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  • Other Sources  (31)
  • American Geophysical Union
  • American Physical Society (APS)
  • Oxford University Press
  • 2005-2009  (15)
  • 2000-2004  (16)
  • 1
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    Doing Science (2001)
    Oxford University Press
    In:  New York, 294 pp., Oxford University Press, vol. 26, no. ALEX(01)-FR-77-01, AFTAC Contract F08606-76-C-0025, pp. 329, (ISBN 0-521-62434-7 hc (0-521-62478-9 pb))
    Details
    Publication Date: 2001
    Keywords: outreach ; communication ; publishing
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    BIBLIOGRAPHY SEISMOLOGY
  • 2
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    The effect of quorum-sensing blockers on the formation of marine microbial communities and larval attachment (2007)
    Oxford University Press
    In:  FEMS Microbiology Ecology, 60 (2). pp. 177-188.
    Details
    Publication Date: 2019-09-24
    Description: We studied the effect of the quorum-sensing (QS) blockers 5-hydroxy-3[(1R)-1-hydroxypropyl]-4-methylfuran-2(5H)-one (FUR1), (5R)-3,4-dihydroxy-5-[(1S)-1,2-dihydroxyethyl]furan-2(5H)-one (FUR2) and triclosan (TRI) on the formation of bacterial biofilms, and the effect of these biofilms on the larval attachment of the polychaete Hydroides elegans and the bryozoan Bugula neritina. 14-day-old subtidal biofilms were harvested from artificial substrata and were allowed to develop in the laboratory with and without QS blockers. QS blockers inhibited the production of violacein by the QS reporter strain Chromobacterium violaceum CV026 and did not affect the metabolic activity of bacteria in multispecies biofilms. At a concentration of 10(-3) M all three tested compounds inhibited the establishment of microbial communities, but at one of 10(-4) M only FUR2 inhibited establishment. The tested QS blockers caused changes in bacterial density and bacterial community structure, as revealed by terminal restriction fragment length polymorphism and FISH. The groups most affected by QS blockers were Alphaproteobacteria, Gammaproteobacteria and the Cytophagales. Larvae of H. elegans and B. neritina avoided settling on biofilms that had developed in the presence of QS blockers. Our results suggest that QS blockers directly control the formation of multi-species biofilms, and indirectly - by means of biofilm properties - affect larval attachment on these modified biofilms.
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  • 3
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    Cyanobacterial diversity in Salar de Huasco, a high altitude saline wetland in Northern Chile, are highly similar to Antarctic cyanobacteria (2008)
    Oxford University Press
    In:  FEMS Microbiology Ecology, 64 . pp. 419-432.
    Details
    Publication Date: 2019-09-23
    Description: The diversity of Cyanobacteria in water and sediment samples from four representative sites of the Salar de Huasco was examined using denaturing gradient gel electrophoresis and analysis of clone libraries of 16S rRNA gene PCR products. Salar de Huasco is a high altitude (3800 m altitude) saline wetland located in the Chilean Altiplano. We analyzed samples from a tributary stream (H0) and three shallow lagoons (H1, H4, H6) that contrasted in their physicochemical conditions and associated biota. Seventy-eight phylotypes were identified in a total of 268 clonal sequences deriving from seven clone libraries of water and sediment samples. Oscillatoriales were frequently found in water samples from sites H0, H1 and H4 and in sediment samples from sites H1 and H4. Pleurocapsales were found only at site H0, while Chroococcales were recovered from sediment samples of sites H0 and H1, and from water samples of site H1. Nostocales were found in sediment samples from sites H1 and H4, and water samples from site H1 and were largely represented by sequences highly similar to Nodularia spumigena. We suggest that cyanobacterial communities from Salar de Huasco are unique - they include sequences related to others previously described from the Antarctic, along with others from diverse, but less extreme environments.
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  • 4
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    Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs (2009)
    Oxford University Press
    In:  Database: The Journal of Biological Databases and Curation, 2009 . bap009.
    Details
    Publication Date: 2019-01-21
    Description: As ecosystem engineers, seagrasses are angiosperms of paramount ecological importance in shallow shoreline habitats around the globe. Furthermore, the ancestors of independent seagrass lineages have secondarily returned into the sea in separate, independent evolutionary events. Thus, understanding the molecular adaptation of this clade not only makes significant contributions to the field of ecology, but also to principles of parallel evolution as well. With the use of Dr. Zompo, the first interactive seagrass sequence database presented here, new insights into the molecular adaptation of marine environments can be inferred. The database is based on a total of 14 597 ESTs obtained from two seagrass species, Zostera marina and Posidonia oceanica, which have been processed, assembled and comprehensively annotated. Dr. Zompo provides experimentalists with a broad foundation to build experiments and consider challenges associated with the investigation of this class of non-domesticated monocotyledon systems. Our database, based on the Ruby on Rails framework, is rich in features including the retrieval of experimentally determined heat-responsive transcripts, mining for molecular markers (SSRs and SNPs), and weighted key word searches that allow access to annotation gathered on several levels including Pfam domains, GeneOntology and KEGG pathways. Well established plant genome sites such as The Arabidopsis Information Resource (TAIR) and the Rice Genome Annotation Project are interfaced by Dr. Zompo. With this project, we have initialized a valuable resource for plant biologists in general and the seagrass community in particular. The database is expected to grow together with more data to come in the near future, particularly with the recent initiation of the Zostera genome sequencing project. The Dr. Zompo database is available at http://drzompo.uni-muenster.de/
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  • 5
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    Legionella pneumophila: an aquatic microbe goes astray (2002)
    Oxford University Press
    In:  FEMS Microbiology Reviews, 26 (2). pp. 149-162.
    Details
    Publication Date: 2020-07-31
    Description: Legionella pneumophila is naturally found in fresh water were the bacteria parasitize within protozoa. It also survives planctonically in water or biofilms. Upon aerosol formation via man-made water systems, L. pneumophila can enter the human lung and cause a severe form of pneumonia, called Legionnaires’ disease. The pathogenesis of Legionnaires’ disease is largely due to the ability of L. pneumophila to invade and grow within macrophages. An important characteristic of the intracellular survival strategy is the replication within the host vacuole that does not fuse with endosomes or lysosomes. In recent times a great number of bacterial virulence factors which affect growth of L. pneumophila in both macrophages and protozoa have been identified. The ongoing Legionella genome project and the use of genetically tractable surrogate hosts are expected to significantly contribute to the understanding of bacterium–host interactions and the regulation of virulence traits during the infection cycle. Since person-to-person transmission of legionellosis has never been observed, the measures for disease prevention have concentrated on eliminating the pathogen from water supplies. In this respect detection and analysis of Legionella in complex environmental consortia become increasingly important. With the availability of new molecular tools this area of applied research has gained new momentum.
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  • 6
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    Nonstationary Gaussian processes in wavelet domain: Synthesis, estimation, and significance testing (2007)
    American Physical Society (APS)
    In:  Physical Review E, 75 (016707).
    Details
    Publication Date: 2017-01-03
    Description: We propose an equivalence class of nonstationary Gaussian stochastic processes defined in the wavelet domain. These processes are characterized by means of wavelet multipliers and exhibit well-defined time-dependent spectral properties. They allow one to generate realizations of any wavelet spectrum. Based on this framework, we study the estimation of continuous wavelet spectra, i.e., we calculate variance and bias of arbitrary estimated continuous wavelet spectra. Finally, we develop an areawise significance test for continuous wavelet spectra to overcome the difficulties of multiple testing; it uses basic properties of continuous wavelet transform to decide whether a pointwise significant result is a real feature of the process or indistinguishable from typical stochastic fluctuations. This test is compared to the conventional one in terms of sensitivity and specificity. A software package for continuous wavelet spectral analysis and synthesis is presented.
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  • 7
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    Phylogeny and distribution of the soxB gene among thiosulfate-oxidizing bacteria (2001)
    Oxford University Press
    In:  FEMS Microbiology Letters, 197 . pp. 171-178.
    Details
    Publication Date: 2019-08-05
    Description: A PCR protocol for the detection of sulfur-oxidizing bacteria based on soxB genes that are essential for thiosulfate oxidation by sulfur-oxidizing bacteria of various phylogenetic groups which use the 'Paracoccus sulfur oxidation' pathway was developed. Five degenerate primers were used to specifically amplify fragments of soxB genes from different sulfur-oxidizing bacteria previously shown to oxidize thiosulfate. The PCR yielded a soxB fragment of approximately 1000 bp from most of the bacteria. Amino acid and nucleotide sequences of soxB from reference strains as well as from new isolates and environmental DNA from a hydrothermal vent habitat in the North Fiji Basin were compared and used to infer relationships of soxB between sulfur-oxidizing bacteria belonging to various 16S rDNA-based phylogenetic groups. Major phylogenetic lines derived from 16S rDNA were confirmed by soxB phylogeny. Thiosulfate-oxidizing green sulfur bacteria formed a coherent group by their soxB sequences. Likewise, clearly separated branches demonstrated the distant relationship of representatives of alpha-, beta-, and gamma-Proteobacteria including representative species of the former genus Thiobacillus (now Halothiobacillus - gamma-Proteobacteria, Thiobacillus - beta-Proteobacteria and Starkeya - alpha-Proteobacteria). This general picture emerged although apparent evidence for lateral transfer of the soxB gene is indicated and comparison of soxB phylogeny and 16S rDNA phylogeny points to the significance of this gene transfer in hydrothermal vent bacterial communities of the North Fiji Basin.
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  • 8
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    Collapses of two-dimensional granular columns (2005)
    American Physical Society (APS)
    In:  Physical Review E, 72 (041301).
    Details
    Publication Date: 2017-01-03
    Description: The first detailed quantitative observations of the two-dimensional collapse of a granular column along a horizontal channel are presented for a variety of materials. Together with the complementary study for the axisymmetric situation, we conclude that for granular collapses the generally accepted approaches, that are highly dependent on frictional parameters, do not describe the main flow phenomena. The motion divides in two main flow regimes at a∼1.8, where the aspect ratio a=hi∕di and hi and di are the initial height and width of the column. We describe the details of collapse by emphasizing the sequential occurrence of a main spreading followed by a final avalanching phase. For the low a regime, a〈1.8, we derive descriptions of the final geometry by direct physical arguments. For the large a regime, a〉1.8, we determine that nearly all details of the collapse, including the position of the flow front as a function of time, the emplacement time, the self-similar final profiles, and especially their maximum vertical and horizontal extension, are established during the spreading phase and can be expressed in terms of the initial geometrical parameters but are independent of basal and internal friction parameters.
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  • 9
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    Comparative analysis of ammonia monooxygenase (amoA) genes in the water column and sediment-water interface of two lakes and the Baltic Sea (2008)
    Oxford University Press
    In:  FEMS Microbiology Ecology, 66 . pp. 367-378.
    Details
    Publication Date: 2019-09-24
    Description: The functional gene amoA was used to compare the diversity of ammonia-oxidizing bacteria (AOB) in the water column and sediment-water interface of the two freshwater lakes Plusssee and Schöhsee and the Baltic Sea. Nested amplifications were used to increase the sensitivity of amoA detection, and to amplify a 789-bp fragment from which clone libraries were prepared. The larger part of the sequences was only distantly related to any of the cultured AOB and is considered to represent new clusters of AOB within the Nitrosomonas/Nitrosospira group. Almost all sequences from the water column of the Baltic Sea and from 1-m depth of Schöhsee were related to different Nitrosospira clusters 0 and 2, respectively. The majority of sequences from Plusssee and Schöhsee were associated with sequences from Chesapeake Bay, from a previous study of Plusssee and from rice roots in Nitrosospira-like cluster A, which lacks sequences from Baltic Sea. Two groups of sequences from Baltic Sea sediment were related to clonal sequences from other brackish/marine habitats in the purely environmental Nitrosospira-like cluster B and the Nitrosomonas-like cluster. This confirms previous results from 16S rRNA gene libraries that indicated the existence of hitherto uncultivated AOB in lake and Baltic Sea samples, and showed a differential distribution of AOB along the water column and sediment of these environments
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  • 10
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    Genetic variability, shell and sperm morphology suggest that the surf clams Donax marincovichi and D. obesulus are one species (2009)
    Oxford University Press
    In:  Journal of Molluscan Studies, 75 (4). pp. 381-390.
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    Publication Date: 2019-08-08
    Description: The taxonomy of two sympatric surf clams Donax marincovichi Coan, 1983 and Donax obesulus Reeve, 1854, inhabiting the coastal Humboldt Current Upwelling System is revisited. Because both species are exploited by artisanal fisheries, it is essential to verify that they are indeed distinct species that have to be managed separately. In this study, both taxa were sampled across their shared distributional area and specimens were indentified according to their respective morphological characteristics. Although width/height and height/length ratios revealed significant differences within sampling areas, the two morphotypes were frequently incongruent for taxonomically important morphometric parameters. In addition, they showed no significant mitochondrial genetic differentiation within or among populations and exhibited indistinguishable sperm ultrastructure. We conclude that the two morphotypes do not represent distinct species and should be included together under D. obesulus.
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