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Liu J.,State Key Laboratory of Genetic Engineering | Liu J.,State Key Laboratory of Surface Physics | Liu J.,fe Research Center | Wang H.,State Key Laboratory of Genetic Engineering | And 8 more authors.
Nucleic Acids Research | Year: 2013

Compared with traditional algorithms for long metagenomic sequence classification, characterizing microorganisms' taxonomic and functional abundance based on tens of millions of very short reads are much more challenging. We describe an efficient composition and phylogeny-based algorithm [Metagenome Composition Vector (MetaCV)] to classify very short metagenomic reads (75-100 bp) into specific taxonomic and functional groups. We applied MetaCV to the Meta-HIT data (371-Gb 75-bp reads of 109 human gut metagenomes), and this single-read-based, instead of assembly-based, classification has a high resolution to characterize the composition and structure of human gut microbiota, especially for low abundance species. Most strikingly, it only took MetaCV 10 days to do all the computation work on a server with five 24-core nodes. To our knowledge, MetaCV, benefited from the strategy of composition comparison, is the first algorithm that can classify millions of very short reads within affordable time. © 2012 The Author(s). Published by Oxford University Press. Source

Zhao J.,University of Akron | Luo Y.,University of Akron | Luo Y.,State Key Laboratory of Surface Physics | Luo Y.,Fudan University | And 7 more authors.
Biochimica et Biophysica Acta - Biomembranes | Year: 2012

Interactions of human islet amyloid polypeptide (hIAPP or amylin) with the cell membrane are correlated with the dysfunction and death of pancreatic islet β-cells in type II diabetes. Formation of receptor-independent channels by hIAPP in the membrane is regarded as one of the membrane-damaging mechanisms that induce ion homeostasis and toxicity in islet β-cells. Here, we investigate the dynamic structure, ion conductivity, and membrane interactions of hIAPP channels in the DOPC bilayer using molecular modeling and molecular dynamics simulations. We use the NMR-derived β-strand-turn-β-strand motif as a building block to computationally construct a series of annular-like hIAPP structures with different sizes and topologies. In the simulated lipid environments, the channels lose their initial continuous β-sheet network and break into oligomeric subunits, which are still loosely associated to form heterogeneous channel conformations. The channels' shapes, morphologies and dimensions are compatible with the doughnut-like images obtained by atomic force microscopy, and with those of modeled channels for Aβ, the β2-microglobulin-derived K3 peptides, and the β-hairpin-based channels of antimicrobial peptide PG-1. Further, all channels induce directional permeability of multiple ions across the bilayers from the lower to the upper leaflet. This similarity suggests that loosely-associated β-structure motifs can be a general feature of toxic, unregulated channels. In the absence of experimental high-resolution atomic structures of hIAPP channels in the membrane, this study represents a first attempt to delineate some of the main structural features of the hIAPP channels, for a better understanding of the origin of amyloid toxicity and the development of pharmaceutical agents. © 2012 Elsevier B.V. Source

Home > Press > A clue to generate electric current without energy consumption at room temperature Abstract: A group of researchers in Japan and China identified the requirements for the development of new types of extremely low power consumption electric devices by studying Cr-doped (Sb, Bi)2Te3 thin films. This study has been reported in Nature Communications. At extremely low temperatures, an electric current flows around the edge of the film without energy loss, and under no external magnetic field. This attractive phenomenon is due to the material's ferromagnetic properties; however, so far, it has been unclear how the material gains this property. For the first time, researchers have revealed the mechanism by which this occurs. "Hopefully, this achievement will lead to the creation of novel materials that operate at room temperature in the future," said Akio Kimura, a professor at Hiroshima University and a member of the research group. Their achievement can be traced back to the discovery of the quantum Hall effect in the 1980's, where an electric current flows along an edge (or interface) without energy loss. However, this requires both a large external magnetic field and an extremely low temperature. This is why practical applications have not been possible. Researchers believed that this problem could be overcome with new materials called topological insulators that have ferromagnetic properties such as those found in Cr-doped (Sb, Bi)2Te3. A topological insulator, predicted in 2005 and first observed in 2007, is neither a metal nor an insulator, and has exotic properties. For example, an electric current is generated only at the surface or the edge of the material, while no electric current is generated inside it. It looks as if only the surface or the edge of the material has metallic properties, while on the inside it is an insulator. At extremely low temperatures, a thin film made of Cr-doped (Sb, Bi)2Te3 shows a peculiar phenomenon. As the film itself is ferromagnetic, an electric current is spontaneously generated without an external magnetic field and electric current flows only around the edge of the film without energy loss. However, it was previously unknown as to why Cr-doped (Sb, Bi)2Te3 had such ferromagnetic properties that allowed it to generate electric current. "That's why we selected the material as the object of our study," said Professor Kimura. Because Cr is a magnetic element, a Cr atom is equivalent to an atomic-sized magnet. The N-S orientations of such atomic-sized magnets tend to be aligned in parallel by the interactions between the Cr atoms. When the N-S orientations of Cr atoms in Cr-doped (Sb, Bi)2Te3 are aligned in parallel, the material exhibits ferromagnetism. However, the interatomic distances between the Cr atoms in the material are, in fact, too long to interact sufficiently to make the material ferromagnetic. The group found that the non-magnetic element atoms, such as the Sb and Te atoms, mediate the magnetic interactions between Cr atoms and serve as the glue to fix the N-S orientations of Cr atoms that face one direction. In addition, the group expects that its finding will provide a way to increase the critical temperature for relevant device applications. The experiments for this research were mainly conducted at SPring-8. "We would not have achieved perfect results without the facilities and the staff there. They devoted themselves to detecting the extremely subtle magnetism that the atoms of non-magnetic elements exhibit with extremely high precision. I greatly appreciate their efforts," Kimura said. Authors and their affiliations: Mao Ye1,2, Wei Li1,2, Siyuan Zhu3, Yukiharu Takeda4, Yuji Saitoh4, Jiajia Wang5, Hong Pan6, Munisa Nurmamat3, Kazuki Sumida3, Fuhao Ji6, Zhen Liu6, Haifeng Yang1, Zhengtai Liu1, Dawei Shen1,2, Akio Kimura3, Shan Qiao1,2,5, and Xiaoming Xie1,2,5 1 State Key Laboratoryof Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences 2 CAS-Shanghai Science Research Center 3 Graduate School of Science, Hiroshima University 4 Condensed Matter Science Division, Quantum Beam Science Center, Japan Atomic Energy Agency 5 School of physical science and technology, ShanghaiTech University 6 Department of Physics, State Key Laboratory of Surface Physics, and Laboratory of Advanced Materials, Fudan University For more information, please click If you have a comment, please us. Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.

Guo C.,State Key Laboratory of Surface Physics | Guo C.,Fudan University | Luo Y.,State Key Laboratory of Surface Physics | Luo Y.,Fudan University | And 4 more authors.
Nanoscale | Year: 2014

Understanding the nature of the self-assembly of peptide nanostructures at the molecular level is critical for rational design of functional bio-nanomaterials. Recent experimental studies have shown that triphenylalanine(FFF)-based peptides can self-assemble into solid plate-like nanostructures and nanospheres, which are different from the hollow nanovesicles and nanotubes formed by diphenylalanine(FF)-based peptides. In spite of extensive studies, the assembly mechanism and the molecular basis for the structural differences between FFF and FF nanostructures remain poorly understood. In this work, we first investigate the assembly process and the structural features of FFF nanostructures using coarse-grained molecular dynamics simulations, and then compare them with FF nanostructures. We find that FFF peptides spontaneously assemble into solid nanometer-sized nanospheres and nanorods with substantial β-sheet contents, consistent with the structural properties of hundred-nanometer-sized FFF nano-plates characterized by FT-IR spectroscopy. Distinct from the formation mechanism of water-filled FF nanovesicles and nanotubes reported in our previous study, intermediate bilayers are not observed during the self-assembly process of FFF nanospheres and nanorods. The peptides in FFF nanostructures are predominantly anti-parallel-aligned, which can form larger sizes of β-sheet-like structures than the FF counterparts. In contrast, FF peptides exhibit lipid-like assembly behavior and assemble into bilayered nanostructures. Furthermore, although the self-assembly of FF and FFF peptides is mostly driven by side chain-side chain (SC-SC) aromatic stacking interactions, the main chain-main chain (MC-MC) interactions also play an important role in the formation of fine structures of the assemblies. The delicate interplay between MC-MC and SC-SC interactions results in the different nanostructures formed by the two peptides. These findings provide new insights into the structure and self-assembly pathway of di-/tri-phenylalanine peptide assemblies, which might be helpful for the design of bioinspired nanostructures. © 2014 The Royal Society of Chemistry. Source

Yuan Y.,Nanchang University | Wang R.,Nanchang University | He J.,Nanchang University | Ma Y.,State Key Laboratory of Surface Physics | And 2 more authors.
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2014

A two-level atomic system as a working substance is used to set up a refrigerator consisting of two quantum adiabatic and two isochoric processes (two constant-frequency processes ωa and ωb with ωa<ωb), during which the two-level system is in contact with two heat reservoirs at temperatures Th and Tc( Source

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