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  • 1
    ISSN: 1432-1793
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Polymerase chain reaction and direct comparison of mitochondrial DNA sequences from a cytochrome b gene fragment were used to identify two morphologically distinct larval types ofXyrichtys, a genus of tropical wrasse (Pisces: Labridae). Both larval types were collected during ichthyoplankton surveys on the Middle Atlantic Bight shelf in the summer of 1988. DNA sequence comparisons indicated that both types were larvae ofXyrichtys novacula (Linnaeus). Back-calculated birthdate distributions for those larvae collected on the Middle Atlantic Bight shelf demonstrated that the two larval types formed two distinct cohorts indicating a biological difference. The two distinct larval types may be a consequence of an ecophenotypic effect, or they may represent offspring from genetically distinct populations. These results emphasize that important biological and oceanographic information can be gained through the use of the polymerase chain reaction and DNA sequencing for larval identificaiton.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1432-1793
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Previously published mtDNA cytochrome b sequences for Xyrichtys novacula (Linnaeus) and two morphologically distinct types of Xyrichtys larvae (Pisces: Labridae) included human cytochrome b sequence, presumably due to sample contamination and/or poor preservation of sample DNA. Those sequences had been used to identify the two types of Xyrichtys larvae as X. novacula, but owing to the contamination, the identifications are invalid. Fresh specimens were collected: X.␣martinicensis (Cuvier and Valenciennes), X. novacula, X. splendens (Castelnau), and Xyrichtys sp. larvae of each of the two morphotypes (dorsal-forward eye and ventral-forward eye). The cytochrome b fragment was amplified from each specimen using the polymerase chain reaction. Comparison of the sequences with human cytochrome b sequence confirmed that the new sequences were not contaminated. The interspecific differences in Xyrichtys sequences were less than previously reported, but still greater than observed in many fish genera. Distance and parsimony analyses indicated that X. novacula and X. martinicensis were more closely related to each other than to X. splendens. This conclusion differs from our previous conclusion that X. martinicensis and X. splendens were more closely related to each other than to X. novacula. Distance and parsimony analyses also demonstrated that both larval morphotypes were X. novacula and, thus, our previous conclusions regarding larval ecology and oceanographic transport remain unchanged.
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Microbial ecology 32 (1996), S. 229-230 
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Microbial ecology 32 (1996), S. 263-281 
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Nitrogen fixation in the sea has attracted the attention of ecologists for decades. Much is known about the habitats in which it occurs and some of the factors that limit N2 fixation activity in different environments, but we still know little about the organisms that fix nitrogen, and what limits the growth and distribution of these organisms in marine environments. Molecular biology technological developments have provided tools for detecting and characterizing N2-fixing organisms in the environment. These techniques hold great promise for unraveling the mysteries and paradoxes of N2 fixation in the sea. In this review, we address the theoretical basis for the use of a molecular approach to N2 fixation, highlight the strengths and weaknesses of the approach, and provide case studies that demonstrate the potential contribution of molecular biology approaches to studies of N2 fixation in the sea.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Hydrobiologia 157 (1988), S. 33-45 
    ISSN: 1573-5117
    Keywords: dissolved organic matter ; nitrogen cycling ; subalpine lake
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Dissolved organic nitrogen (DON) concentrations were measured in meso-oligotrophic Castle Lake, California during the ice-free season in 1982, 1983 and 1984. No consistent relationships were found between DON and particulate-N, primary productivity rates or chlorophyll concentrations. However, increases in DON concentrations were observed in the early growing season of 1982 and 1984 when water temperature was rising and a diatom bloom was senescing. DON increased at a high rate (0.31 mg atom N m−3 day−1), and then rapidly disappeared. Sediment released appared to be the most important source of DON. Dissolved free amino acids were always less than 7.5% of the DON pool, and did not vary in the composition of specific amino acids during the growing season.
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Hydrobiologia 401 (1999), S. 77-96 
    ISSN: 1573-5117
    Keywords: bacterial diversity ; acidification ; Adirondack lakes ; aluminum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Bacterial diversity was examined in six lakes located in the Adirondack Mountains of upstate New York. This region receives significant anthropogenic atmospheric inputs of strong mineral acids resulting in decreases in pH and acid neutralizing capacity (ANC) in many of the lakes. Statistical methods including correlation and cluster analysis were used to determine if there were significant associations between phylotypes and water chemistry variables. Direct effects of acidification, pH and ANC, were not significantly correlated with any of the broadest level taxonomic classifications (equivalent to class or order), but may be correlated with subgroups within these classifications. Indirect influences of acidification were suggested by significant correlations of phylotypes with aluminum chemistry. There were positive correlations between the relative abundance of the γ subdivision of the Proteobacteria and total aluminum (r 2= 0.70,p= 0.04), monomeric aluminum (r 2= 0.78, p= 0.02) and non-labile aluminum (r 2= 0.92, p= 0.002). The ACK1 clade of the β-Proteobacteria (Adirondack clade 1) was correlated with monomeric aluminum (r 2= 0.71, p=0.03) and non-labile aluminum (r 2= 0.73, p= 0.03). Significant negative correlations were found between the relative abundance of the Cytophaga-Flexibacter-Bacteroides phylum and total aluminum (r 2= 0.74, p= 0.03), and the High G+C subdivision of the Gram Positive phylum with total aluminum (r 2 0.70, p= 0.04). Dissolved organic carbon (DOC) concentrations may also influence bacteria through amelioration of aluminum toxicity and as a carbon source. There were significant positive correlations between DOC and the relative abundance of the γ (r 2= 0.66, p= 0.05) and β (r 2= 0.78, p= 0.02) subdivisions and the ACK1 clade (r 2= 0.84, p= 0.01). Additional significant correlations were also noted between specific phylotypes and certain macro- and micro-nutrients. The results of this study indicate that water chemistry can have a direct influence on bacterial lake assemblages and that in acid stressed lakes aluminum chemistry and DOC concentrations may play a particularly important role.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Hydrobiologia 401 (1999), S. 1-7 
    ISSN: 1573-5117
    Keywords: aquatic ecology ; molecular techniques ; molecular ecology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract During the 1980s, many new molecular biology techniques were developed, providing new capabilities for studying the genetics and activities of organisms. Biologists and ecologists saw the promise that these techniques held for studying different aspects of organisms, both in culture and in the natural environment. In less than a decade, these techniques were adopted by a large number of researchers studying many types of organisms in diverse environments. Much of the molecular-level information acquired has been used to address questions of evolution, biogeography, population structure and biodiversity. At this juncture, molecular ecologists are poised to contribute to the study of the fundamental characteristics underlying aquatic community structure. The goal of this overview is to assess where we have been, where we are now and what the future holds for revealing the basis of community structure and function with molecular-level information.
    Type of Medium: Electronic Resource
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  • 8
    Publication Date: 2009-03-17
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 9
    Publication Date: 2007-10-30
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
    Publication Date: 2014-10-04
    Description: Motivation: Studies of the biochemical functions and activities of uncultivated microorganisms in the environment require analysis of DNA sequences for phylogenetic characterization and for the development of sequence-based assays for the detection of microorganisms. The numbers of sequences for genes that are indicators of environmentally important functions such as nitrogen (N 2 ) fixation have been rapidly growing over the past few decades. Obtaining these sequences from the National Center for Biotechnology Information’s GenBank database is problematic because of annotation errors, nomenclature variation and paralogues; moreover, GenBank’s structure and tools are not conducive to searching solely by function. For some genes, such as the nifH gene commonly used to assess community potential for N 2 fixation, manual collection and curation are becoming intractable because of the large number of sequences in GenBank and the large number of highly similar paralogues. If analysis is to keep pace with sequence discovery, an automated retrieval and curation system is necessary. Results: ARBitrator uses a two-step process composed of a broad collection of potential homologues followed by screening with a best hit strategy to conserved domains. 34 420 nifH sequences were identified in GenBank as of November 20, 2012. The false-positive rate is ~0.033%. ARBitrator rapidly updates a public nifH sequence database, and we show that it can be adapted for other genes. Availability and implementation: Java source and executable code are freely available to non-commercial users at http://pmc.ucsc.edu/~wwwzehr/research/database/ . Contact: zehrj@ucsc.edu Supplementary information: Supplementary information is available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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