Programmed assembly of polymer-DNA conjugate nanoparticles with optical readout and sequence-specific activation of biorecognition

Soft micellar nanoparticles can be prepared from DNA conjugates designed to assemble via base pairing such that strands containing a polymer corona and a cholesterol tail generate controlled supramolecular architecture. Functionalization of one DNA conjugate strand with a biorecognition ligand results in shielding of the ligand when in the micelle, while encoding of the DNA sequences with overhangs allows supramolecular unpacking by addition of a complementary strand and sequence-specific unshielding of the ligand. The molecular assembly/disassembly and ‘on–off’ switch of the recognition signal is visualized by FRET pair signalling, PAGE and a facile turbidimetric binding assay, allowing direct and amplified readout of nucleic acid sequence recognition

Carbon antisite clusters in SiC: a possible pathway to the D_{II} center

The photoluminescence center D_{II} is a persistent intrinsic defect which is common in all SiC polytypes. Its fingerprints are the characteristic phonon replicas in luminescence spectra. We perform ab-initio calculations of vibrational spectra for various defect complexes and find that carbon antisite clusters exhibit vibrational modes in the frequency range of the D_{II} spectrum. The clusters possess very high binding energies which guarantee their thermal stability--a known feature of the D_{II} center. The di-carbon antisite (C_{2})_{Si} (two carbon atoms sharing a silicon site) is an important building block of these clusters.Comment: RevTeX 4, 6 pages, 3 figures Changes in version 2: Section headings, footnote included in text, vibrational data now given for neutral split-interstitial, extended discussion of the [(C_2)_Si]_2 defect incl. figure Changes version 3: Correction of binding energy for 3rd and 4th carbon atom at antisite; correction of typo

Virtual annihilation contribution to orthopositronium decay rate

Order alpha^2 contribution to the orthopositronium decay rate due to one-photon virtual annihilation is found to be delta Gamma = (alpha/pi)^2 (pi^2 ln(alpha) - 0.8622(9))Gamma_LO.Comment: 2 pages, no figure

Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem

BACKGROUND : Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. We investigated the role of the modified histone H3K4me3 (trimethylated lysine 4 of histone H3) in gene expression during the early stages of wood formation using ChIP-seq in Eucalyptus grandis, a woody biomass model. RESULTS : Plant chromatin fixation and isolation protocols were optimized for developing xylem tissue collected from field-grown E. grandis trees. A “nano-ChIP-seq” procedure was employed for ChIP DNA amplification. Over 9 million H3K4me3 ChIP-seq and 18 million control paired-end reads were mapped to the E. grandis reference genome for peak-calling using Model-based Analysis of ChIP-Seq. The 12,177 significant H3K4me3 peaks identified covered ~1.5% of the genome and overlapped some 9,623 protein-coding genes and 38 noncoding RNAs. H3K4me3 library coverage, peaking ~600 - 700 bp downstream of the transcription start site, was highly correlated with gene expression levels measured with RNA-seq. Overall, H3K4me3-enriched genes tended to be less tissue-specific than unenriched genes and were overrepresented for general cellular metabolism and development gene ontology terms. Relative expression of H3K4me3-enriched genes in developing secondary xylem was higher than unenriched genes, however, and highly expressed secondary cell wall-related genes were enriched for H3K4me3 as validated using ChIP-qPCR. CONCLUSIONS : In this first genome-wide analysis of a modified histone in a woody tissue, we optimized a ChIP-seq procedure suitable for field-collected samples. In developing E. grandis xylem, H3K4me3 enrichment is an indicator of active transcription, consistent with its known role in sustaining pre-initiation complex formation in yeast. The H3K4me3 ChIP-seq data from this study paves the way to understanding the chromatin landscape and epigenomic architecture of xylogenesis in plants, and complements RNA-seq evidence of gene expression for the future improvement of the E. grandis genome annotation.Additional file 1: Supplementary Note S1.Additional file 2: Figure S1, Figure S2, Figure S3, Figure S4, Figure S5, Figure S6, Figure S6, Figure S7, Figure S8, Figure S9, Figure S10, Figure S11, Figure S12, Figure S13, Figure S14, Figure S15, Figure S16.Additional file 3: Table S1, Table S2, Table S3, Table S4, Table S5, Table S6, Table S7.Additional file 4: Genomic locations and fragment coverage of significant H3K4me3 peaks.Additional file 5: Genomic locations of annotated genes overlapping with significant H3K4me3 peaks.Additional file 6: Genomic locations of low-confidence gene models overlapping with significant H3K4me3 peaks.SH, EM and AM acknowledge funding from the Department of Science and Technology (DST), South Africa, the National Research Foundation of South Africa (NRF) Incentive Funding for Rated Researchers Grant (UID 81111) and NRF Bioinformatics and Functional Genomics Program (UID 71255, UID 86936), Sappi and Mondi through the Forest Molecular Genetics (FMG) Program at the University of Pretoria (UP), and the Technology and Human Resources for Industry Program (THRIP) (UID 80118). AG acknowledges funding from USDA National Institute of Food and Agriculture and the Office of Science (BER), US Department of Energy.http://www.biomedcentral.com/bmcplantbiolam201

Interplay of pairing and multipole interactions in a simple model

The interplay of pairing and other interactions is addressed in this work using a simple single-j model. We show that enhancements in pairing correlations observed through studies of the spectra of deformed systems, moments of inertia, changes in transitional multipole amplitudes, and direct calculations of the pairing component in the wave function, indicate that even without explicit matrix elements responsible for pairing, a paired state can still appear from the kinematic coupling of pairing to deformation and from other geometrical restrictions that are of extreme importance in mesoscopic systems. Furthermore, we demonstrate that macroscopic transitions such as oblate to prolate shape changes can lead to strong dynamic enhancements of pairing correlations. In this work we emphasize that the pairing condensate has an important dynamic and kinematic effect on other residual interactions.Comment: 39 pages, 8 figure

Comparison of structural transformations and superconductivity in compressed Sulfur and Selenium

Density-functional calculations are presented for high-pressure structural phases of S and Se. The structural phase diagrams, phonon spectra, electron-phonon coupling, and superconducting properties of the isovalent elements are compared. We find that with increasing pressure, Se adopts a sequence of ever more closely packed structures (beta-Po, bcc, fcc), while S favors more open structures (beta-Po, simple cubic, bcc). These differences are shown to be attributable to differences in the S and Se core states. All the compressed phases of S and Se considered are calculated to have weak to moderate electron-phonon coupling strengths consistent with superconducting transition temperatures in the range of 1 to 20 K. Our results compare well with experimental data on the beta-Po --> bcc transition pressure in Se and on the superconducting transition temperature in beta-Po S. Further experiments are suggested to search for the other structural phases predicted at higher pressures and to test theoretical results on the electron-phonon interaction and superconducting properties

Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem

Despite the considerable contribution of xylem development (xylogenesis) to plant biomass accumulation, its epigenetic regulation is poorly understood. Furthermore, the relative contributions of histone modifications to transcriptional regulation is not well studied in plants. We investigated the biological relevance of H3K4me3 and H3K27me3 in secondary xylem development using ChIPseq and their association with transcript levels among other histone modifications in woody and herbaceous models. In developing secondary xylem of the woody model Eucalyptus grandis, H3K4me3 and H3K27me3 genomic spans were distinctly associated with xylogenesis-related processes, with (late) lignification pathways enriched for putative bivalent domains, but not early secondary cell wall polysaccharide deposition. H3K27me3-occupied genes, of which 753 (~31%) are novel targets, were enriched for transcriptional regulation and flower development and had significant preferential expression in roots. Linear regression models of the ChIP-seq profiles predicted ~50% of transcript abundance measured with strand-specific RNA-seq, confirmed in a parallel analysis in Arabidopsis where integration of seven additional histone modifications each contributed smaller proportions of unique information to the predictive models. This study uncovers the biological importance of histone modification antagonism and genomic span in xylogenesis and quantifies for the first time the relative correlations of histone modifications with transcript abundance in plants.The Department of Science and Technology (Strategic Grant for the Eucalyptus Genomics Platform), the National Research Foundation (Bioinformatics and Functional Genomics Programme Grant IUD 86936 and 97911), Incentive Funding Grant (AAM) (UID 8111), Mondi Ltd. and Sappi Ltd.http://www.nature.com/srepam2017Forestry and Agricultural Biotechnology Institute (FABI)GeneticsPlant ScienceStatistic

Primary accumulation in the Soviet transition

The Soviet background to the idea of primary socialist accumulation is presented. The mobilisation of labour power and of products into public sector investment from outside are shown to have been the two original forms of the concept. In Soviet primary accumulation the mobilisation of labour power was apparently more decisive than the mobilisation of products. The primary accumulation process had both intended and unintended results. Intended results included bringing most of the economy into the public sector, and industrialisation of the economy as a whole. Unintended results included substantial economic losses, and the proliferation of coercive institutions damaging to attainment of the ultimate goal - the building of a communist society

High Precision Mass Measurements in Ψ\Psi and Υ\Upsilon Families Revisited

High precision mass measurements in $\Psi$ and $\Upsilon$ families performed in 1980-1984 at the VEPP-4 collider with OLYA and MD-1 detectors are revisited. The corrections for the new value of the electron mass are presented. The effect of the updated radiative corrections has been calculated for the $J/\Psi(1S)$ and $\Psi(2S)$ mass measurements.Comment: 5 pages, 1 table, submitted to Phys. Lett.

Constraining fundamental constants of physics with quasar absorption line systems

We summarize the attempts by our group and others to derive constraints on variations of fundamental constants over cosmic time using quasar absorption lines. Most upper limits reside in the range 0.5-1.5x10-5 at the 3sigma level over a redshift range of approximately 0.5-2.5 for the fine-structure constant, alpha, the proton-to-electron mass ratio, mu, and a combination of the proton gyromagnetic factor and the two previous constants, gp(alpha^2/mu)^nu, for only one claimed variation of alpha. It is therefore very important to perform new measurements to improve the sensitivity of the numerous methods to at least <0.1x10-5 which should be possible in the next few years. Future instrumentations on ELTs in the optical and/or ALMA, EVLA and SKA pathfinders in the radio will undoutedly boost this field by allowing to reach much better signal-to-noise ratios at higher spectral resolution and to perform measurements on molecules in the ISM of high redshift galaxies.Comment: 11 pages, 3 figure