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FRED--a framework for T-cell epitope detection

M. Feldhahn, P. Donnes, P. Thiel, O. Kohlbacher
2009 Bioinformatics  
Computational approaches, in particular the prediction of T-cell epitopes using machine learning methods, are at the core of modern vaccine design.  ...  We have developed FRED, an extendable, open source software framework for key tasks in immunoinformatics.  ...  INTRODUCTION The detection of T-cell epitopes is a critical step in vaccine design and a key problem in immunoinformatics. Experimental studies to detect epitopes are expensive and time consuming.  ... 
doi:10.1093/bioinformatics/btp409 pmid:19578173 pmcid:PMC2759545 fatcat:3a6mb3q7hfac7c27ucb7vmxgye

FRED 2: an immunoinformatics framework for Python

Benjamin Schubert, Mathias Walzer, Hans-Philipp Brachvogel, András Szolek, Christopher Mohr, Oliver Kohlbacher
2016 Bioinformatics  
Here we present FRED 2, an open-source immunoinformatics framework offering easy and unified access to methods for epitope prediction and other immunoinformatics applications.  ...  Immunoinformatics approaches are widely used in a variety of applications from basic immunological to applied biomedical research.  ...  We therefore developed FRamework for Epitope Detection (FRED 2) , an opensource, Python-based framework for computational immunology.  ... 
doi:10.1093/bioinformatics/btw113 pmid:27153717 pmcid:PMC4920123 fatcat:n6bpuacbijb33ee5rdnhi6drku

Rational design of low immunogenic anti CD25 recombinant immunotoxin for T cell malignancies by elimination of T cell epitopes in PE38

Ronit Mazor, Gilad Kaplan, Dong Park, Youjin Jang, Fred Lee, Robert Kreitman, Ira Pastan
2017 Cellular Immunology  
Rather than deletion, we identified T cell epitopes in domain II and used alanine substitutions to identify point mutations that diminished those epitopes.  ...  LMB-2, is a potent recombinant immunotoxin (RIT) that is composed of scFv antibody that targets CD25 (Tac) and a toxin fragment (PE38). It is used to treat T cell leukemias and lymphomas.  ...  PE labeled cells were detected using Flow cytometry and affinity was calculated. Fig. 3 . 3 Fig. 3. T cell epitopes in domain II.  ... 
doi:10.1016/j.cellimm.2017.01.003 pmid:28087047 pmcid:PMC5344129 fatcat:loyrf5mikzeflcnmrn4j47cm74

Topological Requirements and Signaling Properties of T Cell–activating, Anti-CD28 Antibody Superagonists

Fred Lühder, Yun Huang, Kevin M. Dennehy, Christine Guntermann, Ingrid Müller, Erna Winkler, Thomas Kerkau, Shinji Ikemizu, Simon J. Davis, Thomas Hanke, Thomas Hünig
2003 Journal of Experimental Medicine  
Antibodies with this property may prove useful for the development of T cell stimulatory drugs.  ...  Our findings indicate that the topologically constrained interactions of anti-CD28 superagonists bypass the requirement for signal 1 in T cell activation.  ...  Lindemann for retroviral vectors, T. Herrmann for the TCR-transfected 58 T cell line, S. Wagner for help in cloning mouse CD28, P. Zigan for lymphocyte preparation, and T. Herrmann and A.  ... 
doi:10.1084/jem.20021024 pmid:12707299 pmcid:PMC2193880 fatcat:uecynz7nwja5bmppmjqloa3ima

A Review on Computational Tools and Databases for the Development of Vaccines Against Infectious Diseases

Qazi Mohammad Sajid Jamal
2019 Turkish Journal of Immunology  
The emergence and successful implementation of bioinformatics and computational technology in the different area of molecular biology has a positive impact on the scientists and researchers.  ...  Acknowledgement: Author is thankful to the all database curator for the maintenance and development of informative portal to the scientific community and students.  ...  [38] FRED 2 FRED 2 is a platform in order to detect the T-cell epitope and vaccine design.  ... 
doi:10.25002/tji.2019.1182 fatcat:cjo5wbc3rvcypot3byqzxkcpsi

Positional information in root epidermis is defined during embryogenesis and acts in domains with strict boundaries

Fred Berger, Jim Haseloff, John Schiefelbein, Liam Dolan
1998 Current Biology  
Fate is not fixed in the developing root, though, as cells that move into a position previously occupied by neighbour cells ablated using laser microsurgery change fate.  ...  The epidermal layer of the Arabidopsis root is made of alternating files of two cell types and thus presents a simple pattern to study positional mechanisms.  ...  Cell corners are, for example, richer in epitopes for antibodies JIM which recognise arabinogalactan protein epitopes (L.D., unpublished observations).  ... 
doi:10.1016/s0960-9822(98)70176-9 pmid:9550701 fatcat:2noveupfnrcz7n3lh57pkot6g4

Development of anti-PD-1 chimeric antigen receptor T cells to target a PD-1+ CD4 T cell population enriched in HIV provirus

K. Eichholz, F. Haeseleer, L. Corey
2019 Journal of virus eradication  
T cell clones, specific for HLA-E presenting the RL9 Gag epitope, have also been isolated and shown to kill HIV-1 infected cells in vitro.  ...  Viability of primary aPD-1 CAR T cells was not affected by the CAR and PD-1 expression was not detectable during cell production.  ... 
doi:10.1016/s2055-6640(20)30228-4 fatcat:sr3w6qgqk5ftbpbmi73rllafw4

Conditions for post-rebound SHIV control in autologous hematopoietic-stem cell transplantation

F. Cardozo, E. Duke, C. Peterson, D. Reeves, B. Mayer, H.P. Kiem, J. Schiffer
2019 Journal of virus eradication  
T cell clones, specific for HLA-E presenting the RL9 Gag epitope, have also been isolated and shown to kill HIV-1 infected cells in vitro.  ...  Viability of primary aPD-1 CAR T cells was not affected by the CAR and PD-1 expression was not detectable during cell production.  ... 
doi:10.1016/s2055-6640(20)30229-6 fatcat:wg5mw2yhrjhmhh63lvhdcnqzxm

Directed Evolution of an Anti-prion Protein scFv Fragment to an Affinity of 1 pM and its Structural Interpretation

Béatrice Luginbühl, Zoltan Kanyo, R. Mark Jones, Robert J. Fletterick, Stanley B. Prusiner, Fred E. Cohen, R. Anthony Williamson, Dennis R. Burton, Andreas Plückthun
2006 Journal of Molecular Biology  
IPTG, isopropylthiogalactoside; KinExA, kinetic exclusion assay; PDEA, 2-(2-pyridinyldithio) ethaneamine hydrochloride; MBo2Mo, mouse/bovine chimeric prion protein (residues 23-231 are mouse, except for  ...  Rich (University of Utah, Salt Lake City, Utah) for many helpful discussions.  ...  ., Boise, Idaho) for his support in KinExA affinity characterization and Dr Annemarie Honegger (University of Zürich, Switzerland) for helpful discussions and introduction into the structural analysis  ... 
doi:10.1016/j.jmb.2006.07.027 pmid:16962610 fatcat:oar34xa34vfh3ltzgev3dzgdqi

Interactions between β-Catenin and the HSlo Potassium Channel Regulates HSlo Surface Expression

Shumin Bian, Jun-Ping Bai, Hannah Chapin, Cathy Le Moellic, Huiping Dong, Michael Caplan, Fred J. Sigworth, Dhasakumar S. Navaratnam, Cara Gottardi
2011 PLoS ONE  
Conclusions and Significance: These studies identify for the first time a central role for b-catenin in mediating Slo surface expression.  ...  Prior work has shown that Slo, through its S10 region, interacts with b-catenin, a key component of the cytoskeleton framework and the Wnt signaling pathway.  ...  Edward Moczydlowski (Clarkson University) for valuable discussions in the beginning of the project, and for providing the rabbit anti BsloC antibody. Dr.  ... 
doi:10.1371/journal.pone.0028264 pmid:22194818 pmcid:PMC3237428 fatcat:l3m2xwysfzapjpnvoc6navmk7u

Genomic actions of estrogen receptor α: what are the targets and how are they regulated?

Willem-Jan Welboren, Fred C G J Sweep, Paul N Span, Hendrik G Stunnenberg
2009 Endocrine-Related Cancer  
The estrogen receptor α (ERα) is a ligand-dependent transcription factor that regulates a large number of genes in many different target tissues and is important in the development and progression of breast  ...  ERα-mediated transcription is a complex process regulated at many different levels.  ...  Acknowledgements The authors would like to thank Dr G Veenstra for critical reading of the manuscript.  ... 
doi:10.1677/erc-09-0086 pmid:19628648 fatcat:73zrhhswvfgh7aq2jmo2ytcyzm

Modeling of Tau-Mediated Synaptic and Neuronal Degeneration in Alzheimer's Disease

Tomasz Jaworski, Sebastian Kügler, Fred Van Leuven
2010 International Journal of Alzheimer's Disease  
A second shift in research focus is from amyloid to tauopathy, and to their mutual relation.  ...  Both hallmarks are inseparable and remain diagnostic as described by Alois Alzheimer more than a century ago.  ...  The authors sincerely thank many collaborators and scientists for technical assistance, advice, materials, and scientific or moral support. T.  ... 
doi:10.4061/2010/573138 pmid:20862366 pmcid:PMC2938448 fatcat:vtrv4h5365d5xkdlditl74yga4

Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape

Fred D Mast, Peter C Fridy, Natalia E Ketaren, Junjie Wang, Erica Y Jacobs, Jean Paul Olivier, Tanmoy Sanyal, Kelly R Molloy, Fabian Schmidt, Magdalena Rutkowska, Yiska Weisblum, Lucille M Rich (+17 others)
2021 eLife  
We therefore generated a large nanobody repertoire to saturate the distinct and highly conserved available epitope space of SARS-CoV-2 spike, including the S1 receptor binding domain, N-terminal domain  ...  and the TMPRSS2+ Vero E6 cells; and the rest of the Aitchison, Chait and Rout laboratories, as well as Fred Cross for technical and intellectual support.  ...  ; Thomas Gallagher and Enya Qing, Loyola University Chicago, for the kind gift of the SARS-CoV-1 and SARS-CoV-2 spike expression plasmids; Andrew McGuire and Leonidas Stamatatos (Fred Hutchinson Cancer  ... 
doi:10.7554/elife.73027 pmid:34874007 pmcid:PMC8651292 fatcat:je5au2hb2bb3po3rz6n4oal2da

The Hog1 Mitogen-Activated Protein Kinase Mediates a Hypoxic Response inSaccharomyces cerevisiae

Mark J. Hickman, Dan Spatt, Fred Winston
2011 Genetics  
Our results have led to a model in which heme and ergosterol depletion alters membrane fluidity, thereby activating Hog1 for hypoxic induction.  ...  We have now identified additional factors required for PAU induction during hypoxia, including Hog1, a mitogen-activated protein kinase (MAPK) whose signaling pathway originates at the membrane.  ...  For real-time PCR, RNA was isolated from cells as described above and then reverse transcribed using a poly(T) primer. The resulting cDNA was quantitated on the Stratagene (La Jolla, CA) MX3000P.  ... 
doi:10.1534/genetics.111.128322 pmid:21467572 pmcid:PMC3122313 fatcat:7srn3gwggbdyxmf3fhwiascm7y

Glial cells maintain synapses by inhibiting an activity-dependent retrograde protease signal

Thomas W. Gould, Bertha Dominguez, Fred de Winter, Gene W. Yeo, Patrick Liu, Balaji Sundararaman, Thomas Stark, Anthony Vu, Jay L. Degen, Weichun Lin, Kuo-Fen Lee, Gregory A. Cox
2019 PLoS Genetics  
Glial cells regulate multiple aspects of synaptogenesis. In the absence of Schwann cells, a peripheral glial cell, motor neurons initially innervate muscle but then degenerate.  ...  Here, using a genetic approach, we show that neural activity-regulated negative factors produced by muscle drive neurodegeneration in Schwann cell-deficient mice.  ...  Bonanomi for helping us with motor explants, S. Pfaff for HB9:GFP mice, Genentech for erbB3 mutant mice and N. Allen for comments on the manuscript. We are grateful to T.  ... 
doi:10.1371/journal.pgen.1007948 pmid:30870413 pmcid:PMC6417855 fatcat:jfadv7riyvddbfivhsjbuqqhfi
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