Design and simulation of losses in Ge/SiGe terahertz quantum cascade laser waveguides.

The waveguide losses from a range of surface plasmon and double metal waveguides for Ge/Si1-xGex THz quantum cascade laser gain media are investigated at 4.79 THz (62.6 µm wavelength). Double metal waveguides demonstrate lower losses than surface plasmonic guiding with minimum losses for a 10 µm thick active gain region with silver metal of 21 cm-1 at 300 K reducing to 14.5 cm-1 at 10 K. Losses for silicon foundry compatible metals including Al and Cu are also provided for comparison and to provide a guide for gain requirements to enable lasers to be fabricated in commercial silicon foundries. To allow these losses to be calculated for a range of designs, the complex refractive index of a range of nominally undoped Si1-xGex with x = 0.7, 0.8 and 0.9 and doped Ge heterolayers were extracted from Fourier transform infrared spectroscopy measurements between 0.1 and 10 THz and from 300 K down to 10 K. The results demonstrate losses comparable to similar designs of GaAs/AlGaAs quantum cascade laser plasmon waveguides indicating that a gain threshold of 15.1 cm-1 and 23.8 cm-1 are required to produce a 4.79 THz Ge/SiGe THz laser at 10 K and 300 K, respectively, for 2 mm long double metal waveguide quantum cascade lasers with facet coatings.

Clinical and genetic characteristics of xeroderma pigmentosum in Nepal.

BACKGROUND: Little is known about xeroderma pigmentosum (XP) in Himalayan countries. OBJECTIVE: To describe clinical characteristics of XP in Nepal and investigate its genetic bases. METHODS: This study was carried out on all consecutive patients referred for XP to a Nepalese tertiary referral centre in 2014-2015. Clinical data were collected using a standardized questionnaire. DNA was extracted from salivary samples, and next-generation sequencing (NGS) was conducted using a panel covering all 8 known XP genes (classical XP (XP-A to XP-G) and XP variant) and a skin cancer modifier gene, the melanocortin 1 receptor gene (MC1R). RESULTS: Seventeen patients (median age: 15 years; range: 1-32) were included. Twelve had skin cancers (including a total of 8 squamous cell carcinomas, 60 basal cell carcinomas, ocular carcinomas requiring an orbital exenteration in 3 patients, but no melanoma). Fifteen patients carried the same homozygous non-sense XPC mutation c.1243C>T, p.R415X. A homozygous non-sense XPA mutation (p.W235X) was found in the only patient with a history of early severe sunburn reaction and associated neurological symptoms. Associated genetic alterations included heterozygous missense variants in XPD/ERCC2 gene and the presence of MC1R variant R163Q in 5 and 9 patients, respectively. CONCLUSION: Although not previously reported, XP seems frequent in Nepal. Patients often presented with a very severe phenotype after a long history of excessive sun exposure without knowledge of the disease. Fifteen of 17 had the same p.R415X XPC mutation, which seems very specific of XP in Nepal, suggesting a founder effect. NGS analyses frequently revealed associated genetic alterations which could play a modifier role in the clinical expression of the disease.

Reducing Phonon-Induced Decoherence in Solid-State Single-Photon Sources with Cavity Quantum Electrodynamics.

Solid-state emitters are excellent candidates for developing integrated sources of single photons. Yet, phonons degrade the photon indistinguishability both through pure dephasing of the zero-phonon line and through phonon-assisted emission. Here, we study theoretically and experimentally the indistinguishability of photons emitted by a semiconductor quantum dot in a microcavity as a function of temperature. We show that a large coupling to a high quality factor cavity can simultaneously reduce the effect of both phonon-induced sources of decoherence. It first limits the effect of pure dephasing on the zero-phonon line with indistinguishabilities above 97% up to 18 K. Moreover, it efficiently redirects the phonon sidebands into the zero-phonon line and brings the indistinguishability of the full emission spectrum from 87% (24%) without cavity effect to more than 99% (76%) at 0K (20K). We provide guidelines for optimal cavity designs that further minimize the phonon-induced decoherence.

Homogeneous array of nanowire-embedded quantum light emitters.

The potential for scale-up coupled with minimized system size is likely to be a major determining factor in the realization of applicable quantum information systems. Nanofabrication technology utilizing the III-V semiconductor system provides a path to scalable quantum bit (qubit) integration and a materials platform with combined electronic/photonic functionality. Here, we address the key requirement of qubit-site and emission energy control for scale-up by demonstrating uniform arrays of III-V nanowires, where each nanowire contains a single quantum dot. Optical studies of single nanowire quantum dots reveal narrow linewidth exciton and biexciton emission and clear state-filling at higher powers. Individual nanowire quantum dots are shown to emit nonclassically with clear evidence of photon antibunching. A model is developed to explain unexpectedly large excited state separations as revealed by photoluminescence emission spectra. From measurements of more than 40 nanowire quantum dots, we find emission energies with an ensemble broadening of 15 meV. The combination of deterministic site control and the narrow distribution in ensemble emission energy results in a system readily capable of scaling for multiqubit quantum information applications.

Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates.

The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000-12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000-67 000 ya using an average mammalian microsatellite mutation rate and at 4700-44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70-110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.

Long lifetimes of quantum-dot intersublevel transitions in the terahertz range.

Carrier relaxation is a key issue in determining the efficiency of semiconductor optoelectronic device operation. Devices incorporating semiconductor quantum dots have the potential to overcome many of the limitations of quantum-well-based devices because of the predicted long quantum-dot excited-state lifetimes. For example, the population inversion required for terahertz laser operation in quantum-well-based devices (quantum-cascade lasers) is fundamentally limited by efficient scattering between the laser levels, which form a continuum in the plane of the quantum well. In this context, semiconductor quantum dots are a highly attractive alternative for terahertz devices, because of their intrinsic discrete energy levels. Here, we present the first measurements, and theoretical description, of the intersublevel carrier relaxation in quantum dots for transition energies in the few terahertz range. Long intradot relaxation times (1.5 ns) are found for level separations of 14 meV (3.4 THz), decreasing very strongly to approximately 2 ps at 30 meV (7 THz), in very good agreement with our microscopic theory of the carrier relaxation process. Our studies pave the way for quantum-dot terahertz device development, providing the fundamental knowledge of carrier relaxation times required for optimum device design.

Glucocorticoids and protein kinase A coordinately modulate transcription factor recruitment at a glucocorticoid-responsive unit.

The rat tyrosine aminotransferase gene is a model system to study transcriptional regulation by glucocorticoid hormones. We analyzed transcription factor binding to the tyrosine aminotransferase gene glucocorticoid-responsive unit (GRU) at kb -2.5, using in vivo footprinting studies with both dimethyl sulfate and DNase I. At this GRU, glucocorticoid activation triggers a disruption of the nucleosomal structure. We show here that various regulatory pathways affect transcription factor binding to this GRU. The binding differs in two closely related glucocorticoid-responsive hepatoma cell lines. In line H4II, glucocorticoid induction promotes the recruitment of hepatocyte nuclear factor 3 (HNF3), presumably through the nucleosomal disruption. However, the footprint of the glucocorticoid receptor (GR) is not visible, even though a regular but transient interaction of the GR is necessary to maintain HNF3 binding. In contrast, in line FTO2B, HNF3 binds to the GRU in the absence of glucocorticoids and nucleosomal disruption, showing that a "closed" chromatin conformation does not repress the binding of certain transcription factors in a uniform manner. In FTO2B cells, the footprint of the GR is detectable, but this requires the activation of protein kinase A. In addition, protein kinase A stimulation also improves the recruitment of HNF3 independently of glucocorticoids and enhances the glucocorticoid response mediated by this GRU in an HNF3-dependent manner. In conclusion, the differences in the behavior of this regulatory sequence in the two cell lines show that various regulatory pathways are integrated at this GRU through modulation of interrelated events: transcription factor binding to DNA and nucleosomal disruption.

Participation of Ets transcription factors in the glucocorticoid response of the rat tyrosine aminotransferase gene.

We have previously shown that two remote glucocorticoid-responsive units (GRUs) of the rat tyrosine aminotransferase (TAT) gene contain multiple binding sites for several transcription factor families, including the glucocorticoid receptor (GR). We report here the identification of two novel binding sites for members of the Ets family of transcription factors in one of these GRUs. One of these binding sites overlaps the major GR-binding site (GRBS), whereas the other is located in its vicinity. Inactivation of the latter binding site leads to a twofold reduction of the glucocorticoid response, whereas inactivation of the site overlapping the GRBS has no detectable effect. In vivo footprinting analysis reveals that the active site is occupied in a glucocorticoid-independent manner, in a TAT-expressing cell line, even though it is located at a position where there is a glucocorticoid-dependent alteration of the nucleosomal structure. This same site is not occupied in a cell line that does not express TAT but expresses Ets-related DNA-binding activities, suggesting the existence of an inhibitory effect of chromatin structure at a hierarchical level above the nucleosome. The inactive Ets-binding site that overlaps the GRBS is not occupied even in TAT-expressing cells. However, this same overlapping site can confer Ets-dependent stimulation of both basal and glucocorticoid-induced levels when it is isolated from the GRU and duplicated. Ets-1 expression in COS cells mimics the activity of the Ets-related activities present in hepatoma cells. These Ets-binding sites could participate in the integration of the glucocorticoid response of the TAT gene with signal transduction pathways triggered by other nonsteroidal extracellular stimuli.

Glucocorticoid receptor, C/EBP, HNF3, and protein kinase A coordinately activate the glucocorticoid response unit of the carbamoylphosphate synthetase I gene.

A single far-upstream enhancer is sufficient to confer hepatocyte-specific, glucocorticoid- and cyclic AMP-inducible periportal expression to the carbamoylphosphate synthetase I (CPS) gene. To identify the mechanism of hormone-dependent activation, the composition and function of the enhancer have been analyzed. DNase I protection and gel mobility shift assays revealed the presence of a cyclic AMP response element, a glucocorticoid response element (GRE), and several sites for the liver-enriched transcription factor families HNF3 and C/EBP. The in vivo relevance of the transcription factors interacting with the enhancer in the regulation of CPS expression in the liver was assessed by the analysis of knockout mice. A strong reduction of CPS mRNA levels was observed in glucocorticoid receptor- and C/EBPalpha-deficient mice, whereas the CPS mRNA was normally expressed in C/EBPbeta knockout mice and in HNF3alpha and -gamma double-knockout mice. (The role of HNFbeta could not be assessed, because the corresponding knockout mice die at embryonic day 10). In hepatoma cells, most of the activity of the enhancer is contained within a 103-bp fragment, which depends for its activity on the simultaneous occupation of the GRE, HNF3, and C/EBP sites, thus meeting the requirement of a glucocorticoid response unit. In fibroblast-like CHO cells, on the other hand, the GRE in the CPS enhancer does not cooperate with the C/EBP and HNF3 elements in transactivation of the CPS promoter. In both hepatoma and CHO cells, stimulation of expression by cyclic AMP depends mainly on the integrity of the glucocorticoid pathway, demonstrating cross talk between this pathway and the cyclic AMP (protein kinase A) pathway.

A cost-effective high-throughput metabarcoding approach powerful enough to genotype ~44 000 year-old rodent remains from Northern Africa.

We present a cost-effective metabarcoding approach, aMPlex Torrent, which relies on an improved multiplex PCR adapted to highly degraded DNA, combining barcoding and next-generation sequencing to simultaneously analyse many heterogeneous samples. We demonstrate the strength of these improvements by generating a phylochronology through the genotyping of ancient rodent remains from a Moroccan cave whose stratigraphy covers the last 120 000 years. Rodents are important for epidemiology, agronomy and ecological investigations and can act as bioindicators for human- and/or climate-induced environmental changes. Efficient and reliable genotyping of ancient rodent remains has the potential to deliver valuable phylogenetic and paleoecological information. The analysis of multiple ancient skeletal remains of very small size with poor DNA preservation, however, requires a sensitive high-throughput method to generate sufficient data. We show this approach to be particularly adapted at accessing this otherwise difficult taxonomic and genetic resource. As a highly scalable, lower cost and less labour-intensive alternative to targeted sequence capture approaches, we propose the aMPlex Torrent strategy to be a useful tool for the genetic analysis of multiple degraded samples in studies involving ecology, archaeology, conservation and evolutionary biology.

Premature termination codons enhance mRNA decapping in human cells.

Nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance process that promotes selective degradation of imperfect messages containing premature translation termination codons (PTCs). In yeast, PTCs trigger both deadenylylation-independent mRNA decapping, thereby allowing their rapid degradation by a 5' to 3' exonuclease, and to a smaller extent accelerated deadenylylation. It is not clear to what extent this decay pathway is conserved in higher eukaryotes. We used a transcriptional pulse strategy relying on a tetracycline-regulated promoter to study the decay of a PTC- containing beta-globin mRNA in human cells. We show that a PTC destabilizes the mRNA and decreases its half-life from >16 h to 3 h. The deadenylylation rate is increased, but not sufficiently to account for the decreased half-life on its own. Using a circularization RT-PCR (cRT-PCR) strategy, we could detect decapped degradation intermediates and measure simultaneously their poly(A) tail length. This allowed us to show that a PTC enhances the rate of mRNA decapping and that decapped products have been deadenylylated to a certain extent. Thus the major feature of the NMD pathway, enhanced decapping, is conserved from yeast to man even though the kinetic details might differ between various mRNAs and/or species.

Coherent manipulation of a solid-state artificial atom with few photons.

In a quantum network based on atoms and photons, a single atom should control the photon state and, reciprocally, a single photon should allow the coherent manipulation of the atom. Both operations require controlling the atom environment and developing efficient atom-photon interfaces, for instance by coupling the natural or artificial atom to cavities. So far, much attention has been drown on manipulating the light field with atomic transitions, recently at the few-photon limit. Here we report on the reciprocal operation and demonstrate the coherent manipulation of an artificial atom by few photons. We study a quantum dot-cavity system with a record cooperativity of 13. Incident photons interact with the atom with probability 0.95, which radiates back in the cavity mode with probability 0.96. Inversion of the atomic transition is achieved for 3.8 photons on average, showing that our artificial atom performs as if fully isolated from the solid-state environment.

In vivo analysis of the model tyrosine aminotransferase gene reveals multiple sequential steps in glucocorticoid receptor action.

We are studying the mechanisms of transcriptional activation by nuclear receptors and we focus our studies on the glucocorticoid regulation of the model tyrosine aminotransferase gene. Rather than using in vitro biochemical approaches, we determine the actual events occurring in the cells. Our experimental approaches include genomic footprinting, chromatin immunoprecipitation, in situ hybridization and transgenic mice. Our results show that the glucocorticoid receptor uses a dynamic multistep mechanism to recruit successively accessory DNA binding proteins that assist in the activation process. Chromatin is first remodelled, DNA is then demethylated, and the synthesis of an accessory factor is induced. Efficient transcription induction is finally achieved upon the formation of a 'stable' multiprotein complex interacting with the regulatory element. We discuss: the relative contribution of histone acetyltransferases and ATP-dependent remodelling machines to the chromatin remodelling event; the nature of the remodelled state; the contribution of regulated DNA demethylation to gene memory during development; the mechanisms of regulated DNA demethylation; the dynamics of protein recruitment at regulatory elements; the control of the frequency of transcription pulses and the control levels of the cell-type specificity of the glucocorticoid response.

Complete complementary DNA of rat tyrosine aminotransferase messenger RNA. Deduction of the primary structure of the enzyme.

The primary structure of rat tyrosine aminotransferase (L-tyrosine:2-oxoglutarate aminotransferase; EC 2.6.1.5), a liver-specific enzyme involved in gluconeogenesis, has been deduced from the nucleotide sequence of a cloned full-length cDNA. The mRNA is 2362 nucleotides long (excluding the poly(A) tail) and codes for a polypeptide of 454 amino acids with a molecular weight of 50634. Unambiguous identification was obtained by comparison of this sequence with the amino acid sequences of several peptides obtained from the purified enzyme.

Stable secondary structures at the 3'-end of the genome of yellow fever virus (17 D vaccine strain).

The sequence of the 3'-terminal 565 nucleotides of yellow fever virus has been determined from a cloned cDNA. Several structures are detectable: three tandemly repeated sequences, a series of inverted repeats and a stable secondary structure involving the 3'-terminal 120 nucleotides.

Local DNA demethylation in vertebrates: how could it be performed and targeted?

In vertebrates, cytosine methylation is an epigenetic DNA modification that participates in genome stability and gene repression. Methylation patterns are either maintained throughout cell division, or modified by global or local de novo methylation and demethylation. Site-specific demethylation is a rather elusive process that occurs mainly in parallel to gene activation during development. In light of our studies of the glucocorticoid-dependent DNA demethylation of the tyrosine aminotransferase gene, we discuss the potential biochemical mechanisms allowing DNA demethylation and its targeting to specific sequences by transcription factors as well as possible links to DNA replication and chromatin remodelling.

Two liver-enriched trans-acting factors support the tissue-specific basal transcription from the rat tyrosine aminotransferase promoter.

The rat tyrosine aminotransferase gene (TAT) is a glucocorticoid-inducible gene, specifically expressed in liver. Using gel retardation assays, we have shown that its promoter (nt + 1 to -350; TAT.35) binds a combination of both ubiquitous and liver-specific trans-acting factors. Cis-acting sequences spanning: (i) nt -65 to -85 bound NF-Y, an ubiquitous "AACCAAT" box binding factor; (ii) nt -157 to -171 bound a liver-enriched member of the NF1 gene family [NF1Liver (NF1L hereafter)]; (iii) nt -266 to -281 bound the liver specific factor HNF1; and (iv) nt -283 to -288 bound ubiquitous "CCAAT" box binding factor(s). Moreover, the TAT gene promoter was able to drive liver-specific basal transcription, even in an in vitro assay using TAT-expressing (liver) vs non-expressing (spleen) crude nuclear extracts (NEs). Competition studies in transcription with both unmutated and mutated ds-oligonucleotides (ds-oligos) demonstrated that NF1L and HNF1 supported approx. 60 and 25% of the basal transcriptional activity sustained by TAT.35 in the liver, respectively. Neither of these oligos affected the very low level of transcription sustained by spleen NEs. This suggests a minor role for HNF1 in liver-specific basal TAT gene expression, consistent with previous observations with dedifferentiated C2 hepatoma cells (which does not express HNF1) [Deschatrette and Weiss. Biochimie 56 (1974) 1603-1611 and Cereghini et al. EMBO Jl9 (1990) 2257-2263]. Competition studies in liver-specific in vitro transcription with ds-oligo -265/-290 yielded a 90% inhibition, suggesting either that sequences spanning nt -283 to -288 sequester "CCAAT-box" binding factor(s) that may be relevant elsewhere for TAT promoter function (e.g. NF-Y which interacts with nt -65 to -85), or that such a factor interacts functionally with HNF1.

Hepatocyte nuclear factor 3 determines the amplitude of the glucocorticoid response of the rat tyrosine aminotransferase gene.

Hepatocyte nuclear factor 3 (HNF3) recognizes two apparently distinct classes of sequence. However, a detailed mutational analysis of a representative binding site of each class reveals that these sequences display common features. We propose a unified consensus sequence for HNF3-binding sites. The basis of the sequence specificity of the interaction of HNF3 with DNA is analyzed in light of the recently determined structure of an HNF3-DNA complex (Clark et al., Nature 364, 412-420, 1993). Particularly, our study reveals that the DNA site used for this structural analysis is too short to account for all HNF3-DNA interactions. The better knowledge of the sequence determinant recognized by HNF3 has allowed us to analyze its function in the glucocorticoid response of the rat tyrosine aminotransferase (TAT) gene. This response is mediated through a complex array of neighboring and overlapping transcription factor binding sites. Selective inactivation of the HNF3-binding sites in this glucocorticoid response unit (GRU) allows us to demonstrate unambiguously that they play a major role in the amplitude of the glucocorticoid response. Furthermore, HNF3 beta overexpression results in a stimulation of the glucocorticoid response that is dependent on the integrity of its binding sites. We also show that the relative level of HNF3 determines the extent of the contribution of one of the glucocorticoid receptor binding sites. Our results indicate that HNF3 accounts for most of the liver-specific activity of this GRU.