Mechanisms of Transposable Element Repression by Piwi Proteins in the piRNA Pathway of Drosophila Germ Cells

The ability to reproduce is a defining characteristic of all living organisms. During reproduction, the integrity of genetic material transferred from one generation to the next is of utmost importance. Organisms have diverse strategies to ensure the fidelity of genomic information inherited between generations of individuals. In sexually reproducing animals, the piRNA pathway is an RNA-interference (RNAi) mechanism that protects the genomes of germ cells from the replication of ‘selfish’ genetic sequences called transposable elements (TE). When left unabated, the replication of TE sequences can cause gene disruption, double-stranded DNA breaks, and germ cell death that results in sterility of the organism. In Drosophila, the piRNA pathway is divided into a cytoplasmic and nuclear branch that involves the functions of three Piwi-clade Argonaute proteins—Piwi, Aubergine (Aub) and Argonaute-3 (Ago3)—which bind piwi-interacting RNA (piRNA) to form the effector complexes that represses deleterious TE sequences.

The work presented in this thesis examines the function and regulation of Piwi proteins in Drosophila germ cells. Chapter 1 presents an introduction to piRNA biogenesis and to the essential roles occupied by each Piwi protein in the repression of TE. We discuss the architecture and function of germ granules as the cellular compartments where much of the piRNA pathway operates. In Chapter 2, we present how Piwi in the nucleus co-transcriptionally targets genomic loci expressing TE sequences to direct the deposition of repressive chromatin marks. Chapter 3 examines the cytoplasmic function of the piRNA pathway, where we find that the protein Krimper coordinates Aub and Ago3 in the piRNA ping-pong pathway to adaptively target and destroy TE transcripts. Chapter 4 explores how interactions of Piwis with associated proteins are modulated by arginine methylation modifications. Lastly, in Chapter 5 I present evidence that the cytoplasmic branch of the piRNA pathway can potentially ‘cross-talk’ with the nuclear branch to transfer sequence information to better target and co-transcriptionally silence the genomic loci coding active TE sequences. Overall, the work presented in this thesis constitutes a part of the first steps in understanding the molecular mechanisms that protect germ cells from invasion by TE sequences.

Histochemical investigations on the interrenal system of the brook lamprey (Lapetra planeri Bloch). [Translation from: Acta biol.med.germ. 24, 553-554, 1970. ]

Histochemical experiments are conducted in order to study the interrenal cells of European brook lamprey (Lampetra planeri).

Scalable Methods for Deterministic Integration of Quantum Emitters in Photonic Crystal Cavities

We investigated four unique methods for achieving scalable, deterministic integration of quantum emitters into ultra-high Q{V photonic crystal cavities, including selective area heteroepitaxy, engineered photoemission from silicon nanostructures, wafer bonding and dimensional reduction of III-V quantum wells, and cavity-enhanced optical trapping. In these areas, we were able to demonstrate site-selective heteroepitaxy, size-tunable photoluminescence from silicon nanostructures, Purcell modification of QW emission spectra, and limits of cavity-enhanced optical trapping designs which exceed any reports in the literature and suggest the feasibility of capturing- and detecting nanostructures with dimensions below 10 nm. In addition to process scalability and the requirement for achieving accurate spectral- and spatial overlap between the emitter and cavity, these techniques paid specific attention to the ability to separate the cavity and emitter material systems in order to allow optimal selection of these independently, and eventually enable monolithic integration with other photonic and electronic circuitry.

We also developed an analytic photonic crystal design process yielding optimized cavity tapers with minimal computational effort, and reported on a general cavity modification which exhibits improved fabrication tolerance by relying exclusively on positional- rather than dimensional tapering. We compared several experimental coupling techniques for device characterization. Significant efforts were devoted to optimizing cavity fabrication, including the use of atomic layer deposition to improve surface quality, exploration into factors affecting the design fracturing, and automated analysis of SEM images. Using optimized fabrication procedures, we experimentally demonstrated 1D photonic crystal nanobeam cavities exhibiting the highest Q/V reported on substrate. Finally, we analyzed the bistable behavior of the devices to quantify the nonlinear optical response of our cavities.

高吸收强度下的波长调制光谱

基于洛伦兹线型近似，研究了高吸收强度下波长调制吸收光谱中谐波信号的行为。得到了二、四、六次谐波幅度与吸收强度的关系的近似解析表达式。解析表达式的结果与数值计算得到的相符合。理论分析的结果在一个用于瓦斯传感的波长调制光谱系统上得到了验证。发现各偶次谐波随吸收强度的变化不仅有最大值还有零点，这一结论对瓦斯传感器的设计具有实际意义。

Double-line-density gratings structure for compression and generation of double femtosecond laser pulses

Grating pairs are widely used for pulse compression and stretching. Normally, the two gratings are identical. We propose a very simple structure with double-line-density reflective gratings for pulse compression and generation of double pulses, which has the advantages of no material dispersion, compact in volume, simple in structure, etc. The use of reflective Dammann gratings fully demonstrated the principle of this structure. The output pulses are well verified by a standard frequency-resolved optical gating apparatus. This structure will be highly interesting in ultrashort pulse compression and other more practical applications of femtosecond laser pulses. (c) 2007 Optical Society of America.

Effects of atmosphere visibility on performances of non-line-of-sight ultraviolet communication systems

Dependence of performances of non-line-of-sight (NLOS) solar-blind ultraviolet (UV) communication systems on atmosphere visibility is investigated numerically by correlating the propagation of UV radiation with the visibility. A simplified solar-blind UV atmospheric propagation model is introduced, and the NLOS UV communication system model is constituted based on the single scattering assumption. Using the model, numerical simulation is conducted for two typical geometry configurations and different modulation formats. The results indicate that the performance of the NLOS UV communication system is insensitive to variation of visibility in quite a large range, and deteriorates significantly only in very low-visibility weather, and is also dependent on the geometry configuration of the system. The results also show that the pulse position modulation (PPM) is preferable due to its high-power efficiency to improve the system performance. (c) 2007 Elsevier GmbH. All rights reserved.

Generation of double pulses in-line by using reflective Dammann gratings

Doubled femtosecond laser pulses in-line are needed in the collinear pump-probe technique, collinear second harmonic generation frequency-resolved optical gating (SHG FROG) and the spectral phase interferometry for direct electric-field reconstruction (SPIDER), etc. Normally, it is generated by using a Michelson's structure. In this paper, we proposed a novel structure with two-layered reflective Dammann gratings and the reflective mirrors to generate doubled femtosecond laser pulses in line without transmission optical elements. Angular dispersion and spectral spatial walk-off are both compensated. In addition, this structure can also compress the positive chirped pulse, which cannot be realized with a Michelson's structure. By adopting triangular grating and blazed gratings, the efficiency of the system would in principle be increased as the Michelson's scheme. Experiments demonstrated that this method should be an alternative approach for generation of the double compressed pulses of femtosecond laser for practical applications. (c) 2006 Elsevier GmbH. All rights reserved.

Split-aperture laser pulse compressor design tolerant to alignment and line-density differences

We introduce a four-pass laser pulse compressor design based on two grating apertures with two gratings per aperture that is tolerant to some alignment errors and, importantly, to grating-to-grating period variations. Each half-beam samples each grating in a diamond-shaped compressor that is symmetric about a central bisecting plane. For any given grating, the two half-beams impinge on opposite sides of its surface normal. It is shown that the two split beams have no pointing difference from paired gratings with different periods. Furthermore, no phase shift between half-beams is incurred as long as the planes containing a grating line and the surface normal for each grating of the pair are parallel. For grating pairs satisfying this condition, gratings surfaces need not be on the same plane, as changes in the gap between the two can compensate to bring the beams back in phase. © 2008 Optical Society of America.

Compliance verification methodology for renewable generation integration. Application to island power grids

261 p.