Invariant template matching in systems with spatiotemporal coding: A matter of instability.

We consider the design principles of algorithms that match templates to images subject to spatiotemporal encoding. Both templates and images are encoded as temporal sequences of samplings from spatial patterns. Matching is required to be tolerant to various combinations of image perturbations.

In vivo tissue response and degradation behavior of PLLA and stereocomplexed PLA nanofibers.

Biocompatibility of PLLA and stereocomplexed PLA nanofibers was evaluated by subcutaneous implantation in rats for 4-12 weeks. Characterization of the nanofibers was performed by GPC, SEM, wide-angle X-ray diffraction, and optical microscopy of hematoxylin-eosin stained ultrathin sections of explanted nanofibers. Stereocomplexed PLA nanofiber showed slower degradation than PLLA nanofiber and thus retained their shape after prolonged implantation.

Formation of highly toxic soluble amyloid beta oligomers by the molecular chaperone prefoldin.

Alzheimer's disease (AD) is a neurological disorder characterized by the presence of amyloid beta (Abeta) peptide fibrils and oligomers in the brain. It has been suggested that soluble Abeta oligomers, rather than Abeta fibrils, contribute to neurodegeneration and dementia due to their higher level of toxicity. Recent studies have shown that Abeta is also generated intracellularly, where it can subsequently accumulate.

Glycosphingolipid deficiency increases the sterol regulatory element-mediated gene transcription.

A major feedback mechanism of cholesterol in transcription of cholesterol metabolism-related genes is mediated by sterol regulatory element-binding protein (SREBP). Involvement of glycosphingolipids (GSLs) in the SREBP pathway is unknown. In this study, we examined the effects of GSL depletion on SRE-mediated gene transcription using GSL-defective cells.

Cloning of poly(aspartic acid) (PAA) hydrolase-1 gene from Pedobacter sp. KP-2 and hydrolysis of thermally synthesized PAA by its gene product.

Pedobacter sp. KP-2 can degrade and metabolize thermally synthesized alpha,beta-poly(D,L-aspartic acid) (tPAA), which contains 70% of unnatural beta-amide units, with high-molecular-weight. In this study, gene cloning and molecular characterization of PAA hydrolase-1 from KP-2 was carried out.

Sulfation of the galactose residues in the glycosaminoglycan-protein linkage region by recombinant human chondroitin 6-O-sulfotransferase-1.

6-O-Sulfated galactose residues have been demonstrated in the glycosaminoglycan-protein linkage region GlcUAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1-O-Ser isolated from shark cartilage chondroitin 6-sulfate (Sugahara, K., Ohi, Y., Harada, T.

Dual-gradient high-performance liquid chromatography for identification of cytosolic high-mannose-type free glycans.

It has been shown that free oligosaccharides derived from N-linked glycans accumulate in the cytosol of animal cells. Most of the glycans have only a single GlcNAc at their reducing termini (Gn1 glycans), whereas the original N-glycans retain N,N'-diacetylchitobiose at their reducing termini (Gn2 glycans). Under the conditions of high-performance liquid chromatography (HPLC) mapping established for pyridylamine (PA)-labeled Gn2 N-glycans, Gn1 glycans are not well retained on reversed-phase HPLC, making simultaneous analysis of Gn1 and Gn2 glycans problematic.

Improvement of dispersion stability and characterization of upconversion nanophosphors covalently modified with PEG as a fluorescence bioimaging probe.

Upconverting (UC) phosphors (UCPs) are ceramic materials doped with rare earth ions. These materials can absorb and upconvert infrared (IR) radiation to emit visible light by the stepwise excitation among discrete energy levels of the rare earth ions. UCPs are potentially useful reagents for use in bioimaging since the use of low energy photons avoids photo-toxicity.

Scaffolds from electrospun polyhydroxyalkanoate copolymers: fabrication, characterization, bioabsorption and tissue response.

Polyhydroxyalkanoate (PHA) copolymers of poly[(R)-3-hydroxybutyrate-co-5mol%-(R)-3-hydroxyhexanoate], poly[(R)-3-hydroxybutyrate-co-7mol%-4-hydroxybutyrate] and poly[(R)-3-hydroxybutyrate-co-97mol%-4-hydroxybutyrate] were electrospun to fabricate scaffolds with enhanced biocompatibility and bioabsorption. Subcutaneous implantation of the fibers in rats was performed to investigate their bioabsorption behavior and tissue response. The fibers before and after the in vivo experiments were characterized using gel permeation chromatography, scanning electron microscopy, X-ray diffraction and tensile test.

1H, 13C and 77Se NMR study of tetraselenafulvalene derivatives supported by novel H(Se)C and H(C)Se triple-resonance experiments at natural abundance.

A series of substituted tetraselenafulvalenes (TSeFs) was studied in solution using 1H, 13C and 77Se NMR spectroscopy. Chemical shifts and heteronuclear coupling constant values were determined and assigned. Novel two-dimensional H(Se)C and H(C)Se triple-resonance correlation experiments were applied at natural abundance in order to accomplish 13C and 77Se signal assignments.

Lysenin: a sphingomyelin specific pore-forming toxin.

Sphingomyelin is a major sphingolipid in mammalian cells. Recent results indicate that sphingomyelin is a reservoir of lipid second messengers, ceramide and sphingosine-1-phosphate. Sphingomyelin is also a major component of sphingolipid and cholesterol-rich membrane domains (lipid rafts).

Characterization of short-chain poly3-hydroxybutyrate in baker's yeast.

A short-chain poly3-hydroxybutyrate including four comonomers, originating from a complex with calcium polyphosphate, was isolated from commercial baker's yeast cells (Saccharomyces cerevisiae) and characterized as the second complexed poly(3-hydroxyalkanoate) (cPHA) in eukaryotes. The number-average molecular weight of 4982.5 Da with a polydispersity index of 1.

First-principles calculations of hydrogen diffusion on rutile TiO2(110) surfaces.

Density functional calculations are performed to study the H-atom diffusion on titanium dioxide (110) surface in the cases of water-molecule dissociation and splitting of the adjacent hydroxyl OH pair. It is shown that, when a water molecule is adsorbed at a surface oxygen-vacancy site, a fragment H atom of the water molecule tends to diffuse toward the nearest-neighboring bridging-oxygen sites by using a straight-line or relay-point path. As the result, a pair of surface hydroxyl OH is formed on the same oxygen row.

Fine structure and enzymatic degradation of poly[(R)-3-hydroxybutyrate] and stereocomplexed poly(lactide) nanofibers.

Fiber morphology and crystalline structure of poly[(R)-3-hydroxybutyrate] (P(3HB)) and stereocomplexed poly(lactide) (PLA) nanofibers were investigated by using scanning and transmission electron microscopies and X-ray and electron diffractions. In the P(3HB) nanofibers spun from less than 1 wt% 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) solution, planar zigzag conformation (beta-form) as well as 2(1) helix conformation (alpha-form) structure was formed. Based on the electron diffraction measurement of single P(3HB) nanofiber, it was revealed that the molecular chains of P(3HB) align parallel to the fiber direction.

Polychlorinated biphenyl/biphenyl degrading gene clusters in Rhodococcus sp. K37, HA99, and TA431 are different from well-known bph gene clusters of Rhodococci.

Four kinds of polychlorinated biphenyl (PCB)-degrading Rhodococcus sp. (TA421, TA431, HA99, and K37) have been isolated from termite ecosystem and under alkaline condition. The bph gene cluster involved in the degradation of PCB/biphenyl has been analyzed in strain TA421.

Curvature-dependent recognition of ethanolamine phospholipids by duramycin and cinnamycin.

Duramycin is a 19-amino-acid tetracyclic lantibiotic closely related to cinnamycin (Ro09-0198), which is known to bind phosphatidylethanolamine (PE). The lipid specificity of duramycin was not established. The present study indicates that both duramycin and cinnamycin exclusively bind to ethanolamine phospholipids (PE and ethanolamine plasmalogen).

Zero-field nuclear magnetic resonance in high field by modulated rf sequences.

The authors propose a novel approach to design and evaluate sequences for zero-field NMR spectra in high field (ZFHF) by using amplitude and phase modulated rf sequences. ZFHF provide sharp peaks for the dipolar interaction between two nuclear spins even if the orientation of the molecules is distributed. The internuclear distance r can be directly obtained from the peak position which is proportional to r-3.

Artificial lymph nodes induce potent secondary immune responses in naive and immunodeficient mice.

We previously demonstrated that artificial lymph nodes (aLNs) could be generated in mice by the implantation of stromal cell-embedded biocompatible scaffolds into their renal subcapsular spaces. T and B cell domains that form in aLNs have immune response functions similar to those of follicles of normal lymphoid tissue. In the present study, we show that the aLNs were transplantable to normal as well as SCID mice, where they efficiently induced secondary immune responses.

In situ hybridization of termite microbes.

In situ hybridization is one of the most direct and reliable ways to ascertain the origin of the gene from complex mixed cellular systems. This method is essential for studying communities of uncultured microorganism in their natural ecosystem. In this chapter, we introduce our protocols for the in situ hybridization of the messenger RNA of uncultured symbiotic protists of termite hindgut and the ribosomal RNA of the symbiotic bacteria of the protists using nonradioactive labeling protocols.

Cholesterol and lipid/protein ratio control the oligomerization of a sphingomyelin-specific toxin, lysenin.

Lysenin is a pore-forming toxin that specifically binds sphingomyelin (SM). The binding of the toxin to the membrane is accompanied by the oligomerization of the protein, leading to pore formation. The interaction of lysenin with SM is affected by the presence of other lipids found in the plasma membrane.

Enzymatic generation of the antimetabolite gamma,gamma-dichloroaminobutyrate by NRPS and mononuclear iron halogenase action in a streptomycete.

Four adjacent open reading frames, cytC1-C4, were cloned from a cytotrienin-producing strain of a Streptomyces sp. by using primers derived from the conserved region of a gene encoding a nonheme iron halogenase, CmaB, in coronamic acid biosynthesis. CytC1-3 were active after expression in Escherichia coli, and CytC4 was active after expression in Pseudomonas putida.

Stereoselective synthesis of a fragment of mycobacterial arabinan.

Strategies for the stereoselective synthesis of mycobacterial arabinan were explored. Arabinofuranosyl donors with various protective groups were screened in terms of suitability for beta-(1,2-cis)-selective glycosylation. The protective group was found to affect the stereoselectivity of arabinofuranosylation.

Effects of mutations in the substrate-binding domain of poly[(R)-3-hydroxybutyrate] (PHB) depolymerase from Ralstonia pickettii T1 on PHB degradation.

Poly[(R)-3-hydroxybutyrate] (PHB) depolymerase from Ralstonia pickettii T1 (PhaZ(RpiT1)) adsorbs to denatured PHB (dPHB) via its substrate-binding domain (SBD) to enhance dPHB degradation. To evaluate the amino acid residues participating in dPHB adsorption, PhaZ(RpiT1) was subjected to a high-throughput screening system consisting of PCR-mediated random mutagenesis targeted to the SBD gene and a plate assay to estimate the effects of mutations in the SBD on dPHB degradation by PhaZ(RpiT1). Genetic analysis of the isolated mutants with lowered activity showed that Ser, Tyr, Val, Ala, and Leu residues in the SBD were replaced by other residues at high frequency.