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FRED--a framework for T-cell epitope detection
2009
Bioinformatics
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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
2016
Bioinformatics
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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
2017
Cellular Immunology
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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
2003
Journal of Experimental Medicine
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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
2019
Turkish Journal of Immunology
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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
1998
Current Biology
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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
2019
Journal of virus eradication
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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
2019
Journal of virus eradication
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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
2006
Journal of Molecular Biology
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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
2011
PLoS ONE
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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?
2009
Endocrine-Related Cancer
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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
2010
International Journal of Alzheimer's Disease
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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
2021
eLife
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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
2011
Genetics
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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
2019
PLoS Genetics
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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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