and the majority of amacrine cell subtypes in the mouse retina. The Ptf1a-regulated genes and the regulation of Ptf1a activity by transcription cofactors during retinogenesis have been poorly investigated. Using a retrovirus-mediated gene transfer approach, we reported that Ptf1a was sufficient to promote the fates of amacrine and horizontal cells from retinal progenitors and inhibit retinal ganglion cell and photoreceptor differentiation in the chick retina. Both GABAergic H1 and non-GABAergic H3 horizontal cells were induced following the forced expression of Ptf1a. We describe Ptf1a as a strong, negative regulator of Atoh7 expression. Furthermore, the Rbpj-interacting domains of Ptf1a protein were required for its effects on cell fate specification. Together, these data provide a novel insight into the molecular basis of Ptf1a activity on early cell specification in the chick retina.

Imaging symmetry-selected corner plasmon modes in penta-twinned crystalline Ag nanowires

Using dual-plane leakage radiation microscopy, we investigate plasmon propagation in individual penta-twinned crystalline silver nanowires. By measuring the wavevector content of the light emitted in the substrate, we unambiguously determine the effective index and the losses of the mode propagating in these structures. The experimental results, in particular, the unexpectedly low effective index, reveal the direct influence of the nanowire crystallinity and pentagonal structure on the observed plasmon modes. By analogy with molecular orbitals of similar symmetry, the plasmon modes are also determined numerically in good agreement with the observed values. We further investigate the effect of wire geometry (length, diameter) on the effective index and propagation loss. Our results show that, beyond dissipation concerns, the morphological and structural control obtained in crystalline colloidal plasmonic nanostructures can be exploited to finely tune their optical properties.

The skeletal organic matrix from Mediterranean coral Balanophyllia europaea influences calcium carbonate precipitation

Scleractinian coral skeletons are made mainly of calcium carbonate in the form of aragonite. The mineral deposition occurs in a biological confined environment, but it is still a theme of discussion to what extent the calcification occurs under biological or environmental control. Hence, the shape, size and organization of skeletal crystals from the cellular level through the colony architecture, were attributed to factors as diverse as mineral supersaturation levels and organic mediation of crystal growth. The skeleton contains an intra-skeletal organic matrix (OM) of which only the water soluble component was chemically and physically characterized. In this work that OM from the skeleton of the Balanophyllia europaea, a solitary scleractinian coral endemic to the Mediterranean Sea, is studied in vitro with the aim of understanding its role in the mineralization of calcium carbonate. Mineralization of calcium carbonate was conducted by overgrowth experiments on coral skeleton and in calcium chloride solutions containing different ratios of water soluble and/or insoluble OM and of magnesium ions. The precipitates were characterized by diffractometric, spectroscopic and microscopic techniques. The results showed that both soluble and insoluble OM components influence calcium carbonate precipitation and that the effect is enhanced by their co-presence. The role of magnesium ions is also affected by the presence of the OM components. Thus, in vitro, OM influences calcium carbonate crystal morphology, aggregation and polymorphism as a function of its composition and of the content of magnesium ions in the precipitation media. This research, although does not resolve the controversy between environmental or biological control on the deposition of calcium carbonate in corals, sheds a light on the role of OM, which appears mediated by the presence of magnesium ions.

The fitness effects of synonymous mutations in DNA and RNA viruses

Despite being silent with respect to protein sequence, synonymous nucleotide substitutions can be targeted by natural selection directly at the DNA or RNA level. However, there has been no systematic assessment of how frequent this type of selection is. Here, we have constructed 53 single random synonymous substitution mutants of the bacteriophages Qβ and ΦX174 by site-directed mutagenesis and assayed their fitness. Analysis of this mutant collection and of previous studies undertaken with a variety of single-stranded (ss) viruses demonstrates that selection at synonymous sites is stronger in RNA viruses than in DNA viruses. We estimate that this type of selection contributes approximately 18% of the overall mutational fitness effects in ssRNA viruses under our assay conditions and that random synonymous substitutions have a 5% chance of being lethal to the virus, whereas in ssDNA viruses, these figures drop to 1.4% and 0%, respectively. In contrast, the effects of nonsynonymous substitutions appear to be similar in ssRNA and ssDNA viruses.

Alkylnaphthalenes: priority pollutants or minor contributors to the poor health of marine mussels?

Alkylnaphthalenes (AN) are relatively water-soluble hydrocarbons which, following spillages of crude oils, have been widely reported in contaminated marine organisms such as mussels. In the present report we show, by tandem-gas chromatography-time-of-flight-mass spectrometry (GC × GC-ToF-MS), that the range of AN in contaminated wild mussels from the UK extends beyond the previously GC resolved isomers to those with at least seven substituent carbon atoms. Since surprisingly little information on AN toxicity to such marine organisms has been reported we synthesized two C(8) AN and measured the toxicity of C(2-8) AN to mussels (clearance rate assay). C(2-3) AN were appreciably toxic (concentration for 50% clearance rate inhibition, 48 h IC(50) 1.4-2.6 μmol g(-1) dry weight tissue), but several C(4), (6) and C(8) AN, including branched isomers expected to be resistant to biodegradation and more accumulative, were relatively nontoxic (48 h IC(50) > 10 μmol g(-1)) and longer term exposure (8d) failed to elicit a greater toxic response. The accumulation profiles of AN in laboratory mussels exposed to oil were similar to those of the wild mussels. Moreover, laboratory oil-exposed mussels depurated toxic C(2-3) AN within 5 days in clean water and clearance rates recovered. The latter might imply that, in contrast with branched alkyl benzenes tested previously, AN are of less toxic concern, but such a straightforward conclusion cannot necessarily be drawn; a synthetic branched C(8) AN persisted following depuration and was as toxic to mussels as a C(3) AN (IC(50) 1.3 μmol g(-1)). This indicates that the structures of AN are also important.

IRF8 mutations and human dendritic-cell immunodeficiency

BACKGROUND

The genetic analysis of human primary immunodeficiencies has defined the contribution of specific cell populations and molecular pathways in the host defense against infection. Disseminated infection caused by bacille Calmette-Guérin (BCG) vaccines is an early manifestation of primary immunodeficiencies, such as severe combined immunodeficiency. In many affected persons, the cause of disseminated BCG disease is unexplained.

METHODS

We evaluated an infant presenting with features of severe immunodeficiency, including early-onset disseminated BCG disease, who required hematopoietic stem-cell transplantation. We also studied two otherwise healthy subjects with a history of disseminated but curable BCG disease in childhood. We characterized the monocyte and dendritic-cell compartments in these three subjects and sequenced candidate genes in which mutations could plausibly confer susceptibility to BCG disease.

RESULTS

We detected two distinct disease-causing mutations affecting interferon regulatory factor 8 (IRF8). Both K108E and T80A mutations impair IRF8 transcriptional activity by disrupting the interaction between IRF8 and DNA. The K108E variant was associated with an autosomal recessive severe immunodeficiency with a complete lack of circulating monocytes and dendritic cells. The T80A variant was associated with an autosomal dominant, milder immunodeficiency and a selective depletion of CD11c+CD1c+ circulating dendritic cells.

CONCLUSIONS

These findings define a class of human primary immunodeficiencies that affect the differentiation of mononuclear phagocytes. They also show that human IRF8 is critical for the development of monocytes and dendritic cells and for antimycobacterial immunity. (Funded by the Medical Research Council and others.).

The putative RNA helicase HELZ promotes cell proliferation, translation initiation and ribosomal protein S6 phosphorylation

The hypoxia–inducible transcription factor (HIF) is a key component of the cellular adaptation mechanisms to hypoxic conditions. HIFα subunits are degraded by prolyl-4-hydroxylase domain (PHD) enzyme-dependent prolyl-4-hydroxylation of LxxLAP motifs that confer oxygen-dependent proteolytic degradation. Interestingly, only three non-HIFα proteins contain two conserved LxxLAP motifs, including the putative RNA helicase with a zinc finger domain HELZ. However, HELZ proteolytic regulation was found to be oxygen-independent, supporting the notion that a LxxLAP sequence motif alone is not sufficient for oxygen-dependent protein destruction. Since biochemical pathways involving RNA often require RNA helicases to modulate RNA structure and activity, we used luciferase reporter gene constructs and metabolic labeling to demonstrate that HELZ overexpression activates global protein translation whereas RNA-interference mediated HELZ suppression had the opposite effect. Although HELZ interacted with the poly(A)-binding protein (PABP) via its PAM2 motif, PABP was dispensable for HELZ function in protein translation. Importantly, downregulation of HELZ reduced translational initiation, resulting in the disassembly of polysomes, in a reduction of cell proliferation and hypophosphorylation of ribosomal protein S6.

Assortment of GABAergic plasticity in the cortical interneuron melting pot

Cortical structures of the adult mammalian brain are characterized by a spectacular diversity of inhibitory interneurons, which use GABA as neurotransmitter. GABAergic neurotransmission is fundamental for integrating and filtering incoming information and dictating postsynaptic neuronal spike timing, therefore providing a tight temporal code used by each neuron, or ensemble of neurons, to perform sophisticated computational operations. However, the heterogeneity of cortical GABAergic cells is associated to equally diverse properties governing intrinsic excitability as well as strength, dynamic range, spatial extent, anatomical localization, and molecular components of inhibitory synaptic connections that they form with pyramidal neurons. Recent studies showed that similarly to their excitatory (glutamatergic) counterparts, also inhibitory synapses can undergo activity-dependent changes in their strength. Here, some aspects related to plasticity and modulation of adult cortical and hippocampal GABAergic synaptic transmission will be reviewed, aiming at providing a fresh perspective towards the elucidation of the role played by specific cellular elements of cortical microcircuits during both physiological and pathological operations.

Ancient hybridization and an Irish origin for the modern polar bear matriline

BACKGROUND

Polar bears (Ursus maritimus) are among those species most susceptible to the rapidly changing arctic climate, and their survival is of global concern. Despite this, little is known about polar bear species history. Future conservation strategies would significantly benefit from an understanding of basic evolutionary information, such as the timing and conditions of their initial divergence from brown bears (U. arctos) or their response to previous environmental change.

RESULTS

We used a spatially explicit phylogeographic model to estimate the dynamics of 242 brown bear and polar bear matrilines sampled throughout the last 120,000 years and across their present and past geographic ranges. Our results show that the present distribution of these matrilines was shaped by a combination of regional stability and rapid, long-distance dispersal from ice-age refugia. In addition, hybridization between polar bears and brown bears may have occurred multiple times throughout the Late Pleistocene.

CONCLUSIONS

The reconstructed matrilineal history of brown and polar bears has two striking features. First, it is punctuated by dramatic and discrete climate-driven dispersal events. Second, opportunistic mating between these two species as their ranges overlapped has left a strong genetic imprint. In particular, a likely genetic exchange with extinct Irish brown bears forms the origin of the modern polar bear matriline. This suggests that interspecific hybridization not only may be more common than previously considered but may be a mechanism by which species deal with marginal habitats during periods of environmental deterioration.

Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana

Biotrophic eukaryotic plant pathogens require a living host for their growth and form an intimate haustorial interface with parasitized cells. Evolution to biotrophy occurred independently in fungal rusts and powdery mildews, and in oomycete white rusts and downy mildews. Biotroph evolution and molecular mechanisms of biotrophy are poorly understood. It has been proposed, but not shown, that obligate biotrophy results from (i) reduced selection for maintenance of biosynthetic pathways and (ii) gain of mechanisms to evade host recognition or suppress host defence. Here we use Illumina sequencing to define the genome, transcriptome, and gene models for the obligate biotroph oomycete and Arabidopsis parasite, Albugo laibachii. A. laibachii is a member of the Chromalveolata, which incorporates Heterokonts (containing the oomycetes), Apicomplexa (which includes human parasites like Plasmodium falciparum and Toxoplasma gondii), and four other taxa. From comparisons with other oomycete plant pathogens and other chromalveolates, we reveal independent loss of molybdenum-cofactor-requiring enzymes in downy mildews, white rusts, and the malaria parasite P. falciparum. Biotrophy also requires “effectors” to suppress host defence; we reveal RXLR and Crinkler effectors shared with other oomycetes, and also discover and verify a novel class of effectors, the “CHXCs”, by showing effector delivery and effector functionality. Our findings suggest that evolution to progressively more intimate association between host and parasite results in reduced selection for retention of certain biosynthetic pathways, and particularly reduced selection for retention of molybdopterin-requiring biosynthetic pathways. These mechanisms are not only relevant to plant pathogenic oomycetes but also to human pathogens within the Chromalveolata.

Plant pathogens that cannot grow except on their hosts are called obligate biotrophs. How such biotrophy evolves is poorly understood. In this study, we sequenced the genome of the obligate biotroph white rust pathogen (Albugo laibachii, Oomycota) of Arabidopsis. From comparisons with other oomycete plant pathogens, diatoms, and the human pathogen Plasmodium falciparum, we reveal a loss of important metabolic enzymes. We also reveal the appearance of defence-suppressing “effectors”, some carrying motifs known from other oomycete effectors, and discover and experimentally verify a novel class of effectors that share a CHXC motif within 50 amino acids of the signal peptide cleavage site. Obligate biotrophy involves an intimate association within host cells at the haustorial interface (where the parasite penetrates the host cell's cell wall), where nutrients are acquired from the host and effectors are delivered to the host. We found that A. laibachii, like Hyaloperonospora arabidopsidis and Plasmodium falciparum, lacks molybdopterin-requiring biosynthetic pathways, suggesting relaxed selection for retention of, or even selection against, this pathway. We propose that when defence suppression becomes sufficiently effective, hosts become such a reliable source of nutrients that a free-living phase can be lost. These mechanisms leading to obligate biotrophy and host specificity are relevant not only to plant pathogenic oomycetes but also to human pathogens.

Note: High sensitivity pulsed electron spin resonance spectroscopy with induction detection

Commercial electron spin resonance spectroscopy and imaging systems make use of the so-called "induction" or "Faraday" detection, which is based on a radio frequency coil or a microwave resonator. The sensitivity of induction detection does not exceed ~3 × 10(8) spins/√Hz. Here we show that through the use of a new type of surface loop-gap microresonators (inner size of 20 μm), operating at cryogenic temperatures at a field of 0.5 T, one can improve upon this sensitivity barrier by more than 2 orders of magnitude and reach spin sensitivities of ~1.5 × 10(6) spins/√Hz or ~2.5 × 10(4) spins for 1 h.

Uniform nanoparticles by flame-assisted spray pyrolysis (FASP) of low cost precursors

A new flame-assisted spray pyrolysis (FASP) reactor design is presented, which allows the use of inexpensive precursors and solvents (e.g., ethanol) for synthesis of nanoparticles (10-20 nm) with uniform characteristics. In this reactor design, a gas-assisted atomizer generates the precursor solution spray that is mixed and combusted with externally fed inexpensive fuel gases (acetylene or methane) at a defined height above the atomizing nozzle. The gaseous fuel feed can be varied to control the combustion enthalpy content of the flame and onset of particle formation. This way, the enthalpy density of the flame is decoupled from the precursor solution composition. Low enthalpy content precursor solutions are prone to synthesis of non-uniform particles (e.g., bimodal particle size distribution) by standard flame spray pyrolysis (FSP) processes. For example, metal nitrates in ethanol typically produce nanosized particles by gas-to-particle conversion along with larger particles by droplet-to-particle conversion. The present FASP design facilitates the use of such low enthalpy precursor solutions for synthesis of homogeneous nanopowders by increasing the combustion enthalpy density of the flame with low-cost, gaseous fuels. The effect of flame enthalpy density on product properties in the FASP configuration is explored by the example of Bi(2)O(3) nanoparticles produced from bismuth nitrate in ethanol. Product powders were characterized by nitrogen adsorption, X-ray diffraction, X-ray disk centrifuge, and transmission electron microscopy. Homogeneous Bi(2)O(3) nanopowders were produced both by increasing the gaseous fuel content and, most notably, by cutting the air entrainment prior to ignition of the spray.

Attenuation of mirror image and enhancement of the signal-to-noise ratio in a Talbot bands optical coherence tomography system

A Fourier domain optical coherence tomography setup is presented built around an optical configuration that exhibits Talbot bands. A low astigmatism spectrometer is used, employing a spherical mirror and a cylindrical lens between a diffraction grating and a linear CCD camera. To produce Talbot bands, the two interferometer beams--object and reference--are laterally shifted in respect to each other in their way toward the diffraction grating. This allows attenuation of mirror terms and optimization of the sensitivity profile. We evaluate the optimization of the sensitivity profile with depth, in respect to its overall strength and its position peak, which can be shifted toward a larger optical path difference in the interferometer. We demonstrate the efficiency of such a configuration at large depths by imaging a thick phantom and human skin in vivo for different values of the lateral distance between the two beams.

Hypoxic stress and cancer: imaging the axis of evil in tumor metastasis

Tumors emerge as a result of the sequential acquisition of genetic, epigenetic and somatic alterations promoting cell proliferation and survival. The maintenance and expansion of tumor cells rely on their ability to adapt to changes in their microenvironment, together with the acquisition of the ability to remodel their surroundings. Tumor cells interact with two types of interconnected microenvironments: the metabolic cell autonomous microenvironment and the nonautonomous cellular-molecular microenvironment comprising interactions between tumor cells and the surrounding stroma. Hypoxia is a central player in cancer progression, affecting not only tumor cell autonomous functions, such as cell division and invasion, resistance to therapy and genetic instability, but also nonautonomous processes, such as angiogenesis, lymphangiogenesis and inflammation, all contributing to metastasis. Closely related microenvironmental stressors affecting cancer progression include, in addition to hypoxia, elevated interstitial pressure and oxidative stress. Noninvasive imaging offers multiple means to monitor the tumor microenvironment and its consequences, and can thus assist in the understanding of the biological basis of hypoxia and microenvironmental stress in cancer progression, and in the development of strategies to monitor therapies targeted at stress-induced tumor progression.

Dissolution DNP NMR with solvent mixtures: substrate concentration and radical extraction

Dynamic nuclear polarization (DNP) followed by sudden sample dissolution, is a topic of active investigation owing to the method's unique prospects for the delivery of NMR spectra and images with unprecedented sensitivity. This experiment achieves hyperpolarization by the combined effects of electron-nuclear irradiation and cryogenic operation; the exploitation of these states occurs following a sudden melting and flushing of the resulting pellet from its original environment into a conventional, liquid-state setting. This melting and flushing usually demands using the equivalent of a few milliliters of hot solvent, a procedure which although well suited for in vivo studies leads to an excessive sample volume when considering typical analytical settings. The present study explores a way of reducing the ensuing dilution of the hyperpolarized analytes, by employing a combination of immiscible liquids for performing the melting and flushing. It is shown that suitable combinations of immiscible solvents - both in terms of their heat capacities and densities - allow one to melt the targeted cryogenic pellet and dissolve the hyperpolarized analytes in a fraction of the solvent hitherto required. By tailoring the resulting volume to the needs of a conventional 5mm NMR probe, a substantial sensitivity enhancement can be added to the hyperpolarization process. An extra benefit may arise from using radicals that preferentially dissolve in the immiscible organic phase, by way of a lengthening of the relaxation time of the investigated analytes. Examples of these principles are given, and further potential extensions of this approach are discussed.

Synthesis and toxicity of some metabolites of the microbial degradation of synthetic naphthenic acids

Some ill-defined carboxylic acids, termed 'naphthenic acids' (NA), are best known as important constituents of the >720billionlitres of process-affected water associated with the expanding oil sands industries. Other NA are components of some immature and biodegraded crude oils and these may enter the environment via produced water discharges from oil production platforms. Yet others are used as biocides and in the manufacture of steel radial tyres and these may also enter the environment through disposal and/or weathering. The environmental fate of NA, including the mechanisms of biodegradation, therefore needs to be better understood. In order to better elucidate such mechanisms, previously we studied the biodegradation in the laboratory of some alkylcyclohexylbutanoic synthetic NA. However, we could only tentatively identify the metabolites produced. In the present study we report the synthesis and characterisation of six alkylcyclohexylethanoic NA. Each was characterised by gas chromatography-mass spectrometry (GC-MS; trimethylsilyl esters) and we show by co-chromatography that these were indeed the metabolites. Also, a preferential degradation of the trans- isomers was revealed. Assessment of the toxicity of the synthetic NA (Microtox assay), revealed that the relative toxicity of the alkylcyclohexylbutanoic acids was reduced by biotransformation to the alkylcyclohexylethanoic acids, as observed recently for the corresponding aromatic acids. Very recent studies have shown that at least one commercial NA mixture contains cyclohexylbutanoic and alkylcyclohexylethanoic acids, suggesting that the biotransformation of the acids studied herein may be quite relevant to the environmental fate of such acids. A similar study of the acid extractables of one oil sands process-affected water sample suggests that the synthetic acids may be less good 'models' for oil sands NA. The consortia of microbes present in oil sands process-affected water may also be different to those used herein. However, the heterogeneity of oil sands process water is well-known and further detailed studies will need to be made in order to establish whether degradation of oil sands NA proceeds by beta oxidation as observed for the acids herein, or whether the oil sands acids are more resistant to bioremediation.

Experimental and modeling study of the thermal decomposition of methyl decanoate

The experimental study of the thermal decomposition of methyl decanoate was performed in a jet-stirred reactor at temperatures ranging from 773 to 1123 K, at residence times between 1 and 4 s, at a pressure of 800 Torr (106.6 kPa) and at high dilution in helium (fuel inlet mole fraction of 0.0218). Species leaving the reactor were analyzed by gas chromatography. Main reaction products were hydrogen, carbon oxides, small hydrocarbons from C₁ to C₃, large 1-olefins from 1-butene to 1-nonene, and unsaturated esters with one double bond at the end of the alkyl chain from methyl-2-propenoate to methyl-8-nonenoate. At the highest temperatures, the formation of polyunsaturated species was observed: 1,3-butadiene, 1,3-cyclopentadiene, benzene, toluene, indene, and naphthalene. These results were compared with previous ones about the pyrolysis of n-dodecane, an n-alkane of similar size. The reactivity of both molecules was found to be very close. The alkane produces more olefins while the ester yields unsaturated oxygenated compounds. A detailed kinetic model for the thermal decomposition of methyl decanoate has been generated using the version of software EXGAS which was updated to take into account the specific chemistry involved in the oxidation of methyl esters. This model contains 324 species and 3231 reactions. It provided a very good prediction of the experimental data obtained in jet-stirred reactor. The formation of the major products was analyzed. The kinetic analysis showed that the retro-ene reactions of intermediate unsaturated methyl esters are of importance in low reactivity systems.

Spatially resolved photoconductivity of thin films formed by colloidal octapod-shaped CdSe/CdS nanocrystals

We studied the optical absorption and photoconductive properties of thin films consisting of core-shell octapod-shaped nanocrystals, which consisted of CdS pods that branch out from a CdSe core. The current-voltage characteristics were measured at room and cryogenic temperatures and agreed well with a phenomenological exponential fitting model, from which we could extract the sheet resistance and the average voltage barrier for the charge tunneling between the octapods. The temperature dependence of the photocurrent showed temperature activated behavior above 220 K and a non-Arrhenius exponential (T/T(0))(n) dispersion below 220 K. Furthermore, we mapped the photocurrent generation within the octapod film via scanning photocurrent microscopy, which revealed photocurrent enhancement near micron-size voids and spatial shifts of the photocurrent maxima with bias voltage.

Identification of individual acids in a commercial sample of naphthenic acids from petroleum by two-dimensional comprehensive gas chromatography/mass spectrometry

The identification of most individual members of the complex mixtures of carboxylic acids found in petroleum ('naphthenic acids') has eluded chemists for over a century; they remain unresolved by conventional gas chromatographic methods. Recently, however, we successfully used two-dimensional comprehensive gas chromatography/mass spectrometry to identify numerous individual diamondoid acids in the naphthenic acids of oil sands process water (OSPW). We have now applied the same methods to a study of a mixture of commercially available naphthenic acids originally refined from petroleum. The results confirm that OSPW and refined petroleum contain very different distributions of acids, as noted previously, although some of the diamondoid acids recently identified in OSPW were detectable in both. Rather, two-dimensional comprehensive gas chromatography/time-of-flight mass spectrometry (GCxGC/ToF-MS) of the methyl esters of the petroleum acids and of numerous acids synthesised for comparison showed that the former comprised mainly C(8-18) straight-chain, methyl-branched, acyclic isoprenoid, cyclohexyl and isomeric octahydropentalene, perhydroindane and perhydronaphthalene (decalin) acids. Some of the latter bicyclic acids occurred as both the non-alkyl-substituted isomers and the bicyclic ethanoic and propanoic acids. Also present in minor quantities was a range of phenyl carboxylic and substituted phenyl alkanoic acids, and traces of non-acids, including trimethylnaphthalenes, again identified by comparison with the synthesised compounds. These results represent some of the first identifications of multiple individual naphthenic acids in commercial mixtures originating from petroleum and provide a basis for future studies of the petroleum geochemistry, toxicities and environmental impacts of the acids. Furthermore, characterisation of the acids will be important for improving the understanding of the role of naphthenic acids in petroleum engineering, particularly for oil pipeline deposition problems.

N400 amplitude reduction correlates with an increase in pupil size

Pupil dilation is classically associated with increase in cognitive load in humans. Here, we studied the potential link between human pupil dilation and meaning integration effort as indexed by event-related brain potentials (ERPs). We recorded pupil size variation and ERPs simultaneously while participants were presented with matching or unrelated picture-word pairs. Whilst relatedness in meaning between spoken words and pictures typically modulated ERPs, pupil size was also affected quickly after picture onset. Moreover, during the time-window associated with meaning integration, greater pupil dilation correlated with less negative N400 amplitudes elicited by unrelated pictures. Since pupil dilation has been linked to activity of the locus coeruleus-norepinephrine (LC-NE) system, these findings may provide new insights into the suggested link between human high-level cognitive function and activity of the LC-NE system.

The reality of Neandertal symbolic behavior at the Grotte du Renne, Arcy-sur-Cure, France

Background

The question of whether symbolically mediated behavior is exclusive to modern humans or shared with anatomically archaic populations such as the Neandertals is hotly debated. At the Grotte du Renne, Arcy-sur-Cure, France, the Châtelperronian levels contain Neandertal remains and large numbers of personal ornaments, decorated bone tools and colorants, but it has been suggested that this association reflects intrusion of the symbolic artifacts from the overlying Protoaurignacian and/or of the Neandertal remains from the underlying Mousterian.

Methodology/Principal Findings

We tested these hypotheses against the horizontal and vertical distributions of the various categories of diagnostic finds and statistically assessed the probability that the Châtelperronian levels are of mixed composition. Our results reject that the associations result from large or small scale, localized or generalized post-depositional displacement, and they imply that incomplete sample decontamination is the parsimonious explanation for the stratigraphic anomalies seen in the radiocarbon dating of the sequence.

Conclusions/Significance

The symbolic artifacts in the Châtelperronian of the Grotte du Renne are indeed Neandertal material culture.

Social evolution in multispecies biofilms

Microbial ecology is revealing the vast diversity of strains and species that coexist in many environments, ranging from free-living communities to the symbionts that compose the human microbiome. In parallel, there is growing evidence of the importance of cooperative phenotypes for the growth and behavior of microbial groups. Here we ask: How does the presence of multiple species affect the evolution of cooperative secretions? We use a computer simulation of spatially structured cellular groups that captures key features of their biology and physical environment. When nutrient competition is strong, we find that the addition of new species can inhibit cooperation by eradicating secreting strains before they can become established. When nutrients are abundant and many species mix in one environment, however, our model predicts that secretor strains of any one species will be surrounded by other species. This "social insulation" protects secretors from competition with nonsecretors of the same species and can improve the prospects of within-species cooperation. We also observe constraints on the evolution of mutualistic interactions among species, because it is difficult to find conditions that simultaneously favor both within- and among-species cooperation. Although relatively simple, our model reveals the richness of interactions between the ecology and social evolution of multispecies microbial groups, which can be critical for the evolution of cooperation.

DNA interstrand crosslink repair and cancer

Interstrand crosslinks (ICLs) are highly toxic DNA lesions that prevent transcription and replication by inhibiting DNA strand separation. Agents that induce ICLs were one of the earliest, and are still the most widely used, forms of chemotherapeutic drug. Only recently, however, have we begun to understand how cells repair these lesions. Important insights have come from studies of individuals with Fanconi anaemia (FA), a rare genetic disorder that leads to ICL sensitivity. Understanding how the FA pathway links nucleases, helicases and other DNA-processing enzymes should lead to more targeted uses of ICL-inducing agents in cancer treatment and could provide novel insights into drug resistance.

Electrophysiological evidence for impaired attentional engagement with phonologically acceptable misspellings in developmental dyslexia

Event-related potential (ERP) studies of word recognition have provided fundamental insights into the time-course and stages of visual and auditory word form processing in reading. Here, we used ERPs to track the time-course of phonological processing in dyslexic adults and matched controls. Participants engaged in semantic judgments of visually presented high-cloze probability sentences ending either with (a) their best completion word, (b) a homophone of the best completion, (c) a pseudohomophone of the best completion, or (d) an unrelated word, to examine the interplay of phonological and orthographic processing in reading and the stage(s) of processing affected in developmental dyslexia. Early ERP peaks (N1, P2, N2) were modulated in amplitude similarly in the two groups of participants. However, dyslexic readers failed to show the P3a modulation seen in control participants for unexpected homophones and pseudohomophones (i.e., sentence completions that are acceptable phonologically but are misspelt). Furthermore, P3a amplitudes significantly correlated with reaction times in each experimental condition. Our results showed no sign of a deficit in accessing phonological representations during reading, since sentence primes yielded phonological priming effects that did not differ between participant groups in the early phases of processing. On the other hand, we report new evidence for a deficient attentional engagement with orthographically unexpected but phonologically expected words in dyslexia, irrespective of task focus on orthography or phonology. In our view, this result is consistent with deficiency in reading occurring from the point at which attention is oriented to phonological analysis, which may underlie broader difficulties in sublexical decoding.

TFEB links autophagy to lysosomal biogenesis

Autophagy is a cellular catabolic process that relies on the cooperation of autophagosomes and lysosomes. During starvation, the cell expands both compartments to enhance degradation processes. We found that starvation activates a transcriptional program that controls major steps of the autophagic pathway, including autophagosome formation, autophagosome-lysosome fusion, and substrate degradation. The transcription factor EB (TFEB), a master gene for lysosomal biogenesis, coordinated this program by driving expression of autophagy and lysosomal genes. Nuclear localization and activity of TFEB were regulated by serine phosphorylation mediated by the extracellular signal-regulated kinase 2, whose activity was tuned by the levels of extracellular nutrients. Thus, a mitogen-activated protein kinase-dependent mechanism regulates autophagy by controlling the biogenesis and partnership of two distinct cellular organelles.

Pancreatitis-induced inflammation contributes to pancreatic cancer by inhibiting oncogene-induced senescence

Pancreatic acinar cells of adult mice (≥P60) are resistant to transformation by some of the most robust oncogenic insults including expression of K-Ras oncogenes and loss of p16Ink4a/p19Arf or Trp53 tumor suppressors. Yet, these acinar cells yield pancreatic intraepithelial neoplasias (mPanIN) and ductal adenocarcinomas (mPDAC) if exposed to limited bouts of non-acute pancreatitis, providing they harbor K-Ras oncogenes. Pancreatitis contributes to tumor progression by abrogating the senescence barrier characteristic of low-grade mPanINs. Attenuation of pancreatitis-induced inflammation also accelerates tissue repair and thwarts mPanIN expansion. Patients with chronic pancreatitis display senescent PanINs, providing they have received antiinflammatory drugs. These results support the concept that antiinflammatory treatment of people diagnosed with pancreatitis may reduce their risk of developing PDAC.

Flexible intuitions of Euclidean geometry in an Amazonian indigene group

Kant argued that Euclidean geometry is synthesized on the basis of an a priori intuition of space. This proposal inspired much behavioral research probing whether spatial navigation in humans and animals conforms to the predictions of Euclidean geometry. However, Euclidean geometry also includes concepts that transcend the perceptible, such as objects that are infinitely small or infinitely large, or statements of necessity and impossibility. We tested the hypothesis that certain aspects of nonperceptible Euclidian geometry map onto intuitions of space that are present in all humans, even in the absence of formal mathematical education. Our tests probed intuitions of points, lines, and surfaces in participants from an indigene group in the Amazon, the Mundurucu, as well as adults and age-matched children controls from the United States and France and younger US children without education in geometry. The responses of Mundurucu adults and children converged with that of mathematically educated adults and children and revealed an intuitive understanding of essential properties of Euclidean geometry. For instance, on a surface described to them as perfectly planar, the Mundurucu's estimations of the internal angles of triangles added up to ~180 degrees, and when asked explicitly, they stated that there exists one single parallel line to any given line through a given point. These intuitions were also partially in place in the group of younger US participants. We conclude that, during childhood, humans develop geometrical intuitions that spontaneously accord with the principles of Euclidean geometry, even in the absence of training in mathematics.

Context-related acoustic variation in male fallow deer (Dama dama) groans

While social and behavioural contexts are known to affect the acoustic structure of vocal signals in several mammal species, few studies have investigated context-related acoustic variation during inter-sexual advertisement and/or intra-sexual competition. Here we recorded male fallow deer groans during the breeding season and investigated how key acoustic parameters (fundamental frequency and formant frequencies) vary as a function of the social context in which they are produced. We found that in the presence of females, male fallow deer produced groans with higher mean fundamental frequency when vocal males were also present than they did when no vocal males were in close vicinity. We attribute this to the increased arousal state typically associated with this context. In addition, groan minimum formant frequency spacing was slightly, but significantly lower (indicating marginally more extended vocal tracts) when males were alone than when potential mates and/or competitors were nearby. This indicates that, contrary to our predictions, male fallow deer do not exaggerate the acoustic impression of their body size by further lowering their formant frequencies in the presence of potential mating partners and competitors. Furthermore, since the magnitude of the variation in groan minimum formant frequency spacing remains small compared to documented inter-individual differences, our findings are consistent with the hypothesis that formants are reliable static cues to body size during intra- and inter-sexual advertisement that do not concurrently encode dynamic motivation-related information.

Sintering Rate and Mechanism of TiO2 Nanoparticles by Molecular Dynamics

Titania is the dominant white pigment and photocatalytic material, a key component of sunscreens and has promising applications in photovoltaics and sensors of organic vapors. The growth of TiO₂ nanoparticles by sintering, the critical step during their large scale manufacture and processing, is elucidated and quantified by molecular dynamics. Highly mobile ions from the particle surface fill in the initially concave space between nanoparticles (surface diffusion) forming the final, fully-coalesced, spherical-like particle with minimal displacement of inner Ti and O ions (grain boundary diffusion) revealing also the significance and sequence of these two sintering mechanisms of TiO₂. A sintering rate for TiO₂ nanoparticles is extracted that is much faster than that in the literature but nicely converges to it for increasing particle size.

Spatial dynamics of human-origin H1 influenza A virus in North American swine

The emergence and rapid global spread of the swine-origin H1N1/09 pandemic influenza A virus in humans underscores the importance of swine populations as reservoirs for genetically diverse influenza viruses with the potential to infect humans. However, despite their significance for animal and human health, relatively little is known about the phylogeography of swine influenza viruses in the United States. This study utilizes an expansive data set of hemagglutinin (HA1) sequences (n = 1516) from swine influenza viruses collected in North America during the period 2003–2010. With these data we investigate the spatial dissemination of a novel influenza virus of the H1 subtype that was introduced into the North American swine population via two separate human-to-swine transmission events around 2003. Bayesian phylogeographic analysis reveals that the spatial dissemination of this influenza virus in the US swine population follows long-distance swine movements from the Southern US to the Midwest, a corn-rich commercial center that imports millions of swine annually. Hence, multiple genetically diverse influenza viruses are introduced and co-circulate in the Midwest, providing the opportunity for genomic reassortment. Overall, the Midwest serves primarily as an ecological sink for swine influenza in the US, with sources of virus genetic diversity instead located in the Southeast (mainly North Carolina) and South-central (mainly Oklahoma) regions. Understanding the importance of long-distance pig transportation in the evolution and spatial dissemination of the influenza virus in swine may inform future strategies for the surveillance and control of influenza, and perhaps other swine pathogens.

Since 1998, genetically and antigenically diverse influenza A viruses have circulated in North American swine due to continuous cross-species transmission and reassortment with avian and human influenza viruses, presenting a pandemic threat to humans. Millions of swine are transported year-round from the southern United States into the corn-rich Midwest, but the importance of these movements in the spatial dissemination and evolution of the influenza virus in swine is unknown. Using a large data set of influenza virus sequences collected in North American swine during 2003–2010, we investigated the spatial dynamics of two influenza viruses of the H1 subtype that were introduced into swine from humans around 2003. Employing recently developed Bayesian phylogeography methods, we find that the spread of this influenza virus follows the large-scale transport of swine from the South to the Midwest. Based on this pattern of viral migration, we suggest that the genetic diversity of swine influenza viruses in the Midwest is continually augmented by the importation of viruses from source populations located in the South. Understanding the importance of long-distance pig movements in the evolution and spatial dissemination of influenza virus in swine may inform future strategies for the surveillance and control of influenza, and perhaps other swine pathogens.

Translocation of single-wall carbon nanotubes through solid-state nanopores

We report the translocation of individual single-wall carbon nanotubes (SWNTs) through solid-state nanopores. Single-strand DNA oligomers are used to both disperse the SWNTs in aqueous solution and to provide them with a net charge, allowing them to be driven through the nanopores by an applied electric field. The resulting temporary interruptions in the measured nanopore conductance provide quantitative information on the diameter and length of the translocated nanotubes at a single-molecule level. Furthermore, we demonstrate that the technique can be utilized to monitor bundling of SWNT in solution by using complementary nucleotides to induce tube-tube agglomeration.