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(2006)Journal ArticleWe have used a bioinformatics approach to evaluate the completeness and functionality of the reported human immunoglobulin heavy-chain IGHD gene repertoire. Using the hidden Markov-model-based iHMMune-align program, 1,080 relatively unmutated heavy-chain sequences were aligned against the reported repertoire. These alignments were compared with alignments to 1,639 more highly mutated sequences. Comparisons of the frequencies of gene utilization in the two databases, and analysis of features of aligned IGHD gene segments, including their length, the frequency with which they appear to mutate, and the frequency with which specific mutations were seen, were used to determine the reliability of alignments to the less commonly seen IGHD genes. Analysis demonstrates that IGHD4-23 and IGHD5-24, which have been reported to be open reading frames of uncertain functionality, are represented in the expressed gene repertoire; however, the functionality of IGHD6-25 must be questioned. Sequence similarities make the unequivocal identification of members of the IGHD1 gene family problematic, although all genes except IGHD1-14*01 appear to be functional. On the other hand, reported allelic variants of IGHD2-2 and of the IGHD3 gene family appear to be nonfunctional, very rare, or nonexistent. Analysis also suggests that the reported repertoire is relatively complete, although one new putative polymorphism (IGHD3-10*p03) was identified. This study therefore confirms a surprising lack of diversity in the available IGHD gene repertoire, and restriction of the germline sequence databases to the functional set described here will substantially improve the accuracy of IGHD gene alignments and therefore the accuracy of analysis of the V-D-J junction.
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(1997)Journal ArticleFlux pinning force and irreversible line of the melt-textured-growth (MTG) YBa2Cu3O7−y (Y-123) crystals with various sizes of secondary phase particles have been investigated by measuring the magnetization of the samples under a series of magnetic fields up to 55 kOe. The magnetic Jc and the pinning force are found to increase as the particle size decreases. A linear relationship between Jc and 1/D has been obtained where D is the average size of the precipitates. The highest Jc value has reached 4×104 A/cm2 at 77 K and 40 kOe in a sample with a high density of the precipitates in nanometre size. Two peaks are observed in the Fp(H) curve in which the position of the first peak is independent of the particle size. The height and the location of the second peak is sensitive to the particle size, indicating that the peak is associated with the small particles.