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At least 793 records · Page 44Linked to original sources

Evolution of III-V nitride alloy electronic structure: the localized to delocalized transition.

Addition of nitrogen to III-V semiconductor alloys radically changes their electronic properties. We report large-scale electronic structure calculations of GaAsN and GaPN using an approach that allows arbitrary states to emerge, couple, and evolve with composition. We find a novel mechanism of alloy formation where localized cluster states within the gap are gradually overtaken by a downwards moving conduction band edge, composed of both localized and delocalized states. This localized to delocalized transition explains many of the hitherto puzzling experimentally observed anomalies in III-V nitride alloys.

Journal Article↗

Image registration using the Walsh transform.

This paper presents a new algorithm which can be used to register images of the same or different modalities, e.g., images with multiple channels, such as X-rays, temperature or elevation, or simply images of different spectral bands. In particular, a correlation-based scheme is used, but instead of gray values, it correlates numbers formulated by different combinations of the extracted local Walsh coefficients of the images. Each image patch is expanded in terms of Walsh basis functions. Each Walsh basis function can be thought of as measuring a different aspect of local structure, e.g., horizontal edge, corner, etc. The coefficients of the expansion, therefore, can be thought of as dense local features, estimating at each point the degree of presence of, for example, a horizontal edge, a corner with contrast of a certain type, etc. These coefficients are normalized and used as digits in a chosen number system which allows one to create a unique number for each type of local structure. The choice of the basis of the number system allows one to give different emphasis to different types of local feature (e.g., corners versus edges), and, thus, the method we present forms a unified framework in terms of which several feature matching methods may be interpreted. The algorithm is compared with wavelet and contour based approaches, using simulated and real images. The two images are assumed to differ from each other by a rotation and a translation only.

Algorithms↗

Intrinsic DNA bends: an organizer of local chromatin structure for transcription.

DNA with a curved trajectory of its helix axis is called bent DNA, or curved DNA. Interestingly, biologically important DNA regions often contain this structure, irrespective of the origin of DNA. In the last decade, considerable progress has been made in clarifying one role of bent DNA in prokaryotic transcription and its mechanism of action. However, the role of bent DNA in eukaryotic transcription remains unclear. Our recent study raises the possibility that bent DNA is implicated in the "functional packaging" of transcriptional regulatory regions into chromatin. In this article, I review recent progress in bent DNA research in eukaryotic transcription, and summarize the history of bent DNA research and several subjects relevant to this theme. Finally, I propose a hypothesis that bent DNA structures that mimic a negative supercoil, or have a right-handed superhelical writhe, organize local chromatin infrastructure to help the very first interaction between cis-acting DNA elements and activators that trigger transcription.

Chromatin↗

Immunofluorescent localization of structural collagen types in endochondral fracture repair.

A nonimmobilized rat tibial fracture model of endochondral osseous repair was examined for the unique localizations of specific collagen genetic types. At various stages of the healing process, the demineralized callus was reacted with immunofluorescent antibodies directed against the type specific forms of matrix collagen. Type III collagen rapidly appeared (day 8-10) and remained in the primitive mesenchymal callus until remodeled. It was particularly prominent in the highly vasoformative regions and the pericallus encapsulation but not present in preexisting cortical and neoformed lamellar bone. The type II collagen, a marker of cartilage, was uniquely located only in areas of chondroid differentiation and calcification. Type II collagen was absent from all bone and was not identified beneath the repairing intact periosteum. The differentiating chondrocytes synthesized type II collagen on an underlayer of type III collagen already within the mesenchymal matrix. From these studies of genetically unique collagen markers, it appears that only in areas of motion or anoxia does an intermediate of chondroid tissue appear. The utilization of specific type II and type III collagen immunofluorescent antibodies has facilitated the understanding of the fracture repair process and has acted as an indicator for unique matrix components.

Animals↗

Optimally informative backbone structural propensities in proteins.

We use basic ideas from information theory to extract the maximum amount of structural information available in protein sequence data. From a non-redundant set of protein X-ray structures, we construct local-sequence-dependent [phi,psi] distributions that summarize the influence of local sequence on backbone conformation. These distributions, approximations of actual backbone propensities in the folded protein, have the following properties: (1) They compensate for the problem of scarce data by an optimized combination of local-sequence-dependent and single-residue specific distributions; (2) They use multi-residue information; (3) They exploit similarities in the local coding properties of amino acids by collapsing the amino acid alphabet to streamline local sequence description; (4) They are designed to contain the maximum amount of local structural information the data set allows. Our methodology is able to extract around 30 cnats of information from the protein data set out of a total 387 cnats of initial uncertainty or entropy in a finely discretized [phi,psi] dihedral angle space (18 x 18 structural states), or about 7.8%. This was achieved at the hexamer length scale; shorter as well as longer fragments produce reduced information gains. The automatic clustering of amino acids into groups, a component of the optimization procedure, reveals patterns consistent with their local coding properties. While the overall information gain from local sequence is small, there are some local sequences that have significantly narrower structural distributions than others. Distribution width varies from at least 20% less than the average overall entropy to at least 14% above. This spread is an expression of the influence of local sequence on the conformational propensities of the backbone chain. The optimal ensemble of local-sequence-specific backbone distributions produced is useful as a guide to structural predictions from sequence, as well as a tool for further explorations of the nature of the local protein code.

Algorithms↗

Theoretical study of near neutrality. II. Effect of subdivided population structure with local extinction and recolonization.

There are several unsolved problems concerning the model of nearly neutral mutations. One is the interaction of subdivided population structure and weak selection that spatially fluctuates. The model of nearly neutral mutations whose selection coefficient spatially fluctuates has been studied by adopting the island model with periodic extinction-recolonization. Both the number of colonies and the migration rate play significant roles in determining mutants' behavior, and selection is ineffective when the extinction-recolonization is frequent with low migration rate. In summary, the number of mutant substitutions decreases and the polymorphism increases by increasing the total population size, and/or decreasing the extinction-recolonization rate. However, by increasing the total size of the population, the mutant substitution rate does not become as low when compared with that in panmictic populations, because of the extinction-recolonization, especially when the migration rate is limited. It is also found that the model satisfactorily explains the contrasting patterns of molecular polymorphisms observed in sibling species of Drosophila, including heterozygosity, proportion of polymorphism and fixation index.

Animals↗

Curvature instability in passive diffractive resonators.

We study the stability of localized structures in a passive optical bistable system. We show that there is a critical value of the input field intensity above which localized structures are unstable with respect to a curvature instability. Beyond this instability boundary, a transition from the localized branch of solutions to stable hexagons is found.

Journal Article↗

The human glycine receptor subunit alpha3. Glra3 gene structure, chromosomal localization, and functional characterization of alternative transcripts.

The neuronal glycine receptor is a ligand-gated chloride channel composed of ligand binding alpha and structural beta polypeptides. Homology screening of a human fetal brain cDNA library resulted in the identification of two alternative splice variants of the glycine receptor alpha3 subunit. The amino acid sequence predicted for the alpha3L variant was largely identical to the corresponding rat subunit. In contrast, the novel splice variant alpha3K lacked the coding sequence for 15 amino acids located within the cytoplasmic loop connecting transmembrane spanning region 3 (TM3) and TM4. Using P1 artificial chromosome (PAC) clones, the structure of the GLRA3 gene was elucidated and its locus assigned to human chromosomal bands 4q33-q34 by fluorescence in situ hybridization. Two transcripts of 2.4 and 9 kilobases, corresponding to alpha3L and alpha3K, respectively, were identified and found to be widely distributed throughout the human central nervous system. Structural analysis of the GLRA3 gene revealed that the alpha3K transcript resulted from a complex splice event where excision of the novel exon 8A comprising the alternative sequence of 45 base pairs coincides with the persistence of a large intronic sequence in the 3'-untranslated region. Functional expression in HEK 293 cells of alpha3L and alpha3K subunits resulted in the formation of glycine-gated chloride channels that differed significantly in desensitization behavior, thus defining the cytoplasmic loop as an important determinant of channel inactivation kinetics.

Alternative Splicing↗

Haem conformation of amphibian nytrosylhaemoglobins detected by XANES spectroscopy.

We investigated for the first time the haem stereochemistry in the nitrosylated derivative of two amphibian haemoglobins, Xenopus laevis and Ambystoma mexicanum, by means of X-ray absorption spectroscopy technique with the aim to explain the relationships between the active site structure and physiological function of these proteins, compared to that from humans. Our results show that while the Fe site local structure of human HbNO is modulated by an allosteric effector such as IHP shifting the T-R equilibrium towards the T-state, the Fe site local structure of amphibians HbNO is stabilized in a particularly tensed T-state also without IHP.

Absorption↗

Structure and localization of the human insulin-like growth factor-binding protein 2 gene.

Insulin-like growth factor binding proteins (IGFBPs) are extracellular proteins that specifically bind IGF and modulate their effects. The human IGFBP2 gene was studied and shown to be localized to chromosome 2 region q33-q34, by somatic cell hybrid analysis and in situ hybridization. Structural characterization of the gene showed that it consists of four exons with three introns of lengths 27.0, 1.0, and 1.9 kilobase-pairs. Comparison of the encoded protein sequence of each exon in IGFBP1, 2, and 3 reveals the highest amino acid identity, 28%, in exon 1, while the lowest was found in exon 2. However, pairwise sequence comparisons demonstrate 50% identity between the protein sequences encoded by exon 4 in IGFBP1 and 2, while their respective identities with IGFBP3 are only 25 and 30%.

Amino Acid Sequence↗

Optical detection of thymine dinucleoside monophosphate and its cis-syn photodimer by inorganic nanoparticles.

The Watson-Crick DNA double helix is an averaged ideal of multitudinous natural sequence-directed local structural deviations. By effectively derailing normal cellular physiological processes, damaged bases can induce noncanonical irregularities in the local structure of DNA if not efficiently repaired. Pyrimidine bases, especially thymine, are prone to dimerization when exposed to ultraviolet light. A [2 + 2] photocyclo-addition between adjacent thymine bases predominantly produces the cis-syn photodimer. These lesions, implicated in skin cancer, bend DNA by approximately 30 degrees due to their structural and conformational changes. Such changes in molecular properties can be detected by differential quenching of CdS nanoparticle luminescence and by surface-enhanced Raman scattering spectroscopy on metal nanoparticle substrates.

Cadmium Compounds↗

Quantitative analysis of x-ray absorption near edge structure data by a full multiple scattering procedure: the Fe-CO geometry in photolyzed carbonmonoxy-myoglobin single crystal.

We report the first quantitative analysis of the Fe K-edge polarized x-ray absorption near edge structure of the iron protein carbonmonoxy-myoglobin (MbCO) single crystal and of its cryogenic photoproduct Mb(*)CO. The CO-Fe-heme local structure has been determined using a novel fitting procedure based on the full multiple scattering approach. The extracted local structure of Mb(*)CO includes a Fe-CO distance of (3.08+/-0.07) A, with a tilting angle between the heme normal and the Fe-C vector of (37+/-7) degrees, and a bending angle between the Fe-C vector and the C-O bond of (31+/-5) degrees.

Animals↗

Structure, chromosomal localization, and methylation pattern of the human mb-1 gene.

The Ag receptor on B lymphocytes is a multimeric complex that is composed of an Ag-specific component, surface Ig, which is noncovalently associated with at least two other proteins, Ig alpha and Ig beta. These are the glycoprotein products of the B lineage-restricted mb-1 and B29 genes and are crucial for the cell surface expression and function of the Ag receptor on B lymphocytes. To better understand the regulation of mb-1, we have cloned and sequenced a 5.7-kb genomic DNA fragment that contained the human gene. The overall structure of human mb-1 is very similar to that of the murine gene, including the number and approximate size of exons. The promoter region lacks a TATA element, but contains two copies of an early B cell factor-binding motif, which previously has been shown to be important for murine mb-1 expression. Other structural features include two nuclear factor-kappa B binding sites at the 5' end of the gene and a long stretch of AG rich-sequence between exons 3 and 4, downstream of an Alu repeat sequence that contains a potential stem-loop structure. The mb-1 gene was localized to chromosome 19q13.2-13.3 by a combination of two methods, PCR amplification of DNA from a somatic cell hybrid-mapping panel and fluorescence in situ hybridization. An examination of the methylation pattern revealed a striking correlation between demethylation in the 5' region of the gene and expression of mb-1. The demethylated HpaII/MspI sites are adjacent to the nuclear factor-kappa B-binding motifs, which suggests a role for this transcription factor in the regulation of human mb-1 gene expression.

Amino Acid Sequence↗

Localization of structural elements of bee venom phospholipase A2 involved in N-type receptor binding and neurotoxicity.

We have shown previously that neurotoxic venom secretory phospholipases A2 (sPLA2s) have specific receptors in brain membranes called N-type receptors that are likely to play a role in the molecular events leading to neurotoxicity of these proteins. The sPLA2 found in honey bee venom is neurotoxic and binds to this receptor with high affinity. In this paper, we have used a number of mutants of bee venom sPLA2 produced in Escherichia coli to determine the structural elements of this protein that are involved in its binding to N-type receptors. Mutations in the interfacial binding surface, in the Ca2+-binding loop and in the hydrophobic channel lead to a dramatic decrease in binding to N-type receptors, whereas mutations of surface residues localized in other parts of the sPLA2 structure do not significantly modify the binding properties. Neurotoxicity experiments show that mutants with low affinity for N-type receptors are devoid of neurotoxic properties, even though some of them retain high enzymatic activity. These results provide further evidence for the involvement of N-type receptors in neurotoxic processes associated with venom sPLA2s and identify the surface region surrounding the hydrophobic channel of bee venom sPLA2 as the N-type receptor recognition domain.

Animals↗

Annealed crystallization of ultrafine amorphous NiB alloy studied by XAFS.

XAFS has been used to investigate the local structure evolutions of ultrafine amorphous NiB alloy during the annealed crystallization process. A nanocrystalline Ni phase with the local structure of crystalline Ni-like and a crystalline Ni3B, have been produced for ultrafine amorphous NiB alloy under the annealed temperature of 573 K. The results rule out Rojo et al.'s devitrification mechanism of Ni80B20 amorphous alloy in which they considered that an amorphous pure Ni phase is formed in the first exothermic process. However, our results are almost identical with Riveiro et al.'s conclusion in which the intermediate state is interpreted as two metastable crystalline phases of Ni3B and Ni-rich NiB alloy. With the annealed temperature going onto 773 K, the ultrafine NiB sample is further decomposed and crystallized into crystalline Ni with long-range order.

Journal Article↗

Small angle scattering in ribosomal structure research: localization of the messenger RNA within ribosomal elongation states.

Besides EM and biochemical studies small angle scattering (SAS) examinations have contributed significantly to our current knowledge about the ribosomal structure. SAS does not only allow the validation of competing models but permits independent model building. However, the major contribution of SAS to ribosomal structure research derived from its ability to reveal the spatial distribution of the individual ribosomal components (57 in the E. coli ribosome) within the ribosomal structure. More recently, an improved scattering method (proton-spin contrast variation) made it possible also to address the question of mapping functional ligands in defined ribosomal elongation states. Here, we review the contributions of SAS to the current understanding of the ribosome. Furthermore we present the direct localization of a small mRNA fragment within 70S elongation complexes and describe its movement upon the translocation reaction. The successful mapping of this fragment comprising only about 0.6% of the total mass of the complex proves that proton-spin contrast-variation is a powerful tool in modern ribosome research.

Peptide Chain Elongation, Translational↗

Folding initiation sites and protein folding.

The paper discusses the role of local structural preferences of protein segments in the folding of proteins. First a short overview of the local, secondary structures detected in peptides, protein fragments, denatured proteins and early folding intermediates is given. Next the discussion of their role in protein folding is presented based on recent literature and data obtained in our laboratory. In conclusion it is pointed out that, during folding, local structures populated at low levels in denatured state may facilitate the crossing of the folding transition state barrier, and consequently accelerate the rate limiting step in folding. However, the data show that this effect does not follow simple rules.

Animals↗

Genetic structure of local populations of Lutzomyia longipalpis (Diptera: Psychodidae) in central Colombia.

Lutzomyia longipalpis (Lutz & Neiva), the sand fly vector of American visceral leishmaniasis in the New World tropics, has a broad but discontinuous geographical distribution from southern Mexico to Argentina. A baseline for population genetic structure and genetic variability for this species was obtained by analyzing 5 local, peridomestic populations at the approximate center of its distribution, the Magdalena River Valley of central Colombia. Three populations of L. longipalpis from El Callejón, a small rural community, were compared with 2 populations from neighboring areas 12 and 25 km distant for genetic variation at 15 isoenzyme loci. The mean heterozygosity ranged from 11 to 16%, with 1.2 to 2.3 alleles detected per locus. Nei's genetic distances among the populations were very low, ranging from 0.001 to 0.007. Gene flow estimates based on FST indicated high levels of gene flow among local L. longipalpis populations, with minimal population substructuring.

Alleles↗