The potential impacts of exploitation on the ecological roles of fish species targeted by fisheries: A multifunctional perspective.

Examining ecosystem functioning through the lens of trait diversity serves as a valuable proxy. It offers crucial insights into how exploitation affects the specific ecological roles played by fisheries targeted species. The present study investigates the potential impacts of exploitation on the ecological roles of fish species targeted by fisheries through an examination of trait diversity. It focuses on the trait diversity of fish landed by local and coastal fleets in the Azores archipelago over the past four decades. Fourteen functional traits were merged to data on fish assemblages landed by both fishing fleets from 1980 to 2020. These traits corresponded to four fundamental fish functions: habitat use, locomotion, feeding and life history. Variability in functional diversity metrics (i.e., functional richness- FRic, functional evenness- FEve, functional divergence-FDiv, and functional dispersion- FDis) among fleets, functions and across decades was assessed using null models. The results revealed similar trait diversity between assemblages landed by local and coastal fishing fleets with overall trait diversity remaining relatively stable over time. However, fishery activities targeted a wide range of functional traits. Additionally, seasonal availability and increased catches of certain fish species can significantly alter trait diversity and their associated functions. The findings highlight the importance of addressing fishing impacts on species traits and their ecological roles, which is crucial for long-term fisheries and ecological sustainability.

Tumor-agnostic cancer therapy using antibodies targeting oncofetal chondroitin sulfate.

Molecular similarities between embryonic and malignant cells can be exploited to target tumors through specific signatures absent in healthy adult tissues. One such embryonic signature tumors express is oncofetal chondroitin sulfate (ofCS), which supports disease progression and dissemination in cancer. Here, we report the identification and characterization of phage display-derived antibody fragments recognizing two distinct ofCS epitopes. These antibody fragments show binding affinity to ofCS in the low nanomolar range across a broad selection of solid tumor types in vitro and in vivo with minimal binding to normal, inflamed, or benign tumor tissues. Anti-ofCS antibody drug conjugates and bispecific immune cell engagers based on these targeting moieties disrupt tumor progression in animal models of human and murine cancers. Thus, anti-ofCS antibody fragments hold promise for the development of broadly effective therapeutic and diagnostic applications targeting human malignancies.

Trait-based insights into sustainable fisheries: A four-decade perspective in Azores archipelago.

The trait-based approach provides a powerful perspective for analyzing fisheries and their potential impact on marine ecological processes, offering crucial insights into sustainability and ecosystem functioning. This approach was applied to investigate trends in fish assemblages landed by both local and coastal fishing fleets in the Azores archipelago over the past four decades (1980s, 1990s, 2000s, and 2010s). A matrix of ten traits was built to assess functional redundancy (Fred), functional over-redundancy (FOve), and functional vulnerability (FVul) for the fish assemblages caught by every fishing fleet in each decade. The susceptibility of the Azorean fishery to negative impacts on ecosystem functioning was evidenced by low FRed (<1.5 species per functional entity) and high FVul (exceeding 70 %). However, there is reason for optimism, as temporal trends in the 2000s and 2010s showed an increase in FRed and FOve along with a significant decrease in FVul. These trends indicate the adaptation of the fishery to new target species and, notably, the effectiveness of local fish regulations in mitigating the impacts of targeting functionally important species, such as Elasmobranchii, over the past two decades. These regulations have played a pivotal role in preserving ecological functions within the ecosystem, as well as in managing the removal of high biomass of key important species (e.g., Trachurus picturatus, Pagellus bogaraveo, and Katsuwonus pelamis) from the ecosystem. This study contributes to understanding the delicate balance between fishing pressure, ecological resilience, and sustainable resource management in Azorean waters. It also highlights the importance of continued monitoring, adaptive management, and the enforcement of local fishing regulations to ensure the long-term health and sustainability of the fishery and the broader marine ecosystem.

Towards a scientific community consensus on designating Vulnerable Marine Ecosystems from imagery.

Management of deep-sea fisheries in areas beyond national jurisdiction by Regional Fisheries Management Organizations/Arrangements (RFMO/As) requires identification of areas with Vulnerable Marine Ecosystems (VMEs). Currently, fisheries data, including trawl and longline bycatch data, are used by many RFMO/As to inform the identification of VMEs. However, the collection of such data creates impacts and there is a need to collect non-invasive data for VME identification and monitoring purposes. Imagery data from scientific surveys satisfies this requirement, but there currently is no established framework for identifying VMEs from images. Thus, the goal of this study was to bring together a large international team to determine current VME assessment protocols and establish preliminary global consensus guidelines for identifying VMEs from images. An initial assessment showed a lack of consistency among RFMO/A regions regarding what is considered a VME indicator taxon, and hence variability in how VMEs might be defined. In certain cases, experts agreed that a VME could be identified from a single image, most often in areas of scleractinian reefs, dense octocoral gardens, multiple VME species' co-occurrence, and chemosynthetic ecosystems. A decision flow chart is presented that gives practical interpretation of the FAO criteria for single images. To further evaluate steps of the flow chart related to density, data were compiled to assess whether scientists perceived similar density thresholds across regions. The range of observed densities and the density values considered to be VMEs varied considerably by taxon, but in many cases, there was a statistical difference in what experts considered to be a VME compared to images not considered a VME. Further work is required to develop an areal extent index, to include a measure of confidence, and to increase our understanding of what levels of density and diversity correspond to key ecosystem functions for VME indicator taxa. Based on our results, the following recommendations are made: 1. There is a need to establish a global consensus on which taxa are VME indicators. 2. RFMO/As should consider adopting guidelines that use imagery surveys as an alternative (or complement) to using bycatch and trawl surveys for designating VMEs. 3. Imagery surveys should also be included in Impact Assessments. And 4. All industries that impact the seafloor, not just fisheries, should use imagery surveys to detect and identify VMEs.

A modelling framework to assess multiple metals impacts on marine food webs: Relevance for assessing the ecological implications of deep-sea mining based on a systematic review.

Industrial deep-sea mining will release plumes containing metals that may disperse over long distances; however, there is no general understanding of metal effects on marine ecosystems. Thus, we conducted a systematic review in search of models of metal effects on aquatic biota with the future perspective to support Environmental Risk Assessment (ERA) of deep-sea mining. According to results, the use of models to study metal effects is strongly biased towards freshwater species (83% freshwater versus 14% marine); Cu, Hg, Al, Ni, Pb, Cd and Zn are the best-studied metals, and most studies target few species rather than entire food webs. We argue that these limitations restrain ERA on marine ecosystems. To overcome this gap of knowledge, we suggest future research directions and propose a modelling framework to predict the effects of metals on marine food webs, which in our view is relevant for ERA of deep-sea mining.

Deep-sea impacts of climate interventions.

Ocean manipulation to mitigate climate change may harm deep-sea ecosystems.

Delayed response of hermit crabs carrying anemones to a benthic impact experiment at the deep-sea nodule fields of the Peru Basin?

The deep Peru Basin is characterised by a unique abyssal scavenging community featuring large numbers of hermit crabs (Probeebei mirabilis, Decapoda, Crustacea). These are atypical hermit crabs, not carrying a shell, but on some occasions carrying an anemone (Actiniaria). The reason why some hermit crabs carry or not carry anemones is thought to be indicative of a changed environment, outweighing the cost/benefit of their relationship. Here we present the temporal variation of abundances of P. mirabilis with and without anemones, spanning more than two decades, following a benthic impact experiment. An overall decrease in hermit crab densities was observed, most noticeable and significant after 26 years and characterised by a loss of Actiniaria on the Probeebei mirabilis' pleon. Whether this is a delayed response to the benthic impact experiment carried out 26 years' prior or a natural variation in the population remains to be corroborated by an extension of the time-series. Attention is drawn to the limitations of our knowledge over time and space of the abyssal community dynamics and the urgent necessity to fill in these gaps prior to any type of deep-sea exploitation.

MesopTroph, a database of trophic parameters to study interactions in mesopelagic food webs.

Mesopelagic organisms play a crucial role in marine food webs, channelling energy across the predator-prey network and connecting depth strata through their diel vertical migrations. The information available to assess mesopelagic feeding interactions and energy transfer has increased substantially in recent years, owing to the growing interest and research activity in the mesopelagic realm. However, such data have not been systematically collated and are difficult to access, hampering estimation of the contribution of mesopelagic organisms to marine ecosystems. Here we present MesopTroph, a georeferenced database of diet, trophic markers, and energy content of mesopelagic and other marine taxa compiled from 203 published and non-published sources. MesopTroph currently includes data on stomach contents, carbon and nitrogen stable isotopes, major and trace elements, energy density, fatty acids, trophic positions, and diet proportion estimates for 498 species/genera. MesopTroph will be expanded with new data emerging from ongoing studies. MesopTroph provides a unique tool to investigate trophic interactions and energy flow mediated by mesopelagic organisms, and to evaluate the ecosystem services of this community.

Biodiversity, environmental drivers, and sustainability of the global deep-sea sponge microbiome.

In the deep ocean symbioses between microbes and invertebrates are emerging as key drivers of ecosystem health and services. We present a large-scale analysis of microbial diversity in deep-sea sponges (Porifera) from scales of sponge individuals to ocean basins, covering 52 locations, 1077 host individuals translating into 169 sponge species (including understudied glass sponges), and 469 reference samples, collected anew during 21 ship-based expeditions. We demonstrate the impacts of the sponge microbial abundance status, geographic distance, sponge phylogeny, and the physical-biogeochemical environment as drivers of microbiome composition, in descending order of relevance. Our study further discloses that fundamental concepts of sponge microbiology apply robustly to sponges from the deep-sea across distances of >10,000 km. Deep-sea sponge microbiomes are less complex, yet more heterogeneous, than their shallow-water counterparts. Our analysis underscores the uniqueness of each deep-sea sponge ground based on which we provide critical knowledge for conservation of these vulnerable ecosystems.

A knowledge graph to interpret clinical proteomics data.

Implementing precision medicine hinges on the integration of omics data, such as proteomics, into the clinical decision-making process, but the quantity and diversity of biomedical data, and the spread of clinically relevant knowledge across multiple biomedical databases and publications, pose a challenge to data integration. Here we present the Clinical Knowledge Graph (CKG), an open-source platform currently comprising close to 20 million nodes and 220 million relationships that represent relevant experimental data, public databases and literature. The graph structure provides a flexible data model that is easily extendable to new nodes and relationships as new databases become available. The CKG incorporates statistical and machine learning algorithms that accelerate the analysis and interpretation of typical proteomics workflows. Using a set of proof-of-concept biomarker studies, we show how the CKG might augment and enrich proteomics data and help inform clinical decision-making.

Overexpression of miR-124 in Motor Neurons Plays a Key Role in ALS Pathological Processes.

miRNA(miR)-124 is an important regulator of neurogenesis, but its upregulation in SOD1G93A motor neurons (mSOD1 MNs) was shown to associate with neurodegeneration and microglia activation. We used pre-miR-124 in wild-type (WT) MNs and anti-miR-124 in mSOD1 MNs to characterize the miR-124 pathological role. miR-124 overexpression in WT MNs produced a miRNA profile like that of mSOD1 MNs (high miR-125b; low miR-146a and miR-21), and similarly led to early apoptosis. Alterations in mSOD1 MNs were abrogated with anti-miR-124 and changes in their miRNAs mostly recapitulated by their secretome. Normalization of miR-124 levels in mSOD1 MNs prevented the dysregulation of neurite network, mitochondria dynamics, axonal transport, and synaptic signaling. Same alterations were observed in WT MNs after pre-miR-124 transfection. Secretome from mSOD1 MNs triggered spinal microglia activation, which was unno-ticed with that from anti-miR-124-modulated cells. Secretome from such modulated MNs, when added to SC organotypic cultures from mSOD1 mice in the early symptomatic stage, also coun-teracted the pathology associated to GFAP decrease, PSD-95 and CX3CL1-CX3CR1 signaling im-pairment, neuro-immune homeostatic imbalance, and enhanced miR-124 expression levels. Data suggest that miR-124 is implicated in MN degeneration and paracrine-mediated pathogenicity. We propose miR-124 as a new therapeutic target and a promising ALS biomarker in patient sub-populations.

Spatially and cell-type resolved quantitative proteomic atlas of healthy human skin.

Human skin provides both physical integrity and immunological protection from the external environment using functionally distinct layers, cell types and extracellular matrix. Despite its central role in human health and disease, the constituent proteins of skin have not been systematically characterized. Here, we combine advanced tissue dissection methods, flow cytometry and state-of-the-art proteomics to describe a spatially-resolved quantitative proteomic atlas of human skin. We quantify 10,701 proteins as a function of their spatial location and cellular origin. The resulting protein atlas and our initial data analyses demonstrate the value of proteomics for understanding cell-type diversity within the skin. We describe the quantitative distribution of structural proteins, known and previously undescribed proteins specific to cellular subsets and those with specialized immunological functions such as cytokines and chemokines. We anticipate that this proteomic atlas of human skin will become an essential community resource for basic and translational research ( https://skin.science/ ).

Deep-Sea Misconceptions Cause Underestimation of Seabed-Mining Impacts.

Scientific misconceptions are likely leading to miscalculations of the environmental impacts of deep-seabed mining. These result from underestimating mining footprints relative to habitats targeted and poor understanding of the sensitivity, biodiversity, and dynamics of deep-sea ecosystems. Addressing these misconceptions and knowledge gaps is needed for effective management of deep-seabed mining.

Integrative Analysis Identifies Key Molecular Signatures Underlying Neurodevelopmental Deficits in Fragile X Syndrome.

BACKGROUND: Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by epigenetic silencing of FMR1 and loss of FMRP expression. Efforts to understand the molecular underpinnings of the disease have been largely performed in rodent or nonisogenic settings. A detailed examination of the impact of FMRP loss on cellular processes and neuronal properties in the context of isogenic human neurons remains lacking. METHODS: Using CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 to introduce indels in exon 3 of FMR1, we generated an isogenic human pluripotent stem cell model of FXS that shows complete loss of FMRP expression. We generated neuronal cultures and performed genome-wide transcriptome and proteome profiling followed by functional validation of key dysregulated processes. We further analyzed neurodevelopmental and neuronal properties, including neurite length and neuronal activity, using multielectrode arrays and patch clamp electrophysiology. RESULTS: We showed that the transcriptome and proteome profiles of isogenic FMRP-deficient neurons demonstrate perturbations in synaptic transmission, neuron differentiation, cell proliferation and ion transmembrane transporter activity pathways, and autism spectrum disorder-associated gene sets. We uncovered key deficits in FMRP-deficient cells demonstrating abnormal neural rosette formation and neural progenitor cell proliferation. We further showed that FMRP-deficient neurons exhibit a number of additional phenotypic abnormalities, including neurite outgrowth and branching deficits and impaired electrophysiological network activity. These FMRP-deficient related impairments have also been validated in additional FXS patient-derived human-induced pluripotent stem cell neural cells. CONCLUSIONS: Using isogenic human pluripotent stem cells as a model to investigate the pathophysiology of FXS in human neurons, we reveal key neural abnormalities arising from the loss of FMRP.

The proteome landscape of the kingdoms of life.

Proteins carry out the vast majority of functions in all biological domains, but for technological reasons their large-scale investigation has lagged behind the study of genomes. Since the first essentially complete eukaryotic proteome was reported1, advances in mass-spectrometry-based proteomics2 have enabled increasingly comprehensive identification and quantification of the human proteome3-6. However, there have been few comparisons across species7,8, in stark contrast with genomics initiatives9. Here we use an advanced proteomics workflow-in which the peptide separation step is performed by a microstructured and extremely reproducible chromatographic system-for the in-depth study of 100 taxonomically diverse organisms. With two million peptide and 340,000 stringent protein identifications obtained in a standardized manner, we double the number of proteins with solid experimental evidence known to the scientific community. The data also provide a large-scale case study for sequence-based machine learning, as we demonstrate by experimentally confirming the predicted properties of peptides from Bacteroides uniformis. Our results offer a comparative view of the functional organization of organisms across the entire evolutionary range. A remarkably high fraction of the total proteome mass in all kingdoms is dedicated to protein homeostasis and folding, highlighting the biological challenge of maintaining protein structure in all branches of life. Likewise, a universally high fraction is involved in supplying energy resources, although these pathways range from photosynthesis through iron sulfur metabolism to carbohydrate metabolism. Generally, however, proteins and proteomes are remarkably diverse between organisms, and they can readily be explored and functionally compared at www.proteomesoflife.org.

Climate change considerations are fundamental to management of deep-sea resource extraction.

Climate change manifestation in the ocean, through warming, oxygen loss, increasing acidification, and changing particulate organic carbon flux (one metric of altered food supply), is projected to affect most deep-ocean ecosystems concomitantly with increasing direct human disturbance. Climate drivers will alter deep-sea biodiversity and associated ecosystem services, and may interact with disturbance from resource extraction activities or even climate geoengineering. We suggest that to ensure the effective management of increasing use of the deep ocean (e.g., for bottom fishing, oil and gas extraction, and deep-seabed mining), environmental management and developing regulations must consider climate change. Strategic planning, impact assessment and monitoring, spatial management, application of the precautionary approach, and full-cost accounting of extraction activities should embrace climate consciousness. Coupled climate and biological modeling approaches applied in the water and on the seafloor can help accomplish this goal. For example, Earth-System Model projections of climate-change parameters at the seafloor reveal heterogeneity in projected climate hazard and time of emergence (beyond natural variability) in regions targeted for deep-seabed mining. Models that combine climate-induced changes in ocean circulation with particle tracking predict altered transport of early life stages (larvae) under climate change. Habitat suitability models can help assess the consequences of altered larval dispersal, predict climate refugia, and identify vulnerable regions for multiple species under climate change. Engaging the deep observing community can support the necessary data provisioning to mainstream climate into the development of environmental management plans. To illustrate this approach, we focus on deep-seabed mining and the International Seabed Authority, whose mandates include regulation of all mineral-related activities in international waters and protecting the marine environment from the harmful effects of mining. However, achieving deep-ocean sustainability under the UN Sustainable Development Goals will require integration of climate consideration across all policy sectors.

Wait your turn, North Atlantic fin whales share a common feeding ground sequentially.

Highly migratory marine species pose a challenge for the identification of management units due to the absence of clear oceanographic barriers. The population structure of North Atlantic fin whales has been investigated since the start of whaling operations but is still the subject of an ongoing scientific debate. Here we measured stable isotopes of carbon, nitrogen and oxygen in skin samples collected from 151 individuals from western Iceland, Galicia (NW Spain), the Azores archipelago and the Strait of Gibraltar (SoG). We found spatiotemporal differences in stable isotope ratios suggesting that fin whales sampled in these four areas may share a common feeding ground within the Northeast Atlantic at different times during the year. Our results also suggest that SoG whales use this common feeding ground in summer but exploit Mediterranean resources during the winter months, further supporting the existence of a limited but current exchange of individuals between these two basins.