bluuebunny/crossref_metadata_2025 huggingface dataset:
Three-dimensional infrared spectroscopy of isotope-diluted ice Ih
Authors: Perakis Fivos , Borek Joanna A. , Hamm Peter
Published: July 2013

Using three-dimensional infrared (3D-IR) spectroscopy, we investigate the vibrational dynamics of isotope-diluted ice Ih. By probing the OD stretch mode of HOD in H2O, we observe an extremely rapid decay (≈200 fs) of the population from the second vibrational excited state. Quantum simulations based on a two-dimensional Lippincott-Schroeder potential agree nearly quantitatively with the experimental 3D-IR lineshapes and dynamics. The model suggests that energy dissipation is enhanced due to nonadiabatic effects between vibrational states, which arise from strong mode-mixing between the OD stretch mode with lattice degrees of freedom. Furthermore, we compare the simulation results to ab initio based potentials, in which the hydrogen bond anharmonicity is too small to reproduce the experimental 3D-IR spectra. We thus conclude that the Lippincott-Schroeder potential effectively coalesces many degrees of freedom of the crystal into one intermolecular coordinate.
Thermodynamic hydration shell behavior of glycine
Authors: D’Amico Francesco , Bencivenga Filippo , Camisasca Gaia , Gessini Alessandro , Principi Emiliano , Cucini Riccardo , Masciovecchio Claudio
Published: July 2013

Glycine aqueous solutions have been studied as a function of temperature and concentration by means of UV Brillouin and Raman spectroscopes. Brillouin spectra provided information on the average relaxation time τα related to the mechanisms of hydrogen bonds (HBs) formation and breaking. The concentration-temperature behavior of τ has been compared to the vibrational dephasing lifetime of atoms involved in HBs, as derived by a lineshape analysis of Raman spectra. We point out how it is possible to trace the thermodynamic behavior of a selected HB from Raman data. In particular, our results confirm the predominant role played in the hydration process by the water molecules surrounding the hydrophobic groups and, furthermore, evidence how at low temperature the HB strength between these molecules is greater than those found in bulk water and between glycine and water molecules.
Microwires fabricated by glass-coated melt spinning
Authors: Zhao Y. Y. , Li H. , Hao H. Y. , Li M. , Zhang Y. , Liaw P. K.
Published: July 2013

The glass-coated melt spinning method offers a route for the manufacture of metal filaments with a few micrometers in diameter in a single operation directly from the melt. Cobalt-based amorphous wires, Cu-15.0 atomic percent (at. %) Sn shape-memory wires, and Ni2MnGa (atomic percent) ferromagnetic wires were successfully produced by this method. The cobalt-based amorphous wire is flexible, and Cu-15.0 at. % Sn shape-memory wires have the tensile elongation of 14%. However, because of chemical reaction with glass and oxidation, it is hard to make Cu–Al–Ni shape-memory wires and Ni–Nb–Sn amorphous wires. Conditions for preparing these materials were summarized, and the differences of the solidification processes among glass-coated amorphous cobalt-based wires, Cu-15.0 at. % Sn shape-memory wires, and Ni2MnGa wires were analyzed and discussed.
Platinum-graphene counter electrodes for dye-sensitized solar cells
Authors: Cheng Cheng-En , Lin Chi-Yuan , Shan Chien-Hsun , Tsai Shang-Yi , Lin Ko-Wei , Chang Chen-Shiung , Shih-Sen Chien Forest
Published: July 2013

This paper describes the photovoltaic performance of dye-sensitized solar cells (DSSCs) containing graphene-incorporated counter electrodes (CEs). The location and thickness of graphene in CEs are optimized to improve the photovoltaic performance of DSSCs, compared with typical Pt CEs. The DSSC, with a Pt/few-layer graphene (FLG) CE, achieved 8% in short-circuit current density and 13% in power conversion efficiency (PCE). Electrochemical impedance spectroscopy shows that the DSSC, with a Pt/FLG CE, exhibits a series resistance lower than that with a Pt CE. The lower series resistance is attributed to the contact resistance at the interface of platinum and fluorine doped tin oxide. The contact resistance is reduced by the formation of the thin platinum-carbon composite layer. It is demonstrated that the consumption of Pt could be reduced with a Pt/FLG CE. However, graphene/Pt CEs resulted in a slow charge-transfer process and consequently a worse photovoltaic performance of DSSCs.
InGaAs quantum dot superlattice with vertically coupled states in InGaP matrix
Authors: Sugaya Takeyoshi , Oshima Ryuji , Matsubara Koji , Niki Shigeru
Published: July 2013

We report the formation of vertically coupled states in a 20-stack InGaAs quantum dot (QD) superlattice with GaAs spacer layers in an InGaP matrix. The InGaAs QD superlattices in the InGaP matrix have good optical properties even though the interdot spacing is reduced to 4.5 nm. We confirmed the vertically coupled states from the excitation power dependence in photoluminescence (PL) measurements. The PL peak of a QD superlattice shifts to a shorter wavelength as the excitation power is increased. The blue-shifted energy of the PL peak is 10 meV for a QD superlattice with an interdot spacing of 4.5 nm, whereas the blue shift is not observed for a multistacked QD structure with an interdot spacing of 17 nm. The vertically coupled states induce a blue shift in the PL peak wavelength as the excitation power density is increased. The vertical energy transfer between InGaAs QDs in an InGaP matrix is very attractive for use in solar cell devices.
Self-similar expansion of a warm dense plasma
Authors: Djebli Mourad , Moslem Waleed M.
Published: July 2013

The properties of an expanding plasma composed of degenerate electron fluid and non-degenerate ions are studied. For our purposes, we use fluid equations for ions together with the electron momentum equation that include quantum forces (e.g., the quantum statistical pressure, forces due to the electron-exchange and electron correlations effects) and the quasi-neutrality condition. The governing equation is written in a tractable form by using a self-similar transformation. Numerical results for typical beryllium plasma parameters revealed that, during the expansion, the ion acoustic speed decreases for both isothermal and adiabatic ion pressure. When compared with classical hydrodynamic plasma expansion model, the electrons and ions are found to initially escape faster in vacuum creating thus an intense electric field that accelerates most of the particles into the vacuum ahead of the plasma expansion. The relevancy of the present model to beryllium plasma produced by a femto-second laser is highlighted
Transmission electron microscopy study of degradation in transparent indium tin oxide/Ag/indium tin oxide multilayer films
Authors: Jeong Jin-A , Kim Han-Ki , Koo Hyun-Woo , Kim Tae-Woong
Published: July 2013

The degradation mechanism and structural evolution of transparent ITO/Ag/ITO (IAI) multilayer films caused by rapid thermal annealing (RTA) were investigated by high resolution transmission electron microscopy (HRTEM) and synchrotron X-ray scattering analysis. The IAI multilayer with low sheet resistance of 9.51 Ω/square and high transmittance of 88.24% was significantly degraded after 600 °C RTA. Discontinuity, agglomeration of the embedded Ag layer at the interface region of the IAI multilayer, and oxygen diffusion through crystalline ITO grain boundaries into Ag layers led to electrical and optical degradation of the IAI multilayer. Using HRTEM analysis, the microstructures and interfaces of as-deposited and 600 °C annealed IAI multilayer films were compared to explain their electrical and optical degradation mechanisms.
Correlation of electrical spin injection and non-linear charge-transport in Fe/MgO/Si
Authors: Pu Yong , Beardsley J. , Odenthal P. M. , Swartz A. G. , Kawakami R. K. , Hammel P. C. , Johnston-Halperin E. , Sinova Jairo , Pelz J. P.
Published: July 2013

We report measurements and analysis of electrical spin injection and detection in Fe/MgO/Si tunnel diodes using the three terminal Hanle method. The bias dependencies of the spin-resistance-area product and the differential-resistance-area product dVc/dJ are found to be very strong (in contrast to current models) and highly correlated. We demonstrate that within a standard tunneling model a strongly bias-dependent dVc/dJ requires that the tunneling coefficient must be strongly energy- and/or bias-dependent, which produces a corresponding strong bias dependence in the spin-resistance-area product compared to the magnitude of the actual spin accumulation properties. The data are best explained if the actual spin behavior is only weakly bias-dependent, consistent with the weakly bias-depended measured effective spin lifetime.
The charged exciton in an InGaN quantum dot on a GaN pyramid
Authors: Hsu Chih-Wei , Moskalenko Evgenii S. , Eriksson Martin O. , Lundskog Anders , Fredrik Karlsson K. , Forsberg Urban , Janzén Erik , Olof Holtz Per
Published: July 2013

The emission of a charged exciton in an InGaN quantum dot (QD) on top of a GaN pyramid is identified experimentally. The intensity of the charged exciton exhibits the expected competition with that of the single exciton, as observed in temperature-dependent micro-photoluminescence measurements, performed with different excitation energies. The non-zero charge state of this complex is further supported by time resolved micro-photoluminescence measurements, which excludes neutral alternatives of biexciton. The potential fluctuations in the vicinity of the QD that localizes the charge carriers are proposed to be responsible for the unequal supply of electrons and holes into the QD.
Hole electrical transporting properties in organic-Si Schottky solar cell
Authors: Shen Xiaojuan , Zhu Yawen , Song Tao , Lee Shuit-Tong , Sun Baoquan
Published: July 2013

In this work we investigated the hole electrical transporting properties effect on the organic-Si hybrid Schottky solar cells. By changing the post-annealing atmosphere of poly(3,4-ethylenedioxythiophene)/poly(styrenesulfonate) (PEDOT:PSS) film, the power conversion efficiencies of the Schottky Si/PEDOT:PSS cell boosted from 6.40% in air to 9.33% in nitrogen. Current-voltage, capacitance-voltage, external quantum efficiency, and transient photovoltage measurements illustrated that the enhanced power conversion efficiency of the cell was ascribed to the increase in both conductivity and work function (WP) of PEDOT:PSS film. The increased conductivity reduced the series resistance (RS) within the cell, and the higher WP generated the larger built-in potential (Vbi) which resulted in the improvement of the open-circuit voltage. In addition, the decreased RS and enlarged Vbi were beneficial for the efficient charge transport/collection, contributing to the enhancement of the fill factor. Our results indicated that the conductivity as well as the WP of the hole transporting layer played an important role in the organic-Si Schottky solar cell.
Massive assembly and migration of nanoparticles by laser-induced vortex flows
Authors: Xu Rui , Xin Hongbao , Li Baojun
Published: July 2013

This work demonstrates an efficient technique for assembly and migration of nanoparticles by laser-induced vortex flows. The vortex flows were generated by launching a 150 mW laser beam into a fiber tip which was horizontally placed on polystyrene particles suspension surface. The assembly is based on pressure difference in vortex flows where flow velocities vary from 0 to 8000 μm/s. Experiments indicate that after vortex flows were generated for 250 s, particles were assembled with number density increasing by 50 times. By simply moving the fiber tip, the rapid migration of the particles was realized.
Renewable energy consumption and economic efficiency: Evidence from European countries
Authors: Halkos George E. , Tzeremes Nickolaos G.
Published: July 2013

This paper examines the relationship between renewable energy consumption and economic efficiency. For this reason, conditional Data Envelopment Analysis estimators alongside with nonparametric regressions are applied in a sample of 25 European countries for the year 2010 with emphasis given to Eastern and Western European countries. Our results reveal that renewable energy consumption has a positive effect on countries' economic efficiency for lower consumption levels while for higher levels, the analysis reveals mixed effects, which are also subject to regional disparities. Finally, it appears that the effect of renewable energy consumption on countries’ economic efficiency depends also on countries’ specific regional characteristics as well as on the environmental policies adopted.
Current distribution in a parallel configuration superconducting strip-line detector
Authors: Casaburi A. , Heath R. M. , Tanner M. G. , Cristiano R. , Ejrnaes M. , Nappi C. , Hadfield R. H.
Published: July 2013

Superconducting detectors based on parallel microscopic strip-lines are promising candidates for single molecule detection in time-of-flight mass spectrometry. The device physics of this configuration is complex. In this letter, we employ nano-optical techniques to study the variation of current density, count rate, and pulse amplitude transversely across the parallel strip device. Using the phenomenological London theory, we are able to correlate our results to a non-uniform current distribution between the strips, governed by the London magnetic penetration depth. This fresh perspective convincingly explains anomalous behaviour in large area parallel superconducting strip-line detectors reported in previous studies.
High temperature-induced abnormal suppression of sub-threshold swing and on-current degradations under hot-carrier stress in a-InGaZnO thin film transistors
Authors: Tsai Ming-Yen , Chang Ting-Chang , Chu Ann-Kuo , Hsieh Tien-Yu , Chen Te-Chih , Lin Kun-Yao , Tsai Wu-Wei , Chiang Wen-Jen , Yan Jing-Yi
Published: July 2013

This letter investigates the effect of temperature on hot-carrier stress-induced degradation behavior in InGaZnO thin film transistors. After hot-carrier stress at 25 °C, serious on-current and subthreshold swing degradations are observed due to trap state generation near the drain side. For identical stress performed at elevated temperatures, current degradation in the I-V transfer curve under reverse mode is gradually suppressed and the anomalous hump in the gate-to-drain capacitance-voltage curve becomes more severe. These suppressed degradations and the more severe hump can be both attributed to hole-trapping near the drain side due to high drain bias at high temperature.
Ultrafast transition between polariton doublet and alternating current Stark triplet in organic one-dimensional photonic crystal microcavity
Authors: Ishii Kenta , Nakanishi Shunsuke , Tsurumachi Noriaki
Published: July 2013

This work investigates nonlinear transmission properties of cavity polaritons in a one-dimensional photonic crystal microcavity containing pseudoisocyanine J-aggregates. It was observed that an unexpected transmission peak appeared between the two peaks of cavity polaritons, when the incident light intensity was high. The decay time of this third peak, determined by the pump-probe transient transmission spectroscopy, was less than 1 ps. We observed ultrafast transition between the cavity polariton doublet and AC Stark triplet in an organic system.
Spin cycloid destruction in Pr doped BiFeO3 films studied by conversion-electron Mossbauer spectroscopy
Authors: Xiao Renzheng , Pelenovich Vasiliy O. , Fu Dejun
Published: July 2013

Crystalline Bi1−xPrxFeO3 films were fabricated on Si (100) substrates by sol-gel technique. X-ray diffraction revealed a decrease of lattice constants of the doped samples evidencing substitution of Bi by Pr ions. Ferromagnetism with low saturation magnetization Ms = 1–3 emu/cm3 of the films were observed by Vibrating sample magnetometry. Systematic change of Mossbauer parameters of the films with Pr doped concentration increase were obtained by Conversion-electron Mossbauer spectroscopy (CEMS). The results of both one- and two-sextet fittings of the CEMS spectra provide evidence for destruction of the spin cycloid in Pr-doped BiFeO3.
Contrasting Reactivity of Mono- versus Bis-2,2,6,6-tetramethylpiperidide Lithium Aluminates Towards Polydentate Lewis Bases: Co-Complexation Versus Deprotonation
Authors: Campbell Ross , Crosbie Elaine , Kennedy Alan R. , Mulvey Robert E. , Naismith Rachael A. , Robertson Stuart D.
Published: July 2013

Two closely related lithium alkylaluminium amides LiAl(TMP)2iBu2 and LiAl(TMP)iBu3 (TMP: 2,2,6,6-tetramethylpiperidide) have been compared in their reactivity towards six polydentate Lewis bases containing either N or O donor atoms or a mixed N,O donor set. Seven of the twelve potential organometallic products of these reactions, which were carried out in hexane solution, have been crystallographically characterised. Three of these structures, [Li(μ-Me2NCH2CHCH2CH2CHO)(μ-TMP)Al(iBu)2], [Li(μ-Me2NCH2CH2OCH2)(μ-TMP)Al(iBu)2], and [Li(μ-Me2NCH2CH2OCHCH2NMe2)(μ-TMP)Al(iBu)2] reveal that the bis-amide LiAl(TMP)2iBu2 deprotonates (aluminates) the multifunctional Lewis base selectively at the carbon atom adjacent to oxygen with the anion generated captured by the residue of the base. In contrast, the mono-amide LiAl(TMP)iBu3 in general fails to deprotonate the Lewis bases but instead forms co-complexes with them as evidenced by the molecular structures of [Me2NCH2CHCH2CH2CH2O·Li(μ-iBu)(μ-TMP)Al(iBu)2], [Me2NCH2CH2OMe·Li(μ-iBu)(μ-TMP)Al(iBu)2], and [MeOCH2CH2OMe·Li(μ-iBu)(μ-TMP)Al(iBu)2]. Providing an exception to this pattern, the mono-amide reagent deprotonates chiral R,R,-N,N,N′,N′-tetramethylcyclohexanediamine to afford [Li(μ-CH2NMeC6H10NMe2)2Al(iBu)2], the final complex to be crystallographically characterised. All new products have been spectroscopically characterised through 1H, 7 Li, and 13C NMR studies. Reaction mixtures have also been quenched with D2O and analysed by 2D NMR spectroscopy to ascertain the full metallation versus co-complexation picture taking place in solution.
Physiological perspectives of reduced tillering and stunting in the tiller inhibition (tin) mutant of wheat
Authors: Kebrom Tesfamichael H. , Richards Richard A.
Published: July 2013

The number of tillers established in cereal crops far exceeds the number that end up being grain bearing at maturity. Improving the economy in tillering has been proposed to improve cereal yields in both favourable and unfavourable environments. The tiller inhibition mutant (tin) is potentially useful for breeding varieties with a greater economy of tillering. However, its tendency to stunting under long day and low temperatures has limited its use. Recently, the inhibition of tillering in tin has been linked to precocious development of solid basal internodes that compete for sucrose and possibly other resources with the growing tiller buds leading to their developmental arrest. Although the physiological basis of stunting in tin is unknown, both inhibition of tillering and stunting begin during the transition from vegetative to reproductive phase indicating a common physiological basis for both. In this review, we provide overall perspectives for the physiological basis of tiller inhibition and stunting in tin and suggest the direction of research in the future.
Metabolic profile of serum and follicular fluid from postpartum dairy cows during summer and winter
Authors: Alves Benner G. , Alves Kele A. , Martins Muller C. , Braga Lucas S. , Silva Thiago H. , Alves Bruna G. , Santos Ricarda M. , Silva Thiago V. , Viu Marco A. O. , Beletti Marcello E. , Jacomini José O. , Gambarini Maria L.
Published: July 2013

This study was designed to monitor the biochemical profiles of serum and follicular fluid (FF) of postpartum dairy cows during the summer (n = 30) and winter (n = 30). Blood and FF (follicles ≥ 9 mm) were obtained from Girolando cows at 30, 45, 60, 75 and 90 days postpartum. The samples were collected and analysed to determine glucose, total cholesterol (TC), triglyceride (TG), urea, sodium (Na), potassium (K) and calcium (Ca) levels. Throughout the study, the following clinical variables were measured: rectal temperature (RT), respiratory rate (RR) and body condition score (BCS). In addition, the temperature humidity index (THI) was calculated for each season. During the summer season, THI was higher, BCS decreased, there was an increase in RT, and glucose, urea, Na and K serum levels were decreased (P < 0.05). The levels of TC, TG, urea, K and Ca in follicular fluid increased (P < 0.05). Positive correlations (P < 0.05) were observed between the serum and FF levels for glucose (r = 0.29), TC (r = 0.24) and Ca (r = 0.30). Therefore, the biochemical profile of serum and FF of dairy cows under summer heat-stress conditions demonstrates marked changes that may impair fertility during lactation.
Comparative effects of adding β-mercaptoethanol or L-ascorbic acid to culture or vitrification–warming media on IVF porcine embryos
Authors: Castillo-Martín Miriam , Bonet Sergi , Morató Roser , Yeste Marc
Published: July 2013

The aims of the present study were to; (1) determine the effects of supplementation with two antioxidants during in vitro culture (IVC) on embryo development and quality; and (2) test the effects of adding the antioxidants to vitrification–warming media on the cryotolerance of in vitro-produced (IVP) porcine blastocysts. In Experiment 1, presumptive zygotes were cultured without antioxidants, with 50 µM β-mercaptoethanol (β-ME) or with 100 µM l-ascorbic acid (AC). After culture, blastocyst yield, quality and cryotolerance were evaluated in each treatment group. In Experiment 2, survival rates (3 and 24 h), total cell number, apoptosis index and the formation of reactive oxygen species (ROS) in blastocysts vitrified–warmed with 100 µM AC or 50 µM β-ME or without antioxidants added to the vitrification medium were compared. Antioxidant addition during IVC had no effect on embryo development, total cell number or the apoptosis index, and culturing embryos in the presence of β-ME had no effects on cryotolerance. In contrast, ROS levels and survival rates after vitrification–warming were significantly improved in embryos cultured with AC. Furthermore, addition of AC into vitrification–warming media enhanced embryo survival and embryo quality after warming. In conclusion, our results suggest that supplementing culture or vitrification media with 100 µM AC improves the quality and cryosurvival of IVP porcine blastocysts.
Evaluation of mixed-source, low-template DNA profiles in forensic science
Authors: Balding David J.
Published: July 2013

Enhancements in sensitivity now allow DNA profiles to be obtained from only tens of picograms of DNA, corresponding to a few cells, even for samples subject to degradation from environmental exposure. However, low-template DNA (LTDNA) profiles are subject to stochastic effects, such as “dropout” and “dropin” of alleles, and highly variable stutter peak heights. Although the sensitivity of the newly developed methods is highly appealing to crime investigators, courts are concerned about the reliability of the underlying science. High-profile cases relying on LTDNA evidence have collapsed amid controversy, including the case of Hoey in the United Kingdom and the case of Knox and Sollecito in Italy. I argue that rather than the reliability of the science, courts and commentators should focus on the validity of the statistical methods of evaluation of the evidence. Even noisy DNA evidence can be more powerful than many traditional types of evidence, and it can be helpful to a court as long as its strength is not overstated. There have been serious shortcomings in statistical methods for the evaluation of LTDNA profile evidence, however. Here, I propose a method that allows for multiple replicates with different rates of dropout, sporadic dropins, different amounts of DNA from different contributors, relatedness of suspected and alternate contributors, “uncertain” allele designations, and degradation. R code implementing the method is open source, facilitating wide scrutiny. I illustrate its good performance using real cases and simulated crime scene profiles.
Phase separation explains a new class of self-organized spatial patterns in ecological systems
Authors: Liu Quan-Xing , Doelman Arjen , Rottschäfer Vivi , de Jager Monique , Herman Peter M. J. , Rietkerk Max , van de Koppel Johan
Published: July 2013

The origin of regular spatial patterns in ecological systems has long fascinated researchers. Turing’s activator–inhibitor principle is considered the central paradigm to explain such patterns. According to this principle, local activation combined with long-range inhibition of growth and survival is an essential prerequisite for pattern formation. Here, we show that the physical principle of phase separation, solely based on density-dependent movement by organisms, represents an alternative class of self-organized pattern formation in ecology. Using experiments with self-organizing mussel beds, we derive an empirical relation between the speed of animal movement and local animal density. By incorporating this relation in a partial differential equation, we demonstrate that this model corresponds mathematically to the well-known Cahn–Hilliard equation for phase separation in physics. Finally, we show that the predicted patterns match those found both in field observations and in our experiments. Our results reveal a principle for ecological self-organization, where phase separation rather than activation and inhibition processes drives spatial pattern formation.
Posttranslational modification of CENP-A influences the conformation of centromeric chromatin
Authors: Bailey Aaron O. , Panchenko Tanya , Sathyan Kizhakke M. , Petkowski Janusz J. , Pai Pei-Jing , Bai Dina L. , Russell David H. , Macara Ian G. , Shabanowitz Jeffrey , Hunt Donald F. , Black Ben E. , Foltz Daniel R.
Published: July 2013

Centromeres are chromosomal loci required for accurate segregation of sister chromatids during mitosis. The location of the centromere on the chromosome is not dependent on DNA sequence, but rather it is epigenetically specified by the histone H3 variant centromere protein A (CENP-A). The N-terminal tail of CENP-A is highly divergent from other H3 variants. Canonical histone N termini are hotspots of conserved posttranslational modification; however, no broadly conserved modifications of the vertebrate CENP-A tail have been previously observed. Here, we report three posttranslational modifications on human CENP-A N termini using high-resolution MS: trimethylation of Gly1 and phosphorylation of Ser16 and Ser18. Our results demonstrate that CENP-A is subjected to constitutive initiating methionine removal, similar to other H3 variants. The nascent N-terminal residue Gly1 becomes trimethylated on the α-amino group. We demonstrate that the N-terminal RCC1 methyltransferase is capable of modifying the CENP-A N terminus. Methylation occurs in the prenucleosomal form and marks the majority of CENP-A nucleosomes. Serine 16 and 18 become phosphorylated in prenucleosomal CENP-A and are phosphorylated on asynchronous and mitotic nucleosomal CENP-A and are important for chromosome segregation during mitosis. The double phosphorylation motif forms a salt-bridged secondary structure and causes CENP-A N-terminal tails to form intramolecular associations. Analytical ultracentrifugation of phospho-mimetic CENP-A nucleosome arrays demonstrates that phosphorylation results in greater intranucleosome associations and counteracts the hyperoligomerized state exhibited by unmodified CENP-A nucleosome arrays. Our studies have revealed that the major modifications on the N-terminal tail of CENP-A alter the physical properties of the chromatin fiber at the centromere.
Analysis of
Dll4
regulation reveals a combinatorial role for Sox and Notch in arterial development
Authors: Sacilotto Natalia , Monteiro Rui , Fritzsche Martin , Becker Philipp W. , Sanchez-del-Campo Luis , Liu Ke , Pinheiro Philip , Ratnayaka Indrika , Davies Benjamin , Goding Colin R. , Patient Roger , Bou-Gharios George , De Val Sarah
Published: July 2013

The mechanisms by which arterial fate is established and maintained are not clearly understood. Although a number of signaling pathways and transcriptional regulators have been implicated in arterio-venous differentiation, none are essential for arterial formation, and the manner in which widely expressed factors may achieve arterial-specific gene regulation is unclear. Using both mouse and zebrafish models, we demonstrate here that arterial specification is regulated combinatorially by Notch signaling and SoxF transcription factors, via direct transcriptional gene activation. Through the identification and characterization of two arterial endothelial cell-specific gene enhancers for the Notch ligand
Delta-like ligand 4 (Dll4)
, we show that arterial
Dll4
expression requires the direct binding of both the RBPJ/Notch intracellular domain and SOXF transcription factors. Specific combinatorial, but not individual, loss of SOXF and RBPJ DNA binding ablates all
Dll4
enhancer-transgene expression despite the presence of multiple functional ETS binding sites, as does knockdown of
sox7
;
sox18
in combination with loss of Notch signaling. Furthermore, triple knockdown of
sox7
,
sox18
and
rbpj
also results in ablation of endogenous
dll4
expression. Fascinatingly, this combinatorial ablation leads to a loss of arterial markers and the absence of a detectable dorsal aorta, demonstrating the essential roles of SoxF and Notch, together, in the acquisition of arterial identity.
Inverse modulation of plant immune and brassinosteroid signaling pathways by the receptor-like cytoplasmic kinase BIK1
Authors: Lin Wenwei , Lu Dongping , Gao Xiquan , Jiang Shan , Ma Xiyu , Wang Zonghua , Mengiste Tesfaye , He Ping , Shan Libo
Published: July 2013

Maintaining active growth and effective immune responses is often costly for a living organism to survive. Fine-tuning the shared cross-regulators is crucial for metazoans and plants to make a trade-off between growth and immunity. The
Arabidopsis
regulatory receptor-like kinase BAK1 complexes with the receptor kinases FLS2 in bacterial flagellin-triggered immunity and BRI1 in brassinosteroid (BR)-mediated growth. BR homeostasis and signaling unidirectionally modulate FLS2-mediated immune responses at multiple levels. We have shown previously that BIK1, a receptor-like cytoplasmic kinase, is directly phosphorylated by BAK1 and associates with FLS2/BAK1 complex in transducing flagellin signaling. In contrast to its positive role in plant immunity, we report here that BIK1 acts as a negative regulator in BR signaling. The
bik1
mutant displays various BR hypersensitive phenotypes accompanied with increased accumulation of de-phosphorylated BES1 proteins and transcriptional regulation of BZR1 and BES1 target genes. BIK1 associates with BRI1, and is released from BRI1 receptor upon BR treatment, which is reminiscent of FLS2-BIK1 complex dynamics in flagellin signaling. The ligand-induced release of BIK1 from receptor complexes is associated with BIK1 phosphorylation. However, in contrast to BAK1-dependent FLS2-BIK1 dissociation, BAK1 is dispensable for BRI1-BIK1 dissociation. Unlike FLS2 signaling which depends on BAK1 to phosphorylate BIK1, BRI1 directly phosphorylates BIK1 to transduce BR signaling. Thus, BIK1 relays the signaling in plant immunity and BR-mediated growth via distinct phosphorylation by BAK1 and BRI1, respectively. Our studies indicate that BIK1 mediates inverse functions in plant immunity and development via dynamic association with specific receptor complexes and differential phosphorylation events.
Controlled insertional mutagenesis using a LINE-1 (
ORFeus
) gene-trap mouse model
Authors: O’Donnell Kathryn A. , An Wenfeng , Schrum Christina T. , Wheelan Sarah J. , Boeke Jef D.
Published: July 2013

Significance

Transposons are powerful tools widely used for insertional mutagenesis screens because of the straightforward identification of transposon-induced mutations. We developed a conditionally regulated long interspersed element 1 [tetracycline (tet)-
ORFeus
] retrotransposon mouse model that may be used for random mutagenesis and mechanistic studies. High-level expression of the retrotransposon during development results in embryonic lethality due to a significant burden of insertions. At lower levels, transgene induction results in a somatic spotting phenotype due to mutations that likely disrupt melanocyte development, suggesting high activity of tet-
ORFeus
in melanocyte precursors. This model may be used to identify genes and pathways involved in diverse biological processes.
Genetic loss or pharmacological blockade of testes-expressed taste genes causes male sterility
Authors: Mosinger Bedrich , Redding Kevin M. , Parker M. Rockwell , Yevshayeva Valeriya , Yee Karen K. , Dyomina Katerina , Li Yan , Margolskee Robert F.
Published: July 2013

TAS1R taste receptors and their associated heterotrimeric G protein gustducin are involved in sugar and amino acid sensing in taste cells and in the gastrointestinal tract. They are also strongly expressed in testis and sperm, but their functions in these tissues were previously unknown. Using mouse models, we show that the genetic absence of both TAS1R3, a component of sweet and amino acid taste receptors, and the gustducin α-subunit GNAT3 leads to male-specific sterility. To gain further insight into this effect, we generated a mouse model that expressed a humanized form of TAS1R3 susceptible to inhibition by the antilipid medication clofibrate. Sperm formation in animals without functional TAS1R3 and GNAT3 is compromised, with malformed and immotile sperm. Furthermore, clofibrate inhibition of humanized TAS1R3 in the genetic background of
Tas1r3

−/−

,
Gnat3

−/−

doubly null mice led to inducible male sterility. These results indicate a crucial role for these extraoral “taste” molecules in sperm development and maturation. We previously reported that blocking of human TAS1R3, but not mouse TAS1R3, can be achieved by common medications or chemicals in the environment. We hypothesize that even low levels of these compounds can lower sperm count and negatively affect human male fertility, which common mouse toxicology assays would not reveal. Conversely, we speculate that TAS1R3 and GNAT3 activators may help infertile men, particularly those that are affected by some of the mentioned inhibitors and/or are diagnosed with idiopathic infertility involving signaling pathway of these receptors.
Modulation of B-cell exosome proteins by gamma herpesvirus infection
Authors: Meckes David G. , Gunawardena Harsha P. , Dekroon Robert M. , Heaton Phillip R. , Edwards Rachel H. , Ozgur Sezgin , Griffith Jack D. , Damania Blossom , Raab-Traub Nancy
Published: July 2013

Significance

Exosomes are released from tumor cells at high levels, and multiple studies have determined that the secreted exosomes enter recipient cells and can affect their biologic and biochemical properties. In this study, the specific effects of the oncogenic herpesviruses, EBV and Kaposi sarcoma-associated virus, on the proteomes of B-cell exosomes were determined using global quantitative proteomics. The data indicate that the viruses greatly impact the protein content of exosomes with common and distinct changes induced by both viruses. It is likely that these alterations in exosome content modulate the tumor environment, potentially to enhance viral infection and promote tumorigenesis.
Body wall development in lamprey and a new perspective on the origin of vertebrate paired fins
Authors: Tulenko Frank J. , McCauley David W. , MacKenzie Ethan L. , Mazan Sylvie , Kuratani Shigeru , Sugahara Fumiaki , Kusakabe Rie , Burke Ann C.
Published: July 2013

Classical hypotheses regarding the evolutionary origin of paired appendages propose transformation of precursor structures (gill arches and lateral fin folds) into paired fins. During development, gnathostome paired appendages form as outgrowths of body wall somatopleure, a tissue composed of somatic lateral plate mesoderm (LPM) and overlying ectoderm. In amniotes, LPM contributes connective tissue to abaxial musculature and forms ventrolateral dermis of the interlimb body wall. The phylogenetic distribution of this character is uncertain because lineage analyses of LPM have not been generated in anamniotes. We focus on the evolutionary history of the somatopleure to gain insight into the tissue context in which paired fins first appeared. Lampreys diverged from other vertebrates before the acquisition of paired fins and provide a model for investigating the preappendicular condition. We present vital dye fate maps that suggest the somatopleure is eliminated in lamprey as the LPM is separated from the ectoderm and sequestered to the coelomic linings during myotome extension. We also examine the distribution of postcranial mesoderm in catshark and axolotl. In contrast to lamprey, our findings support an LPM contribution to the trunk body wall of these taxa, which is similar to published data for amniotes. Collectively, these data lead us to hypothesize that a persistent somatopleure in the lateral body wall is a gnathostome synapomorphy, and the redistribution of LPM was a key step in generating the novel developmental module that ultimately produced paired fins. These embryological criteria can refocus arguments on paired fin origins and generate hypotheses testable by comparative studies on the source, sequence, and extent of genetic redeployment.
Human placental trophoblasts confer viral resistance to recipient cells
Authors: Delorme-Axford Elizabeth , Donker Rogier B. , Mouillet Jean-Francois , Chu Tianjiao , Bayer Avraham , Ouyang Yingshi , Wang Tianyi , Stolz Donna B. , Sarkar Saumendra N. , Morelli Adrian E. , Sadovsky Yoel , Coyne Carolyn B.
Published: July 2013

Placental trophoblasts form the interface between the fetal and maternal environments and serve to limit the maternal–fetal spread of viruses. Here we show that cultured primary human placental trophoblasts are highly resistant to infection by a number of viruses and, importantly, confer this resistance to nonplacental recipient cells by exosome-mediated delivery of specific microRNAs (miRNAs). We show that miRNA members of the chromosome 19 miRNA cluster, which are almost exclusively expressed in the human placenta, are packaged within trophoblast-derived exosomes and attenuate viral replication in recipient cells by the induction of autophagy. Together, our findings identify an unprecedented paracrine and/or systemic function of placental trophoblasts that uses exosome-mediated transfer of a unique set of placental-specific effector miRNAs to directly communicate with placental or maternal target cells and regulate their immunity to viral infections.
A thioredoxin-like/β-propeller protein maintains the efficiency of light harvesting in
Arabidopsis
Authors: Brooks Matthew D. , Sylak-Glassman Emily J. , Fleming Graham R. , Niyogi Krishna K.
Published: July 2013

Significance

Plants need to regulate light harvesting to match incoming light energy to photosynthetic capacity. Excess excitation can generate reactive oxygen species and damage the photosynthetic machinery. To dissipate excess absorbed light energy, plants have evolved several quenching pathways, each of which acts on a different timescale. Here we identify a chloroplast protein involved in a previously uncharacterized, slowly reversible form of energy dissipation in the photosynthetic antenna. This mutant will be critical in characterizing this quenching pathway and will further our understanding of how plants are able to balance light harvesting and photoprotection to maximize photosynthetic efficiency.
Two independent pathways of regulated necrosis mediate ischemia–reperfusion injury
Authors: Linkermann Andreas , Bräsen Jan Hinrich , Darding Maurice , Jin Mi Kyung , Sanz Ana B. , Heller Jan-Ole , De Zen Federica , Weinlich Ricardo , Ortiz Alberto , Walczak Henning , Weinberg Joel M. , Green Douglas R. , Kunzendorf Ulrich , Krautwald Stefan
Published: July 2013

Regulated necrosis (RN) may result from cyclophilin (Cyp)D-mediated mitochondrial permeability transition (MPT) and receptor-interacting protein kinase (RIPK)1-mediated necroptosis, but it is currently unclear whether there is one common pathway in which CypD and RIPK1 act in or whether separate RN pathways exist. Here, we demonstrate that necroptosis in ischemia–reperfusion injury (IRI) in mice occurs as primary organ damage, independent of the immune system, and that mice deficient for RIPK3, the essential downstream partner of RIPK1 in necroptosis, are protected from IRI. Protection of RIPK3-knockout mice was significantly stronger than of CypD-deficient mice. Mechanistically, in vivo analysis of cisplatin-induced acute kidney injury and hyperacute TNF-shock models in mice suggested the distinctness of CypD-mediated MPT from RIPK1/RIPK3-mediated necroptosis. We, therefore, generated CypD-RIPK3 double-deficient mice that are viable and fertile without an overt phenotype and that survived prolonged IRI, which was lethal to each single knockout. Combined application of the RIPK1 inhibitor necrostatin-1 and the MPT inhibitor sanglifehrin A confirmed the results with mutant mice. The data demonstrate the pathophysiological coexistence and corelevance of two separate pathways of RN in IRI and suggest that combination therapy targeting distinct RN pathways can be beneficial in the treatment of ischemic injury.
Role of a Microcin-C–like biosynthetic gene cluster in allelopathic interactions in marineSynechococcus
Authors: Paz-Yepes Javier , Brahamsha Bianca , Palenik Brian
Published: July 2013

Competition between phytoplankton species for nutrients and light has been studied for many years, but allelopathic interactions between them have been more difficult to characterize. We used liquid and plate assays to determine whether these interactions occur between marine unicellular cyanobacteria of the genusSynechococcus. We have found a clear growth impairment ofSynechococcussp. CC9311 andSynechococcussp. WH8102 when they are cultured in the presence ofSynechococcussp. CC9605. The genome of CC9605 contains a region showing homology to genes of theEscherichia coliMicrocin C (McC) biosynthetic pathway. McC is a ribosome-synthesized peptide that inhibits translation in susceptible strains. We show that the CC9605 McC gene cluster is expressed and that three genes (mccD,mccA, andmccB) are further induced by coculture with CC9311. CC9605 was resistant to McC purified fromE. coli, whereas strains CC9311 and WH8102 were sensitive. Cloning the CC9605 McC biosynthetic gene cluster into sensitive CC9311 led this strain to become resistant to both purifiedE. coliMcC andSynechococcussp. CC9605. A CC9605 mutant lackingmccA1,mccA2, and the N-terminal domain ofmccBdid not inhibit CC9311 growth, whereas the inhibition of WH8102 was reduced. Our results suggest that an McC-like molecule is involved in the allelopathic interactions with CC9605.
Rickettsia
Sca2 has evolved formin-like activity through a different molecular mechanism
Authors: Madasu Yadaiah , Suarez Cristian , Kast David J. , Kovar David R. , Dominguez Roberto
Published: July 2013

Significance

Rickettsia
Sca2 mimics eukaryotic formins by promoting actin filament nucleation and elongation to assemble actin comet tails for
Rickettsia
motility. We show that unlike formins, Sca2 is monomeric, but has N- and C-terminal repeat domains (NRD and CRD) that interact with each other. The structure of NRD reveals a new crescent-like fold. CRD is predicted to share this fold, and might form together with NRD a doughnut-shaped formin-like structure for processive elongation. Between NRD and CRD, proline-rich sequences incorporate profilin-actin for elongation, and WASP-homology 2 (WH2) domains recruit actin monomers for nucleation.
Rickettsia
has therefore “rediscovered” formin-like actin nucleation and elongation.
Nicotinic α7 receptors enhance NMDA cognitive circuits in dorsolateral prefrontal cortex
Authors: Yang Yang , Paspalas Constantinos D. , Jin Lu E. , Picciotto Marina R. , Arnsten Amy F. T. , Wang Min
Published: July 2013

The cognitive function of the highly evolved dorsolateral prefrontal cortex (dlPFC) is greatly influenced by arousal state, and is gravely afflicted in disorders such as schizophrenia, where there are genetic insults in α7 nicotinic acetylcholine receptors (α7-nAChRs). A recent behavioral study indicates that ACh depletion from dlPFC markedly impairs working memory [Croxson PL, Kyriazis DA, Baxter MG (2011)Nat Neurosci14(12):1510–1512]; however, little is known about how α7-nAChRs influence dlPFC cognitive circuits. Goldman-Rakic [Goldman-Rakic (1995)Neuron14(3):477–485] discovered the circuit basis for working memory, whereby dlPFC pyramidal cells excite each other through glutamatergic NMDA receptor synapses to generate persistent network firing in the absence of sensory stimulation. Here we explore α7-nAChR localization and actions in primate dlPFC and find that they are enriched in glutamate network synapses, where they are essential for dlPFC persistent firing, with permissive effects on NMDA receptor actions. Blockade of α7-nAChRs markedly reduced, whereas low-dose stimulation selectively enhanced, neuronal representations of visual space. These findings in dlPFC contrast with the primary visual cortex, where nAChR blockade had no effect on neuronal firing [Herrero JL, et al. (2008)Nature454(7208):1110–1114]. We additionally show that α7-nAChR stimulation is needed for NMDA actions, suggesting that it is key for the engagement of dlPFC circuits. As ACh is released in cortex during waking but not during deep sleep, these findings may explain how ACh shapes differing mental states during wakefulness vs. sleep. The results also explain why genetic insults to α7-nAChR would profoundly disrupt cognitive experience in patients with schizophrenia.
Quantum of optical absorption in two-dimensional semiconductors
Authors: Fang Hui , Bechtel Hans A. , Plis Elena , Martin Michael C. , Krishna Sanjay , Yablonovitch Eli , Javey Ali
Published: July 2013

The optical absorption properties of free-standing InAs nanomembranes of thicknesses ranging from 3 nm to 19 nm are investigated by Fourier transform infrared spectroscopy. Stepwise absorption at room temperature is observed, arising from the interband transitions between the subbands of 2D InAs nanomembranes. Interestingly, the absorptance associated with each step is measured to be ∼1.6%, independent of thickness of the membranes. The experimental results are consistent with the theoretically predicted absorptance quantum,
A
Q
=
πα/n

c

for each set of interband transitions in a 2D semiconductor, where
α
is the fine structure constant and
n

c

is an optical local field correction factor. Absorptance quantization appears to be universal in 2D systems including III–V quantum wells and graphene.
Large population solution of the stochastic Luria–Delbrück evolution model
Authors: Kessler David A. , Levine Herbert
Published: July 2013

Luria and Delbrück introduced a very useful and subsequently widely adopted framework for quantitatively understanding the emergence of new cellular lineages. Here, we provide an analytical treatment of the fully stochastic version of the model, enabled by the fact that population sizes at the time of measurement are invariably very large and mutation rates are low. We show that the Lea–Coulson generating function describes the “inner solution,” where the number of mutants is much smaller than the total population. We find that the corresponding distribution function interpolates between a monotonic

decrease at relatively small populations, (compared with the inverse of the mutation probability), whereas it goes over to a Lévy
α
-stable distribution in the very large population limit. The moments are completely determined by the outer solution, and so are devoid of practical significance. The key to our solution is focusing on the fixed population size ensemble, which we show is very different from the fixed time ensemble due to the extreme variability in the evolutionary process.