bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental investigation of symmetry properties of second harmonic Lamb waves
Authors: Liu Yu , Kim Jin-Yeon , Jacobs Laurence J. , Qu Jianmin , Li Zheng
Published: March 2012

Recent studies by multiple authors show contradictory results concerning the symmetry properties of second harmonic Lamb waves. This research experimentally investigates this symmetry issue by examining both symmetric (s1-s2) and anti-symmetric (a1-a2 and a2-a4) mode pairs in aluminum plates under the same experimental conditions. The wedge technique is used to generate and detect ultrasonic Lamb wave signals of a specific mode, and the Morlet wavelet is applied to extract the fundamental and second harmonic amplitudes. The measured normalized second harmonic amplitudes of the three different mode pairs all show a linear increase with propagation distance. However, the slopes of the two anti-symmetric mode pairs are smaller by two to three orders of magnitude than that of the symmetric mode pair considered. Further investigations of these two anti-symmetric mode pairs for plates with different levels of material nonlinearity reveal consistently small slopes that are independent of the level of material nonlinearity. Therefore, this research experimentally demonstrates that the second harmonic generation in anti-symmetric Lamb wave modes is extremely inefficient; this result is consistent with some recent theoretical predictions and thus shows that the use of these anti-symmetric modes is not favorable for the experimental characterization of material nonlinearity.
Nitrogen δ-doping for band engineering of GaAs-related quantum structures
Authors: Ishikawa Fumitaro , Furuse Shinichiro , Sumiya Kengo , Kinoshita Akihiro , Morifuji Masato
Published: March 2012

We study energy-band engineering with nitrogen delta (δ)-doping in GaAs-related quantum structures. A tight-binding calculation indicates that the band structure can be engineered by introducing the one-dimensional doping profile of nitrogen into GaAs. Using molecular beam epitaxy, we prepare δ-doped samples of AlGaAs/GaAs quantum wells and GaAs/δ-doped nitrogen superlattice structures at the growth temperature 560 °C. Photoluminescence obtained from the samples shows a clear redshift of the spectral peak positions dependent on the nitrogen coverage. The transition energies of the superlattice structures agree well with those obtained from photoreflectance, indicating the feasibility of band modification with a single or a multiple nitrogen δ-doped layer.
Isotropic-medium three-dimensional cloaks for acoustic and electromagnetic waves
Authors: Urzhumov Yaroslav , Landy Nathan , Smith David R.
Published: March 2012

We propose a generalization of the two-dimensional eikonal-limit cloak derived from a conformal transformation to three dimensions. The proposed cloak is a spherical shell composed of only isotropic media; it operates in the transmission mode and requires no mirror or ground plane. Unlike the well-known omnidirectional spherical cloaks, it may reduce visibility of an arbitrary object only for a very limited range of observation angles. In the short-wavelength limit, this cloaking structure restores not only the trajectories of incident rays, but also their phase, which is a necessary ingredient to complete invisibility. Both scalar-wave (acoustic) and transverse vector-wave (electromagnetic) versions are presented.
Non-volatile gated variable resistor based on doped La2CuO4+δ and SrTiO3 heterostructures
Authors: Weber Dieter , Poppe Ulrich
Published: March 2012

Gated variable resistors were manufactured by depositing epitaxial heterostructures of doped La2CuO4+δ and SrTiO3 layers. Their conductance change as function of write current I and write time t followed a simple empirical law of the form ΔG/G = CIAtB. This behavior is in agreement with ionic transport that accelerates exponentially with electrical field strength.
Efficient polymer solar cells based on light-trapping transparent electrodes
Authors: Hu Ziyang , Zhang Jianjun , Zhao Ying
Published: March 2012

Highly efficient and cost-effective polymer solar cells (PSCs) fabricated on textured fluorine doped transparent conductive (FTO) electrodes are achieved. Such electrodes with rough surface in combination with reflective back contacts provide efficient light-trapping by light scattering and multiple reflections to increase the path length of the light. Due to the increased light absorption in active layer, the resultant PSCs base on polymer:fullerene system show 10% and 8% improvement in short current density and efficiency, respectively, compared with the reference cell based on the flat electrodes.
Electron traps in amorphous In–Ga–Zn–O thin films studied by isothermal capacitance transient spectroscopy
Authors: Hayashi Kazushi , Hino Aya , Morita Shinya , Yasuno Satoshi , Okada Hiroshi , Kugimiya Toshihiro
Published: March 2012

Electron traps in amorphous In–Ga–Zn–O (a-IGZO) thin films were studied using isothermal capacitance transient spectroscopy (ICTS). Broad peaks that shifted toward a longer elapsed time with an increase in the filling pulse width were detected from the ICTS spectra for metal-oxide-semiconductor diodes consisting of a Mo/SiO2/a-IGZO structure. The time constant of the peak position at 180 K was found to be from ∼1 m to ∼100 ms, corresponding to a range of energy level from ∼170 to ∼230 meV below the conduction band edge. The total trap density around the peak was estimated to be ∼1 × 1016 cm−3·eV−1. Further, according to the biasing voltage dependence of the ICTS signal, the density of the trap states increases by about three orders of magnitude near the interface between the a-IGZO and the gate dielectric layers. The electron transport in electronic devices using an a-IGZO could be influenced by the trap states detected in the present study.
Interfacial stabilization of bilayered nanolaminates by asymmetric block copolymers
Authors: Gozen Arif O. , Genzer Jan , Spontak Richard J.
Published: March 2012

Block copolymers are macromolecular surfactants that self-assemble into a variety of nanostructural elements or reduce the interfacial tension between incompatible polymers. Here, we examine the ability of diblock copolymers differing in composition to stabilize bilayered homopolymer nanolaminates on flat solid supports. In this arrangement, self-assembly competes with interfacial modification and, in one case, promotes destabilization of the top film. To discern the corresponding mechanism, we investigate nanolaminates with a thin copolymer layer positioned between the homopolymer layers. Stabilization commences when this middle layer is sufficiently thick so that the block that is miscible with the top layer forms a brush.
The enhanced optical conductivity for zigzag-edge graphene nanoribbons with applied gate voltage
Authors: Zhu Wen-Huan , Ding Guo-Hui , Dong Bing
Published: March 2012

We study the optical absorption properties of zigzag-edge graphene nanoribbons (ZGNRs) taking into account the Coulomb interaction effect in the Hartree-Fock approximation. The optical selection rules for the incident light polarized along the longitudinal and transverse directions are investigated. We demonstrate that the excitations from the edge states are essential for the optical properties of ZGNRs in the neutral case. With the chemical potential shifting away from the Dirac point, the optical conductivity is drastically enhanced in the low frequency region for the transverse polarized incident light.
Carbon isotope doping induced interfacial thermal resistance and thermal rectification in graphene
Authors: Pei Qing-Xiang , Zhang Yong-Wei , Sha Zhen-Dong , Shenoy Vivek B.
Published: March 2012

We investigate the thermal transport properties of carbon isotope doped graphene using nonequilibrium molecular dynamics simulations. We find that the interfacial thermal resistance between graphene and the isotope atoms causes severe reduction in thermal conductivity of the doped graphene. Furthermore, we find that thermal rectification occurs in the interface. Tensile strain leads to an increase in the interfacial thermal resistance and thermal rectification, while increasing temperature decreases these parameters. We calculate the phonon spectra and find that the thermal rectification is associated with the overlap areas in the phonon spectra.
Effects of interface disorder on valley splitting in SiGe/Si/SiGe quantum wells
Authors: Jiang Zhengping , Kharche Neerav , Boykin Timothy , Klimeck Gerhard
Published: March 2012

A sharp potential barrier at the Si/SiGe interface introduces valley splitting (VS), which lifts the 2-fold valley degeneracy in strained SiGe/Si/SiGe quantum wells (QWs). This work examines in detail the effects of Si/SiGe interface disorder on the VS in an atomistic tight binding approach based on statistical sampling. VS is analyzed as a function of electric field, QW thickness, and simulation domain size. Strong electric fields push the electron wavefunctions into the SiGe buffer and introduce significant VS variations from device to device. A Gedankenexperiment with ordered alloys sheds light on the importance of different bonding configurations on VS. We conclude that a single SiGe band offset and effective mass cannot comprehend the complex Si/SiGe interface interactions that dominate VS.
Relativistic acceleration of Landau resonant particles as a consequence of Hopf bifurcations
Authors: Osmane A. , Hamza A. M.
Published: March 2012

Using bifurcation theory on a dynamical system simulating the interaction of a particle with an obliquely propagating wave in relativistic regimes, we demonstrate that uniform acceleration arises as a consequence of Hopf bifurcations of Landau resonant particles. The acceleration process arises as a form of surfatron established through the locking in pitch angle, gyrophase, and physical trapping along the wave-vector direction. Integrating the dynamical system for large amplitudes (δB/B0∼0.1) obliquely propagating waves, we find that electrons with initial energies in the keV range can be accelerated to MeV energies on timescales of the order of milliseconds. The Hopf condition of Landau resonant particles could underlie some of the most efficient energization of particles in space and astrophysical plasmas.
Experimental study of ejecta from shock melted lead
Authors: Chen Yongtao , Hu Haibo , Tang Tiegang , Ren Guowu , Li Qingzhong , Wang Rongbo , Buttler William T.
Published: March 2012

This effort investigates the dynamic properties of ejecta from explosively shocked, melted Pb targets. The study shows that the ejecta cloud that expands beyond the shocked surface is characterized by a high density and low velocity fragment layer between the free-surface and the high velocity micro-jetting particle cloud. This slow, dense ejecta layer is liquid micro-spall. The properties of micro-spall layer, such as the mass, density and velocity, were diagnosed in a novel application of an Asay window, while micro-jetting particles by lithium niobate piezoelectric pins and high speed photography. The total mass-velocity distribution of ejecta, including micro-spall fragments and micro-jetting particles, is presented. Furthermore, the sensitivity of ejecta production to slight variations in the shockwave drive using the Asay foil is studied.
Direct surface cyclotron resonance terahertz emission from a quantum cascade structure
Authors: Jasnot François-Régis , de Vaulchier Louis-Anne , Guldner Yves , Bastard Gérald , Vasanelli Angela , Manquest Christophe , Sirtori Carlo , Beck Mattias , Faist Jérôme
Published: March 2012

A strong magnetic field applied along the growth direction of a semiconductor quantum well gives rise to a spectrum of discrete energy states, the Landau levels. By combining quantum engineering of a quantum cascade structure with a static magnetic field, we can selectively inject electrons into the excited Landau level of a quantum well and realize a tunable surface emitting device based on cyclotron emission. By applying the appropriate magnetic field between 0 and 12 T, we demonstrate emission from a single device over a wide range of frequencies (1-2 THz and 3-5 THz).
Dissociation of water on Ti-decorated fullerene clusters
Authors: Xue Yongqiang
Published: March 2012

Spin-polarized density functional theory calculations have been applied to investigate water dissociation catalyzed by Ti adsorbed on icosahedral C20, C60 and C80 fullerene clusters, in order to elucidate the roles that cluster size and Ti-cluster interaction play in the proposed hydrogen generation reaction. We find that two water molecules can be dissociated consecutively by overcoming moderate energy barriers of a few tenths of eV, accompanied by the generation of a H2 molecule for all three clusters. Depending on the cluster size, the fullerene clusters may participate directly in water splitting or indirectly through stereochemical control of the Ti adsorption sites. Our results suggest that fullerene clusters can serve as a flexible platform for rational design of nanostructured catalysts for hydrogen generation.
Where in the beef-cattle supply chain might DNA tests generate value?
Authors: Van Eenennaam Alison L. , Drake Daniel J.
Published: March 2012

DNA information has the potential to generate value for each sector of the beef-cattle industry. The value distribution among sectors (breeding, commercial, feedlot, processing) will differ depending on marketing. The more descendants an animal produces, the more valuable each unit of genetic improvement becomes. Therefore, the value of using DNA testing to increase the accuracy of selection and accelerate the rate of genetic gain is highest in the breeding sector, particularly for replacement stud animals. There is a lesser value associated with increasing the accuracy of yearling commercial bulls. The cost to DNA test commercial sires will likely be incurred by breeders before sale, and must be recouped through higher bull sale prices or increased market share. Commercial farmers could also use DNA tests to improve the accuracy of replacement female selection. This assumes the development of DNA tests that perform well for the low-heritability traits that directly affect maternal performance (e.g. days to calving) in commercial cattle populations. DNA tests may provide the sole source of information for traits that are not routinely measured on commercial farms. In that case, DNA test information will provide new selection criteria to allow for genetic improvement in those traits. As DNA test offerings mature to have improved accuracy for traits of great value to the feedlot (e.g. feed conversion, disease resistance) and processing (e.g. meat quality) sectors, the added value derived from DNA-enabled selection for these traits will need to be efficiently transferred up the beef production chain to incentivise continued investment. The widespread adoption of DNA testing to enhance the accuracy of selection will likely require an approach to share the value realised by downstream sectors of the beef-cattle industry with those upstream sectors incurring DNA collection and testing expenses.
The use of genomics in the management of livestock
Authors: Kinghorn B. P.
Published: March 2012

Variation among animals exists at all stages of our livestock supply chains. In contrast, most manufacturing supply chains possess little, if any, unintended variation within each segment. This variation is generally an unwanted nuisance. However, when properly managed, it can provide opportunities to target multiple product end-points and turn-off dates in a dynamic manner. Moreover, optimal management can lead to high degrees of compliance with the needs of the processing segment of the supply chain and/or end-users. Management decisions can be divided into initial group formation (e.g. mating groups, feedlot entry groups) and ongoing changes to the management plan in the light of new information (including market forces, weather and genetic status of animals). In both cases, the best pattern of decision making depends, explicitly or implicitly, on the predicted effect of these decisions on future animal and processing performance. The present paper provides an overview of key factors that affect these predictions, and hence optimal management, and emphasises the potential role of genetic and genomic information for increasing focus and improving profitability in the beef supply chain.
Genomic selection in French dairy cattle
Authors: Boichard D. , Guillaume F. , Baur A. , Croiseau P. , Rossignol M. N. , Boscher M. Y. , Druet T. , Genestout L. , Colleau J. J. , Journaux L. , Ducrocq V. , Fritz S.
Published: March 2012

Genomic selection is implemented in French Holstein, Montbéliarde, and Normande breeds (70%, 16% and 12% of French dairy cows). A characteristic of the model for genomic evaluation is the use of haplotypes instead of single-nucleotide polymorphisms (SNPs), so as to maximise linkage disequilibrium between markers and quantitative trait loci (QTLs). For each trait, a QTL-BLUP model (i.e. a best linear unbiased prediction model including QTL random effects) includes 300–700 trait-dependent chromosomal regions selected either by linkage disequilibrium and linkage analysis or by elastic net. This model requires an important effort to phase genotypes, detect QTLs, select SNPs, but was found to be the most efficient one among all tested ones. QTLs are defined within breed and many of them were found to be breed specific. Reference populations include 1800 and 1400 bulls in Montbéliarde and Normande breeds. In Holstein, the very large reference population of 18 300 bulls originates from the EuroGenomics consortium. Since 2008, ~65 000 animals have been genotyped for selection by Labogena with the 50k chip. Bulls genomic estimated breeding values (GEBVs) were made official in June 2009. In 2010, the market share of the young bulls reached 30% and is expected to increase rapidly. Advertising actions have been undertaken to recommend a time-restricted use of young bulls with a limited number of doses. In January 2011, genomic selection was opened to all farmers for females. Current developments focus on the extension of the method to a multi-breed context, to use all reference populations simultaneously in genomic evaluation.
Livestock in no-till cropping systems - a story of trade-offs
Authors: Fisher James , Tozer Peter , Abrecht Doug
Published: March 2012

The trade-offs of incorporating livestock into no-till cropping systems were examined with respect to ground cover, water balance, nutrient cycling, pest management, whole-farm economics and farmer preferences. The hypothesis that livestock and no-till cropping enterprises may co-exist was investigated using a review of scientific literature and technical reports, information from farmer focus groups and an economic analysis based on case study data from farm consultants. The scientific review focussed on work from Australia, especially western and southern Australia, but also included research related to systems in northern New South Wales and southern Queensland and some related international work. The focus groups and case studies were from the cereal-sheep systems of western and southern Australia. It was concluded that the use of livestock in a no-till system is determined by the productive capacity of the land, the relative profitability of cropping and livestock, the management of herbicide-resistant weeds, sensitivity of soil to damage from grazing and trampling and the farmer’s passion, preference and willingness to apply increased management to livestock. Livestock are an important source of farm diversification and risk management. While net farm income tends to decline as the proportion of livestock increases, variation in net farm income also decreases, reducing volatility in revenue. Livestock need to comprise above 10–15% of net farm income to provide a positive impact on variability of return. Adaptation of mixed-farming systems through rotational grazing, temporary agistment of livestock or removal to non-cropping areas are all management options that may be utilised to remove or reduce potential negative impacts, improve integration and to realise triple-bottom-line gains.
Industrial perspective: capturing the benefits of genomics to Irish cattle breeding
Authors: Wickham B. W. , Amer P. R. , Berry D. P. , Burke M. , Coughlan S. , Cromie A. , Kearney J. F. , Mc Hugh N. , McParland S. , O'Connell K.
Published: March 2012

Genomics is a technology for increasing the accuracy with which the genetic merit of young potential breeding animals can be determined. It enables earlier selection decisions, thus reducing generation intervals and gives rise to more rapid annual rates of genetic gain. Recently, the cost of genomics has reduced to the point where it enables breeding-program costs to be reduced substantially. Ireland has been a rapid adopter of genomics technology in its dairy-cattle breeding program, with 40% of dairy-cow artificial inseminations in 2010 being from bulls evaluated using genomic information. This rapid adoption has been facilitated by a comprehensive database of phenotypes and genotypes, strong public funding support for applied genomics research, an international network of collaborators, a short path between research and implementation, an overall selection index which farmers use in making breeding decisions, and a motivated and informed breeding industry. The shorter generation interval possible with genomic selection strategies also allows exploitation of the already accelerating rate of genetic progress in Ireland, because elite young dairy bulls are considerably superior to the small numbers of bulls that entered progeny test 6 years ago. In addition, genomics is having a dramatic impact on the artificial-insemination industry by substantially reducing the cost of entry, the cost of operation, and shifting the focus of breeding from bulls to cows. We believe that the current industry structures must evolve substantially if Irish cattle farmers are to realise the full benefits of genomics and be protected from related risks. Our model for future dairy breeding envisages a small number of ‘next generation research herds’, 1000 ‘bull breeder herds’ and an artificial-insemination sector using 30 new genomically selected bulls per year to breed the bulk of replacements in commercial milk-producing herds. Accurate imputation from a low-density to a higher-density chip is a key element of our strategy to enable dairy farmers to afford access to genomics. This model is capable of delivering high rates of genetic gain, realising cost savings, and protecting against the risks of increased inbreeding and suboptimal breeding goals. Our strategy for exploiting genomic selection for beef breeding is currently focussed on genotyping, using a high-density chip, a training population of greater than 2000 progeny-tested bulls representing all the main beef breeds in Ireland. We recognise the need for a larger training population and are seeking collaboration with organisations in other countries and populations.
Foraging trip strategies and habitat use during late pup rearing by lactating Australian fur seals
Authors: Kirkwood Roger , Arnould John P. Y.
Published: March 2012

Australian fur seals (Arctocephalus pusillus doriferus) are the most conspicuous and abundant marine mammal in shelf waters of south-eastern Australia. To successfully rear offspring, the females must encounter sufficient prey on each foraging trip out of a central place for periods up to11 months each year. We investigated foraging trip strategies and habitat use by the females in three winter–spring periods, 2001–03, from four colonies that span the species’ latitudinal range and contribute 80% of pup production. Trip durations of 37 females averaged 6.1 ± 0.5 (s.e.) days, although >90% of the seal’s time at sea was spent <150 km travel (<2 days) away. Most females exhibited strong fidelities to individually preferred hot-spots. Females from colonies adjacent to productive shelf-edge waters generally had shorter trips, had smaller ranges, foraged closer to colonies and exhibited less diversity in trip strategies than did those from colonies more distant from a shelf-edge. From a management perspective, there was minimal overlap (<1%) between where females foraged and a system of marine reserves established in 2007, suggesting that habitats visited by lactating Australian fur seals currently receive minimal legislative protection.
Neutral theory for life histories and individual variability in fitness components
Authors: Steiner Ulrich Karl , Tuljapurkar Shripad
Published: March 2012

Individuals within populations can differ substantially in their life span and their lifetime reproductive success but such realized individual variation in fitness components need not reflect underlying heritable fitness differences visible to natural selection. Even so, biologists commonly argue that large differences in fitness components are likely adaptive, resulting from and driving evolution by natural selection. To examine this argument we use unique formulas to compute exactly the variance in life span and in lifetime reproductive success among individuals with identical (genotypic) vital rates (assuming a common genotype for all individuals). Such individuals have identical fitness but vary substantially in their realized individual fitness components. We show by example that our computed variances and corresponding simulated distribution of fitness components match those observed in real populations. Of course, (genotypic) vital rates in real populations are expected to differ by small but evolutionarily important amounts among genotypes, but we show that such differences only modestly increase variances in fitness components. We conclude that observed differences in fitness components may likely be evolutionarily neutral, at least to the extent that they are indistinguishable from distributions generated by neutral processes. Important consequences of large neutral variation are the following: Heritabilities for fitness components are likely to be small (which is in fact the case), small selective differences in life histories will be hard to measure, and the effects of random drift will be amplified in natural populations by the large variances among individuals.
Bitrophic interactions shape biodiversity in space
Authors: Jabot Franck , Bascompte Jordi
Published: March 2012

Ecologists and conservation biologists often study particular trophic groups in isolation, which precludes an explicit assessment of the impact of multitrophic interactions on community structure and dynamics. Network ecology helps to fill this gap by focusing on species interactions, but it often ignores spatial processes. Here, we are taking a step forward in the integration of metacommunity and network approaches by studying a model of bitrophic interactions in a spatial context. We quantify the effect of bitrophic interactions on the diversity of plants and their animal interactors, and we show their complex dependence on the structure of the interaction network, the strength of interactions, and the dispersal rate. We then develop a method to parameterize our model with real-world networks and apply it to 54 datasets describing three types of interactions: pollination, fungal association, and insect herbivory. In all three network types, bitrophic interactions generally lead to an increase of plant and animal spatial heterogeneity by decreasing local species richness while increasing β-diversity.
Injury-independent induction of reactive gliosis in retina by loss of function of the LIM homeodomain transcription factor Lhx2
Authors: de Melo Jimmy , Miki Katsuaki , Rattner Amir , Smallwood Phil , Zibetti Cristina , Hirokawa Karla , Monuki Edwin S. , Campochiaro Peter A. , Blackshaw Seth
Published: March 2012

Müller glia are the primary glial subtype in the retina and perform a wide range of physiological tasks in support of retinal function, but little is known about the transcriptional network that maintains these cells in their differentiated state. We report that selective deletion of the LIM homeodomain transcription factor Lhx2 from mature Müller glia leads to the induction of reactive retinal gliosis in the absence of injury. Furthermore, Lhx2 expression is also down-regulated in Prph2
Rd2/Rd2
animals immediately before the onset of reactive gliosis. Analysis of conditional Lhx2 knockouts showed that gliosis was hypertrophic but not proliferative. Aging of experimental animals demonstrated that constitutive reactive gliosis induced by deletion of Lhx2 reduced rates of ongoing apoptosis and compromised both rod and cone photoreceptor function. Additionally, these animals showed a dramatically reduced ability to induce expression of secreted neuroprotective factors and displayed enhanced rates of apoptosis in light-damage assays. We provide in vivo evidence that Lhx2 actively maintains mature Müller glia in a nonreactive state, with loss of function initiating a specific program of nonproliferative hypertrophic gliosis.
Folding mechanism of the metastable serpin
α
1
-antitrypsin
Authors: Tsutsui Yuko , Dela Cruz Richard , Wintrode Patrick L.
Published: March 2012

The misfolding of serpins is linked to several genetic disorders including emphysema, thrombosis, and dementia. During folding, inhibitory serpins are kinetically trapped in a metastable state in which a stretch of residues near the C terminus of the molecule are exposed to solvent as a flexible loop (the reactive center loop). When they inhibit target proteases, serpins transition to a stable state in which the reactive center loop forms part of a six-stranded β-sheet. Here, we use hydrogen-deuterium exchange mass spectrometry to monitor region-specific folding of the canonical serpin human
α
1
-antitrypsin (
α
1
-AT). We find large differences in the folding kinetics of different regions. A key region in the metastable → stable transition, β-strand 5A, shows a lag phase of nearly 350 s. In contrast, the “B-C barrel” region shows no lag phase and the incorporation of the C-terminal residues into β-sheets B and C is largely complete before the center of β-sheet A begins to fold. We propose this as the mechanism for trapping
α
1
-AT in a metastable form. Additionally, this separation of timescales in the folding of different regions suggests a mechanism by which
α
1
-AT avoids polymerization during folding.
Constraint shapes convergence in tetrodotoxin-resistant sodium channels of snakes
Authors: Feldman Chris R. , Brodie Edmund D. , Brodie Edmund D. , Pfrender Michael E.
Published: March 2012

Natural selection often produces convergent changes in unrelated lineages, but the degree to which such adaptations occur via predictable genetic paths is unknown. If only a limited subset of possible mutations is fixed in independent lineages, then it is clear that constraint in the production or function of molecular variants is an important determinant of adaptation. We demonstrate remarkably constrained convergence during the evolution of resistance to the lethal poison, tetrodotoxin, in six snake species representing three distinct lineages from around the globe. Resistance-conferring amino acid substitutions in a voltage-gated sodium channel, Na
v
1.4, are clustered in only two regions of the protein, and a majority of the replacements are confined to the same three positions. The observed changes represent only a small fraction of the experimentally validated mutations known to increase Na
v
1.4 resistance to tetrodotoxin. These results suggest that constraints resulting from functional tradeoffs between ion channel function and toxin resistance led to predictable patterns of evolutionary convergence at the molecular level. Our data are consistent with theoretical predictions and recent microcosm work that suggest a predictable path is followed during an adaptive walk along a mutational landscape, and that natural selection may be frequently constrained to produce similar genetic outcomes even when operating on independent lineages.
Quantitative global analysis of the role of climate and people in explaining late Quaternary megafaunal extinctions
Authors: Prescott Graham W. , Williams David R. , Balmford Andrew , Green Rhys E. , Manica Andrea
Published: March 2012

The late Quaternary period saw the rapid extinction of the majority of the world's terrestrial megafauna. The cause of these dramatic losses, especially the relative importance of climatic change and the impacts of newly arrived people, remains highly controversial, with geographically restricted analyses generating conflicting conclusions. By analyzing the distribution and timing of all megafaunal extinctions in relation to climatic variables and human arrival on five landmasses, we demonstrate that the observed pattern of extinctions is best explained by models that combine both human arrival and climatic variables. Our conclusions are robust to uncertainties in climate data and in the dates of megafaunal extinctions and human arrival on different landmasses, and strongly suggest that these extinctions were driven by both anthropogenic and climatic factors.
Ecosystem service tradeoff analysis reveals the value of marine spatial planning for multiple ocean uses
Authors: White Crow , Halpern Benjamin S. , Kappel Carrie V.
Published: March 2012

Marine spatial planning (MSP) is an emerging responsibility of resource managers around the United States and elsewhere. A key proposed advantage of MSP is that it makes tradeoffs in resource use and sector (stakeholder group) values explicit, but doing so requires tools to assess tradeoffs. We extended tradeoff analyses from economics to simultaneously assess multiple ecosystem services and the values they provide to sectors using a robust, quantitative, and transparent framework. We used the framework to assess potential conflicts among offshore wind energy, commercial fishing, and whale-watching sectors in Massachusetts and identify and quantify the value from choosing optimal wind farm designs that minimize conflicts among these sectors. Most notably, we show that using MSP over conventional planning could prevent >$1 million dollars in losses to the incumbent fishery and whale-watching sectors and could generate >$10 billion in extra value to the energy sector. The value of MSP increased with the greater the number of sectors considered and the larger the area under management. Importantly, the framework can be applied even when sectors are not measured in dollars (e.g., conservation). Making tradeoffs explicit improves transparency in decision-making, helps avoid unnecessary conflicts attributable to perceived but weak tradeoffs, and focuses debate on finding the most efficient solutions to mitigate real tradeoffs and maximize sector values. Our analysis demonstrates the utility, feasibility, and value of MSP and provides timely support for the management transitions needed for society to address the challenges of an increasingly crowded ocean environment.
Evaporation rate of water in hydrophobic confinement
Authors: Sharma Sumit , Debenedetti Pablo G.
Published: March 2012

The drying of hydrophobic cavities is believed to play an important role in biophysical phenomena such as the folding of globular proteins, the opening and closing of ligand-gated ion channels, and ligand binding to hydrophobic pockets. We use forward flux sampling, a molecular simulation technique, to compute the rate of capillary evaporation of water confined between two hydrophobic surfaces separated by nanoscopic gaps, as a function of gap, surface size, and temperature. Over the range of conditions investigated (gaps between 9 and 14 Å and surface areas between 1 and 9 nm
2
), the free energy barrier to evaporation scales linearly with the gap between hydrophobic surfaces, suggesting that line tension makes the predominant contribution to the free energy barrier. The exponential dependence of the evaporation rate on the gap between confining surfaces causes a 10 order-of-magnitude decrease in the rate when the gap increases from 9 to 14 Å. The computed free energy barriers are of the order of 50
kT
and are predominantly enthalpic. Evaporation rates per unit area are found to be two orders of magnitude faster in confinement by the larger (9 nm
2
) than by the smaller (1 nm
2
) surfaces considered here, at otherwise identical conditions. We show that this rate enhancement is a consequence of the dependence of hydrophobic hydration on the size of solvated objects. For sufficiently large surfaces, the critical nucleus for the evaporation process is a gap-spanning vapor tube.
Nonmuscle myosin II exerts tension but does not translocate actin in vertebrate cytokinesis
Authors: Ma Xuefei , Kovács Mihály , Conti Mary Anne , Wang Aibing , Zhang Yingfan , Sellers James R. , Adelstein Robert S.
Published: March 2012

During vertebrate cytokinesis it is thought that contractile ring constriction is driven by nonmuscle myosin II (NM II) translocation of antiparallel actin filaments. Here we report in situ, in vitro, and in vivo observations that challenge this hypothesis. Graded knockdown of NM II in cultured COS-7 cells reveals that the amount of NM II limits ring constriction. Restoration of the constriction rate with motor-impaired NM II mutants shows that the ability of NM II to translocate actin is not required for cytokinesis. Blebbistatin inhibition of cytokinesis indicates the importance of myosin strongly binding to actin and exerting tension during cytokinesis. This role is substantiated by transient kinetic experiments showing that the load-dependent mechanochemical properties of mutant NM II support efficient tension maintenance despite the inability to translocate actin. Under loaded conditions, mutant NM II exhibits a prolonged actin attachment in which a single mechanoenzymatic cycle spans most of the time of cytokinesis. This prolonged attachment promotes simultaneous binding of NM II heads to actin, thereby increasing tension and resisting expansion of the ring. The detachment of mutant NM II heads from actin is enhanced by assisting loads, which prevent mutant NM II from hampering furrow ingression during cytokinesis. In the 3D context of mouse hearts, mutant NM II-B R709C that cannot translocate actin filaments can rescue multinucleation in NM II-B ablated cardiomyocytes. We propose that the major roles of NM II in vertebrate cell cytokinesis are to bind and cross-link actin filaments and to exert tension on actin during contractile ring constriction.
Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome
Authors: Pessia Eugénie , Makino Takashi , Bailly-Bechet Marc , McLysaght Aoife , Marais Gabriel A. B.
Published: March 2012

How and why female somatic X-chromosome inactivation (XCI) evolved in mammals remains poorly understood. It has been proposed that XCI is a dosage-compensation mechanism that evolved to equalize expression levels of X-linked genes in females (2X) and males (1X), with a prior twofold increase in expression of X-linked genes in both sexes (“Ohno's hypothesis”). Whereas the parity of X chromosome expression between the sexes has been clearly demonstrated, tests for the doubling of expression levels globally along the X chromosome have returned contradictory results. However, changes in gene dosage during sex-chromosome evolution are not expected to impact on all genes equally, and should have greater consequences for dosage-sensitive genes. We show that, for genes encoding components of large protein complexes (≥ 7 members)—a class of genes that is expected to be dosage-sensitive—expression of X-linked genes is similar to that of autosomal genes within the complex. These data support Ohno's hypothesis that XCI acts as a dosage-compensation mechanism, and allow us to refine Ohno's model of XCI evolution. We also explore the contribution of dosage-sensitive genes to X aneuploidy phenotypes in humans, such as Turner (X0) and Klinefelter (XXY) syndromes. X aneuploidy in humans is common and is known to have mild effects because most of the supernumerary X genes are inactivated and not affected by aneuploidy. Only genes escaping XCI experience dosage changes in X-aneuploidy patients. We combined data on dosage sensitivity and XCI to compute a list of candidate genes for X-aneuploidy syndromes.
Earliest Carboniferous tetrapod and arthropod faunas from Scotland populate Romer's Gap
Authors: Smithson Timothy R. , Wood Stanley P. , Marshall John E. A. , Clack Jennifer A.
Published: March 2012

Devonian tetrapods (limbed vertebrates), known from an increasingly large number of localities, have been shown to be mainly aquatic with many primitive features. In contrast, the post-Devonian record is marked by an Early Mississippian temporal gap ranging from the earliest Carboniferous (Tournaisian and early Viséan) to the mid-Viséan. By the mid-Viséan, tetrapods had become effectively terrestrial as attested by the presence of stem amniotes, developed an essentially modern aspect, and given rise to the crown group. Up to now, only two localities have yielded tetrapod specimens from the Tournaisian stage: one in Scotland with a single articulated skeleton and one in Nova Scotia with isolated bones, many of uncertain identity. We announce a series of discoveries of Tournaisian-age localities in Scotland that have yielded a wealth of new tetrapod and arthropod fossils. These include both terrestrial and aquatic forms and new taxa. We conclude that the gap in the fossil record has been an artifact of collection failure.
Bid-induced mitochondrial membrane permeabilization waves propagated by local reactive oxygen species (ROS) signaling
Authors: Garcia-Perez Cecilia , Roy Soumya Sinha , Naghdi Shamim , Lin Xuena , Davies Erika , Hajnóczky György
Published: March 2012

Bid-induced mitochondrial membrane permeabilization and cytochrome
c
release are central to apoptosis. It remains a mystery how tiny amounts of Bid synchronize the function of a large number of discrete organelles, particularly in mitochondria-rich cells. Looking at cell populations, the rate and lag time of the Bid-induced permeabilization are dose-dependent, but even very low doses lead eventually to complete cytochrome
c
release. By contrast, individual mitochondria display relatively rapid and uniform kinetics, indicating that the dose dependence seen in populations is due to a spreading of individual events in time. We report that Bid-induced permeabilization and cytochrome
c
release regularly demonstrate a wave-like pattern, propagating through a cell at a constant velocity without dissipation. Such waves do not depend on caspase activation or permeability transition pore opening. However, reactive oxygen species (ROS) scavengers suppressed the coordination of cytochrome
c
release and also inhibited Bid-induced cell death, whereas both superoxide and hydrogen peroxide sensitized mitochondria to Bid-induced permeabilization. Thus, Bid engages a ROS-dependent, local intermitochondrial potentiation mechanism that amplifies the apoptotic signal as a wave.
Wnt/β-catenin signaling promotes differentiation, not self-renewal, of human embryonic stem cells and is repressed by Oct4
Authors: Davidson Kathryn C. , Adams Allison M. , Goodson Jamie M. , McDonald Circe E. , Potter Jennifer C. , Berndt Jason D. , Biechele Travis L. , Taylor Russell J. , Moon Randall T.
Published: March 2012

Signal transduction pathways play diverse, context-dependent roles in vertebrate development. In studies of human embryonic stem cells (hESCs), conflicting reports claim Wnt/β-catenin signaling promotes either self-renewal or differentiation. We use a sensitive reporter to establish that Wnt/β-catenin signaling is not active during hESC self-renewal. Inhibiting this pathway over multiple passages has no detrimental effect on hESC maintenance, whereas activating signaling results in loss of self-renewal and induction of mesoderm lineage genes. Following exposure to pathway agonists, hESCs exhibit a delay in activation of β-catenin signaling, which led us to postulate that Wnt/β-catenin signaling is actively repressed during self-renewal. In support of this hypothesis, we demonstrate that OCT4 represses β-catenin signaling during self-renewal and that targeted knockdown of OCT4 activates β-catenin signaling in hESCs. Using a fluorescent reporter of β-catenin signaling in live hESCs, we observe that the reporter is activated in a very heterogeneous manner in response to stimulation with Wnt ligand. Sorting cells on the basis of their fluorescence reveals that hESCs with elevated β-catenin signaling express higher levels of differentiation markers. Together these data support a dominant role for Wnt/β-catenin signaling in the differentiation rather than self-renewal of hESCs.
Combined linkage and association mapping revealsCYCD5;1as a quantitative trait gene for endoreduplication inArabidopsis
Authors: Sterken Roel , Kiekens Raphaël , Boruc Joanna , Zhang Fanghong , Vercauteren Annelies , Vercauteren Ilse , De Smet Lien , Dhondt Stijn , Inzé Dirk , De Veylder Lieven , Russinova Eugenia , Vuylsteke Marnik
Published: March 2012

Endoreduplication is the process where a cell replicates its genome without mitosis and cytokinesis, often followed by cell differentiation. This alternative cell cycle results in various levels of endoploidy, reaching 4× or higher one haploid set of chromosomes. Endoreduplication is found in animals and is widespread in plants, where it plays a major role in cellular differentiation and plant development. Here, we show that variation in endoreduplication betweenArabidopsis thalianaaccessions Columbia-0 and Kashmir is controlled by two major quantitative trait loci, ENDO-1 and ENDO-2. A local candidate gene association analysis in a set of 87 accessions, combined with expression analysis, identifiedCYCD5;1as the most likely candidate gene underlying ENDO-2, operating as a rate-determining factor of endoreduplication. In accordance, both the overexpression and silencing ofCYCD5;1were effective in changing DNA ploidy levels, confirmingCYCD5;1to be a previously undescribed quantitative trait gene underlying endoreduplication inArabidopsis.
Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography
Authors: Rigort Alexander , Bäuerlein Felix J. B. , Villa Elizabeth , Eibauer Matthias , Laugks Tim , Baumeister Wolfgang , Plitzko Jürgen M.
Published: March 2012

Cryoelectron tomography provides unprecedented insights into the macromolecular and supramolecular organization of cells in a close-to-living state. However because of the limited thickness range (< 0.5–1 μm) that is accessible with today’s intermediate voltage electron microscopes only small prokaryotic cells or peripheral regions of eukaryotic cells can be examined directly. Key to overcoming this limitation is the ability to prepare sufficiently thin samples. Cryosectioning can be used to prepare thin enough sections but suffers from severe artefacts, such as substantial compression. Here we describe a procedure, based upon focused ion beam (FIB) milling for the preparation of thin (200–500 nm) lamellae from vitrified cells grown on electron microscopy (EM) grids. The self-supporting lamellae are apparently free of distortions or other artefacts and open up large windows into the cell’s interior allowing tomographic studies to be performed on any chosen part of the cell. We illustrate the quality of sample preservation with a structure of the nuclear pore complex obtained from a single tomogram.