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  • Elsevier  (19)
  • Wiley  (11)
  • Copernicus Publications (EGU)  (6)
  • Oxford University Press  (6)
  • American Institute of Physics
  • Blackwell Publishing Ltd
  • Molecular Diversity Preservation International (MDPI)
  • Nature Publishing Group
  • 2020-2024  (42)
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  • 1
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    Factors controlling plankton community production, export flux, and particulate matter stoichiometry in the coastal upwelling system off Peru (2020)
    Copernicus Publications (EGU)
    Details
    Publication Date: 2023-02-08
    Description: Eastern boundary upwelling systems (EBUS) are among the most productive marine ecosystems on Earth. The production of organic material is fueled by upwelling of nutrient-rich deep waters and high incident light at the sea surface. However, biotic and abiotic factors can modify surface production and related biogeochemical processes. Determining these factors is important because EBUS are considered hotspots of climate change, and reliable predictions of their future functioning requires understanding of the mechanisms driving the biogeochemical cycles therein. In this field experiment, we used in situ mesocosms as tools to improve our mechanistic understanding of processes controlling organic matter cycling in the coastal Peruvian upwelling system. Eight mesocosms, each with a volume of ∼55 m3, were deployed for 50 d ∼6 km off Callao (12∘ S) during austral summer 2017, coinciding with a coastal El Niño phase. After mesocosm deployment, we collected subsurface waters at two different locations in the regional oxygen minimum zone (OMZ) and injected these into four mesocosms (mixing ratio ≈1.5 : 1 mesocosm: OMZ water). The focus of this paper is on temporal developments of organic matter production, export, and stoichiometry in the individual mesocosms. The mesocosm phytoplankton communities were initially dominated by diatoms but shifted towards a pronounced dominance of the mixotrophic dinoflagellate (Akashiwo sanguinea) when inorganic nitrogen was exhausted in surface layers. The community shift coincided with a short-term increase in production during the A. sanguinea bloom, which left a pronounced imprint on organic matter C : N : P stoichiometry. However, C, N, and P export fluxes did not increase because A. sanguinea persisted in the water column and did not sink out during the experiment. Accordingly, export fluxes during the study were decoupled from surface production and sustained by the remaining plankton community. Overall, biogeochemical pools and fluxes were surprisingly constant for most of the experiment. We explain this constancy by light limitation through self-shading by phytoplankton and by inorganic nitrogen limitation which constrained phytoplankton growth. Thus, gain and loss processes remained balanced and there were few opportunities for blooms, which represents an event where the system becomes unbalanced. Overall, our mesocosm study revealed some key links between ecological and biogeochemical processes for one of the most economically important regions in the oceans.
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  • 2
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    Nitrogen loss processes in response to upwelling in a Peruvian coastal setting dominated by denitrification – a mesocosm approach (2021)
    Copernicus Publications (EGU)
    Details
    Publication Date: 2024-02-07
    Description: Upwelling of nutrient-rich deep waters make eastern boundary upwelling systems (EBUSs), such as the Humboldt Current system, hot spots of marine productivity. Associated settling of organic matter to depth and consecutive aerobic decomposition results in large subsurface water volumes being oxygen depleted. Under these circumstances, organic matter remineralisation can continue via denitrification, which represents a major loss pathway for bioavailable nitrogen. Additionally, anaerobic ammonium oxidation can remove significant amounts of nitrogen in these areas. Here we assess the interplay of suboxic water upwelling and nitrogen cycling in a manipulative offshore mesocosm experiment. Measured denitrification rates in incubations with water from the oxygen-depleted bottom layer of the mesocosms (via 15N label incubations) mostly ranged between 5.5 and 20 nmol N2 L−1 h−1 (interquartile range), reaching up to 80 nmol N2 L−1 h−1. However, actual in situ rates in the mesocosms, estimated via Michaelis–Menten kinetic scaling, did most likely not exceed 0.2–4.2 nmol N2 L−1 h−1 (interquartile range) due to substrate limitation. In the surrounding Pacific, measured denitrification rates were similar, although indications of substrate limitation were detected only once. In contrast, anammox (anaerobic ammonium oxidation) made only a minor contribution to the overall nitrogen loss when encountered in both the mesocosms and the Pacific Ocean. This was potentially related to organic matter C / N stoichiometry and/or process-specific oxygen and hydrogen sulfide sensitivities. Over the first 38 d of the experiment, total nitrogen loss calculated from in situ rates of denitrification and anammox was comparable to estimates from a full nitrogen budget in the mesocosms and ranged between ∼ 1 and 5.5 µmol N L−1. This represents up to ∼  20 % of the initially bioavailable inorganic and organic nitrogen standing stocks. Interestingly, this loss is comparable to the total amount of particulate organic nitrogen that was exported into the sediment traps at the bottom of the mesocosms at about 20 m depth. Altogether, this suggests that a significant portion, if not the majority of nitrogen that could be exported to depth, is already lost, i.e. converted to N2 in a relatively shallow layer of the surface ocean, provided that there are oxygen-deficient conditions like those during coastal upwelling in our study. Published data for primary productivity and nitrogen loss in all EBUSs reinforce such conclusion.
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  • 3
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    The founding charter of the Omic Biodiversity Observation Network (Omic BON) (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.
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  • 4
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    An Equal Burden (2021)
    Oxford University Press
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    Publication Date: 2024-04-01
    Description: "An Equal Burden forms the first scholarly study of the Army Medical Services in the First World War to focus on the roles and experiences of the men of the ranks of the Royal Army Medical Corps (RAMC). These men, through their work as stretcher bearers and orderlies, provided a range of labour, both physical and emotional, in aid of the sick and wounded. They were not professional medical caregivers, yet were called upon to provide medical care, however rudimentary; they served in uniform, under military discipline, yet were forbidden, as non-combatants, from carrying weapons. Their service as men in wartime, was thus unique. Structured both chronologically and thematically, this study examines both the work that RAMC rankers undertook and its importance to the running of the chain of medical evacuation. It additionally explores the gendered status of these men within the medical, military and cultural hierarchies of a society engaged in total war, locating their service within the context of that of doctors, female nurses and combatant servicemen. Through close readings of official documents, personal papers, and cultural representations, both verbal and visual, it argues that the ranks of the RAMC formed a space in which non-commissioned servicemen, through their many roles, defined and redefined medical caregiving as men’s work in wartime."
    Keywords: Royal Army Medical Corps ; First World War ; masculinity ; non-combatants ; military medicine ; care giving ; gender history ; cultural representation ; thema EDItEUR::N History and Archaeology ; thema EDItEUR::3 Time period qualifiers::3M c 1500 onwards to present day::3MP 20th century, c 1900 to c 1999 ; thema EDItEUR::N History and Archaeology::NH History::NHW Military history::NHWR Specific wars and campaigns::NHWR5 First World War ; thema EDItEUR::3 Time period qualifiers::3M c 1500 onwards to present day::3MP 20th century, c 1900 to c 1999::3MPB Early 20th century c 1900 to c 1950::3MPBF c 1910 to c 1919::3MPBFB c 1914 to c 1918 (World War One period) ; thema EDItEUR::M Medicine and Nursing
    Language: English
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  • 5
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    Habitat light sets the boundaries for the rapid evolution of cichlid fish vision, while sexual selection can tune it within those limits (2020)
    Wiley
    Details
    Publication Date: 2023-02-08
    Description: Cichlid fishes’ famous diversity in body coloration is accompanied by a highly diverse and complex visual system. Although cichlids possess an unusually high number of seven cone opsin genes, they express only a subset of these during their ontogeny, accounting for their astonishing interspecific variation in visual sensitivities. Much of this diversity is thought to have been shaped by natural selection as cichlids inhabit a variety of habitats with distinct light environments. Also, sexual selection might have contributed to the observed visual diversity, and sexual dimorphism in coloration potentially co‐evolved with sexual dimorphism in opsin expression. We investigated sex‐specific opsin expression of several cichlids from Africa and the Neotropics and collected and integrated datasets on sex‐specific body coloration, species‐specific visual sensitivities, lens transmission and habitat light properties for some of them. We comparatively analyzed this wide range of molecular and ecological data, illustrating how integrative approaches can address specific questions on the factors and mechanisms driving diversification, and the evolution of cichlid vision in particular. We found that both sexes expressed opsins at the same levels ‐ even in sexually dimorphic cichlid species – which argues against coevolution of sexual dichromatism and differences in sex‐specific visual sensitivity. Rather, a combination of environmental light properties and body coloration shaped the diversity in spectral sensitivities among cichlids. We conclude that although cichlids are particularly colorful and diverse and often sexually dimorphic, it would appear that natural rather than sexual selection is a more powerful force driving visual diversity in this hyper‐diverse lineage.
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  • 6
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    Diving into divergence: Differentiation in swimming performances, physiology and gene expression between locally‐adapted sympatric cichlid fishes (2020)
    Wiley
    Details
    Publication Date: 2023-02-08
    Description: Sympatric speciation occurs without geographical barriers and is thought to often be driven by ecological specialization of individuals that eventually diverge genetically and phenotypically. Distinct morphologies between sympatric populations occupying different niches have been interpreted as such differentiating adaptive phenotypes, yet differences in performance and thus likely adaptiveness between them were rarely tested. Here, we investigated if divergent body shapes of two sympatric crater lake cichlid species from Nicaragua, one being a shore‐associated (benthic) species while the other prefers the open water zones (limnetic), affect cruising (Ucrit) and sprinting (Usprint) swimming abilities ‐ performances particularly relevant to their respective lifestyles. Furthermore, we investigated species differences in oxygen consumption (MO2) across different swimming speeds and compare gene expression in gills and white muscle at rest and during exercise. We found a superior cruising ability in the limnetic Amphilophus zaliosus compared to the benthic A. astorquii, while sprinting was not different, suggesting that their distinct morphologies affect swimming performance. Increased cruising swimming ability in A. zaliosus was linked to a higher oxygen demand during activity (but not rest), indicating different metabolic rates during exercise ‐ a hypothesis supported by coinciding gene expression patterns of gill transcriptomes. We identified differentially expressed genes linked to swimming physiology, regulation of swimming behaviour and oxygen intake. A combination of physiological and morphological differences may thus underlie adaptations to these species’ distinct niches. This complex ecological specialization likely resulted in morphological and physiological trade‐offs that contributed to the rapid establishment and maintenance of divergence with gene flow.
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  • 7
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    Experimental parasite infection causes genome-wide changes in DNA methylation (2020)
    Oxford University Press
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    Publication Date: 2023-02-08
    Description: Parasites are arguably among the strongest drivers of natural selection, constraining hosts to evolve resistance and tolerance mechanisms. Although, the genetic basis of adaptation to parasite infection has been widely studied, little is known about how epigenetic changes contribute to parasite resistance and eventually, adaptation. Here, we investigated the role of host DNA methylation modifications to respond to parasite infections. In a controlled infection experiment, we used the three-spined stickleback fish, a model species for host-parasite studies, and their nematode parasite Camallanus lacustris. We showed that the levels of DNA methylation are higher in infected fish. Results furthermore suggest correlations between DNA methylation and shifts in key fitness and immune traits between infected and control fish, including respiratory burst and functional trans-generational traits such as the concentration of motile sperm. We revealed that genes associated with metabolic, developmental and regulatory processes (cell death and apoptosis) were differentially methylated between infected and control fish. Interestingly, genes such as the neuropeptide FF receptor 2 and the integrin alpha 1 as well as molecular pathways including the Th1 and Th2 cell differentiation were hypermethylated in infected fish, suggesting parasite-mediated repression mechanisms of immune responses. Altogether, we demonstrate that parasite infection contributes to genome-wide DNA methylation modifications. Our study brings novel insights into the evolution of vertebrate immunity and suggests that epigenetic mechanisms are complementary to genetic responses against parasite-mediated selection.
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  • 8
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    A genomic cluster containing novel and conserved genes is associated with cichlid fish dental developmental convergence (2020)
    Oxford University Press
    Details
    Publication Date: 2023-02-08
    Description: The two toothed jaws of cichlid fishes provide textbook examples of convergent evolution. Tooth phenotypes such as enlarged molar-like teeth used to process hard-shelled molluscs have evolved numerous times independently during cichlid diversification. While the ecological benefit of molar-like teeth to crush prey is known, it is unclear whether the same molecular mechanisms underlie these convergent traits. To identify genes involved in the evolution and development of enlarged cichlid teeth, we performed RNA-seq on the serially homologous toothed oral and pharyngeal jaws as well as the fourth toothless gill arch of Astatoreochromis alluaudi. We identified 27 genes that are highly upregulated on both tooth-bearing jaws compared to the toothless gill arch. Most of these genes have never been reported to play a role in tooth formation. Two of these genes (unk, rpfA) are not found in other vertebrate genomes but are present in all cichlid genomes. They also cluster genomically with two other highly expressed tooth genes (odam, scpp5) that exhibit conserved expression during vertebrate odontogenesis. Unk and rpfA were confirmed via in situ hybridization to be expressed in developing teeth of Astatotilapia burtoni. We then examined expression of the cluster's four genes in six evolutionarily independent and phylogenetically disparate cichlid species pairs each with a large- and a small-toothed species. Odam and unk commonly and scpp5 and rpfA always showed higher expression in larger-toothed cichlid jaws. Convergent trophic adaptations across cichlid diversity are associated with the repeated developmental deployment of this genomic cluster containing conserved and novel cichlid-specific genes.
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  • 9
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    Detection and quantification of a release of carbon dioxide gas at the seafloor using pH eddy covariance and measurements of plume advection (2021)
    Elsevier
    Details
    Publication Date: 2024-02-07
    Description: Highlights ● We developed a pH eddy covariance system to detect a sub-seafloor CO2 release. ● It detected CO2 emission to the water column at injection rates of 5.7–143 kg d − 1. ● It was also sensitive enough to quantify benthic biological CO2 production. ● Close to bubble streams, the kinetics of aqueous CO2 equilibration are important. ● This system can be used to detect, attribute, and quantify seafloor sources of CO2. We detected a controlled release of CO2 (g) with pH eddy covariance. We quantified CO2 emission using measurements of water velocity and pH in the plume of aqueous CO2 generated by the bubble streams, and using model predictions of vertical CO2 dissolution and its dispersion downstream. CO2 (g) was injected 3 m below the floor of the North Sea at rates of 5.7–143 kg d − 1. Instruments were 2.6 m from the center of the bubble streams. In the absence of injected CO2, pH eddy covariance quantified the proton flux due to naturally-occurring benthic organic matter mineralization (equivalent to a dissolved inorganic carbon flux of 7.6 ± 3.3 mmol m − 2 d − 1, s.e., n = 33). At the lowest injection rate, the proton flux due to CO2 dissolution was 20-fold greater than this. To accurately quantify emission, the kinetics of the carbonate system had to be accounted for. At the peak injection rate, 73 ± 13% (s.d.) of the injected CO2 was emitted, but when kinetics were neglected, the calculated CO2 emission was one-fifth of this. Our results demonstrate that geochemical techniques can detect and quantify very small seafloor sources of CO2 and attribute them to natural or abiotic origins.
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  • 10
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    Genomic basis of evolutionary adaptation in a warm-blooded fish (2022)
    Elsevier
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    Publication Date: 2024-02-07
    Description: PUBLIC SUMMARY: Endothermy has evolved multiple times not only in mammals and birds but also in fishes (teleosts and chondrichthyans) A chromosome-level genome sequence of the whole-body endothermic opah was generated, explaining genetic changes in heat production, sensory, and adaptive immune system Convergent evolution in endothermic vertebrate lineages was investigated, and genes essential for heart function and metabolic heat production were screened Analyses of the unique pectoral muscle of opah revealed that numerous proteins were co-opted from dorsal swimming muscles for thermogenesis and oxidative phosphorylation ABSTRACT: Few fishes have evolved elevated body temperatures compared to ambient temperatures and only in opah (Lampris spp) is the entire body affected. To understand the molecular basis of endothermy, we analyzed the opah genome and identified 23 genes with convergent amino acid substitutions across fish, birds, and mammals, including slc8b1, which encodes the mitochondrial Na+/Ca2+ exchanger and is essential for heart function and metabolic heat production. Among endothermic fishes, 44 convergent genes with suggestive metabolic functions were identified, such as glrx3, encoding a crucial protein for hemoglobin maturation. Numerous genes involved in the production and retention of metabolic heat were also found to be under positive selection. Analyses of opah’s unique inner heat-producing pectoral muscle layer, an evolutionary key-innovation, revealed that many proteins were co-opted from dorsal swimming muscles for thermogenesis and oxidative phosphorylation. Thus, the opah genome provides valuable resources and opportunities to uncover the genetic basis of thermal adaptations in fish.
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