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(2000)Conference Paper
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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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(2000)Journal ArticleIn-plane fluctuations of superconductivity have been investigated for Al-doped Bi-2212 single crystals with different resistivity anisotropy. The experimental results of in-plane paraconductivity are in good agreement with the Lawrence and Doniach model. The interlayer coupling is found to decrease with the resistivity anisotropy.
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(2000)Journal ArticleHigh quality, large size Bi2Sr2CaCu2O8 (Bi-2212) single crystals have been grown by a self-flux method in a horizontal temperature gradient. We found that the presence of the horizontal temperature gradient is helpful for the crystal growing along the ab-plane direction. However, non-uniform distribution of temperature in the vertical direction in the furnace often causes imperfections along the c direction. This may be one of the critical reasons why crystals produced by flux method are very thin and easy to cleave along the ab-plane, compared with the crystals grown by the floating zone method. The influence of the growth conditions and post-heat treatment on the resistivity anisotropy of the crystals has been investigated. Crystals grown in the condition where the temperature is non-uniformly distributed along the vertical direction often have higher anisotropy in resistivity. In addition, the post-heat treatment in the nitrogen atmosphere reduces the anisotropy of the resistivity of the crystal. Possible mechanisms are discussed.