Atom ordering in cuboctahedral Ni-Al nanoalloys

Energy calculations have been carried out on high-symmetry cuboctahedral Ni-Al nanoalloy clusters, of varying composition, with the interatomic interactions modelled by the Gupta many-body potential. Relaxations of cuboctahedral fragments cut from the bulk lattice of Ni₃Al, with 13-561 atoms, were undertaken, as were relaxations of high symmetry clusters with 55 and 147 atoms. The lowest energy isomers were found to be dominated by three factors: the tendency toward mixing due to the favourable energy of mixing, Δ_mixE; the size difference between nickel and aluminium; and the higher cohesive and surface energy of nickel compared to aluminium. The latter two factors favour Al-segregation to the surface. The most stable Ni:Al composition approaches 3:1 for larger clusters.     

In vitro chiral nematic ordering of chitin crystallites

Microfibrillar fragments of purified crab and shrimp chitin were prepared by hydrolysis in 3 HCl at its boiling point (104°C). After removal of the acid by centrifugal washing and dialysis, an ultrasound treatment converts the residual product to a colloidal suspension stabilized by NH₃⁺ charges. When dewatered to a critical concentration, spontaneous formation of a two-phase equilibrium system occurs. The upper phase (lower concentration) is isotropic and the lower phase is anisotropic. The latter displays chiral nematic order and dries to a solid film which mimics the helicoid organization characteristic of the chitin microfibrils in the cuticle of arthropods.     

Efficient multipoint mapping: making use of dominant repulsion-phase markers

The paper is devoted to the problem of multipoint gene ordering with a particular focus on "dominance" complication that acts differently in conditions of coupling-phase and repulsion-phase markers. To solve the problem we split the dataset into two complementary subsets each containing shared codominant markers and dominant markers in the coupling-phase only. Multilocus ordering in the proposed algorithm is based on pairwise recombination frequencies and using the well-known travelling salesman problem (TSP) formalization. To obtain accurate results, we developed a multiphase algorithm that includes synchronized-marker ordering of two subsets assisted by re-sampling-based map verification, combining the resulting maps into an integrated map followed by verification of the integrated map. A new synchronized Evolution-Strategy discrete optimization algorithm was developed here for the proposed multilocus ordering approach in which common codominant markers facilitate stabilization of the marker order of the two complementary maps. High performance of the employed algorithm allows systematic treatment for the problem of verification of the obtained multilocus orders, based on computing-intensive bootstrap and jackknife technologies for detection and removing unreliable marker scores. The efficiency of the proposed algorithm was demonstrated on simulated and real data.Communicated by J.W. Snape     

Crystal structure of aspartyl dipeptidase from Xenopus laevis revealed ligand binding induced loop ordering and catalytic triad assembly

Gene encoding aspartyl dipeptidase from Xenopus levies (PepExl) is upregulated by thyroid hormone and is proposed to play a significant role in resorption of tadpole tail during metamorphosis. However, the importance of peptidase activity for the resorption of the tail remain elusive. Here we report the crystal structures of first eukaryotic S51 peptidase, PepExl, in its ligand-free and Asp-bound states at 1.4 and 1.8 Å resolutions, respectively. The active site is located at dimeric interface and the catalytic triad is found to be dissembled in ligand-free and assembled in Asp-bound state. Structural comparison and molecular dynamic simulations of ligand-free and Asp-bound states shows that distinct loop (loop-A) plays an important role in active site shielding, substrate binding and enzyme activation. This study illuminates the Asp-X dipeptide binding in PepExl is associated with ordering of the loop-A and assembly of residues of catalytic triad in active conformation for enzymatic activity.     

On identification of the number of best treatments using the Newman-Keuls test

In this paper, we provide a stochastic ordering of the Studentized range statistics under a balanced one-way ANOVA model. Based on this result we show that, when restricted to the multiple comparisons with the best, the Newman-Keuls (NK) procedure strongly controls experimentwise error rate for a sequence of null hypotheses regarding the number of largest treatment means. In other words, the NK procedure provides an upper confidence bound for the number of best treatments.     

Alteration of membrane lipid biophysical properties and resistance of human lung adenocarcinoma A_(549) cells to cisplatin

Alterations of membrane lipid biophysical properties of sensitive A549 and resistant A549/DDP cells to the Cis-dichlorodiammine platinum (Cisplatin) were performed by measurements of fluorescence and flow cytometry approaches using fluorescence dyes of DPH, N-AS and Mero-cyanine 540 (MC 540) respectively. Fatty acids of membrane lipid of the two cell lines were analyzed by gas chromatography. The results indicated clearly that fluorescence polarization (P) of the DPH probe is 0.169 for the sensitive A549 cell and 0.194 for the resistant A549/DDP cells. Statistical analysis showed significant difference between the two cell lines. The polarizations of 2-AS and 7-AS which reflect the fluidity of surface and middle of lipid bilayer are 0.134 and 0.144 for the sensitive A549 cells as well as 0.171 and 0.178 for the resistant A549/DDP cells respectively, but there is no significant difference of the polarization of 12-AS between the two cell lines. This shows that alterations of the membrane fluidity of both     

Solution NMR views of dynamical ordering of biomacromolecules

Background

To understand the mechanisms related to the ‘dynamical ordering’ of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells.