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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) Green, R; Waite, T; Melville, MichaelJournal Article
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.
(2006) Green, Rosalind; Melville, Michael; Waite, T; Mcdonald, BJournal ArticleThe water quality of drainage discharged via pumping from an acid sulfate soil (ASS) affected catchment used for sugar cane farming is temporally very variable and is influenced by the various rain event magnitudes, their antecedents, and the particular phase of the discharge in any rain event. Rainfall episodes can cause substantial changes in acidity and dissolved metal concentrations in ASS drainage waters over very short time scales with minimum pH often reached within a few hours of initiation of the rainfall event. The initial increase in acidity and dissolved metals concentrations often observed can be attributed mainly to `first flush` effects resulting from mobilization of salts present in the upper soil profile. During the middle of a large rainfall event dilution effects may result in a decrease in concentrations of dissolved species, but increases in acidity and dissolved metals (particularly aluminium) concentrations in the recession portion of the hydrograph often occur as small field drains discharge into main channels. These observations assist both in understanding of the hydrogeochemical processes leading to acid and metals release from acid sulfate soils affected catchments, and in developing appropriate strategies to treat contaminated discharge waters from such catchments. © 2005.
(2006) Murphy, Kathleen; Ruiz, G; Dunsmuir, William; Waite, TJournal ArticleMid-ocean ballast water exchange is mandatory for ships discharging foreign ballast in US territorial waters in order to reduce the risk of biological invasions. However, a reliable tool for determining whether the procedure took place is lacking. We investigated chromophoric dissolved organic matter (CDOM) fluorescence as a tracer of mid-ocean exchange on nine research cruises out of Asia, Europe, and the USA, focusing on challenging source conditions (high salinity, low CDOM). Using parallel factor analysis, we identified nine independent fluorescent components present in varying concentrations in the ocean and in ballast water. One component was sufficient for predicting the coastal vs oceanic source of most ballast water samples. Across nine cruises, thresholds (1.7 and 0.7 ppb quinine sulfate equivalent units) at two fixed wavelength pairs (lambda(ex)/lambda(em) = 320/414 and 370/496 nm, respectively) discriminated coastal from oceanic ballast water in >95% of samples (N = 514). Our results suggest that single- and dual-channel fluorometers could be optimized for verifying ballast water exchange.
Characteristics of the acidity in acid sulfate soil drainage waters, McLeods Creek, northeastern NSW, Australia(2006) Green, Rosalind; Waite, T; Melville, Michael; Macdonald, BennettJournal ArticleCatchments that contain acid sulfate soils can discharge large quantities of acid and dissolved metals into waterways. At McLeods Creek in far northern NSW, Australia, the acidity from the hydrolysis of dissolved metal species, particularly aluminium and iron, contributes to greater than 70% of the total acidity. Therefore, a poor relationship exists between both calculated and titrated acidity and pH because of the dominant influence of these hydrolyzable metal species. Determination of the so-called `cold acidity` by direct titration with NaOH yields results that are difficult to replicate because of the buffering effects of suspended solids, carbon dioxide ingassing, and/or Mn-II and Fe-II oxidation in the sample as the titration end-point is approached. Samples that are pre-treated with sulfuric acid and hydrogen peroxide produce results ( of `hot acidity`) that can be easily replicated and are similar to calculated acidities based on elemental analysis and speciation calculations. The cold acidity values for titrations of 105 water samples from the chosen field site are often higher than hot acidity values as a result of the loss of carbonate acidity during pre-treatment of samples for hot acidity analysis.