Atomic-level structural and chemical analysis of Cr-doped Bi2Se3 thin films

We present a study of the structure and chemical composition of the Cr-doped 3D topological insulator Bi2Se3. Single-crystalline thin films were grown by molecular beam epitaxy on Al2O3 (0001), and their structural and chemical properties determined on an atomic level by aberration-corrected scanning transmission electron microscopy and electron energy loss spectroscopy. A regular quintuple layer stacking of the Bi2Se3 film is found, with the exception of the first several atomic layers in the initial growth. The spectroscopy data gives direct evidence that Cr is preferentially substituting for Bi in the Bi2Se3 host. We also show that Cr has a tendency to segregate at internal grain boundaries of the Bi2Se3 film

Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements

<p>Abstract</p> <p>Background</p> <p>Transcription factor binding to DNA requires both an appropriate binding element and suitably open chromatin, which together help to define regulatory elements within the genome. Current methods of identifying regulatory elements, such as promoters or enhancers, typically rely on sequence conservation, existing gene annotations or specific marks, such as histone modifications and p300 binding methods, each of which has its own biases.</p> <p>Results</p> <p>Herein we show that an approach based on clustering of transcription factor peaks from high-throughput sequencing coupled with chromatin immunoprecipitation (Chip-Seq) can be used to evaluate markers for regulatory elements. We used 67 data sets for 54 unique transcription factors distributed over two cell lines to create regulatory element clusters. By integrating the clusters from our approach with histone modifications and data for open chromatin, we identified general methylation of lysine 4 on histone H3 (H3K4me) as the most specific marker for transcription factor clusters. Clusters mapping to annotated genes showed distinct patterns in cluster composition related to gene expression and histone modifications. Clusters mapping to intergenic regions fall into two groups either directly involved in transcription, including miRNAs and long noncoding RNAs, or facilitating transcription by long-range interactions. The latter clusters were specifically enriched with H3K4me1, but less with acetylation of lysine 27 on histone 3 or p300 binding.</p> <p>Conclusion</p> <p>By integrating genomewide data of transcription factor binding and chromatin structure and using our data-driven approach, we pinpointed the chromatin marks that best explain transcription factor association with different regulatory elements. Our results also indicate that a modest selection of transcription factors may be sufficient to map most regulatory elements in the human genome.</p

The Cardiac Transcription Network Modulated by Gata4, Mef2a, Nkx2.5, Srf, Histone Modifications, and MicroRNAs

The transcriptome, as the pool of all transcribed elements in a given cell, is regulated by the interaction between different molecular levels, involving epigenetic, transcriptional, and post-transcriptional mechanisms. However, many previous studies investigated each of these levels individually, and little is known about their interdependency. We present a systems biology study integrating mRNA profiles with DNA–binding events of key cardiac transcription factors (Gata4, Mef2a, Nkx2.5, and Srf), activating histone modifications (H3ac, H4ac, H3K4me2, and H3K4me3), and microRNA profiles obtained in wild-type and RNAi–mediated knockdown. Finally, we confirmed conclusions primarily obtained in cardiomyocyte cell culture in a time-course of cardiac maturation in mouse around birth. We provide insights into the combinatorial regulation by cardiac transcription factors and show that they can partially compensate each other's function. Genes regulated by multiple transcription factors are less likely differentially expressed in RNAi knockdown of one respective factor. In addition to the analysis of the individual transcription factors, we found that histone 3 acetylation correlates with Srf- and Gata4-dependent gene expression and is complementarily reduced in cardiac Srf knockdown. Further, we found that altered microRNA expression in Srf knockdown potentially explains up to 45% of indirect mRNA targets. Considering all three levels of regulation, we present an Srf-centered transcription network providing on a single-gene level insights into the regulatory circuits establishing respective mRNA profiles. In summary, we show the combinatorial contribution of four DNA–binding transcription factors in regulating the cardiac transcriptome and provide evidence that histone modifications and microRNAs modulate their functional consequence. This opens a new perspective to understand heart development and the complexity cardiovascular disorders

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Conducting polymer nanocomposite-based supercapacitors

The use of nanocomposites of electronically-conducting polymers for supercapacitors has increased significantly over the past years, due to their high capacitances and abilities to withstand many charge-discharge cycles. We have recently been investigating the use of nanocomposites of electronically-conducting polymers containing conducting and non-conducting nanomaterials such as carbon nanotubes and cellulose nanocrystals, for use in supercapacitors. In this contribution, we provide a summary of some of the key issues in this area of research. This discussion includes some history, fundamental concepts, the physical and chemical processes involved, and the challenges that these nanocomposite materials must overcome in order to become technologically viable. Due to space limitations, this is not a complete review of all the work that has been done in this field and we have focused on common themes that appear in the published work. Our aim is that this chapter will help readers to understand the advantages and challenges involved in the use of these materials in supercapacitors and to identify areas for further development

Design and analysis of 1.3 mu m GaAs-based quantum dot vertical-cavity surface-emitting lasers

A theoretical study on 1.3 mu m GaAs-based quantum dot vertical-cavity surface-emitting lasers (VCSELs) was made. Investigation of the influence of VCSELs on the optical confinement factors and the optical loss and the calculation of the material gain of the assembled InGaAs/GaAs quantum dots. Analysis of the threshold characteristic was made and the multi-wavelength cavity and multilayer quantum-dot stack structure is found to be more suitable for quantum dot VCSELs

Electrical conductivity of a single Au/polyaniline microfiber

International audienceWe report the measurements of conductivity, I-V curve, and magnetoresistance of a single Au/polyaniline microfiber with a core-shell structure, on which a pair of platinum microleads was attached by focused ion beam. The Au/polyaniline microfiber shows a much higher conductivity (~110 S/cm at 300 K) and a much weaker temperature dependence of resistance [R(4 K)/R(300 K)=5.1] as compared with those of a single polyaniline microtube [sigmaRT=30–40 S/cm and R(4 K)/R(300 K)=16.2]. The power-law dependence of R(T)[proportional]T–beta, with beta=0.38, indicates that the measured Au/polyaniline microfiber is lying in the critical regime of the metal-insulator transition. In addition, the microfiber shows a H2 dependent positive magnetoresistance at 2, 4, and 6 K