Hybrids and polyploids are very common in plants and some animals. Although hybrid vigor or heterosis has been widely adopted in agricultural practices, the underlying mechanisms are poorly understood partly because of their multigenic nature and the lack of a good model system for the study. Allotetraploidy is an emerging model system for investigating molecular mechanisms of hybrid vigor. An allotetraploid is formed by interspecific hybridization followed by chromosome doubling or hybridization between two autotetraploid parents and is genetically stable. A previous study showed nonadditive expression (different from the mid-parent value) of over 5% of genes in the allotetraploids, suggesting altered transcriptional and post-transcriptional regulation. Here oligo-gene microarray analysis of mRNA stability in allotetraploids was carried out to investigate how nonadditive gene regulation upon allopolyploidization is achieved at the posttranscriptional level. Approximately 1% of annotated genes were identified as unstable transcripts, and their estimated half-life is less than 60 minutes. The unstable transcripts in Arabidopsis allotetraploids are associated with nonadditive gene expression and with stress and environmental responses. The nonadditively expressed genes identified in the previous study include those encoding proteins involved in energy and metabolic pathways, which are putative targets of circadian clock regulators. To test how circadian clock genes affect downstream genes and pathways, expression of CIRCADIAN CLOCK ASSOCIATED1 (CCA1) was up- or down-regulated by overexpressing CCA1 or cca1(RNAi) driven by the promoter of TIMING OF CAB EXPRESSION 1 (TOC1). Upregulation of CCA1 was associated with repression of downstream genes in chlorophyll biosynthesis and starch metabolism, whereas down-regulation of CCA1 correlated with upregulation of these downstream genes. As a result, chlorophyll and starch content was ~10% higher in the TOC1::cca1(RNAi) transgenic plants than the controls, while the growth vigor is lower in the TOC1::CCA1 transgenic plants. To further test the effects of clock genes in growth vigor, CCA1 expression was examined in reciprocal hybrids of A. thaliana ecotypes. The maternal effect on starch content was observed in several combinations of hybrids, which was correlated with preferential expression of maternal CCA1 during early stages of seed development. Although the cause of parent-of-origin effects is still unclear, the data have clearly documented parent-of-origin effects on circadian clock gene expression and starch metabolism in hybrids. / text

Baud-rate clock recovery (CR) is gradually gaining popularity in modern serial data transmission systems since these CR techniques do not require edge-samples for extracting timing information. However, previous baud-rate techniques for high-speed serial links either rely on specific 4-bit patterns or uncorrelated random data. This work describes the modeling and design of analog filter front-end aided baud-rate CR schemes. Unlike other baud-rate schemes, this technique is not constrained by the properties of the input random data. Firstly, the thesis develops a hardware-efficient baud-rate algorithm that requires only the slope information of the incoming random data. Called modified sign-sign minimum mean squared error (SSMMSE), this algorithm adjusts the clock sampling phase until the slope is zero through a bang-bang control loop. Secondly, the performance of a modified SSMMSE phase detector is investigated and compared with a conventional edge-sampled phase detector. It is shown that, at severe noise levels, the proposed modified SSMMSE method has better performance compared to the edge-sampled method for equal loop bandwidths.Thirdly, the thesis investigates different hardware-efficient slope detection techniques. Both passive and active filter based slope detection techniques are demonstrated in this work. In addition to slope generation, the active filter performs linear equalization as well. However, the passive filter generates the slope information at higher speeds than the active filter and also consumes less power. The two filters are used to recover a 2-GHz clock by using an external bang-bang loop. In short, the thesis demonstrates that area and power savings can be achieved by utilizing slope information from front-end filters without compromising the performance of the CR unit.

Thèse-Université de Neuchâtel.

Circadian rhythms are the outward manifestation of an internal timing system that measures time in 24-hr increments. The mammalian circadian system is hierarchical, with a pacemaker in the suprachiasmatic nucleus (SCN) synchronizing cell-autonomous oscillators in peripheral tissues. Much of what we know about rhythmicity in peripheral tissues comes from studies monitoring bioluminescence rhythms in PERIOD2::LUCIFERASE knock-in mice. A limitation with this model is that rhythmicity cannot be monitored in specific cells due to widespread reporter expression. To address this shortcoming, we generated a mouse that expresses luciferase from the Dbp locus only after Cre-mediated recombination. I validated this conditional mouse to provide a tool for monitoring circadian rhythms in a tissue/cell-specific manner. Crossing the conditional reporter mice with mice expressing Cre recombinase in various cell types allowed detection of rhythmic bioluminescence in the expected tissues, in vivo and ex vivo, as well as in slice cultures containing the SCN. The phase of bioluminescence rhythms from explants of mouse peripheral tissues indicated that DbpLuc/+ bioluminescence rhythms have an earlier phase than PER2::LUC/+ rhythms. Importantly, we confirmed that editing of the Dbp locus did not alter the period of circadian locomotor activity rhythms and did not alter liver Dbp RNA rhythms. Finally, the reporter mouse allows for monitoring rhythms in specific tissues in ambulatory mice. Thus, this mouse line is useful for studying circadian rhythms in a tissue/cell-type specific manner, which can be used to better monitor phase relationships between tissues at baseline and after environmental perturbations that disrupt circadian rhythms.

No description available.

As the CMOS technology continues to scale into the deep sub-micron regime, the demand for higher frequencies and higher levels of integration poses a significant challenge for the clock generation and distribution design of microprocessors. Hence, skew optimization schemes are necessary to limit clock inaccuracies to a small fraction of the clock period. In this thesis, a crude deskew buffer (CDB) is designed to facilitate an adaptive deskewing scheme that reduces the clock skew in an ASIC clock network under manufacturing process, supply voltage, and temperature (PVT)variations. The crude deskew buffer adopts a DLL structure and functions on a 1GHz nominal clock frequency with an operating frequency range of 800MHz to 1.2GHz. An approximate 91.6ps phase resolution is achieved for all simulation conditions including various process corners and temperature variation. When the crude deskew buffer is applied to seven ASIC clock networks with each under various PVT variations, a maximum of 67.1% reduction in absolute maximum clock skew has been achieved. Furthermore, the maximum phase difference between all the clock signals in the seven networks have been reduced from 957.1ps to 311.9ps, a reduction of 67.4%. Overall, the CDB serves two important purposes in the proposed deskewing methodology: reducing the absolute maximum clock skew and synchronizes all the clock signals to a certain limit for the fine deskewing scheme. By generating various clock phases, the CDB can also be potentially useful in high speed debugging and testing where the clock duty cycle can be adjusted accordingly. Various positive and negative duty cycle values can be generated based on the phase resolution and the number of clock phases being “hot swapped”. For a 500ps duty cycle, the following values can be achieved for both the positive and negative duty cycle: 224ps, 316ps, 408ps, 592ps, 684ps, and 776ps.

As the CMOS technology continues to scale into the deep sub-micron regime, the demand for higher frequencies and higher levels of integration poses a significant challenge for the clock generation and distribution design of microprocessors. Hence, skew optimization schemes are necessary to limit clock inaccuracies to a small fraction of the clock period. In this thesis, a crude deskew buffer (CDB) is designed to facilitate an adaptive deskewing scheme that reduces the clock skew in an ASIC clock network under manufacturing process, supply voltage, and temperature (PVT)variations. The crude deskew buffer adopts a DLL structure and functions on a 1GHz nominal clock frequency with an operating frequency range of 800MHz to 1.2GHz. An approximate 91.6ps phase resolution is achieved for all simulation conditions including various process corners and temperature variation. When the crude deskew buffer is applied to seven ASIC clock networks with each under various PVT variations, a maximum of 67.1% reduction in absolute maximum clock skew has been achieved. Furthermore, the maximum phase difference between all the clock signals in the seven networks have been reduced from 957.1ps to 311.9ps, a reduction of 67.4%. Overall, the CDB serves two important purposes in the proposed deskewing methodology: reducing the absolute maximum clock skew and synchronizes all the clock signals to a certain limit for the fine deskewing scheme. By generating various clock phases, the CDB can also be potentially useful in high speed debugging and testing where the clock duty cycle can be adjusted accordingly. Various positive and negative duty cycle values can be generated based on the phase resolution and the number of clock phases being “hot swapped”. For a 500ps duty cycle, the following values can be achieved for both the positive and negative duty cycle: 224ps, 316ps, 408ps, 592ps, 684ps, and 776ps.

No description available.

No description available.

The involvement of clock genes in the temporal regulation of the function and lifespan of the corpus luteum (CL) has not been investigated in detail. Immunohistochemistry and real-time quantitative PCR techniques were used to examine the expression of the canonical clock genes: period1, period2, period3, cryptochrome1, cryptochrome2, clock and bmal1, at protein and mRNA levels respectively. The expression of the clock genes was examined in the human CL, cultured luteinised granulosa cells, cultured luteal fibroblast-like cells and the ovine CL. The main findings were that clock genes are expressed in the human and ovine CL; that this expression is manifest at mRNA and protein level in all discernible cell types within the human and ovine CL, and that the pattern of mRNA expression differs between the early luteal phase compared to the late luteal phase. The circadian expression of the clock genes was established in the ovine CL during the late luteal phase and could not be determined in the human CL, although indications from cultured luteinised granulosa cells and luteal fibroblast-like cells suggest that this may also be the case in humans. With the exception of per2, the circadian pattern of clock gene expression emerged in the late luteal phase CL when the early luteal phase CL did not demonstrate circadian clock gene expression. This emergence later in the lifespan of the CL was akin to that observed in embryonic development, where the clock genes are initially non-rhythmic but then acquire circadian rhythmicity with age. In this case, the clock genes have been proposed to perform a non-classical circadian timing role in the timing of embryonic development. The per2 gene was also found to be special, in its loss rather than gain of rhythmic gene expression across the luteal lifespan and in its protein localisation in the cytoplasm of some granulosa-lutein cells. The exceptional behaviour of per2 is consistent with a growing body of evidence supporting its role as a unique clock gene in many respects, able to maintain circadian protein levels in the absence of circadian gene expression, integrating peripheral clock inputs and outputs and acting as a tumour suppressor gene. The CL was also found to be a potential target of melatonin regulation, based on its possession of melatonin MT1 receptors and the timing of circadian cry1 gene expression in the late luteal phase. The expression of cry1 is known to be directly melatonin-induced in the PT and appeared to be similarly activated, downstream of a melatonin signal, in the CL. This supports the evolving view of a hierarchical organisation of the central and peripheral clocks, which are integrated in order to establish information feedback loops that maintain circadian homeostasis, and which can regulate seasonal physiology.