A5101469963- Circadian rhythm and melatonin
- Genetics, Aging, and Longevity in Model Organisms
- Light effects on plants
- Muscle Physiology and Disorders
- Dietary Effects on Health
- Neurobiology and Insect Physiology Research
- Bioinformatics and Genomic Networks
- RNA modifications and cancer
- Gene Regulatory Network Analysis
- Neonatal Respiratory Health Research
- Spaceflight effects on biology
- Long-Term Effects of COVID-19
- Sleep and Wakefulness Research
- Psychological and Temporal Perspectives Research
- RNA Research and Splicing
- Metabolomics and Mass Spectrometry Studies
- scientometrics and bibliometrics research
- Topological and Geometric Data Analysis
- Fractal and DNA sequence analysis
- Meta-analysis and systematic reviews
- IL-33, ST2, and ILC Pathways
- Drug Transport and Resistance Mechanisms
- Climate Change and Health Impacts
- Behavioral Health and Interventions
- Academic Publishing and Open Access
Washington University in St. Louis
2017-2024
Pulmonary and Critical Care Associates
2021
Yale University
2010-2018
University of Missouri–St. Louis
2014-2016
Translational Therapeutics (United States)
2009-2014
University of Pennsylvania
2007-2014
Howard Hughes Medical Institute
2011
Institute of Clinical Research
2005
Nottingham General Hospital
1976
Significance We generated high-resolution multiorgan expression data showing that nearly half of all genes in the mouse genome oscillate with circadian rhythm somewhere body. Such widespread transcriptional oscillations have not been previously reported mammals. Applying pathway analysis, we observed new clock-mediated spatiotemporal relationships. Moreover, found a majority best-selling drugs United States target gene products. Many these relatively short half-lives, and our predict which...
Circadian rhythms are oscillations of physiology, behavior, and metabolism that have period lengths near 24 hours. In several model organisms humans, circadian clock genes been characterized found to be transcription factors. Because this, researchers used microarrays characterize global regulation gene expression algorithmic approaches detect cycling. This article presents a new algorithm, JTK_CYCLE, designed efficiently identify cycling variables in large data sets. Compared with COSOPT...
The circadian clock is a molecular and cellular oscillator found in most mammalian tissues that regulates rhythmic physiology behavior. Numerous investigations have addressed the contribution of rhythmicity to cellular, organ, organismal physiology. We recently developed method look at transcriptional oscillations with unprecedented precision accuracy using high-density time sampling. Here, we report comparison oscillating transcription from mouse liver, NIH3T3, U2OS cells. Several...
Abstract Summary: Detecting periodicity in large scale data remains a challenge. While efforts have been made to identify best of breed algorithms, relatively little research has gone into integrating these methods generalizable method. Here, we present MetaCycle, an R package that incorporates ARSER, JTK_CYCLE and Lomb-Scargle conveniently evaluate time-series data. MetaCycle two functions, meta2d meta3d, designed analyze two-dimensional three-dimensional datasets, respectively. Meta2d...
Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout day. These methods hold significant promise for future discovery, when combined with computational modeling. However, genome-scale experiments are costly laborious, yielding “big data” that conceptually statistically difficult analyze. There is no obvious consensus...
Eukaryotic circadian clocks include transcriptional/translational feedback loops that drive 24-h rhythms of transcription. These transcriptional underlie oscillations protein abundance, thereby mediating behavior, physiology, and metabolism. Numerous studies over the last decade have used microarrays to profile in various organisms tissues. Here we use RNA sequencing (RNA-seq) transcriptome Drosophila melanogaster brain from wild-type period -null clock-defective animals. We identify several...
Skeletal muscle comprises a family of diverse tissues with highly specialized functions. Many acquired diseases, including HIV and COPD, affect specific muscles while sparing others. Even monogenic muscular dystrophies selectively certain groups. These observations suggest that factors intrinsic to influence their resistance disease. Nevertheless, most studies have not addressed transcriptional diversity among skeletal muscles. Here we use RNAseq profile mRNA expression in skeletal, smooth,...
Over the last decades, researchers have characterized a set of "clock genes" that drive daily rhythms in physiology and behavior. This arduous work has yielded results with far-reaching consequences metabolic, psychiatric, neoplastic disorders. Recent attempts to expand our understanding circadian regulation moved beyond mutagenesis screens identified first clock components, employing higher throughput genomic proteomic techniques. In order further accelerate gene discovery, we utilized...
The circadian regulatory network is organized in a hierarchical fashion, with central oscillator the suprachiasmatic nuclei (SCN) orchestrating oscillations peripheral tissues. nature of relationship between and oscillators, however, poorly understood. We used tetOFF expression system to specifically restore Clock function brains Clock(Δ19) mice, which have compromised clocks. Rescued mice showed normal locomotor rhythms constant darkness, activity period lengths approximating wildtype...
Epithelial cells are charged with protection at barrier sites, but whether this normally beneficial response might sometimes become dysfunctional still needs definition. Here, we recognized a pattern of imbalance marked by basal epithelial cell growth and differentiation that replaced normal airspaces in mouse model progressive postviral lung disease due to the Sendai virus. Single-cell lineage-tracing technologies identified distinct subset stem (basal ESCs) extended into gas-exchange...
In Brief Summary Background Data: Duodenogastric–esophageal reflux disease is directly linked to Barrett's esophagus and the development of esophageal adenocarcinoma. Despite this link, little known about mutagenic potential refluxed material on mucosa. We hypothesize that gastric duodenal content causes mutations in mucosa vivo. Methods: Seven Sprague Dawley/Big Blue F1 lacI transgenic rats underwent esophagoduodenostomy (ED) surgically create duodeno–gastric–esophageal reflux. Fourteen...
Abstract Intertidal inhabitants are exposed to the 24-hour solar day, and 12.4 hour rising falling of tides. One or both these cycles govern intertidal organisms’ behaviour physiology, yet little is known about molecular clockworks tidal rhythmicity. Here, we show that limpet Cellana rota exhibits robust tidally rhythmic gene expression. We assembled a de-novo transcriptome, identifying novel tidal, along with circadian clock genes. Surprisingly, most putative genes, lack typical identified...
Epithelial barriers are programmed for defense and repair but also the site of long-term structural remodeling disease. In general, this paradigm features epithelial stem cells (ESCs) that called on to regenerate damaged tissues can be reprogrammed detrimental remodeling. Here we identified a Wfdc21-dependent monocyte-derived dendritic cell (moDC) population functioned as an early sentinel niche basal ESC reprogramming in mouse models injury after respiratory viral infection. Niche function...
In both the suprachiasmatic nucleus (SCN) and peripheral tissues, circadian oscillator drives rhythmic transcription of downstream target genes. Recently, a number studies have used DNA microarrays to systematically identify oscillating transcripts in plants, fruit flies, rats, mice. These identified several dozen many hundred rhythmically expressed genes by sampling tissues every 4 hours for 1, 2, or more days. To extend this work, we performed microarray analysis on RNA derived from mouse...
It is well known that spontaneously hypertensive rats (SHR) develop muscle pathologies with hypertension and heart failure, though the mechanism remains poorly understood. Woon et al. (2007) linked circadian clock gene Bmal1 to metabolic dysfunction in SHR. Building on these findings, we compared expression pattern of several core-clock genes gastrocnemius aged SHR (80 weeks; overt failure) aged-matched control WKY strain. Heart failure was associated marked effects Bmal1, Clock Rora...
The circadian clock regulates many cellular processes, notably including the cell cycle, metabolism and aging. Mitochondria play essential roles in are major sites of reactive oxygen species (ROS) production cell. mitochondrial functions by driving daily changes NAD+ levels Sirt3 activity. In addition to this central route, present study, we find that expression some genes is also rhythmic liver, there rhythms disrupted ClockΔ19 mutation young mice, suggesting they regulated core oscillator....
Circadian rhythms refer to biologic processes that oscillate with an approximate 24-h period. These direct nearly all aspects of animal behavior and physiology. The aim our study was determine if Toll-like receptor (TLR) expression responsiveness exhibit time-of-day dependent differences. Therefore, we isolated adherent splenocyte population, which consisted primarily B cells, dendritic macrophages, over the course a light-dark period measured daily changes in Tlr1-8 mRNA levels cytokine...
Circadian rhythms coordinate an organism's activities and biological processes to the optimal time in 24-h daylight cycle. We previously demonstrated that male C57BL/6 mice develop sepsis more rapidly when disease is induced nighttime versus daytime. In this report, we elucidate mechanism of diurnal difference. Sepsis was via cecal ligation puncture (CLP) at zeitgeber (ZT)-19 (2 am) or ZT-7 pm). Like males used our prior study, female had a worse outcome CLP ZT-19 ZT-7, these effects...
lzheimer disease (AD) is a neurodegenerative disorder that the leading cause of dementia in people aged 65 years or older.At present, there no cure and are survivors; all AD cases end death.More than 5 million Americans have AD, it recently passed diabetes mellitus to become sixth death United States. 1 Worldwide, more 35 live with related dementias, ultimately resulting costs exceeding $600 billion. 2 To put this number perspective, approximately 1% world's gross domestic product used care...
ABSTRACT Summary: Detecting periodicity in large scale data remains a challenge. Different algorithms offer strengths and weaknesses statistical power, sensitivity to outliers, ease of use, sampling requirements. While efforts have been made identify best breed algorithms, relatively little research has gone into integrating these methods generalizable method. Here we present MetaCycle, an R package that incorporates ARSER, JTK_CYCLE, Lomb-Scargle conveniently evaluate time-series data....