Observation of Transparency of Erbium-doped Silicon nitride in photonic crystal nanobeam cavities

One-dimensional nanobeam photonic crystal cavities are fabricated in an Er-doped amorphous silicon nitride layer. Photoluminescence from the cavities around 1.54 um is studied at cryogenic and room temperatures at different optical pump powers. The resonators demonstrate Purcell enhanced absorption and emission rates, also confirmed by time-resolved measurements. Resonances exhibit linewidth narrowing with pump power, signifying absorption bleaching and the onset of stimulated emission in the material at both 5.5 K and room temperature. We estimate from the cavity linewidths that Er has been pumped to transparency at the cavity resonance wavelength.Comment: 10 pages, 7 figure

Developing an online academic writing tutorial for non-native English speaking international graduate students in diverse programs of studies

This presentation introduces a research/practice project that aims to help non-native English speaking international graduate students improve academic literature review writing through a series of extracurricular online tutorials. The presentation introduces the tutorial delivered via Moodle (an open-source learning management system) and supported by h5p interactive content. To support learners’ academic discourse socialization process, we have added interactive elements such as peer review, collaborative writing, and instructor feedback to the main writing tasks in the tutorials. The participants come from two Canadian universities and represent six different first languages and four disciplines. We report the preliminary results regarding the following research questions: what the participants’ challenges in academic writing are; and what kind of learning experiences they are getting from the tutorial (their genre awareness, reflection of collaborative writing practices, tutorial materials, etc.)

Rethinking origin licensing

Human cells that lack a subunit in their origin recognition complex are viable, which suggests the existence of alternative mechanisms to initiate DNA replication

Enhanced Light Emission from Erbium Doped Silicon Nitride in Plasmonic Metal-Insulator-Metal Structures

Plasmonic gratings and nano-particle arrays in a metal-insulator-metal structures are fabricated on an erbium doped silicon nitride layer. This material system enables simple fabrication of the structure, since the active nitride layer can be directly grown on metal. Enhancement of collected emission of up to 12 is observed on resonance, while broad off-resonant enhancement is also present. The output polarization behavior of the gratings and nano-particle arrays is investigated and matched to plasmonic resonances, and the behavior of coupled modes as a function of inter-particle distance is also discussed.Comment: 9 pages, 6 figures updated because pdf was still non-functiona

Improved genome editing in human cell lines using the CRISPR method

The Cas9/CRISPR system has become a popular choice for genome editing. In this system, binding of a single guide (sg) RNA to a cognate genomic sequence enables the Cas9 nuclease to induce a double-strand break at that locus. This break is next repaired by an error-prone mechanism, leading to mutation and gene disruption. In this study we describe a range of refinements of the method, including stable cell lines expressing Cas9, and a PCR based protocol for the generation of the sgRNA. We also describe a simple methodology that allows both elimination of Cas9 from cells after gene disruption and re-introduction of the disrupted gene. This advance enables easy assessment of the off target effects associated with gene disruption, as well as phenotype-based structure-function analysis. In our study, we used the Fan1 DNA repair gene as control in these experiments. Cas9/CRISPR-mediated Fan1 disruption occurred at frequencies of around 29%, and resulted in the anticipated spectrum of genotoxin hypersensitivity, which was rescued by re-introduction of Fan1

Coupled fiber taper extraction of 1.53 um photoluminescence from erbium doped silicon nitride photonic crystal cavities

Optical fiber tapers are used to collect photoluminescence emission at ~1.5 um from photonic crystal cavities fabricated in erbium doped silicon nitride on silicon. Photoluminescence collection via fiber taper is enhanced 2.5 times relative to free space, with a total taper collection efficiency of 53%. By varying the fiber taper offset from the cavity, a broad tuning range of coupling strength is obtained. This material system combined with fiber taper collection is promising for building on-chip optical amplifiers.Comment: 10 pages, 7 figure

Rapid generation of endogenously driven transcriptional reporters in cells through CRISPR/Cas9

CRISPR/Cas9 technologies have been employed for genome editing to achieve gene knockouts and knock-ins in somatic cells. Similarly, certain endogenous genes have been tagged with fluorescent proteins. Often, the detection of tagged proteins requires high expression and sophisticated tools such as confocal microscopy and flow cytometry. Therefore, a simple, sensitive and robust transcriptional reporter system driven by endogenous promoter for studies into transcriptional regulation is desirable. We report a CRISPR/Cas9-based methodology for rapidly integrating a firefly luciferase gene in somatic cells under the control of endogenous promoter, using the TGFβ-responsive gene PAI-1. Our strategy employed a polycistronic cassette containing a non-fused GFP protein to ensure the detection of transgene delivery and rapid isolation of positive clones. We demonstrate that firefly luciferase cDNA can be efficiently delivered downstream of the promoter of the TGFβ-responsive gene PAI-1. Using chemical and genetic regulators of TGFβ signalling, we show that it mimics the transcriptional regulation of endogenous PAI-1 expression. Our unique approach has the potential to expedite studies on transcription of any gene in the context of its native chromatin landscape in somatic cells, allowing for robust high-throughput chemical and genetic screens

ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.go

Automatic Determination of Stellar Atmospheric Parameters and Construction of Stellar Spectral Templates of the Guoshoujing Telescope (LAMOST)

A number of spectroscopic surveys have been carried out or are planned to study the origin of the Milky Way. Their exploitation requires reliable automated methods and softwares to measure the fundamental parameters of the stars. Adopting the ULySS package, we have tested the effect of different resolutions and signal-to-noise ratios (SNR) on the measurement of the stellar atmospheric parameters (effective temperature Teff, surface gravity log g, and metallicity [Fe/H]). We show that ULySS is reliable to determine these parameters with medium-resolution spectra (R~2000). Then, we applied the method to measure the parameters of 771 stars selected in the commissioning database of the Guoshoujing Telescope (GSJT). The results were compared with the SDSS/SEGUE Stellar Parameter Pipeline (SSPP), and we derived precisions of 167 K, 0.34 dex, and 0.16 dex for Teff, log g and [Fe/H] respectively. Furthermore, 120 of these stars are selected to construct the primary stellar spectra template library (Version 1.0) of GSJT, and will be deployed as basic ingredients for the GSJT automated parametrization pipeline.Comment: 23 pages, 15 figures, accepted by RA

Modulating signaling networks by CRISPR/Cas9-mediated transposable element insertion

In a recent past, transposable elements (TEs) were referred to as selfish genetic components only capable of copying themselves with the aim of increasing the odds of being inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into host genome comprises an important evolutionary mechanism capable of increasing the adaptive fitness. As insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility of setting the host functions, although the lack of appropriate genome engineering tools has unpaved it. Fortunately, the emergence of genome editing technologies based on programmable nucleases, and especially the arrival of a multipurpose RNA-guided Cas9 endonuclease system, has made it possible to reconsider this challenge. For such purpose, a particular type of transposons referred to as miniature inverted-repeat transposable elements (MITEs) has shown a series of interesting characteristics for designing functional drivers. Here, recent insights into MITE elements and versatile RNA-guided CRISPR/Cas9 genome engineering system are given to understand how to deploy the potential of TEs for control of the host transcriptional activity.Fil: Vaschetto, Luis Maria Benjamin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Cátedra de Diversidad Animal I; Argentin