Cell systems最新文献_第10页

Observations and implication of thermal tolerance in the Arabidopsis proteome. 拟南芥蛋白质组耐热性的观察和意义。

Cell systems Pub Date : 2023-10-18 DOI: 10.1016/j.cels.2023.09.001

Alisdair R Fernie, Youjun Zhang

引用次数: 0

Promotion of plasmid maintenance by heterogeneous partitioning of microbial communities. 通过微生物群落的异质分配促进质粒维持。

Cell systems Pub Date : 2023-10-18 Epub Date: 2023-10-10 DOI: 10.1016/j.cels.2023.09.002

Andrea Weiss, Teng Wang, Lingchong You

引用次数: 0

Genomic footprinting uncovers global transcription factor responses to amino acids in Escherichia coli. 基因组足迹揭示了大肠杆菌对氨基酸的全局转录因子反应。

Cell systems Pub Date : 2023-10-18 Epub Date: 2023-10-10 DOI: 10.1016/j.cels.2023.09.003

Julian Trouillon, Peter F Doubleday, Uwe Sauer

引用次数: 0

Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth. 异质性支架包埋的体积压缩促进大脑类器官成熟，不会阻碍生长。

Cell systems Pub Date : 2023-10-18 Epub Date: 2023-10-10 DOI: 10.1016/j.cels.2023.09.004

Xiaowei Tang, Zitian Wang, Davit Khutsishvili, Yifan Cheng, Jiaqi Wang, Jiyuan Tang, Shaohua Ma

{"title":"Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth.","authors":"Xiaowei Tang, Zitian Wang, Davit Khutsishvili, Yifan Cheng, Jiaqi Wang, Jiyuan Tang, Shaohua Ma","doi":"10.1016/j.cels.2023.09.004","DOIUrl":"10.1016/j.cels.2023.09.004","url":null,"abstract":"Although biochemical regulation has been extensively studied in organoid modeling protocols, the role of mechanoregulation in directing stem cell fate and organoid development has been relatively unexplored. To accurately replicate the dynamic organoid development observed in nature, in this study, we present a method of heterogeneous embedding using an alginate-shell-Matrigel-core system. This approach allows for cell-Matrigel remodeling by the inner layer and provides short-term moderate-normal compression through the soft alginate outer layer. Our results show that the time-limited confinement contributes to increased expression of neuronal markers such as neurofilament (NF) and microtubule-associated protein 2 (MAP2). Compared with non-alginate embedding and alginate compression groups, volume growth remains unimpeded. Our findings demonstrate the temporary mechanical regulation of cerebral organoid growth, which exhibits a regular growth profile with enhanced maturation. These results highlight the importance and potential practical applications of mechanoregulation in the establishment of brain organoids. A record of this paper's transparent peer review process is included in the supplemental information.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41223584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs. RNA从染色质解离的全基因组测量通过其动力学对转录物进行分类，并揭示增强子lncRNA的快速解离。

Cell systems Pub Date : 2023-10-18 DOI: 10.1016/j.cels.2023.09.005

Evgenia Ntini, Stefan Budach, Ulf A Vang Ørom, Annalisa Marsico

{"title":"Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs.","authors":"Evgenia Ntini, Stefan Budach, Ulf A Vang Ørom, Annalisa Marsico","doi":"10.1016/j.cels.2023.09.005","DOIUrl":"10.1016/j.cels.2023.09.005","url":null,"abstract":"Long non-coding RNAs (lncRNAs) are involved in gene expression regulation in cis. Although enriched in the cell chromatin fraction, to what degree this defines their regulatory potential remains unclear. Furthermore, the factors underlying lncRNA chromatin tethering, as well as the molecular basis of efficient lncRNA chromatin dissociation and its impact on enhancer activity and target gene expression, remain to be resolved. Here, we developed chrTT-seq, which combines the pulse-chase metabolic labeling of nascent RNA with chromatin fractionation and transient transcriptome sequencing to follow nascent RNA transcripts from their transcription on chromatin to release and allows the quantification of dissociation dynamics. By incorporating genomic, transcriptomic, and epigenetic metrics, as well as RNA-binding protein propensities, in machine learning models, we identify features that define transcript groups of different chromatin dissociation dynamics. Notably, lncRNAs transcribed from enhancers display reduced chromatin retention, suggesting that, in addition to splicing, their chromatin dissociation may shape enhancer activity.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49686336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids. 用于类器官的高通量纵向表型和选择性检索的微孔平台。

Cell systems Pub Date : 2023-09-20 DOI: 10.1016/j.cels.2023.08.002

Alexandra Sockell, Wing Wong, Scott Longwell, Thy Vu, Kasper Karlsson, Daniel Mokhtari, Julia Schaepe, Yuan-Hung Lo, Vincent Cornelius, Calvin Kuo, David Van Valen, Christina Curtis, Polly M Fordyce

{"title":"A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids.","authors":"Alexandra Sockell, Wing Wong, Scott Longwell, Thy Vu, Kasper Karlsson, Daniel Mokhtari, Julia Schaepe, Yuan-Hung Lo, Vincent Cornelius, Calvin Kuo, David Van Valen, Christina Curtis, Polly M Fordyce","doi":"10.1016/j.cels.2023.08.002","DOIUrl":"10.1016/j.cels.2023.08.002","url":null,"abstract":"Organoids are powerful experimental models for studying the ontogeny and progression of various diseases including cancer. Organoids are conventionally cultured in bulk using an extracellular matrix mimic. However, bulk-cultured organoids physically overlap, making it impossible to track the growth of individual organoids over time in high throughput. Moreover, local spatial variations in bulk matrix properties make it difficult to assess whether observed phenotypic heterogeneity between organoids results from intrinsic cell differences or differences in the microenvironment. Here, we developed a microwell-based method that enables high-throughput quantification of image-based parameters for organoids grown from single cells, which can further be retrieved from their microwells for molecular profiling. Coupled with a deep learning image-processing pipeline, we characterized phenotypic traits including growth rates, cellular movement, and apical-basal polarity in two CRISPR-engineered human gastric organoid models, identifying genomic changes associated with increased growth rate and changes in accessibility and expression correlated with apical-basal polarity. A record of this paper's transparent peer review process is included in the supplemental information.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41108086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

What cannot be seen correctly in 2D visualizations of single-cell 'omics data? 在单细胞组学数据的2D可视化中不能正确看到什么？

Cell systems Pub Date : 2023-09-20 DOI: 10.1016/j.cels.2023.07.002

Shu Wang, Eduardo D Sontag, Douglas A Lauffenburger

引用次数: 0

Ligand-receptor promiscuity enables cellular addressing. 配体-受体杂交使细胞能够寻址。

Cell systems Pub Date : 2022-05-18 Epub Date: 2022-04-13 DOI: 10.1016/j.cels.2022.03.001

Christina J Su, Arvind Murugan, James M Linton, Akshay Yeluri, Justin Bois, Heidi Klumpe, Matthew A Langley, Yaron E Antebi, Michael B Elowitz

{"title":"Ligand-receptor promiscuity enables cellular addressing.","authors":"Christina J Su, Arvind Murugan, James M Linton, Akshay Yeluri, Justin Bois, Heidi Klumpe, Matthew A Langley, Yaron E Antebi, Michael B Elowitz","doi":"10.1016/j.cels.2022.03.001","DOIUrl":"10.1016/j.cels.2022.03.001","url":null,"abstract":"In multicellular organisms, secreted ligands selectively activate, or \"address,\" specific target cell populations to control cell fate decision-making and other processes. Key cell-cell communication pathways use multiple promiscuously interacting ligands and receptors, provoking the question of how addressing specificity can emerge from molecular promiscuity. To investigate this issue, we developed a general mathematical modeling framework based on the bone morphogenetic protein (BMP) pathway architecture. We find that promiscuously interacting ligand-receptor systems allow a small number of ligands, acting in combinations, to address a larger number of individual cell types, defined by their receptor expression profiles. Promiscuous systems outperform seemingly more specific one-to-one signaling architectures in addressing capability. Combinatorial addressing extends to groups of cell types, is robust to receptor expression noise, grows more powerful with increases in the number of receptor variants, and is maximized by specific biochemical parameter relationships. Together, these results identify design principles governing cellular addressing by ligand combinations.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10897978/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139699134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Decoupling of Rates of Protein Synthesis from Cell Expansion Leads to Supergrowth. 蛋白质合成速率与细胞扩增的解耦导致超生长。

Cell systems Pub Date : 2019-11-27 Epub Date: 2019-11-06 DOI: 10.1016/j.cels.2019.10.001

Benjamin D Knapp, Pascal Odermatt, Enrique R Rojas, Wenpeng Cheng, Xiangwei He, Kerwyn Casey Huang, Fred Chang

{"title":"Decoupling of Rates of Protein Synthesis from Cell Expansion Leads to Supergrowth.","authors":"Benjamin D Knapp, Pascal Odermatt, Enrique R Rojas, Wenpeng Cheng, Xiangwei He, Kerwyn Casey Huang, Fred Chang","doi":"10.1016/j.cels.2019.10.001","DOIUrl":"https://doi.org/10.1016/j.cels.2019.10.001","url":null,"abstract":"Cell growth is a complex process in which cells synthesize cellular components while they increase in size. It is generally assumed that the rate of biosynthesis must somehow be coordinated with the rate of growth in order to maintain intracellular concentrations. However, little is known about potential feedback mechanisms that could achieve proteome homeostasis or the consequences when this homeostasis is perturbed. Here, we identify conditions in which fission yeast cells are prevented from volume expansion but nevertheless continue to synthesize biomass, leading to general accumulation of proteins and increased cytoplasmic density. Upon removal of these perturbations, this biomass accumulation drove cells to undergo a multi-generational period of \"supergrowth\" wherein rapid volume growth outpaced biosynthesis, returning proteome concentrations back to normal within hours. These findings demonstrate a mechanism for global proteome homeostasis based on modulation of volume growth and dilution.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.cels.2019.10.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49686271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data. 利用单细胞 RNA 测序数据校正差异变异性测试的均方差依赖性

Cell systems Pub Date : 2019-10-23 DOI: 10.1016/j.cels.2019.08.003

Nils Eling, Arianne C Richard, Sylvia Richardson, John C Marioni, Catalina A Vallejos

引用次数: 0