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  • 1
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Authors 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Functional & Integrative Genomics 10 (2010): 97-110, doi:10.1007/s10142-009-0142-y.
    Beschreibung: Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. Genomic characteristics underlying this variability across species are largely unknown. In this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced Shewanella species. We have employed two novel approaches based on association of a phenotypic trait with the number of the trait-specific protein families (Pfam domains) and on the conservation of synteny (order in the genome) of the trait-related genes. Our first approach is top-down and involves experimental evaluation and quantification of the species’ cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved synteny. The second, a bottom-up approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network clustering. Using the first approach, we find a link between cold and salt tolerance of the species and the presence in the genome of a Na+/H+ antiporter gene cluster. Other cold-tolerance-related genes include peptidases, chemotaxis sensory transducer proteins, a cysteine exporter, and helicases. Using the bottom-up approach, we found several novel phenotypes in the newly sequenced Shewanella species, including degradation of aromatic compounds by an aerobic hybrid pathway in Shewanella woodyi, degradation of ethanolamine by Shewanella benthica, and propanediol degradation by Shewanella putrefaciens CN32 and Shewanella sp. W3-18-1.
    Beschreibung: This research was supported by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research under the Genomics: GTL Program via the Shewanella Federation consortium.
    Schlagwort(e): Phenotypic trait ; Bacteria ; Molecular mechanisms of cold tolerance ; Shewanella ; Protein families
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 2
    Publikationsdatum: 2022-05-26
    Beschreibung: © 2009 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 9 (2009): 292, doi:10.1186/1471-2148-9-292.
    Beschreibung: Bacterial endosymbiosis has a recurring significance in the evolution of insects. An estimated 10-20% of insect species depend on bacterial associates for their nutrition and reproductive viability. Members of the ant tribe Camponotini, the focus of this study, possess a stable, intracellular bacterial mutualist. The bacterium, Blochmannia, was first discovered in Camponotus and has since been documented in a distinct subgenus of Camponotus, Colobopsis, and in the related genus Polyrhachis. However, the distribution of Blochmannia throughout the Camponotini remains in question. Documenting the true host range of this bacterial mutualist is an important first step toward understanding the various ecological contexts in which it has evolved, and toward identifying its closest bacterial relatives. In this study, we performed a molecular screen, based on PCR amplification of 16S rDNA, to identify bacterial associates of diverse Camponotini species. Phylogenetic analyses of 16S rDNA gave four important insights: (i) Blochmannia occurs in a broad range of Camponotini genera including Calomyrmex, Echinopla, and Opisthopsis, and did not occur in outgroups related to this tribe (e.g., Notostigma). This suggests that the mutualism originated in the ancestor of the tribe Camponotini. (ii) The known bacteriocyte-associated symbionts of ants, in Formica, Plagiolepis, and the Camponotini, arose independently. (iii) Blochmannia is nestled within a diverse clade of endosymbionts of sap-feeding hemipteran insects, such as mealybugs, aphids, and psyllids. In our analyses, a group of secondary symbionts of mealybugs are the closest relatives of Blochmannia. (iv) Blochmannia has cospeciated with its known hosts, although deep divergences at the genus level remain uncertain. The Blochmannia mutualism occurs in Calomyrmex, Echinopla, and Opisthopsis, in addition to Camponotus, and probably originated in the ancestral lineage leading to the Camponotini. This significant expansion of its known host range implies that the mutualism is more ancient and ecologically diverse than previously documented. Blochmannia is most closely related to endosymbionts of sap-feeding hemipterans, which ants tend for their carbohydrate-rich honeydew. Based on phylogenetic results, we propose Camponotini might have originally acquired this bacterial mutualist through a nutritional symbiosis with other insects.
    Beschreibung: Funding for this research was provided by grants from the NSF (MCB-0604177) and NIH (R01GM062626) to JJW, and from the NSF-supported Ant AToL project (EF-0431330) to PSW and SGB.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 3
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Authors, 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Estuaries and Coasts 33 (2010): 15-29, doi:10.1007/s12237-009-9244-y.
    Beschreibung: Future estuarine geomorphic change, in response to climate change, sea-level rise, and watershed sediment supply, may govern ecological function, navigation, and water quality. We estimated geomorphic changes in Suisun Bay, CA, under four scenarios using a tidal-timescale hydrodynamic/sediment transport model. Computational expense and data needs were reduced using the morphological hydrograph concept and the morphological acceleration factor. The four scenarios included (1) present-day conditions; (2) sea-level rise and freshwater flow changes of 2030; (3) sea-level rise and decreased watershed sediment supply of 2030; and (4) sea-level rise, freshwater flow changes, and decreased watershed sediment supply of 2030. Sea-level rise increased water levels thereby reducing wave-induced bottom shear stress and sediment redistribution during the wind-wave season. Decreased watershed sediment supply reduced net deposition within the estuary, while minor changes in freshwater flow timing and magnitude induced the smallest overall effect. In all future scenarios, net deposition in the entire estuary and in the shallowest areas did not keep pace with sea-level rise, suggesting that intertidal and wetland areas may struggle to maintain elevation. Tidal-timescale simulations using future conditions were also used to infer changes in optical depth: though sea-level rise acts to decrease mean light irradiance, decreased suspended-sediment concentrations increase irradiance, yielding small changes in optical depth. The modeling results also assisted with the development of a dimensionless estuarine geomorphic number representing the ratio of potential sediment import forces to sediment export forces; we found the number to be linearly related to relative geomorphic change in Suisun Bay. The methods implemented here are widely applicable to evaluating future scenarios of estuarine change over decadal timescales.
    Beschreibung: This study was supported by the US Geological Survey’s Priority Ecosystems Science program, CALFED Bay/ Delta Program, and the University of California Center for Water Resources.
    Schlagwort(e): Numerical modeling ; Geomorphology ; Scenarios ; Sediment transport
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 4
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial License. The definitive version was published in Ecosystems 13 (2010): 239-248, doi:10.1007/s10021-010-9315-8.
    Beschreibung: Ecosystem nutrient budgets often report values for pools and fluxes without any indication of uncertainty, which makes it difficult to evaluate the significance of findings or make comparisons across systems. We present an example, implemented in Excel, of a Monte Carlo approach to estimating error in calculating the N content of vegetation at the Hubbard Brook Experimental Forest in New Hampshire. The total N content of trees was estimated at 847 kg ha−1 with an uncertainty of 8%, expressed as the standard deviation divided by the mean (the coefficient of variation). The individual sources of uncertainty were as follows: uncertainty in allometric equations (5%), uncertainty in tissue N concentrations (3%), uncertainty due to plot variability (6%, based on a sample of 15 plots of 0.05 ha), and uncertainty due to tree diameter measurement error (0.02%). In addition to allowing estimation of uncertainty in budget estimates, this approach can be used to assess which measurements should be improved to reduce uncertainty in the calculated values. This exercise was possible because the uncertainty in the parameters and equations that we used was made available by previous researchers. It is important to provide the error statistics with regression results if they are to be used in later calculations; archiving the data makes resampling analyses possible for future researchers. When conducted using a Monte Carlo framework, the analysis of uncertainty in complex calculations does not have to be difficult and should be standard practice when constructing ecosystem budgets.
    Schlagwort(e): Monte Carlo ; Hubbard Brook ; Forest biomass ; Allometric equations ; Error analysis ; Ecosystem N budget
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 5
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Authors 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Biogeochemistry 99 (2010): 1-13, doi:10.1007/s10533-009-9392-y.
    Beschreibung: Human activities have profoundly altered the global nitrogen (N) cycle. Increases in anthropogenic N have had multiple effects on the atmosphere, on terrestrial, freshwater and marine ecosystems, and even on human health. Unfortunately, methodological limitations challenge our ability to directly measure natural N inputs via biological N fixation (BNF)—the largest natural source of new N to ecosystems. This confounds efforts to quantify the extent of anthropogenic perturbation to the N cycle. To address this gap, we used a pair of indirect methods—analytical modeling and N balance—to generate independent estimates of BNF in a presumed hotspot of N fixation, a tropical rain forest site in central Rondônia in the Brazilian Amazon Basin. Our objectives were to attempt to constrain symbiotic N fixation rates in this site using indirect methods, and to assess strengths and weaknesses of this approach by looking for areas of convergence and disagreement between the estimates. This approach yielded two remarkably similar estimates of N fixation. However, when compared to a previously published bottom-up estimate, our analysis indicated much lower N inputs via symbiotic BNF in the Rondônia site than has been suggested for the tropics as a whole. This discrepancy may reflect errors associated with extrapolating bottom-up fluxes from plot-scale measures, those resulting from the indirect analyses, and/or the relatively low abundance of legumes at the Rondônia site. While indirect methods have some limitations, we suggest that until the technological challenges of directly measuring N fixation are overcome, integrated approaches that employ a combination of model-generated and empirically-derived data offer a promising way of constraining N inputs via BNF in natural ecosystems.
    Beschreibung: We acknowledge and are grateful for financial support from the Andrew W. Mellon Foundation (C.C. and B.H.), the National Science Foundation (NSF DEB-0515744 to C.C. and A.T. and DEB-0315656 to C.N.), and the NASA LBA Program (NCC5-285 to C.N.).
    Schlagwort(e): Amazon Basin ; Ecosystem modeling ; Mass balance ; Nitrogen fixation ; Nutrient cycling ; Rondonia ; Tropical forest
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
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  • 6
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 11 (2010): 559, doi:10.1186/1471-2164-11-559.
    Beschreibung: Bathymodiolus azoricus is a deep-sea hydrothermal vent mussel found in association with large faunal communities living in chemosynthetic environments at the bottom of the sea floor near the Azores Islands. Investigation of the exceptional physiological reactions that vent mussels have adopted in their habitat, including responses to environmental microbes, remains a difficult challenge for deep-sea biologists. In an attempt to reveal genes potentially involved in the deep-sea mussel innate immunity we carried out a high-throughput sequence analysis of freshly collected B. azoricus transcriptome using gills tissues as the primary source of immune transcripts given its strategic role in filtering the surrounding waterborne potentially infectious microorganisms. Additionally, a substantial EST data set was produced and from which a comprehensive collection of genes coding for putative proteins was organized in a dedicated database, "DeepSeaVent" the first deep-sea vent animal transcriptome database based on the 454 pyrosequencing technology. A normalized cDNA library from gills tissue was sequenced in a full 454 GS-FLX run, producing 778,996 sequencing reads. Assembly of the high quality reads resulted in 75,407 contigs of which 3,071 were singletons. A total of 39,425 transcripts were conceptually translated into amino-sequences of which 22,023 matched known proteins in the NCBI non-redundant protein database, 15,839 revealed conserved protein domains through InterPro functional classification and 9,584 were assigned with Gene Ontology terms. Queries conducted within the database enabled the identification of genes putatively involved in immune and inflammatory reactions which had not been previously evidenced in the vent mussel. Their physical counterpart was confirmed by semi-quantitative quantitative Reverse-Transcription-Polymerase Chain Reactions (RT-PCR) and their RNA transcription level by quantitative PCR (qPCR) experiments. We have established the first tissue transcriptional analysis of a deep-sea hydrothermal vent animal and generated a searchable catalog of genes that provides a direct method of identifying and retrieving vast numbers of novel coding sequences which can be applied in gene expression profiling experiments from a non-conventional model organism. This provides the most comprehensive sequence resource for identifying novel genes currently available for a deep-sea vent organism, in particular, genes putatively involved in immune and inflammatory reactions in vent mussels. The characterization of the B. azoricus transcriptome will facilitate research into biological processes underlying physiological adaptations to hydrothermal vent environments and will provide a basis for expanding our understanding of genes putatively involved in adaptations processes during post-capture long term acclimatization experiments, at "sea-level" conditions, using B. azoricus as a model organism.
    Beschreibung: We acknowledge the Portuguese Foundation for Science and Technology, FCT-Lisbon and the Regional Azorean Directorate for Science and Technology, DRCT-Azores, for pluri-annual and programmatic PIDDAC and FEDER funding to IMAR/DOP Research Unit #531 and the Associated Laboratory #9 (ISR-Lisboa); the Luso-American Foundation FLAD (Project L-V- 173/2006); the Biotechnology and Biomedicine Institute of the Azores (IBBA), project M.2.1.2/I/029/2008-BIODEEPSEA and the project n° FCOMP-01-0124- FEDER-007376 (ref: FCT PTDC/MAR/65991/2006-IMUNOVENT; coordinated by RB) under the auspices of the COMPETE program.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 7
    Publikationsdatum: 2022-05-24
    Beschreibung: National seismic risk maps are an important risk mitigation tool as they can be used for the prioritization of regions within a country where retrofitting of the building stock or other risk mitigation measures should take place. The production of a seismic risk map involves the convolution of seismic hazard data, vulnerability predictions for the building stock and exposure data. The seismic risk maps produced in Italy over the past 10 years are compared in this paper with recent proposals for seismic risk maps based on state-of-the-art seismic hazard data and mechanics-based vulnerability assessment procedures. The aim of the paper is to open the discussion for the way in which future seismic risk maps could be produced, making use of the most up-to-date information in the fields of seismic hazard evaluation and vulnerability assessment.
    Beschreibung: Published
    Beschreibung: 149–180
    Beschreibung: 4.2. TTC - Modelli per la stima della pericolosità sismica a scala nazionale
    Beschreibung: JCR Journal
    Beschreibung: open
    Schlagwort(e): Seismic risk ; Seismic hazard ; 04. Solid Earth::04.06. Seismology::04.06.11. Seismic risk
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 8
    Publikationsdatum: 2021-06-25
    Beschreibung: A multi-model set of atmospheric simulations forced by historical sea surface temperature (SST) or SSTs plus Greenhouse gases and aerosol forcing agents for the period of 1950–1999 is studied to identify and understand which components of the Asian–Australian monsoon (A–AM) variability are forced and reproducible. The analysis focuses on the summertime monsoon circulations, comparing model results against the observations. The priority of different components of the A–AM circulations in terms of reproducibility is evaluated. Among the subsystems of the wide A–AM, the South Asian monsoon and the Australian monsoon circulations are better reproduced than the others, indicating they are forced and well modeled. The primary driving mechanism comes from the tropical Pacific. The western North Pacific monsoon circulation is also forced and well modeled except with a slightly lower reproducibility due to its delayed response to the eastern tropical Pacific forcing. The simultaneous driving comes from the western Pacific surrounding the maritime continent region. The Indian monsoon circulation has a moderate reproducibility, partly due to its weakened connection to June–July–August SSTs in the equatorial eastern Pacific in recent decades. Among the A–AM subsystems, the East Asian summer monsoon has the lowest reproducibility and is poorly modeled. This is mainly due to the failure of specifying historical SST in capturing the zonal land-sea thermal contrast change across the East Asia. The prescribed tropical Indian Ocean SST changes partly reproduce the meridional wind change over East Asia in several models. For all the A–AM subsystem circulation indices, generally the MME is always the best except for the Indian monsoon and East Asian monsoon circulation indices.
    Beschreibung: Published
    Beschreibung: 1051-1068
    Beschreibung: 3.7. Dinamica del clima e dell'oceano
    Beschreibung: JCR Journal
    Beschreibung: open
    Schlagwort(e): CLIVAR C20C ; Asian-Australian monsoon circulation ; AGCM ; Reproducibility ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 9
    Publikationsdatum: 2020-11-16
    Beschreibung: Active volcanoes characterized by open conduit conditions generate sonic and infrasonic signals, whose investigation provides useful information for both monitoring purposes and studying the dynamics of explosive processes. In this work, we discuss the automatic procedures implemented for a real-time application to the data acquired by a permanent network of five infrasound stations running at Mt. Etna volcano. The infrasound signals at Mt. Etna consist in amplitude transients, called infrasound events. The adopted procedure uses a multi-algorithm approach for event detection, counting, characterization and location. It is designed for an efficient and accurate processing of infrasound records provided by single-site and array stations. Moreover, the source mechanism of these events can be investigated off-line or in near real-time by using three different models: i) Strombolian bubble; ii) resonating conduit and iii) Helmholtz resonator. The infrasound waveforms allow us to choose the most suitable model, to get quantitative information about the source and to follow the time evolution of the source parameters.
    Beschreibung: Published
    Beschreibung: 1215–1231
    Beschreibung: 6V. Pericolosità vulcanica e contributi alla stima del rischio
    Beschreibung: JCR Journal
    Beschreibung: open
    Schlagwort(e): infrasound ; monitoring system ; Mt. Etna ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 10
    Publikationsdatum: 2020-11-16
    Beschreibung: The presence of quarry and mine blasts in seismic catalogues is detected using the Wiemer and Baer (Bull Seism Soc Am 90(2):525–530, 2000) algorithm. The procedure is based on the observation that quarry blasts generally take place during daytime hours: the areas with a high ratio of daytime and night-time events are likely to be regions with quarry activity. In the first part of this work we have tested the method, using both a synthetic and a regional catalogue; in the second part the procedure has been applied to some of the European regional catalogues available on line. The comparison between the results obtained and the location of known quarries and mines for the analysed catalogues confirms the reliability of the methodology in identifying mining areas.
    Beschreibung: This research was partially supported by the transnational access activity of the European Union project NERIES (contract number 026130)
    Beschreibung: Published
    Beschreibung: 229–249
    Beschreibung: 4IT. Banche dati
    Beschreibung: JCR Journal
    Beschreibung: open
    Schlagwort(e): quarry blast; mine blast; seismic catalogue ; 05. General::05.01. Computational geophysics::05.01.04. Statistical analysis
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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