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Boneschanscher Mark P - - 2012
Atomic force microscopy (AFM) images of graphene and graphite show contrast with atomic periodicity. However, the contrast patterns vary depending on the atomic termination of the AFM tip apex and the tip-sample distance, hampering the identification of the atomic positions. Here, we report quantitative AFM imaging of epitaxial graphene using ...
Rana Malay Kumar - - 2012
Molecular dynamics simulations have been performed to investigate the solvation characteristics of neutral fullerene (C(60)) and charged fulleride anion (C(60) (5-)) in liquid ammonia. Potassium ions are present as counterions in the system containing fulleride ion. In addition to solvation characteristics, dynamical properties of solvation shells are also found out ...
Toffoli Daniele - - 2012
A general implementation of the lowest nonvanishing order perturbation theory for the calculation of molecular multiphoton ionization cross sections is proposed in the framework of density functional theory. Bound and scattering wave functions are expanded in a multicentric basis set and advantage is taken of the full molecular point group ...
Amano T - - 2012
In view of recent tremendous advance in astronomical observations in the submillimeter to THz region brought by the Herschel space craft, laboratory high-resolution spectroscopic investigations in that frequency region into unstable molecules, in particular, light hydride ions, are urgently needed. As a part of such endeavor, rotational transitions of H(2)F(+) ...
Ferrara C Gastón - - 2012
Due to the importance of the hydrophobic interaction in protein folding, we decided to study the effect of pressure and temperature on the phase transitions of non-polar solutes in water, and thereby their solubility, using molecular dynamics simulations. The main results are: (1) within a certain range, temperature induces the ...
Vynck Kevin - - 2012
Elaborating reliable and versatile strategies for efficient light coupling between free space and thin films is of crucial importance for new technologies in energy efficiency. Nanostructured materials have opened unprecedented opportunities for light management, notably in thin-film solar cells. Efficient coherent light trapping has been accomplished through the careful design ...
Hanauer Matthias - - 2012
The reason for the lack of size extensivity in the valence space in current implementations of internally contracted multireference coupled cluster theories is the procedure used to eliminate redundant components from the cluster operator. We present a simple way to restore full size extensivity by performing this critical step in ...
Yasuda Satoshi - - 2012
A protein folds into its native structure with the α-helix and∕or β-sheet in aqueous solution under the physiological condition. The relative content of these secondary structures largely varies from protein to protein. However, such structural variability is not exhibited in nonaqueous environment. For example, there is a strong trend that ...
Martínez-Ratón Yuri - - 2012
We use a fundamental-measure density functional for hard board-like polydisperse particles, in the restricted-orientation approximation, to explain the phase behaviour of platelet colloidal suspensions studied in recent experiments. In particular, we focus our attention on the behavior of the total packing fraction of the mixture, η, in the region of ...
Kibsgaard Jakob - - 2012
Controlling surface structure at the atomic scale is paramount to developing effective catalysts. For example, the edge sites of MoS(2) are highly catalytically active and are thus preferred at the catalyst surface over MoS(2) basal planes, which are inert. However, thermodynamics favours the presence of the basal plane, limiting the ...
Muramatsu Rieko - - 2012
Angiogenesis is a prominent feature of central nervous system (CNS) disease and has roles in both the continued promotion of inflammation and the subsequent repair processes. Here we report that prostacyclin (or prostaglandin I(2) (PGI(2))) derived from new vessels promotes axonal remodeling of injured neuronal networks after CNS inflammation. In ...
Kryvohuz M - - 2012
The semiclassical instanton approach discussed by Kryvohuz [J. Chem. Phys. 134, 114103 (2011)] is applied to calculate kinetic H/D isotope effect (KIE) of intramolecular hydrogen transfer in cis-1,3-pentadiene. All 33 vibrational degrees of freedom are treated quantum mechanically with semiclassical approximation. Nuclear quantum effects such as tunneling under the barrier ...
Pendás A Martín - - 2012
The Ehrenfest force is the force acting on the electrons in a molecule due to the presence of the other electrons and the nuclei. There is an associated force field in three-dimensional space that is obtained by the integration of the corresponding Hermitian quantum force operator over the spin coordinates ...
Ten-No Seiichiro - - 2012
We propose explicitly correlated Ansatz for four-component relativistic methods within the framework of the no-pair approximation. Kinetically balanced geminal basis is derived to satisfy the cusp conditions in the non-relativistic limit based on the Lévy-Leblend-like equation. Relativistic variants of strong-orthogonality projection operator (Ansätze 2α and 2β) suitable for practical calculations ...
Meng Qingyong - - 2012
Full dimensional multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) calculations of the dynamics of the three difluorobenzene cationic isomers in five lowest-lying doublet electronic states using the ab initio multistate multimode vibronic coupling Hamiltonian (MMVCH) model are carried out using the Heidelberg MCTDH package. The same dynamical problems, but treated with the ...
Min Lihua - - 2012
Understanding stage-dependent oncogenic mechanisms is critical to develop not only targeted therapies, but also diagnostic markers and preventive strategies. The mechanisms acting during cancer initiation remain elusive, largely owing to a lack of suitable animal models and limited availability of human precancerous lesions. Here we show using genetic mouse models ...
Yamatodani Takashi - - 2012
The study showed the value of using intravital microscopy (IVM) analysis for the study of neoangiogenesis. It demonstrated that the model and the analytical methodology could be used to evaluate in detail the effects of treatment strategies for solid tumours. Neoangiogenesis is a key component of tumour progression, invasion and ...
Cho Mi Hyeon - - 2012
The regulation of cellular activities in a controlled manner is one of the most challenging issues in fields ranging from cell biology to biomedicine. Nanoparticles have the potential of becoming useful tools for controlling cell signalling pathways in a space and time selective fashion. Here, we have developed magnetic nanoparticles ...
Litcofsky Kevin D - - 2012
We present a methodology for the design, construction and modification of synthetic gene networks. This method emphasizes post-assembly modification of constructs based on network behavior, thus facilitating iterative design strategies and rapid tuning and repurposing of gene networks. The ease of post-construction modification afforded by this approach and the ever-increasing ...
Li Lenong - - 2012
E3-19K binds to and retains MHC class I molecules in the endoplasmic reticulum, suppressing anti-adenovirus activities of T cells. We determined the structure of the adenovirus serotype 2 (Ad2, species C) E3-19K-HLA-A2 complex to 1.95-Å resolution. Ad2 E3-19K binds to the N terminus of the HLA-A2 groove, contacting the α1, ...
Dethoff Elizabeth A - - 2012
The visualization of RNA conformational changes has provided fundamental insights into how regulatory RNAs carry out their biological functions. The RNA structural transitions that have been characterized so far involve long-lived species that can be captured by structure characterization techniques. Here we report the nuclear magnetic resonance visualization of RNA ...
Falconer Ester - - 2012
DNA rearrangements such as sister chromatid exchanges (SCEs) are sensitive indicators of genomic stress and instability, but they are typically masked by single-cell sequencing techniques. We developed Strand-seq to independently sequence parental DNA template strands from single cells, making it possible to map SCEs at orders-of-magnitude greater resolution than was ...
Metzger Louis E LE - - 2012
Enzymes in lipid metabolism acquire and deliver hydrophobic substrates and products from within lipid bilayers. The structure at 2.55 Å of one isozyme of a constitutive enzyme in lipid A biosynthesis, LpxI from Caulobacter crescentus, has a novel fold. Two domains close around a completely sequestered substrate, UDP-2,3-diacylglucosamine, and open ...
Zhong Bo - - 2012
Interleukin 17 (IL-17) is important in infection and autoimmunity; how it signals remains poorly understood. In this study, we identified the ubiquitin-specific protease USP25 as a negative regulator of IL-17-mediated signaling and inflammation. Overexpression of USP25 inhibited IL-17-triggered signaling, whereas USP25 deficiency resulted in more phosphorylation of the inhibitor IκBα ...
Hahn Thomas T G - - 2012
Persistent activity is thought to mediate working memory during behavior. Can it also occur during sleep? We found that the membrane potential of medial entorhinal cortex layer III (MECIII) neurons, a gateway between neocortex and hippocampus, showed spontaneous, stochastic persistent activity in vivo in mice during Up-Down state oscillations (UDS). ...
Deery Evelyne - - 2012
The biosynthesis of many vitamins and coenzymes has often proven difficult to elucidate owing to a combination of low abundance and kinetic lability of the pathway intermediates. Through a serial reconstruction of the cobalamin (vitamin B(12)) pathway in Escherichia coli and by His tagging the terminal enzyme in the reaction ...
Erb Tobias J - - 2012
Functional assignment of uncharacterized proteins is a challenge in the era of large-scale genome sequencing. Here, we combine in extracto NMR, proteomics and transcriptomics with a newly developed (knock-out) metabolomics platform to determine a potential physiological role for a ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Rhodospirillum rubrum. Our studies unraveled an ...
Leão Richardson N - - 2012
The vast diversity of GABAergic interneurons is believed to endow hippocampal microcircuits with the required flexibility for memory encoding and retrieval. However, dissection of the functional roles of defined interneuron types has been hampered by the lack of cell-specific tools. We identified a precise molecular marker for a population of ...
Zhang Qiong - - 2012
ABSTRACT: BACKGROUND: Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of perfect microsatellites in assembled ...
Southwell Derek G - - 2012
Cortical inhibitory circuits are formed by γ-aminobutyric acid (GABA)-secreting interneurons, a cell population that originates far from the cerebral cortex in the embryonic ventral forebrain. Given their distant developmental origins, it is intriguing how the number of cortical interneurons is ultimately determined. One possibility, suggested by the neurotrophic hypothesis, is ...
Roy Dipankar - - 2012
We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion ...
Tao Peng - - 2012
An algorithm is presented to maintain rigid structures in Verlet based cartesian molecular dynamics (MD) simulations. After each unconstrained MD step, the coordinates of selected particles are corrected to maintain rigid structures through an iterative procedure of rotation matrix computation. This algorithm, named as SHAPE and implemented in CHARMM program ...
Bowman Gregory R - - 2012
Markov state models (MSMs)--or discrete-time master equation models--are a powerful way of modeling the structure and function of molecular systems like proteins. Unfortunately, MSMs with sufficiently many states to make a quantitative connection with experiments (often tens of thousands of states even for small systems) are generally too complicated to ...
Hou Guangjin - - 2012
(13)C and (15)N chemical shift (CS) interaction is a sensitive probe of structure and dynamics in a wide variety of biological and inorganic systems, and in the recent years several magic angle spinning NMR approaches have emerged for residue-specific measurements of chemical shift anisotropy (CSA) tensors in uniformly and sparsely ...
Greives Nicholas - - 2012
A method developed by Northrup et al. [J. Chem. Phys. 80, 1517 (1984)] for calculating protein-ligand binding rate constants (k(a)) from brownian dynamics (BD) simulations has been widely used for rigid molecules. Application to flexible molecules is limited by the formidable computational cost to treat conformational fluctuations during the long ...
Kim Hyung J HJ Department of Medicine, University of Utah Health Sciences Center, Salt Lake City, UT 84132, - - 2012
Succinate dehydrogenase (SDH) requires a covalent addition of FAD for catalytic function. Mutational analyses of Sdh1 implicate C-terminal region Arg residues involvement in covalent flavinylation and SDH assembly. SDH assembly is dependent on FAD binding to Sdh1 but not covalent binding. These results document the basis for the SDH deficiency ...
Duan Da D Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, - - 2012
Kar3Vik1 is a heterodimeric kinesin with one catalytic subunit (Kar3) and one noncatalytic subunit (Vik1). Vik1 experiences conformational changes in regions analogous to the force-producing elements in catalytic kinesins. A molecular mechanism by which Kar3 could trigger Vik1's release from microtubules was revealed. These findings will serve as the prototype ...
Graziano Vito V Biology Department, Brookhaven National Laboratory, Upton, New York 11973, - - 2013
Late in an adenovirus infection, the viral proteinase (AVP) becomes activated to process virion precursor proteins used in virus assembly. AVP is activated by two cofactors, the viral DNA and pVIc, an 11-amino acid peptide originating from the C terminus of the precursor protein pVI. There is a conundrum in ...
Graziano Vito V Biology Department, Brookhaven National Laboratory, Upton, New York 11973, - - 2013
The precursor to adenovirus protein VI, pVI, is a multifunctional protein with different roles early and late in virus infection. Here, we focus on two roles late in infection, binding of pVI to DNA and to the major capsid protein hexon. pVI bound to DNA as a monomer independent of ...
Blainey Paul C PC Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, - - 2013
Precursor proteins used in the assembly of adenovirus virions must be processed by the virally encoded adenovirus proteinase (AVP) before the virus particle becomes infectious. An activated adenovirus proteinase, the AVP-pVIc complex, was shown to slide along viral DNA with an extremely fast one-dimensional diffusion constant, 21.0 ± 1.9 × ...
Baniecki Mary Lynn ML Biology Department, Brookhaven National Laboratory, Upton, New York 11973, - - 2013
The adenovirus proteinase (AVP), the first member of a new class of cysteine proteinases, is essential for the production of infectious virus, and here we report its structure at 0.98 Å resolution. AVP, initially synthesized as an inactive enzyme, requires two cofactors for maximal activity: pVIc, an 11-amino acid peptide, ...
Moon Tae Seok TS Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, - - 2012
Genetic programs function to integrate environmental sensors, implement signal processing algorithms and control expression dynamics. These programs consist of integrated genetic circuits that individually implement operations ranging from digital logic to dynamic circuits, and they have been used in various cellular engineering applications, including the implementation of process control in ...
Davis Emily J EJ Medical Research Council Protein Phosphorylation Unit, Sir James Black Centre, University of Dundee, Dundee, Scotland, - - 2012
Ubiquitin-binding domains (UBDs) are crucial for recruiting many proteins to sites of DNA damage. Here we characterize C1orf124 (Spartan; referred to as DVC1), which has an UBZ4-type UBD found predominantly in DNA repair proteins. DVC1 associates with DNA replication factories and localizes to sites of DNA damage in human cells, ...
Freyer Christoph C Max Planck Institute for Biology of Ageing, Cologne, - - 2012
A genetic bottleneck explains the marked changes in mitochondrial DNA (mtDNA) heteroplasmy that are observed during the transmission of pathogenic mutations, but the precise timing of these changes remains controversial, and it is not clear whether selection has a role. These issues are important for the genetic counseling of prospective ...
Manjarrez-Orduño Nataly N Center for Autoimmune and Musculoskeletal Disorders, The Feinstein Institute for Medical Research, North Shore-Long Island Jewish, Manhasset, New York, - - 2012
The c-Src tyrosine kinase, Csk, physically interacts with the intracellular phosphatase Lyp (encoded by PTPN22) and can modify the activation state of downstream Src kinases, such as Lyn, in lymphocytes. We identified an association of CSK with systemic lupus erythematosus (SLE) and refined its location to the intronic polymorphism rs34933034 ...
McLaughlin Richard N RN Jr Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, - - 2012
Statistical analysis of protein evolution suggests a design for natural proteins in which sparse networks of coevolving amino acids (termed sectors) comprise the essence of three-dimensional structure and function. However, proteins are also subject to pressures deriving from the dynamics of the evolutionary process itself--the ability to tolerate mutation and ...
Galbán Craig J CJ Department of Radiology, University of Michigan, Ann Arbor, MI, - - 2012
Chronic obstructive pulmonary disease (COPD) is increasingly being recognized as a highly heterogeneous disorder, composed of varying pathobiology. Accurate detection of COPD subtypes by image biomarkers is urgently needed to enable individualized treatment, thus improving patient outcome. We adapted the parametric response map (PRM), a voxel-wise image analysis technique, for ...
Volbeda Franke - - 2013
Control of asthma is the goal of asthma management worldwide. The Global Initiative for Asthma defined control by a composite measure of clinical findings and future risk but without using markers of airway inflammation, the hallmark of asthma. We investigated whether clinical asthma control reflects eosinophilic inflammation in a broad ...
- - 2012
Bovine TB, veterinary surveillance, dog breeding and 'one health' were all subjects on which the UK's chief veterinary officers answered questions at this year's BVA Congress. Kathryn Clark reports on the 'Ask the CVOs' session, at which the four CVOs gave their views on a range of topical issues raised ...
Schachtman Daniel P - - 2012
This research highlight does not have an abstract.
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