ABSTRACT
To establish a relation between an protein amino acid sequence and its tendencies to generate antibody response, and to investigate an improved in silico method for linear B-cell epitope (LBE) prediction. We present a sequence-based LBE predictor developed using deep maxout network (DMN) with dropout training techniques. A graphics processing unit (GPU) was used to reduce the training time of the model. A 10-fold cross-validation test on a large, non-redundant and experimentally verified dataset (Lbtope_Fixed_ non_redundant) was performed to evaluate the performance. DMN-LBE achieved an accuracy of 68.33% and an area under the receiver operating characteristic curve (AUC) of 0.743, outperforming other prediction methods in the field. A web server, DMN-LBE, of the improved prediction model has been provided for public free use. We anticipate that DMN-LBE will be beneficial to vaccine development, antibody production, disease diagnosis, and therapy.
Subject(s)
Amino Acid Sequence , Computational Biology , Methods , Epitopes, B-Lymphocyte , Chemistry , Allergy and Immunology , ROC CurveABSTRACT
<p><b>OBJECTIVE</b>To construct a cDNA library of osteosarcoma SAOS-2 cells and screen the proteins interacting with the bone morphogenetic protein-2 (BMP-2) to explore the role of BMP-2 in the development of prostate cancer.</p><p><b>METHODS</b>The total RNA was extracted from SAOS-2 cells, from which poly(A)(+)RNA was purified to generate the cDNA using RT-PCR with primer SMARTIII and primer CDSIIIoligo(dT). The library was constructed and screened by cotransformation of the double-stranded cDNA (dscDNA) and linearized pGADT7-Rec with the bait plasmid to the yeast AH109. The proteins interacting with BMP-2 were screened by AH109 mating with the bait strain Y187, and the interaction was confirmed using far-Western blot analysis.</p><p><b>RESULTS</b>The cDNA library of human osteosarcoma SAOS-2 cells was constructed, which was characterized by high diversity and sufficient capacity. The dscDNA size range was between 250-5000 bp, with a cotransformation efficiency of 4.3 x 10(5) and recombination efficiency of 1.9 x 10(6), and 4.3 x 10(5) clones were screened. The mating efficiency was 32% and 1.0 x 10(6) clones were screened by the bait of BMP-2, and 4 positive clones was obtained and sequenced.</p><p><b>CONCLUSION</b>The diversity and capacity of the cDNA library meet the needs for screening genes related to prostate cancer.</p>
Subject(s)
Humans , Male , Bone Morphogenetic Protein 2 , Genetics , Cell Line, Tumor , Gene Library , Osteosarcoma , Genetics , Prostatic Neoplasms , Genetics , RNA, Neoplasm , Genetics , Two-Hybrid System TechniquesABSTRACT
This article introduces a new-type anti-rotation reduction internal fixator, which can be applied in various spine fractures and dislocations in order to shorten the operation time, to raise reduction effect, and to reduce the complications such as the loss of reduction, broken nail, broken rod etc. Biomechanical tests and clinical applications have proved that the internal fixator has the features of a short operation time, a definite fixation and few complications.