Browsing by Author "Chen, Yang"

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    Beam pointing stabilization of an acousto-optic modulator with thermal control
    (OSA, 2019-04) Zhang, Xiao; Chen, Yang; Fang, Jianxiong; Wang, Tishuo; Li, Jiaming; Luo, Le; Physics, School of Science
    Diffraction beams generated by an acousto-optic modulator (AOM) are widely used in various optical experiments, some of which require high angular stability with the temporal modulation of optical power. Usually, it is difficult to realize both angular stability and high-power modulation in a passive setup without a servo system of radio-frequency compensation. Here, we present a method to suppress the angular drift and pointing noise only with the thermal management of the AOM crystal. We analyze the dependence of the angular drift on the refractive index variation and find that the angular drift is very sensitive to the temperature gradient, which could induce the refractive index gradient inside the AOM crystal. It reminds us that such angular drift could be significantly suppressed by carefully overlapping the zero temperature gradient area with the position of the acousto-optic interaction zone. We implement a water-cooling setup and find that the angular drift of an AOM is reduced over 100 times during the thermal transient and the angular noise is also suppressed to one-third of the non-cooled case. It should be emphasized that this thermal control method generally used to suppress the beam drift in both the diffraction and the perpendicular-to-diffraction directions. The refractive index thermal coefficient of tellurium dioxide crystal at 1064 nm determined by this angular drift-temperature model is 16×10 −6 K −1, consistent with previous studies. This thermal control technique provides potential applications for optical trapping and remote sensoring that demand for intensity ramps.
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    Genome-wide circadian rhythm detection methods: systematic evaluations and practical guidelines
    (Oxford University Press, 2021-05-20) Mei, Wenwen; Jiang, Zhiwen; Chen, Yang; Chen, Li; Sancar, Aziz; Jiang, Yuchao; Medicine, School of Medicine
    Circadian rhythms are oscillations of behavior, physiology and metabolism in many organisms. Recent advancements in omics technology make it possible for genome-wide profiling of circadian rhythms. Here, we conducted a comprehensive analysis of seven existing algorithms commonly used for circadian rhythm detection. Using gold-standard circadian and non-circadian genes, we systematically evaluated the accuracy and reproducibility of the algorithms on empirical datasets generated from various omics platforms under different experimental designs. We also carried out extensive simulation studies to test each algorithm’s robustness to key variables, including sampling patterns, replicates, waveforms, signal-to-noise ratios, uneven samplings and missing values. Furthermore, we examined the distributions of the nominal equation M1-values under the null and raised issues with multiple testing corrections using traditional approaches. With our assessment, we provide method selection guidelines for circadian rhythm detection, which are applicable to different types of high-throughput omics data.
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    Isha is a su(Hw) mRNA-binding protein required for gypsy insulator function
    (Oxford University Press, 2022) Bag, Indira; Chen, Yang; D’Orazio, Karole; Lopez, Prisma; Wenzel, Sabine; Takagi, Yuichiro; Lei, Elissa P.; Biochemistry and Molecular Biology, School of Medicine
    Chromatin insulators are DNA-protein complexes localized throughout the genome capable of establishing independent transcriptional domains. It was previously reported that the Drosophila su(Hw) mRNA physically associates with the gypsy chromatin insulator protein complex within the nucleus and may serve a noncoding function to affect insulator activity. However, how this mRNA is recruited to the gypsy complex is not known. Here, we utilized RNA-affinity pulldown coupled with mass spectrometry to identify a novel RNA-binding protein, Isha (CG4266), that associates with su(Hw) mRNA in vitro and in vivo. Isha harbors a conserved RNA recognition motif and RNA Polymerase II C-terminal domain-interacting domain (CID). We found that Isha physically interacts with total and elongating Polymerase II and associates with chromatin at the 5' end of genes in an RNA-dependent manner. Furthermore, ChIP-seq analysis reveals Isha overlaps particularly with the core gypsy insulator component CP190 on chromatin. Depletion of Isha reduces enhancer-blocking and barrier activities of the gypsy insulator and disrupts the nuclear localization of insulator bodies. Our results reveal a novel factor Isha that promotes gypsy insulator activity that may act as a nuclear RNA-binding protein adapter for su(Hw) noncoding mRNA.
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    Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome
    (Frontiers, 2019-03-19) Zhang, Jianbin; Nie, Qiangqiang; Si, Chaozeng; Wang, Cheng; Chen, Yang; Sun, Weiliang; Pan, Lin; Guo, Jing; Kong, Jie; Cui, Yiyao; Wang, Feng; Fan, Xueqiang; Ye, Zhidong; Wen, Jianyan; Liu, Peng; Medicine, School of Medicine
    Objective: Varicose veins are a common problem worldwide and can cause significant impairments in health-related quality of life, but the etiology and pathogenesis remain not well defined. This study aims to elucidate transcriptomic regulations of varicose veins by detecting differentially expressed genes, pathways and regulator genes. Methods: We harvested great saphenous veins (GSV) from patients who underwent coronary artery bypass grafting (CABG) and varicose veins from conventional stripping surgery. RNA-Sequencing (RNA-Seq) technique was used to obtain the complete transcriptomic data of both GSVs from CABG patients and varicose veins. Weighted Gene Co-expression network analysis (WGCNA) and further analyses were then carried out with the aim to elucidate transcriptomic regulations of varicose veins by detecting differentially expressed genes, pathways and regulator genes. Results: From January 2015 to December 2016, 7 GSVs from CABG patients and 13 varicose veins were obtained. WGCNA identified 4 modules. In the brown module, gene ontology (GO) analysis showed that the biological processes were focused on response to stimulus, immune response and inflammatory response, etc. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that the biological processes were focused on cytokine-cytokine receptor interaction and TNF signaling pathway, etc. In the gray module, GO analysis showed that the biological processes were skeletal myofibril assembly related. The immunohistochemistry staining showed that the expression of ASC, Caspase-1 and NLRP3 were increased in GSVs from CABG patients compared with varicose veins. Histopathological analysis showed that in the varicose veins group, the thickness of vascular wall, tunica intima, tunica media and collagen/smooth muscle ratio were significantly increased, and that the elastic fiber/internal elastic lamina ratio was decreased. Conclusion: This study shows that there are clear differences in transcriptomic information between varicose veins and GSVs from CABG patients. Some inflammatory RNAs are down-regulated in varicose veins compared with GSVs from CABG patients. Skeletal myofibril assembly pathway may play a crucial role in the pathogenesis of varicose veins. Characterization of these RNAs may provide new targets for understanding varicose veins diagnosis, progression, and treatment.