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Reconsidering the human immunoglobulin heavy-chain locus: 1. An evaluation of the expressed human IGHD gene repertoire(2006) Lee, Cathryn; Gaeta, Bruno; Malming, H; Bain, Michael; Sewell, William; Collins, AndrewJournal 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.
(2006) Bain, Michael; Ahsan, Nasir; Potter, John; Gaeta, Bruno; Temple, Mark; Dawes, IanConference Paper
The FeL model of iron acquisition: Nondissociative reduction of ferric complexes in the marine environment(2006) Salmon, Timothy; Rose, Andrew; Neilan, Brett; Waite, TJournal ArticleRecently there has been recognition of the importance of reductive processes in the acquisition of iron by microorganisms in marine environments with Fe(III) reduction induced by either membrane-bound reductases or by superoxide, a powerful Fe(III) reducing agent generated either by photochemical or biological means. We have measured the relative rates of iron uptake achieved by the cyanobacterium L. majuscula in the presence of a variety of model- and naturally-derived organic ligands exhibiting a broad range of conditional ferric and ferrous stability constants. Additionally, we have investigated the effect upon iron uptake rate of varying the concentration of both iron and the iron-binding ligands. We have reconciled this data with previous work in which we measured rates of reduction by exogenous superoxide of Fe(III) bound to these same complexes. We show that the rate of formation of ferrous iron and the rate of uptake of iron by Lyngbya majuscula are each independent of the concentration of Fe′ and demonstrate that this is consistent with our previous finding that this organism acquires iron via nondissociative reduction of ferric complexes. We also show that the rate of reoxidation of organically complexed Fe(II) is a critical determinant of the subsequent bioavailability of iron, a feature not previously addressed in the literature. In view of the central importance of the complexation and redox behavior of the iron-organic complexes to iron uptake rate, we propose a new kinetic model of iron acquisition, termed the FeL model, that is consistent with presented and previously published data and which describes processes both in natural and artificial conditions. © 2006, by the American Society of Limnology and Oceanography, Inc.