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Discrete data on hydrography (from CTD casts) and chemical analyses of dissolved nutrients and organic carbon on the Louisiana-Texas shelf in the Gulf of Mexico from R/V Pelican cruise 28 September – 11 October 2017
No full textDataset: Discrete Samples Oct 2017Discrete data on hydrography (from CTD casts) and chemical analyses of dissolved nutrients and organic carbon on the Louisiana-Texas shelf in the Gulf of Mexico from R/V Pelican cruise 28 September – 11 October 2017.
For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/844721NSF Division of Ocean Sciences (NSF OCE) OCE-176068
Impacts of coastal infrastructure on shoreline response to major hurricanes in southwest Louisiana
Get PDF© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cadigan, J., Bekkaye, J., Jafari, N., Zhu, L., Booth, A., Chen, Q., Raubenheimer, B., Harris, B., O’Connor, C., Lane, R., Kemp, G., Day, J., Day, J., & Ulloa, H. Impacts of coastal infrastructure on shoreline response to major hurricanes in southwest Louisiana. Frontiers in Built Environment, 8, (2022): 885215. https://doi.org/10.3389/fbuil.2022.885215.The Rockefeller Wildlife Refuge, located along the Chenier Plain in Southwest Louisiana, was the location of the sequential landfall of two major hurricanes in the 2020 hurricane season. To protect the rapidly retreating coastline along the Refuge, a system of breakwaters was constructed, which was partially completed by the 2020 hurricane season. Multi-institutional, multi-disciplinary rapid response deployments of wave gauges, piezometers, geotechnical measurements, vegetation sampling, and drone surveys were conducted before and after Hurricanes Laura and Delta along two transects in the Refuge; one protected by a breakwater system and one which was the natural, unprotected shoreline. Geomorphological changes were similar on both transects after Hurricane Laura, while after Delta there was higher inland sediment deposition on the natural shoreline. Floodwaters drained from the transect with breakwater protection more slowly than the natural shoreline, though topography profiles are similar, indicating a potential dampening or complex hydrodynamic interactions between the sediment—wetland—breakwater system. In addition, observations of a fluidized mud deposit in Rollover Bayou in the Refuge are presented and discussed in context of the maintenance of wetland elevation and stability in the sediment starved Chenier Plain.Funding for the study has been partially provided by the National Science Foundation through grants NSF 2139882, 2139883, 1829136, 1848650, and 1939275, as well as through the United States Army Corps of Engineers Regional Sediment Management program. Student support provided through the National Science Foundation Graduate Research Fellowship Program and the Louisiana Coastal Science Assistantship Program
Endogenous retroviruses augment amphibian (Xenopus laevis) tadpole antiviral protection
No full textAuthor Posting. © American Society for Microbiology , 2022. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Kalia, N., Hauser, K., Burton, S., Hossainey, M., Zelle, M., Horb, M., & Grayfer, L. Endogenous retroviruses augment amphibian (Xenopus laevis) tadpole antiviral protection. Journal of Virology, 96(11), (2022): e00634-22, https://doi.org/10.1128/jvi.00634-22.The global amphibian declines are compounded by infections with members of the Ranavirus genus such as Frog Virus 3 (FV3). Premetamorphic anuran amphibians are believed to be significantly more susceptible to FV3 while this pathogen targets the kidneys of both pre- and postmetamorphic animals. Paradoxically, FV3-challenged Xenopus laevis tadpoles exhibit lower kidney viral loads than adult frogs. Presently, we demonstrate that X. laevis tadpoles are intrinsically more resistant to FV3 kidney infections than cohort-matched metamorphic and postmetamorphic froglets and that this resistance appears to be epigenetically conferred by endogenous retroviruses (ERVs). Using a X. laevis kidney-derived cell line, we show that enhancing ERV gene expression activates cellular double-stranded RNA-sensing pathways, resulting in elevated mRNA levels of antiviral interferon (IFN) cytokines and thus greater anti-FV3 protection. Finally, our results indicate that large esterase-positive myeloid-lineage cells, rather than renal cells, are responsible for the elevated ERV/IFN axis seen in the tadpole kidneys. This conclusion is supported by our observation that CRISPR-Cas9 ablation of colony-stimulating factor-3 results in abolished homing of these myeloid cells to tadpole kidneys, concurrent with significantly abolished tadpole kidney expression of both ERVs and IFNs. We believe that the manuscript marks an important step forward in understanding the mechanisms controlling amphibian antiviral defenses and thus susceptibility and resistance to pathogens like FV3.This work was supported by grants from NSF-IOS 1749427 to L.G. and NIH R24OD030008 and P40OD010997 to M.E.H.2022-11-1
Eight-page manuscript list of Albatross salinities
No full textAlbatross salinities, see MC20-1.1.11. Date inferred from cover letter
Two-page typescript letter from Edward P. Rankin to the commissioner of the Bureau of Fisheries
No full textCover letter accompanying a detailed description of haddock experiments perfomed on the Albatross in spring, 1920. See item MC20-1.1.
Two-page typescript report on the haddock egg experiments.
No full textDetailed description of haddock experiments performed on the Albatross in spring, 1920. See item MC20-1.1.
Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain
Get PDF© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Petrosino, G., Ponte, G., Volpe, M., Zarrella, I., Ansaloni, F., Langella, C., Di Cristina, G., Finaurini, S., Russo, M., Basu, S., Musacchia, F., Ristoratore, F., Pavlinic, D., Benes, V., Ferrante, M., Albertin, C., Simakov, O., Gustincich, S., Fiorito, G., & Sanges, R. Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain. BMC Biology, 20(1) (2022): 116, https://doi.org/10.1186/s12915-022-01303-5.Background
Transposable elements (TEs) widely contribute to the evolution of genomes allowing genomic innovations, generating germinal and somatic heterogeneity, and giving birth to long non-coding RNAs (lncRNAs). These features have been associated to the evolution, functioning, and complexity of the nervous system at such a level that somatic retrotransposition of long interspersed element (LINE) L1 has been proposed to be associated to human cognition. Among invertebrates, octopuses are fascinating animals whose nervous system reaches a high level of complexity achieving sophisticated cognitive abilities. The sequencing of the genome of the Octopus bimaculoides revealed a striking expansion of TEs which were proposed to have contributed to the evolution of its complex nervous system. We recently found a similar expansion also in the genome of Octopus vulgaris. However, a specific search for the existence and the transcription of full-length transpositionally competent TEs has not been performed in this genus.
Results
Here, we report the identification of LINE elements competent for retrotransposition in Octopus vulgaris and Octopus bimaculoides and show evidence suggesting that they might be transcribed and determine germline and somatic polymorphisms especially in the brain. Transcription and translation measured for one of these elements resulted in specific signals in neurons belonging to areas associated with behavioral plasticity. We also report the transcription of thousands of lncRNAs and the pervasive inclusion of TE fragments in the transcriptomes of both Octopus species, further testifying the crucial activity of TEs in the evolution of the octopus genomes.
Conclusions
The neural transcriptome of the octopus shows the transcription of thousands of putative lncRNAs and of a full-length LINE element belonging to the RTE class. We speculate that a convergent evolutionary process involving retrotransposons activity in the brain has been important for the evolution of sophisticated cognitive abilities in this genus.The work has been supported by Progetto Premiale MolEcOC (Italian Ministry of Education, University and Research, MIUR), Flagship project RITMARE (MIUR and Stazione Zoologica), and BIOforIU PON Project (MIUR and European Regional Development Fund, FESR). Giuseppe Petrosino, Swaraj Basu, Massimiliano Volpe, and Giulia Di Cristina have been supported by a SZN PhD fellowship
NCBI accession numbers describing nifH amplicon sequences from sediment samples collected offshore of San Francisco, Califronia, USA in March 2017 on R/V Oceanus cruise OC1703A
No full textDataset: OC1703A Sediment nifH amplicon sequencesThese data are raw, demultiplexed nifH amplicon sequences generated from Illumina MiSeq for the investigation of potential diazotroph diversity along a continental margin transect. Raw Illumina MiSeq 2×250 bp sequence data can be accessed in the NCBI SRA database under accession numbers ERP130242 and ERP120468 and BioProject accession numbers PRJEB46054 and PRJEB37167. Data under accession number ERP120468 and BioProject accession number PRJEB37167 were published in Kapili and Dekas, 2021. The generation of these data was completed on June 29, 2021.
For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/863192NSF Division of Ocean Sciences (NSF OCE) OCE-163429
Detection and characterization of coastal tidal wetland change in the northeastern US using Landsat time series
Get PDF© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Yang, X., Zhu, Z., Qiu, S., Kroeger, K. D., Zhu, Z., & Covington, S. Detection and characterization of coastal tidal wetland change in the northeastern US using Landsat time series. Remote Sensing of Environment, 276, (2022): 113047, https://doi.org/10.1016/j.rse.2022.113047.Coastal tidal wetlands are highly altered ecosystems exposed to substantial risk due to widespread and frequent land-use change coupled with sea-level rise, leading to disrupted hydrologic and ecologic functions and ultimately, significant reduction in climate resiliency. Knowing where and when the changes have occurred, and the nature of those changes, is important for coastal communities and natural resource management. Large-scale mapping of coastal tidal wetland changes is extremely difficult due to their inherent dynamic nature. To bridge this gap, we developed an automated algorithm for DEtection and Characterization of cOastal tiDal wEtlands change (DECODE) using dense Landsat time series. DECODE consists of three elements, including spectral break detection, land cover classification and change characterization. DECODE assembles all available Landsat observations and introduces a water level regressor for each pixel to flag the spectral breaks and estimate harmonic time-series models for the divided temporal segments. Each temporal segment is classified (e.g., vegetated wetlands, open water, and others – including unvegetated areas and uplands) based on the phenological characteristics and the synthetic surface reflectance values calculated from the harmonic model coefficients, as well as a generic rule-based classification system. This harmonic model-based approach has the advantage of not needing the acquisition of satellite images at optimal conditions (i.e., low tide status) to avoid underestimating coastal vegetation caused by the tidal fluctuation. At the same time, DECODE can also characterize different kinds of changes including land cover change and condition change (i.e., land cover modification without conversion). We used DECODE to track status of coastal tidal wetlands in the northeastern United States from 1986 to 2020. The overall accuracy of land cover classification and change detection is approximately 95.8% and 99.8%, respectively. The vegetated wetlands and open water were mapped with user's accuracy of 94.6% and 99.0%, and producer's accuracy of 98.1% and 93.5%, respectively. The cover change and condition change were mapped with user's accuracy of 68.0% and 80.0%, and producer's accuracy of 80.5% and 97.1%, respectively. Approximately 3283 km2 of the coastal landscape within our study area in the northeastern United States changed at least once (12% of the study area), and condition changes were the dominant change type (84.3%). Vegetated coastal tidal wetland decreased consistently (~2.6 km2 per year) in the past 35 years, largely due to conversion to open water in the context of sea-level rise.This study was supported by USGS North Atlantic Coast Cooperative Ecosystem Studies Unit (CESU) Program for Detection and Characterization of Coastal Tidal Wetland Change (G19AC00354)
Pool-seq data from laboratory selection lines of copepods collected from Kiel Canal in Germany in 2017 and 2018
No full textDataset: Evolve and re-sequence experiment - laboratory selection linesThis dataset represents pool-seq data from laboratory selection lines of E. affinis collected from Kiel Canal in Kiel, Germany (latitude = 54° 19' 59.88"N, longitude = 10° 9' 0"W) in 2017 (approximately 1000 copepods) and on May 30, 2018 (85 gravid females and 40 juveniles). Individual copepods (ranging from 50 to 200 in number) were pooled and their DNA was extracted. Paired-end whole-genome sequencing libraries were prepared using the Illumina Nextera DNA kit (Illumina, Inc.) and sequenced on five lanes of an Illumina HiSeq 4000 sequencer, generating an average of approximately 176 million paired-end (100 bp) reads per pool. These data have been deposited in NCBI under BioProject number PRJNA844002.
For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/878335NSF Division of Ocean Sciences (NSF OCE) OCE-165851