Cell systems最新文献_第10页

Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture. 复杂相关模式的层次结构支持大脑动态，定义了一个强大的功能架构。

Cell systems Pub Date : 2024-08-21 Epub Date: 2024-08-13 DOI: 10.1016/j.cels.2024.07.003

Levente Varga, Vasile V Moca, Botond Molnár, Laura Perez-Cervera, Mohamed Kotb Selim, Antonio Díaz-Parra, David Moratal, Balázs Péntek, Wolfgang H Sommer, Raul C Mureșan, Santiago Canals, Maria Ercsey-Ravasz

{"title":"Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture.","authors":"Levente Varga, Vasile V Moca, Botond Molnár, Laura Perez-Cervera, Mohamed Kotb Selim, Antonio Díaz-Parra, David Moratal, Balázs Péntek, Wolfgang H Sommer, Raul C Mureșan, Santiago Canals, Maria Ercsey-Ravasz","doi":"10.1016/j.cels.2024.07.003","DOIUrl":"10.1016/j.cels.2024.07.003","url":null,"abstract":"Functional magnetic resonance imaging (fMRI) provides insights into cognitive processes with significant clinical potential. However, delays in brain region communication and dynamic variations are often overlooked in functional network studies. We demonstrate that networks extracted from fMRI cross-correlation matrices, considering time lags between signals, show remarkable reliability when focusing on statistical distributions of network properties. This reveals a robust brain functional connectivity pattern, featuring a sparse backbone of strong 0-lag correlations and weaker links capturing coordination at various time delays. This dynamic yet stable network architecture is consistent across rats, marmosets, and humans, as well as in electroencephalogram (EEG) data, indicating potential universality in brain dynamics. Second-order properties of the dynamic functional network reveal a remarkably stable hierarchy of functional correlations in both group-level comparisons and test-retest analyses. Validation using alcohol use disorder fMRI data uncovers broader shifts in network properties than previously reported, demonstrating the potential of this method for identifying disease biomarkers.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":" ","pages":"770-786.e5"},"PeriodicalIF":0.0,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141984113","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

Systematic identification of transcriptional activation domains from non-transcription factor proteins in plants and yeast. 系统鉴定植物和酵母中非转录因子蛋白的转录激活结构域。

Cell systems Pub Date : 2024-07-17 Epub Date: 2024-06-11 DOI: 10.1016/j.cels.2024.05.007

Niklas F C Hummel, Kasey Markel, Jordan Stefani, Max V Staller, Patrick M Shih

{"title":"Systematic identification of transcriptional activation domains from non-transcription factor proteins in plants and yeast.","authors":"Niklas F C Hummel, Kasey Markel, Jordan Stefani, Max V Staller, Patrick M Shih","doi":"10.1016/j.cels.2024.05.007","DOIUrl":"10.1016/j.cels.2024.05.007","url":null,"abstract":"Transcription factors can promote gene expression through activation domains. Whole-genome screens have systematically mapped activation domains in transcription factors but not in non-transcription factor proteins (e.g., chromatin regulators and coactivators). To fill this knowledge gap, we employed the activation domain predictor PADDLE to analyze the proteomes of Arabidopsis thaliana and Saccharomyces cerevisiae. We screened 18,000 predicted activation domains from >800 non-transcription factor genes in both species, confirming that 89% of candidate proteins contain active fragments. Our work enables the annotation of hundreds of nuclear proteins as putative coactivators, many of which have never been ascribed any function in plants. Analysis of peptide sequence compositions reveals how the distribution of key amino acids dictates activity. Finally, we validated short, \"universal\" activation domains with comparable performance to state-of-the-art activation domains used for genome engineering. Our approach enables the genome-wide discovery and annotation of activation domains that can function across diverse eukaryotes.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":" ","pages":"662-672.e4"},"PeriodicalIF":0.0,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141312522","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

SEMPER: Stoichiometric expression of mRNA polycistrons by eukaryotic ribosomes for compact, ratio-tunable multi-gene expression. SEMPER：真核核糖体对 mRNA 多单元的定量表达，实现紧凑、比例可调的多基因表达。

Cell systems Pub Date : 2024-07-17 Epub Date: 2024-07-05 DOI: 10.1016/j.cels.2024.06.001

Mengtong Duan, Ishaan Dev, Andrew Lu, Goar Ayrapetyan, Mei Yi You, Mikhail G Shapiro

{"title":"SEMPER: Stoichiometric expression of mRNA polycistrons by eukaryotic ribosomes for compact, ratio-tunable multi-gene expression.","authors":"Mengtong Duan, Ishaan Dev, Andrew Lu, Goar Ayrapetyan, Mei Yi You, Mikhail G Shapiro","doi":"10.1016/j.cels.2024.06.001","DOIUrl":"10.1016/j.cels.2024.06.001","url":null,"abstract":"Here, we present a method for expressing multiple open reading frames (ORFs) from single transcripts using the leaky scanning model of translation initiation. In this approach termed \"stoichiometric expression of mRNA polycistrons by eukaryotic ribosomes\" (SEMPER), adjacent ORFs are translated from a single mRNA at tunable ratios determined by their order in the sequence and the strength of their translation initiation sites. We validate this approach by expressing up to three fluorescent proteins from one plasmid in two different cell lines. We then use it to encode a stoichiometrically tuned polycistronic construct encoding gas vesicle acoustic reporter genes that enables efficient formation of the multi-protein complex while minimizing cellular toxicity. We also demonstrate that SEMPER enables polycistronic expression of recombinant monoclonal antibodies from plasmid DNA and of two fluorescent proteins from single mRNAs made through in vitro transcription. Finally, we provide a probabilistic model to elucidate the mechanisms underlying SEMPER. A record of this paper's transparent peer review process is included in the supplemental information.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":" ","pages":"597-609.e4"},"PeriodicalIF":0.0,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11298409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141545640","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

Highly parallel production of designer organoids by mosaic patterning of progenitors. 通过对祖细胞进行镶嵌图案化，高度并行地生产出设计器官。

Cell systems Pub Date : 2024-07-17 Epub Date: 2024-07-08 DOI: 10.1016/j.cels.2024.06.004

Catherine M Porter, Grace C Qian, Samuel H Grindel, Alex J Hughes

{"title":"Highly parallel production of designer organoids by mosaic patterning of progenitors.","authors":"Catherine M Porter, Grace C Qian, Samuel H Grindel, Alex J Hughes","doi":"10.1016/j.cels.2024.06.004","DOIUrl":"10.1016/j.cels.2024.06.004","url":null,"abstract":"Organoids derived from human stem cells are a promising approach for disease modeling, regenerative medicine, and fundamental research. However, organoid variability and limited control over morphological outcomes remain as challenges. One open question is the extent to which engineering control over culture conditions can guide organoids to specific compositions. Here, we extend a DNA \"velcro\" cell patterning approach, precisely controlling the number and ratio of human induced pluripotent stem cell-derived progenitors contributing to nephron progenitor (NP) organoids and mosaic NP/ureteric bud (UB) tip cell organoids within arrays of microwells. We demonstrate long-term control over organoid size and morphology, decoupled from geometric constraints. We then show emergent trends in organoid tissue proportions that depend on initial progenitor cell composition. These include higher nephron and stromal cell representation in mosaic NP/UB organoids vs. NP-only organoids and a \"goldilocks\" initial cell ratio in mosaic organoids that optimizes the formation of proximal tubule structures.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":" ","pages":"649-661.e9"},"PeriodicalIF":0.0,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11257788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141565354","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

Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis. 大肠杆菌趋化过程中的信号整合与适应性感觉多样性调整

Cell systems Pub Date : 2024-07-17 Epub Date: 2024-07-08 DOI: 10.1016/j.cels.2024.06.003

Jeremy Philippe Moore, Keita Kamino, Rafaela Kottou, Thomas S Shimizu, Thierry Emonet

引用次数: 0

The unreasonable effectiveness of equilibrium gene regulation through the cell cycle. 细胞周期中平衡基因调控的不合理有效性。

Cell systems Pub Date : 2024-07-17 Epub Date: 2024-07-08 DOI: 10.1016/j.cels.2024.06.002

Jose M G Vilar, Leonor Saiz

引用次数: 0

Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter. 利用基于相分离的荧光报告器实现亚显微蛋白质团簇的简单可视化。

Cell systems Pub Date : 2024-06-19 Epub Date: 2024-05-25 DOI: 10.1016/j.cels.2024.05.003

Thomas R Mumford, Diarmid Rae, Emily Brackhahn, Abbas Idris, David Gonzalez-Martinez, Ayush Aditya Pal, Michael C Chung, Juan Guan, Elizabeth Rhoades, Lukasz J Bugaj

引用次数: 0

Tissue module discovery in single-cell-resolution spatial transcriptomics data via cell-cell interaction-aware cell embedding. 通过细胞-细胞交互感知细胞嵌入在单细胞分辨率空间转录组学数据中发现组织模块

Cell systems Pub Date : 2024-06-19 Epub Date: 2024-05-31 DOI: 10.1016/j.cels.2024.05.001

Yuzhe Li, Jinsong Zhang, Xin Gao, Qiangfeng Cliff Zhang

{"title":"Tissue module discovery in single-cell-resolution spatial transcriptomics data via cell-cell interaction-aware cell embedding.","authors":"Yuzhe Li, Jinsong Zhang, Xin Gao, Qiangfeng Cliff Zhang","doi":"10.1016/j.cels.2024.05.001","DOIUrl":"10.1016/j.cels.2024.05.001","url":null,"abstract":"Computational methods are desired for single-cell-resolution spatial transcriptomics (ST) data analysis to uncover spatial organization principles for how individual cells exert tissue-specific functions. Here, we present ST data analysis via interaction-aware cell embedding (SPACE), a deep-learning method for cell-type identification and tissue module discovery from single-cell-resolution ST data by learning a cell representation that captures its gene expression profile and interactions with its spatial neighbors. SPACE identified spatially informed cell subtypes defined by their special spatial distribution patterns and distinct proximal-interacting cell types. SPACE also automatically discovered \"cell communities\"-tissue modules with discernible boundaries and a uniform spatial distribution of constituent cell types. For each cell community, SPACE outputs a characteristic proximal cell-cell interaction network associated with physiological processes, which can be used to refine ligand-receptor-based intercellular signaling analyses. We envision that SPACE can be used in large-scale ST projects to understand how proximal cell-cell interactions contribute to emergent biological functions within cell communities. A record of this paper's transparent peer review process is included in the supplemental information.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":" ","pages":"578-592.e7"},"PeriodicalIF":0.0,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141186041","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

Stimulus-response signaling dynamics characterize macrophage polarization states. 刺激-反应信号动态描述了巨噬细胞的极化状态。

Cell systems Pub Date : 2024-06-19 Epub Date: 2024-06-05 DOI: 10.1016/j.cels.2024.05.002

Apeksha Singh, Supriya Sen, Michael Iter, Adewunmi Adelaja, Stefanie Luecke, Xiaolu Guo, Alexander Hoffmann

{"title":"Stimulus-response signaling dynamics characterize macrophage polarization states.","authors":"Apeksha Singh, Supriya Sen, Michael Iter, Adewunmi Adelaja, Stefanie Luecke, Xiaolu Guo, Alexander Hoffmann","doi":"10.1016/j.cels.2024.05.002","DOIUrl":"10.1016/j.cels.2024.05.002","url":null,"abstract":"The functional state of cells is dependent on their microenvironmental context. Prior studies described how polarizing cytokines alter macrophage transcriptomes and epigenomes. Here, we characterized the functional responses of 6 differentially polarized macrophage populations by measuring the dynamics of transcription factor nuclear factor κB (NF-κB) in response to 8 stimuli. The resulting dataset of single-cell NF-κB trajectories was analyzed by three approaches: (1) machine learning on time-series data revealed losses of stimulus distinguishability with polarization, reflecting canalized effector functions. (2) Informative trajectory features driving stimulus distinguishability (\"signaling codons\") were identified and used for mapping a cell state landscape that could then locate macrophages conditioned by an unrelated condition. (3) Kinetic parameters, inferred using a mechanistic NF-κB network model, provided an alternative mapping of cell states and correctly predicted biochemical findings. Together, this work demonstrates that a single analyte's dynamic trajectories may distinguish the functional states of single cells and molecular network states underlying them. A record of this paper's transparent peer review process is included in the supplemental information.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":" ","pages":"563-577.e6"},"PeriodicalIF":0.0,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11226196/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141285663","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

The substrate quality of CK2 target sites has a determinant role on their function and evolution. CK2 目标位点的底物质量对其功能和进化具有决定性作用。

Cell systems Pub Date : 2024-06-19 Epub Date: 2024-06-10 DOI: 10.1016/j.cels.2024.05.005

David Bradley, Chantal Garand, Hugo Belda, Isabelle Gagnon-Arsenault, Moritz Treeck, Sabine Elowe, Christian R Landry

{"title":"The substrate quality of CK2 target sites has a determinant role on their function and evolution.","authors":"David Bradley, Chantal Garand, Hugo Belda, Isabelle Gagnon-Arsenault, Moritz Treeck, Sabine Elowe, Christian R Landry","doi":"10.1016/j.cels.2024.05.005","DOIUrl":"10.1016/j.cels.2024.05.005","url":null,"abstract":"Most biological processes are regulated by signaling modules that bind to short linear motifs. For protein kinases, substrates may have full or only partial matches to the kinase recognition motif, a property known as \"substrate quality.\" However, it is not clear whether differences in substrate quality represent neutral variation or if they have functional consequences. We examine this question for the kinase CK2, which has many fundamental functions. We show that optimal CK2 sites are phosphorylated at maximal stoichiometries and found in many conditions, whereas minimal substrates are more weakly phosphorylated and have regulatory functions. Optimal CK2 sites tend to be more conserved, and substrate quality is often tuned by selection. For intermediate sites, increases or decreases in substrate quality may be deleterious, as we demonstrate for a CK2 substrate at the kinetochore. The results together suggest a strong role for substrate quality in phosphosite function and evolution. A record of this paper's transparent peer review process is included in the supplemental information.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":" ","pages":"544-562.e8"},"PeriodicalIF":0.0,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141307628","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