Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans

We have used whole genome paired-end Illumina sequence data to identify tandem duplications in 20 isofemale lines of D. yakuba, and 20 isofemale lines of D. simulans and performed genome wide validation with PacBio long molecule sequencing. We identify 1,415 tandem duplications that are segregating in D. yakuba as well as 975 duplications in D. simulans, indicating greater variation in D. yakuba. Additionally, we observe high rates of secondary deletions at duplicated sites, with 8% of duplicated sites in D. simulans and 17% of sites in D. yakuba modified with deletions. These secondary deletions are consistent with the action of the large loop mismatch repair system acting to remove polymorphic tandem duplication, resulting in rapid dynamics of gain and loss in duplicated alleles and a richer substrate of genetic novelty than has been previously reported. Most duplications are present in only single strains, suggesting deleterious impacts are common. D. simulans shows larger numbers of whole gene duplications in comparison to larger proportions of gene fragments in D. yakuba. D. simulans displays an excess of high frequency variants on the X chromosome, consistent with adaptive evolution through duplications on the D. simulans X or demographic forces driving duplicates to high frequency. We identify 78 chimeric genes in D. yakuba and 38 chimeric genes in D. simulans, as well as 143 cases of recruited non-coding sequence in D. yakuba and 96 in D. simulans, in agreement with rates of chimeric gene origination in D. melanogaster. Together, these results suggest that tandem duplications often result in complex variation beyond whole gene duplications that offers a rich substrate of standing variation that is likely to contribute both to detrimental phenotypes and disease, as well as to adaptive evolutionary change.Comment: Revised Version- Accepted at Molecular Biology and Evolutio

Photon statistics from coupled quantum dots

We present an optical study of closely-spaced self-assembled InAs/GaAs quantum dots. The energy spectrum and correlations between photons subsequently emitted from a single pair provide not only clear evidence of coupling between the quantum dots but also insight into the coupling mechanism. Our results are in agreement with recent theories predicting that tunneling is largely suppressed between nonidentical quantum dots and that the interaction is instead dominated by dipole-dipole coupling and phonon-assisted energy transfer processes.Comment: 4 pages, 4 figures, to appear in Phys. Re

Frequency control of photonic crystal membrane resonators by mono-layer deposition

We study the response of GaAs photonic crystal membrane resonators to thin film deposition. Slow spectral shifts of the cavity mode of several nanometers are observed at low temperatures, caused by cryo-gettering of background molecules. Heating the membrane resets the drift and shielding will prevent drift altogether. In order to explore the drift as a tool to detect surface layers, or to intentionally shift the cavity resonance frequency, we studied the effect of self-assembled monolayers of polypeptide molecules attached to the membranes. The 2 nm thick monolayers lead to a discrete step in the resonance frequency and partially passivate the surface.Comment: 3 pages, 4 figures, submitted to Appl. Phys. Let

Mouse Rad1 deletion enhances susceptibility for skin tumor development

Cells are constantly exposed to stresses from cellular metabolites as well as environmental genotoxins. DNA damage caused by these genotoxins can be efficiently fixed by DNA repair in cooperation with cell cycle checkpoints. Unrepaired DNA lesions can lead to cell death, gene mutation and cancer. The Rad1 protein, evolutionarily conserved from yeast to humans, exists in cells as monomer as well as a component in the 9-1-1 protein complex. Rad1 plays crucial roles in DNA repair and cell cycle checkpoint control, but its contribution to carcinogenesis is unknown. To address this question, we constructed mice with a deletion of Mrad1. Matings between heterozygous Mrad1 mutant mice produced Mrad1+/+ and Mrad1+/- but no Mrad1-/- progeny, suggesting the Mrad1 null is embryonic lethal. Mrad1+/- mice demonstrated no overt abnormalities up to one and half years of age. DMBA-TPA combinational treatment was used to induce tumors on mouse skin. Tumors were larger, more numerous, and appeared earlier on the skin of Mrad1+/- mice compared to Mrad1+/+ animals. Keratinocytes isolated from Mrad1+/- mice had significantly more spontaneous DNA double strand breaks, proliferated slower and had slightly enhanced spontaneous apoptosis than Mrad1+/+ control cells. These data suggest that Mrad1 is important for preventing tumor development, probably through maintaining genomic integrity. The effects of heterozygous deletion of Mrad1 on proliferation and apoptosis of keratinocytes is different from those resulted from Mrad9 heterozygous deletion (from our previous study), suggesting that Mrad1 also functions independent of Mrad9 besides its role in the Mrad9-Mrad1-Mhus1 complex in mouse cells

O-Band Subwavelength Grating Filters in a Monolithic Photonics Technology

The data communications industry has begun transitioning from electrical to optical interconnects in datacenters in order to overcome performance bottlenecks and meet consumer needs. To mitigate the costs associated with this change and achieve performance for 5G and beyond, it is crucial to explore advanced photonic devices that can enable high-bandwidth interconnects via wavelength-division multiplexing (WDM) in photonic integrated circuits. Subwavelength grating (SWG) filters have shown great promise for WDM applications. However, the small feature sizes necessary to implement these structures have prohibited them from penetrating into industrial applications. To explore the manufacturability and performance of SWG filters in an industrial setting, we fabricate and characterize O-band subwavelength grating filters using the monolithic photonics technology at GLOBALFOUNDRIES (GF). We demonstrate a low drop channel loss of -1.2 dB with a flat-top response, a high extinction ratio of -30 dB, a 3 dB channel width of 5 nm and single-source thermal tunability without shape distortion. This filter structure was designed using elements from the product design kit provided by GF and functions in a compact footprint of 0.002 mm2 with a minimum feature size of 150 nm.Comment: 4 pages, 3 figure

Diagnosing and predicting wind turbine faults from SCADA data using support vector machines

Unscheduled or reactive maintenance on wind turbines due to component failure incurs significant downtime and, in turn, loss of revenue. To this end, it is important to be able to perform maintenance before it's needed. To date, a strong effort has been applied to developing Condition Monitoring Systems (CMSs) which rely on retrofitting expensive vibration or oil analysis sensors to the turbine. Instead, by performing complex analysis of existing data from the turbine's Supervisory Control and Data Acquisition (SCADA) system, valuable insights into turbine performance can be obtained at a much lower cost. In this paper, fault and alarm data from a turbine on the Southern coast of Ireland is analysed to identify periods of nominal and faulty operation. Classification techniques are then applied to detect and diagnose faults by taking into account other SCADA data such as temperature, pitch and rotor data. This is then extended to allow prediction and diagnosis in advance of specific faults. Results are provided which show recall scores generally above 80\% for fault detection and diagnosis, and prediction up to 24 hours in advance of specific faults, representing significant improvement over previous techniques