REVIEW | doi:10.20944/preprints202305.0598.v1
Subject: Biology And Life Sciences, Aging Keywords: circadian rhythms; aging; suprachiasmatic nucleus; peripheral clock; inflammatory response
Online: 9 May 2023 (08:19:43 CEST)
The circadian clock regulates daily changes in behavioral, endocrine and metabolic activities in mammals. Circadian rhythms in cellular physiology are significantly affected by aging. In particular, we previously found that aging has profound impact on daily rhythms in mitochondrial functions, leading to increased oxidative stress. However, this is unlikely due to malfunction of molecular clocks in the suprachiasmatic nucleus or peripheral tissues, as robust clock oscillations are observed therein in old animals. Nonetheless, aging induces changes in gene expression levels and rhythms in various peripheral and probably central tissues. In this article, we review findings on the roles of the circadian clock and aging in regulating mitochondrial rhythms and redox homeostasis. Chronic sterile inflammation is implicated in mitochondrial dysfunction and increased oxidative stress during aging. In particular, upregulation of CD38 by inflammatory response can disturb mitochondrial functions in multiple ways.
REVIEW | doi:10.20944/preprints202306.1927.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: circadian rhythms; transcription; pausing; mammalian; mouse
Online: 27 June 2023 (14:32:42 CEST)
Cell autonomous circadian oscillation is present in central and various peripheral tissues. The intrinsic tissue clock and various extrinsic cues drive gene expression rhythms. Transcription regulation is thought to be the main driving force for gene rhythms. However, how transcription rhythms arise remains to be fully characterized, due to the fact that transcription is regulated at multiple steps. In particular, Pol II recruitment and pause release are two critical regulatory steps that determine the status of Pol II pausing. Recently, we showed that Pol II pausing exhibits genomewide changes during daily transcription in mouse liver. In this article, we review historical as well as recent findings on the regulation of transcription rhythms. We also discuss the possible mechanisms for daily changes in Pol II pausing and the critical involvement of Pol II pausing regulation in generating rhythmic transcription output.
ARTICLE | doi:10.20944/preprints201802.0032.v1
Subject: Physical Sciences, Acoustics Keywords: inverse acoustic problem; helicopter rotor; Ffowcs Williams and Hawkings equation; aerodynamic constraint; Thikhonov method
Online: 5 February 2018 (11:34:30 CET)
An inverse aeroacoustic problem for a helicopter rotor combined with aerodynamic constraint is proposed based on Ffowcs Williams and Hawkings equation in subsonic. The rotor noise includes thickness noise and loading noise when quadrupole noise is neglected. Thickness noise is related to geometry and motion conditions. Loading noise is related to the pressure on the wall. Therefore, the equation between pressure on the wall and far-field noise can be established, thus the pressure on the wall can be obtained by solving this equation. Since this equation is an ill-posed, the singular value decomposition combined with the regulation method is applied and the aerodynamic constraint is taken into account. The direct noise prediction is verify firstly and then the inverse problem is solved. The reconstruction pressure is compared to the input data. The result is in good agreement with the input value. At the same time, the influence of interference noise is also considered. Under low signal-to-noise ratio, the reconstruction result is also reasonable.
Subject: Biology And Life Sciences, Plant Sciences Keywords: BrassicaEDB; Brassica napus; gene expression profile; coexpression
Online: 12 July 2020 (15:25:37 CEST)
The Brassica family contains several economically important crops, including rapeseed (Brassica napus, 2n = 38, AACC), the second largest source of seed oil and protein meal worldwide. However, research in rapeseed is hampered because it is complicated and time-consuming for researchers to access different types of expression data. We therefore developed the Brassica Expression Database (BrassicaEDB, https://biodb.swu.edu.cn/brassica/) for the research community. We conducted RNA sequencing (RNA-Seq) of 103 tissues from rapeseed cultivar ZhongShuang11 (ZS11) at seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, and maturation). We determined the expression patterns of 101,040 genes via FPKM analysis and displayed the results using the eFP browser. We also analyzed transcriptome data for rapeseed from 70 BioProjects in the SRA database and obtained three types of expression level data (FPKM, TPM, and read counts). We used this information to develop the BrassicaEDB, including eFP, Treatment, Coexpression, and SRA Project modules based on gene expression profiles and Gene Feature, qPCR Primer, and BLAST modules based on gene sequences. The BrassicaEDB provides comprehensive gene expression profile information and a user-friendly visualization interface for Brassica crop researchers. Using this database, researchers can quickly retrieve the expression level data for target genes in different tissues and in response to different treatments to elucidate gene functions and explore the biology of rapeseed at the transcriptome level.