Shotgun protein sequencing by tandem mass spectra assembly

The analysis of mass spectrometry data is still largely based on identification of single MS/MS spectra and does not attempt to make use of the extra information available in multiple MS/MS spectra from partially or completely overlapping peptides. Analysis of MS/MS spectra from multiple overlapping peptides opens up the possibility of assembling MS/MS spectra into entire proteins, similarly to the assembly of overlapping DNA reads into entire genomes. In this paper, we present for the first time a way to detect, score, and interpret overlaps between uninterpreted MS/MS spectra in an attempt to sequence entire proteins rather than individual peptides. We show that this approach not only extends the length of reconstructed amino acid sequences but also dramatically improves the quality of de novo peptide sequencing, even for low mass accuracy MS/MS data.     

Thermal Expansion of BaO · 2B<Subscript>2</Subscript>O<Subscript>3</Subscript> in the Vitreous and Crystalline States: I. Thermal Expansion and Density of Barium Diborate Prepared from Monolithic Glass of the Same Composition

The thermal expansion and density of vitreous and polycrystalline barium diborates prepared by crystallization of monolithic glasses of stoichiometric composition are investigated in the temperature range 20–700°C. The glass crystallizes in the form of the α and β modifications depending on the heat treatment conditions. The α phase nucleates on the surface of the monolithic sample and grows inward the sample in the form of textured layers. The β phase nucleates in the melt bulk and grows in the form of spherulites. Textured polycrystalline barium diborate in the form of the α phase possesses a pronounced anisotropy of thermal expansion with respect to the direction of crystalline-layer growth. This is associated with the negative expansion along one of the crystallographic axes. The effective temperature coefficients of thermal expansion in the temperature range 20–600°C increase in the order: α phase-glass-β phase. Upon heating above 690°C, the β phase transforms partially into the α phase. This is accompanied by a considerable increase in the volume. The densities of the glass and polycrystalline samples in the temperature range 20–700°C increase in the order: glass-α phase–β phase.     

Engineering in genomics-combinatorial methods for DNA physicalmapping

To build a physical map biologists use different biochemical techniques to derive indirect information about the map and combinatorial methods to reconstruct the map from these data. Several experimental approaches to DNA physical mapping exist, each with its own advantages and disadvantages. They lead to different combinatorial problems but unfortunately, for most of these problems polynomial algorithms are still unknown; moreover, many of them are NP-complete. To solve some of these problem a number of combinatorial techniques have been suggested, in particular: homometric sets analysis, interval graphs, flows in networks, separation theory and minimum cycles mean in graphs. The author discusses: small-scale mapping; probed partial digestion; progress toward a basic map     

Silver–polyimide nanocomposite membranes: Macromolecular‐matrix‐mediated metallization of an aromatic,fluorinated polyimide yielding highly reflective films at low metal concentrations

Highly reflective, surface‐metalized, flexible polyimide films were prepared by the incorporation of a soluble silver‐ion complex, (hexafluoroacetylacetonato)silver(I) (AgHFA), into dimethylacetamide solutions of poly(amic acid) prepared from 2,2‐bis(3,4‐dicarboxyphenyl)hexafluoropropane dianhydride and 2,2‐bis[4‐(4‐aminophenoxy)phenyl]hexafluoropropane. The thermal curing of solution‐cast silver(I)–poly(amic acid) films to 300°C led to cycloimidization of the amic acid with concomitant silver(I) reduction and the formation of a reflective, air‐side‐silvered surface at very low (2 wt % and 0.3 vol %) silver concentrations. The reflective surface evolved only when the cure temperature reached about 275°C, although X‐ray diffraction showed metallic silver in the hybrid film by 200°C. After a maximum specular reflectivity greater than 80% was achieved for the 2 wt % silver film, the specular reflectivity diminished sharply with further heating at a constant temperature of 300°C. Incorporating the AgHFA complex into the soluble, fully imidized form of poly{(1,3‐dihydro‐1,3‐dioxo‐2H‐isoindole‐2,5‐diyl)[2,2,2‐trifluoro‐1‐(trifluoromethyl)ethylidene](1,3‐dihydro‐1,3‐dioxo‐2H‐isoindole‐5,2‐diyl)‐1,4‐phenyleneoxy‐1,4‐phenylene[2,2,2‐trifluoro‐1‐(trifluoromethyl)ethylidene]‐1,4‐phenyleneoxy‐1,4‐phenylene} gave films that were 25% less reflective than those beginning with poly(amic acid). Though highly reflective, the films were not electrically conductive. The metalized membranes were thermally stable and maintained mechanical properties similar to those of the parent polyimide. Transmission electron microscopy revealed an air‐side, near‐surface layer of silver that was about 40 nm thick; the interior of the film had well‐dispersed metal particles with diameters mostly less than 2 nm. The near‐surface silver layer maintained its integrity because of physical entrapment of the metal nanoparticles beneath a thin layer of polyimide; that is, the practical adhesion of the metal layer was good. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 103: 2409–2418, 2007     

Particle clearance and histopathology in lungs of F344/N rats and B6C3F1 mice inhaling nickel oxide or nickel sulfate

The goals of this study were to (1) determine the effects of repeated inhalation of relatively insoluble nickel oxide (NiO) and highly soluble nickel sulfate hexahydrate (NiSO4.6H2O) on lung particle clearance, (2) investigate the effects of repeated inhalation of NiO or NiSO4 on the pulmonary clearance of subsequently inhaled 85Sr-labeled microspheres, (3) correlate the observed effects on clearance with accumulated Ni lung burden and associated pathological changes in the lung, and (4) compare responses in F344 rats and B6C3F1 mice. Male F344/N rats and B6C3F1 mice were exposed whole-body to either NiO or NiSO4.6H2O 6 hr/day, 5 days/week for up to 6 months. NiO exposure concentrations were 0, 0.62, and 2.5 mg NiO/m3 for rats and 0, 1.25, and 5.0 mg NiO/m3 for mice. NiSO4.6H2O exposure concentrations were 0, 0.12, and 0.5 mg NiSO4.6H2O/m3 for rats and 0, 0.25, and 1.0 mg NiSO4.6H2O/m3 for mice. After 2 and 6 months of whole-body exposure, groups of rats and mice were acutely exposed nose-only to 63NiO (NiO-exposed animals only), 63NiSO4.6H2O (NiSO4.6H2O-exposed animals only), or to 85Sr-labeled polystyrene latex (PSL) microspheres (both NiO- and NiSO4.6H2O-exposed animals) to evaluate lung clearance. In addition, groups of rats and mice were euthanized after 2 and 6 months of exposure and at 2 and 4 months after the whole-body exposures were completed to evaluate histopathological changes in the left lung and to quantitate Ni in the right lung. Repeated inhalation of NiO results in accumulation of Ni in lungs of both rats and mice, but to a greater extent in lungs of rats. During the 4 months after the end of the whole-body exposures, some clearance of the accumulated Ni burden occurred from the lungs of rats and mice exposed to the lower, but not the higher NiO exposure concentrations. Clearance of acutely inhaled 63NiO was also impaired in both rats and mice, with the extent of impairment related to both exposure concentration and duration. However, the clearance of acutely inhaled 85Sr PSL microspheres was not impaired. The repeated inhalation of NiO resulted in alveolar macrophage (AM) hyperplasia with accumulation of NiO particles in both rats and mice, chronic alveolitis in rats, and interstitial pneumonia in mice. These lesions persisted throughout the 4-month recovery period after the NiO whole-body exposures were terminated. In contrast, repeated inhalation of NiSO4.6H2O did not result in accumulation of Ni in lungs of either rats or mice and did not affect the clearance of 63NiSO4.6H2O inhaled after either 2 or 6 months of NiSO4.6H2O exposure. Clearance of the 85Sr-labeled microspheres was significantly impaired only in rats exposed to the microspheres after 2 months of exposure to NiSO4.6H2O. Histopathological changes in rats were qualitatively similar to those seen in NiO-exposed rats. Only minimal histopathological changes were observed in NiSO4.6H2O-exposed mice. These results suggest that repeated inhalation of NiO at levels resulting in AM hyperplasia and alveolitis may impair clearance of subsequently inhaled NiO. The potential effects of repeated inhalation of soluble NiSO4.6H2O on the clearance of subsequently inhaled poorly soluble particles are less clear.     

Giant Chromatic Lipid/Polydiacetylene Vesicles for Detection and Visualization of Membrane Interactions

We present the construction of microscopic vesicular particles comprising phospholipids and polydiacetylene (PDA), a polymer with unique color and fluorescence properties. We show that the vesicle‐embedded PDA domains function as chromatic reporters of membrane events, undergoing dramatic colorimetric and fluorescence transformations induced by interactions with membrane‐active species. In particular, the micrometer sizes of the giant vesicles facilitate their utilization for visual inspection of membrane events by conventional microscopy techniques. The morphology, size, and chromatic properties of the vesicular aggregates depend upon the type of phospholipids and the molecular ratio between the phospholipids and diacetylene, indicating that the lipids and polymer form interdependent domains within the vesicles. The giant chromatic aggregates have been employed for detection and microscopic visualization of varied membrane processes, including lipid interactions of lipophilic drugs, binding of antimicrobial peptides, and membrane attachment by virus particles.