Deep and shallow electronic states associated to doping, contamination and intrinsic defects in ε-Ga2O3 epilayers

Deep and shallow electronic states in undoped and Si-doped ε-Ga2O3 epilayers grown by MOVPE on c-oriented Al2O3 were investigated by cathodoluminescence, optical absorption, photocurrent spectroscopy, transport measurements, and electron-paramagnetic-resonance. Nominally undoped films were highly resistive, with a room temperature resistivity varying in the range 107- 1013 Ωcm depending on the carrier gas used during growth. Films grown with He carrier were generally more resistive than those grown with H2 carrier and exhibited a Fermi level located at about 0.8 eV below the conduction band edge, which tends to shift deeper with temperature. This can tentatively be attributed to the combined action of deep donors (probably carbon impurities and oxygen vacancies) and deep acceptors (Ga vacancies and related complexes), which compensate residual shallow donors. There are strong experimental hints that nitrogen also behaves as deep acceptor. Room temperature resistivity as low as 0.42 Ωcm and electron concentrations around 1018 cm−3 were obtained by silicon doping. Si was confirmed to act as shallow donor with sufficiently high solubility. A variable range hopping conduction was observed in a wide temperature interval in the n-type layers, and compensation by native acceptors also plays a major role on conduction mechanisms. Previous evaluations of curvature and anisotropy of the conduction band are confirmed, which allows for the estimation of the electron effective mass. The present experimental data are discussed considering the theoretical predictions for point defect formation in the ε-polymorph as well as literature data on extrinsic and intrinsic defects in β-Ga2O3

Silver-enriched ZnO:Ag thin films deposited by magnetron co-sputtering: Post annealing effects on structural and physical properties

The ZnO semiconductor is probably among the most mentioned compounds in the scientific literature during the last decade, which is mainly due to its wide spectrum of applications. Compounds based on ZnO (in doped or composite form) are of great relevance for the development of high-tech devices. In this work, we present the growth and characterization of samples deposited by DC Magnetron co-sputtering from two pure Zn and Ag targets in an O2 / Ar atmosphere. The samples were characterized as deposited and after an annealing treatment in a reducing atmosphere. We have used XRD, RBS, ellipsometry, UV visible photoluminescence, and electrical measurements for sample characterization. The results revealed the amorphization of ZnO when the Ag content increases and, after annealing, a mixture of crystalline phases was detected for the samples with higher Ag content. It is also demonstrated the strong effect of the presence of Ag atoms in the stimulated optical and electrical responses from ZnO:Ag compounds obtained in this wor

Posterior Association Networks and Functional Modules Inferred from Rich Phenotypes of Gene Perturbations

Combinatorial gene perturbations provide rich information for a systematic exploration of genetic interactions. Despite successful applications to bacteria and yeast, the scalability of this approach remains a major challenge for higher organisms such as humans. Here, we report a novel experimental and computational framework to efficiently address this challenge by limiting the ‘search space’ for important genetic interactions. We propose to integrate rich phenotypes of multiple single gene perturbations to robustly predict functional modules, which can subsequently be subjected to further experimental investigations such as combinatorial gene silencing. We present posterior association networks (PANs) to predict functional interactions between genes estimated using a Bayesian mixture modelling approach. The major advantage of this approach over conventional hypothesis tests is that prior knowledge can be incorporated to enhance predictive power. We demonstrate in a simulation study and on biological data, that integrating complementary information greatly improves prediction accuracy. To search for significant modules, we perform hierarchical clustering with multiscale bootstrap resampling. We demonstrate the power of the proposed methodologies in applications to Ewing's sarcoma and human adult stem cells using publicly available and custom generated data, respectively. In the former application, we identify a gene module including many confirmed and highly promising therapeutic targets. Genes in the module are also significantly overrepresented in signalling pathways that are known to be critical for proliferation of Ewing's sarcoma cells. In the latter application, we predict a functional network of chromatin factors controlling epidermal stem cell fate. Further examinations using ChIP-seq, ChIP-qPCR and RT-qPCR reveal that the basis of their genetic interactions may arise from transcriptional cross regulation. A Bioconductor package implementing PAN is freely available online at http://bioconductor.org/packages/release/bioc/html/PANR.html

Identifying Determinants of Cullin Binding Specificity Among the Three Functionally Different Drosophila melanogaster Roc Proteins via Domain Swapping

BACKGROUND: Cullin-dependent E3 ubiquitin ligases (CDL) are key regulators of protein destruction that participate in a wide range of cell biological processes. The Roc subunit of CDL contains an evolutionarily conserved RING domain that binds ubiquitin charged E2 and is essential for ubiquitylation. Drosophila melanogaster contains three highly related Roc proteins: Roc1a and Roc2, which are conserved in vertebrates, and Roc1b, which is specific to Drosophila. Our previous genetic data analyzing Roc1a and Roc1b mutants suggested that Roc proteins are functionally distinct, but the molecular basis for this distinction is not known. METHODOLOGY/PRINCIPAL FINDINGS: Using co-immunoprecipitation studies we show that Drosophila Roc proteins bind specific Cullins: Roc1a binds Cul1-4, Roc1b binds Cul3, and Roc2 binds Cul5. Through domain swapping experiments, we demonstrate that Cullin binding specificity is strongly influenced by the Roc NH(2)-terminal domain, which forms an inter-molecular beta sheet with the Cullin. Substitution of the Roc1a RING domain with that of Roc1b results in a protein with similar Cullin binding properties to Roc1a that is active as an E3 ligase but cannot complement Roc1a mutant lethality, indicating that the identity of the RING domain can be an important determinant of CDL function. In contrast, the converse chimeric protein with a substitution of the Roc1b RING domain with that of Roc1a can rescue the male sterility of Roc1b mutants, but only when expressed from the endogenous Roc1b promoter. We also identified mutations of Roc2 and Cul5 and show that they cause no overt developmental phenotype, consistent with our finding that Roc2 and Cul5 proteins are exclusive binding partners, which others have observed in human cells as well. CONCLUSIONS: The Drosophila Roc proteins are highly similar, but have diverged during evolution to bind a distinct set of Cullins and to utilize RING domains that have overlapping, but not identical, function in vivo

Human Genetics in Rheumatoid Arthritis Guides a High-Throughput Drug Screen of the CD40 Signaling Pathway

Although genetic and non-genetic studies in mouse and human implicate the CD40 pathway in rheumatoid arthritis (RA), there are no approved drugs that inhibit CD40 signaling for clinical care in RA or any other disease. Here, we sought to understand the biological consequences of a CD40 risk variant in RA discovered by a previous genome-wide association study (GWAS) and to perform a high-throughput drug screen for modulators of CD40 signaling based on human genetic findings. First, we fine-map the CD40 risk locus in 7,222 seropositive RA patients and 15,870 controls, together with deep sequencing of CD40 coding exons in 500 RA cases and 650 controls, to identify a single SNP that explains the entire signal of association (rs4810485, P = 1.4×10(−9)). Second, we demonstrate that subjects homozygous for the RA risk allele have ∼33% more CD40 on the surface of primary human CD19+ B lymphocytes than subjects homozygous for the non-risk allele (P = 10(−9)), a finding corroborated by expression quantitative trait loci (eQTL) analysis in peripheral blood mononuclear cells from 1,469 healthy control individuals. Third, we use retroviral shRNA infection to perturb the amount of CD40 on the surface of a human B lymphocyte cell line (BL2) and observe a direct correlation between amount of CD40 protein and phosphorylation of RelA (p65), a subunit of the NF-κB transcription factor. Finally, we develop a high-throughput NF-κB luciferase reporter assay in BL2 cells activated with trimerized CD40 ligand (tCD40L) and conduct an HTS of 1,982 chemical compounds and FDA–approved drugs. After a series of counter-screens and testing in primary human CD19+ B cells, we identify 2 novel chemical inhibitors not previously implicated in inflammation or CD40-mediated NF-κB signaling. Our study demonstrates proof-of-concept that human genetics can be used to guide the development of phenotype-based, high-throughput small-molecule screens to identify potential novel therapies in complex traits such as RA

A redox state-dictated signalling pathway deciphers the malignant cell specificity of CD40-mediated apoptosis

CD40, a member of the tumour necrosis factor receptor (TNFR) superfamily, has the capacity to cause extensive apoptosis in carcinoma cells, while sparing normal epithelial cells. Yet, apoptosis is only achieved by membrane-presented CD40 ligand (mCD40L), as soluble receptor agonists are but weakly pro-apoptotic. Here, for the first time we have identified the precise signalling cascade underpinning mCD40L-mediated death as involving sequential TRAF3 stabilisation, ASK1 phosphorylation, MKK4 (but not MKK7) activation and JNK/AP-1 induction, leading to a Bak- and Bax-dependent mitochondrial apoptosis pathway. TRAF3 is central in the activation of the NADPH oxidase (Nox)-2 component p40phox and the elevation of reactive oxygen species (ROS) is essential in apoptosis. Strikingly, CD40 activation resulted in down-regulation of Thioredoxin (Trx)-1 to permit ASK1 activation and apoptosis. Although soluble receptor agonist alone could not induce death, combinatorial treatment incorporating soluble CD40 agonist and pharmacological inhibition of Trx-1 was functionally equivalent to the signal triggered by mCD40L. Finally, we demonstrate using normal, ‘para-malignant’ and tumour-derived cells that progression to malignant transformation is associated with increase in oxidative stress in epithelial cells, which coincides with increased susceptibility to CD40 killing, while in normal cells CD40 signalling is cytoprotective. Our studies have revealed the molecular nature of the tumour specificity of CD40 signalling and explained the differences in pro-apoptotic potential between soluble and membrane-bound CD40 agonists. Equally importantly, by exploiting a unique epithelial culture system that allowed us to monitor alterations in the redox-state of epithelial cells at different stages of malignant transformation, our study reveals how pro-apoptotic signals can elevate ROS past a previously hypothesised ‘lethal pro-apoptotic threshold’ to induce death; an observation that is both of fundamental importance and carries implications for cancer therap

Point defect localization and cathodoluminescence emission in undoped ϵ-Ga2O3

In this study, experimental and theoretical investigations have been performed on nominally undoped ϵ-Ga2O3 films deposited on (0001)-Al2O3 substrates by metal-organic vapor phase epitaxy using different O and Ga precursor ratios. Hydrogen and helium were used as carrier gas. Low-temperature cathodoluminescence (CL) broad emissions extending over the range 1.5-3.4 eV were deconvoluted in five peaks, whose position, integrated intensity, and full width at half maximum were investigated in the temperatures range 80 K-300 K. A non-monotonic behavior of the extracted CL peaks is observed, which is attributed to localization phenomena connected with families of point defects. The behavior of two main luminescence emissions with temperature has been simulated using the localized state ensemble model. The derived parameters agree with the experimental observations and provide a new interpretation of micro-and macroscale disorder inside ϵ-Ga2O3 and related potential fluctuations