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  • Copernicus  (79,874)
  • BioMed Central
  • 2020-2022  (14,179)
  • 2015-2019  (110,508)
  • 2000-2004  (5,991)
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  • 1
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    Coastal dynamics and submarine permafrost in shallow water of the central Laptev Sea, East Siberia (2016)
    Copernicus
    In:  EPIC3The Cryosphere, Copernicus, 9(4), pp. 1449-1462, ISSN: 1994-0416
    Details
    Publication Date: 2024-04-29
    Description: Coastal erosion and flooding transform terrestrial landscapes into marine environments. In the Arctic, these processes inundate terrestrial permafrost with seawater and create submarine permafrost. Permafrost begins to warm under marine conditions, which can destabilize the sea floor and may release greenhouse gases. We report on the transition of terrestrial to submarine permafrost at a site where the timing of inundation can be inferred from the rate of coastline retreat. On Muostakh Island in the central Laptev Sea, East Siberia, changes in annual coastline position have been measured for decades and vary highly spatially. We hypothesize that these rates are inversely related to the inclination of the upper surface of submarine ice-bonded permafrost (IBP) based on the consequent duration of inundation with increasing distance from the shoreline. We compared rapidly eroding and stable coastal sections of Muostakh Island and find permafrost-table inclinations, determined using direct current resistivity, of 1 and 5 %, respectively. Determinations of submarine IBP depth from a drilling transect in the early 1980s were compared to resistivity profiles from 2011. Based on borehole observations, the thickness of unfrozen sediment overlying the IBP increased from 0 to 14m below sea level with increasing distance from the shoreline. The geoelectrical profiles showed thickening of the unfrozen sediment overlying ice-bonded permafrost over the 28 years since drilling took place. We use geoelectrical estimates of IBP depth to estimate permafrost degradation rates since inundation. Degradation rates decreased from over 0.4ma-1 following inundation to around 0.1ma-1 at the latest after 60 to 110 years and remained constant at this level as the duration of inundation increased to 250 years. We suggest that long-term rates are lower than these values, as the depth to the IBP increases and thermal and porewater solute concentration gradients over depth decrease. For the study region, recent increases in coastal erosion rate and changes in benthic temperature and salinity regimes are expected to affect the depth to submarine permafrost, leading to coastal regions with shallower IBP.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 2
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    Stable isotope signatures of Holocene syngenetic permafrost trace seabird presence in the Thule District (NW Greenland) (2019)
    Copernicus
    In:  EPIC3Biogeosciences, Copernicus, 16(21), pp. 4261-4275, ISSN: 1726-4170
    Details
    Publication Date: 2023-07-05
    Description: Holocene permafrost from ice wedge polygons in the vicinity of large seabird breeding colonies in the Thule District, NW Greenland, was drilled to explore the relation between permafrost aggradation and seabird presence. The latter is reliant on the presence of the North Water Polynya (NOW) in the northern Baffin Bay. The onset of peat accumulation associated with the arrival of little auks (Alle alle) in a breeding colony at Annikitisoq, north of Cape York, is radiocarbon-dated to 4400 cal BP. A thick-billed murre (Uria lomvia) colony on Appat (Saunders Island) in the mouth of the Wolstenholme Fjord started 5650 cal BP. Both species provide marine-derived nutrients (MDNs) that fertilize vegetation and promote peat growth. The geochemical signature of organic matter left by the birds is traceable in the frozen Holocene peat. The peat accumulation rates at both sites are highest after the onset, decrease over time, and were about 2-times faster at the little auk site than at the thick-billed murre site. High accumulation rates induce shorter periods of organic matter (OM) decomposition before it enters the perennially frozen state. This is seen in comparably high C=N ratios and less depleted 13C, pointing to a lower degree of OM decomposition at the little auk site, while the opposite pattern can be discerned at the thick-billed murre site. Peat accumulation rates correspond to 15N trends, where decreasing accumulation led to increasing depletion in 15N as seen in the little-auk-related data. In contrast, the more decomposed OM of the thick-billed murre site shows almost stable 15N. Late Holocene wedge ice fed by cold season precipitation was studied at the little auk site and provides the first stable-water isotopic record from Greenland with mean 18O of 8:00:8, mean D of 36:25:7, mean d excess of 7:70:7, and a 18O-D slope of 7.27, which is close to those of the modern Thule meteoric water line. The syngenetic ice wedge polygon development is mirrored in testacean records of the little auk site and delineates polygon low-center, dry-out, and polygon-high-center stages. The syngenetic permafrost formation directly depending on peat growth (controlled by bird activity) falls within the period of neoglacial cooling and the establishment of the NOW, thus indirectly following the Holocene climate trends.
    Repository Name: EPIC Alfred Wegener Institut
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  • 3
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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
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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
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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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    Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis (2016)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 4 (2016): 16, doi:10.1186/s40168-016-0161-6.
    Description: The epidemiology of bacterial vaginosis (BV) suggests it is sexually transmissible, yet no transmissible agent has been identified. It is probable that BV-associated bacterial communities are transferred from male to female partners during intercourse; however, the microbiota of sexual partners has not been well-studied. Pyrosequencing analysis of PCR-amplified 16S rDNA was used to examine BV-associated bacteria in monogamous couples with and without BV using vaginal, male urethral, and penile skin specimens. The penile skin and urethral microbiota of male partners of women with BV was significantly more similar to the vaginal microbiota of their female partner compared to the vaginal microbiota of non-partner women with BV. This was not the case for male partners of women with normal vaginal microbiota. Specific BV-associated species were concordant in women with BV and their male partners. In monogamous heterosexual couples in which the woman has BV, the significantly higher similarity between the vaginal microbiota and the penile skin and urethral microbiota of the male partner, supports the hypothesis that sexual exchange of BV-associated bacterial taxa is common.
    Description: This work was supported by National Institute of Health Grant R01 AI079071-01A1.
    Keywords: Bacterial vaginosis ; Microbiome ; Sexual transmission ; Penile skin ; Urethra ; Vagina
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  • 7
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    Erratum to: Merging scleractinian genera: the overwhelming genetic similarity between solitary Desmophyllum and colonial Lophelia (2016)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 16 (2016): 149, doi:10.1186/s12862-016-0703-3.
    Description: As a result of vendor errors being introduced during processing, the original version of this article was published with some duplication errors in Table 1.
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Transcriptome of the Caribbean stony coral Porites astreoides from three developmental stages (2016)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 5 (2016): 33, doi:10.1186/s13742-016-0138-1.
    Description: Porites astreoides is a ubiquitous species of coral on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most other coral species. We assembled and annotated a transcriptome from this coral using Illumina sequences from three different developmental stages collected over several years: free-swimming larvae, newly settled larvae, and adults (〉10 cm in diameter). This resource will aid understanding of coral calcification, larval settlement, and host–symbiont interactions. A de novo transcriptome for the P. astreoides holobiont (coral plus algal symbiont) was assembled using 594 Mbp of raw Illumina sequencing data generated from five age-specific cDNA libraries. The new transcriptome consists of 867 255 transcript elements with an average length of 685 bases. The isolated P. astreoides assembly consists of 129 718 transcript elements with an average length of 811 bases, and the isolated Symbiodinium sp. assembly had 186 177 transcript elements with an average length of 1105 bases. This contribution to coral transcriptome data provides a valuable resource for researchers studying the ontogeny of gene expression patterns within both the coral and its dinoflagellate symbiont.
    Description: Bioinformatic analysis was performed in part on computing resources at the University of Puerto Rico (UPR) Puerto Rico Center for Environmental Neuroscience (PRCEN)’s High Performance Computing Facility, which is supported by: Institutional Development Award Networks of Biomedical Research Excellent (INBRE) grant P20GM103475 from the National Institute of General Medical Sciences, National Institutes of Health; the Institute for Functional Nanomaterials (IFN) award from the Experimental Program to Stimulate Competitive Research (EPSCoR) Track 1 program of the National Science Foundation (NSF); and EPSCoR Track 2 awards for computational nanoscience (EPS 1002410, EPS 1010094). Funding and support of the research was provided by PRCEN thanks to an NSF Centers of Research Excellent in Science and Technology (CREST) award, number HRD-1137725.
    Keywords: Porites astreoides ; Calcification ; Biomineralization ; Coral ; Symbiodinium ; Dinoflagellate ; Zooxanthellae ; Symbiosis ; Swimming larvae ; Larval settlement
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  • 9
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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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  • 10
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    Simulating social-ecological systems : the Island Digital Ecosystem Avatars (IDEA) consortium (2016)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 5 (2016): 14, doi:10.1186/s13742-016-0118-5.
    Description: Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine–terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions.
    Description: Work was supported in part by: the Institute of Theoretical Physics and the Pauli Center at ETH Zurich; the US National Science Foundation (NSF Moorea Coral Reef Long Term Ecological Research Site, OCE-1236905; Socio-Ecosystem Dynamics of Natural-Human Networks on Model Islands, CNH-1313830; Coastal SEES: Adaptive Capacity, Resilience, and Coral Reef State Shifts in Social-ecological Systems, OCE-1325652, OCE-1325554); the Gordon and Betty Moore Foundation (Berkeley Initiative in Global Change Biology; Genomic Standards Consortium); Courtney Ross and the Ross Institute; UC Berkeley Vice Chancellor for Research; CRIOBE; and the France Berkeley Fund (FBF 2014-0015).
    Keywords: Computational ecology ; Biodiversity ; Genomics ; Biocode ; Earth observations ; Social-ecological system ; Ecosystem dynamics ; Climate change scenarios ; Predictive modeling
    Repository Name: Woods Hole Open Access Server
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