Cell Systems最新文献

What’s driving rhythmic gene expression: Sleep or the clock? 是什么在驱动有节奏的基因表达？睡眠还是时钟？

IF 9.3 1区生物学

Cell Systems Pub Date : 2024-07-17 DOI: 10.1016/j.cels.2024.06.006

引用次数: 0

Model integration of circadian- and sleep-wake-driven contributions to rhythmic gene expression reveals distinct regulatory principles 昼夜节律和睡眠-觉醒对节律性基因表达贡献的模型整合揭示了不同的调控原理

IF 9.3 1区生物学

Cell Systems Pub Date : 2024-07-09 DOI: 10.1016/j.cels.2024.06.005

Maxime Jan, Sonia Jimenez, Charlotte N. Hor, Derk-Jan Dijk, Anne C. Skeldon, Paul Franken

{"title":"Model integration of circadian- and sleep-wake-driven contributions to rhythmic gene expression reveals distinct regulatory principles","authors":"Maxime Jan, Sonia Jimenez, Charlotte N. Hor, Derk-Jan Dijk, Anne C. Skeldon, Paul Franken","doi":"10.1016/j.cels.2024.06.005","DOIUrl":"https://doi.org/10.1016/j.cels.2024.06.005","url":null,"abstract":"Analyses of gene-expression dynamics in research on circadian rhythms and sleep homeostasis often describe these two processes using separate models. Rhythmically expressed genes are, however, likely to be influenced by both processes. We implemented a driven, damped harmonic oscillator model to estimate the contribution of circadian- and sleep-wake-driven influences on gene expression. The model reliably captured a wide range of dynamics in cortex, liver, and blood transcriptomes taken from mice and humans under various experimental conditions. Sleep-wake-driven factors outweighed circadian factors in driving gene expression in the cortex, whereas the opposite was observed in the liver and blood. Because of tissue- and gene-specific responses, sleep deprivation led to a long-lasting intra- and inter-tissue desynchronization. The model showed that recovery sleep contributed to these long-lasting changes. The results demonstrate that the analyses of the daily rhythms in gene expression must take the complex interactions between circadian and sleep-wake influences into account. A record of this paper’s transparent peer review process is included in the supplemental information.","PeriodicalId":54348,"journal":{"name":"Cell Systems","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141576476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

On knowing a gene: A distributional hypothesis of gene function 认识基因基因功能分布假说

IF 9.3 1区生物学

Cell Systems Pub Date : 2024-05-28 DOI: 10.1016/j.cels.2024.04.008

Jason J. Kwon, Joshua Pan, Guadalupe Gonzalez, William C. Hahn, Marinka Zitnik

引用次数: 0

Acute response to pathogens in the early human placenta at single-cell resolution 以单细胞分辨率观察早期人类胎盘对病原体的急性反应

IF 9.3 1区生物学

Cell Systems Pub Date : 2024-05-03 DOI: 10.1016/j.cels.2024.04.002

Regina Hoo, Elias R. Ruiz-Morales, Iva Kelava, Mukul Rawat, Cecilia Icoresi Mazzeo, Elizabeth Tuck, Carmen Sancho-Serra, Sara Chelaghma, Alexander V. Predeus, Simon Murray, David Fernandez-Antoran, Ross F. Waller, Damiana Álvarez-Errico, Marcus C.S. Lee, Roser Vento-Tormo

{"title":"Acute response to pathogens in the early human placenta at single-cell resolution","authors":"Regina Hoo, Elias R. Ruiz-Morales, Iva Kelava, Mukul Rawat, Cecilia Icoresi Mazzeo, Elizabeth Tuck, Carmen Sancho-Serra, Sara Chelaghma, Alexander V. Predeus, Simon Murray, David Fernandez-Antoran, Ross F. Waller, Damiana Álvarez-Errico, Marcus C.S. Lee, Roser Vento-Tormo","doi":"10.1016/j.cels.2024.04.002","DOIUrl":"https://doi.org/10.1016/j.cels.2024.04.002","url":null,"abstract":"The placenta is a selective maternal-fetal barrier that provides nourishment and protection from infections. However, certain pathogens can attach to and even cross the placenta, causing pregnancy complications with potential lifelong impacts on the child’s health. Here, we profiled at the single-cell level the placental responses to three pathogens associated with intrauterine complications—Plasmodium falciparum, Listeria monocytogenes, and Toxoplasma gondii. We found that upon exposure to the pathogens, all placental lineages trigger inflammatory responses that may compromise placental function. Additionally, we characterized the responses of fetal macrophages known as Hofbauer cells (HBCs) to each pathogen and propose that they are the probable niche for T. gondii. Finally, we revealed how P. falciparum adapts to the placental microenvironment by modulating protein export into the host erythrocyte and nutrient uptake pathways. Altogether, we have defined the cellular networks and signaling pathways mediating acute placental inflammatory responses that could contribute to pregnancy complications.","PeriodicalId":54348,"journal":{"name":"Cell Systems","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140828058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Combinatorial interpretation of BMP and WNT controls the decision between primitive streak and extraembryonic fates BMP和WNT的组合解释控制着原始条纹和胚外命运之间的抉择

IF 9.3 1区生物学

Cell Systems Pub Date : 2024-04-30 DOI: 10.1016/j.cels.2024.04.001

Elena Camacho-Aguilar, Sumin T. Yoon, Miguel A. Ortiz-Salazar, Siqi Du, M. Cecilia Guerra, Aryeh Warmflash

{"title":"Combinatorial interpretation of BMP and WNT controls the decision between primitive streak and extraembryonic fates","authors":"Elena Camacho-Aguilar, Sumin T. Yoon, Miguel A. Ortiz-Salazar, Siqi Du, M. Cecilia Guerra, Aryeh Warmflash","doi":"10.1016/j.cels.2024.04.001","DOIUrl":"https://doi.org/10.1016/j.cels.2024.04.001","url":null,"abstract":"BMP signaling is essential for mammalian gastrulation, as it initiates a cascade of signals that control self-organized patterning. As development is highly dynamic, it is crucial to understand how time-dependent combinatorial signaling affects cellular differentiation. Here, we show that BMP signaling duration is a crucial control parameter that determines cell fates upon the exit from pluripotency through its interplay with the induced secondary signal WNT. BMP signaling directly converts cells from pluripotent to extraembryonic fates while simultaneously upregulating Wnt signaling, which promotes primitive streak and mesodermal specification. Using live-cell imaging of signaling and cell fate reporters together with a simple mathematical model, we show that this circuit produces a temporal morphogen effect where, once BMP signal duration is above a threshold for differentiation, intermediate and long pulses of BMP signaling produce specification of mesoderm and extraembryonic fates, respectively. Our results provide a systems-level picture of how these signaling pathways control the landscape of early human development.","PeriodicalId":54348,"journal":{"name":"Cell Systems","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140828160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The resilience of Ukrainian scientists 乌克兰科学家的复原力

IF 9.3 1区生物学

Cell Systems Pub Date : 2024-04-17 DOI: 10.1016/j.cels.2024.03.006

Oksana Piven, Valerii Pokrytiuk, Nadiia Kasianchuk, Bohdan Ostash, Svitlana Dekina, Rostyslav Panchuk, Oleksiy Boldyriev, Vitalina Bashynska, Andrii Zaremba, Yuliia Faidiuk, Maria Yu Obolenskaya, Anastasiia Polishchuk, Oleksandr Petrenko

引用次数: 0

Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy 整合多重成像和多尺度建模，确定肿瘤表型转换是治疗性 T 细胞疗效的关键组成部分

IF 9.3 1区生物学

Cell Systems Pub Date : 2024-04-17 DOI: 10.1016/j.cels.2024.03.004

引用次数: 0

Context matters: DNA virus infection reshapes DNA damage response pathways 背景很重要：DNA病毒感染重塑DNA损伤应答途径

IF 9.3 1区生物学

Cell Systems Pub Date : 2024-04-17 DOI: 10.1016/j.cels.2024.03.008

Jeffrey R. Johnson

引用次数: 0

Evaluation of McCauley et al.: A framework for systematic evaluation of tissue signaling responses by single-cell RNA-seq 对 McCauley 等人的评价通过单细胞 RNA-seq 系统评估组织信号反应的框架

IF 9.3 1区生物学

Cell Systems Pub Date : 2024-04-17 DOI: 10.1016/j.cels.2024.03.007

Laure-Emmanuelle Zaragosi

引用次数: 0

Truncated protein isoforms generate diversity of protein localization and function in yeast 截短蛋白质异构体在酵母中产生蛋白质定位和功能的多样性

IF 9.3 1区生物学

Cell Systems Pub Date : 2024-04-17 DOI: 10.1016/j.cels.2024.03.005

Andrea L. Higdon, Nathan H. Won, Gloria A. Brar

{"title":"Truncated protein isoforms generate diversity of protein localization and function in yeast","authors":"Andrea L. Higdon, Nathan H. Won, Gloria A. Brar","doi":"10.1016/j.cels.2024.03.005","DOIUrl":"https://doi.org/10.1016/j.cels.2024.03.005","url":null,"abstract":"Genome-wide measurement of ribosome occupancy on mRNAs has enabled empirical identification of translated regions, but high-confidence detection of coding regions that overlap annotated coding regions has remained challenging. Here, we report a sensitive and robust algorithm that revealed the translation of 388 N-terminally truncated proteins in budding yeast—more than 30-fold more than previously known. We extensively experimentally validated them and defined two classes. The first class lacks large portions of the annotated protein and tends to be produced from a truncated transcript. We show that two such cases, Yap5truncation and Pus1truncation, have condition-specific regulation and distinct functions from their respective annotated isoforms. The second class of truncated protein isoforms lacks only a small region of the annotated protein and is less likely to be produced from an alternative transcript isoform. Many display different subcellular localizations than their annotated counterpart, representing a common strategy for dual localization of otherwise functionally identical proteins.A record of this paper’s transparent peer review process is included in the supplemental information.","PeriodicalId":54348,"journal":{"name":"Cell Systems","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140636785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0