Dynamic condensation of linker histone C-terminal domain regulates chromatin structure.

The basic and intrinsically disordered C-terminal domain (CTD) of the linker histone (LH) is essential for chromatin compaction. However, its conformation upon nucleosome binding and its impact on chromatin organization remain unknown. Our mesoscale chromatin model with a flexible LH CTD captures a dynamic, salt-dependent condensation mechanism driven by charge neutralization between the LH and linker DNA. Namely, at low salt concentration, CTD condenses, but LH only interacts with the nucleosome and one linker DNA, resulting in a semi-open nucleosome configuration; at higher salt, LH interacts with the nucleosome and two linker DNAs, promoting stem formation and chromatin compaction. CTD charge reduction unfolds the domain and decondenses chromatin, a mechanism in consonance with reduced counterion screening in vitro and phosphorylated LH in vivo. Divalent ions counteract this decondensation effect by maintaining nucleosome stems and expelling the CTDs to the fiber exterior. Additionally, we explain that the CTD folding depends on the chromatin fiber size, and we show that the asymmetric structure of the LH globular head is responsible for the uneven interaction observed between the LH and the linker DNAs. All these mechanisms may impact epigenetic regulation and higher levels of chromatin folding

A Mouse Amidase Specific for N-terminal Asparagine: the gene, the enzyme, and their function in the N-end rule pathway

The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. In both fungi and mammals, the tertiary destabilizing N-terminal residues asparagine and glutamine function through their conversion, by enzymatic deamidation, into the secondary destabilizing residues aspartate and glutamate, whose destabilizing activity requires their enzymatic conjugation to arginine, one of the primary destabilizing residues. We report the isolation and analysis of a mouse cDNA and the corresponding gene (termed Ntan1) that encode a 310-residue amidohydrolase (termed NtN-amidase) specific for N-terminal asparagine. The ~17-kilobase pair Ntan1 gene is located in the proximal region of mouse chromosome 16 and contains 10 exons ranging from 54 to 177 base pairs in length. The ~1.4-kilobase pair Ntan1 mRNA is expressed in all of the tested mouse tissues and cell lines and is down-regulated upon the conversion of myoblasts into myotubes. The Ntan1 promoter is located ~500 base pairs upstream of the Ntan1 start codon. The deduced amino acid sequence of mouse NtN-amidase is 88% identical to the sequence of its porcine counterpart, but bears no significant similarity to the sequence of the NTA1-encoded N-terminal amidohydrolase of the yeast Saccharomyces cerevisiae, which can deamidate either N-terminal asparagine or glutamine. The expression of mouse NtN-amidase in S. cerevisiae nta1Delta was used to verify that NtN-amidase retains its asparagine selectivity in vivo and can implement the asparagine-specific subset of the N-end rule. Further dissection of mouse Ntan1, including its null phenotype analysis, should illuminate the functions of the N-end rule, most of which are still unknown

Influence of complex impact of the picosecond electron beam and volume discharge in atmospheric-pressure air on the electronic properties of MCT epitaxial films surface

In the present report we studied the distribution of surface potential of the HgCdTe epitaxial films grown by molecular beam epitaxy after the impact of picosecond electron beam and volume discharge in atmospheric-pressure air. The surface potential distribution was studied by the Kelvin Force Probe Microscopy. The experimental data obtained for the variation of the contact potential difference (ΔCPD) between the V-defect and the main matrix of the epitaxial film. The investigation of the origin epitaxial films show that variation of the spatial distribution of surface potential in the V-defect region can be related to the variation of the material composition. The experimental data obtained for the irradiated samples show that the mean value of ΔCPD for the original surface differs from the one for the irradiated surface for 55 eV. At the same time the mean value of ΔCPD changes its sign indicating that the original surface of the epitaxial HgCdTe film predominantly contains the grains with increased cadmium content while after the irradiation the grains possess an increased content of mercury. Therefore, during the irradiation process a decrease of the mercury content in the near-surface region of the semiconductor takes place resulting in the alteration of the electrophysical properties in the films near-surface region. © (2015) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only

Influence of pulsed nanosecond volume discharge in atmospheric-pressure air on the electrical characteristics of MCT epitaxial films

The purpose of this paper was investigating the effect of volume nanosecond discharge in air at atmospheric pressure on the electro-physical properties of the HgCdTe (MCT) epitaxial films grown by molecular beam epitaxy. Hall measurements of electro-physical parameters of MCT samples after irradiation have shown that there is a layer of epitaxial films exhibiting n-type conductivity that is formed in the near-surface area. After more than 600 pulses of influence parameters and thickness of the resulting n-layer is such that the measured field dependence of Hall coefficient corresponds to the material of n-type conductivity. Also it is shown that the impact of the discharge leads to significant changes in electro-physical characteristics of MIS structures. This fact is demonstrated by increase in density of positive fixed charge, change in the hysteresis type of the capacitance-voltage characteristic, an increase in density of surface states. The preliminary results show that it is possible to use such actions in the development of technologies of the controlled change in the properties of MCT. © (2015) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only

The Fabrication of Bioresorbable Implants for Bone Defects Replacement Using Computer Tomogram and 3D Printing

The present work demonstrates the possibility of production of personalized implants from bioresorbable polymers designed for replacement of bone defects. The stages of creating a personalized implant are described, which include the obtaining of 3D model from a computer tomogram, development of the model with respect to shape of bone fitment bore using Autodesk Meshmixer software, and 3D printing process from bioresorbable polymers. The results of bioresorbable polymer scaffolds implantation in pre-clinical tests on laboratory animals are shown. The biological properties of new bioresorbable polymers based on poly(lactic acid) were studied during their subcutaneous, intramuscular, bone and intraosseous implantation in laboratory animals. In all cases, there was a lack of a fibrous capsule formation around the bioresorbable polymer over time. Also, during the performed study, conclusions were made on osteogenesis intensity depending on the initial state of bone tissue

The Fabrication of Bioresorbable Implants for Bone Defects Replacement Using Computer Tomogram and 3D Printing

The present work demonstrates the possibility of production of personalized implants from bioresorbable polymers designed for replacement of bone defects. The stages of creating a personalized implant are described, which include the obtaining of 3D model from a computer tomogram, development of the model with respect to shape of bone fitment bore using Autodesk Meshmixer software, and 3D printing process from bioresorbable polymers. The results of bioresorbable polymer scaffolds implantation in pre-clinical tests on laboratory animals are shown. The biological properties of new bioresorbable polymers based on poly(lactic acid) were studied during their subcutaneous, intramuscular, bone and intraosseous implantation in laboratory animals. In all cases, there was a lack of a fibrous capsule formation around the bioresorbable polymer over time. Also, during the performed study, conclusions were made on osteogenesis intensity depending on the initial state of bone tissue

Effect of a boron implantation on the electrical properties of epitaxial HgCdTe with different material composition

In this work the experimental results of investigations of the dynamics of accumulation and spatial distribution of electrically active radiation defects when irradiating epitaxial films of Hg1-xCdxTe (MCT) with different material composition (x). The films, grown by molecular beam epitaxy (MBE) were irradiated by B ions at room temperature in the radiation dose range 1012 -1015 ions/cm2 and with ion energy 100 keV. The results give the differences in implantation profiles, damage accumulation and electrical properties as a function of the material composition of the film

Conformational Change in the Chromatin Remodelling Protein MENT

Chromatin condensation to heterochromatin is a mechanism essential for widespread suppression of gene transcription, and the means by which a chromatin-associated protein, MENT, induces a terminally differentiated state in cells. MENT, a protease inhibitor of the serpin superfamily, is able to undergo conformational change in order to effect enzyme inhibition. Here, we sought to investigate whether conformational change in MENT is ‘fine-tuned’ in the presence of a bound ligand in an analogous manner to other serpins, such as antithrombin where such movements are reflected by a change in intrinsic tryptophan fluorescence. Using this technique, MENT was found to undergo structural shifts in the presence of DNA packaged into nucleosomes, but not naked DNA. The contribution of the four Trp residues of MENT to the fluorescence change was mapped using deconvolution analysis of variants containing single Trp to Phe mutations. The analysis indicated that the overall emission spectra is dominated by a helix-H tryptophan, but this residue did not dominate the conformational change in the presence of chromatin, suggesting that other Trp residues contained in the A-sheet and RCL regions contribute to the conformational change. Mutagenesis revealed that the conformational change requires the presence of the DNA-binding ‘M-loop’ and D-helix of MENT, but is independent of the protease specificity determining ‘reactive centre loop’. The D-helix mutant of MENT, which is unable to condense chromatin, does not undergo a conformational change, despite being able to bind chromatin, indicating that the conformational change may contribute to chromatin condensation by the serpin

Regulation of Orai1/STIM1 mediated ICRAC by intracellular pH

Ca²⁺ release activated Ca²⁺-(CRAC) channels composed of two cellular proteins, Ca²⁺-sensing stromal interaction molecule 1 (STIM1) and pore-forming Orai1, are the main mediators of the Ca²⁺ entry pathway activated in response to depletion of intracellular Ca²⁺ stores. Previously it has been shown that the amplitude of CRAC current (ICRAC) strongly depends on extracellular and intracellular pH. Here we investigate the intracellular pH (pHi) dependence of ICRAC mediated by Orai1 and STIM1ectopically expressed in HEK293 cells. The results indicate that pHi affects not only the amplitude of the current, but also Ca²⁺ dependent gating of CRAC channels. Intracellular acidification changes the kinetics of ICRAC, introducing prominent re-activation component in the currents recorded in response to voltage steps to strongly negative potentials. ICRAC with similar kinetics can be observed at normal pHi if the expression levels of Orai1 are increased, relative to the expression levels of STIM1. Mutations in the STIM1 inactivation domain significantly diminish the dependence of ICRAC kinetics on pHi, but have no effect on pHi dependence of ICRAC amplitude, implying that more than one mechanism is involved in CRAC channel regulation by intracellular pH.D. Gavriliouk, N.R. Scrimgeour, S. Grigoryev, L. Ma, F.H. Zhou, G.J. Barritt, G.Y. Rychko

A Single Heterochromatin Boundary Element Imposes Position-Independent Antisilencing Activity in Saccharomyces cerevisiae Minichromosomes

Chromatin boundary elements serve as cis-acting regulatory DNA signals required to protect genes from the effects of the neighboring heterochromatin. In the yeast genome, boundary elements act by establishing barriers for heterochromatin spreading and are sufficient to protect a reporter gene from transcriptional silencing when inserted between the silencer and the reporter gene. Here we dissected functional topography of silencers and boundary elements within circular minichromosomes in Saccharomyces cerevisiae. We found that both HML-E and HML-I silencers can efficiently repress the URA3 reporter on a multi-copy yeast minichromosome and we further showed that two distinct heterochromatin boundary elements STAR and TEF2-UASrpg are able to limit the heterochromatin spreading in circular minichromosomes. In surprising contrast to what had been observed in the yeast genome, we found that in minichromosomes the heterochromatin boundary elements inhibit silencing of the reporter gene even when just one boundary element is positioned at the distal end of the URA3 reporter or upstream of the silencer elements. Thus the STAR and TEF2-UASrpg boundary elements inhibit chromatin silencing through an antisilencing activity independently of their position or orientation in S. cerevisiae minichromosomes rather than by creating a position-specific barrier as seen in the genome. We propose that the circular DNA topology facilitates interactions between the boundary and silencing elements in the minichromosomes