bluuebunny/crossref_metadata_2025 huggingface dataset:
Coded cooperation: generalised outage analysis
Authors: Sharma Prabhat Kumar , Garg Parul
Published: February 2014

In this study, the authors derive the exact closed‐form expression of the outage probability for coded cooperation using power‐based approach. They consider a generalised system model with n relays (n > 1) over Nakagami‐m fading channels. They also obtain the optimal number of relays for the given outage performance. Furthermore, they find analytically the critical cooperation ratio at which the total outage probability is minimum.
Raman spectra of aligned carbon micro-coils and their impedance characteristics under loads
Authors: Tao Wang , Yabo Zhu , Heliang Fan , Zhicheng Ju , Lei Chen , Zhengyuan Wang
Published: February 2014

Scanning and transmission electron microscopy were used to characterize the morphology of the carbon microcoils (CMCs). The Raman spectra showed that CMCs had local regular structure as ID/IG = 0.841. Then, aligned CMCs/silicone–rubber composites (5 × 5 × 1 mm3) were fabricated by coating of silicone rubber on the CMCs. Their alternating current impedance characteristics were measured as a function of applied load and the pressure sensitivity was discussed. The results showed that the impedance decreased as the increasing applied load, and the sample with less CMCs owned high pressure sensitivity, which indicated a novel composite film could act as an alternative of tactile sensor.
First principles study of the structural, electronic, and transport properties of triarylamine-based nanowires
Authors: Akande Akinlolu , Bhattacharya Sandip , Cathcart Thomas , Sanvito Stefano
Published: February 2014

We investigate with state of the art density functional theory the structural, electronic, and transport properties of a class of recently synthesized nanostructures based on triarylamine derivatives. First, we consider the single molecule precursors in the gas phase and calculate their static properties, namely (i) the geometrical structure of the neutral and cationic ions, (ii) the electronic structure of the frontier molecular orbitals, and (iii) the ionization potential, hole extraction potential, and internal reorganization energy. This initial study does not evidence any direct correlation between the properties of the individual molecules and their tendency to self-assembly. Subsequently, we investigate the charge transport characteristics of the triarylamine derivatives nanowires, by using Marcus theory. For one derivative we further construct an effective Hamiltonian including intermolecular vibrations and evaluate the mobility from the Kubo formula implemented with Monte Carlo sampling. These two methods, valid respectively in the sequential hopping and polaronic band limit, give us values for the room-temperature mobility in the range 0.1–12 cm2/Vs. Such estimate confirms the superior transport properties of triarylamine-based nanowires, and make them an attracting materials platform for organic electronics.
The origin of 2.7 eV luminescence and 5.2 eV excitation band in hafnium oxide
Authors: Perevalov T. V. , Aliev V. Sh. , Gritsenko V. A. , Saraev A. A. , Kaichev V. V. , Ivanova E. V. , Zamoryanskaya M. V.
Published: February 2014

The origin of a blue luminescence band at 2.7 eV and a luminescence excitation band at 5.2 eV of hafnia has been studied in stoichiometric and non-stoichiometric hafnium oxide films. Experimental and calculated results from the first principles valence band spectra showed that the stoichiometry violation leads to the formation of the peak density of states in the band gap caused by oxygen vacancies. Cathodoluminescence in the non-stoichiometric film exhibits a band at 2.65 eV that is excited at the energy of 5.2 eV. The optical absorption spectrum calculated for the cubic phase of HfO2 with oxygen vacancies shows a peak at 5.3 eV. Thus, it could be concluded that the blue luminescence band at 2.7 eV and HfOx excitation peak at 5.2 eV are due to oxygen vacancies. The thermal trap energy in hafnia was estimated.
Temperature sensor based on 4H-silicon carbide pn diode operational from 20 °C to 600 °C
Authors: Zhang Nuo , Lin Chih-Ming , Senesky Debbie G. , Pisano Albert P.
Published: February 2014

A high-performance temperature sensor based on 4H-SiC pn diode is demonstrated. The sensor is capable of stable operation in a temperature range from 20 °C to 600 °C. The forward voltage of the pn diode has a linear dependence on temperature variation at a constant current, and recombination current dominates the current flowing in the 4H-SiC pn diode in the measured current range. At a forward current density of 0.44 mA/cm2, the device achieves a sensitivity of 3.5 mV/ °C. This type of temperature sensor can be integrated with SiC power management and control circuitry to create a sensing module that is capable of working at extremely high temperatures.
Neutron source reconstruction from pinhole imaging at National Ignition Facility
Authors: Volegov P. , Danly C. R. , Fittinghoff D. N. , Grim G. P. , Guler N. , Izumi N. , Ma T. , Merrill F. E. , Warrick A. L. , Wilde C. H. , Wilson D. C.
Published: February 2014

The neutron imaging system at the National Ignition Facility (NIF) is an important diagnostic tool for measuring the two-dimensional size and shape of the neutrons produced in the burning deuterium-tritium plasma during the ignition stage of inertial confinement fusion (ICF) implosions at NIF. Since the neutron source is small (∼100 μm) and neutrons are deeply penetrating (>3 cm) in all materials, the apertures used to achieve the desired 10-μm resolution are 20-cm long, single-sided tapers in gold. These apertures, which have triangular cross sections, produce distortions in the image, and the extended nature of the pinhole results in a non-stationary or spatially varying point spread function across the pinhole field of view. In this work, we have used iterative Maximum Likelihood techniques to remove the non-stationary distortions introduced by the aperture to reconstruct the underlying neutron source distributions. We present the detailed algorithms used for these reconstructions, the stopping criteria used and reconstructed sources from data collected at NIF with a discussion of the neutron imaging performance in light of other diagnostics.
Laser-ablative engineering of phase singularities in plasmonic metamaterial arrays for biosensing applications
Authors: Aristov Andrey I. , Zywietz Urs , Evlyukhin Andrey B. , Reinhardt Carsten , Chichkov Boris N. , Kabashin Andrei V.
Published: February 2014

By using methods of laser-induced transfer combined with nanoparticle lithography, we design and fabricate large-area gold nanoparticle-based metamaterial arrays exhibiting extreme Heaviside-like phase jumps in reflected light due to a strong diffractive coupling of localized plasmons. When employed in sensing schemes, these phase singularities provide the sensitivity of 5 × 104 deg. of phase shift per refractive index unit change that is comparable with best values reported for plasmonic biosensors. The implementation of sensor platforms on the basis of such metamaterial arrays promises a drastic improvement of sensitivity and cost efficiency of plasmonic biosensing devices.
Quantification of initial-data uncertainty on a shock-accelerated gas cylinder
Authors: Tritschler V. K. , Avdonin A. , Hickel S. , Hu X. Y. , Adams N. A.
Published: February 2014

We quantify initial-data uncertainties on a shock accelerated heavy-gas cylinder by two-dimensional well-resolved direct numerical simulations. A high-resolution compressible multicomponent flow simulation model is coupled with a polynomial chaos expansion to propagate the initial-data uncertainties to the output quantities of interest. The initial flow configuration follows previous experimental and numerical works of the shock accelerated heavy-gas cylinder. We investigate three main initial-data uncertainties, (i) shock Mach number, (ii) contamination of SF6 with acetone, and (iii) initial deviations of the heavy-gas region from a perfect cylindrical shape. The impact of initial-data uncertainties on the mixing process is examined. The results suggest that the mixing process is highly sensitive to input variations of shock Mach number and acetone contamination. Additionally, our results indicate that the measured shock Mach number in the experiment of Tomkins et al. [“An experimental investigation of mixing mechanisms in shock-accelerated flow,” J. Fluid. Mech. 611, 131 (2008)] and the estimated contamination of the SF6 region with acetone [S. K. Shankar, S. Kawai, and S. K. Lele, “Two-dimensional viscous flow simulation of a shock accelerated heavy gas cylinder,” Phys. Fluids 23, 024102 (2011)] exhibit deviations from those that lead to best agreement between our simulations and the experiment in terms of overall flow evolution.
Angular dependence of the magnetic properties of cylindrical diameter modulated Ni80Fe20 nanowires
Authors: Tejo F. , Vidal-Silva N. , Espejo A. P. , Escrig J.
Published: February 2014

We have investigated numerically the angular dependence of the coercivity and remanence of cylindrical diameter modulated Ni80Fe20 nanowires. We observed that the system always starts reversing its magnetization through the thickest segment by means of a quite complex reversal process, considering the propagation of two vortex domain walls. Furthermore, we observed a transition from vortex domain walls to coherent-mode rotation for the thinnest segment as a function of the angle in which the external magnetic field is applied. In addition, we obtained a non-monotonic behavior for the coercivity and saturation field as a function of the angle at which the external magnetic field is applied. Finally, diameter modulation is an attractive way to handle over the motion of magnetic domain walls, a phenomenon proposed as a future data storage platform.
Atomistic tight-binding study of electronic structure and interband optical transitions in GaBixAs1−x/GaAs quantum wells
Authors: Usman Muhammad , O'Reilly Eoin P.
Published: February 2014

Large-supercell tight-binding calculations are presented for GaBixAs1−x/GaAs single quantum wells (QWs) with Bi fractions x of 3.125% and 12.5%. Our results highlight significant distortion of the valence band states due to the alloy disorder. A large full-width-half-maximum (FWHM) is estimated in the ground state interband transition energy (≈33 meV) at 3.125% Bi, consistent with recent photovoltage measurements for similar Bi compositions. Additionally, the alloy disorder effects are predicted to become more pronounced as the QW width is increased. However, they are less strong at the higher Bi composition (12.5%) required for the design of temperature-stable lasers, with a calculated FWHM of ≈23.5 meV at x = 12.5%.
Effect of growth temperature on defects in epitaxial GaN film grown by plasma assisted molecular beam epitaxy
Authors: Kushvaha S. S. , Pal P. , Shukla A. K. , Joshi Amish G. , Gupta Govind , Kumar M. , Singh S. , Gupta Bipin K. , Haranath D.
Published: February 2014

We report the effect of growth temperature on defect states of GaN epitaxial layers grown on 3.5 μm thick GaN epi-layer on sapphire (0001) substrates using plasma assisted molecular beam epitaxy. The GaN samples grown at three different substrate temperatures at 730, 740 and 750 °C were characterized using atomic force microscopy and photoluminescence spectroscopy. The atomic force microscopy images of these samples show the presence of small surface and large hexagonal pits on the GaN film surfaces. The surface defect density of high temperature grown sample is smaller (4.0 × 108 cm−2 at 750 °C) than that of the low temperature grown sample (1.1 × 109 cm−2 at 730 °C). A correlation between growth temperature and concentration of deep centre defect states from photoluminescence spectra is also presented. The GaN film grown at 750 °C exhibits the lowest defect concentration which confirms that the growth temperature strongly influences the surface morphology and affects the optical properties of the GaN epitaxial films.
Electron transport characteristics of silicon nanowires by metal-assisted chemical etching
Authors: Qi Yangyang , Wang Zhen , Zhang Mingliang , Wang Xiaodong , Ji An , Yang Fuhua
Published: February 2014

The electron transport characteristics of silicon nanowires (SiNWs) fabricated by metal-assisted chemical etching with different doping concentrations were studied. By increasing the doping concentration of the starting Si wafer, the resulting SiNWs were prone to have a rough surface, which had important effects on the contact and the electron transport. A metal-semiconductor-metal model and a thermionic field emission theory were used to analyse the current-voltage (I-V) characteristics. Asymmetric, rectifying and symmetric I-V curves were obtained. The diversity of the I-V curves originated from the different barrier heights at the two sides of the SiNWs. For heavily doped SiNWs, the critical voltage was one order of magnitude larger than that of the lightly doped, and the resistance obtained by differentiating the I-V curves at large bias was also higher. These were attributed to the lower electron tunnelling possibility and higher contact barrier, due to the rough surface and the reduced doping concentration during the etching process.
Identification of QTLs for shoot and root growth under ionic–osmotic stress in Lotus, using a RIL population
Authors: Quero Gastón , Gutíerrez Lucía , Lascano Ramiro , Monza Jorge , Sandal Niels , Borsani Omar
Published: February 2014

The genus Lotus includes a group of forage legume species including genotypes of agronomic interest and model species. In this work, an experimental hydroponic growth system allowed the discrimination of growth responses to ionic–osmotic stress in a population of recombinant inbred lines (RILs) developed from L. japonicus × L. burttii and the identification of the associated quantitative trait loci (QTLs). The analyses led to the identification of eight QTLs: three for shoot growth localised on chromosome 3, 5 and 6; one for root growth on chromosome 1; three for total growth on chromosome 1, 4 and 5; and one associated with shoot/root ratio on chromosome 3. An interaction of QTL × stress condition was established and the effect of the environment quantified. In summary, it was established that the allele from L. burttii explained most responses to osmotic stress, while the alleles of L. japonicus explained the responses related to ionic stress conditions. Of 49 markers linked to all QTLs identified, 41 expressed superiority of the L. burttii parental allele in the osmotic stress condition, but when an iso-osmotic concentration of NaCl was applied, L. burttii lost superiority in 21 of these markers. This shows the superiority of the L. japonicus parental allele in ionic stress conditions. This study is the first report in which a RIL population of lotus is analysed with the aim of providing molecular markers associated with plant responses to ionic or osmotic stress.
Telomeric transcripts stimulate telomere recombination to suppress senescence in cells lacking telomerase
Authors: Yu Tai-Yuan , Kao Yu-wen , Lin Jing-Jer
Published: February 2014

Significance

Telomerase expression is essential for the long-term proliferation of most cancer cells. In cancer cells lacking telomerase, an alternative lengthening of telomeres (ALT) pathway is activated to maintain telomere length through telomere recombination. Using yeast as a model system, we found that the noncoding telomeric repeat-containing RNA (TERRA) plays a major role in recombination-mediated maintenance of telomere in telomerase-deficient cells. Increased levels of telomere-associated TERRA result in the accumulation of telomeric DNA–RNA hybrids and induce telomere recombination. Because the structure and function of TERRA are conserved among eukaryotes, our findings suggest that the accumulation of telomere-associated TERRA might also have a role in modulating the occurrence of ALT in cancer cells.
Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy
Authors: Loenarz Christoph , Sekirnik Rok , Thalhammer Armin , Ge Wei , Spivakovsky Ekaterina , Mackeen Mukram M. , McDonough Michael A. , Cockman Matthew E. , Kessler Benedikt M. , Ratcliffe Peter J. , Wolf Alexander , Schofield Christopher J.
Published: February 2014

Significance

The processing of DNA sequences into proteins is fine-tuned to meet the conflicting demands of accuracy and speed. DNA mutations can introduce premature stop codons, leading to inactive proteins. We report that oxygen-dependent posttranslational modification of the ribosomal decoding center affects stop codon readthrough in an mRNA sequence-dependent manner. Our work demonstrates that oxygenases catalyzing RPS23 hydroxylation are conserved in eukaryotes, including yeasts, flies, and humans. In basal eukaryotes, RPS23 undergoes two hydroxylations, whereas in animals we only observe one hydroxylation. Yeast ribosomes lacking hydroxylation manifest altered stop codon readthrough up to ∼10-fold. The results reveal oxygen-dependent modifications that regulate translational accuracy and suggest unprecedented approaches to modulating ribosomal accuracy for medicinal application.
Intercellular propagated misfolding of wild-type Cu/Zn superoxide dismutase occurs via exosome-dependent and -independent mechanisms
Authors: Grad Leslie I. , Yerbury Justin J. , Turner Bradley J. , Guest William C. , Pokrishevsky Edward , O’Neill Megan A. , Yanai Anat , Silverman Judith M. , Zeineddine Rafaa , Corcoran Lisa , Kumita Janet R. , Luheshi Leila M. , Yousefi Masoud , Coleman Bradley M. , Hill Andrew F. , Plotkin Steven S. , Mackenzie Ian R. , Cashman Neil R.
Published: February 2014

Significance

Amyotrophic lateral sclerosis (ALS), an incurable motor neuron disease, is associated with mutation and misfolding of the Cu/Zn superoxide dismutase (SOD1) protein. Prior studies found that mutant misfolded SOD1 can convert wild-type (WT) SOD1 to a misfolded form inside living cells in a prion-like fashion. We now report that misfolded WT SOD1 can be transmitted from cell to cell, and that propagated protein misfolding can be perpetuated. Misfolded SOD1 transmission between cells can be mediated through release and uptake of protein aggregates or via small membrane-bounded transport vesicles called exosomes. These mechanisms may help explain why sporadic ALS, without a known genetic cause, can spread systematically from region to region in a progressive manner.
Toxoplasmaaldolase is required for metabolism but dispensable for host-cell invasion
Authors: Shen Bang , Sibley L. David
Published: February 2014

Significance

Previous studies have suggested that aldolase plays an essential role in parasite motility and host-cell invasion by connecting surface-adhesive proteins to the actin–myosin motor of the parasite. However, our studies show thatToxoplasmaaldolase is critical for metabolism but not directly required for parasite motility or invasion. Aldolase-depletedT. gondiicells were sensitive to glucose but showed normal motility and host-cell invasion when grown without glucose, indicating that aldolase does not fulfill an essential role in these important aspects of parasite biology. This conclusion was also supported by studies from adhesin mutants with altered interactions with aldolase in vitro. Taken together, our results force a revision to the current model for host-cell invasion of apicomplexan parasites.
Cortisol shifts financial risk preferences
Authors: Kandasamy Narayanan , Hardy Ben , Page Lionel , Schaffner Markus , Graggaber Johann , Powlson Andrew S. , Fletcher Paul C. , Gurnell Mark , Coates John
Published: February 2014

Significance

Many influential models in economics, finance, and neurobiology assume risk preferences are a stable trait. In this study we find they are not. We examine the effects of chronic stress on financial risk taking by raising cortisol levels in volunteers over an 8-d period using individually tailored hydrocortisone regimens. We find that they become more risk-averse and that the overweighting of small probabilities becomes more exaggerated among men relative to women. We designed our protocol to maintain ecological validity: The increase in cortisol among participants replicated levels we had previously observed in real traders when faced with uncertainty and market volatility. Physiology-induced shifts in risk preferences may thus be a cause of market instability that has been hitherto overlooked by economists, risk managers, and central bankers.
Chemical-biogeographic survey of secondary metabolism in soil
Authors: Charlop-Powers Zachary , Owen Jeremy G. , Reddy Boojala Vijay B. , Ternei Melinda A. , Brady Sean F.
Published: February 2014

Significance

A comparative analysis of conserved domain fragments amplified from nonribosomal peptide and polyketide-type gene clusters present in diverse soil microbiomes revealed a link between soil type, species composition, and biosynthetic richness, as well as an unexpected conservation of the meta-secondary metabolome present within microbiomes from similar soil types. Although the functional consequences of these enrichment patterns is not yet clear, it suggests that similar soil types contain functionally related collections of secondary metabolites that likely play conserved roles in the ecology of these soils. This work provides a model for the large-scale extension of molecular phylogenetic-type analyses directly to the study, characterization, and comparison of secondary metabolite biosynthetic gene clusters that remain hidden in diverse soil microbiomes.
Pregnancy without progesterone in horses defines a second endogenous biopotent progesterone receptor agonist, 5α-dihydroprogesterone
Authors: Scholtz Elizabeth L. , Krishnan Shweta , Ball Barry A. , Corbin C. Jo , Moeller Benjamin C. , Stanley Scott D. , McDowell Karen J. , Hughes Austin L. , McDonnell Donald P. , Conley Alan J.
Published: February 2014

Significance

We have characterized the relative bioactivity of the physiological progestin, dihydroprogesterone (DHP), showing in vivo it maintains equine gestation in the absence of progesterone, generally believed the only steroid capable of supporting pregnancy. DHP activates the equine progesterone receptor (PR) as potently as progesterone itself, and the human PR potently enough to suggest support for human pregnancy. Thus, DHP joins this steroid class as the only other naturally synthesized progestin so defined. This settles five decades of speculation that DHP sustains equine pregnancies in the second half of gestation when circulating progesterone becomes undetectable. Expanding the progestin class in horses reminds us that the limited suite of physiologically relevant sex steroids currently recognized may be incomplete across taxa.
Gene expression differences underlying genotype-by-genotype specificity in a host–parasite system
Authors: Barribeau Seth M. , Sadd Ben M. , du Plessis Louis , Schmid-Hempel Paul
Published: February 2014

Significance

Some genotypes of parasites can infect some genotypes of hosts but not others, whereas hosts also vary in susceptibility to a given parasite genotype. Variation in genes important for defenses against parasites could produce this specificity. Here, we find that variation in gene expression depended on both the genotype of the host and the genotype of the parasite. Moreover, we found that bumblebees that were exposed to infectious genotypes of a trypanosome parasite had low gene expression of immune genes but upregulation of genes that control expression. A poorly infecting parasite genotype, however, induced expression of immune genes. These results suggest that variation in the regulation of gene expression may also contribute to producing genotype-by-genotype specificity.
Detecting and visualizing cell phenotype differences from microscopy images using transport-based morphometry
Authors: Basu Saurav , Kolouri Soheil , Rohde Gustavo K.
Published: February 2014

Significance

Much of what is currently known about how cells work has been derived through visual interpretation of microscopy images. Computational methods for image analysis have emerged as quantitative alternatives to visual interpretation. We describe an analysis pipeline for cell image databases that combines statistical pattern recognition with the mathematics of optimal mass transport. The approach is fully automated and does not require the use of ad hoc numerical features. It enables the identification of discriminant phenotypic variations, or biomarkers, between sets of cells (e.g., normal vs. diseased) while at the same time allowing for the visualization of meaningful differences. The approach can be used for fully automated high content screening with a variety of microscopic image modalities.
Circulating giant macrophages as a potential biomarker of solid tumors
Authors: Adams Daniel L. , Martin Stuart S. , Alpaugh R. Katherine , Charpentier Monica , Tsai Susan , Bergan Raymond C. , Ogden Irene M. , Catalona William , Chumsri Saranya , Tang Cha-Mei , Cristofanilli Massimo
Published: February 2014

Significance

Using microfiltration as a liquid biopsy for the recovery of circulating tumor cells (CTCs) has revealed an accompanying macrophage subset that we use as a highly sensitive biomarker for solid tumors. We supply evidence that this circulating giant cell is a subset of disseminated tumor-associated macrophages capable of binding CTCs in peripheral blood of cancer patients. The presence of this cell expands the concept of using a liquid biopsy not only to indicate cancer presence but also to track cancer treatment effects sequentially using other circulating blood cells. Further, we supply observational evidence hypothesizing a metastasis pathway model in which CTCs migrate with pro-angiogenic macrophages, linking cancer cell intravasation, migration, and extravasation and the formation of metastatic microenvironments.
Central role for hydrogen peroxide in P2Y1 ADP receptor-mediated cellular responses in vascular endothelium
Authors: Kalwa Hermann , Sartoretto Juliano L. , Martinelli Roberta , Romero Natalia , Steinhorn Benjamin S. , Tao Ming , Ozaki C. Keith , Carman Christopher V. , Michel Thomas
Published: February 2014

Significance

ADP is best known as a constituent of nucleic acids and for its role in energy metabolism. ADP is also an important signaling molecule that activates cell surface receptors in a broad range of cells. ADP receptor antagonists are widely used to treat cardiovascular disease. We studied the signaling pathways activated by ADP receptors in endothelial cells, which form the lining of blood vessels. Vascular disease states cause abnormalities in endothelial function. We identified a critical role for the reactive oxygen species hydrogen peroxide (H
2
O
2
) in mediating cellular responses to ADP. We discovered that P2Y1 ADP receptors promote transactivation of the receptor tyrosine kinase Flt3, suggesting a new mechanism whereby cancer chemotherapy with receptor tyrosine kinase inhibitors cause vascular dysfunction.
Dynamic look at DNA unwinding by a replicative helicase
Authors: Lee Seung-Jae , Syed Salman , Enemark Eric J. , Schuck Stephen , Stenlund Arne , Ha Taekjip , Joshua-Tor Leemor
Published: February 2014

Significance

Precise replication of the genome is essential for maintaining the integrity of genetic information in all forms of life. A key step in this process is the unwinding of the DNA double helix, a subject of intensive research and debate. We took a multifaceted approach to study fundamental mechanisms of helicase function, using the E1 helicase from papillomavirus. Our findings reveal that E1 employs a strand exclusion mechanism to unwind DNA with the N-terminal side leading at the replication fork. Intriguingly, DNA unwinding by E1 is modulated by the origin-recognition domain, suggesting a previously unsuspected role for this domain in regulating helicase activity.
Stochasticity, succession, and environmental perturbations in a fluidic ecosystem
Authors: Zhou Jizhong , Deng Ye , Zhang Ping , Xue Kai , Liang Yuting , Van Nostrand Joy D. , Yang Yunfeng , He Zhili , Wu Liyou , Stahl David A. , Hazen Terry C. , Tiedje James M. , Arkin Adam P.
Published: February 2014

Significance

The study of ecological succession remains at the core of ecology. Understanding the trajectories and mechanisms controlling ecological succession is crucial to predicting the responses of ecosystems to environmental change and projecting their future states. By definition, deterministic succession is expected under homogeneous abiotic and biotic starting conditions. This study, however, shows that the succession of groundwater microbial communities in response to nutrient amendment is primarily stochastic, but that the drivers controlling biodiversity and succession are dynamic rather than static. By identifying the mechanisms controlling microbial community assembly and succession, this study makes fundamental contribution to the mechanistic understanding essential for a predictive microbial ecology of many systems ranging from microbiomes of humans and plants to natural and managed ecosystems.
Detecting grain rotation at the nanoscale
Authors: Chen Bin , Lutker Katie , Lei Jialin , Yan Jinyuan , Yang Shizhong , Mao Ho-kwang
Published: February 2014

Significance

The plastic deformation of nanomaterials has long been wrapped in mystery. Grain rotation is suggested to be a dominant mechanism of plastic deformation for ultrafine nanomaterials. However, the in situ observation of grain rotation has been made possible only for coarse-grained materials. Here we report the in situ high-pressure detection of grain rotation at the nanoscale. The surprising observation is that the texture strength of the same-sized platinum drops rapidly with decreasing grain size of the nickel medium, indicating that more active grain rotation occurs in the smaller nickel nanocrystals. Insight into these processes provides a better understanding of the plastic deformation of nanomaterials at a few-nanometer length scale.
Oxygen requirements of the earliest animals
Authors: Mills Daniel B. , Ward Lewis M. , Jones CarriAyne , Sweeten Brittany , Forth Michael , Treusch Alexander H. , Canfield Donald E.
Published: February 2014

Significance

The relationship between the origin of animals and the oxygen content of the atmosphere is a pressing issue in historical geology. Here we challenge the widely held view that low levels of atmospheric oxygen delayed the origin of animals up until 850–542 million years ago. We provide experimental evidence suggesting that the last common ancestor of animals could have thrived in oxygen levels as low as 0.5% to 4% of present atmospheric levels, which were likely met on Earth well before animals evolved. This was achieved by observing the survival of sponges, basal animals similar to the earliest metazoans, under low-oxygen conditions in the laboratory. These results encourage us to reconsider the environmental constraints on the origin of animal life.
Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in
Arabidopsis
Authors: Feng Zhengyan , Mao Yanfei , Xu Nanfei , Zhang Botao , Wei Pengliang , Yang Dong-Lei , Wang Zhen , Zhang Zhengjing , Zheng Rui , Yang Lan , Zeng Liang , Liu Xiaodong , Zhu Jian-Kang
Published: February 2014

Significance

The CRISPR (clustered regularly interspaced short palindromic repeat)/Cas (CRISPR-associated) system has been used to generate targeted gene editing in plants. However, it is not known whether CRISPR/Cas-induced gene modifications in plants occur in somatic cells only or whether some or all of the modifications can enter the germ line to become heritable. Through systematic and multigenerational analysis, this study demonstrates that although the majority of gene modifications detected in the first generation CRISPR/Cas transgenic
Arabidopsis
plants were somatic mutations only, heritable mutations could be found in subsequent generations. In addition, deep sequencing of CRISPR/Cas-modified
Arabidopsis
genomes did not detect any off-targets. The work demonstrates that the CRISPR/Cas method can effectively create specific gene modifications
in planta
that are stably transmitted through the germ line to future generations.
Local immunostimulation leading to rejection of accepted male skin grafts by female mice as a model for cancer immunotherapy
Authors: Bourdeaux Christophe , Lurquin Christophe , Jacquemart Isabelle , Lethé Bernard , Brasseur Francis , van Baren Nicolas , Baurain Jean-François , Dyson Julian , Van Snick Jacques , Uyttenhove Catherine , Boon Thierry
Published: February 2014

Significance

Many cancer patients mount a spontaneous T-lymphocyte response against their tumor. In metastatic progressing patients, this response has evidently been incomplete. Moreover, it has stalled, and an immunosuppressive environment appears to be present within the tumor. This may constitute a major factor preventing success of immunotherapies such as antitumoral vaccination. Similar stalled responses are occasionnally observed in the area of tissue transplantation. In a mouse strain named CBA, this phenomenon is observed when male skin is grafted onto females. We used this system to find combinations of cytokines and Toll receptor ligands that, when applied locally, relieve the immunosuppression and reactivate the response. The combinations reported here may prove generally useful to boost the efficacy of cancer immunotherapy.
Dissociation of the trimeric gp41 ectodomain at the lipid–water interface suggests an active role in HIV-1 Env-mediated membrane fusion
Authors: Roche Julien , Louis John M. , Grishaev Alexander , Ying Jinfa , Bax Adriaan
Published: February 2014

Significance

Infection by HIV-1 requires fusion of viral and host cell membranes, a process mediated by viral protein gp41. Although extensive structural detail on both pre- and postfusion gp41 states is available from X-ray crystallography and cryo-EM studies, little is known about the actual transition. This NMR study of a trimeric gp41 ectodomain, which connects viral and host cell membranes in the prefusion state, suggests a fusion model, where this domain unzippers from opposite ends because of the affinity of its two α-helices for viral and host cell membranes. In this model, the change in orientation of the ectodomain helices, which is associated with membrane binding, provides the driving force that pulls the membranes into the close juxtaposition required for fusion.
Inhibition of Cullin-RING E3 ubiquitin ligase 7 by simian virus 40 large T antigen
Authors: Hartmann Thomas , Xu Xinsong , Kronast Mira , Muehlich Susanne , Meyer Kathleen , Zimmermann Wolfgang , Hurwitz Jerard , Pan Zhen-Qiang , Engelhardt Stefan , Sarikas Antonio
Published: February 2014

Significance

Simian virus 40 (SV40) large tumor antigen (LT) is a viral oncoprotein with the ability to induce tumors by inhibition of cellular tumor suppressors such as p53 and members of the retinoblastoma protein family. Here we present evidence for a role of SV40 LT in suppressing the activity of Cullin-RING E3 ubiquitin ligase 7 in mediating the ubiquitin-dependent degradation of insulin receptor substrate 1 (IRS1). This SV40 LT-mediated protection of IRS1 leads to enhanced activation of promitogenic downstream signaling pathways AKT and Erk mitogen-activated pathway kinase, which may contribute to viral-induced oncogenic transformation.
The potential impact of climate change on the infectious diseases of commercially important shellfish populations in the Irish Sea—a review
Authors: Rowley Andrew F. , Cross Maud E. , Culloty Sarah C. , Lynch Sharon A. , Mackenzie Clara L. , Morgan Emer , O'Riordan Ruth M. , Robins Peter E. , Smith Amanda L. , Thrupp Tara J. , Vogan Claire L. , Wootton Emma C. , Malham Shelagh K.
Published: February 2014

The Irish Sea and surrounding regions are a rich source of shellfish production as a result of captive fishing and aquaculture. Key species produced include lobsters (Homarus gammarus), edible crabs (Cancer pagurus), langoustines (Nephrops norvegicus), flat oysters (Ostrea edulis), cockles (Cerestoderma edule) and blue mussels (Mytilus edulis). The role played by infectious disease in limiting the sustainability of the production of these species is largely neglected. This review summarizes our knowledge of the key diseases of commercially important crustaceans and bivalve molluscs and attempts to determine their role in limiting the population of animals available for food production both at present and in the future. It shows that the key diseases threatening the sustainability of shellfish production are bitter crab disease in langoustines and edible crabs, and a wide range of diseases caused by micro- and macro-parasites in some bivalve molluscs including oysters and cockles. Oceanographic models are also employed to predict how changes in climate over the next half century may affect these key diseases and their hosts as found in the Irish Sea. It is concluded that the paucity of information on the potential transfer of some disease agents in pelagic larval stages of hosts and vectors is a major hurdle in predicting how some changes in environmental conditions may influence the prevalence and severity of shellfish diseases in coming years.
Genes without prominence: a reappraisal of the foundations of biology
Authors: Annila Arto , Baverstock Keith
Published: February 2014

The sequencing of the human genome raises two intriguing questions: why has the prediction of the inheritance of common diseases from the presence of abnormal alleles proved so unrewarding in most cases and how can some 25 000 genes generate such a rich complexity evident in the human phenotype? It is proposed that light can be shed on these questions by viewing evolution and organisms as natural processes contingent on the second law of thermodynamics, equivalent to the principle of least action in its original form. Consequently, natural selection acts on variation in any mechanism that consumes energy from the environment rather than on genetic variation. According to this tenet cellular phenotype, represented by a minimum free energy attractor state comprising active gene products, has a causal role in giving rise, by a self-similar process of cell-to-cell interaction, to morphology and functionality in organisms, which, in turn, by a self-similar process entailing Darwin'sproportional numbersare influencing their ecosystems. Thus, genes are merely a means of specifying polypeptides: those that serve free energy consumption in a given surroundings contribute to cellular phenotype as determined by the phenotype. In such natural processes, everything depends on everything else, and phenotypes are emergent properties of their systems.
Quantification of single-cell nanoparticle concentrations and the distribution of these concentrations in cell population
Authors: Rashkow Jason T. , Patel Sunny C. , Tappero Ryan , Sitharaman Balaji
Published: February 2014

Quantification of nanoparticle uptake into cells is necessary for numerous applications in cellular imaging and therapy. Herein, synchrotron X-ray fluorescence (SXRF) microscopy, a promising tool to quantify elements in plant and animal cells, was employed to quantify and characterize the distribution of titanium dioxide (TiO
2
) nanosphere uptake in a population of single cells. These results were compared with average nanoparticle concentrations per cell obtained by widely used inductively coupled plasma mass spectrometry (ICP-MS). The results show that nanoparticle concentrations per cell quantified by SXRF were of one to two orders of magnitude greater compared with ICP-MS. The SXRF results also indicate a Gaussian distribution of the nanoparticle concentration per cell. The results suggest that issues relevant to the field of single-cell analysis, the limitation of methods to determine physical parameters from large population averages leading to potentially misleading information and the lack of any information about the cellular heterogeneity are equally relevant for quantification of nanoparticles in cell populations.
Surface contact and design of fibrillar ‘friction pads’ in stick insects (Carausius morosus): mechanisms for large friction coefficients and negligible adhesion
Authors: Labonte David , Williams John A. , Federle Walter
Published: February 2014

Many stick insects and mantophasmids possess tarsal ‘heel pads’ (euplantulae) covered by arrays of conical, micrometre-sized hairs (acanthae). These pads are used mainly under compression; they respond to load with increasing shear resistance, and show negligible adhesion. Reflected-light microscopy in stick insects (Carausius morosus) revealed that the contact area of ‘heel pads’ changes with normal load on three hierarchical levels. First, loading brought larger areas of the convex pads into contact. Second, loading increased the density of acanthae in contact. Third, higher loads changed the shape of individual hair contacts gradually from circular (tip contact) to elongated (side contact). The resulting increase in real contact area can explain the load dependence of friction, indicating a constant shear stress between acanthae and substrate. As the euplantula contact area is negligible for small loads (similar to hard materials), but increases sharply with load (resembling soft materials), these pads show high friction coefficients despite little adhesion. This property appears essential for the pads’ use in locomotion. Several morphological characteristics of hairy friction pads are in apparent contrast to hairy pads used for adhesion, highlighting key adaptations for both pad types. Our results are relevant for the design of fibrillar structures with high friction coefficients but small adhesion.
Molecular heterochrony and the evolution of sociality in bumblebees (
Bombus terrestris
)
Authors: Woodard S. Hollis , Bloch Guy M. , Band Mark R. , Robinson Gene E.
Published: February 2014

Sibling care is a hallmark of social insects, but its evolution remains challenging to explain at the molecular level. The hypothesis that sibling care evolved from ancestral maternal care in primitively eusocial insects has been elaborated to involve heterochronic changes in gene expression. This elaboration leads to the prediction that workers in these species will show patterns of gene expression more similar to foundress queens, who express maternal care behaviour, than to established queens engaged solely in reproductive behaviour. We tested this idea in bumblebees (
Bombus terrestris
) using a microarray platform with approximately 4500 genes. Unlike the wasp
Polistes metricus
, in which support for the above prediction has been obtained, we found that patterns of brain gene expression in foundress and queen bumblebees were more similar to each other than to workers. Comparisons of differentially expressed genes derived from this study and gene lists from microarray studies in
Polistes
and the honeybee
Apis mellifera
yielded a shared set of genes involved in the regulation of related social behaviours across independent eusocial lineages. Together, these results suggest that multiple independent evolutions of eusociality in the insects might have involved different evolutionary routes, but nevertheless involved some similarities at the molecular level.
Inactivation of pecS restores the virulence of mutants devoid of osmoregulated periplasmic glucans in the phytopathogenic bacterium Dickeya dadantii
Authors: Bontemps-Gallo Sébastien , Madec Edwige , Lacroix Jean-Marie
Published: February 2014

Dickeya dadantii is a phytopathogenic enterobacterium that causes soft rot disease in a wide range of plant species. Maceration, an apparent symptom of the disease, is the result of the synthesis and secretion of a set of plant cell wall-degrading enzymes (PCWDEs), but many additional factors are required for full virulence. Among these, osmoregulated periplasmic glucans (OPGs) and the PecS transcriptional regulator are essential virulence factors. Several cellular functions are controlled by both OPGs and PecS. Strains devoid of OPGs display a pleiotropic phenotype including total loss of virulence, loss of motility and severe reduction in the synthesis of PCWDEs. PecS is one of the major regulators of virulence in D. dadantii, acting mainly as a repressor of various cellular functions including virulence, motility and synthesis of PCWDEs. The present study shows that inactivation of the pecS gene restored virulence in a D. dadantii strain devoid of OPGs, indicating that PecS cannot be de-repressed in strains devoid of OPGs.
The ontogeny of learned inhibition
Authors: Meyer Heidi C. , Bucci David J.
Published: February 2014

Previous studies have examined the maturation of learning and memory abilities during early stages of development. By comparison, much less is known about the ontogeny of learning and memory during later stages of development, including adolescence. In Experiment 1, we tested the ability of adolescent and adult rats to learn a Pavlovian negative occasion setting task. This procedure involves learning to inhibit a behavioral response when signaled by a cue in the environment. During reinforced trials, a target stimulus (a tone) was presented and immediately followed by a food reward. On nonreinforced trials, a feature stimulus (a light) was presented 5 sec prior to the tone and indicated the absence of reward following presentation of the tone. Both adult and adolescent rats learned to discriminate between two different trial types and withhold responding when the light preceded the tone. However, adolescent rats required more sessions than adults to discriminate between reinforced and nonreinforced trials. The results of Experiment 2 revealed that adolescents could learn the task rules but were specifically impaired in expressing that learning in the form of withholding behavior on nonreinforced trials. In Experiment 3, we found that adolescents were also impaired in learning a different version of the task in which the light and tone were presented simultaneously during the nonreinforced trials. These findings add to existing literature by indicating that impairments in inhibitory behavior during adolescence do not reflect an inability to learn to inhibit a response, but instead reflect a specific deficit in expressing that learning.
Inhibition of acid‐sensing ion channel currents by propofol in rat dorsal root ganglion neurons
Authors: Lei Zhen , Li Xiaoyu , Wang Guizhi , Fei Jianchun , Meng Tao , Zhang Xinyu , Yu Jingya , Yu Jingui , Li Jingxin
Published: February 2014

Acid‐sensing ion channels (ASICs), part of the epithelial sodium channel/degenerin family, are activated by extracellular protons. The ASICs play a significant role in the acidosis‐mediated perception of pain. The anaesthetic agent propofol also exerts antinociceptive effects, but the underlying mechanisms for this effect are not clear.

We used whole‐cell patch clamping to investigate the effect of propofol on proton‐gated currents in: (i) rat dorsal root ganglion (DRG) neurons; and (ii) HEK293 cells transfected with either ASIC1a or ASIC3.

Propofol inhibited the amplitude of proton‐gated currents in DRG neurons, but did not change the sensitivity of ASICs to H+. Notably, propofol altered acid‐evoked excitability of rat DRG neurons and decreased the number of action potentials induced by acid stimuli. In addition, we demonstrated that propofol inhibited ASICs by directly binding with these channels in HEK293 cells.

These results suggest that propofol inhibits proton‐gated currents in DRG neurons and that inhibition of proton‐gated currents explains, in part, the antinociceptive effects of propofol in primary afferent neurons.