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  • Open Access English
    Authors: 
    Martina Červená; František Šťáhlavský; Vladimír Papáč; Ľubomír Kováč; Jana Christophoryová;
    Publisher: Pensoft Publishers

    A redescription is provided of the adult, tritonymph and deutonymph life stages of the troglobitic Neobisium (Blothrus) slovacum Gulička, 1977, which is known from Slovakia and Hungary. Material examined included 35 previously deposited museum specimens and 15 newly collected specimens. In addition, the karyotype and distribution of 18S rDNA clusters are described, using fluorescence in situ hybridization (FISH). The male karyotype ofN.slovacumcomprises 69 chromosomes, with a predominance of biarmed chromosomes, and an X0 sex chromosome system. Two pairs of signals for 18S rDNA on biarmed chromosomes (submetacentric and metacentric) of different sizes were identified. The present study provides the first information about the distribution of these clusters in the arachnid order Pseudoscorpiones. The geographic distribution of the species is summarized and mapped.Neobisiumslovacumis endemic to the Slovak and Aggtelek Karst area in southern Slovakia and north-western Hungary, where it has been recorded from 16 caves. One of these, Hačavská cave (in Slovakia), is the northernmost locality known for any species of the subgenus Blothrus.

  • Publication . Other literature type . Article . Preprint . 2017
    Open Access English
    Authors: 
    G. Laaha; T. Gauster; L. M. Tallaksen; J.-P. Vidal; K. Stahl; C. Prudhomme; C. Prudhomme; B. Heudorfer; R. Vlnas; R. Vlnas; +16 more
    Publisher: HAL CCSD
    Countries: Germany, France, Netherlands, Netherlands, United Kingdom

    Abstract. In 2015 large parts of Europe were affected by drought. In this paper, we analyze the hydrological footprint (dynamic development over space and time) of the drought of 2015 in terms of both severity (magnitude) and spatial extent and compare it to the extreme drought of 2003. Analyses are based on a range of low flow and hydrological drought indices derived for about 800 streamflow records across Europe, collected in a community effort based on a common protocol. We compare the hydrological footprints of both events with the meteorological footprints, in order to learn from similarities and differences of both perspectives and to draw conclusions for drought management. The region affected by hydrological drought in 2015 differed somewhat from the drought of 2003, with its center located more towards eastern Europe. In terms of low flow magnitude, a region surrounding the Czech Republic was the most affected, with summer low flows that exhibited return intervals of 100 years and more. In terms of deficit volumes, the geographical center of the event was in southern Germany, where the drought lasted a particularly long time. A detailed spatial and temporal assessment of the 2015 event showed that the particular behavior in these regions was partly a result of diverging wetness preconditions in the studied catchments. Extreme droughts emerged where preconditions were particularly dry. In regions with wet preconditions, low flow events developed later and tended to be less severe. For both the 2003 and 2015 events, the onset of the hydrological drought was well correlated with the lowest flow recorded during the event (low flow magnitude), pointing towards a potential for early warning of the severity of streamflow drought. Time series of monthly drought indices (both streamflow- and climate-based indices) showed that meteorological and hydrological events developed differently in space and time, both in terms of extent and severity (magnitude). These results emphasize that drought is a hazard which leaves different footprints on the various components of the water cycle at different spatial and temporal scales. The difference in the dynamic development of meteorological and hydrological drought also implies that impacts on various water-use sectors and river ecology cannot be informed by climate indices alone. Thus, an assessment of drought impacts on water resources requires hydrological data in addition to drought indices based solely on climate data. The transboundary scale of the event also suggests that additional efforts need to be undertaken to make timely pan-European hydrological assessments more operational in the future.

  • Open Access English
    Authors: 
    Kamil Hupało; Markus Majaneva; Molly Victoria Czachur; Lucas Sire; Daniel Marquina; Dario A Lijtmaer; Vladislav Ivanov; Sonja Leidenberger; Fedor Čiampor; Zuzana Čiamporová-Zaťovičová; +11 more
    Countries: Germany, Australia, Switzerland, France, Argentina, Norway, Norway, Germany, Sweden

    As global biodiversity declines, there is an increasing need to create an educated and engaged society. Having people of all ages participate in measuring biodiversity where they live helps to create awareness. Recently, the use of environmental DNA (eDNA) for biodiversity surveys has gained momentum. Here, we explore whether sampling eDNA and sequencing it can be used as a means of rapidly surveying urban biodiversity for educational purposes. We sampled 2 × 1 L of water from each of 15 locations in the city of Trondheim, Norway, including a variety of freshwater, marine, and brackish habitats. DNA was extracted, amplified in triplicate targeting the barcoding fragment of COI gene, and sequenced. The obtained data were analyzed on the novel mBRAVE platform, an online open-access software and computing resource. The water samples were collected in 2 days by two people, and the laboratory analysis was completed in 5 days by one person. Overall, we detected the presence of 506 BINs identified as belonging to 435 taxa, representing at least 265 putative species. On average, only 5.4% of the taxa were shared among six replicates per site. Based on the observed diversity, three distinct clusters were detected and related to the geographic distribution of sites. There were some taxa shared between the habitats, with a substantial presence of terrestrial biota. Here we propose a new form of BioBlitz, where with noninvasive sampling effort combined with swift processing and straightforward online analyses, hundreds of species can be detected. Thus, using eDNA analysis of water is useful for rapid biodiversity surveys and valuable for educational purposes. We show that rapid eDNA surveys, combined with openly available services and software, can be used as an educational tool to raise awareness about the importance of biodiversity. Environmental DNA, 3 (1) ISSN:2637-4943

  • Open Access English
    Authors: 
    David Bajnai; Jens Fiebig; Adam Tomašových; Sara Milner Garcia; Claire Rollion-Bard; Jacek Raddatz; Niklas Löffler; Cristina Primo-Ramos; Uwe Brand;
    Publisher: HAL CCSD
    Countries: France, Germany, France
    Project: EC | BASE-LiNE Earth (643084)

    AbstractBrachiopod shells are the most widely used geological archive for the reconstruction of the temperature and the oxygen isotope composition of Phanerozoic seawater. However, it is not conclusive whether brachiopods precipitate their shells in thermodynamic equilibrium. In this study, we investigated the potential impact of kinetic controls on the isotope composition of modern brachiopods by measuring the oxygen and clumped isotope compositions of their shells. Our results show that clumped and oxygen isotope compositions depart from thermodynamic equilibrium due to growth rate-induced kinetic effects. These departures are in line with incomplete hydration and hydroxylation of dissolved CO2. These findings imply that the determination of taxon-specific growth rates alongside clumped and bulk oxygen isotope analyses is essential to ensure accurate estimates of past ocean temperatures and seawater oxygen isotope compositions from brachiopods.

  • Open Access English
    Authors: 
    Klionsky, Daniel; Abdel-Aziz, Amal Kamal; Abdelfatah, Sara; Abdellatif, Mahmoud; Abdoli, Asghar; Abel, Steffen; Abeliovich, Hagai; Abildgaard, Marie; Abudu, Yakubu Princely; Acevedo-Arozena, Abraham; +760 more
    Publisher: HAL CCSD
    Countries: Netherlands, Croatia, Netherlands, Netherlands, Italy, Palestinian-administered areas, United Kingdom, France, Italy
    Project: EC | ENTRAPMENT (772853), EC | RobustSynapses (646671), EC | ChemBioAP (678899), EC | FIRM (819600)

    International audience; In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

  • Open Access English
    Authors: 
    Gordon H. Copp; Lorenzo Vilizzi; Hui Wei; Shan Li; Marina Piria; Abbas J. Al-Faisal; David Almeida; Usman Atique; Zainab Al-Wazzan; Rigers Bakiu; +66 more
    Countries: Russian Federation, Netherlands, France, Croatia

    Abstract Environmental changes due to non-native species introductions and translocations are a global concern. Whilst understanding the causes of bioinvasions is important, there is need for decision-support tools that facilitate effective communication of the potential risks of invasive non-native species to stakeholders. Decision-support tools have been developed mostly in English language only, which increases linguistic uncertainty associated with risk assessments undertaken by assessors not of English mother tongue and who need to communicate outcomes to local stakeholders. To reduce language-based uncertainty, the ‘ecology-of-language’ paradigm was applied when developing the Aquatic Species Invasiveness Screening Kit (AS-ISK), a decision-support tool that offers 32 languages in which to carry out screenings and communicate outcomes to stakeholders. Topics discussed include uncertainty related to language-specific issues encountered during the AS-ISK translation and the potential benefits of a multilingual decision-support tool for reducing linguistic uncertainty and enhancing communication between scientists, environmental managers, and policy and decision makers.

  • Open Access English
    Authors: 
    Lorenzo Vilizzi; Gordon H. Copp; Jeffrey E. Hill; B. V. Adamovich; Luke Aislabie; Daniel R. Akin; Abbas J. Al-Faisal; David Almeida; M. N.Amal Azmai; Rigers Bakiu; +183 more
    Countries: Denmark, Lithuania, Turkey, Russian Federation, Norway, Netherlands, Norway, France, Poland, France ...

    The threat posed by invasive non-native species worldwide requires a global approach to identify which introduced species are likely to pose an elevated risk of impact to native species and ecosystems. To inform policy, stakeholders and management decisions on global threats to aquatic ecosystems, 195 assessors representing 120 risk assessment areas across all six inhabited continents screened 819 non-native species from 15 groups of aquatic organisms (freshwater, brackish, marine plants and animals) using the Aquatic Species Invasiveness Screening Kit. This multi-lingual decision-support tool for the risk screening of aquatic organisms provides assessors with risk scores for a species under current and future climate change conditions that, following a statistically based calibration, permits the accurate classification of species into high-, medium-and low-risk categories under current and predicted climate conditions. The 1730 screenings undertaken encompassed wide geographical areas (regions, political entities, parts thereof, water bodies, river basins, lake drainage basins, and marine regions), which permitted thresholds to be identified for almost all aquatic organismal groups screened as well as for tropical, temperate and continental climate classes, and for tropical and temperate marine ecoregions. In total, 33 species were identified as posing a 'very high risk' of being or becoming invasive, and the scores of several of these species under current climate increased under future climate conditions, primarily due to their wide thermal tolerances. The risk thresholds determined for taxonomic groups and climate zones provide a basis against which area-specific or climate-based calibrated thresholds may be interpreted. In turn, the risk rankings help decision-makers identify which species require an immediate 'rapid' management action (e.g. eradication, control) to avoid or mitigate adverse impacts, which require a full risk assessment, and which are to be restricted or banned with regard to importation and/or sale as ornamental or aquarium/fishery enhancement. (c) 2021 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http:// creativecommons.org/licenses/by/4.0/). Cefas Science Excellence fund; [TKP2020-NKA-16] This study is dedicated to our co-author, the late Prof. Olaf Weyl, whose sudden passing during field work in November 2020 was received by us with great sadness. This study represents a contribution to the term of reference 'd' (Advance knowledge base to further develop indicators to evaluate the status and impact of non-indigenous species in marine environments) of the ICES working group on Introductions and Transfers of Marine Organisms. The participation of GHC was supported by the Cefas Science Excellence fund. AW and AF were supported by TKP2020-NKA-16 project. WOS:000663799700017 2-s2.0-85106630815 PubMed: 34134389

  • Open Access
    Authors: 
    Roman Kuchta; Marcus Enrique Serrano-Martínez; Tomáš Scholz;
    Publisher: Centers for Disease Control and Prevention (CDC)
    Country: Peru

    The Pacific broad tapeworm Adenocephalus pacificus (syn. Diphyllobothrium pacificum) is the causative agent of the third most common fish-borne cestodosis among humans. Although most of the nearly 1,000 cases among humans have been reported in South America (Peru, Chile, and Ecuador), cases recently imported to Europe demonstrate the potential for spread of this tapeworm throughout the world as a result of global trade of fresh or chilled marine fish and travel or migration of humans. We provide a comprehensive survey of human cases of infection with this zoonotic parasite, summarize the history of this re-emerging disease, and identify marine fish species that may serve as a source of human infection when eaten raw or undercooked. Certain types of marine fish, eaten raw or undercooked, may serve as a source of human infection with these parasites.

  • Publication . Article . Other literature type . 2020
    Open Access English
    Authors: 
    Rute R. da Fonseca; Alvarina Couto; André M. Machado; Brona Brejova; Carolin B Albertin; Filipe Silva; Paul P. Gardner; Tobias Baril; Alexander Hayward; Alexandre Campos; +34 more
    Publisher: Oxford University Press
    Countries: United States, Germany, Austria, Portugal, Spain, Denmark, Norway, United Kingdom, Denmark
    Project: FCT | SFRH/BD/126560/2016 (SFRH/BD/126560/2016), WT , UKRI | South West Biosciences: A... (BB/M009122/1), NWO | Age of Deep-Sea Squid (5618), WT | ENSEMBL (108749), FCT | PTDC/CTA-AMB/31774/2017 (PTDC/CTA-AMB/31774/2017), UKRI | Architects of genomic cha... (BB/N020146/1), FCT | PTDC/MAR/115347/2009 (PTDC/MAR/115347/2009), EC | MAIZEKEY (272927), FCT | UID/Multi/04423/2019 (UID/Multi/04423/2019)

    Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked. Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments. R.R.F. thanks the Villum Fonden for grant VKR023446 (Vil-lum Fonden Young Investigator Grant), the Portuguese Science Foundation (FCT) for grant PTDC/MAR/115347/2009; COMPETE-FCOMP-01-012; FEDER-015453, Marie Curie Actions (FP7-PEOPLE-2010-IEF, Proposal 272927), and the Danish National Research Foundation (DNRF96) for its funding of the Center for Macroe-cology, Evolution, and Climate. H.O. thanks the Rede Nacional de Espectrometria de Massa, ROTEIRO/0028/2013, ref. LISBOA-01-0145-FEDER-022125, supported by COMPETE and North Portugal Regional Operational Programme (Norte2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). A.C. thanks FCT for project UID/Multi/04423/2019. M.P. acknowledges the support from the Wellcome Trust (grant number WT108749/Z/15/Z) and the European Molecular Biology Laboratory. M.P.T.G. thanks the Danish National Research Foundation for its funding of the Center for GeoGenetics (grant DNRF94) and Lundbeck Foundation for grant R52–5062 on Pathogen Palaeogenomics. S.R. was supported by the Novo Nordisk Foundation grant NNF14CC0001. A.H. is supported by a Biotechnology and Biological Sciences Research Council David Phillips Fellowship (fellowship reference: BB/N020146/1). T.B. is supported by the Biotechnology and Biological Sciences Research Council-funded South West Biosciences Doctoral Training Partnership (training grant reference BB/M009122/1). This work was partially funded by the Lundbeck Foundation (R52-A4895 to B.B.). H.J.T.H. was supported by the David and Lucile Packard Foundation, the Netherlands Organization for Scientific Research (#825.09.016), and currently by the Deutsche Forschungsgemeinschaft (DFG) under grant HO 5569/2-1 (Emmy Noether Junior Research Group). T.V. and B. Brejova were supported by grantsfrom the Slovak grant agency VEGA (1/0684/16, 1/0458/18). F.S. was supported by a PhD grant (SFRH/BD/126560/2016) from FCT. A.A. was partly supported by the FCT project PTDC/CTAAMB/ 31774/2017. C.C. and Y.W. are partly supported by grant IIS-1526415 from the US National Science Foundation. Computation for the work described in this article was partially supported by the DeiC National Life Science Supercomputer at DTU.

  • Open Access English
    Authors: 
    Kyung Hun Lee; Kyoung Bun Lee; Tae Yong Kim; Sae-Won Han; Do Youn Oh; Seock-Ah Im; Tae-You Kim; Nam-Joon Yi; Kwang-Woong Lee; Kyung-Suk Suh; +2 more
    Publisher: BioMed Central

    Background More knowledge about genetic and molecular features of cholangiocarcinoma is needed to develop effective therapeutic strategies. We investigated the clinical and pathological significance of ROS1 expression in intrahepatic cholangiocarcinoma. Methods One hundred ninety-four patients with curatively resected intrahepatic cholangiocarcinoma were included in this study. Tumor tissue specimens were collected and analyzed for ROS1 gene rearrangement using fluorescence in situ hybridization (FISH) and ROS1 protein expression using immunohistochemistry (IHC). Results ROS1 immunohistochemistry was positive (moderate or strong staining) in 72 tumors (37.1 %). ROS1 protein expression was significantly correlated with well differentiated tumors, papillary or mucinous histology, oncocytic/hepatoid or intestinal type tumors, and periductal infiltrating or intraductal growing tumors (vs. mass-forming cholangiocarcinoma). ROS-expressing tumors were associated with better disease-free survival (30.1 months for ROS1 expression (+) tumors vs. 9.0 months for ROS1 (−) tumors, p = 0.006). Moreover, ROS1 expression was an independent predictor of better disease-free survival in a multivariate analysis (HR 0.607, 95 % CI 0.377–0.976; p = 0.039). Although break-apart FISH was successfully performed in 102 samples, a split pattern indicative of ROS1 gene rearrangement was not found in the examined samples. Conclusion ROS1 protein expression was associated with well-differentiated histology and better survival in our patients with resected intrahepatic cholangiocarcinoma. ROS1 gene rearrangement by break-apart FISH was not found in the examined samples.

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The following results are related to European Marine Science. Are you interested to view more results? Visit OpenAIRE - Explore.
62 Research products, page 1 of 7
  • Open Access English
    Authors: 
    Martina Červená; František Šťáhlavský; Vladimír Papáč; Ľubomír Kováč; Jana Christophoryová;
    Publisher: Pensoft Publishers

    A redescription is provided of the adult, tritonymph and deutonymph life stages of the troglobitic Neobisium (Blothrus) slovacum Gulička, 1977, which is known from Slovakia and Hungary. Material examined included 35 previously deposited museum specimens and 15 newly collected specimens. In addition, the karyotype and distribution of 18S rDNA clusters are described, using fluorescence in situ hybridization (FISH). The male karyotype ofN.slovacumcomprises 69 chromosomes, with a predominance of biarmed chromosomes, and an X0 sex chromosome system. Two pairs of signals for 18S rDNA on biarmed chromosomes (submetacentric and metacentric) of different sizes were identified. The present study provides the first information about the distribution of these clusters in the arachnid order Pseudoscorpiones. The geographic distribution of the species is summarized and mapped.Neobisiumslovacumis endemic to the Slovak and Aggtelek Karst area in southern Slovakia and north-western Hungary, where it has been recorded from 16 caves. One of these, Hačavská cave (in Slovakia), is the northernmost locality known for any species of the subgenus Blothrus.

  • Publication . Other literature type . Article . Preprint . 2017
    Open Access English
    Authors: 
    G. Laaha; T. Gauster; L. M. Tallaksen; J.-P. Vidal; K. Stahl; C. Prudhomme; C. Prudhomme; B. Heudorfer; R. Vlnas; R. Vlnas; +16 more
    Publisher: HAL CCSD
    Countries: Germany, France, Netherlands, Netherlands, United Kingdom

    Abstract. In 2015 large parts of Europe were affected by drought. In this paper, we analyze the hydrological footprint (dynamic development over space and time) of the drought of 2015 in terms of both severity (magnitude) and spatial extent and compare it to the extreme drought of 2003. Analyses are based on a range of low flow and hydrological drought indices derived for about 800 streamflow records across Europe, collected in a community effort based on a common protocol. We compare the hydrological footprints of both events with the meteorological footprints, in order to learn from similarities and differences of both perspectives and to draw conclusions for drought management. The region affected by hydrological drought in 2015 differed somewhat from the drought of 2003, with its center located more towards eastern Europe. In terms of low flow magnitude, a region surrounding the Czech Republic was the most affected, with summer low flows that exhibited return intervals of 100 years and more. In terms of deficit volumes, the geographical center of the event was in southern Germany, where the drought lasted a particularly long time. A detailed spatial and temporal assessment of the 2015 event showed that the particular behavior in these regions was partly a result of diverging wetness preconditions in the studied catchments. Extreme droughts emerged where preconditions were particularly dry. In regions with wet preconditions, low flow events developed later and tended to be less severe. For both the 2003 and 2015 events, the onset of the hydrological drought was well correlated with the lowest flow recorded during the event (low flow magnitude), pointing towards a potential for early warning of the severity of streamflow drought. Time series of monthly drought indices (both streamflow- and climate-based indices) showed that meteorological and hydrological events developed differently in space and time, both in terms of extent and severity (magnitude). These results emphasize that drought is a hazard which leaves different footprints on the various components of the water cycle at different spatial and temporal scales. The difference in the dynamic development of meteorological and hydrological drought also implies that impacts on various water-use sectors and river ecology cannot be informed by climate indices alone. Thus, an assessment of drought impacts on water resources requires hydrological data in addition to drought indices based solely on climate data. The transboundary scale of the event also suggests that additional efforts need to be undertaken to make timely pan-European hydrological assessments more operational in the future.

  • Open Access English
    Authors: 
    Kamil Hupało; Markus Majaneva; Molly Victoria Czachur; Lucas Sire; Daniel Marquina; Dario A Lijtmaer; Vladislav Ivanov; Sonja Leidenberger; Fedor Čiampor; Zuzana Čiamporová-Zaťovičová; +11 more
    Countries: Germany, Australia, Switzerland, France, Argentina, Norway, Norway, Germany, Sweden

    As global biodiversity declines, there is an increasing need to create an educated and engaged society. Having people of all ages participate in measuring biodiversity where they live helps to create awareness. Recently, the use of environmental DNA (eDNA) for biodiversity surveys has gained momentum. Here, we explore whether sampling eDNA and sequencing it can be used as a means of rapidly surveying urban biodiversity for educational purposes. We sampled 2 × 1 L of water from each of 15 locations in the city of Trondheim, Norway, including a variety of freshwater, marine, and brackish habitats. DNA was extracted, amplified in triplicate targeting the barcoding fragment of COI gene, and sequenced. The obtained data were analyzed on the novel mBRAVE platform, an online open-access software and computing resource. The water samples were collected in 2 days by two people, and the laboratory analysis was completed in 5 days by one person. Overall, we detected the presence of 506 BINs identified as belonging to 435 taxa, representing at least 265 putative species. On average, only 5.4% of the taxa were shared among six replicates per site. Based on the observed diversity, three distinct clusters were detected and related to the geographic distribution of sites. There were some taxa shared between the habitats, with a substantial presence of terrestrial biota. Here we propose a new form of BioBlitz, where with noninvasive sampling effort combined with swift processing and straightforward online analyses, hundreds of species can be detected. Thus, using eDNA analysis of water is useful for rapid biodiversity surveys and valuable for educational purposes. We show that rapid eDNA surveys, combined with openly available services and software, can be used as an educational tool to raise awareness about the importance of biodiversity. Environmental DNA, 3 (1) ISSN:2637-4943

  • Open Access English
    Authors: 
    David Bajnai; Jens Fiebig; Adam Tomašových; Sara Milner Garcia; Claire Rollion-Bard; Jacek Raddatz; Niklas Löffler; Cristina Primo-Ramos; Uwe Brand;
    Publisher: HAL CCSD
    Countries: France, Germany, France
    Project: EC | BASE-LiNE Earth (643084)

    AbstractBrachiopod shells are the most widely used geological archive for the reconstruction of the temperature and the oxygen isotope composition of Phanerozoic seawater. However, it is not conclusive whether brachiopods precipitate their shells in thermodynamic equilibrium. In this study, we investigated the potential impact of kinetic controls on the isotope composition of modern brachiopods by measuring the oxygen and clumped isotope compositions of their shells. Our results show that clumped and oxygen isotope compositions depart from thermodynamic equilibrium due to growth rate-induced kinetic effects. These departures are in line with incomplete hydration and hydroxylation of dissolved CO2. These findings imply that the determination of taxon-specific growth rates alongside clumped and bulk oxygen isotope analyses is essential to ensure accurate estimates of past ocean temperatures and seawater oxygen isotope compositions from brachiopods.

  • Open Access English
    Authors: 
    Klionsky, Daniel; Abdel-Aziz, Amal Kamal; Abdelfatah, Sara; Abdellatif, Mahmoud; Abdoli, Asghar; Abel, Steffen; Abeliovich, Hagai; Abildgaard, Marie; Abudu, Yakubu Princely; Acevedo-Arozena, Abraham; +760 more
    Publisher: HAL CCSD
    Countries: Netherlands, Croatia, Netherlands, Netherlands, Italy, Palestinian-administered areas, United Kingdom, France, Italy
    Project: EC | ENTRAPMENT (772853), EC | RobustSynapses (646671), EC | ChemBioAP (678899), EC | FIRM (819600)

    International audience; In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

  • Open Access English
    Authors: 
    Gordon H. Copp; Lorenzo Vilizzi; Hui Wei; Shan Li; Marina Piria; Abbas J. Al-Faisal; David Almeida; Usman Atique; Zainab Al-Wazzan; Rigers Bakiu; +66 more
    Countries: Russian Federation, Netherlands, France, Croatia

    Abstract Environmental changes due to non-native species introductions and translocations are a global concern. Whilst understanding the causes of bioinvasions is important, there is need for decision-support tools that facilitate effective communication of the potential risks of invasive non-native species to stakeholders. Decision-support tools have been developed mostly in English language only, which increases linguistic uncertainty associated with risk assessments undertaken by assessors not of English mother tongue and who need to communicate outcomes to local stakeholders. To reduce language-based uncertainty, the ‘ecology-of-language’ paradigm was applied when developing the Aquatic Species Invasiveness Screening Kit (AS-ISK), a decision-support tool that offers 32 languages in which to carry out screenings and communicate outcomes to stakeholders. Topics discussed include uncertainty related to language-specific issues encountered during the AS-ISK translation and the potential benefits of a multilingual decision-support tool for reducing linguistic uncertainty and enhancing communication between scientists, environmental managers, and policy and decision makers.

  • Open Access English
    Authors: 
    Lorenzo Vilizzi; Gordon H. Copp; Jeffrey E. Hill; B. V. Adamovich; Luke Aislabie; Daniel R. Akin; Abbas J. Al-Faisal; David Almeida; M. N.Amal Azmai; Rigers Bakiu; +183 more
    Countries: Denmark, Lithuania, Turkey, Russian Federation, Norway, Netherlands, Norway, France, Poland, France ...

    The threat posed by invasive non-native species worldwide requires a global approach to identify which introduced species are likely to pose an elevated risk of impact to native species and ecosystems. To inform policy, stakeholders and management decisions on global threats to aquatic ecosystems, 195 assessors representing 120 risk assessment areas across all six inhabited continents screened 819 non-native species from 15 groups of aquatic organisms (freshwater, brackish, marine plants and animals) using the Aquatic Species Invasiveness Screening Kit. This multi-lingual decision-support tool for the risk screening of aquatic organisms provides assessors with risk scores for a species under current and future climate change conditions that, following a statistically based calibration, permits the accurate classification of species into high-, medium-and low-risk categories under current and predicted climate conditions. The 1730 screenings undertaken encompassed wide geographical areas (regions, political entities, parts thereof, water bodies, river basins, lake drainage basins, and marine regions), which permitted thresholds to be identified for almost all aquatic organismal groups screened as well as for tropical, temperate and continental climate classes, and for tropical and temperate marine ecoregions. In total, 33 species were identified as posing a 'very high risk' of being or becoming invasive, and the scores of several of these species under current climate increased under future climate conditions, primarily due to their wide thermal tolerances. The risk thresholds determined for taxonomic groups and climate zones provide a basis against which area-specific or climate-based calibrated thresholds may be interpreted. In turn, the risk rankings help decision-makers identify which species require an immediate 'rapid' management action (e.g. eradication, control) to avoid or mitigate adverse impacts, which require a full risk assessment, and which are to be restricted or banned with regard to importation and/or sale as ornamental or aquarium/fishery enhancement. (c) 2021 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http:// creativecommons.org/licenses/by/4.0/). Cefas Science Excellence fund; [TKP2020-NKA-16] This study is dedicated to our co-author, the late Prof. Olaf Weyl, whose sudden passing during field work in November 2020 was received by us with great sadness. This study represents a contribution to the term of reference 'd' (Advance knowledge base to further develop indicators to evaluate the status and impact of non-indigenous species in marine environments) of the ICES working group on Introductions and Transfers of Marine Organisms. The participation of GHC was supported by the Cefas Science Excellence fund. AW and AF were supported by TKP2020-NKA-16 project. WOS:000663799700017 2-s2.0-85106630815 PubMed: 34134389

  • Open Access
    Authors: 
    Roman Kuchta; Marcus Enrique Serrano-Martínez; Tomáš Scholz;
    Publisher: Centers for Disease Control and Prevention (CDC)
    Country: Peru

    The Pacific broad tapeworm Adenocephalus pacificus (syn. Diphyllobothrium pacificum) is the causative agent of the third most common fish-borne cestodosis among humans. Although most of the nearly 1,000 cases among humans have been reported in South America (Peru, Chile, and Ecuador), cases recently imported to Europe demonstrate the potential for spread of this tapeworm throughout the world as a result of global trade of fresh or chilled marine fish and travel or migration of humans. We provide a comprehensive survey of human cases of infection with this zoonotic parasite, summarize the history of this re-emerging disease, and identify marine fish species that may serve as a source of human infection when eaten raw or undercooked. Certain types of marine fish, eaten raw or undercooked, may serve as a source of human infection with these parasites.

  • Publication . Article . Other literature type . 2020
    Open Access English
    Authors: 
    Rute R. da Fonseca; Alvarina Couto; André M. Machado; Brona Brejova; Carolin B Albertin; Filipe Silva; Paul P. Gardner; Tobias Baril; Alexander Hayward; Alexandre Campos; +34 more
    Publisher: Oxford University Press
    Countries: United States, Germany, Austria, Portugal, Spain, Denmark, Norway, United Kingdom, Denmark
    Project: FCT | SFRH/BD/126560/2016 (SFRH/BD/126560/2016), WT , UKRI | South West Biosciences: A... (BB/M009122/1), NWO | Age of Deep-Sea Squid (5618), WT | ENSEMBL (108749), FCT | PTDC/CTA-AMB/31774/2017 (PTDC/CTA-AMB/31774/2017), UKRI | Architects of genomic cha... (BB/N020146/1), FCT | PTDC/MAR/115347/2009 (PTDC/MAR/115347/2009), EC | MAIZEKEY (272927), FCT | UID/Multi/04423/2019 (UID/Multi/04423/2019)

    Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked. Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments. R.R.F. thanks the Villum Fonden for grant VKR023446 (Vil-lum Fonden Young Investigator Grant), the Portuguese Science Foundation (FCT) for grant PTDC/MAR/115347/2009; COMPETE-FCOMP-01-012; FEDER-015453, Marie Curie Actions (FP7-PEOPLE-2010-IEF, Proposal 272927), and the Danish National Research Foundation (DNRF96) for its funding of the Center for Macroe-cology, Evolution, and Climate. H.O. thanks the Rede Nacional de Espectrometria de Massa, ROTEIRO/0028/2013, ref. LISBOA-01-0145-FEDER-022125, supported by COMPETE and North Portugal Regional Operational Programme (Norte2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). A.C. thanks FCT for project UID/Multi/04423/2019. M.P. acknowledges the support from the Wellcome Trust (grant number WT108749/Z/15/Z) and the European Molecular Biology Laboratory. M.P.T.G. thanks the Danish National Research Foundation for its funding of the Center for GeoGenetics (grant DNRF94) and Lundbeck Foundation for grant R52–5062 on Pathogen Palaeogenomics. S.R. was supported by the Novo Nordisk Foundation grant NNF14CC0001. A.H. is supported by a Biotechnology and Biological Sciences Research Council David Phillips Fellowship (fellowship reference: BB/N020146/1). T.B. is supported by the Biotechnology and Biological Sciences Research Council-funded South West Biosciences Doctoral Training Partnership (training grant reference BB/M009122/1). This work was partially funded by the Lundbeck Foundation (R52-A4895 to B.B.). H.J.T.H. was supported by the David and Lucile Packard Foundation, the Netherlands Organization for Scientific Research (#825.09.016), and currently by the Deutsche Forschungsgemeinschaft (DFG) under grant HO 5569/2-1 (Emmy Noether Junior Research Group). T.V. and B. Brejova were supported by grantsfrom the Slovak grant agency VEGA (1/0684/16, 1/0458/18). F.S. was supported by a PhD grant (SFRH/BD/126560/2016) from FCT. A.A. was partly supported by the FCT project PTDC/CTAAMB/ 31774/2017. C.C. and Y.W. are partly supported by grant IIS-1526415 from the US National Science Foundation. Computation for the work described in this article was partially supported by the DeiC National Life Science Supercomputer at DTU.

  • Open Access English
    Authors: 
    Kyung Hun Lee; Kyoung Bun Lee; Tae Yong Kim; Sae-Won Han; Do Youn Oh; Seock-Ah Im; Tae-You Kim; Nam-Joon Yi; Kwang-Woong Lee; Kyung-Suk Suh; +2 more
    Publisher: BioMed Central

    Background More knowledge about genetic and molecular features of cholangiocarcinoma is needed to develop effective therapeutic strategies. We investigated the clinical and pathological significance of ROS1 expression in intrahepatic cholangiocarcinoma. Methods One hundred ninety-four patients with curatively resected intrahepatic cholangiocarcinoma were included in this study. Tumor tissue specimens were collected and analyzed for ROS1 gene rearrangement using fluorescence in situ hybridization (FISH) and ROS1 protein expression using immunohistochemistry (IHC). Results ROS1 immunohistochemistry was positive (moderate or strong staining) in 72 tumors (37.1 %). ROS1 protein expression was significantly correlated with well differentiated tumors, papillary or mucinous histology, oncocytic/hepatoid or intestinal type tumors, and periductal infiltrating or intraductal growing tumors (vs. mass-forming cholangiocarcinoma). ROS-expressing tumors were associated with better disease-free survival (30.1 months for ROS1 expression (+) tumors vs. 9.0 months for ROS1 (−) tumors, p = 0.006). Moreover, ROS1 expression was an independent predictor of better disease-free survival in a multivariate analysis (HR 0.607, 95 % CI 0.377–0.976; p = 0.039). Although break-apart FISH was successfully performed in 102 samples, a split pattern indicative of ROS1 gene rearrangement was not found in the examined samples. Conclusion ROS1 protein expression was associated with well-differentiated histology and better survival in our patients with resected intrahepatic cholangiocarcinoma. ROS1 gene rearrangement by break-apart FISH was not found in the examined samples.