A structural analysis of M protein in coronavirus assembly and morphology

The M protein of coronavirus plays a central role in virus assembly, turning cellular membranes into workshops where virus and host factors come together to make new virus particles. We investigated how M structure and organization is related to virus shape and size using cryo-electron microscopy, tomography and statistical analysis. We present evidence that suggests M can adopt two conformations and that membrane curvature is regulated by one M conformer. Elongated M protein is associated with rigidity, clusters of spikes and a relatively narrow range of membrane curvature. In contrast, compact M protein is associated with flexibility and low spike density. Analysis of several types of virus-like particles and virions revealed that S protein, N protein and genomic RNA each help to regulate virion size and variation, presumably through interactions with M. These findings provide insight into how M protein functions to promote virus assembly.

Prediction of novel and analogous folds using fragment assembly and fold recognition

A number of new and newly improved methods for predicting protein structure developed by the Jones–University College London group were used to make predictions for the CASP6 experiment. Structures were predicted with a combination of fold recognition methods (mGenTHREADER, nFOLD, and THREADER) and a substantially enhanced version of FRAGFOLD, our fragment assembly method. Attempts at automatic domain parsing were made using DomPred and DomSSEA, which are based on a secondary structure parsing algorithm and additionally for DomPred, a simple local sequence alignment scoring function. Disorder prediction was carried out using a new SVM-based version of DISOPRED. Attempts were also made at domain docking and “microdomain” folding in order to build complete chain models for some targets.

Self-assembly and bioactivity of a polymer/peptide conjugate containing the RGD cell adhesion motif and PEG

The self-assembly and bioactivity of the peptide–polymer conjugate DGRFFF–PEG3000 containing the RGD cell adhesion motif has been examined, in aqueous solution. The conjugate is designed to be amphiphilic by incorporation of three hydrophobic phenylalanine residues as well as the RGD unit and a short poly(ethylene glycol) (PEG) chain of molar mass 3000 kg mol-1. Above a critical aggregation concentration, determined by fluorescence measurements, signals of b-sheet structure are revealed by spectroscopic measurements, as well as X-ray diffraction. At high concentration, a self-assembled fibril nanostructure is revealed by electron microscopy. The fibrils are observed despite PEG crystallization which occurs on drying. This suggests that DGRFFF has an aggregation tendency that is sufficiently strong not to be prevented by PEG crystallization. The adhesion, viability and proliferation of human corneal fibroblasts was examined for films of the conjugate on tissue culture plates (TCPs) as well as low attachment plates. On TCP, DGRFFF–PEG3000 films prepared at sufficiently low concentration are viable, and cell proliferation is observed. However, on low attachment surfaces, neither cell adhesion nor proliferation was observed, indicating that the RGD motif was not available to enhance cell adhesion. This was ascribed to the core–shell architecture of the self-assembled fibrils with a peptide core surrounded by a PEG shell which hinders access to the RGD unit.

Hepatic denervation impairs the assembly and secretion of VLDL-TAG

VLDL secretion is a regulated process that depends on the availability of lipids, apoB and MTP. Our aim was to investigate the effect of liver denervation upon the secretion of VLDL and the expression of proteins involved in this process. Denervation was achieved by applying a 85% phenol solution onto the portal tract, while control animals were treated with 9% NaCl. VLDL secretion was evaluated by the Tyloxapol method. The hepatic concentration of TAG and cholesterol, and the plasma concentration of TAG, cholesterol, VLDL-TAG, VLDL-cholesterol and HDL-cholesterol were measured, as well as mRNA expression of proteins involved in the process of VLDL assembly. Hepatic acinar distribution of MTP and apoB was evaluated by immunohistochemistry. Denervation increased plasma concentration of cholesterol (125.3 +/- 10.1 vs. 67.1 +/- 4.9 mg dL(-1)) and VLDL-cholesterol (61.6 +/- 5.6 vs. 29.4 +/- 3.3 mg dL(-1)), but HDL-cholesterol was unchanged (45.5 +/- 6.1 vs. 36.9 +/- 3.9 mg dL(-1)). Secretion of VLDL-TAG (47.5 +/- 23.8 vs. 148.5 +/- 27.4 mg dL h(-1)) and mRNA expression of CPT I and apoB were reduced (p < 0.01) in the denervated animals. MTP and apoB acinar distribution was not altered in the denervated animals, but the intensity of the reaction was reduced in relation to controls. Copyright (C) 2008 John Wiley & Sons, Ltd.

Large-scale biological sequence assembly and alignment by using computing grid

Large-scale sequence assembly and alignment are fundamental parts of biological computing. However, most of the large-scale sequence assembly and alignment require intensive computing power and normally take very long time to complete. To speedup the assembly and alignment process, this paper parallelizes the Euler sequence assembly and pair-wise/multiple sequence assembly, two important sequence assembly methods, and takes advantage of Computing Grid which has a colossal computing capacity to meet the large-scale biological computing demand.

Chinese consumers' perceptions of country design, assembly and parts capabilities : does country considered or consumer acculturation matter?

Chinese consumers are facing a diverse range of choices in regards to products produced wholly or in part overseas or by overseas corporations based in China. This study examines how consumers from China, both residing at home and abroad, perceived capability of Germany, Japan, US and China in regard to three dimensions of country capabilities- design, assembly and parts/components. The findings show that consumers have different perceptions concerning country capabilities and that Chinese consumers residing overseas appear to have more positive perceptions of foreign countries’ capabilities.

Self-assembly and film stability of a micelle of a single-chain quaternary ammonium amphiphile containing azobenzene on mica

The self-assembling behavior of a single-chain quaternary ammonium amphiphile bearing azobenzene (C₁₂AzoC₆N⁺) on freshly cleaved mica sheet has been investigated by atomic force microscopy (AFM) method. Confocal microscopic Raman spectra confirm the adsorption of the self-assembled monolayer structure. Ex-situ AFM reveals that C₁₂AzoC₆N⁺ forms branch-like stripes indicating the fusion and reorganization of the micelles during drying in air as the in-situ AFM has revealed that surfactant forms spherical micelles on the mica surface. The nano-sized surface structure is strongly dependent on the change of molecular structure, which resulted from photo-induced isomerization. The nano-sized stripe is quite stable even being annealed at 90 °C for 4 h.

Birth of a biome : insights into the assembly and maintenance of the Australian arid zone biota

The integration of phylogenetics, phylogeography and palaeoenvironmental studies is providing major insights into the historical forces that have shaped the Earth’s biomes. Yet our present view is biased towards arctic and temperate/tropical forest regions, with very little focus on the extensive arid regions of the planet. The Australian arid zone is one of the largest desert landform systems in the world, with a unique, diverse and relatively well-studied biota. With foci on palaeoenvironmental and molecular data, we here review what is known about the assembly and maintenance of this biome in the context of its physical history, and in comparison with other mesic biomes. Aridification of Australia began in the Mid-Miocene, around 15 million years, but fully arid landforms in central Australia appeared much later, around 1–4 million years. Dated molecular phylogenies of diverse taxa show the deepest divergences of arid-adapted taxa from the Mid-Miocene, consistent with the onset of desiccation. There is evidence of arid-adapted taxa evolving from mesicadapted ancestors, and also of speciation within the arid zone. There is no evidence for an increase in speciation rate during the Pleistocene, and most arid-zone species lineages date to the Pliocene or earlier. The last 0.8 million years have seen major fluctuations of the arid zone, with large areas covered by mobile sand dunes during glacial maxima. Some large, vagile taxa show patterns of recent expansion and migration throughout the arid zone, in parallel with the ice sheet-imposed range shifts in Northern Hemisphere taxa. Yet other taxa show high lineage diversity and strong phylogeographical structure, indicating persistence in multiple localised refugia over several glacial maxima. Similar to the Northern Hemisphere, Pleistocene range shifts have produced suture zones, creating the opportunity for diversification and speciation through hybridisation, polyploidy and parthenogenesis. This review highlights the opportunities that development of arid conditions provides for rapid and diverse evolutionary radiations, and re-enforces the emerging view that Pleistocene environmental change can have diverse impacts on genetic structure and diversity in different biomes. There is a clear need for more detailed and targeted phylogeographical studies of Australia’s arid biota and we suggest a framework and a set of a priori hypotheses by which to proceed.

Coupling between snoRNP assembly and 3' processing controls box C/D snoRNA biosynthesis in yeast

RNA polymerase II transcribes genes encoding proteins and a large number of small stable RNAs. While pre-mRNA 3'-end formation requires a machinery ensuring tight coupling between cleavage and polyadenylation, small RNAs utilize polyadenylation-independent pathways. In yeast, specific factors required for snRNA and snoRNA 3'-end formation were characterized as components of the APT complex that is associated with the core complex of the cleavage/polyadenylation machinery (core-CPF). Other essential factors were identified as independent components: Nrd1p, Nab3p and Sen1p. Here we report that mutations in the conserved box D of snoRNAs and in the snoRNP-specific factor Nop1p interfere with transcription and 3'-end formation of box C/D snoRNAs. We demonstrate that Nop1p is associated with box C/D snoRNA genes and that it interacts with APT components. These data suggest a mechanism of quality control in which efficient transcription and 3'-end formation occur only when nascent snoRNAs are successfully assembled into functional particles.

Self-assembly and competitive hydrogen bonding interactions of double crystalline diblock copolymer/homopolymer blends

In the present work, nanostructured blends were prepared from double crystalline diblock copolymer poly(ɛ-caprolactone)-block-poly(ethylene oxide) and homopolymer poly(4-vinyl phenol) (PVPh). The diblock copolymer PEO-b-PCL consists of two immiscible crystallizable blocks wherein both PEO and PCL blocks can form hydrogen bonds with PVPh. In these A-b-B/C diblock copolymer/homopolymer blends, microphase separation takes place due to the disparity in intermolecular interactions; specifically, PVPh and PEO block interact strongly whereas PVPh and PCL block interact weakly. The TEM and SAXS results show that the cubic PEO-b-PCL diblock copolymer changes into ordered hexagonal cylindrical morphology upon addition of 20 wt % PVPh followed by disordered bicontinuous phase in the blend with 40 wt % PVPh and then to homogeneous phase at 60 wt % PVPh and above blends. Up to 40 wt % PVPh there is only weak interaction between PVPh and PCL due to the selective hydrogen bonding between PVPh and PEO. However, with higher PVPh concentration, the blends become homogeneous since a sufficient amount of PVPh is available to form hydrogen bonds with both PEO and PCL. A structural model was proposed to explain the self-assembly and microphase morphology of these blends based on the experimental results obtained. The formation of nanostructures and changes in morphologies depend on the relative strength of hydrogen bonding interaction between each block of the block copolymer and the homopolymer.

Self-assembly and morphology in double crystalline diblock copolymer/homopolymer blends with competitive hydrogen bonding

Block copolymers are of particular interest due to their ability to form a rich variety of nanostructures via self-assembly [1]. The self-assembly via competitive hydrogen bonding is a novel concept which is based on the competition between different blocks of the block copolymer to form more than one kind of intermolecular interaction with the complimentary polymer in the system. Recently, Guo and co-workers have proven that careful selection of the polymers specifically the block copolymer, and the experimental conditions can lead to self-assembled structures in blends and complexes exhibiting competitive hydrogen bonding [2-5].