Cell Systems最新文献_第4页

In vitro continuous protein evolution empowered by machine learning and automation. 在体外，通过机器学习和自动化实现持续的蛋白质进化。

IF 9.3 1区生物学

Cell Systems Pub Date : 2023-08-16 DOI: 10.1016/j.cels.2023.04.006

Tianhao Yu, Aashutosh Girish Boob, Nilmani Singh, Yufeng Su, Huimin Zhao

引用次数: 3

How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design? 对于希望利用人工智能工具进行蛋白质结构预测和设计的生物学家来说，蛋白质设计领域如何才能为他们提供最佳支持？

IF 9.3 1区生物学

Cell Systems Pub Date : 2023-08-16 DOI: 10.1016/j.cels.2023.07.005

Birte Höcker, Peilong Lu, Anum Glasgow, Debora S Marks, Pranam Chatterjee, Joanna S G Slusky, Ora Schueler-Furman, Possu Huang

引用次数: 0

Virtual stress plays tricks on cells. 虚拟压力对细胞起作用。

IF 9.3 1区生物学

Cell Systems Pub Date : 2023-07-19 DOI: 10.1016/j.cels.2023.06.006

Alexander Loewer

引用次数: 0

What do you most hope spatial molecular profiling will help us understand? Part 2. 您最希望空间分子剖析能帮助我们了解什么？第 2 部分.

IF 9.3 1区生物学

Cell Systems Pub Date : 2023-07-19 DOI: 10.1016/j.cels.2023.06.007

Itai Yanai, Elana J Fertig, Mingyao Li, Fabian Coscia, Johanna Klughammer, Qing Nie, Jinmiao Chen, Ahmet F Coskun

引用次数: 0

Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape. 光遗传控制的综合应激反应揭示了比例编码和应激记忆景观。

IF 9.3 1区生物学

Cell Systems Pub Date : 2023-07-19 DOI: 10.1016/j.cels.2023.06.001

Taivan Batjargal, Francesca Zappa, Ryan J Grant, Robert A Piscopio, Alex Chialastri, Siddharth S Dey, Diego Acosta-Alvear, Maxwell Z Wilson

{"title":"Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape.","authors":"Taivan Batjargal, Francesca Zappa, Ryan J Grant, Robert A Piscopio, Alex Chialastri, Siddharth S Dey, Diego Acosta-Alvear, Maxwell Z Wilson","doi":"10.1016/j.cels.2023.06.001","DOIUrl":"https://doi.org/10.1016/j.cels.2023.06.001","url":null,"abstract":"The integrated stress response (ISR) is a conserved signaling network that detects aberrations and computes cellular responses. Dissecting these computations has been difficult because physical and chemical inducers of stress activate multiple parallel pathways. To overcome this challenge, we engineered a photo-switchable control over the ISR sensor kinase PKR (opto-PKR), enabling virtual, on-target activation. Using light to control opto-PKR dynamics, we traced information flow through the transcriptome and for key downstream ISR effectors. Our analyses revealed a biphasic, proportional transcriptional response with two dynamic modes, transient and gradual, that correspond to adaptive and terminal outcomes. We then constructed an ordinary differential equation (ODE) model of the ISR, which demonstrated the dependence of future stress responses on past stress. Finally, we tested our model using high-throughput light-delivery to map the stress memory landscape. Our results demonstrate that cells encode information in stress levels, durations, and the timing between encounters. 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":"2023-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9947129","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

β-catenin repositions over time. 随着时间的推移，β-catenin 会重新定位。

IF 9 1区生物学

Cell Systems Pub Date : 2023-07-19 DOI: 10.1016/j.cels.2023.06.008

Sarah M Leichter, Steven Henikoff

引用次数: 0

BayesTME: An end-to-end method for multiscale spatial transcriptional profiling of the tissue microenvironment. BayesTME：组织微环境多尺度空间转录谱分析的端到端方法。

IF 9 1区生物学

Cell Systems Pub Date : 2023-07-19 DOI: 10.1016/j.cels.2023.06.003

Haoran Zhang, Miranda V Hunter, Jacqueline Chou, Jeffrey F Quinn, Mingyuan Zhou, Richard M White, Wesley Tansey

{"title":"BayesTME: An end-to-end method for multiscale spatial transcriptional profiling of the tissue microenvironment.","authors":"Haoran Zhang, Miranda V Hunter, Jacqueline Chou, Jeffrey F Quinn, Mingyuan Zhou, Richard M White, Wesley Tansey","doi":"10.1016/j.cels.2023.06.003","DOIUrl":"10.1016/j.cels.2023.06.003","url":null,"abstract":"Spatial variation in cellular phenotypes underlies heterogeneity in immune recognition and response to therapy in cancer and many other diseases. Spatial transcriptomics holds the potential to quantify such variation, but existing analysis methods are limited by their focus on individual tasks such as spot deconvolution. We present BayesTME, an end-to-end Bayesian method for analyzing spatial transcriptomics data. BayesTME unifies several previously distinct analysis goals under a single, holistic generative model. This unified approach enables BayesTME to deconvolve spots into cell phenotypes without any need for paired single-cell RNA-seq. BayesTME then goes beyond spot deconvolution to uncover spatial expression patterns among coordinated subsets of genes within phenotypes, which we term spatial transcriptional programs. BayesTME achieves state-of-the-art performance across myriad benchmarks. On human and zebrafish melanoma tissues, BayesTME identifies spatial transcriptional programs that capture fundamental biological phenomena such as bilateral symmetry and tumor-associated fibroblast and macrophage reprogramming. BayesTME is open source.","PeriodicalId":54348,"journal":{"name":"Cell Systems","volume":null,"pages":null},"PeriodicalIF":9.0,"publicationDate":"2023-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10368078/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10159341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SiftCell: A robust framework to detect and isolate cell-containing droplets from single-cell RNA sequence reads. SiftCell：从单细胞 RNA 序列读数中检测和分离含细胞液滴的稳健框架。

IF 9 1区生物学

Cell Systems Pub Date : 2023-07-19 DOI: 10.1016/j.cels.2023.06.002

Jingyue Xi, Sung Rye Park, Jun Hee Lee, Hyun Min Kang

{"title":"SiftCell: A robust framework to detect and isolate cell-containing droplets from single-cell RNA sequence reads.","authors":"Jingyue Xi, Sung Rye Park, Jun Hee Lee, Hyun Min Kang","doi":"10.1016/j.cels.2023.06.002","DOIUrl":"10.1016/j.cels.2023.06.002","url":null,"abstract":"Single-cell RNA sequencing (scRNA-seq) massively profiles transcriptomes of individual cells encapsulated in barcoded droplets in parallel. However, in real-world scRNA-seq data, many barcoded droplets do not contain cells, but instead, they capture a fraction of ambient RNAs released from damaged or lysed cells. A typical first step to analyze scRNA-seq data is to filter out cell-free droplets and isolate cell-containing droplets, but distinguishing them is often challenging; incorrect filtering may mislead the downstream analysis substantially. We propose SiftCell, a suite of software tools to identify and visualize cell-containing and cell-free droplets in manifold space via randomization (SiftCell-Shuffle) to classify between the two types of droplets (SiftCell-Boost) and to quantify the contribution of ambient RNAs for each droplet (SiftCell-Mix). By applying our method to datasets obtained by various single-cell platforms, we show that SiftCell provides a streamlined way to perform upstream quality control of scRNA-seq, which is more comprehensive and accurate than existing methods.","PeriodicalId":54348,"journal":{"name":"Cell Systems","volume":null,"pages":null},"PeriodicalIF":9.0,"publicationDate":"2023-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10411962/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10018347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","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 time-resolved genomic impact of Wnt/β-catenin signaling. Wnt/β-catenin信号的时间解析基因组影响。

IF 9.3 1区生物学

Cell Systems Pub Date : 2023-07-19 DOI: 10.1016/j.cels.2023.06.004

Pierfrancesco Pagella, Simon Söderholm, Anna Nordin, Gianluca Zambanini, Valeria Ghezzi, Amaia Jauregi-Miguel, Claudio Cantù

{"title":"The time-resolved genomic impact of Wnt/β-catenin signaling.","authors":"Pierfrancesco Pagella, Simon Söderholm, Anna Nordin, Gianluca Zambanini, Valeria Ghezzi, Amaia Jauregi-Miguel, Claudio Cantù","doi":"10.1016/j.cels.2023.06.004","DOIUrl":"https://doi.org/10.1016/j.cels.2023.06.004","url":null,"abstract":"Wnt signaling orchestrates gene expression via its effector, β-catenin. However, it is unknown whether β-catenin binds its target genomic regions simultaneously and how this impacts chromatin dynamics to modulate cell behavior. Using a combination of time-resolved CUT&RUN against β-catenin, ATAC-seq, and perturbation assays in different cell types, we show that Wnt/β-catenin physical targets are tissue-specific, β-catenin \"moves\" on different loci over time, and its association to DNA accompanies changing chromatin accessibility landscapes that determine cell behavior. In particular, Wnt/β-catenin progressively shapes the chromatin of human embryonic stem cells (hESCs) as they undergo mesodermal differentiation, a behavior that we define as \"plastic.\" In HEK293T cells, on the other hand, Wnt/β-catenin drives a transient chromatin opening, followed by re-establishment of the pre-stimulation state, a response that we define as \"elastic.\" Future experiments shall assess whether other cell communication mechanisms, in addition to Wnt signaling, are ruled by time, cellular idiosyncrasies, and chromatin constraints. 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":"2023-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10251043","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

Biphasic JNK-Erk signaling separates the induction and maintenance of cell senescence after DNA damage induced by topoisomerase II inhibition. 双相JNK-Erk信号传导分离拓扑异构酶II抑制诱导的DNA损伤后细胞衰老的诱导和维持。

IF 9 1区生物学

Cell Systems Pub Date : 2023-07-19 DOI: 10.1016/j.cels.2023.06.005

Tatiana S Netterfield, Gerard J Ostheimer, Andrea R Tentner, Brian A Joughin, Alexandra M Dakoyannis, Charvi D Sharma, Peter K Sorger, Kevin A Janes, Douglas A Lauffenburger, Michael B Yaffe

{"title":"Biphasic JNK-Erk signaling separates the induction and maintenance of cell senescence after DNA damage induced by topoisomerase II inhibition.","authors":"Tatiana S Netterfield, Gerard J Ostheimer, Andrea R Tentner, Brian A Joughin, Alexandra M Dakoyannis, Charvi D Sharma, Peter K Sorger, Kevin A Janes, Douglas A Lauffenburger, Michael B Yaffe","doi":"10.1016/j.cels.2023.06.005","DOIUrl":"10.1016/j.cels.2023.06.005","url":null,"abstract":"Genotoxic stress in mammalian cells, including those caused by anti-cancer chemotherapy, can induce temporary cell-cycle arrest, DNA damage-induced senescence (DDIS), or apoptotic cell death. Despite obvious clinical importance, it is unclear how the signals emerging from DNA damage are integrated together with other cellular signaling pathways monitoring the cell's environment and/or internal state to control different cell fates. Using single-cell-based signaling measurements combined with tensor partial least square regression (t-PLSR)/principal component analysis (PCA) analysis, we show that JNK and Erk MAPK signaling regulates the initiation of cell senescence through the transcription factor AP-1 at early times after doxorubicin-induced DNA damage and the senescence-associated secretory phenotype (SASP) at late times after damage. These results identify temporally distinct roles for signaling pathways beyond the classic DNA damage response (DDR) that control the cell senescence decision and modulate the tumor microenvironment and reveal fundamental similarities between signaling pathways responsible for oncogene-induced senescence (OIS) and senescence caused by topoisomerase II inhibition. 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":9.0,"publicationDate":"2023-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10627503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10045327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0