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Xue Han, Jianxun Qi, Hao Song, Qihui Wang, Yanfang Zhang, Ying Wu, Guangwen Lu, Kwok-Yung Yuen, Yi Shi, George F Gao
Accumulating evidence indicates that MERS-CoV originated from bat coronaviruses (BatCoVs). Previously, we demonstrated that both MERS-CoV and BatCoV HKU4 use CD26 as a receptor, but how the BatCoVs evolved to bind CD26 is an intriguing question. Here, we solved the crystal structure of the S1 subunit C-terminal domain of HKU5 (HKU5-CTD), another BatCoV that is phylogenetically related to MERS-CoV but cannot bind to CD26. We observed that the conserved core subdomain and those of other betacoronaviruses (betaCoVs) have a similar topology of the external subdomain, indicating the same ancestor of lineage C betaCoVs...
April 19, 2017: Virology
Brendan Francis Abrahams, David Dharma, Paul Stephen Donnelly, Timothy Adam Hudson, Cameron J Kepert, Richard Robson, Peter D Southon, Keith Forrest White
The uptake of inhalation anesthetics by three topologically identical frameworks is described. The 3D network materials, which possess square channels of different dimensions, are formed from the relatively simple combination of Zn(II) centres and dianionic ligands that contain a phenolate and a carboxylate group at opposite ends. All three framework materials are able to adsorb N2O, Xe and isoflurane. Whilst the framework with the widest channels is able to adsorb large quantities of the various guests from the gas phase, the frameworks with the narrower channels have superior binding enthalpies and exhibit higher levels of retention...
April 22, 2017: Chemistry: a European Journal
Harish Shukla, Rohit Shukla, Amit Sonkar, Tripti Pandey, Timir Tripathi
Isocitrate lyase (ICL), a potential anti-tubercular drug target, catalyzes the first step of the glyoxylate shunt. In the present investigation, we studied the conformational flexibility of MtbICL to better understand its stability and catalytic activity. Our biochemical results showed that a point mutation at Phe345, which is topologically distant (>10 Å) to the active site signature sequence ((189)KKCGH(193)), completely abolishes the activity of the enzyme. In depth computational analyses were carried out for understanding the structural alterations using molecular dynamics, time-dependent secondary structure and principal component analysis...
April 21, 2017: Scientific Reports
Haixia Chen, Li He, Hairong Huang, Chengmin Shi, Xumin Ni, Guangming Dai, Liang Ma, Weimin Li
Mycobacterium tuberculosis (M. tuberculosis) genotyping has dramatically improved the understanding of the epidemiology of tuberculosis (TB). In this study, 187 M. tuberculosis isolates from Xinjiang Uygur Autonomous Region (Xinjiang) and Gansu province in China were genotyped using large sequence polymorphisms (LSPs) and variable number tandem repeats (VNTR). Ten isolates, which represent major nodes of VNTR-based minimum spanning tree, were selected and subsequently subjected to multi-locus sequence analyses (MLSA) that include 82 genes...
April 21, 2017: Scientific Reports
Guang-Hao Shao, Shao-Cheng Yan, Wei Luo, Guo-Wei Lu, Yan-Qing Lu
We propose and numerically demonstrate a conversion and multicasting scheme of orbital angular momentum (OAM) states by using N-core supermode fiber (NCSF), where the topological charges of converted OAM states mainly depend on the injected OAM state and the number of fiber cores. The conversion efficiency (CE) of the converted OAM states could be optimized by properly designing the fiber structure. Take N = 6 as an example, ~37% CE could be achieved at telecom bands. Moreover, even for a fabricated NCSF, the CE could be dynamically changed by stretching the fiber or by adjusting the refractive index of the fiber cores through external control of the environmental conditions...
April 21, 2017: Scientific Reports
Detlef Vullhorst, Tanveer Ahmad, Irina Karavanova, Carolyn Keating, Andres Buonanno
The Neuregulin (NRG) family of ErbB ligands is comprised of numerous variants originating from the use of different genes, alternative promoters and splice variants. NRGs have generally been thought to be transported to axons and presynaptic terminals where they signal via ErbB3/4 receptors in paracrine or juxtacrine mode. However, we recently demonstrated that unprocessed pro-NRG2 accumulates on cell bodies and proximal dendrites, and that NMDAR activity is required for shedding of its ectodomain by metalloproteinases...
April 21, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
Heidi Vitrac, William Dowhan, Mikhail Bogdanov
The final topology of membrane proteins is thought to be dictated primarily by the encoding sequence. However, according to the Charge Balance Rule the topogenic signals within nascent membrane proteins are interpreted in agreement with the Positive Inside Rule as influenced by the protein phospholipid environment. The role of long-range protein-lipid interactions in establishing a final uniform or dual topology is unknown. In order to address this role, we determined the positional dependence of the potency of charged residues as topological signals within Escherichia coli sucrose permease (CscB) in cells in which the zwitterionic phospholipid phosphatidylethanolamine (PE), acting as topological determinant, was either eliminated or tightly titrated...
April 18, 2017: Biochimica et Biophysica Acta
Ayse Julius, Lisa Laur, Christoph Schanzenbach, Dieter Langosch
Parallel and antiparallel transmembrane helix-helix interactions support the folding and non-covalent assembly of many integral membrane proteins. While several genetic tools are currently in use to study parallel transmembrane helix-helix interactions, antiparallel associations have been difficult to determine. Here, we present a novel genetic approach, termed BLaTM 2.0, which can be used in combination with the recently presented BLaTM 1.2 to compare the efficiency of antiparallel and parallel TMD interactions in a natural membrane...
April 18, 2017: Journal of Molecular Biology
Lefteris Koumakis, Panos Roussos, George Potamias
Minepath ( is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles...
April 20, 2017: Nucleic Acids Research
Gilles Didier, Marine Fau, Michel Laurin
Since the diversification process cannot be directly observed at the human scale, it has to be studied from the information available, namely the extant taxa and the fossil record. In this sense, phylogenetic trees including both extant taxa and fossils are the most complete representations of the diversification process that one can get. Such phylogenetic trees can be reconstructed from molecular and morphological data, to some extent. Among the temporal information of such phylogenetic trees, fossil ages are by far the most precisely known (divergence times are inferences calibrated mostly with fossils)...
April 18, 2017: Systematic Biology
Huw A Ogilvie, Remco R Bouckaert, Alexei J Drummond
Fully Bayesian multispecies coalescent (MSC) methods like *BEAST estimate species trees from multiple sequence alignments. Today thousands of genes can be sequenced for a given study, but using that many genes with *BEAST is intractably slow. An alternative is to use heuristic methods which compromise accuracy or completeness in return for speed. A common heuristic is concatenation, which assumes that the evolutionary history of each gene tree is identical to the species tree. This is an inconsistent estimator of species tree topology, a worse estimator of divergence times, and induces spurious substitution rate variation when incomplete lineage sorting is present...
April 14, 2017: Molecular Biology and Evolution
Nansu Zong, Hyeoneui Kim, Victoria Ngo, Olivier Harismendy
Motivation: A heterogeneous network topology possessing abundant interactions between biomedical entities has yet to be utilized in similarity-based methods for predicting drug-target associations based on the array of varying features of drugs and their targets. Deep learning reveals features of vertices of a large network that can be adapted in accommodating the similarity-based solutions to provide a flexible method of drug-target prediction. Results: We propose a similarity-based drug-target prediction method that enhances existing association discovery methods by using a topology-based similarity measure...
April 18, 2017: Bioinformatics
Maren Schmiester, Ilja Demuth
hSNM1B/Apollo is a member of the highly conserved β-CASP subgroup within the MBL superfamily of proteins. It interacts with several DNA repair proteins and functions within the Fanconi anemia pathway in response to DNA interstrand crosslinks. As a shelterin accessory protein, hSNM1B/Apollo is also vital for the generation and maintenance of telomeric overhangs. In this review, we will summarize studies on hSNM1B/Apollo's function, including its contribution to DNA damage signaling, replication fork maintenance, control of topological stress and telomere protection...
April 5, 2017: Oncotarget
Shaobo Cheng, Jun Li, Myung-Geun Han, Shiqing Deng, Guotai Tan, Xixiang Zhang, Jing Zhu, Yimei Zhu
We report structural transformation of sixfold vortex domains into two-, four-, and eightfold vortices via a different type of topological defect in hexagonal manganites. Combining high-resolution electron microscopy and Landau-theory-based numerical simulations, we investigate the remarkable atomic arrangement and the intertwined relationship between the vortex structures and the topological defects. The roles of their displacement field, formation temperature, and nucleation sites are revealed. All conceivable vortices in the system are topologically classified using homotopy group theory, and their origins are identified...
April 7, 2017: Physical Review Letters
Fengcheng Wu, Timothy Lovorn, A H MacDonald
Moiré patterns are common in van der Waals heterostructures and can be used to apply periodic potentials to elementary excitations. We show that the optical absorption spectrum of transition metal dichalcogenide bilayers is profoundly altered by long period moiré patterns that introduce twist-angle dependent satellite excitonic peaks. Topological exciton bands with nonzero Chern numbers that support chiral excitonic edge states can be engineered by combining three ingredients: (i) the valley Berry phase induced by electron-hole exchange interactions, (ii) the moiré potential, and (iii) the valley Zeeman field...
April 7, 2017: Physical Review Letters
Tsuneya Yoshida, Akito Daido, Youichi Yanase, Norio Kawakami
In this paper, we propose CeCoIn_{5}/YbCoIn_{5} superlattice systems as a test bed for the reduction of topological classification in free fermions. We find that the system with a quadlayer of CeCoIn_{5} shows a topological crystalline superconducting phase with the mirror Chern number eight at the noninteracting level. Furthermore, we demonstrate that in the presence of two-body interactions, gapless edge modes are no longer protected by the symmetry in the system with a quadlayer, but are protected in the system with a bilayer or trilayer...
April 7, 2017: Physical Review Letters
Zhongbo Yan, Ren Bi, Zhong Wang
Majorana zero modes are usually attributed to topological superconductors. We study a class of two-dimensional topologically trivial superconductors without chiral edge modes, which nevertheless host robust Majorana zero modes in topological defects. The construction of this minimal single-band model is facilitated by the Hopf map and the Hopf invariant. This work will stimulate investigations of Majorana zero modes in superconductors in the topologically trivial regime.
April 7, 2017: Physical Review Letters
S Prokhorenko, Y Nahas, L Bellaiche
Homotopy theory and first-principles-based effective Hamiltonian simulations are combined to investigate the stability of topological defects in proper ferroelectric crystals. We show that, despite a nearly trivial topology of the order parameter space, these materials can exhibit stable topological point defects in their tetragonal polar phase and stable topological line defects in their orthorhombic polar phase. The stability of such defects originates from a novel mechanism of topological protection related to finite-temperature fluctuations of local dipoles...
April 7, 2017: Physical Review Letters
Ryo Ozawa, Satoru Hayami, Yukitoshi Motome
Magnetic Skyrmions are swirling spin textures with topologically protected noncoplanarity. Recently, Skyrmions with the topological number of unity have been extensively studied in both experiment and theory. We here show that a Skyrmion crystal with an unusually high topological number of two is stabilized in itinerant magnets at a zero magnetic field. The results are obtained for a minimal Kondo lattice model on a triangular lattice by an unrestricted large-scale numerical simulation and variational calculations...
April 7, 2017: Physical Review Letters
M Micoulaut, M Bauchy
Upon cooling, the dynamics of supercooled liquids exhibits a growing transient spatial distribution of relaxation times that is known as dynamic heterogeneities. The relationship between this now well-established crucial feature of the glass transition and some underlying liquid properties remains challenging and elusive in many respects. Here we report on computer simulations of liquids with a changing network structure (densified silicates), and show that there is a deep and important link between the mechanical nature characterized by topological constraints and the spatial extent of such fluctuations...
April 7, 2017: Physical Review Letters
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