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  • Articles  (1,341,352)
  • Springer  (775,555)
  • American Chemical Society  (410,191)
  • Oxford University Press  (107,405)
  • BioMed Central  (48,201)
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  • 1975-1979  (325,244)
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  • 11
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    Macroseismic effects highlight site response in Rome and its geological signature (2012)
    Springer
    Details
    Publication Date: 2023-06-05
    Description: A detailed analysis of the earthquake effects on the urban area of Rome has been conducted for the L’Aquila sequence, which occurred in April 2009, by using an on-line macroseismic questionnaire. Intensity residuals calculated using the mainshock and four aftershocks are analyzed in the light of a very accurate and original geological reconstruction of the subsoil of Rome based on a large amount of wells. The aim of this work is to highlight ground motion amplification areas and to find a correlation with the geological settings at a sub-regional scale, putting in evidence the extreme complexity of the phenomenon and the difficulty of making a simplified model. Correlations between amplification areas and both near-surface and deep geology were found. Moreover, the detailed scale of investigation has permitted us to find a correlation between seismic amplification in recent alluvial settings and subsiding zones, and between heard seismic sound and Tiber alluvial sediments.
    Description: Published
    Description: 425-443
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: open
    Keywords: Earthquakes ; Intensity residuals ; Urban geosciences ; Macroseismic effects ; Amplification areas ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion ; 04. Solid Earth::04.06. Seismology::04.06.11. Seismic risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
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    Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes (2010)
    Springer
    Details
    Publication Date: 2022-05-26
    Description: © 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.
    Description: 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.
    Description: 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.
    Keywords: Phenotypic trait ; Bacteria ; Molecular mechanisms of cold tolerance ; Shewanella ; Protein families
    Repository Name: Woods Hole Open Access Server
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  • 13
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    Identification and developmental expression of the full complement of Cytochrome P450 genes in Zebrafish (2011)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © 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): 643, doi:10.1186/1471-2164-11-643.
    Description: Increasing use of zebrafish in drug discovery and mechanistic toxicology demands knowledge of cytochrome P450 (CYP) gene regulation and function. CYP enzymes catalyze oxidative transformation leading to activation or inactivation of many endogenous and exogenous chemicals, with consequences for normal physiology and disease processes. Many CYPs potentially have roles in developmental specification, and many chemicals that cause developmental abnormalities are substrates for CYPs. Here we identify and annotate the full suite of CYP genes in zebrafish, compare these to the human CYP gene complement, and determine the expression of CYP genes during normal development. Zebrafish have a total of 94 CYP genes, distributed among 18 gene families found also in mammals. There are 32 genes in CYP families 5 to 51, most of which are direct orthologs of human CYPs that are involved in endogenous functions including synthesis or inactivation of regulatory molecules. The high degree of sequence similarity suggests conservation of enzyme activities for these CYPs, confirmed in reports for some steroidogenic enzymes (e.g. CYP19, aromatase; CYP11A, P450scc; CYP17, steroid 17a-hydroxylase), and the CYP26 retinoic acid hydroxylases. Complexity is much greater in gene families 1, 2, and 3, which include CYPs prominent in metabolism of drugs and pollutants, as well as of endogenous substrates. There are orthologous relationships for some CYP1 s and some CYP3 s between zebrafish and human. In contrast, zebrafish have 47 CYP2 genes, compared to 16 in human, with only two (CYP2R1 and CYP2U1) recognized as orthologous based on sequence. Analysis of shared synteny identified CYP2 gene clusters evolutionarily related to mammalian CYP2 s, as well as unique clusters. Transcript profiling by microarray and quantitative PCR revealed that the majority of zebrafish CYP genes are expressed in embryos, with waves of expression of different sets of genes over the course of development. Transcripts of some CYP occur also in oocytes. The results provide a foundation for the use of zebrafish as a model in toxicological, pharmacological and chemical disease research.
    Description: This work was supported by NIH grants R01ES015912 and P42ES007381 (Superfund Basic Research Program at Boston University) (to JJS). MEJ was a Guest Investigator at the Woods Hole Oceanographic Institution (WHOI) and was supported by grants from the Swedish research council Formas and Carl Trygger's foundation. AK was a Post-doctoral Fellow at WHOI, and was supported by a fellowship from the Japanese Society for Promotion of Science (JSPS). JZ and TP were Guest Students at the WHOI and were supported by a CAPES Ph.D. Fellowship and CNPq Ph.D. Sandwich Fellowship (JZ), and by a CNPq Ph.D. Fellowship (TP), from Brazil.
    Repository Name: Woods Hole Open Access Server
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  • 14
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    Comparative transcriptome analysis of obligately asexual and cyclically sexual rotifers reveals genes with putative functions in sexual reproduction, dormancy, and asexual egg production (2013)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 14 (2013): 412, doi:10.1186/1471-2164-14-412.
    Description: Sexual reproduction is a widely studied biological process because it is critically important to the genetics, evolution, and ecology of eukaryotes. Despite decades of study on this topic, no comprehensive explanation has been accepted that explains the evolutionary forces underlying its prevalence and persistence in nature. Monogonont rotifers offer a useful system for experimental studies relating to the evolution of sexual reproduction due to their rapid reproductive rate and close relationship to the putatively ancient asexual bdelloid rotifers. However, little is known about the molecular underpinnings of sex in any rotifer species. We generated mRNA-seq libraries for obligate parthenogenetic (OP) and cyclical parthenogenetic (CP) strains of the monogonont rotifer, Brachionus calyciflorus, to identify genes specific to both modes of reproduction. Our differential expression analysis identified receptors with putative roles in signaling pathways responsible for the transition from asexual to sexual reproduction. Differential expression of a specific copy of the duplicated cell cycle regulatory gene CDC20 and specific copies of histone H2A suggest that such duplications may underlie the phenotypic plasticity required for reproductive mode switch in monogononts. We further identified differential expression of genes involved in the formation of resting eggs, a process linked exclusively to sex in this species. Finally, we identified transcripts from the bdelloid rotifer Adineta ricciae that have significant sequence similarity to genes with higher expression in CP strains of B. calyciflorus. Our analysis of global gene expression differences between facultatively sexual and exclusively asexual populations of B. calyciflorus provides insights into the molecular nature of sexual reproduction in rotifers. Furthermore, our results offer insight into the evolution of obligate asexuality in bdelloid rotifers and provide indicators important for the use of monogononts as a model system for investigating the evolution of sexual reproduction.
    Description: This work was funded by National Institutes of Health Institute of General Medical Sciences (grant number 5R01GM079484, to JML and DMW).
    Keywords: Evolution of sexual reproduction ; Differential expression analysis ; Gene ontology analysis ; Meiosis ; Gametogenesis ; Resting eggs ; Mixis induction
    Repository Name: Woods Hole Open Access Server
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  • 15
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    VAMPS : a website for visualization and analysis of microbial population structures (2014)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 15 (2014): 41, doi:10.1186/1471-2105-15-41.
    Description: The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 105–108 reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing. We developed the free web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu webcite) to address these challenges and to facilitate research by individuals or collaborating groups working on projects with large-scale sequencing data. Users can upload marker gene sequences and associated metadata; reads are quality filtered and assigned to both taxonomic structures and to taxonomy-independent clusters. A simple point-and-click interface allows users to select for analysis any combination of their own or their collaborators’ private data and data from public projects, filter these by their choice of taxonomic and/or abundance criteria, and then explore these data using a wide range of analytic methods and visualizations. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships. VAMPS allows researchers using marker gene sequence data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download data, results, and images for publication. VAMPS obviates the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret massive amounts of next-generation sequence data. Any web-capable device can be used to upload, process, explore, and extract data and results from VAMPS. VAMPS encourages researchers to share sequence and metadata, and fosters collaboration between researchers of disparate biomes who recognize common patterns in shared data.
    Description: Funding provided by the National Science Foundation [grant NSF/BDI 0960626 to SMH] and the Sloan Foundation through a collaborative project with the Microbiology of the Built Environment program.
    Keywords: Microbiome ; Microbial ecology ; Microbial diversity ; Data visualization ; Website ; Bacteria ; SSU rRNA ; Next-generation sequencing
    Repository Name: Woods Hole Open Access Server
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  • 16
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    Distribution of surface plastic debris in the eastern Pacific Ocean from an 11-Year data set (2014)
    American Chemical Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Chemical Society, 2014. This article is posted here by permission of American Chemical Society for personal use, not for redistribution. The definitive version was published in Environmental Science and Technology 38 (2014): 4732–4738, doi:10.1021/es4053076.
    Description: We present an extensive survey of floating plastic debris in the eastern North and South Pacific Oceans from more than 2500 plankton net tows conducted between 2001 and 2012. From these data we defined an accumulation zone (25 to 41°N, 130 to 180°W) in the North Pacific subtropical gyre that closely corresponds to centers of accumulation resulting from the convergence of ocean surface currents predicted by several oceanographic numerical models. Maximum plastic concentrations from individual surface net tows exceeded 106 pieces km–2, with concentrations decreasing with increasing distance from the predicted center of accumulation. Outside the North Pacific subtropical gyre the median plastic concentration was 0 pieces km–2. We were unable to detect a robust temporal trend in the data set, perhaps because of confounded spatial and temporal variability. Large spatiotemporal variability in plastic concentration causes order of magnitude differences in summary statistics calculated over short time periods or in limited geographic areas. Utilizing all available plankton net data collected in the eastern Pacific Ocean (17.4°S to 61.0°N; 85.0 to 180.0°W) since 1999, we estimated a minimum of 21 290 t of floating microplastic.
    Description: This work was supported by Sea Education Association, NFWF-NOAA Marine Debris Program (Nos. 2009-0062-002, NA10OAR4320148, Amend. 71), and NSF (Nos. OCE-0087528, OCE-1155379, OCE-1260403, OCE-1352422).
    Repository Name: Woods Hole Open Access Server
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  • 17
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    Scientific names of organisms : attribution, rights, and licensing (2014)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Research Notes 7 (2014): 79, doi:10.1186/1756-0500-7-79.
    Description: As biological disciplines extend into the ‘big data’ world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world. The laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their efforts. A ‘blue list’ identifies elements of checklists, classifications and monographs to which intellectual property rights do not apply. To promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors. Mechanisms for achieving this are discussed.
    Keywords: Scientific names ; Taxonomy ; Copyright ; Intellectual property rights ; Name-based infrastructure ; Big data
    Repository Name: Woods Hole Open Access Server
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  • 18
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    Seasonal and hydrologic drivers of dissolved organic matter and nutrients in the upper Kuparuk River, Alaskan Arctic (2011)
    Springer
    Details
    Publication Date: 2022-05-26
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Biogeochemistry 103 (2011): 109-124, doi:10.1007/s10533-010-9451-4.
    Description: As the planet warms, widespread changes in Arctic hydrology and biogeochemistry have been documented and these changes are expected to accelerate in the future. Improved understanding of the behavior of water-borne constituents in Arctic rivers with varying hydrologic conditions, including seasonal variations in discharge–concentration relationships, will improve our ability to anticipate future changes in biogeochemical budgets due to changing hydrology. We studied the relationship between seasonal water discharge and dissolved organic carbon and nitrogen (DOC and DON) and nutrient concentrations in the upper Kuparuk River, Arctic Alaska. Fluxes of most constituents were highest during initial snowmelt runoff in spring, indicating that this historically under-studied period contributes significantly to total annual export. In particular, the initial snowmelt period (the stream is completely frozen during the winter) accounted for upwards of 35% of total export of DOC and DON estimated for the entire study period. DOC and DON concentrations were positively correlated with discharge whereas nitrate (NO3 −) and silicate were negatively correlated with discharge throughout the study. However, discharge-specific DOC and DON concentrations (i.e. concentrations compared at the same discharge level) decreased over the summer whereas discharge-specific concentrations of NO3 − and silicate increased. Soluble reactive phosphorus (SRP) and ammonium (NH4 +) were negatively correlated with discharge during the spring thaw, but were less predictable with respect to discharge thereafter. These data provide valuable information on how Arctic watershed biogeochemistry will be affected by future changes in temperature, snowfall, and rainfall in the Arctic. In particular, our results add to a growing body of research showing that nutrient export per unit of stream discharge, particularly NO3 −, is increasing in the Arctic.
    Description: Funding provided by the National Science Foundation, NSF-OPP- 0436118.
    Keywords: Arctic ; Stream ; Headwaters ; Carbon ; Nitrogen ; Nutrients
    Repository Name: Woods Hole Open Access Server
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  • 19
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    The use (and misuse) of sediment traps in coral reef environments : theory, observations, and suggested protocols (2011)
    Springer
    Details
    Publication Date: 2022-05-26
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coral Reefs 30 (2011): 23-38, doi:10.1007/s00338-010-0705-3.
    Description: Sediment traps are commonly used as standard tools for monitoring “sedimentation” in coral reef environments. In much of the literature where sediment traps were used to measure the effects of “sedimentation” on corals, it is clear from deployment descriptions and interpretations of the resulting data that information derived from sediment traps has frequently been misinterpreted or misapplied. Despite their widespread use in this setting, sediment traps do not provide quantitative information about “sedimentation” on coral surfaces. Traps can provide useful information about the relative magnitude of sediment dynamics if trap deployment standards are used. This conclusion is based first on a brief review of the state of knowledge of sediment trap dynamics, which has primarily focused on traps deployed high above the seabed in relatively deep water, followed by our understanding of near-bed sediment dynamics in shallow-water environments that characterize coral reefs. This overview is followed by the first synthesis of near-bed sediment trap data collected with concurrent hydrodynamic information in coral reef environments. This collective information is utilized to develop nine protocols for using sediment traps in coral reef environments, which focus on trap parameters that researchers can control such as trap height (H), trap mouth diameter (D), the height of the trap mouth above the substrate (z o ), and the spacing between traps. The hydrodynamic behavior of sediment traps and the limitations of data derived from these traps should be forefront when interpreting sediment trap data to infer sediment transport processes in coral reef environments.
    Keywords: Sediment trap ; Coral reefs ; Sedimentation ; Waves ; Currents ; Shear stress
    Repository Name: Woods Hole Open Access Server
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  • 20
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    Characterization of differential transcript abundance through time during Nematostella vectensis development (2013)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 14 (2013): 266, doi:10.1186/1471-2164-14-266.
    Description: Nematostella vectensis, a burrowing sea anemone, has become a popular species for the study of cnidarian development. In previous studies, the expression of a variety of genes has been characterized during N. vectensis development with in situ mRNA hybridization. This has provided detailed spatial resolution and a qualitative perspective on changes in expression. However, little is known about broad transcriptome-level patterns of gene expression through time. Here we examine the expression of N. vectensis genes through the course of development with quantitative RNA-seq. We provide an overview of changes in the transcriptome through development, and examine the maternal to zygotic transition, which has been difficult to investigate with other tools. We measured transcript abundance in N. vectensis with RNA-seq at six time points in development: zygote (2 hours post fertilization (HPF)), early blastula (7 HPF), mid-blastula (12 HPF), gastrula (24 HPF), planula (5 days post fertilization (DPF)) and young polyp (10 DPF). The major wave of zygotic expression appears between 7–12 HPF, though some changes occur between 2–7 HPF. The most dynamic changes in transcript abundance occur between the late blastula and early gastrula stages. More transcripts are upregulated between the gastrula and planula than downregulated, and a comparatively lower number of transcripts significantly change between planula and polyp. Within the maternal to zygotic transition, we identified a subset of maternal factors that decrease early in development, and likely play a role in suppressing zygotic gene expression. Among the first genes to be expressed zygotically are genes whose proteins may be involved in the degradation of maternal RNA. The approach presented here is highly complementary to prior studies on spatial patterns of gene expression, as it provides a quantitative perspective on a broad set of genes through time but lacks spatial resolution. In addition to addressing the problems identified above, our work provides an annotated matrix that other investigators can use to examine genes and developmental events that we do not examine in detail here.
    Description: This work was supported by seed funds from the Brown-MBL Partnership and the National Science Foundation Graduate Student Research Fellowship. Infrastructure for data transfer from the sequencer was supported by the National Science Foundation EPSCoR Program under Grant No. 1004057 (Infrastructure to Advance Life Sciences in the Ocean State).
    Keywords: Nematostella vectensis ; Transcriptome ; Gene expression ; Maternal to zygotic transition ; Development
    Repository Name: Woods Hole Open Access Server
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