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The following results are related to European Marine Science. Are you interested to view more results? Visit OpenAIRE - Explore.

  • European Marine Science
  • 2014-2023
  • Open Access
  • Research data
  • Other research products
  • EU
  • CA
  • English

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: De Luca, Daniele; Bellardini, Daniele; Calicchio, Rosalia; Dattolo, Emanuela; +3 Authors

    This dataset includes the annotated metabarcoding Amplicon Sequence Variants (ASVs) resulting from the analysis of environmental DNA (eDNA) collected as water samples in the area of Marina di Camerota (Campania region, Italy) and filtered in loco by citizens. The first sheet includes sequence information, relative abundance and taxonomic annotation of the organisms identified using the hypervariable region V4 of the nuclear 18S rRNA; the second sheet includes the same information but for organisms (metazoans) identified using a fragment of the mitochondrial COI gene. Data were sequenced at the Sequencing facility of the SZN (RIMAR Dept.) using the GeneStudio S5 and processed through the dada2 pipeline. The dataset was produced during the Citizen Science Initiative Integrating biodiversity monitoring and awareness-raising in coastal peripheries, by engaging citizen-science sailors as focal nodes in the process of local community empowerment (Acronym: BIOMARCS; Nickname: Reknotting Marine Biodiversity) funded by the European project IMPETUS (https://impetus4cs.eu/; Grant agreement ID: 101058677; DOI: 10.3030/101058677). IMPETUS is funded by the European Union's Horizon Europe research and innovation programme under grant agreement number 101058677. Views and opinions expressed are, however, those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Executive Agency (REA). Neither the European Union nor the granting authority can be held responsible for them.

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    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: Datacite
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      ZENODO
      Dataset . 2023
      License: CC BY
      Data sources: ZENODO
      ZENODO
      Dataset . 2023
      License: CC BY
      Data sources: Datacite
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    Authors: Prokkola, Jenni; Aykanat, Tutku;

    Folder with two datasets of enzyme activities (CS and LDH) with associated details of fish, incuding genotypes, body size, and metabolic rates, and R codes for linear mixed models as described in the manuscript Prokkola et al (submitted 2023). See README file for more information.

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    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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      ZENODO
      Dataset . 2023
      License: CC BY
      Data sources: ZENODO
      ZENODO
      Dataset . 2023
      License: CC BY
      Data sources: Datacite
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    Authors: Breton, Sophie;

    HeLa cells (n=3 replicates) were washed with PBS and harvested in a lysing buffer containing 10 mM HEPES, 150 mM NaCl and a cocktail of protease inhibitors (benzamidine, PMSF, aprotinin and leupeptin). Cells were then lysed with a sonic dismembrator sonicator (Fisher) 3 times for 30 seconds before adding 100 µl of Triton X-100 10%. Cell lysates were incubated on ice for 20 minutes and then centrifuged for 15 minutes at 15000 RPM at 4˚C. The supernatant was kept. 20 µl of protein A agarose was added to 1 ml of samples and incubated at 4˚C for 1 hour. Samples were then centrifuged at 15000 rpm for 1 minute at 4˚C and the supernatant was kept. 20 µl of rabbit anti-MTALTND4 antibody and 20 µl of protein A agarose were added to the samples before incubating at 4˚C overnight. 20 µl of rabbit pre-immune serum was used as control. Samples were washed 6 times with lysing buffer. Samples were then sent to the proteomics platform of the McGill University Health Center (MUHC) Research Institute for mass spectrometry analysis. Samples were loaded onto a single stacking gel band to remove lipids, detergents and salts. The single gel band containing all proteins was reduced with DTT, alkylated with iodoacetic acid and digested with trypsin. 2 µg of extracted peptides were re-solubilized in 0.1% aqueous formic acid and loaded onto a Thermo Acclaim Pepmap (Thermo, 75µM ID X 2 cm C18 3 µM beads) precolumn and then onto an Acclaim Pepmap Easyspray (Thermo, 75 µM X 15 cm with 2 µM C18 beads) analytical column separation using a Dionex Ultimate 3000 uHPLC at 250 nl·min-1 with a gradient of 2–35% organic (0.1% formic acid in acetonitrile) over 3 hours. Peptides were analyzed using a Thermo Orbitrap Fusion mass spectrometer operating at 120,000 resolutions (FWHM in MS1) with HCD sequencing (15,000 resolution) at top speed for all peptides with a charge of 2+ or greater. The raw data were converted into *.mgf format (Mascot generic format) for searching using the Mascot 2.6.2 search engine (Matrix Science) against Human Uniprot sequences (2022). The database search results were loaded onto Scaffold Q+ Scaffold_4.9.0 (Proteome Sciences) for statistical treatment and data visualization (Table S4). Background: Mitochondria have a central role in cellular functions, aging and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties. This is radically different from bacterial genomes, which are also circular but much larger, and in which we can find genes inside other genes. These sequences, different from the reference coding sequences, are called alternative open reading frames or altORFs, and they are involved in key biological functions. However, whether altORFs exist in mitochondrial protein-coding genes or elsewhere in the human mitogenome has not been fully addressed. Results: We found a downstream alternative ATG initiation codon in the +3 reading frame of the human mitochondrial nd4 gene. This newly characterized altORF encodes a 99-amino acids long polypeptide, MTALTND4, which is conserved in primates. Our custom antibody, but not the pre-immune serum, was able to immunoprecipitate MTALTND4 from HeLa cell lysates, confirming the existence of an endogenous MTALTND4 peptide. The protein is localized in mitochondria and cytoplasm and is also found in the plasma, and it impacts cell and mitochondrial physiology. Conclusions: Many human-mitochondrial-translated ORFs might have so far gone unnoticed. By ignoring mtaltORFs, we have underestimated the coding potential of the mitogenome. Alternative mitochondrial peptides such as MTALTND4 may offer a new framework for the investigation of mitochondrial functions and diseases.

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    DRYAD; ZENODO
    Dataset . 2023
    License: CC 0
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      DRYAD; ZENODO
      Dataset . 2023
      License: CC 0
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    Authors: Kramer, Lena; Schulze, Tobias; Klüver, Nils; Altenburger, Rolf; +3 Authors

    Chemicals in the aquatic environment can be harmful to organisms and ecosystems. Knowledge on effect concentrations as well as on mechanisms and modes of interaction with biological molecules and signaling pathways is necessary to perform chemical risk assessment and identify toxic compounds. To this end, we developed criteria and a pipeline for harvesting and summarizing effect concentrations from the US ECOTOX database for the three aquatic species groups algae, crustaceans, and fish and researched the modes of action of more than 3,300 environmentally relevant chemicals in literature and databases. We provide a curated dataset ready to be used for risk assessment based on monitoring data and the first comprehensive collection and categorization of modes of action of environmental chemicals. Authorities, regulators, and scientists can use this data for the grouping of chemicals, the establishment of meaningful assessment groups, and the development of in vitro and in silico approaches for chemical testing and assessment.

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    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Dataset . 2023
    Data sources: Datacite
    ZENODO
    Dataset . 2023
    Data sources: ZENODO
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      ZENODO
      Dataset . 2023
      License: CC BY
      Data sources: ZENODO
      ZENODO
      Dataset . 2023
      Data sources: Datacite
      ZENODO
      Dataset . 2023
      Data sources: ZENODO
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    Authors: Düsedau, Luisa; Frediksen, Stein; Brand, Markus; Fischer, Philipp; +4 Authors

    Macroalgal surveys were performed at Hansneset, Blomstrand in Kongsfjorden, Svalbard, from the infralittoral fringe down to 15 m depth in June – August 2021. This dataset is part of a time series currently spanning over 25 years and complements the studies conducted in 1996/98 (Hop et al., 2012) and 2012-14 (Bartsch et al., 2016). The aim was to document changes in Arctic kelp forest dynamics in an Arctic fjord system influenced by glacial melt by repeatedly sampling the same site in a standardized manner. As ocean temperatures in the Arctic have risen substantially and underwater light climate continuously deteriorated over this time period, alterations were observed in the seaweed community, especially kelps as major coastal foundation species. This Zenodo upload contains all datasets supporting the findings of the manuscript Düsedau et al. (2023) "Arctic kelp forest decline - a consequence of melting glaciers?".

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: Datacite
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      ZENODO
      Dataset . 2023
      License: CC BY
      Data sources: ZENODO
      ZENODO
      Dataset . 2023
      License: CC BY
      Data sources: Datacite
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    Authors: Francesco Papi; Robert Behrens de Luna; Joseph Saverin; David Marten; +4 Authors

    In work package 2 of FLOATECH a detailed validation and verification of the capabilities of QBlade-Ocean was performed. Thereby, three wind turbine models mounted on floating substructures with differing characteristics serve as the means for the validation.This dataset contains Floating Offshore Wind Turbine (FOWT) calculations in various design situations, computed with three different codes. In more detail, three floating platform archetypes are used in the code-to-code comparison ongoing in work package 2: a semi-submersible-type floater and a spar-type floater as well as the Hexafloat® concept recently proposed by Saipem®. The three test-cases are the NREL 5MW RWT mounted on the DeepCwind semi-submersible platform, the DTU 10MW RWT mounted on the SOFTWIND spar-type platform and the DTU 10MW RWT mounted on the Hexafloat® platform. More details regarding the dataset structure and the testcases can be found in the accompanying document. Changelog: Version 5.0.0 Changed structural damping ratio (increased) in OpenFAST results (SOFTWIND and Hexafloat models) to match structural damping ratios in QBlade Added wave time series at platform undisplaced position Added TurbSim input files for wind field generation. TurbSim v2.0.0 (https://www.nrel.gov/wind/nwtc/turbsim.html - National Renewable Energy Laboratory) Added detailed DLC and simulation information in "DLC&SimulationList.xlsx" Version 4.0.0 Correction of bugs in QB 5MWOC4 and 10MWSOFT models: wind shear exponent in wind fields (0.11 -> 0.14) Update of hydrodynamic database used in OpenFAST and QBlade results of 10MWSOFT model Data in version 5.0.0 is used in WES publication: Papi, F., Troise, G., Behrens de Luna, R., Saverin, J., Perez-Becker, S., Marten, D., Ducasse, M.-L., and Bianchini, A.: A Code-to-Code Comparison for Floating Offshore Wind Turbine Simulation in Realistic Environmental Conditions: Quantifying the Impact of Modeling Fidelity on Different Substructure Concepts, Wind Energ. Sci. Discuss. [preprint], https://doi.org/10.5194/wes-2023-107, in review, 2023.

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    ZENODO
    Dataset . 2022
    License: CC BY
    Data sources: ZENODO
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    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: ZENODO
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    ZENODO
    Dataset . 2022
    License: CC BY
    Data sources: ZENODO
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    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: ZENODO
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    ZENODO
    Dataset . 2022
    License: CC BY
    Data sources: ZENODO
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    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: ZENODO
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    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: Datacite
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    Authors: Pensieri Sara; Bozzano Roberto;

    Time series data of physical oceanography (salinity, temperature) and meteorology (atmospheric pressure, wind speed and direction, air temperature and humidity, shortwave radiation, longwave radiation and rain) collected from October 2020 to July 2021 by observatory W1M3A at 1h interval. The file contains tabular data (tab delimited) with the following columns: Day; Month; Year; UTC Hour; Minute ; Longitude [deg]; Latitude [deg]; Atmospheric Pressure [hPa]; Wind speed [m/s]; Wind direction [deg]; Air Temperature [°C]; Relative air humidity [%]; Short wave Radiation [W/m2]; Long wave radiation [W/m2]; Rainfall [mm/h]; Sea temperature @ 6 m [°C]; Sea temperature @ 20 m [°C]; Sea temperature @ 36 m [°C]; Salinity @ 6 m [psu]; Salinity @ 20 m [psu], Salinity @ 36 m [psu].

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    ZENODO
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    ZENODO
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    Authors: Audh, Riesna R.; Burger, Jessica; Collins, Dayna; Deary, Amelia; +3 Authors

    This dataset provides an overview of data produced during South African voyages in the Southern Ocean aboard the R/V S.A. Agulhas II and contains a document detailing the data that are presented (AvailableData.pdf) and an .xlsx file that contains the metadata and links to the published datasets (AvailableData.xlsx). Each voyage has a dedicated sheet within the .xlsx file. This dataset will be updated, and a new version published as more data becomes available. Please refer to the most recent version on https://zenodo.org/communities/scale_south_africa/ This is a data curation document only. Any use of the data mentioned in this document should reference the original dataset and authors.

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    Authors: Pensieri Sara; Bozzano Roberto;

    Time series data of physical oceanography (salinity, temperature) and meteorology (atmospheric pressure, wind speed and direction, air temperature and humidity, shortwave radiation, longwave radiation and rain) collected from July 2021 to April 2022 by observatory W1M3A at 1h interval. The file contains tabular data (tab delimited) with the following columns: Day; Month; Year; UTC Hour; Minute ; Longitude [deg]; Latitude [deg]; Atmospheric Pressure [hPa]; Wind speed [m/s]; Wind direction [deg]; Air Temperature [°C]; Relative air humidity [%]; Short wave Radiation [W/m2]; Long wave radiation [W/m2]; Rainfall [mm/h]; Sea temperature @ 6 m [°C]; Sea temperature @ 20 m [°C]; Sea temperature @ 36 m [°C]; Salinity @ 6 m [psu]; Salinity @ 20 m [psu], Salinity @ 36 m [psu].

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    ZENODO
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    Authors: Pensieri Sara; Bozzano Roberto;

    Time series data of physical oceanography (salinity, temperature) and meteorology (atmospheric pressure, wind speed and direction, air temperature and humidity, shortwave radiation, longwave radiation and rain) collected from March 2015 to December 2015 by observatory W1M3A at 1h interval. The file contains tabular data (tab delimited) with the following columns: Day; Month; Year; UTC Hour; Minute ; Longitude [deg]; Latitude [deg]; Atmospheric Pressure [hPa]; Wind speed [m/s]; Wind direction [deg]; Air Temperature [°C]; Relative air humidity [%]; Short wave Radiation [W/m2]; Long wave radiation [W/m2]; Rainfall [mm/h]; Sea temperature @ 6 m [°C]; Sea temperature @ 20 m [°C]; Sea temperature @ 36 m [°C]; Salinity @ 6 m [psu]; Salinity @ 20 m [psu], Salinity @ 36 m [psu]. {"references": ["P. Picco, M.E. Schiano, S. Incardone, L.Repetti, M. Demarte, S. Pensieri, R. Bozzano. Detection and Characterization of Meteotsunamis in the Gulf of Genoa. J. Mar. Sci. Eng. 2019, 7(8), 275; https://doi.org/10.3390/jmse7080275"]} The data acquisition was partially supported by the Italian project RITMARE- COFUND BANDIERA ("Best Action for National Development of International Expert Researchers Activities")

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    ZENODO
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: De Luca, Daniele; Bellardini, Daniele; Calicchio, Rosalia; Dattolo, Emanuela; +3 Authors

    This dataset includes the annotated metabarcoding Amplicon Sequence Variants (ASVs) resulting from the analysis of environmental DNA (eDNA) collected as water samples in the area of Marina di Camerota (Campania region, Italy) and filtered in loco by citizens. The first sheet includes sequence information, relative abundance and taxonomic annotation of the organisms identified using the hypervariable region V4 of the nuclear 18S rRNA; the second sheet includes the same information but for organisms (metazoans) identified using a fragment of the mitochondrial COI gene. Data were sequenced at the Sequencing facility of the SZN (RIMAR Dept.) using the GeneStudio S5 and processed through the dada2 pipeline. The dataset was produced during the Citizen Science Initiative Integrating biodiversity monitoring and awareness-raising in coastal peripheries, by engaging citizen-science sailors as focal nodes in the process of local community empowerment (Acronym: BIOMARCS; Nickname: Reknotting Marine Biodiversity) funded by the European project IMPETUS (https://impetus4cs.eu/; Grant agreement ID: 101058677; DOI: 10.3030/101058677). IMPETUS is funded by the European Union's Horizon Europe research and innovation programme under grant agreement number 101058677. Views and opinions expressed are, however, those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Executive Agency (REA). Neither the European Union nor the granting authority can be held responsible for them.

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    ZENODO
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    Authors: Prokkola, Jenni; Aykanat, Tutku;

    Folder with two datasets of enzyme activities (CS and LDH) with associated details of fish, incuding genotypes, body size, and metabolic rates, and R codes for linear mixed models as described in the manuscript Prokkola et al (submitted 2023). See README file for more information.

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    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: Datacite
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      ZENODO
      Dataset . 2023
      License: CC BY
      Data sources: ZENODO
      ZENODO
      Dataset . 2023
      License: CC BY
      Data sources: Datacite
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    Authors: Breton, Sophie;

    HeLa cells (n=3 replicates) were washed with PBS and harvested in a lysing buffer containing 10 mM HEPES, 150 mM NaCl and a cocktail of protease inhibitors (benzamidine, PMSF, aprotinin and leupeptin). Cells were then lysed with a sonic dismembrator sonicator (Fisher) 3 times for 30 seconds before adding 100 µl of Triton X-100 10%. Cell lysates were incubated on ice for 20 minutes and then centrifuged for 15 minutes at 15000 RPM at 4˚C. The supernatant was kept. 20 µl of protein A agarose was added to 1 ml of samples and incubated at 4˚C for 1 hour. Samples were then centrifuged at 15000 rpm for 1 minute at 4˚C and the supernatant was kept. 20 µl of rabbit anti-MTALTND4 antibody and 20 µl of protein A agarose were added to the samples before incubating at 4˚C overnight. 20 µl of rabbit pre-immune serum was used as control. Samples were washed 6 times with lysing buffer. Samples were then sent to the proteomics platform of the McGill University Health Center (MUHC) Research Institute for mass spectrometry analysis. Samples were loaded onto a single stacking gel band to remove lipids, detergents and salts. The single gel band containing all proteins was reduced with DTT, alkylated with iodoacetic acid and digested with trypsin. 2 µg of extracted peptides were re-solubilized in 0.1% aqueous formic acid and loaded onto a Thermo Acclaim Pepmap (Thermo, 75µM ID X 2 cm C18 3 µM beads) precolumn and then onto an Acclaim Pepmap Easyspray (Thermo, 75 µM X 15 cm with 2 µM C18 beads) analytical column separation using a Dionex Ultimate 3000 uHPLC at 250 nl·min-1 with a gradient of 2–35% organic (0.1% formic acid in acetonitrile) over 3 hours. Peptides were analyzed using a Thermo Orbitrap Fusion mass spectrometer operating at 120,000 resolutions (FWHM in MS1) with HCD sequencing (15,000 resolution) at top speed for all peptides with a charge of 2+ or greater. The raw data were converted into *.mgf format (Mascot generic format) for searching using the Mascot 2.6.2 search engine (Matrix Science) against Human Uniprot sequences (2022). The database search results were loaded onto Scaffold Q+ Scaffold_4.9.0 (Proteome Sciences) for statistical treatment and data visualization (Table S4). Background: Mitochondria have a central role in cellular functions, aging and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties. This is radically different from bacterial genomes, which are also circular but much larger, and in which we can find genes inside other genes. These sequences, different from the reference coding sequences, are called alternative open reading frames or altORFs, and they are involved in key biological functions. However, whether altORFs exist in mitochondrial protein-coding genes or elsewhere in the human mitogenome has not been fully addressed. Results: We found a downstream alternative ATG initiation codon in the +3 reading frame of the human mitochondrial nd4 gene. This newly characterized altORF encodes a 99-amino acids long polypeptide, MTALTND4, which is conserved in primates. Our custom antibody, but not the pre-immune serum, was able to immunoprecipitate MTALTND4 from HeLa cell lysates, confirming the existence of an endogenous MTALTND4 peptide. The protein is localized in mitochondria and cytoplasm and is also found in the plasma, and it impacts cell and mitochondrial physiology. Conclusions: Many human-mitochondrial-translated ORFs might have so far gone unnoticed. By ignoring mtaltORFs, we have underestimated the coding potential of the mitogenome. Alternative mitochondrial peptides such as MTALTND4 may offer a new framework for the investigation of mitochondrial functions and diseases.

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    DRYAD; ZENODO
    Dataset . 2023
    License: CC 0
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      DRYAD; ZENODO
      Dataset . 2023
      License: CC 0
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    Authors: Kramer, Lena; Schulze, Tobias; Klüver, Nils; Altenburger, Rolf; +3 Authors