Journal of Biological Rhythms最新文献

{"title":"How to Deal With Darkness: Modeling and Visualization of Zero-Inflated Personal Light Exposure Data on a Logarithmic Scale.","authors":"Johannes Zauner, Carolina Guidolin, Manuel Spitschan","doi":"10.1177/07487304251336624","DOIUrl":"10.1177/07487304251336624","url":null,"abstract":"<p><p>Measuring and analyzing personal light exposure has become increasingly important in circadian and myopia research. Very small measurement values in light exposure patterns, especially zero, are regularly recorded in field studies. These zero-lux values are problematic for commonly applied logarithmic transformations and should neither be dismissed nor be unduly influential in visualizations and statistical modeling. We compare 4 ways to visualize such data on a linear, logarithmic, hybrid, or symlog scale, and we model the light exposure patterns with a generalized additive model by removing zero-lux values, adding a very small or -1 log₁₀ lux value to the dataset, or using the Tweedie error distribution. We show that a <i>symlog</i>-transformed visualization, implemented in <i>LightLogR</i>, displays relevant features of light exposure across scales, including zero-lux, while reducing the emphasis on the small values (<1 lux). <i>Symlog</i> is well-suited to visualize differences in light exposure covering heavy-tailed negative values. We further show that small but not negligible value additions to the light exposure data of -1 log₁₀ lux for statistical modeling allow for acceptable models on a logarithmic scale, while very small values distort results. We also demonstrate the utility of the Tweedie distribution, which does not require prior transformations, models data on a logarithmic scale, and includes zero-lux values, capturing personal light exposure patterns satisfactorily. Data from field studies of personal light exposure require appropriate handling of zero-lux values in a logarithmic context. <i>Symlog</i> scales for visualizations and an appropriate addition to input values for modeling, or the Tweedie distribution, provide a solid basis. Beyond light exposure, other time-series data relevant to biological rhythms, such as accelerometry for ambulatory sleep scoring in humans or wheel-running in animal models, exhibit zero inflation and can benefit from the methods introduced here.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"480-490"},"PeriodicalIF":3.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12426318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144528100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Circadian Rhythms in Health and Disease (CRHD 2024).","authors":"Sandipan Ray, Srishti Banerjee","doi":"10.1177/07487304251349350","DOIUrl":"10.1177/07487304251349350","url":null,"abstract":"","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"411-413"},"PeriodicalIF":2.1,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144560212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Takao Kondo.","authors":"Hideo Iwasaki, Ayano Ogihara, Ikuno Ohashi, Ken-Ichi Honma, Takashi Yoshimura, Susan S Golden, Carl Hirschie Johnson","doi":"10.1177/07487304251352036","DOIUrl":"10.1177/07487304251352036","url":null,"abstract":"","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"403-408"},"PeriodicalIF":2.1,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12426316/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144667704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Neurotransmitter and Receptor Mapping in <i>Drosophila</i> Circadian Clock Neurons via T2A-GAL4 Screening.","authors":"Ayumi Fukuda, Aika Saito, Taishi Yoshii","doi":"10.1177/07487304251349887","DOIUrl":"10.1177/07487304251349887","url":null,"abstract":"<p><p>The circadian neuronal network in the brain comprises central pacemaker neurons and associated input and output pathways. These components work together to generate coherent rhythmicity, synchronize with environmental time cues, and convey circadian information to downstream neurons that regulate behaviors such as the sleep/wake cycle. To mediate these functions, neurotransmitters and neuromodulators play essential roles in transmitting and modulating signals between neurons. In <i>Drosophila melanogaster</i>, approximately 240 brain neurons function as clock neurons. Previous studies have identified several neurotransmitters and neuromodulators, including the Pigment-dispersing factor (PDF) neuropeptide, along with their corresponding receptors in clock neurons. However, our understanding of the neurotransmitters and receptors involved in the circadian system remains incomplete. In this study, we conducted a T2A-GAL4-based screening for neurotransmitter and receptor genes expressed in clock neurons. We identified 2 neurotransmitter-related genes and 22 receptor genes. Notably, while previous studies had reported the expression of 6 neuropeptide receptor genes in large ventrolateral neurons (l-LN_v), we also found that 14 receptor genes-including those for dopamine, serotonin, and γ-aminobutyric acid-are expressed in l-LN_v neurons. These findings suggest that l-LN_v neurons serve as key integrative hubs within the circadian network, receiving diverse external signals.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"491-497"},"PeriodicalIF":2.1,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144600471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Time of Day-Dependent Responses to Cisplatin Treatment in a Male Mouse Model of Hepatoma.","authors":"Yasemin Kubra Akyel, Christopher P Selby, Aziz Sancar, Ashraf N Abdo","doi":"10.1177/07487304251349893","DOIUrl":"10.1177/07487304251349893","url":null,"abstract":"<p><p>The circadian clock maintains oscillations in gene expression with a 24-hour periodicity in nearly every cell of the body and confers rhythmic patterns to many aspects of behavior and physiology. The presence of circadian rhythms in tumors leads to the question of whether tumors may respond differently to chemotherapy given at different times of day. We addressed this question using a male mouse model of hepatoma by treating mice in the morning (ZT2) or evening (ZT14) with cisplatin, and measuring gross effects on body weight, blood counts and chemistry, gene expression, and cellular proliferation. We found that among cisplatin-treated mice, there was a reduction in expression of the proliferation marker protein Ki-67 in tumors of mice treated at ZT14 as compared to ZT2. Corresponding hepatotoxicity, as measured by elevated serum alanine aminotransferase (ALT), and body weight loss were also reduced at ZT14. Overall gene expression at ZT14 was more similar to healthy liver than expression at ZT2. Mitogen-activated protein kinase (MAPK) and Ras-related protein-1 (Rap-1) signaling pathways were specifically downregulated in tumors following treatment at ZT14, which may be related to the decreased proliferation, at this treatment time. These findings align with the possible use of timed chemotherapy to enhance drug efficacy.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"441-454"},"PeriodicalIF":3.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12303536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144698608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sleep Identification Enabled by Supervised Training Algorithms (SIESTA): An Open-Source Platform for Automatic Sleep Staging of Rodent Electrocorticographic and Electromyographic Data.","authors":"Asad I Beck, Carlos S Caldart, Miriam Ben-Hamo, Tenley A Weil, Jazmine G Perez, Franck Kalume, Bingni W Brunton, Horacio O de la Iglesia, Raymond E A Sanchez","doi":"10.1177/07487304251336649","DOIUrl":"10.1177/07487304251336649","url":null,"abstract":"<p><p>Accurately capturing the temporal distribution of polysomnographic sleep stages is critical for the study of sleep function, regulation, and disorders in higher vertebrates. In laboratory rodents, scoring of electrocorticography (ECoG) and electromyography (EMG) recordings is usually performed manually by categorizing 5- to 10-sec epochs as 1 of 3 specific stages: wakefulness, rapid-eye-movement (REM) sleep, and non-REM (NREM) sleep. This process is laborious, time-consuming, and particularly impractical for large experimental cohorts with recordings lasting longer than 24 h, which are critical for the study of the circadian regulation of sleep. To circumvent this problem, we developed an open-source Python toolkit, Sleep Identification Enabled by Supervised Training Algorithms (SIESTA), that automates the detection of these 3 main behavioral stages in mice. We used a supervised machine learning algorithm that extracts features from the ECoG and EMG signals and autonomously scores recordings with a hierarchical classifier based on using logistic regression. We evaluated this approach on data collected from wild-type mice housed under both normal and different lighting conditions, as well as from mutant mouse lines with abnormal sleep phenotypes and from rats. We obtained mean F₁ scores 0.94 for wakefulness, 0.94 for NREM, and 0.74 for REM, and followed up by validating SIESTA with manually scored data from 3 other laboratories. SIESTA has a user-friendly interface that can be used without coding expertise. To our knowledge, this is the first time that such a strategy has been developed using all open-source and freely available resources. Our aim is that SIESTA becomes a useful tool that facilitates further research in sleep on rodent models.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"330-346"},"PeriodicalIF":2.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12263331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chronic Phase Shifts Are Associated With Higher Systolic Blood Pressure and Impaired Glucose Tolerance Independently of Estrogen Deficiency in Female Spontaneously Hypertensive Rats.","authors":"Refentshe Amandu's Nthlane, Karine Scheuermaier, Siluleko Advice Mkhize, Frédéric Sébastien Michel","doi":"10.1177/07487304251347464","DOIUrl":"10.1177/07487304251347464","url":null,"abstract":"<p><p>Postmenopausal shift workers face increased cardiometabolic risk due to estrogen decline and shift work-induced circadian misalignment. Yet, their combined effects remain poorly understood, especially in hypertensive individuals. This study investigated whether circadian misalignment worsens cardiometabolic parameters in a hypertensive ovariectomized rat model. Female spontaneously hypertensive rats (SHR) were ovariectomized or sham-operated (7-week-old), and then exposed to a chronic phase shift (CPS) protocol or a control light schedule for 10 weeks (<i>n</i> = 9 per group). Measurements included body mass, food and water intake, blood pressure (BP), fasting glucose, glucose tolerance, organ masses, and low-density lipoprotein (LDL) concentration. Ovariectomized rats were heavier and had greater food intake and organ masses than sham-operated rats. However, food intake and organ masses were reduced relative to body mass. CPS rats had greater water intake and reduced liver mass than control light rats. In addition, ovariectomized rats showed lower glucose concentration than sham-operated rats, whereas CPS rats showed higher glucose concentration than control light rats during the oral glucose tolerance test. Moreover, the CPS rats had higher systolic BP. The LDL and fasting glucose concentrations were similar. No interaction between ovariectomy and CPS was observed. These findings suggest that estrogen deficiency increases body mass, but does not worsen cardiometabolic parameters in female SHR. CPS-induced circadian misalignment altered water intake, liver mass, systolic BP and glucose tolerance in the CPS condition in female SHR. This study was unable to monitor physiological or behavioral indicators to confirm circadian misalignment by the CPS protocol. However, the findings provide novel insights into how CPSs independently impair cardiometabolic outcomes in female SHR, with implications for understanding risk in postmenopausal shift workers.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"384-399"},"PeriodicalIF":2.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12255845/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144333200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sex and the Clock: Time to Consider Sexually Dimorphic Rhythms in Circadian Research.","authors":"Ronan Lordan","doi":"10.1177/07487304251333548","DOIUrl":"10.1177/07487304251333548","url":null,"abstract":"","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"315-317"},"PeriodicalIF":2.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12255844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tracking Daily Variations in Rest-Wake to Guide Personalized Timing of Temozolomide for High-Grade Glioma Patients.","authors":"Maria F Gonzalez-Aponte, Anna R Damato, Ruth G N Katumba, Grayson R Talcott, Jian L Campian, Omar H Butt, Marc D Ruben, Joshua B Rubin, Erik D Herzog, Olivia J Walch","doi":"10.1177/07487304251336826","DOIUrl":"10.1177/07487304251336826","url":null,"abstract":"<p><p>High-grade gliomas, like glioblastoma multiforme (GBM), are the most common malignant brain tumors in adults and are treated with the chemotherapy drug temozolomide (TMZ). In humans, a retrospective analysis of patients' overall survival suggests that morning dosing may confer a benefit over evening dosing. Circadian variation in O6-methylguanine-DNA methyltransferase (MGMT) gene expression and promoter methylation has been implicated in increased tumor cell sensitivity to TMZ in the morning. Although patient compliance with timed oral administration of TMZ was high in a prospective trial, it is not known whether differences in daily sleep patterns of patients impact the biological time of drug administration or overall survival. Using wrist actigraphy collected from 10 high-grade glioma patients, we quantified the moment of oral TMZ delivery in terms of wall clock time and internal biological time during the months after surgical tumor resection. We found that variation of daily rhythms within and between individuals caused dosing times to vary more in their internal biological time than wall clock time so that, for example, some doses taken by patients assigned for the evening (2000 h) were closer to the patient's internal biological morning. We conclude that wrist actigraphy provides a reliable and non-invasive estimate of personal circadian time that could improve efficacy and precision of TMZ delivery. These findings may inform personalized circadian medicine and optimized times for TMZ delivery in the clinic.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"320-329"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12263323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144159255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Circadian regulation of maternal and feeding behaviors in lactating mice.","authors":"Atsumi Murakami, Haruo Masai, Koyuki Kawamura, Kanako Matsumoto, Hitoshi Okamura, Keiko Tominaga","doi":"10.1177/07487304251345655","DOIUrl":"https://doi.org/10.1177/07487304251345655","url":null,"abstract":"<p><p>Maternal care is essential for offspring survival. Circadian regulation of maternal behavior and feeding behavior was determined in mice after parturition. The maternal crouching behavior (covering over pups) occurred intensively in the late half of the dark phase (nighttime), referred to as the \"crouching-dominant time.\" Interestingly, a rapid decrease in body temperature preceded the onset of crouching-dominant time. Feeding behavior during lactation increased in line with the increased energy demand. However, during the night, feeding behavior intensively occurred in the first half of the nighttime, as seen during the non-lactation period, and intermittent feeding behavior was added during the daytime. The clock genes expression of the suprachiasmatic nucleus (SCN) showed robust oscillation even during lactation. In contrast, marked changes in expression profiles of peroxisome proliferator-activated receptor α (PPARα)-regulated metabolic genes in the liver during lactation (postpartum 7 to 12 days) were dissociated from the peripheral clock control, compared to those in virgin mice. During lactation, a critical time for the survival of the species, the maternal circadian clock may regulate multiple important behaviors so that they can occur in the appropriate time frame while adapting to energy requirements.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":"40 4","pages":"365-383"},"PeriodicalIF":2.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144642632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}