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  • BioMed Central  (10,457)
  • American Geophysical Union
  • 2015-2019  (16,933)
  • 2010-2014
  • 2015  (16,933)
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  • 2015-2019  (16,933)
  • 2010-2014
Year
  • 1
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    Active alkaline traps to determine acidic-gas ratios in volcanic plumes: Sampling techniques and analytical methods (2015)
    American Geophysical Union
    Details
    Publication Date: 2023-01-19
    Description: In situ measurements have been the basis for monitoring volcanic gas emissions for many years and—being complemented by remote sensing techniques—still play an important role to date. Concerning in situ techniques for sampling a dilute plume, an increase in accuracy and a reduction of detection limits are still necessary for most gases (e.g., CO2, SO2, HCl, HF, HBr, HI). In this work, the Raschig-Tube technique (RT) is modified and utilized for application on volcanic plumes. The theoretical and experimental absorption properties of the RT and the Drechsel bottle (DB) setups are characterized and both are applied simultaneously to the well-established Filter packs technique (FP) in the field (on Stromboli Island and Mount Etna). The comparison points out that FPs are the most practical to apply but the results are errorprone compared to RT and DB, whereas the RT results in up to 13 times higher analyte concentrations than the DB in the same sampling time. An optimization of the analytical procedure, including sample pretreatment and analysis by titration, Ion Chromatography, and Inductively Coupled Plasma Mass Spectrometry, led to a comprehensive data set covering a wide range of compounds. In particular, less abundant species were quantified more accurately and iodine was detected for the first time in Stromboli’s plume. Simultaneously applying Multiaxis Differential Optical Absorption Spectroscopy (MAX-DOAS) the chemical transformation of emitted bromide into bromine monoxide (BrO) from Stromboli and Etna was determined to 3–6% and 7%, respectively, within less than 5 min after the gas release from the active vents.
    Description: Published
    Description: 2797–2820
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: restricted
    Keywords: plume ; volcano ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    The ocean sampling day consortium (2015)
    BioMed Central
    Details
    Publication Date: 2022-10-18
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 4 (2015): 27, doi:10.1186/s13742-015-0066-5.
    Description: Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
    Description: This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589.
    Keywords: Ocean sampling day ; OSD ; Biodiversity ; Genomics ; Health index ; Bacteria ; Microorganism ; Metagenomics ; Marine ; Micro B3 ; Standards
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
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    Rayleigh wave dispersion measurements reveal low-velocity zones beneath the new crust in the Gulf of California (2015)
    American Geophysical Union
    Details
    Publication Date: 2022-06-14
    Description: Rayleigh wave tomography provides images of the shallow mantle shear wave velocity structure beneath the Gulf of California. Low-velocity zones (LVZs) are found on axis between 26 and 50 km depth beneath the Guaymas Basin but mostly off axis under the other rift basins, with the largest feature underlying the Ballenas Transform Fault. We interpret the broadly distributed LVZs as regions of partial melting in a solid mantle matrix. The pathway for melt migration and focusing is more complex than an axis-centered source aligned above a deeper region of mantle melt and likely reflects the magmatic evolution of rift segments. We also consider the existence of solid lower continental crust in the Gulf north of the Guaymas Basin, where the association of the LVZs with asthenospheric upwelling suggests lateral flow assisted by a heat source. These results provide key constraints for numerical models of mantle upwelling and melt focusing in this young oblique rift.
    Description: Published
    Description: 1766–1774
    Description: 1T. Geodinamica e interno della Terra
    Description: JCR Journal
    Description: open
    Keywords: Low velocities in the Gulf upper mantle are interpreted as partial melting ; Partial melting under the Guaymas Basin and off axis of the other rift basins ; Lower crustal flow assisted by heat source in N Gulf near mantle upwelling ; 04. Solid Earth::04.01. Earth Interior::04.01.03. Mantle and Core dynamics ; 04. Solid Earth::04.06. Seismology::04.06.07. Tomography and anisotropy ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Forensic analysis of the microbiome of phones and shoes (2015)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 3 (2015): 21, doi:10.1186/s40168-015-0082-9.
    Description: Microbial interaction between human-associated objects and the environments we inhabit may have forensic implications, and the extent to which microbes are shared between individuals inhabiting the same space may be relevant to human health and disease transmission. In this study, two participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2-day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences. Samples taken from different surface types maintained significantly different microbial community structures. The impact of the floor microbial community on that of the shoe environments was strong and immediate, as evidenced by Procrustes analysis of shoe replicates and significant correlation between shoe and floor samples taken at the same time point. Supervised learning was highly effective at determining which participant had taken a given shoe or phone sample, and a Bayesian method was able to determine which participant had taken each shoe sample based entirely on its similarity to the floor samples. Both shoe and phone samples taken by conference participants clustered into distinct groups based on location, though much more so when an unweighted distance metric was used, suggesting sharing of low-abundance microbial taxa between individuals inhabiting the same space. Correlations between microbial community sources and sinks allow for inference of the interactions between humans and their environment.
    Description: This work was enabled by the generous support of the Alfred P Sloan foundation. This work was supported in part by the U.S. Dept. of Energy under Contract DE-AC02-06CH11357. S.M.G. was supported by an EPA STAR Graduate Fellowship and by a National Institutes of Health Training Grant 5 T-32 EB-009412.
    Keywords: Forensic microbiology ; Source-sink dynamics ; Shoe microbiome ; Phone microbiome ; Microbial time series
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
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    Transcriptional profiling of reproductive development, lipid storage and molting throughout the last juvenile stage of the marine copepod Calanus finmarchicus (2015)
    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 Frontiers in Zoology 11 (2014): 91, doi:10.1186/s12983-014-0091-8.
    Description: Calanus finmarchicus, a highly abundant copepod that is an important primary consumer in North Atlantic ecosystems, has a flexible life history in which copepods in the last juvenile developmental stage (fifth copepodid, C5) may either delay maturation and enter diapause or molt directly into adults. The factors that regulate this developmental plasticity are poorly understood, and few tools have been developed to assess the physiological condition of individual copepods. We sampled a cultured population of C. finmarchicus copepods daily throughout the C5 stage and assessed molt stage progression, gonad development and lipid storage. We used high-throughput sequencing to identify genes that were differentially expressed during progression through the molt stage and then used qPCR to profile daily expression of individual genes. Based on expression profiles of twelve genes, samples were statistically clustered into three groups: (1) an early period occurring prior to separation of the cuticle from the epidermis (apolysis) when expression of genes associated with lipid synthesis and transport (FABP and ELOV) and two nuclear receptors (ERR and HR78) was highest, (2) a middle period of rapid change in both gene expression and physiological condition, including local minima and maxima in several nuclear receptors (FTZ-F1, HR38b, and EcR), and (3) a late period when gonads were differentiated and expression of genes associated with molting (Torso-like, HR38a) peaked. The ratio of Torso-like to HR38b strongly differentiated the early and late groups. This study provides the first dynamic profiles of gene expression anchored with morphological markers of lipid accumulation, development and gonad maturation throughout a copepod molt cycle. Transcriptomic profiling revealed significant changes over the molt cycle in genes with presumed roles in lipid synthesis, molt regulation and gonad development, suggestive of a coupling of these processes in Calanus finmarchicus. Finally, we identified gene expression profiles that strongly differentiate between early and late development within the C5 copepodid stage. We anticipate that these findings and continued development of robust gene expression biomarkers that distinguish between diapause preparation and continuous development will ultimately enable novel studies of the intrinsic and extrinsic factors that govern diapause initiation in Calanus finmarchicus.
    Description: This work was supported by grant number OCE-1132567 from the National Science Foundation to MFB and AMT. Additional supported was provided by WHOI Early Career Scientist Awards provided to MFB and AMT.
    Keywords: Arthropod ; Crustacean ; Gene expression ; Molt cycle ; Transcriptomics
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus) (2015)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 16 (2015): 243, doi:10.1186/s12864-015-1288-8.
    Description: With its unique ability to produce high-voltage electric discharges in excess of 600 volts, the South American strong voltage electric eel (Electrophorus electricus) has played an important role in the history of science. Remarkably little is understood about the molecular nature of its electric organs. We present an in-depth analysis of the genome of E. electricus, including the transcriptomes of eight mature tissues: brain, spinal cord, kidney, heart, skeletal muscle, Sachs’ electric organ, main electric organ, and Hunter’s electric organ. A gene set enrichment analysis based on gene ontology reveals enriched functions in all three electric organs related to transmembrane transport, androgen binding, and signaling. This study also represents the first analysis of miRNA in electric fish. It identified a number of miRNAs displaying electric organ-specific expression patterns, including one novel miRNA highly over-expressed in all three electric organs of E. electricus. All three electric organ tissues also express three conserved miRNAs that have been reported to inhibit muscle development in mammals, suggesting that miRNA-dependent regulation of gene expression might play an important role in specifying an electric organ identity from its muscle precursor. These miRNA data were supported using another complete miRNA profile from muscle and electric organ tissues of a second gymnotiform species. Our work on the E. electricus genome and eight tissue-specific gene expression profiles will greatly facilitate future research on determining the coding and regulatory sequences that specify the function, development, and evolution of electric organs. Moreover, these data and future studies will be informed by the first comprehensive analysis of miRNA expression in an electric fish presented here.
    Description: This project has been funded in part by NSF Grant MCB No. 1144012 (MRS), NSF Grant DEB No. 0741450 (JSA), NSF Grant CNS No. 1248109 (GAU), W.M. Keck Foundation Distinguished Young Scholars in Medical Research (CDN), NIH R01 GM084879 (HZ), NIH grant R01 GM088670 (RA), NIH grant 1SC1GM092297-01A1 (GAU), the Morgridge Graduate Fellowship (JDV and LLT), University of Wisconsin Genetics NIH Graduate Training Grant (LLT); and the Cornell University Center for Vertebrate Genomics (JRG).
    Keywords: Electric eel ; Genome ; Transcriptome ; miRNA ; Gene ontology
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum (2015)
    BioMed Central
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 16 (2015): 805, doi:10.1186/s12864-015-2052-9.
    Description: Organelle retention is a form of mixotrophy that allows organisms to reap metabolic benefits similar to those of photoautotrophs through capture of algal prey and sequestration of their plastids. Mesodinium rubrum is an abundant and broadly distributed photosynthetic marine ciliate that steals organelles from cryptophyte algae, such as Geminigera cryophila. M. rubrum is unique from most other acquired phototrophs because it also steals a functional nucleus that facilitates genetic control of sequestered plastids and other organelles. We analyzed changes in G. cryophila nuclear gene expression and transcript abundance after its incorporation into the cellular architecture of M. rubrum as an initial step towards understanding this complex system. We compared Illumina-generated transcriptomes of the cryptophyte Geminigera cryophila as a free-living cell and as a sequestered nucleus in M. rubrum to identify changes in protein abundance and gene expression. After KEGG annotation, proteins were clustered by functional categories, which were evaluated for over- or under-representation in the sequestered nucleus. Similarly, coding sequences were grouped by KEGG categories/pathways, which were then evaluated for over- or under-expression via read count strategies. At the time of sampling, the global transcriptome of M. rubrum was dominated (~58–62 %) by transcription from its stolen nucleus. A comparison of transcriptomes from free-living G. cryophila cells to those of the sequestered nucleus revealed a decrease in gene expression and transcript abundance for most functional protein categories within the ciliate. However, genes coding for proteins involved in photosynthesis, oxidative stress reduction, and several other metabolic pathways revealed striking exceptions to this general decline. Major changes in G. cryophila transcript expression after sequestration by M. rubrum and the ciliate’s success as a photoautotroph imply some level of control or gene regulation by the ciliate and at the very least reflect a degree of coordination between host and foreign organelles. Intriguingly, cryptophyte genes involved in protein transport are significantly under-expressed in M. rubrum, implicating a role for the ciliate’s endomembrane system in targeting cryptophyte proteins to plastid complexes. Collectively, this initial portrait of an acquired transcriptome within a dynamic and ecologically successful ciliate highlights the remarkable cellular and metabolic chimerism of this system.
    Description: The authors wish to acknowledge the support of NSF award 1354773.
    Keywords: Mesodinium rubrum ; Geminigera cryophila ; Karyoklepty ; Acquired phototrophy ; Transcriptome ; Differential gene expression ; Chimeric metabolism ; Organelle retention ; Mixotrophy
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Athletic equipment microbiota are shaped by interactions with human skin (2015)
    BioMed Central
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 3 (2015): 25, doi:10.1186/s40168-015-0088-3.
    Description: Americans spend the vast majority of their lives in built environments. Even traditionally outdoor pursuits, such as exercising, are often now performed indoors. Bacteria that colonize these indoor ecosystems are primarily derived from the human microbiome. The modes of human interaction with indoor surfaces and the physical conditions associated with each surface type determine the steady-state ecology of the microbial community. Bacterial assemblages associated with different surfaces in three athletic facilities, including floors, mats, benches, free weights, and elliptical handles, were sampled every other hour (8 am to 6 pm) for 2 days. Surface and equipment type had a stronger influence on bacterial community composition than the facility in which they were housed. Surfaces that were primarily in contact with human skin exhibited highly dynamic bacterial community composition and non-random co-occurrence patterns, suggesting that different host microbiomes—shaped by selective forces—were being deposited on these surfaces through time. However, bacterial assemblages found on the floors and mats changed less over time, and species co-occurrence patterns appeared random, suggesting more neutral community assembly. These longitudinal patterns highlight the dramatic turnover of microbial communities on surfaces in regular contact with human skin. By uncovering these longitudinal patterns, this study promotes a better understanding of microbe-human interactions within the built environment.
    Description: MW was supported by a Weinberg College of Arts and Sciences Summer Grant from Northwestern University. This work was supported in part by the U.S. Dept. of Energy under Contract DE-AC02-06CH11357. This work was also supported by the Alfred P Sloan Foundation’s Microbiology of the Built Environment research program. SMG was supported by an EPA STAR Graduate Fellowship and the National Institutes of Health Training Grant 5 T-32 EB-009412.
    Keywords: Gym microbiome ; Athletic equipment ; Microbiology ; Niche communities ; Next-generation sequencing
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Tectonic control on the petrophysical properties of foredeep sandstone in the Central Apennines, Italy (2015)
    American Geophysical Union
    Details
    Publication Date: 2022-04-29
    Description: Petrophysical properties of rocks and their applicability at larger scale are a challenging topic in Earth sciences. Petrophysical properties of rocks are severely affected by boundary conditions, rock fabric/microstructure, and tectonics that require a multiscale approach to be properly defined. Here we (1) report laboratory measurements of density, porosity, permeability, and P wave velocities at increasing confining pressure conducted on Miocene foredeep sandstones (Frosinone Formation); (2) compare the laboratory results with larger-scale geophysical investigations; and (3) discuss the effect of thrusting on the properties of sandstones. At ambient pressure, laboratory porosity varied from 2.2% to 13.8% and P wave velocities (Vp) from 1.5 km/s to 2.7 km/s. The P wave velocity increased with confining pressure, reaching between 3.3 km/s and 4.7 km/s at 100 MPa. In situ Vp profiles, measured using sonic logs, matched the ultrasonic laboratory measurement well. The permeability varied between 1.4 × 10 15m2 and 3.9 × 10 15m2 and was positively correlated with porosity. The porosity and permeability of samples taken at various distances to the Olevano–Antrodoco fault plane progressively decreased with distance while P wave velocity increased. At about 1 km from the fault plane, the relative variations reached 43%, 65%, and 20% for porosity, permeability, and P wave velocity, respectively. This suggests that tectonic loading changed the petrophysical properties inherited from sedimentation and diagenesis. Using field constraints and assuming overburden-related inelastic compaction in the proximity of the fault plane, we conclude that the fault reached the mechanical condition for rupture in compression at differential stress of 64.8 MPa at a depth of 1500 m.
    Description: Published
    Description: 9077-9094
    Description: 2IT. Laboratori sperimentali e analitici
    Description: JCR Journal
    Description: open
    Keywords: Petrophysical properties of sandstone ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
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    Applying a curl-B technique to Swarm vector data to estimate nighttime F region current intensities (2015)
    American Geophysical Union
    Details
    Publication Date: 2022-03-01
    Description: The innovative geometry of European Space Agency Swarm constellation opens the way for new investigations based on magnetic data. Since the knowledge of a vector field on two spherical surfaces allows calculating its curl, we propose a new technique to estimate the curl of the ionospheric magnetic field measured by Swarm satellites A and B, orbiting the Earth at two different altitudes from March to September 2014. Using this technique, we mapped the amplitude of the radial, meridional, and zonal components and of total intensity of the ionospheric current density at the satellite's altitudes, i.e., the F region of the ionosphere, during two local nighttime intervals: before and after midnight. Most of the obtained results are consistent with some of the known features of nighttime F region currents; others need further investigation. The proposed technique could contribute in selecting magnetic data with minimum contamination from nighttime F region electric currents for magnetic modeling purposes.
    Description: Published
    Description: 6162-6169
    Description: 1A. Geomagnetismo e Paleomagnetismo
    Description: JCR Journal
    Description: restricted
    Keywords: Swarm magnetic data ; current density ; F region ; 01. Atmosphere::01.02. Ionosphere::01.02.99. General or miscellaneous ; 04. Solid Earth::04.05. Geomagnetism::04.05.08. Instruments and techniques ; 05. General::05.01. Computational geophysics::05.01.01. Data processing
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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