bluuebunny/crossref_metadata_2025 huggingface dataset:
Liquid viscosity sensing using nonlinear vibration of a fiberoptic sensor
Authors: Wang Wei-Chih , Liu Chao-Shih
Published: July 2013

This paper investigates the nonlinear dynamic motion of a vibrating optical fiber viscosity sensor through representative cases of primary and super-harmonic resonance. The results show that a nonlinear effect drastically improves the sensitivity of the viscosity measurement by nearly an order of magnitude from the previously developed linear systems. Experimental results and several applications of the viscosity sensor are also presented.
Measurement of cloud point temperature in polymer solutions
Authors: Mannella G. A. , La Carrubba V. , Brucato V.
Published: July 2013

A temperature-controlled turbidity measurement apparatus for the characterization of polymer solutions has been instrumented and set up. The main features are the coupled temperature-light transmittance measurement and the accurate temperature control, achieved by means of peltier cells. The apparatus allows to measure cloud point temperatures by adopting different cooling protocols: low rate for quasi-equilibrium measurements and high rate for detect kinetic effects. A ternary polymeric solution was adopted as case study system showing that cooling rate affects the measured cloud point temperature.
Functional composites of plasmas and metamaterials: Flexible waveguides, and variable attenuators with controllable phase shift
Authors: Sakai Osamu , Maeda Jun , Shimomura Takuya , Urabe Keiichiro
Published: July 2013

Numerical predictions and experimental results in this study verify that plasmas with negative permittivity work as functional media for electromagnetic waves and that their composites with metallic metamaterials show further extraordinary properties. Chain structures of individual plasmas with negative permittivity, forming a straight line and a L-shaped bent line, serve flexible waveguides via coupling structures of localized surface waves standing around each plasma. Further progresses as wave controllers are achievable in an array of the composites of plasmas and micro metallic resonators; functions of phase shifters and attenuators are individually controlled, with rotation of working points on the complex refractive index plane by varying gas conditions and permeability modulation. Such proposed sets of flexible combination will lead to advanced scientific products with novel functions.
Protein immobilization techniques for microfluidic assays
Authors: Kim Dohyun , Herr Amy E.
Published: July 2013

Microfluidic systems have shown unequivocal performance improvements over conventional bench-top assays across a range of performance metrics. For example, specific advances have been made in reagent consumption, throughput, integration of multiple assay steps, assay automation, and multiplexing capability. For heterogeneous systems, controlled immobilization of reactants is essential for reliable, sensitive detection of analytes. In most cases, protein immobilization densities are maximized, while native activity and conformation are maintained. Immobilization methods and chemistries vary significantly depending on immobilization surface, protein properties, and specific assay goals. In this review, we present trade-offs considerations for common immobilization surface materials. We overview immobilization methods and chemistries, and discuss studies exemplar of key approaches—here with a specific emphasis on immunoassays and enzymatic reactors. Recent “smart immobilization” methods including the use of light, electrochemical, thermal, and chemical stimuli to attach and detach proteins on demand with precise spatial control are highlighted. Spatially encoded protein immobilization using DNA hybridization for multiplexed assays and reversible protein immobilization surfaces for repeatable assay are introduced as immobilization methods. We also describe multifunctional surface coatings that can perform tasks that were, until recently, relegated to multiple functional coatings. We consider the microfluidics literature from 1997 to present and close with a perspective on future approaches to protein immobilization.
Simulation study of wave phenomena from the sheath region in single frequency capacitively coupled plasma discharges; field reversals and ion reflection
Authors: Sharma S. , Turner M. M.
Published: July 2013

Capacitively coupled radio-frequency (RF) discharges have great significance for industrial applications. Collisionless electron heating in such discharges is important, and sometimes is the dominant mechanism. This heating is usually understood to originate in a stochastic interaction between electrons and the electric fields. However, other mechanisms may also be important. There is evidence of wave emission with a frequency near the electron plasma frequency, i.e., ωpe, from the sheath region in collisionless capacitive RF discharges. This is the result of a progressive breakdown of quasi-neutrality close to the electron sheath edge. These waves are damped in a few centimeters during their propagation from the sheath towards the bulk plasma. The damping occurs because of the Landau damping or some related mechanism. This research work reports that the emission of waves is associated with a field reversal during the expanding phase of the sheath. Trapping of electrons near to this field reversal region is observed. The amplitude of the wave increases with increasing RF current density amplitude J̃0 until some maximum is reached, beyond which the wave diminishes and a new regime appears. In this new regime, the density of the bulk plasma suddenly increases because of ion reflection, which occurs due to the presence of strong field reversal near sheath region. Our calculation shows that these waves are electron plasma waves. These phenomena occur under extreme conditions (i.e., higher J̃0 than in typical experiments) for sinusoidal current waveforms, but similar effects may occur with non-sinusoidal pulsed waveforms for conditions of experimental interest, because the rate of change of current is a relevant parameter. The effect of electron elastic collisions on plasma waves is also investigated.
Droplet deformation and manipulation in an electrified microfluidic channel
Authors: Wehking Jonathan D. , Chew Larry , Kumar Ranganathan
Published: July 2013

This letter studies electrically induced droplet deformation to predictably pin and route droplets in a T-junction microchannel. Droplets of various sizes are shown to deform differently and respond to steep electric potential gradients. The relative magnitudes of inertial and electric forces are responsible for droplet deceleration and pinning, and may be manipulated to route a droplet in either direction of a T-junction.
Coaction and distinguishment of converse piezoelectric and field effects in La0.7Ca0.3MnO3/SrTiO3/0.68Pb(Mg1/3Nb2/3)O3-0.32PbTiO3 heterostructures
Authors: Jiang Tao , Yang Shengwei , Liu Yukuai , Yin Yuewei , Dong Sining , Zhao Wenbo , Li Xiaoguang
Published: July 2013

The volatile and nonvolatile electroresistances related to the converse piezoelectric induced strain and ferroelectric field effects are improved in La0.7Ca0.3MnO3/SrTiO3/0.68Pb(Mg1/3Nb2/3)O3-0.32PbTiO3 heterostructures by inserting a SrTiO3 buffer layer. Due to the coaction of the strain and field effects, the tri-resistance states are observed, and the relative contributions of the two effects on the resistance changes can be quantitatively distinguished by a programmable control of the polarization electric fields in “ON” and “OFF” modes, respectively. Our results indicate that the well-designed heterostructure exhibits potential for application in multifunctional devices.
Controlling the activation energy of graphene-like thin films through disorder induced localization
Authors: Coleman Christopher , McIntosh Ross , Bhattacharyya Somnath
Published: July 2013

The influence of disorder on the activation energy in few layer graphitic films is demonstrated through combined Raman and temperature dependent transport studies. A laser ablation technique is employed which allows the level of disorder in the sp2-C phase to be controlled and conditions for minimizing the level of disorder are determined. As conditions vary from optimal, Raman measurements show increasing D and G bandwidths while the activation energy, negligible for optimal growth conditions, can be correlated with the level of disorder. This laser ablation technique allows the specific effects of structural disorder in the sp2 phase to be probed while defects act as effective barriers resulting in localization of charge carriers. Electron transmission spectra, calculated with a tight-binding model, account for the change of localization length as a result of disorder in the sp2 hybridized phase. This tandem experimental and theoretical approach shows that the localization length of the thin graphitic films can be tuned with the level of disorder which is controlled through synthesis parameters. This study, which addresses the role of disorder in graphene-like materials, is a prerequisite for device applications.
Spin-relaxation modulation and spin-pumping control by transverse spin-wave spin current in Y3Fe5O12
Authors: Kajiwara Y. , Uchida K. , Kikuchi D. , An T. , Fujikawa Y. , Saitoh E.
Published: July 2013

Heat-current-induced manipulation of spin relaxation in Y3Fe5O12 under an in-plane temperature gradient is investigated. We show that the linewidth of the ferromagnetic resonance spectrum, i.e., the spin relaxation, in an Y3Fe5O12 film increases or decreases depending on the temperature-gradient direction and that this modulation is attributed to the spin-transfer torque caused by a thermally induced transverse spin-wave spin current in the Y3Fe5O12 film. The experimental results also show that the spin-current magnitude generated by spin pumping in an attached Pt film is inversely proportional to the square of the modulated Gilbert damping constant, consistent with a phenomenological spin-pumping model.
Biaxial anisotropy driven asymmetric kinked magnetization reversal in exchange-biased IrMn/NiFe bilayers
Authors: Fulara Himanshu , Chaudhary Sujeet , Kashyap Subhash C.
Published: July 2013

The significant biaxial anisotropy contribution below 50 K is evidenced and identified as a cause of asymmetric “kinked” magnetization reversal behaviour and strong single cycle training effect in ion-beam sputtered IrMn/NiFe bilayers. The minor loop measurement clearly suggests that the magnetization reversal along the descending branch of the hysteresis loop takes place in two distinct steps comprising initial magnetization rotation followed by irreversible domain processes. Our experimental observations of characteristic magnetoresistance and minor loop measurements unambiguously endorse the recent theoretical prediction of Hoffmann suggesting the critical role of the symmetry of antiferromagnetic anisotropy on the reversal asymmetry and training effect.
Unidirectional acoustic transmission through a prism with near-zero refractive index
Authors: Li Yong , Liang Bin , Gu Zhong-ming , Zou Xin-ye , Cheng Jian-chun
Published: July 2013

We propose a two-dimensional model of acoustic prism comprising metamaterials with near-zero refractive index to yield high efficiency unidirectional transmission and demonstrate an implementation by coiling up space. Due to the acoustic tunneling effect, the waveform is kept consistent between input and output waves, and the transmitted angle can be controlled by reshaping the prism, even in the presence of hard scatterer. A directional waveguide is also designed whose transmission property can be freely switched between all possible states. Our design may have potential for practical applications of acoustic one-way devices in various fields such as ultrasound imaging and treatment.
Charge transfer between reduced graphene oxide sheets on insulating substrates
Authors: Shen Yue , Zhang Xueqiang , Wang Ying , Zhou Xuejiao , Hu Jun , Guo Shouwu , Zhang Yi
Published: July 2013

Understanding the electrical communications between graphene sheets placed on insulating substrates is of great value to rational design of functional graphene nanoelectronics. In this paper, we report charge transfer between reduced graphene oxide (rGO) sheets separated in hundreds of nanometers on insulating substrates. We found that the rGO sheet collects charges from the adjacent charged rGO sheet through the dielectric surfaces. The efficiency of charge transfer between the separated rGO sheets is dependent on their separation distance, gap length, and the substrate type. The findings suggest that the charge interflow should not be neglected in a graphene circuit.
Effects of ZnO-nanostructure antireflection coatings on sulfurization-free Cu2ZnSnS4 absorber deposited by single-step co-sputtering process
Authors: Jheng Bao-Tang , Liu Po-Tsun , Wang Min-Chuan , Wu Meng-Chyi
Published: July 2013

ZnO nanostructures as anti-reflective coatings were synthesized by using hydrothermal technique for a sulfurization-free Cu2ZnSnS4 absorber prepared by co-sputtering deposition. By controlling the morphology of solution-grown ZnO nanostructures, the average reflectance of the Cu2ZnSnS4 solar cell with branched ZnO nanorods decreased from 7.6% to 1.12%, and the energy conversion efficiency promoted by 10.4% from the initial value of 4.8% to 5.3%. The efficiency improvement was well studied with the effects of the gradually increased refractive index between the air and the top electrode of Cu2ZnSnS4 solar device, due to the presence of the ZnO nanostructure.
Optical absorption in silicon layers in the presence of charge inversion/accumulation or ion implantation
Authors: Alloatti L. , Lauermann M. , Sürgers C. , Koos C. , Freude W. , Leuthold J.
Published: July 2013

We determine the optical losses in gate-induced charge accumulation/inversion layers at a Si/SiO2 interface. Comparison between gate-induced charge layers and ion-implanted thin silicon films having an identical sheet resistance shows that optical losses can be significantly lower for gate-induced layers. For a given sheet resistance, holes produce higher optical loss than electrons. Measurements have been performed at λ = 1550 nm.
Heat rectification effect of serially coupled quantum dots
Authors: Tseng Yen-Chun , Kuo David M. T. , Chang Yia-chung , Lin Yan-Ting
Published: July 2013

The nonlinear thermoelectric properties of serially coupled quantum dots (SCQDs) embedded in a nanowire connected to metallic electrodes are theoretically studied in the Coulomb blockade regime. We demonstrate that the electron heat current of SCQDs exhibits a direction-dependent behavior (heat rectification) in an asymmetrical structure in which the electron Coulomb interactions are significant. The phonon thermal conductivity of the nanowire is also calculated, which is used to estimate the phonon heat current. Finally, we discuss how to reduce phonon heat current to allow observation of electron heat rectification behavior in the SCQD junction system in low temperature regime.
Communication: Long-range angular correlations in liquid water
Authors: Liu Yu , Wu Jianzhong
Published: July 2013

At ambient conditions the intermolecular correlation in liquid water is generally believed to be short ranged as shown in the atomic pair distribution functions (PDFs) obtained from scattering experiments or from theoretical predictions. However, atom-atom PDFs provide only a partial description of the higher dimensional intermolecular correlation function that depends on both the positions and orientations of water molecules. Here we study the atomic PDFs of liquid water as well as the angular correlation function (ACF) using a classical density functional theory. We demonstrate that, different from the PDFs, the ACF exhibits long-range oscillatory decay extending up to tens of molecular diameters. The theoretical predictions are in good agreement with molecular simulations and corroborate recent experimental results from the second harmonic light scattering experiments.
Interface characterization of metal-HfO2-InAs gate stacks using hard x-ray photoemission spectroscopy
Authors: Persson O. , Lind E. , Lundgren E. , Rubio-Zuazo J. , Castro G. R. , Wernersson L.-E. , Mikkelsen A. , Timm R.
Published: July 2013

MOS devices based on III-V semiconductors and thin high-k dielectric layers offer possibilities for improved transport properties. Here, we have studied the interface structure and chemical composition of realistic MOS gate stacks, consisting of a W or Pd metal film and a 6- or 12-nm-thick HfO2 layer deposited on InAs, with Hard X-ray Photoemission Spectroscopy. In and As signals from InAs buried more than 18 nm below the surface are clearly detected. The HfO2 layers are found to be homogeneous, and no influence of the top metal on the sharp InAs-HfO2 interface is observed. These results bridge the gap between conventional photoemission spectroscopy studies on various metal-free model samples with very thin dielectric layers and realistic MOS gate stacks.
Low lattice thermal conductivity suppressed by Sr-deficiency in Sr0.9Ca0.1Si2
Authors: Lue C. S. , Tseng Y. S. , Huang J. Y. , Hsieh H. L. , Liao H. Y. , Kuo Y. K.
Published: July 2013

We present a study of the temperature-dependent electrical resistivity, Seebeck coefficient, and thermal conductivity in Sr0.9-δCa0.1Si2 alloys to shed light on Sr-deficient effect on the thermoelectric performance, as characterized by the dimensionless thermoelectric figure-of-merit, ZT. It is found that the thermal conductivity is considerably reduced upon introducing Sr deficiency in Sr0.9Ca0.1Si2. In particular, a marked low lattice thermal conductivity of about 1.1 W/m-K at room temperature is achieved for Sr0.77Ca0.1Si2. Such a promising result leads to a relatively high ZT of 0.27 at room temperature for this material. Furthermore, with the extrapolation of thermoelectric parameters to high temperatures, a possible maximum ZT of about 0.52 at 850 K can be realistically estimated for Sr0.77Ca0.1Si2.
Effect on wireless power transmission with different layout of left-handed materials
Authors: Huang Ying , Tang Hou-Jun , Chen En-Ce , Yao Chen
Published: July 2013

In order to improve the efficiency and to increase the distance of the wireless power transmission system, we studied the application of the left-handed materials on it. From the point of view of evanescent waves as well as the negative refraction effect, verified left-handed materials’ ability to improve efficiency. The contribution of the four layouts named single flatbed, dual flatbeds, full bracketing and semi-bracketing model were compared and analyzed. Furthermore, the influence of different location and thickness was also discussed, and their results were explained theoretically. Finally, we proposed the superiority of the dual flatbeds model, for its highest efficiency improvement, easy production and convenience.
Jitter analysis of a superconducting nanowire single photon detector
Authors: You Lixing , Yang Xiaoyan , He Yuhao , Zhang Wenxing , Liu Dengkuan , Zhang Weijun , Zhang Lu , Zhang Ling , Liu Xiaoyu , Chen Sijing , Wang Zhen , Xie Xiaoming
Published: July 2013

Jitter is one of the key parameters for a superconducting nanowire single photon detector (SNSPD). Using an optimized time-correlated single photon counting system for jitter measurement, we extensively studied the dependence of system jitter on the bias current and working temperature. The signal-to-noise ratio of the single-photon-response pulse was proven to be an important factor in system jitter. The final system jitter was reduced to 18 ps by using a high-critical-current SNSPD, which showed an intrinsic SNSPD jitter of 15 ps. A laser ranging experiment using a 15-ps SNSPD achieved a record depth resolution of 3 mm at a wavelength of 1550 nm.
Analysis of magnetic structures of iron nitrides by Landau's theory of second-order phase transitions
Authors: Fang H. N. , Zhang R. , Liu B. , Tao Z. K. , Xiao M. W. , Wang X. F. , Xie Z. L. , Xiu X. Q. , Zheng Y. D.
Published: July 2013

The magnetic structures of iron nitrides are studied by Landau's theory of second-order phase transitions. It is found that the magnetization direction of ɛ-Fe3N must be parallel to the c-axis of the hexagonal structure, which may conclude the debates on the easy axes of ɛ-Fe3N in this field. The easy axes of α″-Fe16N2 are turned out to be along [001], or [100], or [110] direction, with the former two cases already found by the experiments. The magnetization along [111] is forbidden, which solves rigorously the puzzle why the easy axes of the α″-Fe16N2 on InGaAs and Fe are different from each other. Finally, the magnetic structure of γ′-Fe4N is also determined, and the result shows that there are three possibilities for the magnetization: parallel to the axial, or the body diagonal, or the face diagonal direction of the cubic structure, among which the first case has been found in experiments.
Partitioning hydraulic resistance in Sorghum bicolor leaves reveals unique correlations with stomatal conductance during drought
Authors: Ocheltree Troy W. , Nippert Jesse B. , Kirkham Mary Beth , Prasad P. Vara V.
Published: July 2013

The hydraulic architecture of leaves represents the final path along which liquid water travels through the plant and comprises a significant resistance for water movement, especially for grasses. We partitioned leaf hydraulic resistance of six genotypes of Sorghum bicolor L. (Moench) into leaf specific hydraulic resistance within the large longitudinal veins (r*LV) and outside the large veins (r*OLV), and correlated these resistances with the response of stomatal conductance (gs) and photosynthesis (A) to drought. Under well-watered conditions, gs was tightly correlated with r*OLV (r2 = 0.95), but as soil moisture decreased, gs was more closely correlated with r*LV (r2 = 0.97). These results suggest that r*OLV limits maximum rates of gas exchange, but the ability to efficiently move water long distances (low r*LV) becomes more important for the maintenance of cell turgor and gas exchange as soil moisture declines. Hydraulic resistance through the leaf was negatively correlated with evapotranspiration (P < 0.001) resulting in more conservative water use in genotypes with large leaf resistance. These results illustrate the functional significance of leaf resistance partitioning to declining soil moisture in a broadly-adapted cereal species.
Heparan sulfate proteoglycans mediate internalization and propagation of specific proteopathic seeds
Authors: Holmes Brandon B. , DeVos Sarah L. , Kfoury Najla , Li Mei , Jacks Rachel , Yanamandra Kiran , Ouidja Mohand O. , Brodsky Frances M. , Marasa Jayne , Bagchi Devika P. , Kotzbauer Paul T. , Miller Timothy M. , Papy-Garcia Dulce , Diamond Marc I.
Published: July 2013

Significance

Prion-like propagation of proteopathic seeds may underlie the progression of neurodegenerative diseases, including the tauopathies and synucleinopathies. Aggregate entry into the cell is a crucial step in transcellular propagation. We used chemical, enzymatic, and genetic methods to identify heparan sulfate proteoglycans as critical mediators of tau aggregate binding and uptake, and subsequent seeding of normal intracellular tau. This pathway mediates aggregate uptake in cultured cells, primary neurons, and brain. α-Synuclein fibrils use the same entry mechanism to seed intracellular aggregation, whereas huntingtin fibrils do not. This establishes the molecular basis for a key step in aggregate propagation.
SIRT2 directs the replication stress response through CDK9 deacetylation
Authors: Zhang Hui , Park Seong-Hoon , Pantazides Brooke G. , Karpiuk Oleksandra , Warren Matthew D. , Hardy Claire W. , Duong Duc M. , Park So-Jeong , Kim Hyun-Seok , Vassilopoulos Athanassios , Seyfried Nicholas T. , Johnsen Steven A. , Gius David , Yu David S.
Published: July 2013

Sirtuin 2 (SIRT2) is a sirtuin family deacetylase that directs acetylome signaling, protects genome integrity, and is a murine tumor suppressor. We show that SIRT2 directs replication stress responses by regulating the activity of cyclin-dependent kinase 9 (CDK9), a protein required for recovery from replication arrest. SIRT2 deficiency results in replication stress sensitivity, impairment in recovery from replication arrest, spontaneous accumulation of replication protein A to foci and chromatin, and a G2/M checkpoint deficit. SIRT2 interacts with and deacetylates CDK9 at lysine 48 in response to replication stress in a manner that is partially dependent on ataxia telangiectasia and Rad3 related (ATR) but not cyclin T or K, thereby stimulating CDK9 kinase activity and promoting recovery from replication arrest. Moreover, wild-type, but not acetylated CDK9, alleviates the replication stress response impairment of SIRT2 deficiency. Collectively, our results define a function for SIRT2 in regulating checkpoint pathways that respond to replication stress through deacetylation of CDK9, providing insight into how SIRT2 maintains genome integrity and a unique mechanism by which SIRT2 may function, at least in part, as a tumor suppressor protein.
Characterization of an early-stage fusion intermediate of Sindbis virus using cryoelectron microscopy
Authors: Cao Sheng , Zhang Wei
Published: July 2013

The sequential steps in the alphavirus membrane fusion pathway have been postulated based on the prefusion and postfusion crystal structures of the viral fusion protein E1 in conjunction with biochemical studies. However, the molecular structures of the hypothesized fusion intermediates have remained obscure due to difficulties inherent in the dynamic nature of the process. We developed an experimental system that uses liposomes as the target membrane to capture Sindbis virus, a prototypical alphavirus, in its membrane-binding form at pH 6.4. Cryoelectron micrograph analyses and 3D reconstructions showed that the virus retains its overall icosahedral structure at this mildly acidic pH, except in the membrane-binding region, where monomeric E1 associates with the target membrane and the E2 glycoprotein retains its original trimeric organization. The remaining E2 trimers may hinder E1 homotrimerization and are a potential target for antiviral drugs.
Rapid shifts in dispersal behavior on an expanding range edge
Authors: Lindström Tom , Brown Gregory P. , Sisson Scott A. , Phillips Benjamin L. , Shine Richard
Published: July 2013

Dispersal biology at an invasion front differs from that of populations within the range core, because novel evolutionary and ecological processes come into play in the nonequilibrium conditions at expanding range edges. In a world where species’ range limits are changing rapidly, we need to understand how individuals disperse at an invasion front. We analyzed an extensive dataset from radio-tracking invasive cane toads (
Rhinella marina
) over the first 8 y since they arrived at a site in tropical Australia. Movement patterns of toads in the invasion vanguard differed from those of individuals in the same area postcolonization. Our model discriminated encamped versus dispersive phases within each toad’s movements and demonstrated that pioneer toads spent longer periods in dispersive mode and displayed longer, more directed movements while they were in dispersive mode. These analyses predict that overall displacement per year is more than twice as far for toads at the invasion front compared with those tracked a few years later at the same site. Studies on established populations (or even those a few years postestablishment) thus may massively underestimate dispersal rates at the leading edge of an expanding population. This, in turn, will cause us to underpredict the rates at which invasive organisms move into new territory and at which native taxa can expand into newly available habitat under climate change.
Prereplicative repair of oxidized bases in the human genome is mediated by NEIL1 DNA glycosylase together with replication proteins
Authors: Hegde Muralidhar L. , Hegde Pavana M. , Bellot Larry J. , Mandal Santi M. , Hazra Tapas K. , Li Guo-Min , Boldogh Istvan , Tomkinson Alan E. , Mitra Sankar
Published: July 2013

Significance

Repair of mutagenic oxidized bases in the genome is required before replication to prevent mutations. It is unknown how such base lesions, which do not block replication, are flagged for repair in the single-stranded replicating template. We demonstrate here that the repair-initiating, S-phase–activated Nei-like (NEIL) 1 DNA glycosylase binds to but does not excise the base lesion and cleave the template DNA strand, which would lead to a lethal double-strand break. Instead, NEIL1 blocks progression of the replication fork, which then regresses to allow lesion repair. In the absence of NEIL1, the related glycosylase NEIL2 serves as a backup enzyme.
Ant colonies outperform individuals when a sensory discrimination task is difficult but not when it is easy
Authors: Sasaki Takao , Granovskiy Boris , Mann Richard P. , Sumpter David J. T. , Pratt Stephen C.
Published: July 2013

“Collective intelligence” and “wisdom of crowds” refer to situations in which groups achieve more accurate perception and better decisions than solitary agents. Whether groups outperform individuals should depend on the kind of task and its difficulty, but the nature of this relationship remains unknown. Here we show that colonies of
Temnothorax
ants outperform individuals for a difficult perception task but that individuals do better than groups when the task is easy. Subjects were required to choose the better of two nest sites as the quality difference was varied. For small differences, colonies were more likely than isolated ants to choose the better site, but this relationship was reversed for large differences. We explain these results using a mathematical model, which shows that positive feedback between group members effectively integrates information and sharpens the discrimination of fine differences. When the task is easier the same positive feedback can lock the colony into a suboptimal choice. These results suggest the conditions under which crowds do or do not become wise.
Coarse-grained, foldable, physical model of the polypeptide chain
Authors: Chakraborty Promita , Zuckermann Ronald N.
Published: July 2013

Although nonflexible, scaled molecular models like Pauling–Corey’s and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report here the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees of freedom in the peptide backbone. The coarse-grained backbone model consists of repeating amide and α-carbon units, connected by mechanical bonds (corresponding to φ and ψ) that include realistic barriers to rotation that closely approximate those found at the molecular scale. Longer-range hydrogen-bonding interactions are also incorporated, allowing the chain to readily fold into stable secondary structures. The model is easily constructed with readily obtainable parts and promises to be a tremendous educational aid to the intuitive understanding of chain folding as the basis for macromolecular structure. Furthermore, this physical model can serve as the basis for linking tangible biomacromolecular models directly to the vast array of existing computational tools to provide an enhanced and interactive human–computer interface.
Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses
Authors: Kampa Annette , Gagunashvili Andrey N. , Gulder Tobias A. M. , Morinaka Brandon I. , Daolio Cristina , Godejohann Markus , Miao Vivian P. W. , Piel Jörn , Andrésson Ólafur S.
Published: July 2013

Significance

Remarkable chemical families are being recognized by studying diverse symbioses. We identified, through metagenomics, the first cyanobacterial
trans
-AT polyketide biosynthetic pathway in the
Nostoc
symbiont of the lichen
Peltigera membranacea
and showed its expression in natural thalli. An isotope-based technique designed for characterizing minute amounts of material confirmed predictions that its product, nosperin, is a distinct member of the pederin family of compounds that was previously thought exclusive to animal–bacteria associations. The unexpected discovery of nosperin in lichen expands the structural range and known distribution of this family of natural products and suggests a role associated with symbiosis.
Multiple antigen-presenting system (MAPS) to induce comprehensive B- and T-cell immunity
Authors: Zhang Fan , Lu Ying-Jie , Malley Richard
Published: July 2013

Vaccines are among the most effective approaches to prevent and control many infectious diseases. Because of safety and reproducibility concerns, whole-cell vaccines (WCVs), made from live or killed microorganisms and including hundreds of antigenic components, have been mostly replaced by acellular or subunit vaccines composed of well-defined, purified antigen components. The efficacy of acellular vaccines is inferior to that of WCVs, however, for two major reasons: limited antigen diversity and reduced immunogenicity, especially in a lack of activation of antigen-specific T-cell immunity, which plays an important role in protection against mucosal and intracellular pathogens. Here we present the multiple antigen-presenting system (MAPS), which enables the creation of a macromolecular complex that mimics the properties of WCVs by integrating various antigen components, including polysaccharides and proteins, in the same construct and that induces multipronged immune responses, including antibody, Th1, and Th17 responses. Using antigens from various pathogens (Streptococcus pneumoniae,Salmonella typhi, andMycobacterium tuberculosis), we demonstrate the versatility of the MAPS system and its feasibility for the design of unique defined-structure subunit vaccines to confer comprehensive protection via multiple immune mechanisms. Moreover, MAPS can serve as a tool for structure-activity analysis of cellular immunogens.
A bacterial symbiont is converted from an inedible producer of beneficial molecules into food by a single mutation in the
gacA
gene
Authors: Stallforth Pierre , Brock Debra A. , Cantley Alexandra M. , Tian Xiangjun , Queller David C. , Strassmann Joan E. , Clardy Jon
Published: July 2013

Stable multipartite mutualistic associations require that all partners benefit. We show that a single mutational step is sufficient to turn a symbiotic bacterium from an inedible but host-beneficial secondary metabolite producer into a host food source. The bacteria’s host is a “farmer” clone of the social amoeba
Dictyostelium discoideum
that carries and disperses bacteria during its spore stage. Associated with the farmer are two strains of
Pseudomonas fluorescens
, only one of which serves as a food source. The other strain produces diffusible small molecules: pyrrolnitrin, a known antifungal agent, and a chromene that potently enhances the farmer’s spore production and depresses a nonfarmer’s spore production. Genome sequence and phylogenetic analyses identify a derived point mutation in the food strain that generates a premature stop codon in a global activator (
gacA
), encoding the response regulator of a two-component regulatory system. Generation of a knockout mutant of this regulatory gene in the nonfood bacterial strain altered its secondary metabolite profile to match that of the food strain, and also, independently, converted it into a food source. These results suggest that a single mutation in an inedible ancestral strain that served a protective role converted it to a “domesticated” food source.
Behavioral diversity in microbes and low-dimensional phenotypic spaces
Authors: Jordan David , Kuehn Seppe , Katifori Eleni , Leibler Stanislas
Published: July 2013

Systematic studies of phenotypic diversity—required for understanding evolution—lag behind investigations of genetic diversity. Here we develop a quantitative approach to studying behavioral diversity, which we apply to swimming of the ciliate
Tetrahymena.
We measure the full-lifetime behavior of hundreds of individual organisms at high temporal resolution, over several generations and in diverse nutrient conditions. To characterize population diversity and temporal variability we introduce a unique statistical framework grounded in the notion of a phenotypic space of behaviors. We show that this space is effectively low dimensional with dimensions that correlate with a two-state “roaming and dwelling” model of swimming behavior. Temporal variability over the lifetime of an individual is correlated with the fraction of time spent roaming whereas diversity between individuals is correlated with the speed of roaming. Quantifying the dynamics of behavioral variation shows that behavior over the lifetime of an individual is strongly nonstationary. Analysis of behavioral dynamics between generations reveals complex patterns of behavioral heritability that point to the importance of considering correlations beyond mothers and daughters. Our description of a low-dimensional behavioral space should enable the systematic study of the evolutionary and ecological bases of phenotypic constraints. Future experimental and theoretical studies of behavioral diversity will have to account for the possibility of nonstationary and environmentally dependent behavioral dynamics that we observe.
Induction of IL-17 and nonclassical T-cell activation by HIV-Tat protein
Authors: Johnson Tory P. , Patel Karan , Johnson Kory R. , Maric Dragan , Calabresi Peter A. , Hasbun Rodrigo , Nath Avindra
Published: July 2013

Chronic immune activation is a major complication of antiretroviral therapy (ART) for HIV infection and can cause a devastating immune reconstitution inflammatory syndrome (IRIS) in the brain. The mechanism of T-cell activation in this population is not well understood. We found HIV-Tat protein and IL-17–expressing mononuclear cells in the brain of an individual with IRIS. Tat was also present in the CSF of individuals virologically controlled on ART. Hence we examined if Tat protein could directly activate T cells. Tat transcriptionally dysregulated 94 genes and induced secretion of 11 cytokines particularly activation of IL-17 signaling pathways supporting the development of a proinflammatory state. Tat increased IL-17 transcription and secretion in T cells. Tat entered the T cells rapidly by clathrin-mediated endocytosis and localized to both the cytoplasm and the nucleus. Tat activated T cells through a nonclassical pathway dependent upon vascular endothelial growth factor receptor-2 and downstream secondary signaling pathways but independent of the T-cell receptor. However, Tat stimulation of T cells did not induce T-cell proliferation but increased viral infectivity. This study demonstrates Tat’s role as a virulence factor, by driving T-cell activation and contributing to IRIS pathophysiology. This supports the necessity of an anti-Tat therapy in conjunction with ART and identifies multiple targetable pathways to prevent Tat-mediated T-cell activation.
Break-induced replication occurs by conservative DNA synthesis
Authors: Donnianni Roberto A. , Symington Lorraine S.
Published: July 2013

Break-induced replication (BIR) refers to recombination-dependent DNA synthesis initiated from one end of a DNA double-strand break and can extend for more than 100 kb. BIR initiates by Rad51-catalyzed strand invasion, but the mechanism for DNA synthesis is not known. Here, we used BrdU incorporation to track DNA synthesis during BIR and found that the newly synthesized strands segregate with the broken chromosome, indicative of a conservative mode of DNA synthesis. Furthermore, we show the frequency of BIR is reduced and product formation is progressively delayed when the donor is placed at an increasing distance from the telomere, consistent with replication by a migrating D-loop from the site of initiation to the telomere.
RARα-PLZF oncogene inhibits C/EBPα function in myeloid cells
Authors: Girard Nathalie , Tremblay Mathieu , Humbert Magali , Grondin Benoît , Haman André , Labrecque Jean , Chen Bing , Chen Zhu , Chen Sai-Juan , Hoang Trang
Published: July 2013

In acute promyelocytic leukemia, granulocytic differentiation is arrested at the promyelocyte stage. The variant t(11;17) translocation produces two fusion proteins, promyelocytic leukemia zinc finger-retinoic acid receptor α (PLZF-RARα) and RARα-PLZF, both of which participate in leukemia development. Here we provide evidence that the activity of CCAAT/enhancer binding protein α (C/EBPα), a master regulator of granulocytic differentiation, is severely impaired in leukemic promyelocytes with the t(11;17) translocation compared with those associated with the t(15;17) translocation. We show that RARα-PLZF inhibits myeloid cell differentiation through interactions with C/EBPα tethered to DNA, using ChIP and DNA capture assays. Furthermore, RARα-PLZF recruits HDAC1 and causes histone H3 deacetylation at C/EBPα target loci, thereby decreasing the expression of C/EBPα target genes. In line with these results, HDAC inhibitors restore in part C/EBPα target gene expression. These findings provide molecular evidence for a mechanism through which RARα-PLZF acts as a modifier oncogene that subverts differentiation in the granulocytic lineage by associating with C/EBPα and inhibiting its activity.
An integrated reweighting theory of perceptual learning
Authors: Dosher Barbara Anne , Jeter Pamela , Liu Jiajuan , Lu Zhong-Lin
Published: July 2013

Improvements in performance on visual tasks due to practice are often specific to a retinal position or stimulus feature. Many researchers suggest that specific perceptual learning alters selective retinotopic representations in early visual analysis. However, transfer is almost always practically advantageous, and it does occur. If perceptual learning alters location-specific representations, how does it transfer to new locations? An integrated reweighting theory explains transfer over retinal locations by incorporating higher level location-independent representations into a multilevel learning system. Location transfer is mediated through location-independent representations, whereas stimulus feature transfer is determined by stimulus similarity at both location-specific and location-independent levels. Transfer to new locations/positions differs fundamentally from transfer to new stimuli. After substantial initial training on an orientation discrimination task, switches to a new location or position are compared with switches to new orientations in the same position, or switches of both. Position switches led to the highest degree of transfer, whereas orientation switches led to the highest levels of specificity. A computational model of integrated reweighting is developed and tested that incorporates the details of the stimuli and the experiment. Transfer to an identical orientation task in a new position is mediated via more broadly tuned location-invariant representations, whereas changing orientation in the same position invokes interference or independent learning of the new orientations at both levels, reflecting stimulus dissimilarity. Consistent with single-cell recording studies, perceptual learning alters the weighting of both early and midlevel representations of the visual system.
JIP1 regulates the directionality of APP axonal transport by coordinating kinesin and dynein motors
Authors: Fu Meng-meng , Holzbaur Erika L.F.
Published: July 2013

Regulation of the opposing kinesin and dynein motors that drive axonal transport is essential to maintain neuronal homeostasis. Here, we examine coordination of motor activity by the scaffolding protein JNK-interacting protein 1 (JIP1), which we find is required for long-range anterograde and retrograde amyloid precursor protein (APP) motility in axons. We identify novel interactions between JIP1 and kinesin heavy chain (KHC) that relieve KHC autoinhibition, activating motor function in single molecule assays. The direct binding of the dynactin subunit p150Glued to JIP1 competitively inhibits KHC activation in vitro and disrupts the transport of APP in neurons. Together, these experiments support a model whereby JIP1 coordinates APP transport by switching between anterograde and retrograde motile complexes. We find that mutations in the JNK-dependent phosphorylation site S421 in JIP1 alter both KHC activation in vitro and the directionality of APP transport in neurons. Thus phosphorylation of S421 of JIP1 serves as a molecular switch to regulate the direction of APP transport in neurons.
A new method for high-resolution imaging of Ku foci to decipher mechanisms of DNA double-strand break repair
Authors: Britton Sébastien , Coates Julia , Jackson Stephen P.
Published: July 2013

DNA double-strand breaks (DSBs) are the most toxic of all genomic insults, and pathways dealing with their signaling and repair are crucial to prevent cancer and for immune system development. Despite intense investigations, our knowledge of these pathways has been technically limited by our inability to detect the main repair factors at DSBs in cells. In this paper, we present an original method that involves a combination of ribonuclease- and detergent-based preextraction with high-resolution microscopy. This method allows direct visualization of previously hidden repair complexes, including the main DSB sensor Ku, at virtually any type of DSB, including those induced by anticancer agents. We demonstrate its broad range of applications by coupling it to laser microirradiation, super-resolution microscopy, and single-molecule counting to investigate the spatial organization and composition of repair factories. Furthermore, we use our method to monitor DNA repair and identify mechanisms of repair pathway choice, and we show its utility in defining cellular sensitivities and resistance mechanisms to anticancer agents.
The inner and outer compartments of mitochondria are sites of distinct cAMP/PKA signaling dynamics
Authors: Lefkimmiatis Konstantinos , Leronni Daniela , Hofer Aldebaran M.
Published: July 2013

Cyclic AMP (cAMP)-dependent phosphorylation has been reported to exert biological effects in both the mitochondrial matrix and outer mitochondrial membrane (OMM). However, the kinetics, targets, and effectors of the cAMP cascade in these organellar domains remain largely undefined. Here we used sensitive FRET-based sensors to monitor cAMP and protein kinase A (PKA) activity in different mitochondrial compartments in real time. We found that cytosolic cAMP did not enter the matrix, except during mitochondrial permeability transition. Bicarbonate treatment (expected to activate matrix-bound soluble adenylyl cyclase) increased intramitochondrial cAMP, but along with membrane-permeant cAMP analogues, failed to induce measureable matrix PKA activity. In contrast, the OMM proved to be a domain of exceptionally persistent cAMP-dependent PKA activity. Although cAMP signaling events measured on the OMM mirrored those of the cytosol, PKA phosphorylation at the OMM endured longer as a consequence of diminished control by local phosphatases. Our findings demonstrate that mitochondria host segregated cAMP cascades with distinct functional and kinetic signatures.