Current protocols in chemical biology最新文献_第3页

Activity-Based Kinome Profiling Using Chemical Proteomics and ATP Acyl Phosphates 利用化学蛋白质组学和ATP酰基磷酸进行基于活性的基因组分析

Current protocols in chemical biology Pub Date : 2019-08-23 DOI: 10.1002/cpch.72

Caroline E. Franks, Ku-Lung Hsu

引用次数: 7

Elucidating Compound Mechanism of Action and Predicting Cytotoxicity Using Machine Learning Approaches, Taking Prediction Confidence into Account 利用机器学习方法阐明复合作用机制和预测细胞毒性，考虑预测置信度

Current protocols in chemical biology Pub Date : 2019-08-11 DOI: 10.1002/cpch.73

Georgios Drakakis, Isidro Cortés-Ciriano, Ben Alexander-Dann, Andreas Bender

{"title":"Elucidating Compound Mechanism of Action and Predicting Cytotoxicity Using Machine Learning Approaches, Taking Prediction Confidence into Account","authors":"Georgios Drakakis, Isidro Cortés-Ciriano, Ben Alexander-Dann, Andreas Bender","doi":"10.1002/cpch.73","DOIUrl":"10.1002/cpch.73","url":null,"abstract":"The modes of action (MoAs) of drugs frequently are unknown, because many are small molecules initially identified from phenotypic screens, giving rise to the need to elucidate their MoAs. In addition, the high attrition rate for candidate drugs in preclinical studies due to intolerable toxicity has motivated the development of computational approaches to predict drug candidate (cyto)toxicity as early as possible in the drug-discovery process. Here, we provide detailed instructions for capitalizing on bioactivity predictions to elucidate the MoAs of small molecules and infer their underlying phenotypic effects. We illustrate how these predictions can be used to infer the underlying antidepressive effects of marketed drugs. We also provide the necessary functionalities to model cytotoxicity data using single and ensemble machine-learning algorithms. Finally, we give detailed instructions on how to calculate confidence intervals for individual predictions using the conformal prediction framework. © 2019 by John Wiley & Sons, Inc.","PeriodicalId":38051,"journal":{"name":"Current protocols in chemical biology","volume":"11 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpch.73","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43437220","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: 1

Purification and Application of Genetically Encoded Potassium Ion Indicators for Quantification of Potassium Ion Concentrations within Biological Samples 基因编码钾离子指示剂的纯化及在生物样品钾离子浓度定量中的应用

Current protocols in chemical biology Pub Date : 2019-07-26 DOI: 10.1002/cpch.71

H. Bischof, S. Burgstaller, N. Vujic, T. Madl, D. Kratky, W. F. Graier, R. Malli

{"title":"Purification and Application of Genetically Encoded Potassium Ion Indicators for Quantification of Potassium Ion Concentrations within Biological Samples","authors":"H. Bischof, S. Burgstaller, N. Vujic, T. Madl, D. Kratky, W. F. Graier, R. Malli","doi":"10.1002/cpch.71","DOIUrl":"10.1002/cpch.71","url":null,"abstract":"Vital cells maintain a steep potassium ion (K+) gradient across the plasma membrane. Intracellular potassium ion concentrations ([K+]) and especially the [K+] within the extracellular matrix are strictly regulated, the latter within a narrow range of ∼3.5 to 5.0 mM. Alterations of the extracellular K+ homeostasis are associated with severe pathological alterations and systemic diseases including hypo- or hypertension, heart rate alterations, heart failure, neuronal damage or abnormal skeleton muscle function. In higher eukaryotic organisms, the maintenance of the extracellular [K+] is mainly achieved by the kidney, responsible for K+ excretion and reabsorption. Thus, renal dysfunctions are typically associated with alterations in serum- or plasma [K+]. Generally, [K+] quantifications within bodily fluids are performed using ion selective electrodes. However, tracking such alterations in experimental models such as mice features several difficulties, mainly due to the small blood volume of these animals, hampering the repetitive collection of sample volumes required for measurements using ion selective electrodes. We have recently developed highly sensitive, genetically encoded potassium ion indicators, the GEPIIs, applicable for in vitro determinations of [K+]. In addition to the determination of [K+] within bodily fluids, GEPIIs proved suitable for the real-time visualization of cell viability over time and the exact determination of the number of dead cells. © 2019 The Authors.","PeriodicalId":38051,"journal":{"name":"Current protocols in chemical biology","volume":"11 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpch.71","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46845023","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: 1

Genetic Engineering by DNA Recombineering DNA重组的基因工程

Current protocols in chemical biology Pub Date : 2019-06-27 DOI: 10.1002/cpch.70

Louis J. Papa III, Matthew D. Shoulders

{"title":"Genetic Engineering by DNA Recombineering","authors":"Louis J. Papa III, Matthew D. Shoulders","doi":"10.1002/cpch.70","DOIUrl":"10.1002/cpch.70","url":null,"abstract":"Recombineering inserts PCR products into DNA using homologous recombination. A pair of short homology arms (50 base pairs) on the ends of a PCR cassette target the cassette to its intended location. These homology arms can be easily introduced as 5′ primer overhangs during the PCR reaction. The flexibility to choose almost any pair of homology arms enables the precise modification of virtually any DNA for purposes of sequence deletion, replacement, insertion, or point mutation. Recombineering often offers significant advantages relative to previous homologous recombination methods that require the construction of cassettes with large homology arms, and relative to traditional cloning methods that become intractable for large plasmids or DNA sequences. However, the tremendous number of variables, options, and pitfalls that can be encountered when designing and performing a recombineering protocol for the first time introduce barriers that can make recombineering a challenging technique for new users to adopt. This article focuses on three recombineering protocols we have found to be particularly robust, providing a detailed guide for choosing the simplest recombineering method for a given application and for performing and troubleshooting experiments. © 2019 by John Wiley & Sons, Inc.","PeriodicalId":38051,"journal":{"name":"Current protocols in chemical biology","volume":"11 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpch.70","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45157698","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: 2

Issue Information TOC 发布信息TOC

Current protocols in chemical biology Pub Date : 2019-06-13 DOI: 10.1002/cpch.55

引用次数: 0

Cell Culture and Coculture for Oncological Research in Appropriate Microenvironments 适宜微环境下肿瘤研究的细胞培养和共培养

Current protocols in chemical biology Pub Date : 2019-06-05 DOI: 10.1002/cpch.65

Apekshya Chhetri, Shirisha Chittiboyina, Farzaneh Atrian, Yunfeng Bai, Davide A. Delisi, Rahim Rahimi, John Garner, Yuri Efremov, Kinam Park, Rabih Talhouk, Sophie A. Lelièvre

{"title":"Cell Culture and Coculture for Oncological Research in Appropriate Microenvironments","authors":"Apekshya Chhetri, Shirisha Chittiboyina, Farzaneh Atrian, Yunfeng Bai, Davide A. Delisi, Rahim Rahimi, John Garner, Yuri Efremov, Kinam Park, Rabih Talhouk, Sophie A. Lelièvre","doi":"10.1002/cpch.65","DOIUrl":"10.1002/cpch.65","url":null,"abstract":"With the increase in knowledge on the importance of the tumor microenvironment, cell culture models of cancers can be adapted to better recapitulate physiologically relevant situations. Three main microenvironmental factors influence tumor phenotype: the biochemical components that stimulate cells, the fibrous molecules that influence the stiffness of the extracellular matrix, and noncancerous cells like epithelial cells, fibroblasts, endothelial cells, and immune cells. Here we present methods for the culture of carcinomas in the presence of a matrix of specific stiffness, and for the coculture of tumors and fibroblasts as well as epithelial cells in the presence of matrix. Information is provided to help with choice and assessment of the matrix support and in working with serum-free medium. Using the example of a tissue chip recapitulating the environmental geometry of carcinomas, we also highlight the development of engineered platforms that provide exquisite control of cell culture parameters necessary in research and development. © 2019 by John Wiley & Sons, Inc.","PeriodicalId":38051,"journal":{"name":"Current protocols in chemical biology","volume":"11 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpch.65","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37310473","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: 10

Issue Information TOC 问题信息TOC

Current protocols in chemical biology Pub Date : 2019-03-01 DOI: 10.1111/ilrs.12082

引用次数: 0

Novel Approaches to Access Arylfluorosulfates and Sulfamoyl Fluorides Based on Sulfur (VI) Fluoride Exchange 基于硫(VI)氟交换获取芳基氟磺酸和磺酰氟的新方法

Current protocols in chemical biology Pub Date : 2019-02-28 DOI: 10.1002/cpch.64

Zilei Liu, Genyi Meng, Taijie Guo, Jiajia Dong, Peng Wu

引用次数: 4

Issue Information TOC 发布信息TOC

Current protocols in chemical biology Pub Date : 2019-02-21 DOI: 10.1002/cpch.54

引用次数: 0

Biochemical Stimulation of Immune Cells and Measurement of Mechanical Responses Using Atomic Force Microscopy 免疫细胞的生化刺激和使用原子力显微镜测量机械反应

Current protocols in chemical biology Pub Date : 2019-02-01 DOI: 10.1002/cpch.63

Kenneth H. Hu, Marc A. Bruce, Jianwei Liu, Manish J. Butte

引用次数: 1