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The immune system is a complex network of specialized cells that coordinate to eliminate immune challenges while minimally damaging self. Understanding the role of each cell in that network requires accurate quantification of informative biological features of single cells. Here, we innovated and applied single-cell methods and purpose- driven computational analyses to problems in basic and translational immunology. We developed a highly-multiplexed screen to quantify the co-expression of 351 surface molecules on millions of human B cells. We identified differentially expressed molecules and aligned their variance with isotype usage, VDJ sequence, metabolic profile, biosynthesis activity, and signaling response. Based on these analyses, we proposed a classification scheme to segregate B cells from four lymphoid tissues into twelve unique subsets, providing a framework for further investigations of human B cell identity and function. Additionally, we introduced morphometry, a high-throughput, quantitative, single-cell mass-cytometry-based assay that measures cell morphological features by their underlying molecular components. We applied multiplexed morphometric profiling and surface molecule immunophenotyping to 71 diverse clinical hematopathology samples and demonstrated that our approach was superior to flow cytometry and comparable to expert microscopy for tumor cell identification and enumeration. We introduced linear discriminant analysis (LDA) to generate morphometric maps that facilitate visualization and quantification of tumor cells. This contextualization of traditional surface markers on independent morphometric frameworks permits more sensitive and automated diagnosis of complex hematopoietic diseases.
Revealing Unchartered Biology with Single Intact Cells: Case Studies explores the path to research success, key projects, the role of techniques, the selection process, other alternatives considered, what other paths have led to dead ends, detailed protocols followed, and how the analysis of generated data allowed researchers to visualize unchartered biology. Focusing on the research journey that led to the publication of each article, the book's editors interviewed the researchers on the use of the Multiplex Single Cell technique and how it helped hone in on the biological quest. These methods can be expanded to a wide variety of research objectives. In conclusion to each chapter, the authors critically review their process and provide suggestions of improvement or alternate techniques that could be employed. This book is the ideal reference for researchers new to the world of single-cell multiplex techniques. The discussion on failures encountered along the research path provides insights on how to avoid repeating the same errors. Provides insights into the path to success of key research articles based on Multiplex Single-Cell analysis techniques results Contains detailed method information Discusses strengths and limitations of techniques applied to each research domain covered Includes discussions on the failures encountered along the research path and how to avoid them
A step-by-step guide to commonly used procedures, Methods in Cellular Immunology addresses both human and murine models, in addition to such topics as PCR and apoptosis. The basic format of the original version has been maintained, and the goal remains the same: to make it a useful and easy-to-use tool for investigators employing cellular immunolog
The volume focuses on the genomics, proteomics, metabolomics, and bioinformatics of a single cell, especially lymphocytes and on understanding the molecular mechanisms of systems immunology. Based on the author's personal experience, it provides revealing insights into the potential applications, significance, workflow, comparison, future perspectives and challenges of single-cell sequencing for identifying and developing disease-specific biomarkers in order to understand the biological function, activation and dysfunction of single cells and lymphocytes and to explore their functional roles and responses to therapies. It also provides detailed information on individual subgroups of lymphocytes, including cell characters, function, surface markers, receptor function, intracellular signals and pathways, production of inflammatory mediators, nuclear receptors and factors, omics, sequencing, disease-specific biomarkers, bioinformatics, networks and dynamic networks, their role in disease and future prospects. Dr. Xiangdong Wang is a Professor of Medicine, Director of Shanghai Institute of Clinical Bioinformatics, Director of Fudan University Center for Clinical Bioinformatics, Director of the Biomedical Research Center of Zhongshan Hospital, Deputy Director of Shanghai Respiratory Research Institute, Shanghai, China. .
The volume focuses on the genomics, proteomics, metabolomics, and bioinformatics of a single cell, especially lymphocytes and on understanding the molecular mechanisms of systems immunology. Based on the author’s personal experience, it provides revealing insights into the potential applications, significance, workflow, comparison, future perspectives and challenges of single-cell sequencing for identifying and developing disease-specific biomarkers in order to understand the biological function, activation and dysfunction of single cells and lymphocytes and to explore their functional roles and responses to therapies. It also provides detailed information on individual subgroups of lymphocytes, including cell characters, function, surface markers, receptor function, intracellular signals and pathways, production of inflammatory mediators, nuclear receptors and factors, omics, sequencing, disease-specific biomarkers, bioinformatics, networks and dynamic networks, their role in disease and future prospects. Dr. Xiangdong Wang is a Professor of Medicine, Director of Shanghai Institute of Clinical Bioinformatics, Director of Fudan University Center for Clinical Bioinformatics, Director of the Biomedical Research Center of Zhongshan Hospital, Deputy Director of Shanghai Respiratory Research Institute, Shanghai, China.
Topic Editor Qihui Shi is the scientific co-founder of JunHealth, a company aiming to developing single-cell sequencing technologies for clinical applications, and received research funding from BeiGene.
The Immunology Methods Manual is a four-volume set comprising a comprehensive sourcebook of immunological methods and techniques. Unique in its project-oriented, rather than protocol-oriented approach, the emphasis is placed on describing the environment in which each method was developed and is used. The manual contains both advanced methods and descriptions and basic protocols. It is essential not only for those who study the immune system of man or mouse, but also those applying methods to other species. This new compilation of methods answers the needs of immunologists; molecular, developmental, and cell biologists; students and advanced researchers, and workers in clinical and diagnostic laboratories. Protocols are provided to guide day-to-day laboratory work as well as the development of long-term strategies. Vital contact information also encourages useful dialogue and interaction between authors and method-users. More than 35 section editors and 350 authors have contributed to compile this four-volume practical guide to methods that work! Key Features * Provides essential hands-on methods * Presents protocols with background information * Ideally suited for use in a laboratory * Covers all molecular and cellular techniques Key Features of the CD-ROM * Compatible with Windows, Mac, and UNIX platforms * Features a full range of advanced search capabilities * Includes a personalized note creation feature enabling the user to add bookmarks and "post-its" * Offers full cut, copy, and paste capabilities allowing printing, exporting, and editing * Provides hyperlinks between solutions/reagents and their recipes; figures/tables and their text citations; and reference citations to their bibliographic listings * Contains a Pathway feature which allows recording of content during a particular session or loading a pre-recorded tutorial * Includes the animated film "The Immune System" by André Traunecker and Stefan Meyer
This open access book explores techniques for working in the field of immunogenetics, i.e. fundamental and translational research into the adaptive immune receptor repertoire. Many chapters are dedicated to lab protocols, bioinformatics, and immunoinformatics analysis of high-resolution immunome analysis, exemplified by numerous applications. Additionally, the newest technological variations on these protocols are discussed, including non-amplicon, single-cell, and cell-free strategies. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Immunogenetics: Methods and Protocols covers a broad spectrum of methodologies for applications in research and clinical diagnostics to illustrate the impact that immunogenetics has achieved and will further expand in all fields of medicine, from infection and (auto)immunity, to vaccination, to lymphoid malignancy and tumor immunity.
This book provides a brief overview of single-cell analysis using recent advanced technologies. The different sections cover different aspect of single cell analysis and applications with their advantages, limitations, and future challenges. The book has covered how different physical energies such as optical, electrical, and mechanical energy have been applied for single cell therapy and analysis. The recent advanced micro/nanofluidic devices have been employed for single-cell counting, manipulation, cultivation, separation, isolation, lysis, printing and patterning and host-viral interaction at single-cell level. Various chemical approaches for single-cell analysis have been discussed, such as liposome mediated materials transfer at single-cell and their analysis, discovery of antibody via single-cell, high-throughput screening of antigen-specific antibody-secreting cells, and biomolecular secretion analysis of individual cells. Moreover, different single-cell omics such as genomics, proteomics and transcriptomics have been discussed using microfluidic technologies as well as conventional approaches. The role of single cell analysis in system biology and biocatalysis have been discussed in detail. The book describes single-cell phenotyping of heterogeneous tissue, stimulation, and instant reaction quenching technology for biochemical kinetic analysis, large scale single-cell assay for the identification of biocatalysts and analytical techniques for single-cell studies in microbiology. The role of single-cell analysis in cancer, such as single-cell adhesion and cancer progression, single-cell technologies for cancer therapy, analytical technology for single cancer cell analysis, and biophysical markers for cancer cell analysis have been discussed. The flow cytometry based high throughput single-cell analysis have been well emphasized. Finally this book has covered single-cell electrophysiology, single-cell sensing and size measurement using mechanical and microwave resonators, molecular force spectroscopy for cell adhesion measurement, micro-tweezers and force microscopy techniques for single-cell mechanobiological analysis, mass spectrometry and acoustic tweezers for single-cell manipulation and analysis. This book is intended for academic and industrial researchers, undergraduate and graduate students in the fields of biomedical engineering, bio-micro/nanoengineering, and bio-micro/nano fabrication for single-cell analysis. It can be used for courses on bio-MEMS/bio-NEMS, biomicrofluidics, bio-micro/nanofabrications, micro/nanofluidics, biophysics, single cell analysis, bionanotechnology, drug delivery systems and biomedical microdevices. Collective contributions from respected experts, have brought diverse aspects of single-cell technologies in a single hand book. This will benefit researchers and practitioners in the biotechnology industry for different diseases analysis, therapeutics, diagnostics, drug discovery, drug screening etc. In addition to hard copies, the book will be available online and will often be updated by the authors.