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Ab-origin: An Improved Tool of Heavy Chain Rearrangement Analysis for Human Immunoglobulin [chapter]

Xiaojing Wang, Wu Wei, SiYuan Zheng, Z. W. Cao, Yixue Li
2007 Lecture Notes in Computer Science  
An improved tool to explore the origin of human immunoglobulin heavy chains, named Ab-origin, has been developed.  ...  Though only taking the human heavy chain for an example here, the algorithm also suits for the analysis of all immunoglobulin and TCR sequences.  ...  technology commission of Shanghai municipality (04DZ19850, 06PJ14072).  ... 
doi:10.1007/978-3-540-72586-2_52 fatcat:cin2po2eqredbalvvpk4uaobca

Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies

Xiaojing Wang, Di Wu, Siyuan Zheng, Jing Sun, Lin Tao, Yixue Li, Zhiwei Cao
2008 BMC Bioinformatics  
Moreover, none of them give a confidence for immunoglobulin heavy diversity (IGHD) identification.  ...  Developing fast, efficient and enhanced tools is always needed with the booming of immunological data. Results: Here, a program named Ab-origin is presented.  ...  Yeo WeeKiang for helping us improving the English writing, and the anonymous reviewers for their constructive comments. We also thank Dr. Wu Wei for fruitful and helpful discussion.  ... 
doi:10.1186/1471-2105-9-s12-s20 pmid:19091020 pmcid:PMC2638160 fatcat:daeylty7cvczzbpb2rfqb2jbye

Benchmarking the performance of human antibody gene alignment utilities using a 454 sequence dataset

Katherine J. L. Jackson, Scott Boyd, Bruno A. Gaëta, Andrew M. Collins
2010 Computer applications in the biosciences : CABIOS  
Motivation: Immunoglobulin heavy chain genes are formed by recombination of genes randomly selected from sets of IGHV, IGHD and IGHJ genes.  ...  The Stanford_S22 dataset and an evaluation tool is available at  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btq604 pmid:21036814 fatcat:ogxlmhcdevdxtlg4iphdchbjdy

Clustering-based identification of clonally-related immunoglobulin gene sequence sets

Zhiliang Chen, Andrew M Collins, Yan Wang, Bruno A Gaëta
2010 Immunome Research  
Results: We have developed and implemented an algorithm for identifying sets of clonally-related sequences in large human immunoglobulin heavy chain gene variable region sequence sets.  ...  The identification of groups of rearranged immunoglobulin gene sequences descended from the same rearrangement (clonally-related sets) in very large sets of sequences is facilitated by the availability  ...  Acknowledgements The authors thank Michael Bain and Katherine Jackson for helpful comments and feedback. This article has been published as part of Immunome Research  ... 
doi:10.1186/1745-7580-6-s1-s4 pmid:20875155 pmcid:PMC2946782 fatcat:2kkcexky3bgexmz5zrtgwqklby

Assigning and visualizing germline genes in antibody repertoires

Simon D. W. Frost, Ben Murrell, A. S. Md. Mukarram Hossain, Gregg J. Silverman, Sergei L. Kosakovsky Pond
2015 Philosophical Transactions of the Royal Society of London. Biological Sciences  
datasets of human immunoglobulin heavy chain sequences.  ...  Identifying the germline genes involved in immunoglobulin rearrangements is an essential first step in the analysis of antibody repertoires.  ...  We thank the two anonymous reviewers for their comments, which helped to improve the manuscript.  ... 
doi:10.1098/rstb.2014.0240 pmid:26194754 pmcid:PMC4528417 fatcat:d7ybn2675vfmdc3sh6mp7xsbze

Recovery of a human natural antibody against the noncollagenous-1 domain of type IV collagen using humanized models

Inge M Worni-Schudel, Amy G Clark, Tiffany Chien, Kwan-Ki Hwang, Benny J Chen, Mary H Foster
2015 Journal of Translational Medicine  
Ab target the noncollagenous 1 (NC1) domain of alpha3(IV) collagen, but little is known about Ab origins or structure.  ...  The aim of this study was to assess the suitability of two humanized models for this purpose.  ...  We thank Divino Deoliveira for help with humanized models, Michael Cook for help with flow cytometry, Emma Zhao for help with immunoassays and animal husbandry, Julie Fuller of the Surgical Sciences Histopathology  ... 
doi:10.1186/s12967-015-0539-4 pmid:26048777 pmcid:PMC4467618 fatcat:p2wyhhw3r5gdro4tbyhjqbbv6y

Multispecificity of a recombinant anti-ras monoclonal antibody

John W. Schrader, Gary R. McLean
2017 Journal of Molecular Recognition  
Whilst studying the cellular molecular switch protein m-ras, a recombinant monoclonal antibody to m-ras was generated for use as a research tool.  ...  The cross reactive binding of the monoclonal Ab to h-ras was defined by peptide array blot revealing that the Ab showed preference for peptide sequences containing multiple positively charged amino acid  ...  Conflicts of Interests: The authors declare they have no conflicts of interests.  ... 
doi:10.1002/jmr.2683 pmid:29115701 fatcat:oog2ybuexve3bmevzma7pvnana

Ontogeny of Recognition Specificity and Functionality for the Broadly Neutralizing Anti-HIV Antibody 4E10

Kathryn A. K. Finton, Della Friend, James Jaffe, Mesfin Gewe, Margaret A. Holmes, H. Benjamin Larman, Andrew Stuart, Kevin Larimore, Philip D. Greenberg, Stephen J. Elledge, Leonidas Stamatatos, Roland K. Strong (+1 others)
2014 PLoS Pathogens  
The process of antibody ontogeny typically improves affinity, on-rate, and thermostability, narrows polyspecificity, and rigidifies the combining site to the conformer optimal for binding from the broader  ...  The ontogeny of 4E10, an autoreactive antibody with unexpected combining site flexibility, was delineated through structural and biophysical comparisons of the mature antibody with multiple potential precursors  ...  Acknowledgments We would like to thank Tim Vanden Bos and Madeline LaPatra for assistance with protein production. Author Contributions  ... 
doi:10.1371/journal.ppat.1004403 pmid:25254371 pmcid:PMC4177983 fatcat:hjjydmof35aqjdvhtgzipmobcy

Abstract Book, XIII International Congress of Histochemistry and Cytochemistry ICHC2008, Imaging of Cell Dynamics, 23rd-27th August 2008, Medical University of Gdansk, Poland

FHC Redaction
2008 Folia Histochemica et Cytobiologica  
line (Ab) originated from the melanotic form by a spontaneous alteration, differing in many biological properties.  ...  We will describe a new tool for the high-throughput analysis of alternative splicing.  ...  To reach this goal, changes in the chemical coding of sympathetic neurons supplying porcine urinary bladder, an animal which can be used as a very good model for human lower urinary tract, have been elucidated  ... 
doi:10.5603/4388 doaj:cdebe86bf2604301b2401e99ae9a504c fatcat:7j6nazvgnjf2bhooy5awdzq7uy

Immunoregulation in myasthenia gravis

Robin L. Kaufman
1989
Additionally, in order to gain access to an appropriate patient base for our study, we established a further modification with improved sensitivity for detection of serum nAchR Ab.  ...  Myasthenia Gravis (MG) is an autoimmune disorder of neuromuscular transmission. Clinically, the disease is manifested by abnormal muscle fatigue with recovery on resting.  ...  We have established two modifications of the nAchR Ab originally described by Lindstrom et al (1977) .  ... 
doi:10.14288/1.0100307 fatcat:szzwzbhof5fetf75d2d4mffbly