DMAPS: a database of multiple alignments for protein structures

The database of multiple alignments for protein structures (DMAPS) provides instant access to pre-computed multiple structure alignments for all protein structure families in the Protein Data Bank (PDB). Protein structure families have been obtained from four distinct classification methods including SCOP, CATH, ENZYME and CE, and multiple structure alignments have been built for all families containing at least three members, using CE-MC software. Currently, multiple structure alignments are available for 3050 SCOP-, 3087 CATH-, 664 ENZYME- and 1707 CE-based families. A web-based query system has been developed to retrieve multiple alignments for these families using the PDB chain ID of any member of a family. Multiple alignments can be viewed or downloaded in six different formats, including JOY/html, TEXT, FASTA, PDB (superimposed coordinates), JOY/postscript and JOY/rtf. DMAPS is accessible online at

Spin-polarized electronic structure of the core-shell ZnO/ZnO:Mn nanowires probed by x-ray absorption and emission spectroscopy

The combination of x-ray spectroscopy methods complemented with theoretical analysis unravels the coexistence of paramagnetic and antiferromagnetic phases in the Zn_0.9Mn_0.1O shell deposited onto array of wurtzite ZnO nanowires. The shell is crystalline with orientation toward the ZnO growth axis, as demonstrated by X-ray linear dichroism. EXAFS analysis confirmed that more than 90% of Mn atoms substituted Zn in the shell while fraction of secondary phases was below 10%. The value of manganese spin magnetic moment was estimated from the Mn K{\beta} X-ray emission spectroscopy to be 4.3{\mu}B which is close to the theoretical value for substitutional Mn_Zn. However the analysis of L_2,3 x-ray magnetic circular dichroism data showed paramagnetic behaviour with saturated spin magnetic moment value of 1.95{\mu}B as determined directly from the spin sum rule. After quantitative analysis employing atomic multiplet simulations such difference was explained by a coexistence of paramagnetic phase and local antiferromagnetic coupling of Mn magnetic moments. Finally, spin-polarized electron density of states was probed by the spin-resolved Mn K-edge XANES spectroscopy and consequently analyzed by band structure calculations.Comment: Supplementary information available at http://www.rsc.org/suppdata/ja/c3/c3ja50153a/c3ja50153a.pdf J. Anal. At. Spectrom., 201

Polarization bistability and resultant spin rings in semiconductor microcavities

The transmission of a pump laser resonant with the lower polariton branch of a semiconductor microcavity is shown to be highly dependent on the degree of circular polarization of the pump. Spin dependent anisotropy of polariton-polariton interactions allows the internal polarization to be controlled by varying the pump power. The formation of spatial patterns, spin rings with high degree of circular polarization, arising as a result of polarization bistability, is observed. A phenomenological model based on spin dependent Gross-Pitaevskii equations provides a good description of the experimental results. Inclusion of interactions with the incoherent exciton reservoir, which provides spin-independent blueshifts of the polariton modes, is found to be essential.Comment: 5 pages, 3 figure

Effect of interactions on vortices in a nonequilibrium polariton condensate

We demonstrate the creation of vortices in a macroscopically occupied polariton state formed in a semiconductor microcavity. A weak external laser beam carrying orbital angular momentum (OAM) is used to imprint a vortex on the condensate arising from the polariton optical parametric oscillator (OPO). The vortex core radius is found to decrease with increasing pump power, and is determined by polariton-polariton interactions. As a result of OAM conservation in the parametric scattering process, the excitation consists of a vortex in the signal and a corresponding antivortex in the idler of the OPO. The experimental results are in good agreement with a theoretical model of a vortex in the polariton OPO

Crisis in the NICU and the Medley with Midazolam

Epidemiologic studies of human patients have revealed a correlation between childhood exposure to general anesthetic and sedative agents and subsequent cognitive deficits. This association is supported by data from animal models, which shows that developmental exposure to both anesthetics and sedatives causes lasting impairments in learning. This study focused on midazolam (MDZ), a common benzodiazepine regularly used as a sedative agent on neonates in the Neonatal Intensive Care Unit (NICU). However, a knowledge gap that remains is how long-term exposure to MDZ during very early stages of life impacts synaptic alterations and neurobiological mechanisms. Elucidation of these mechanisms is of high clinical importance and may develop neuroprotective therapeutic strategies for optimizing outcomes for uniquely vulnerable NICU populations. Using a preclinical rodent model system, we mimicked a dose-escalation regimen from postnatal day 3 (P3) pups until P21 to comprehensively characterize how early-life exposure to MDZ impacts neurodevelopment outcomes at different tiers ─ phenotypic, molecular, behavioral, and high throughput- “omics” levels. Our data demonstrated that repetitive exposure to MDZ at an early age stunts neurodevelopment during the early stages of life disrupts the blood-brain barrier, and alters the synaptic components and neurochemistry, which may be indicative of behavioral deficits at later development. Additionally, our bioinformatics analysis from purified synaptosome identified enrichment of proteins associated with actin-binding and protein depolymerization process. One potential hit identified was alpha adducin (ADD1), belonging to the family of cytoskeleton proteins, upregulated in the MDZ group and whose expression was further validated by western blot. Our study has provided a comprehensive characterization of MDZ effects on development at multiple tiers yielding novel insights on how long-term exposure to MDZ impacts development. Notably, the identification of ADD1 as a potential target and further characterization of its downstream mechanisms can give additional insights into its role as a potential therapeutic for treating neurodevelopmental alterations associated with long-term MDZ use in neonates.https://digitalcommons.unmc.edu/chri_forum/1056/thumbnail.jp

Synthesis and characterization of MnCrO4, a new mixed-valence antiferromagnet

A new orthorhombic phase, MnCrO4, isostructural with MCrO 4 (M = Mg, Co, Ni, Cu, Cd) was prepared by evaporation of an aqueous solution, (NH4)2Cr2O7 + 2 Mn(NO 3)2, followed by calcination at 400 C. It is characterized by redox titration, Rietveld analysis of the X-ray diffraction pattern, Cr K edge and Mn K edge XANES, ESR, magnetic susceptibility, specific heat and resistivity measurements. In contrast to the high-pressure MnCrO4 phase where both cations are octahedral, the new phase contains Cr in a tetrahedral environment suggesting the charge balance Mn2+Cr 6+O4. However, the positions of both X-ray absorption K edges, the bond lengths and the ESR data suggest the occurrence of some mixed-valence character in which the mean oxidation state of Mn is higher than 2 and that of Cr is lower than 6. Both the magnetic susceptibility and the specific heat data indicate an onset of a three-dimensional antiferromagnetic order at TN ≈ 42 K, which was confirmed also by calculating the spin exchange interactions on the basis of first principles density functional calculations. Dynamic magnetic studies (ESR) corroborate this scenario and indicate appreciable short-range correlations at temperatures far above T N. MnCrO4 is a semiconductor with activation energy of 0.27 eV; it loses oxygen on heating above 400 C to form first Cr 2O3 plus Mn3O4 and then Mn 1.5Cr1.5O4 spinel. © 2013 American Chemical Society

Whole genomic sequence analysis of \u3ci\u3eBacillus infantis\u3c/i\u3e: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe

Background: We recently reported the identification of Bacillus sp. NRRL B-14911 that induces heart autoimmunity by generating cardiac-reactive T cells through molecular mimicry. This marine bacterium was originally isolated from the Gulf of Mexico, but no associations with human diseases were reported. Therefore, to characterize its biological and medical significance, we sought to determine and analyze the complete genome sequence of Bacillus sp. NRRL B-14911. Results: Based on the phylogenetic analysis of 16S ribosomal RNA (rRNA) genes, sequence analysis of the 16S-23S rDNA intergenic transcribed spacers, phenotypic microarray, and matrix-assisted laser desorption ionization time-offlight mass spectrometry, we propose that this organism belongs to the species Bacillus infantis, previously shown to be associated with sepsis in a newborn child. Analysis of the complete genome of Bacillus sp. NRRL B-14911 revealed several virulence factors including adhesins, invasins, colonization factors, siderophores and transporters. Likewise, the bacterial genome encodes a wide range of methyl transferases, transporters, enzymatic and biochemical pathways, and insertion sequence elements that are distinct from other closely related bacilli. Conclusions: The complete genome sequence of Bacillus sp. NRRL B-14911 provided in this study may facilitate genetic manipulations to assess gene functions associated with bacterial survival and virulence. Additionally, this bacterium may serve as a useful tool to establish a disease model that permits systematic analysis of autoimmune events in various susceptible rodent strains