bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional domains of the mouse β3-adrenoceptor associated with differential G-protein coupling
Authors: Sato M. , Hutchinson D.S. , Evans B.A. , Summers R.J.
Published: August 2015

Localization of G-protein-coupled receptors within membrane microdomains is associated with differential signalling pathway activation. We have shown that two mouse β3-AR (β3-adrenoceptor) isoforms encoded by alternatively spliced mRNAs differ in their signalling properties; the β3a-AR couples only with Gs, whereas the β3b-AR couples with both Gs and Gi. Our previous studies indicated that the β3a-AR is restrained from coupling with Gi due to the interaction of residues in the C-terminus with other protein(s). We have investigated the hypothesis that the β3a-AR interacts with caveolin. Disruption of caveolae in CHO (Chinese-hamster ovary)-K1 cells expressing wild-type β3a-ARs with filipin III, or mutation of a putative caveolin-binding site in the β3a-AR, causes cAMP accumulation to become PTX (pertussis toxin)-sensitive. Likewise, filipin treatment of mouse brown adipocytes that express endogenous β3a-ARs produces a substantial reduction in agonist-stimulated cAMP production that is rescued by pre-treatment with PTX. These studies suggest that β3a-ARs may be restricted to caveolae and that localization of the receptor may play a specific role in G-protein-mediated signalling.
The pumps that fuel a sperm's journey
Authors: Clausen Michael Jakob , Nissen Poul , Poulsen Hanne
Published: August 2015

The sole purpose of a sperm cell is to carry genetic information from a male to a female egg. In order to accomplish this quest, the sperm cell must travel a long distance through a constantly changing environment. The success of this journey depends on membrane proteins that are uniquely expressed in sperm cells. One of these proteins is the α4 isoform of the sodium pump. This pump is optimized to cope with the ionic environment characteristic of the female reproductive tract, and its activity may be tightly coupled with secondary transporters that maintain cytoplasmic pH. Pharmacological inhibition of α4 is sufficient to inhibit sperm motility, and significant differences around the inhibitor-binding site compared with the ubiquitous α1 isoform, make α4 a feasible target in rational drug development.
Mapping lipid and detergent molecules at the surface of membrane proteins
Authors: Cogdell Richard J. , Gardiner Alastair T. , Roszak Aleksander W. , Stončius Sigitas , Kočovský Pavel , Isaacs Neil W.
Published: August 2015

Electron-density maps for the crystal structures of membrane proteins often show features suggesting binding of lipids and/or detergent molecules on the hydrophobic surface, but usually it is difficult to identify the bound molecules. In our studies, heavy-atom-labelled phospholipids and detergents have been used to unequivocally identify these binding sites at the surfaces of test membrane proteins, the reaction centres from Rhodobacter sphaeroides and Blastochloris viridis. The generality of this method is discussed in the present article.
The mitochondrial-encoded subunits of respiratory complex I (NADH:ubiquinone oxidoreductase): identifying residues important in mechanism and disease
Authors: Bridges Hannah R. , Birrell James A. , Hirst Judy
Published: August 2015

Complex I (NADH:ubiquinone oxidoreductase) is crucial to respiration in many aerobic organisms. The hydrophilic domain of complex I, containing nine or more redox cofactors, and comprising seven conserved core subunits, protrudes into the mitochondrial matrix or bacterial cytoplasm. The α-helical membrane-bound hydrophobic domain contains a further seven core subunits that are mitochondrial-encoded in eukaryotes and named the ND subunits (ND1–ND6 and ND4L). Complex I couples the oxidation of NADH in the hydrophilic domain to ubiquinone reduction and proton translocation in the hydrophobic domain. Although the mechanisms of NADH oxidation and intramolecular electron transfer are increasingly well understood, the mechanisms of ubiquinone reduction and proton translocation remain only poorly defined. Recently, an α-helical model of the hydrophobic domain of bacterial complex I [Efremov, Baradaran and Sazanov (2010) Nature 465, 441–447] revealed how the 63 transmembrane helices of the seven core subunits are arranged, and thus laid a foundation for the interpretation of functional data and the formulation of mechanistic proposals. In the present paper, we aim to correlate information from sequence analyses, site-directed mutagenesis studies and mutations that have been linked to human diseases, with information from the recent structural model. Thus we aim to identify and discuss residues in the ND subunits of mammalian complex I which are important in catalysis and for maintaining the enzyme's structural and functional integrity.
The basic building blocks and evolution of CRISPR–Cas systems
Authors: Makarova Kira S. , Wolf Yuri I. , Koonin Eugene V.
Published: August 2015

CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) is an adaptive immunity system in bacteria and archaea that functions via a distinct self/non-self recognition mechanism that involves unique spacers homologous with viral or plasmid DNA and integrated into the CRISPR loci. Most of the Cas proteins evolve under relaxed purifying selection and some underwent dramatic structural rearrangements during evolution. In many cases, CRISPR–Cas system components are replaced either by homologous or by analogous proteins or domains in some bacterial and archaeal lineages. However, recent advances in comparative sequence analysis, structural studies and experimental data suggest that, despite this remarkable evolutionary plasticity, all CRISPR–Cas systems employ the same architectural and functional principles, and given the conservation of the principal building blocks, share a common ancestry. We review recent advances in the understanding of the evolution and organization of CRISPR–Cas systems. Among other developments, we describe for the first time a group of archaeal cas1 gene homologues that are not associated with CRISPR–Cas loci and are predicted to be involved in functions other than adaptive immunity.
D-Serine metabolism: new insights into the modulation of D-amino acid oxidase activity
Authors: Sacchi Silvia
Published: August 2015

Over the years, accumulating evidence has indicated that D-serine represents the main endogenous ligand of NMDA (N-methyl-D-aspartate) receptors. In the brain, the concentration of D-serine stored in cells is defined by the activity of two enzymes: serine racemase (responsible for both the synthesis and degradation) and D-amino acid oxidase (which catalyses D-serine degradation). The present review is focused on human D-amino acid oxidase, discussing the mechanisms involved in modulating enzyme activity and stability, with the aim to substantiate the pivotal role of D-amino acid oxidase in brain D-serine metabolism.
Autophagy and mammalian development
Authors: Wu Xiaoting , Won Hyeran , Rubinsztein David C.
Published: August 2015

Autophagy is a highly conserved cytoplasmic degradation pathway that has an impact on many physiological and disease states, including immunity, tumorigenesis and neurodegeneration. Recent studies suggest that autophagy may also have important functions in embryogenesis and development. Many autophagy gene-knockout mice have embryonic lethality at different stages of development. Furthermore, interactions of autophagy with crucial developmental pathways such as Wnt, Shh (Sonic Hedgehog), TGFβ (transforming growth factor β) and FGF (fibroblast growth factor) have been reported. This suggests that autophagy may regulate cell fate decisions, such as differentiation and proliferation. In the present article, we discuss how mammalian autophagy may affect phenotypes associated with development.
Spatial control of mitotic commitment in fission yeast
Authors: Hagan Iain M. , Grallert Agnes
Published: August 2015

The activation of the Cdk1 (cyclin-dependent kinase 1)–cyclin B complex to promote commitment to mitosis is controlled by the phosphorylation status of the Cdk1 catalytic subunit. Cdk1 phosphorylation by Wee1 kinases blocks activation until Cdc25 (cell division cycle 25) phosphatases remove this phosphate to drive division. Feedback inhibition of Wee1 and promotion of Cdc25 activities by the newly activated Cdk1–cyclin B complexes ensure that the transition from interphase to mitosis is a rapid and complete bi-stable switch. Although this level of molecular understanding of the mitotic commitment switch has been clear for over two decades, it is still unclear how the switch is engaged to promote division at the right time for a particular context. We discuss recent work in fission yeast that shows how the spatial organization of signalling networks, in particular events on the centrosome equivalent, the spindle pole body, plays a key role in ensuring that the timing of cell division is coupled to environmental cues.
The programme of DNA replication: beyond genome duplication
Authors: Gómez-Escoda Blanca , Wu Pei-Yun Jenny
Published: August 2015

The accurate duplication and transmission of genetic information is critical for cell growth and proliferation, and this is ensured in part by the multi-layered regulation of DNA synthesis. One of the key steps in this process is the selection and activation of the sites of replication initiation, or origins, across the genome. Interestingly, origin usage changes during development and in different pathologies, suggesting an integral interplay between the establishment of replication initiation along the chromosomes and cellular function. The present review discusses how the spatiotemporal organization of replication origin activation may play crucial roles in the control of biological events.
Role of Cdc42 dynamics in the control of fission yeast cell polarization
Authors: Das Maitreyi , Verde Fulvia
Published: August 2015

Cell polarization is fundamental to many cellular processes, including cell differentiation, cell motility and cell fate determination. A key regulatory enzyme in the control of cell morphogenesis is the conserved Rho GTPase Cdc42, which breaks symmetry via self-amplifying positive-feedback mechanisms. Additional mechanisms of control, including competition between different sites of polarized cell growth and time-delayed negative feedback, define a cellular-level system that promotes Cdc42 oscillatory dynamics and modulates activated Cdc42 intracellular distribution.
Evolutionary causes and consequences of diversified CRISPR immune profiles in natural populations
Authors: England Whitney E. , Whitaker Rachel J.
Published: August 2015

Host–pathogen co-evolution is a significant force which shapes the ecology and evolution of all types of organisms, and such interactions are driven by resistance and immunity mechanisms of the host. Diversity of resistance and immunity can affect the co-evolutionary trajectory of both host and pathogen. The microbial CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) system is one host immunity mechanism which offers a tractable model for examining the dynamics of diversity in an immune system. In the present article, we review CRISPR variation observed in a variety of natural populations, examine the forces which can push CRISPRs towards high or low diversity, and investigate the consequences of various levels of diversity on microbial populations.
Periplasmic quality control in biogenesis of outer membrane proteins
Authors: Lyu Zhi Xin , Zhao Xin Sheng
Published: August 2015

The β-barrel outer membrane proteins (OMPs) are integral membrane proteins that reside in the outer membrane of Gram-negative bacteria and perform a diverse range of biological functions. Synthesized in the cytoplasm, OMPs must be transported across the inner membrane and through the periplasmic space before they are assembled in the outer membrane. In Escherichia coli, Skp, SurA and DegP are the most prominent factors identified to guide OMPs across the periplasm and to play the role of quality control. Although extensive genetic and biochemical analyses have revealed many basic functions of these periplasmic proteins, the mechanism of their collaboration in assisting the folding and insertion of OMPs is much less understood. Recently, biophysical approaches have shed light on the identification of the intricate network. In the present review, we summarize recent advances in the characterization of these key factors, with a special emphasis on the multifunctional protein DegP. In addition, we present our proposed model on the periplasmic quality control in biogenesis of OMPs.
Probing DNA interactions with proteins using a single-molecule toolbox: inside the cell, in a test tube and in a computer
Authors: Wollman Adam J. M. , Miller Helen , Zhou Zhaokun , Leake Mark C.
Published: August 2015

DNA-interacting proteins have roles in multiple processes, many operating as molecular machines which undergo dynamic meta-stable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and the proteins that bind to it must ideally be interrogated at a single molecule level in their native in vivo environments, in a time-resolved manner, fast enough to sample the molecular transitions across the free-energy landscape. Progress has been made over the past decade in utilizing cutting-edge tools of the physical sciences to address challenging biological questions concerning the function and modes of action of several different proteins which bind to DNA. These physiologically relevant assays are technically challenging but can be complemented by powerful and often more tractable in vitro experiments which confer advantages of the chemical environment with enhanced detection signal-to-noise of molecular signatures and transition events. In the present paper, we discuss a range of techniques we have developed to monitor DNA–protein interactions in vivo, in vitro and in silico. These include bespoke single-molecule fluorescence microscopy techniques to elucidate the architecture and dynamics of the bacterial replisome and the structural maintenance of bacterial chromosomes, as well as new computational tools to extract single-molecule molecular signatures from live cells to monitor stoichiometry, spatial localization and mobility in living cells. We also discuss recent developments from our laboratory made in vitro, complementing these in vivo studies, which combine optical and magnetic tweezers to manipulate and image single molecules of DNA, with and without bound protein, in a new super-resolution fluorescence microscope.
Molecular simulation studies of hydrophobic gating in nanopores and ion channels
Authors: Trick Jemma L. , Aryal Prafulla , Tucker Stephen J. , Sansom Mark S. P.
Published: August 2015

Gating in channels and nanopores plays a key role in regulating flow of ions across membranes. Molecular simulations provide a ‘computational microscope’ which enables us to examine the physical nature of gating mechanisms at the level of the single channel molecule. Water enclosed within the confines of a nanoscale pore may exhibit unexpected behaviour. In particular, if the molecular surfaces lining the pore are hydrophobic this promotes de-wetting of the pore. De-wetting is observed as stochastic liquid–vapour transitions within a pore, and may lead to functional closure of a pore to the flow of ions and/or water. Such behaviour was first observed in simulations of simple model nanopores and referred to as ‘hydrophobic gating’. Simulations of both the nicotinic acetylcholine receptor and of TWIK-1 potassium channels (the latter alongside experimental studies) suggest hydrophobic gating may occur in some biological ion channels. Current studies are focused on designing hydrophobic gates into biomimetic nanopores.
Elevated venous thromboembolism risk in preeclampsia: molecular mechanisms and clinical impact
Authors: Egan Karl , Kevane Barry , Áinle Fionnuala Ní
Published: August 2015

Venous thromboembolism (VTE) remains a leading cause of maternal death and morbidity in the developed world. Strategies for prevention of VTE in pregnancy have been the subject of recent guidelines and consensus statements. These guidelines recommend thrombosis prevention in women who have risk factors associated with an elevated VTE risk. Preeclampsia is characterized by maternal hypertension and proteinuria developing after 20 weeks gestation, complicating up to 7% of pregnancies and is associated with a massive annual morbidity and mortality burden. Women with preeclampsia have been shown to be at increased risk of VTE with studies to date suggesting that this risk may be up to 5-fold greater than the risk of pregnancy-associated VTE in the general population. Despite the fact that preeclampsia is so common and potentially devastating, our understanding of its pathogenesis and potential therapeutic strategies remain poor. In addition, the mechanisms underlying the prothrombotic phenotype in preeclampsia are also poorly characterized although a number of potential mechanisms have been postulated. Derangements of platelet and endothelial activation and impairment of endogenous anti-coagulant pathways have been reported and may contribute to the observed VTE risk. Recently, evidence for the role of neutrophil extracellular traps (NETs) and cell-free DNA in the pathogenesis of VTE has emerged and some evidence exists to suggest that this may be of relevance in preeclampsia. Future studies aimed at understanding the diagnostic and potential therapeutic relevance of this procoagulant state are likely to be of enormous clinical benefit for pregnant women affected with this potentially devastating condition.
Interplay between cytosolic disulfide reductase systems and the Nrf2/Keap1 pathway
Authors: Schmidt Edward E.
Published: August 2015

NADPH transfers reducing power from bioenergetic pathways to thioredoxin reductase-1 (TrxR1) and glutathione reductase (GR) to support essential reductive systems. Surprisingly, it was recently shown that mouse livers lacking both TrxR1 and GR (‘TR/GR-null’) can sustain redox (reduction-oxidation) homoeostasis using a previously unrecognized NADPH-independent source of reducing power fuelled by dietary methionine. The NADPH-dependent systems are robustly redundant in liver, such that disruption of either TrxR1 or GR alone does not cause oxidative stress. However, disruption of TrxR1 induces transcription factor Nrf2 (nuclear factor erythroid-derived 2-like-2) whereas disruption of GR does not. This suggests the Nrf2 pathway responds directly to the status of the thioredoxin-1 (Trx1) system. The proximal regulator of Nrf2 is Keap1 (Kelch-like ECH-associated protein-1), a cysteine (Cys)-rich protein that normally interacts transiently with Nrf2, targeting it for degradation. During oxidative stress, this interaction is stabilized, preventing degradation of newly synthesized Nrf2, thereby allowing Nrf2 accumulation. Within the Trx1 system, TrxR1 and peroxiredoxins (Prxs) contain some of the most reactive nucleophilic residues in the cell, making them likely targets for oxidants or electrophiles. We propose that Keap1 activity and therefore Nrf2 is regulated by interactions of Trx1 system enzymes with oxidants. In TR/GR-null livers, Nrf2 activity is further induced, revealing that TrxR-independent systems also repress Nrf2 and these might be induced by more extreme challenges.
Introduction to the Special Session on Intervention and Outcomes of Children With Hearing Loss
Authors: Ching Teresa Y. C.
Published: August 2015

Purpose

This research forum article introduces the special session on “Intervention and Outcomes of Children with Hearing Loss” presented at the HEaring Across the Lifespan (HEAL) Conference in 2014.

Method

The method involved a narrative summary of the key findings of two papers presented during the session.

Results

Early intervention was effective in improving outcomes of children with significant bilateral hearing loss. Preliminary findings on children with mild or unilateral hearing loss showed communicative development on par with their normal-hearing peers.

Conclusion

Children with bilateral hearing loss benefited from early detection and intervention.
Anomalous behavior of trapping in extended dendrimers with a perfect trap
Authors: Zhang Zhongzhi , Li Huan , Yi Yuhao
Published: August 2015

Compact and extended dendrimers are two important classes of dendritic polymers. The impact of the underlying structure of compact dendrimers on dynamical processes has been much studied, yet the relation between the dynamical and structural properties of extended dendrimers remains not well understood. In this paper, we study the trapping problem in extended dendrimers with generation-dependent segment lengths, which is different from that of compact dendrimers where the length of the linear segments is fixed. We first consider a particular case that the deep trap is located at the central node, and derive an exact formula for the average trapping time (ATT) defined as the average of the source-to-trap mean first passage time over all starting points. Then, using the obtained result we deduce a closed-form expression for the ATT to an arbitrary trap node, based on which we further obtain an explicit solution to the ATT corresponding to the trapping issue with the trap uniformly distributed in the polymer systems. We show that the trap location has a substantial influence on the trapping efficiency measured by the ATT, which increases with the shortest distance from the trap to the central node, a phenomenon similar to that for compact dendrimers. In contrast to this resemblance, the leading terms of ATTs for the three trapping problems differ drastically between extended and compact dendrimers, with the trapping processes in the extended dendrimers being less efficient than in compact dendrimers.
Effects of polymer stiffness on surface tension and pressure in confinement
Authors: Milchev Andrey
Published: August 2015

We study the effect of chain rigidity on the behavior of semiflexible polymers in the vicinity of flat walls in a slit, and of surfactants at the liquid-liquid interface between immiscible liquids. Using molecular dynamics simulations, it is demonstrated that the impact of bending angle forces is particularly strong within the depletion layer at the phase boundary whereas at distance Re away from the interface, where Re is the mean distance between the ends of a semiflexible chain, the contribution of these non-local triplet interactions to pressure tensor virtually disappears. The present study also demonstrates that growing stiffness of the macromolecules leads to an increase in surface tension and total pressure.
Full self-similar solutions of the subsonic radiative heat equations
Authors: Shussman Tomer , Heizler Shay I.
Published: August 2015

We study the phenomenon of diffusive radiative heat waves (Marshak waves) under general boundary conditions. In particular, we derive full analytic solutions for the subsonic case that include both the ablation and the shock wave regions. Previous works in this regime, based on the work of R. Pakula and R. Sigel [Phys. Fluids. 28, 232 (1985)], present self-similar solutions for the ablation region alone, since, in general, the shock region and the ablation region are not self-similar together. Analytic results for both regions were obtained only for the specific case in which the ratio between the ablation front velocity and the shock velocity is constant. In this work, we derive a full analytic solution for the whole problem in general boundary conditions. Our solution is composed of two different self-similar solutions, one for each region, that are patched at the heat front. The ablative region of the heat wave is solved in a manner similar to previous works. Then, the pressure at the front, which is derived from the ablative region solution, is taken as a boundary condition to the shock region, while the other boundary is described by Hugoniot relations. The solution is compared to full numerical simulations in several representative cases. The numerical and analytic results are found to agree within 1% in the ablation region, and within 2%–5% in the shock region. This model allows better prediction of the physical behavior of radiation induced shock waves, and can be applied for high energy density physics experiments.
In situ observation the interface undercooling of freezing colloidal suspensions with differential visualization method
Authors: You Jiaxue , Wang Lilin , Wang Zhijun , Li Junjie , Wang Jincheng , Lin Xin , Huang Weidong
Published: August 2015

Interface undercooling is one of the most significant parameters in the solidification of colloidal suspensions. However, quantitative measurement of interface undercooling of colloidal suspensions is still a challenge. Here, a new experimental facility and gauging method are designed to directly reveal the interface undercooling on both static and dynamic cases. The interface undercooling is visualized through the discrepancy of solid/liquid interface positions between the suspensions and its solvent in a thermal gradient apparatus. The resolutions of the experimental facility and gauging method are proved to be 0.01 K. The high precision of the method comes from the principle of converting temperature measurement into distance measurement in the thermal gradient platform. Moreover, both static and dynamic interface undercoolings can be quantitatively measured.
On the mechanism of Zn4O-acetate precursors ripening to ZnO: How dimerization is promoted by hydroxide incorporation
Authors: Milek Theodor , Kirschbaum Rolf W. , v. Gernler Marc S. , Lübbert Christian , Segets Doris , Drewello Thomas , Peukert Wolfgang , Zahn Dirk
Published: August 2015

We report on a combined experimental and molecular modelling study on Zn4O ion clusters stabilized by acetate molecules (OAc). In particular, ab initio calculations of acetate substitution by hydroxide ions are compared with mass spectrometry data. Though quantum calculations in the gas phase indicate strong energetic preference, no experimental evidence of stable Zn4O(OAc)6−x(OH)x clusters in ethanolic solutions could be observed. This apparent contradiction is rationalized by identifying the supportive role of hydroxide ions for the association of (OAc− → OH− substituted) Zn4O(OAc)6 and Zn4O(OAc)5+ clusters. Mass spectrometry and quantum calculations hint at the stability of (Zn4O)2(OAc)12−x(OH)x dimers with x = 1, 2. Therein, the hydroxide ions establish salt-bridges that allow for the formation of additional Zn3 motifs with the OH above the triangle center—a structural motif close to that of the ZnO-crystal. The association of Zn4O(OAc)6 clusters is thus suggested to involve OAc− → OH− substitution as an activation step, quickly followed by dimerization and the subsequent agglomeration of oligomers.
Large-eddy simulation of 3-D corner separation in a linear compressor cascade
Authors: Gao Feng , Ma Wei , Zambonini Gherardo , Boudet Jérôme , Ottavy Xavier , Lu Lipeng , Shao Liang
Published: August 2015

The increase of the thrust/weight ratio of aircraft engines is extremely restricted by different 3-D flow loss mechanisms. One of them is the corner separation that can form at the junction between a blade suction side and a hub or shroud. In this paper, in order to further investigate the turbulent characteristics of corner separation, large-eddy simulation (LES) is conducted on a compressor cascade configuration using NACA65 blade profiles (chord based Reynolds number: 3.82 × 105), in comparison with the previous obtained experimental data. Using the shear-improved Smagorinsky model as subgrid-scale model, the LES gives a good description of the mean aerodynamics of the corner separation, especially for the blade surface static pressure coefficient and the total pressure losses. The turbulent dynamics is then analyzed in detail, in consideration of the turbulent structures, the one-point velocity spectra, and the turbulence anisotropy. Within the recirculation region, the energy appears to concentrate around the largest turbulent eddies, with fairly isotropic characteristics. Concerning the dynamics, an aperiodic shedding of hairpin vortices seems to induce an unsteadiness of the separation envelope.
Enhanced thermoelectric properties of phase-separating bismuth selenium telluride thin films via a two-step method
Authors: Takashiri Masayuki , Kurita Kensuke , Hagino Harutoshi , Tanaka Saburo , Miyazaki Koji
Published: August 2015

A two-step method that combines homogeneous electron beam (EB) irradiation and thermal annealing has been developed to enhance the thermoelectric properties of nanocrystalline bismuth selenium telluride thin films. The thin films, prepared using a flash evaporation method, were treated with EB irradiation in a N2 atmosphere at room temperature and an acceleration voltage of 0.17 MeV. Thermal annealing was performed under Ar/H2 (5%) at 300 °C for 60 min. X-ray diffraction was used to determine that compositional phase separation between bismuth telluride and bismuth selenium telluride developed in the thin films exposed to higher EB doses and thermal annealing. We propose that the phase separation was induced by fluctuations in the distribution of selenium atoms after EB irradiation, followed by the migration of selenium atoms to more stable sites during thermal annealing. As a result, thin film crystallinity improved and mobility was significantly enhanced. This indicates that the phase separation resulting from the two-step method enhanced, rather than disturbed, the electron transport. Both the electrical conductivity and the Seebeck coefficient were improved following the two-step method. Consequently, the power factor of thin films that underwent the two-step method was enhanced to 20 times (from 0.96 to 21.0 μW/(cm K2) that of the thin films treated with EB irradiation alone.
Stability of an elliptical vortex in a strongly coupled dusty plasma
Authors: Jana Sayanee , Banerjee Debabrata , Chakrabarti Nikhil
Published: August 2015

The stability of a long scale equilibrium vortex structure to short scale perturbations is studied in a strongly coupled dusty plasma in the framework of a generalized hydrodynamic model. It is shown that the free energy associated with the velocity shear of the vortex can drive secondary instabilities consisting of transverse shear waves when the resonance condition between the vortex rotation frequency and the secondary wave frequency is met. Such a process can transfer energy from the long scale vortex to the short scale secondary wave and thereby provide a saturation mechanism for long scale vortices in plasmas in a manner analogous to that in neutral fluids.
Radiative heat transport instability in a laser produced inhomogeneous plasma
Authors: Bychenkov V. Yu. , Rozmus W.
Published: August 2015

A laser produced high-Z plasma in which an energy balance is achieved due to radiation emission and radiative heat transfer supports ion acoustic instability. A linear dispersion relation is derived, and instability is compared to the radiation cooling instability [R. G. Evans, Plasma Phys. Controlled Fusion 27, 751 (1985)]. Under conditions of indirect drive fusion experiments, the driving term for the instability is the radiative heat flux and, in particular, the density dependence of the radiative heat conductivity. A specific example of thermal Bremsstrahlung radiation source has been considered. This instability may lead to plasma jet formation and anisotropic x-ray generation, thus affecting inertial confinement fusion related experiments.
Communication: Antibody stability and behavior on surfaces
Authors: Bush Derek B. , Knotts Thomas A.
Published: August 2015

Antibody microarrays have the potential to revolutionize molecular detection in scientific, medical, and other biosensor applications, but their current use is limited because of poor reliability. It is hypothesized that one reason for their poor performance results from strong antibody-surface interactions that destabilize the antibody structure and create steric interference for antigen recognition. Using a recently developed coarse-grain protein-surface model that has been parameterized against experimental data, antibody-surface interactions for two antibody orientations on two types of surfaces have been investigated. The results show that regardless of attachment geometry, antibodies tend to collapse onto hydrophobic surfaces and exhibit lower overall stability compared to antibodies on hydrophilic surfaces or in bulk solution. The results provide an unprecedented view into the dynamics of antibodies on surfaces and offer new insights into the poor performance exhibited by current antibody microarrays.
Counterion-only electrical double layers: An application of density functional theory
Authors: Liu Longcheng
Published: August 2015

Within the framework of density functional theory, a self-consistent approach of weighted correlation approximation is developed to give an accurate account of the cross correlations between the Coulombic interaction and the hard-sphere exclusion in the counterion-only electrical double layers. Application of the approach to the cases of practical interest, against the Monte Carlo simulations, shows that it is excellent in describing the structural properties and the pressures of the confined solutions involving both mono- and divalent counterions between two planar charged walls. In particular, the study suggests that the relative importance of electrostatic correlations in comparison to the effects of ionic excluded volume and direct Coulomb interactions depends on the valency of the counterions and the surface charge density. In a clay system with mixed counterions, the competition between the mono- and divalent ions results in a large swelling when the fraction of surface charge compensated by monovalent counterions is greater than 30%. In the opposite situation involving mostly divalent counterions, a limited swelling is found and the attraction between the clay particles favors the formation of stacks incorporating a water layer of about 1.0 nm. These findings are consistent with experimental observations, giving insight into some mechanisms governing the stability of colloidal clay in salt-free or dilute solutions.
Anaerobic microorganisms and bioremediation of organohalide pollution
Authors: Lee Matthew , Marquis Chris , Judger Bat-Erdene , Manefield Mike
Published: August 2015

Organohalide pollution of subsurface environments is ubiquitous across all industrialised countries. Fortunately, strictly anaerobic microorganisms exist that have evolved using naturally occurring organohalides as their terminal electron acceptor. These unusual organisms are now being utilised to clean anthropogenic organohalide pollution.
Performance of GPS collars on free-ranging bison (Bison bison) in north-western Canada
Authors: Jung Thomas S. , Kuba Kazuhisa
Published: August 2015

Context Global positioning system (GPS) collars are increasingly used to study animal ecology. However, understanding their real-world performance is important so that biases in data collection can be addressed. These biases may be species specific. Few studies have examined the influence of sex or temporal variation on locational fix success rates (FSR), and none has assessed GPS-collar performance on bison (Bison bison). Aims To test for sex- and temporal-based biases on the performance of GPS collars on free-ranging bison. Methods Data from 59 deployments of 37 GPS collars on 27 female and seven male bison was used to test for temporal variation and differences between sexes on collar-deployment success rates and four fix acquisition metrics. Key results Most (72.9%) of the 55 GPS collars retrieved malfunctioned before reaching their expected deployment schedule (2 years). We observed a significant difference in the performance of GPS collars deployed on male and females, with those on females functioning almost three times longer. All four fix metrics differed between sexes, with males having significantly better metrics. For females, nightly fix metrics were better than the daytime ones, whereas for males, there was no difference. We observed a significant difference in fix metrics between seasons for females, but not males. Conclusions Although the data from GPS collars may be useful in understanding animal ecology, understanding associated biases can aid in the design of field studies using, and the interpretation of results stemming from, GPS collars. Temporal variation in our study was apparent for females, but not males, and likely related to differences in habitat use and movements. Overall, sex had a significant influence on the success of GPS-collar deployments on bison, and should be examined for other species as well. Implications Bison damage to the collars was the main reason for collar failures. Researchers should plan for catastrophic failures and malfunctions when deploying GPS collars on bison, particularly adult males. Significant differences observed between daily and seasonal FSR for females were small (≤4.9%), and do not warrant post hoc treatment before analyses.
Elasticity, friction, and pathway of γ-subunit rotation in F
o
F
1
-ATP synthase
Authors: Okazaki Kei-ichi , Hummer Gerhard
Published: August 2015

Significance

F
o
F
1
-ATP synthase produces the ATP essential for cellular functions from bacteria to humans. Rotation of its central γ-subunit couples proton translocation in the membrane-embedded F
o
motor to ATP synthesis in the catalytic F
1
motor. To explain its high efficiency, determine its top speed, and characterize its mechanism, we construct a viscoelastic model of the F
1
rotary motor from molecular dynamics simulation trajectories. We find that the γ-subunit is just flexible enough to compensate for the incommensurate eightfold and threefold rotational symmetries of mammalian F
o
and F
1
motors, respectively. The resulting energetic constraints dictate a unique pathway for the coupled rotations of the F
o
and F
1
rotary motors, and explain the fine stepping seen in single-molecule experiments.
Experimental evidence that short-range intermolecular aggregation is sufficient for efficient charge transport in conjugated polymers
Authors: Wang Suhao , Fabiano Simone , Himmelberger Scott , Puzinas Skomantas , Crispin Xavier , Salleo Alberto , Berggren Magnus
Published: August 2015

Significance

Understanding the nature of charge transport and its limitations has guided the rational design of organic semiconductors. Research has mainly focused on increasing the crystallinity of conjugated polymers as a strategy to improve the long-range charge transport properties. Here, we demonstrate that local aggregation over very few chains is a sufficient mesoscopic structure to ensure high mobility, with charge transport mainly occurring along the polymer backbones, and that extended crystallinity is not necessary. These results provide an explanation for the high mobilities observed in seemingly disordered polymers and set molecular-design guidelines for next-generation conjugated polymers.
MeCP2 regulates the timing of critical period plasticity that shapes functional connectivity in primary visual cortex
Authors: Krishnan Keerthi , Wang Bor-Shuen , Lu Jiangteng , Wang Lang , Maffei Arianna , Cang Jianhua , Huang Z. Josh
Published: August 2015

Significance

Rett syndrome is a neurodevelopmental disorder caused by mutations in methyl-CpG-binding protein 2 (
MeCP2
). It is thought to result from altered neuronal connectivity and/or plasticity, possibly through abnormal experience-dependent synapse development, but the underlying mechanisms remain obscure. Using
MeCP2
-null mice, we examined experience-dependent development of neural circuits in the primary visual cortex where GABAergic interneurons regulate a critical period of neural plasticity. We provide evidence that a precocious maturation of parvalbumin
+
GABAergic interneurons correlates with the altered timing of the critical period and deficient visual function in the absence of MECP2. Our study begins to establish a link from specific molecular changes in GABAergic neurons to critical period of circuit development and to functional alterations in a mouse model of Rett syndrome.
Production diversity and dietary diversity in smallholder farm households
Authors: Sibhatu Kibrom T. , Krishna Vijesh V. , Qaim Matin
Published: August 2015

Significance

Given that hunger and malnutrition are still widespread problems in many developing countries, the question of how to make agriculture and food systems more nutrition-sensitive is of high relevance for research and policy. Many of the undernourished people in Africa and Asia are small-scale subsistence farmers. Diversifying production on these farms is often perceived as a promising strategy to improve dietary quality and diversity. This hypothesis is tested with data from smallholder farm households in Indonesia, Kenya, Ethiopia, and Malawi. Higher farm production diversity significantly contributes to dietary diversity in some situations, but not in all. Improving small farmers’ access to markets seems to be a more effective strategy to improve nutrition than promoting production diversity on subsistence farms.
Correlating steric hydration forces with water dynamics through surface force and diffusion NMR measurements in a lipid–DMSO–H
2
O system
Authors: Schrader Alex M. , Donaldson Stephen H. , Song Jinsuk , Cheng Chi-Yuan , Lee Dong Woog , Han Songi , Israelachvili Jacob N.
Published: August 2015

Significance

We use the common biological additive DMSO to show quantitatively the impact that surface-bound water has on interactions between lipid bilayers, the membranes that separate the interior of cells from the surroundings. We present a number of metrics to gauge the hydration of the bilayer surfaces and show how the metrics are affected by the concentration of DMSO in the solvent. This work further connects measurements of surface forces, surface structure and dynamics, and surface water diffusion with significant and broad implications for soft matter systems.
Biologically active LIL proteins built with minimal chemical diversity
Authors: Heim Erin N. , Marston Jez L. , Federman Ross S. , Edwards Anne P. B. , Karabadzhak Alexander G. , Petti Lisa M. , Engelman Donald M. , DiMaio Daniel
Published: August 2015

Significance

Most proteins are long polymers of amino acids with 20 or more chemically distinct side-chains, whereas transmembrane domains are short membrane-spanning protein segments with mainly hydrophobic amino acids. Here, we have defined the minimal chemical diversity sufficient for a protein to display specific biological activity by isolating artificial 26-aa-long transmembrane proteins consisting of random sequences of only two hydrophobic amino acids, leucine and isoleucine. A small fraction of proteins with this composition interact with the transmembrane domain of a growth factor receptor to specifically activate the receptor, resulting in growth transformation. These findings change our view of what can constitute an active protein and have important implications for protein evolution, protein engineering, and synthetic biology.
The effect of nitrate supplementation on muscle contraction in healthy adults
Authors: Hoon Matthew W. , Fornusek Ché , Chapman Phillip G. , Johnson Nathan A.
Published: August 2015

This study examined the effect of dietary supplementation with inorganic nitrate () on markers of contractile function in human knee extensors. In a double‐blinded, randomized cross‐over design, 18 (12 M) healthy participants undertook four days of supplementation with either nitrate‐rich beetroot juice (NITRATE; days 1–3: 525 mg , day 4: 1050 mg ) or nitrate‐depleted beetroot juice (PLACEBO). On the fourth day, isometric knee extension force was assessed during a series of voluntary and electrically evoked (stimulation) tests. In addition, muscular fatigue was examined in two separate continuous‐stimulation (0.8 s tetanus with a 1:1 work:rest ratio for 102.4 s) fatigue tests, one with and one without blood flow restriction. There were no differences for maximum voluntary contraction, peak twitch force, half‐relaxation time and the force–frequency relationship for stimulations up to 100 Hz between the NITRATE and PLACEBO trials. No differences between trials were observed in the non‐restricted fatigue test, however NITRATE was found to attenuate the decline in force during the restricted test, such that the force at the 80 s mark (PLACEBO: 66 ± 11 vs. NITRATE 74 ± 9% of initial force; P = .01) and 102 s mark (PLACEBO: 47 ± 8% vs. NITRATE 55 ± 8%; P < .01) were significantly higher. These results suggest that four days of supplementation elicits peripheral responses in muscle that attenuate muscular fatigue during exhaustive exercise under hypovolemic conditions. This ergogenic action is likely attributable to improved Ca2+ handling in the muscle, or enhanced perfusion during ischemia.
Non-muscle myosin IIB is critical for nuclear translocation during 3D invasion
Authors: Thomas Dustin G. , Yenepalli Aishwarya , Denais Celine Marie , Rape Andrew , Beach Jordan R. , Wang Yu-li , Schiemann William P. , Baskaran Harihara , Lammerding Jan , Egelhoff Thomas T.
Published: August 2015

Non-muscle myosin II (NMII) is reported to play multiple roles during cell migration and invasion. However, the exact biophysical roles of different NMII isoforms during these processes remain poorly understood. We analyzed the contributions of NMIIA and NMIIB in three-dimensional (3D) migration and in generating the forces required for efficient invasion by mammary gland carcinoma cells. Using traction force microscopy and microfluidic invasion devices, we demonstrated that NMIIA is critical for generating force during active protrusion, and NMIIB plays a major role in applying force on the nucleus to facilitate nuclear translocation through tight spaces. We further demonstrate that the nuclear membrane protein nesprin-2 is a possible linker coupling NMIIB-based force generation to nuclear translocation. Together, these data reveal a central biophysical role for NMIIB in nuclear translocation during 3D invasive migration, a result with relevance not only to cancer metastasis but for 3D migration in other settings such as embryonic cell migration and wound healing.
Exchanging Land for Solidarity: Solidarity Transfers among Voluntarily Resettled and Non‐resettled Land‐Reform Beneficiaries
Authors: Gobien Simone , Vollan Björn
Published: August 2015

Mutual aid among villagers in developing countries is often the only means of insuring against economic shocks. We use “lab‐in‐the‐field experiments” in Cambodian villages to study solidarity in established and newly resettled communities. Our experimental participants were part of an agricultural land‐distribution project for which they signed up voluntarily. Half of our sample voluntarily resettled one and a half years before this study. Playing a version of the “solidarity game,” we identify the effect of voluntary resettlement on willingness to help anonymous fellow villagers. We find that resettled farmers transfer substantially less money to their fellow villagers than farmers who have not resettled. Our experimental results indicate greater vulnerability on the part of resettled households in the initial years after resettlement.