Analyzing a putative enhancer of optic disc morphology.

BACKGROUND: Genome-wide association studies have identified the CDC7-TGFBR3 intergenic region on chromosome 1 to be strongly associated with optic disc area size. The mechanism of its function remained unclear until new data on eQTL markers emerged from the Genotype-Tissue Expression project. The target region was found to contain a strong silencer of the distal (800 kb) Transcription Factor (TF) gene GFI1 (Growth Factor Independent Transcription Repressor 1) specifically in neuroendocrine cells (pituitary gland). GFI1 has also been reported to be involved in the development of sensory neurons and hematopoiesis. Therefore, GFI1, being a developmental gene, is likely to affect optic disc area size by altering the expression of the associated genes via long-range interactions. RESULTS: Distribution of haplotypes in the putative enhancer region has been assessed using the data on four continental supergroups generated by the 1000 Genomes Project. The East Asian (EAS) populations were shown to manifest a highly homogenous unimodal haplotype distribution pattern within the region with the major haplotype occurring with the frequency of 0.9. Another European specific haplotype was observed with the frequency of 0.21. The major haplotype appears to be involved in silencing GFI1repressor gene expression, which might be the cause of increased optic disc area characteristic of the EAS populations. The enhancer/eQTL region overlaps AluJo element, which implies that this particular regulatory element is primate-specific and confined to few tissues. CONCLUSION: Population specific distribution of GFI1 enhancer alleles may predispose certain ethnic groups to glaucoma.

Contribution of the Multiplicity Fluctuation in the Temperature Dependence of Phonon Spectra of Rare-Earth Cobaltites.

We have studied, both experimentally and theoretically, the unusual temperature dependence of the phonon spectra in NdCoO3, SmCoO3 and GdCoO3, where the Co3+ ion is in the low-spin (LS) ground state, and at the finite temperature, the high-spin (HS) term has a nonzero concentration nHS due to multiplicity fluctuations. We measured the absorption spectra in polycrystalline and nanostructured samples in the temperature range 3-550 K and found a quite strong breathing mode softening that cannot be explained by standard lattice anharmonicity. We showed that the anharmonicity in the electron-phonon interaction is responsible for this red shift proportional to the nHS concentration.

Effect of Multiplicity Fluctuation in Cobalt Ions on Crystal Structure, Magnetic and Electrical Properties of NdCoO3 and SmCoO3.

The structural, magnetic, electrical, and dilatation properties of the rare-earth NdCoO3 and SmCoO3 cobaltites were investigated. Their comparative analysis was carried out and the effect of multiplicity fluctuations on physical properties of the studied cobaltites was considered. Correlations between the spin state change of cobalt ions and the temperature dependence anomalies of the lattice parameters, magnetic susceptibility, volume thermal expansion coefficient, and electrical resistance have been revealed. A comparison of the results with well-studied GdCoO3 allows one to single out both the general tendencies inherent in all rare-earth cobaltites taking into account the lanthanide contraction and peculiar properties of the samples containing Nd and Sm.

Mass spectrometry and biochemical analysis of RNA polymerase II: targeting by protein phosphatase-1.

Transcription of eukaryotic genes is regulated by phosphorylation of serine residues of heptapeptide repeats of the carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII). We previously reported that protein phosphatase-1 (PP1) dephosphorylates RNAPII CTD in vitro and inhibition of nuclear PP1-blocked viral transcription. In this article, we analyzed the targeting of RNAPII by PP1 using biochemical and mass spectrometry analysis of RNAPII-associated regulatory subunits of PP1. Immunoblotting showed that PP1 co-elutes with RNAPII. Mass spectrometry approach showed the presence of U2 snRNP. Co-immunoprecipitation analysis points to NIPP1 and PNUTS as candidate regulatory subunits. Because NIPP1 was previously shown to target PP1 to U2 snRNP, we analyzed the effect of NIPP1 on RNAPII phosphorylation in cultured cells. Expression of mutant NIPP1 promoted RNAPII phosphorylation suggesting that the deregulation of cellular NIPP1/PP1 holoenzyme affects RNAPII phosphorylation and pointing to NIPP1 as a potential regulatory factor in RNAPII-mediated transcription.

Roles of the outer membrane protein AsmA of Salmonella enterica in the control of marRAB expression and invasion of epithelial cells.

A genetic screen for suppressors of bile sensitivity in DNA adenine methylase (dam) mutants of Salmonella enterica serovar Typhimurium yielded insertions in an uncharacterized locus homologous to the Escherichia coli asmA gene. Disruption of asmA suppressed bile sensitivity also in phoP and wec mutants of S. enterica and increased the MIC of sodium deoxycholate for the parental strain ATCC 14028. Increased levels of marA mRNA were found in asmA, asmA dam, asmA phoP, and asmA wec strains of S. enterica, suggesting that lack of AsmA activates expression of the marRAB operon. Hence, asmA mutations may enhance bile resistance by inducing gene expression changes in the marRAB-controlled Mar regulon. In silico analysis of AsmA structure predicted the existence of one transmembrane domain. Biochemical analysis of subcellular fractions revealed that the asmA gene of S. enterica encodes a protein of approximately 70 kDa located in the outer membrane. Because AsmA is unrelated to known transport and/or efflux systems, we propose that activation of marRAB in asmA mutants may be a consequence of envelope reorganization. Competitive infection of BALB/c mice with asmA(+) and asmA isogenic strains indicated that lack of AsmA attenuates Salmonella virulence by the oral route but not by the intraperitoneal route. Furthermore, asmA mutants showed a reduced ability to invade epithelial cells in vitro.

Novel pressure-induced magnetic transition in magnetite (Fe3O4).

Fe K-edge x-ray magnetic circular dichroism of magnetite (Fe3O4) powders was measured with synchrotron radiation under variable pressure and temperature conditions in diamond anvil cell. The magnetic dichroism was observed to decrease discontinuously by approximately 50% between 12 and 16 GPa, independent of temperature. The magnetic transition is attributed to a high-spin to intermediate-spin transition of Fe2+ ions in the octahedral sites and could account for previously observed structural and electrical anomalies in magnetite at this pressure range. The interpretation of x-ray magnetic circular dichroism data is supported by x-ray emission spectroscopy and theoretical cluster calculations.

Resonance method of electric-dipole-moment measurements in storage rings.

A "resonance method" of measuring the electric dipole moment (EDM) of nuclei in storage rings is described, based on two new ideas: (1) Oscillating particles' velocities in resonance with spin precession, and (2) alternately producing two sub-beams with different betatron tunes--one sub-beam to amplify and thus make it easier to correct ring imperfections that produce false signals imitating EDM signals, and the other to make the EDM measurement.