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https://www.readbyqxmd.com/read/27926846/alamethicin-supramolecular-organization-in-lipid-membranes-from-19-f-solid-state-nmr
#1
Evgeniy S Salnikov, Jesus Raya, Marta De Zotti, Ekaterina Zaitseva, Cristina Peggion, Gema Ballano, Claudio Toniolo, Jan Raap, Burkhard Bechinger
Alamethicins (ALMs) are antimicrobial peptides of fungal origin. Their sequences are rich in hydrophobic amino acids and strongly interact with lipid membranes, where they cause a well-defined increase in conductivity. Therefore, the peptides are thought to form transmembrane helical bundles in which the more hydrophilic residues line a water-filled pore. Whereas the peptide has been well characterized in terms of secondary structure, membrane topology, and interactions, much fewer data are available regarding the quaternary arrangement of the helices within lipid bilayers...
December 6, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27925796/a-severe-asthma-disease-signature-from-gene-expression-profiling-of-peripheral-blood-from-u-biopred-cohorts
#2
Jeannette Bigler, Michael Boedigheimer, James P R Schofield, Paul J Skipp, Julie Corfield, Anthony Rowe, Ana R Sousa, Martin Timour, Lori Twehues, Xuguang Hu, Graham Roberts, Andrew A Welcher, Wen Yu, Kian F Chung, Ian M Adcock, Peter J Sterk, Ratko Djukanović
RATIONALE: Stratification of asthma at the molecular level, especially using accessible biospecimens, could greatly enable patient selection for targeted therapy. OBJECTIVES: To determine the value of blood to identify transcriptional differences between clinically defined asthmatic and non-asthmatic groups, identify potential patient subgroups based on gene expression, and explore biological pathways associated with identified differences. METHODS: Transcriptomics profiles were generated by microarray analysis of blood from 610 asthmatic and control participants in U-BIOPRED...
December 7, 2016: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/27925756/temperature-effects-in-the-band-structure-of-topological-insulators
#3
Bartomeu Monserrat, David Vanderbilt
We study the effects of temperature on the band structure of the Bi_{2}Se_{3} family of topological insulators using first-principles methods. Increasing temperature drives these materials towards the normal state, with similar contributions from thermal expansion and from electron-phonon coupling. The band gap changes with temperature reach 0.3 eV at 600 K, of similar size to the changes caused by electron correlation. Our results suggest that temperature-induced topological phase transitions should be observable near critical points of other external parameters...
November 25, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27925749/persistent-skyrmion-lattice-of-noninteracting-electrons-with-spin-orbit-coupling
#4
Jiyong Fu, Poliana H Penteado, Marco O Hachiya, Daniel Loss, J Carlos Egues
A persistent spin helix (PSH) is a robust helical spin-density pattern arising in disordered 2D electron gases with Rashba α and Dresselhaus β spin-orbit (SO) tuned couplings, i.e., α=±β. Here, we investigate the emergence of a persistent Skyrmion lattice (PSL) resulting from the coherent superposition of PSHs along orthogonal directions-crossed PSHs-in wells with two occupied subbands ν=1, 2. For realistic GaAs wells, we show that the Rashba α_{ν} and Dresselhaus β_{ν} couplings can be simultaneously tuned to equal strengths but opposite signs, e...
November 25, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27925739/static-einstein-maxwell-black-holes-with-no-spatial-isometries-in-ads-space
#5
Carlos A R Herdeiro, Eugen Radu
We explicitly construct static black hole solutions to the fully nonlinear, D=4, Einstein-Maxwell-anti-de Sitter (AdS) equations that have no continuous spatial symmetries. These black holes have a smooth, topologically spherical horizon (section), but without isometries, and approach, asymptotically, global AdS spacetime. They are interpreted as bound states of a horizon with the Einstein-Maxwell-AdS solitons recently discovered, for appropriate boundary data. In sharp contrast to the uniqueness results for a Minkowski electrovacuum, the existence of these black holes shows that single, equilibrium, black hole solutions in an AdS electrovacuum admit an arbitrary multipole structure...
November 25, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27925728/traveling-majorana-solitons-in-a-low-dimensional-spin-orbit-coupled-fermi-superfluid
#6
Peng Zou, Joachim Brand, Xia-Ji Liu, Hui Hu
We investigate traveling solitons of a one- or two-dimensional spin-orbit-coupled Fermi superfluid in both topologically trivial and nontrivial regimes by solving the static and time-dependent Bogoliubov-de Gennes equations. We find a critical velocity v_{h} for traveling solitons that is much smaller than the value predicted using the Landau criterion due to spin-orbit coupling. Above v_{h}, our time-dependent simulations in harmonic traps indicate that traveling solitons decay by radiating sound waves. In the topological phase, we predict the existence of peculiar Majorana solitons, which host two Majorana fermions and feature a phase jump of π across the soliton, irrespective of the velocity of travel...
November 25, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27925726/acoustic-type-ii-weyl-nodes-from-stacking-dimerized-chains
#7
Zhaoju Yang, Baile Zhang
Lorentz-violating type-II Weyl fermions, which were missed in Weyl's prediction of nowadays classified type-I Weyl fermions in quantum field theory, have recently been proposed in condensed matter systems. The semimetals hosting type-II Weyl fermions offer a rare platform for realizing many exotic physical phenomena that are different from type-I Weyl systems. Here we construct the acoustic version of a type-II Weyl Hamiltonian by stacking one-dimensional dimerized chains of acoustic resonators. This acoustic type-II Weyl system exhibits distinct features in a finite density of states and unique transport properties of Fermi-arc-like surface states...
November 25, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27925722/realization-of-the-haldane-kane-mele-model-in-a-system-of-localized-spins
#8
Se Kwon Kim, Héctor Ochoa, Ricardo Zarzuela, Yaroslav Tserkovnyak
We study a spin Hamiltonian for spin-orbit-coupled ferromagnets on the honeycomb lattice. At sufficiently low temperatures supporting the ordered phase, the effective Hamiltonian for magnons, the quanta of spin-wave excitations, is shown to be equivalent to the Haldane model for electrons, which indicates the nontrivial topology of the band and the existence of the associated edge state. At high temperatures comparable to the ferromagnetic-exchange strength, we take the Schwinger-boson representation of spins, in which the mean-field spinon band forms a bosonic counterpart of the Kane-Mele model...
November 25, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27925719/synthetic-dimensions-and-spin-orbit-coupling-with-an-optical-clock-transition
#9
L F Livi, G Cappellini, M Diem, L Franchi, C Clivati, M Frittelli, F Levi, D Calonico, J Catani, M Inguscio, L Fallani
We demonstrate a novel way of synthesizing spin-orbit interactions in ultracold quantum gases, based on a single-photon optical clock transition coupling two long-lived electronic states of two-electron ^{173}Yb atoms. By mapping the electronic states onto effective sites along a synthetic "electronic" dimension, we have engineered fermionic ladders with synthetic magnetic flux in an experimental configuration that has allowed us to achieve uniform fluxes on a lattice with minimal requirements and unprecedented tunability...
November 25, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27925584/topological-analysis-and-gaussian-decision-tree-effective-representation-and-classification-of-biosignals-of-small-sample-size
#10
Zhifei Zhang, Yang Song, Haochen Cui, Jayne Wu, Fernando Schwartz, Hairong Qi
GOAL: Bucking the trend of big data, in microdevice engineering, small sample size is common, especially when the device is still at the proof-of-concept stage. The small sample size, small inter-class variation, and large intra-class variation, have brought biosignal analysis new challenges. Novel representation and classification approaches need to be developed to effectively recognize targets of interests with the absence of a large training set. METHODS: Moving away from the traditional signal analysis in the spatiotemporal domain, we exploit the biosignal representation in the topological domain that would reveal the intrinsic structure of point clouds generated from the biosignal...
December 2, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/27925323/synthesis-binding-properties-and-differences-on-cell-uptake-of-g-quadruplex-ligands-based-on-carbohydrate-naphthalene-diimide-conjugates
#11
Matilde Arevalo, Filippo Doria, Efres Belmonte-Reche, Aurore De Rache, Jenny Campos-Salinas, Ricardo Lucas, Eva Falomir, Miguel Carda, Jose María Pérez-Victoria, Jean-Louis Mergny, Mauro Freccero, Juan Carlos Morales
G-quadruplex (G4) are currently being explored as therapeutic targets in cancer and other pathologies. We have synthesized six carbohydrate naphthalene diimide conjugates (carb-NDIs) as G4 ligands to investigate their potential selectivity on G4 binding and on cell penetration. Carb-NDIs have shown certain selectivity for G4 structures against DNA duplexes but the different sugar moieties did not induce a preference for a specific G4 topology. Interestingly, when monosaccharides were attached through a short ethylene linker to the NDI scaffold their cellular uptake was 2-3 fold more efficient than when the sugar was directly attached through its anomeric position...
December 7, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27924954/eeg-functional-network-topology-is-associated-with-disability-in-patients-with-amyotrophic-lateral-sclerosis
#12
Matteo Fraschini, Matteo Demuru, Arjan Hillebrand, Lorenza Cuccu, Silvia Porcu, Francesca Di Stefano, Monica Puligheddu, Gianluca Floris, Giuseppe Borghero, Francesco Marrosu
Amyotrophic Lateral Sclerosis (ALS) is one of the most severe neurodegenerative diseases, which is known to affect upper and lower motor neurons. In contrast to the classical tenet that ALS represents the outcome of extensive and progressive impairment of a fixed set of motor connections, recent neuroimaging findings suggest that the disease spreads along vast non-motor connections. Here, we hypothesised that functional network topology is perturbed in ALS, and that this reorganization is associated with disability...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924812/interstitial-oxygen-as-a-source-of-p-type-conductivity-in-hexagonal-manganites
#13
Sandra H Skjærvø, Espen T Wefring, Silje K Nesdal, Nikolai H Gaukås, Gerhard H Olsen, Julia Glaum, Thomas Tybell, Sverre M Selbach
Hexagonal manganites, h-RMnO3 (R=Sc, Y, Ho-Lu), have been intensively studied for their multiferroic properties, magnetoelectric coupling, topological defects and electrically conducting domain walls. Although point defects strongly affect the conductivity of transition metal oxides, the defect chemistry of h-RMnO3 has received little attention. We use a combination of experiments and first principles electronic structure calculations to elucidate the effect of interstitial oxygen anions, Oi, on the electrical and structural properties of h-YMnO3...
December 7, 2016: Nature Communications
https://www.readbyqxmd.com/read/27924325/lirb2lab2o6-a-new-rare-earth-borate-with-a-mof-5-like-topological-structure-and-a-short-uv-cut-off-edge
#14
Dongdong Xu, Fangfang Zhang, Yanzhou Sun, Zhihua Yang, Binghua Lei, Lili Liu, Shilie Pan
A new rare-earth borate LiRb2LaB2O6 (LB-1) has been synthesized using a high-temperature solution method. Interestingly, it shares its topological structure with the famous porous material MOF-5, which is formed from Zn4O(BDC)3 (BDC = 1,4-benzenedicarboxylate). The nodes [OZn4] and organic linkers [BDC] of MOF-5 are carefully substituted with La(3+) rare-earth cations and the inorganic linkers [BO3] and [LiO4], respectively, in order to construct a pure inorganic open framework. LB-1 exhibits good thermal and water stability...
December 7, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/27924190/network-analysis-of-human-post-mortem-microarrays-reveals-novel-genes-micrornas-and-mechanistic-scenarios-of-potential-importance-in-fighting-huntington-s-disease
#15
Sreedevi Chandrasekaran, Danail Bonchev
Huntington's disease is a progressive neurodegenerative disorder characterized by motor disturbances, cognitive decline, and neuropsychiatric symptoms. In this study, we utilized network-based analysis in an attempt to explore and understand the underlying molecular mechanism and to identify critical molecular players of this disease condition. Using human post-mortem microarrays from three brain regions (cerebellum, frontal cortex and caudate nucleus) we selected in a four-step procedure a seed set of highly modulated genes...
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27924036/folding-and-misfolding-pathways-of-g-quadruplex-dna
#16
Adrien Marchand, Valérie Gabelica
G-quadruplexes adopt various folding topologies, but information on their folding pathways remains scarce. Here, we used electrospray mass spectrometry to detect and quantify the specifically bound potassium ions, and circular dichroism to characterize the stacking topology of each ensemble. For human telomeric (hTel) sequences containing the d((GGGTTA)3GGG) core, K(+) binding affinity and cooperativity strongly depends on the chosen construct. The shortest sequences bind only one K(+) at low KCl concentration, and this 2-quartet G-quadruplex is antiparallel...
October 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923713/when-transcription-goes-on-holliday-double-holliday-junctions-block-rna-polymerase-ii-transcription-in-vitro
#17
Anne Pipathsouk, Boris P Belotserkovskii, Philip C Hanawalt
Non-canonical DNA structures can obstruct transcription. This transcription blockage could have various biological consequences, including genomic instability and gratuitous transcription-coupled repair. Among potential structures causing transcription blockage are Holliday junctions (HJ), which can be generated as intermediates in homologous recombination or during processing of stalled replication forks. Of particular interest is the double Holliday junction (DHJ), which contains two HJs. Topological considerations impose the constraint that the total number of helical turns in the DNA duplexes between the junctions cannot be altered as long as the flanking DNA duplexes are intact...
December 3, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27923179/structural-dynamics-of-casein-kinase-i-cki-from-malarial-parasite-plasmodium-falciparum-isolate-3d7-insights-from-theoretical-modelling-and-molecular-simulations
#18
Budheswar Dehury, Santosh Kumar Behera, Namita Mahapatra
The protein kinases (PKs), belonging to serine/threonine kinase (STKs), are important drug targets for a wide spectrum of diseases in human. Among protein kinases, the Casein Kinases (CKs) are vastly expanded in various organisms, where, the malarial parasite Plasmodium falciparum possesses a single member i.e., PfCKI, which can phosphorylate various proteins in parasite extracts in vitro condition. But, the structure-function relationship of PfCKI and dynamics of ATP binding is yet to be understood. Henceforth, an attempt was made to study the dynamics, stability, and ATP binding mechanisms of PfCKI through computational modelling, docking, molecular dynamics (MD) simulations, and MM/PBSA binding free energy estimation...
November 21, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27923117/examining-topological-domain-influence-on-enhancer-function
#19
Robert A Beagrie, Ana Pombo
Enhancers regulate the expression of target genes across large genomic distances, but it is unclear how recently discovered topological domains affect this regulation. Reporting in this issue of Developmental Cell, Symmons et al. (2016) show that the endogenous Shh topological domain promotes functional interactions between Shh and its remote enhancer.
December 5, 2016: Developmental Cell
https://www.readbyqxmd.com/read/27923064/sparse-regression-based-structure-learning-of-stochastic-reaction-networks-from-single-cell-snapshot-time-series
#20
Anna Klimovskaia, Stefan Ganscha, Manfred Claassen
Stochastic chemical reaction networks constitute a model class to quantitatively describe dynamics and cell-to-cell variability in biological systems. The topology of these networks typically is only partially characterized due to experimental limitations. Current approaches for refining network topology are based on the explicit enumeration of alternative topologies and are therefore restricted to small problem instances with almost complete knowledge. We propose the reactionet lasso, a computational procedure that derives a stepwise sparse regression approach on the basis of the Chemical Master Equation, enabling large-scale structure learning for reaction networks by implicitly accounting for billions of topology variants...
December 2016: PLoS Computational Biology
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