Periodic structures with a sub-wavelength pitch have been known since Hertz conducted his first experiments on the polarization of electromagnetic waves. While the use of these structures in waveguide optics was proposed in the 1990s, it has been with the more recent developments of silicon photonics and high-precision lithography techniques that sub-wavelength structures have found widespread application in the field of photonics. This review first provides an introduction to the physics of sub-wavelength structures. An overview of the applications of sub-wavelength structures is then given including: anti-reflective coatings, polarization rotators, high-efficiency fiber-chip couplers, spectrometers, high-reflectivity mirrors, athermal waveguides, multimode interference couplers, and dispersion engineered, ultra-broadband waveguide couplers among others. Particular attention is paid to providing insight into the design strategies for these devices. The concluding remarks provide an outlook on the future development of sub-wavelength structures and their impact in photonics.

The B cell–specific enzyme activation-induced cytidine deaminase (AID) has been shown to be essential for isotype switching and affinity maturation of antibody genes during the immune response. Conversely, AID activity has also been linked to autoimmunity and tumorigenesis. Determining how AID expression is regulated in vivo is therefore central to understanding its role in health and disease. Here we use phylogenetic footprinting and high-resolution histone acetylation mapping to accurately demarcate AID gene regulatory boundaries. Based on this strategy, we identify a novel, positive regulatory element required for AID transcription. Furthermore, we generate two AID indicator mouse strains using bacterial artificial chromosomes that faithfully recapitulate endogenous AID expression. The first strain uses a green fluorescent protein reporter to identify B cells that actively express AID during the immune response. In the second strain, AID transcription affects the permanent expression of a yellow fluorescent protein reporter in post–germinal center and terminally differentiated lymphocytes. We demonstrate the usefulness of these novel strains by resolving recent contradictory observations on AID expression during B cell ontogeny.

Chromosomal translocations juxtaposing the MYC protooncogene with regulatory sequences of immunoglobulin (Ig) H chain or kappa (Igκ) or lambda (Igλ) L chain genes and effecting deregulated expression of MYC are the hallmarks of human Burkitt lymphoma (BL). Here we report that lymphomas with striking similarities to BL develop in mice bearing a mutated human MYC gene controlled by a reconstructed Igλ locus encompassing all the elements required for establishment of locus control in vitro. Diffusely infiltrating lymphomas with a typical starry sky appearance occurred in multiple founders and an established line, indicating independence from positional effects. Monoclonal IgM+CD5−CD23− tumors developed from an initially polyclonal population of B cells. These results demonstrate that the phenotype of B lineage lymphomas induced by MYC dysregulation is highly dependent on cooperativity among the regulatory elements that govern expression of the protooncogene and provide a new system for studying the pathogenesis of BL.

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Murine models of human carcinogenesis are exceedingly valuable tools to understand genetic mechanisms of neoplastic growth. The identification of recurrent chromosomal rearrangements by cytogenetic techniques serves as an initial screening test for tumour specific aberrations. In murine models of human carcinogenesis, however, karyotype analysis is technically demanding because mouse chromosomes are acrocentric and of similar size. Fluorescence in situ hybridization (FISH) with mouse chromosome specific painting probes can complement conventional banding analysis. Although sensitive and specific, FISH analyses are restricted to the visualization of only a few mouse chromosomes at a time. Here we apply a novel imaging technique that we developed recently for the visualization of human chromosomes to the simultaneous discernment of all mouse chromosomes. The approach is based on spectral imaging to measure chromosome-specific spectra after FISH with differentially labelled mouse chromosome painting probes. Utilizing a combination of Fourier spectroscopy, CCD-imaging and conventional optical microscopy, spectral imaging allows simultaneous measurement of the fluorescence emission spectrum at all sample points. A spectrum-based classification algorithm has been adapted to karyotype mouse chromosomes. We have applied spectral karyotyping (SKY) to chemically induced plasmocytomas, mammary gland tumours from transgenic mice overexpressing the c-myc oncogene and thymomas from mice deficient for the ataxia telangiectasia (Atm) gene. Results from these analyses demonstrate the potential of SKY to identify complex chromosomal aberrations in mouse models of human carcinogenesis.

We propose a new method for mode conversion and coupling between an optical fiber and a sub-micrometer waveguide using a subwavelength grating (SWG) with a period less than the 1st order Bragg period. The coupler principle is based on gradual modification of the waveguide mode effective index by the SWG effect that at the same time frustrates diffraction and minimizes reflection loss. We demonstrate the proposed principle by two-dimensional Finite Difference Time Domain (FDTD) calculations of various SWG structures designed for the silicon-on-insulator (SOI) platform with a Si core thickness of 0.3 microm. We found a coupling loss as small as 0.9 dB for a 50 microm-long SWG device and low excess loss due to fiber misalignment, namely 0.07 dB for a transverse misalignment of +/-1 microm, and 0.24 dB for an angular misalignment of +/-2 degrees. Scaling of the SWG coupler length down to 10 microm is also reported on an example of a 2D slab waveguide coupling structure including aspect ratio dependent etching and micro-loading effects. Finally, advantages of the proposed coupling principle for fabricating 3D coupling structures are discussed.

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