bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering Functional Membrane–Membrane Interfaces by InterSpy
Authors: Moghimianavval Hossein , Patel Chintan , Mohapatra Sonisilpa , Hwang Sung‐Won , Kayikcioglu Tunc , Bashirzadeh Yashar , Liu Allen P. , Ha Taekjip 
Published: May 2022

AbstractEngineering synthetic interfaces between membranes has potential applications in designing non‐native cellular communication pathways and creating synthetic tissues. Here, InterSpy is introduced as a synthetic biology tool consisting of a heterodimeric protein engineered to form and maintain membrane–membrane interfaces between apposing synthetic as well as cell membranes through the SpyTag/SpyCatcher interaction. The inclusion of split fluorescent protein fragments in InterSpy allows tracking of the formation of a membrane–membrane interface and reconstitution of functional fluorescent protein in the space between apposing membranes. First, InterSpy is demonstrated by testing split protein designs using a mammalian cell‐free expression (CFE) system. By utilizing co‐translational helix insertion, cell‐free synthesized InterSpy fragments are incorporated into the membrane of liposomes and supported lipid bilayers with the desired topology. Functional reconstitution of split fluorescent protein between the membranes is strictly dependent on SpyTag/SpyCatcher. Finally, InterSpy is demonstrated in mammalian cells by detecting fluorescence reconstitution of split protein at the membrane–membrane interface between two cells each expressing a component of InterSpy. InterSpy demonstrates the power of CFE systems in the functional reconstitution of synthetic membrane interfaces via proximity‐inducing proteins. This technology may also prove useful where cell‐cell contacts and communication are recreated in a controlled manner using minimal components.
Organic Small Molecules with Electrochemical‐Active Phenolic Enolate Groups for Ready‐to‐Charge Organic Sodium‐Ion Batteries
Authors: Zhang Hang , Gao Yun , Chen Mingzhe , Li Lin , Li Li , Qiao Yun , Li Weijie , Wang Jiazhao , Chou Shu‐Lei 
Published: May 2022

AbstractOrganic materials have attracted much attention in sodium ion batteries (SIBs) because of their advantages such as being environmentally benign and having high designability. Capacities and cycle life of organic materials are the most important parameters in most research which has been paid much effort to obtain an impressive electrochemical performance on the material level, and the sodium‐detachable ability of these materials to directly match with the sodium‐free anode is neglected. In this work, one organic sodium salt (C6H2Na2O6) exhibits the unique ability (charging first in half cell) unlike other reported organic cathode materials (normally discharging first) for SIBs. The redox mechanism and structure change are investigated by in situ and ex situ tests to give a better understanding for C6H2Na2O6. Satisfying electrochemical performance (74% capacity retention after 600 cycles at 0.05 A g−1 and 63% capacity retention at 5 A g−1 when compared with capacity at 0.05 A g−1) is achieved by the C6H2Na2O6 electrode. In addition, matched with hard carbon, full cells are assembled successfully like other transition metal containing cathode materials because C6H2Na2O6 electrode can deliver its sodium ions to a sodium‐free anode directly without any presodiation.
NGS-Based B-Cell Receptor Repertoire AnalysisRepertoire analyses in the Context of Inborn Errors of Immunity
Authors: van Schouwenburg Pauline A. , van der Burg Mirjam , IJspeert Hanna 
Published: May 2022

AbstractInborn errors of immunity (IEI) are genetic defects that can affect both the innate and the adaptive immune system. Patients with IEI usually present with recurrent infections, but many also suffer from immune dysregulation, autoimmunity, and malignancies.Inborn errors of the immune system can cause defects in the development and selection of the B-cell receptor (BCR) repertoire. Patients with IEI can have a defect in one of the key processes of immune repertoire formation like V(D)J recombination, somatic hypermutation (SHM), class switch recombination (CSR), or (pre-)BCR signalling and proliferation. However, also other genetic defects can lead to quantitative and qualitative differences in the immune repertoire.In this chapter, we will give an overview of protocols that can be used to study the immune repertoire in patients with IEI, provide considerations to take into account before setting up experiments, and discuss analysis of the immune repertoire data using Antigen Receptor Galaxy (ARGalaxy).
Generic Multiplex Digital PCR for Accurate Quantification of T Cells in Copy Number Stable and Unstable DNA Samples
Authors: Nell Rogier J. , Zoutman Willem H. , Versluis Mieke , van der Velden Pieter A. 
Published: May 2022

AbstractAn accurate T cell quantification is prognostically and therapeutically relevant in various clinical applications, including oncology care and research. In this chapter, we describe how T cell quantifications can be obtained from bulk DNA samples with a multiplex digital PCR experiment. The experimental setup includes the concurrent quantification of three different DNA targets within one reaction: a unique T cell DNA marker, a regional corrector, and a reference DNA marker. The T cell marker is biallelically absent in T cells due to VDJ rearrangements, while the reference is diploid in all cells. The so-called regional corrector allows to correct for possible copy number alterations at the T cell marker locus in cancer cells. By mathematically integrating the measurements of all three markers, T cells can be accurately quantified in both copy number stable and unstable DNA samples.
Gene Engineering T Cells with T-Cell Receptor for Adoptive Therapy
Authors: Kortleve Dian , van Brakel Mandy , Wijers Rebecca , Debets Reno , Hammerl Dora 
Published: May 2022

AbstractPrior to clinical testing of adoptive T-cell therapy with T-cell receptor (TCR)-engineered T cells, TCRs need to be retrieved, annotated, gene-transferred, and extensively tested in vitro to accurately assess specificity and sensitivity of target recognition. Here, we present a fundamental series of protocols that cover critical preclinical parameters, thereby enabling the selection of candidate TCRs for clinical testing.
AIRR Community Guide to Planning and Performing AIRR-Seq Experiments
Authors: Eugster Anne , Bostick Magnolia L. , Gupta Nidhi , Mariotti-Ferrandiz Encarnita , Kraus Gloria , Meng Wenzhao , Soto Cinque , Trück Johannes , Stervbo Ulrik , Luning Prak Eline T. ,   on behalf of the AIRR Community
Published: May 2022

AbstractThe development of high-throughput sequencing of adaptive immune receptor repertoires (AIRR-seq of IG and TR rearrangements) has provided a new frontier for in-depth analysis of the immune system. The last decade has witnessed an explosion in protocols, experimental methodologies, and computational tools. In this chapter, we discuss the major considerations in planning a successful AIRR-seq experiment together with basic strategies for controlling and evaluating the outcome of the experiment. Members of the AIRR Community have authored several chapters in this edition, which cover step-by-step instructions to successfully conduct, analyze, and share an AIRR-seq project.
Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation
Authors: Babrak Lmar , Marquez Susanna , Busse Christian E. , Lees William D. , Miho Enkelejda , Ohlin Mats , Rosenfeld Aaron M. , Stervbo Ulrik , Watson Corey T. , Schramm Chaim A. ,   on behalf of the AIRR Community
Published: May 2022

AbstractHigh-throughput sequencing of adaptive immune receptor repertoires (AIRR, i.e., IG and TR) has revolutionized the ability to carry out large-scale experiments to study the adaptive immune response. Since the method was first introduced in 2009, AIRR sequencing (AIRR-Seq) has been applied to survey the immune state of individuals, identify antigen-specific or immune-state-associated signatures of immune responses, study the development of the antibody immune response, and guide the development of vaccines and antibody therapies. Recent advancements in the technology include sequencing at the single-cell level and in parallel with gene expression, which allows the introduction of multi-omics approaches to understand in detail the adaptive immune response. Analyzing AIRR-seq data can prove challenging even with high-quality sequencing, in part due to the many steps involved and the need to parameterize each step. In this chapter, we outline key factors to consider when preprocessing raw AIRR-Seq data and annotating the genetic origins of the rearranged receptors. We also highlight a number of common difficulties with common AIRR-seq data processing and provide strategies to address them.
Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis
Authors: Marquez Susanna , Babrak Lmar , Greiff Victor , Hoehn Kenneth B. , Lees William D. , Luning Prak Eline T. , Miho Enkelejda , Rosenfeld Aaron M. , Schramm Chaim A. , Stervbo Ulrik ,   on behalf of the AIRR Community
Published: May 2022

AbstractAdaptive immune receptor repertoires (AIRRs) are rich with information that can be mined for insights into the workings of the immune system. Gene usage, CDR3 properties, clonal lineage structure, and sequence diversity are all capable of revealing the dynamic immune response to perturbation by disease, vaccination, or other interventions. Here we focus on a conceptual introduction to the many aspects of repertoire analysis and orient the reader toward the uses and advantages of each. Along the way, we note some of the many software tools that have been developed for these investigations and link the ideas discussed to chapters on methods provided elsewhere in this volume.
Bulk gDNA Sequencing of Antibody Heavy-Chain Gene Rearrangements for Detection and Analysis of B-Cell Clone Distribution: A Method by the AIRR Community
Authors: Rosenfeld Aaron M. , Meng Wenzhao , Horne Kalisse I. , Chen Elaine C. , Bagnara Davide , Stervbo Ulrik , Luning Prak Eline T. ,   on behalf of the AIRR Community
Published: May 2022

AbstractIn this method we illustrate how to amplify, sequence, and analyze antibody/immunoglobulin (IG) heavy-chain gene rearrangements from genomic DNA that is derived from bulk populations of cells by next-generation sequencing (NGS). We focus on human source material and illustrate how bulk gDNA-based sequencing can be used to examine clonal architecture and networks in different samples that are sequenced from the same individual. Although bulk gDNA-based sequencing can be performed on both IG heavy (IGH) or kappa/lambda light (IGK/IGL) chains, we focus here on IGH gene rearrangements because IG heavy chains are more diverse, tend to harbor higher levels of somatic hypermutations (SHM), and are more reliable for clone identification and tracking. We also provide a procedure, including code, and detailed instructions for processing and annotation of the NGS data. From these data we show how to identify expanded clones, visualize the overall clonal landscape, and track clonal lineages in different samples from the same individual. This method has a broad range of applications, including the identification and monitoring of expanded clones, the analysis of blood and tissue-based clonal networks, and the study of immune responses including clonal evolution.
Next-Generation Sequencing-Based Clonality Detection of Immunoglobulin Gene Rearrangements in B-Cell Lymphoma
Authors: van Bladel Diede A. G. , van der Last-Kempkes Jessica L. M. , Scheijen Blanca , Groenen Patricia J. T. A. ,   on behalf of the EuroClonality Consortium
Published: May 2022

AbstractImmunoglobulin (IG) clonality assessment is a widely used supplementary test for the diagnosis of suspected lymphoid malignancies. The specific rearrangements of the immunoglobulin (IG) heavy and light chain genes act as a unique hallmark of a B-cell lymphoma, a feature that is used in clonality assessment. The widely used BIOMED-2/EuroClonality IG clonality assay, visualized by GeneScanning or heteroduplex analysis, has an unprecedented high detection rate because of the complementarity of this approach. However, the BIOMED-2/EuroClonality clonality assays have been developed for the assessment of specimens with optimal DNA quality. Further improvements for the assessment of samples with suboptimal DNA quality, such as from formalin-fixed paraffin-embedded (FFPE) specimens or specimens with a limited tumor burden, are required. The EuroClonality-NGS Working Group recently developed a next-generation sequencing (NGS)-based clonality assay for the detection of the IG heavy and kappa light chain rearrangements, using the same complementary approach as in the conventional assay. By employing next-generation sequencing, both the sensitivity and specificity of the clonality assay have increased, which not only is very useful for diagnostic clonality testing but also allows robust comparison of clonality patterns in a patient with multiple lymphoma’s that have suboptimal DNA quality. Here, we describe the protocols for IG-NGS clonality assessment that are compatible for Ion Torrent and Illumina sequencing platforms including pre-analytical DNA isolation, the analytical phase, and the post-analytical data analysis.
Immune Repertoire Analysis on High-Performance Computing Using VDJServer V1: A Method by the AIRR Community
Authors: Christley Scott , Stervbo Ulrik , Cowell Lindsay G. ,   on behalf of the AIRR Community
Published: May 2022

AbstractAIRR-seq data sets are usually large and require specialized analysis methods and software tools. A typical Illumina MiSeq sequencing run generates 20–30 million 2 × 300 bp paired-end sequence reads, which roughly corresponds to 15 GB of sequence data to be processed. Other platforms like NextSeq, which is useful in projects where the full V gene is not needed, create about 400 million 2 × 150 bp paired-end reads. Because of the size of the data sets, the analysis can be computationally expensive, particularly the early analysis steps like preprocessing and gene annotation that process the majority of the sequence data. A standard desktop PC may take 3–5 days of constant processing for a single MiSeq run, so dedicated high-performance computational resources may be required.VDJServer provides free access to high-performance computing (HPC) at the Texas Advanced Computing Center (TACC) through a graphical user interface (Christley et al. Front Immunol 9:976, 2018). VDJServer is a cloud-based analysis portal for immune repertoire sequence data that provides access to a suite of tools for a complete analysis workflow, including modules for preprocessing and quality control of sequence reads, V(D)J gene assignment, repertoire characterization, and repertoire comparison. Furthermore, VDJServer has parallelized execution for tools such as IgBLAST, so more compute resources are utilized as the size of the input data grows. Analysis that takes days on a desktop PC might take only a few hours on VDJServer. VDJServer is a free, publicly available, and open-source licensed resource. Here, we describe the workflow for performing immune repertoire analysis on VDJServer’s high-performance computing.
Data Sharing and Reuse: A Method by the AIRR Community
Authors: Corrie Brian D. , Christley Scott , Busse Christian E. , Cowell Lindsay G. , Neller Kira C. M. , Rubelt Florian , Schwab Nicholas ,   on behalf of the AIRR Community
Published: May 2022

AbstractHigh-throughput sequencing of adaptive immune receptor repertoires (AIRR, i.e., IG and TR) has revolutionized the ability to study the adaptive immune response via large-scale experiments. Since 2009, AIRR sequencing (AIRR-seq) has been widely applied to survey the immune state of individuals (see “The AIRR Community Guide to Repertoire Analysis” chapter for details). One of the goals of the AIRR Community is to make the resulting AIRR-seq data FAIR (Findable, Accessible, Interoperable, and Reusable) (Wilkinson et al. Sci Data 3:1–9, 2016), with a primary goal of making it easy for the research community to reuse AIRR-seq data (Breden et al. Front Immunol 8:1418, 2017; Scott and Breden. Curr Opin Syst Biol 24:71–77, 2020). The basis for this is the MiAIRR data standard (Rubelt et al. Nat Immunol 18:1274–1278, 2017). For long-term preservation, it is recommended that researchers store their sequence read data in an INSDC repository. At the same time, the AIRR Community has established the AIRR Data Commons (Christley et al. Front Big Data 3:22, 2020), a distributed set of AIRR-compliant repositories that store the critically important annotated AIRR-seq data based on the MiAIRR standard, making the data findable, interoperable, and, because the data are annotated, more valuable in its reuse. Here, we build on the other AIRR Community chapters and illustrate how these principles and standards can be incorporated into AIRR-seq data analysis workflows. We discuss the importance of careful curation of metadata to ensure reproducibility and facilitate data sharing and reuse, and we illustrate how data can be shared via the AIRR Data Commons.
IMGT/3Dstructure-DB: T-Cell Receptor TR Paratope and Peptide/Major Histocompatibility pMH Contact Sites and Epitope
Authors: Lefranc Marie-Paule , Lefranc Gérard 
Published: May 2022

AbstractT-cell receptors (TR), the antigen receptors of T cells, specifically recognize peptides presented by the major histocompatibility (MH) proteins, as peptide/MH (pMH), on the cell surface. The structure characterization of the trimolecular TR/pMH complexes is crucial to the fields of immunology, vaccination, and immunotherapy. IMGT/3Dstructure-DB is the three-dimensional (3-D) structure database of IMGT®, the international ImMunoGenetics information system®. By its creation, IMGT®marks the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. The IMGT®immunoglobulin (IG) and TR gene and allele nomenclature (CLASSIFICATION axiom) and the IMGT unique numbering and IMGT/Collier-de-Perles (NUMEROTATION axiom) are the two founding breakthroughs of immunoinformatics. IMGT-ONTOLOGY concepts and IMGT Scientific chart rules generated from these axioms allowed IMGT®bridging genes, structures, and functions. IMGT/3Dstructure-DB contains 3-D structures of IG or antibodies, TR and MH proteins of the adaptive immune responses of jawed vertebrates (gnathostomata), IG or TR complexes with antigens (IG/Ag, TR/pMH), related proteins of the immune system of any species belonging to the IG and MH superfamilies, and fusion proteins for immune applications. The focus of this chapter is on the TR V domains and MH G domains and the contact analysis comparison in TR/pMH interactions. Standardized molecular characterization includes “IMGT pMH contact sites” for peptide and MH groove interactions and “IMGT paratopes and epitopes” for TR/pMH complexes. Data are available in the IMGT/3Dstructure database, at the IMGT Home pagehttp://www.imgt.org.
Purpose-Built Immunoinformatics for BcR IG/TR Repertoire Data Analysis
Authors: Galigalidou Chrysi , Zaragoza-Infante Laura , Chatzidimitriou Anastasia , Stamatopoulos Kostas , Psomopoulos Fotis , Agathangelidis Andreas 
Published: May 2022

AbstractThe study of antigen receptor gene repertoires using next-generation sequencing (NGS) technologies has disclosed an unprecedented depth of complexity, requiring novel computational and analytical solutions. Several bioinformatics workflows have been developed to this end, including the T-cell receptor/immunoglobulin profiler (TRIP), a web application implemented in R shiny, specifically designed for the purposes of comprehensive repertoire analysis, which is the focus of this chapter. TRIP has the potential to perform robust immunoprofiling analysis through the extraction and processing of the IMGT/HighV-Quest output, via a series of functions, ensuring the analysis of high-quality, biologically relevant data through a multilevel process of data filtering. Subsequently, it provides in-depth analysis of antigen receptor gene rearrangements, including (a) clonality assessment; (b) extraction of variable (V), diversity (D), and joining (J) gene repertoires; (c) CDR3 characterization at both the nucleotide and amino acid level; and (d) somatic hypermutation analysis, in the case of immunoglobulin gene rearrangements. Relevant to mention, TRIP enables a high level of customization through the integration of various options in key aspects of the analysis, such as clonotype definition and computation, hence allowing for flexibility without compromising on accuracy.
One-Step Next-Generation Sequencing of Immunoglobulin and T-Cell Receptor Gene Recombinations for MRD Marker Identification in Acute Lymphoblastic Leukemia
Authors: Villarese Patrick , Abdo Chrystelle , Bertrand Matthieu , Thonier Florian , Giraud Mathieu , Salson Mikaël , Macintyre Elizabeth 
Published: May 2022

AbstractWithin the EuroClonality-NGS group, immune repertoire analysis for target identification in lymphoid malignancies was initially developed using two-stage amplicon approaches, essentially as a progressive modification of preceding methods developed for Sanger sequencing. This approach has, however, limitations with respect to sample handling, adaptation to automation, and risk of contamination by amplicon products. We therefore developed one-step PCR amplicon methods with individual barcoding for batched analysis for IGH, IGK, TRD, TRG, and TRB rearrangements, followed by Vidjil-based data analysis.
Minimal Residual Disease Analysis by Monitoring Immunoglobulin and T-Cell Receptor Gene Rearrangements by Quantitative PCR and Droplet Digital PCR
Authors: Starza Irene Della , Eckert Cornelia , Drandi Daniela , Cazzaniga Giovanni ,   on behalf of the EuroMRD Consortium
Published: May 2022

AbstractAnalysis of immunoglobulin and T-cell receptor gene rearrangements by real-time quantitative polymerase chain reaction (RQ-PCR) is the gold standard for sensitive and accurate minimal residual disease (MRD) monitoring; it has been extensively standardized and guidelines have been developed within the EuroMRD consortium (www.euromrd.org). However, new generations of PCR-based methods are standing out as potential alternatives to RQ-PCR, such as digital PCR technology (dPCR), the third-generation implementation of conventional PCR, which has the potential to overcome some of the limitations of RQ-PCR such as allowing the absolute quantification of nucleic acid targets without the need for a calibration curve. During the last years, droplet digital PCR (ddPCR) technology has been compared to RQ-PCR in several hematologic malignancies showing its proficiency for MRD analysis. So far, no established guidelines for ddPCR MRD analysis and data interpretation have been defined and its potential is still under investigation. However, a major standardization effort is underway within the EuroMRD consortium (www.euromrd.org) for future application of ddPCR in standard clinical practice.
Quality Control for IG/TR Marker Identification and MRD Analysis
Authors: Fronkova Eva , Svaton Michael , Trka Jan 
Published: May 2022

AbstractSelection of the proper target is crucial for clinically relevant monitoring of minimal residual disease (MRD) in patients with acute lymphoblastic leukemia using the quantitation of clonal-specific immunoreceptor (immunoglobulin/T cell receptor) gene rearrangements. Consequently, correct interpretation of the results of the entire analysis is of utmost importance. Here we present an overview of the quality control measures that need to be implemented into the process of marker identification, selection, and subsequent quantitation of the MRD level.