Biology subjects

Casini, M.

Publications and source records attributed to Casini, M..

11 recordsLinked to original sources

bioRxiv2025

Peroxisome protein import deficiency causes heart failure in mouse and human

Peroxisomes are ubiquitous cellular organelles with potentially vital roles in lipid and reactive oxygen metabolism. The metabolic demands of the heart are substantial; however, the contribution of peroxisomes to cardiac development, health, and their role in heart failure (HF) remain largely unexplored. We developed and examined a mouse and an engineered human myocardium (EHM) model with a deficiency in cardiac peroxisome biogenesis to investigate the role of peroxisomes in cardiac function and pathology. In the EHM, loss of peroxisome protein import and subsequent peroxisomal metabolic impairment trigger mitochondrial damage and compromise cellular respiration and energy production. Peroxisome dysfunction results in incoherent electrical conduction, defective Ca2+-handling, and ultimately presentation of a HF phenotype with pathological force generation. These phenotypes are mirrored in an orthogonal murine model system with defective cardiac peroxisome biogenesis. Preload-dependent deficits in force generation due to insufficient energy supply are eventually fatal. Thus, peroxisomes play an important role in sustaining normal heart operations. Vice versa, peroxisome maintenance is compromised in pressure overload-induced HF, establishing peroxisomes as potential modulators of pathology and targets of therapy.

cell biology↗

bioRxiv2025

Weak effects of local prey density and spatial overlap on predation intensity in a temperate marine ecosystem

Quantifying the impact of lower trophic level species abundance on higher trophic level predators (and vice versa) is critical for understanding marine ecosystem dynamics and for implementing ecosystem-based management. Trophic ecosystem models generally predict a tight coupling between prey and fish predators, such that higher abundance of lower trophic species increases abundance of higher trophic level predators. This assumes that predator feeding rates are limited by prey availability to some degree. Despite being a key component of predator-prey interactions and multi-species fisheries management, relatively few studies have assessed the impacts of prey availability on predation patterns of mobile, generalist fish predators using spatiotemporal models and local-scale stomach content, predator, and prey data. In this study, we explore the association between local density of key prey and predator stomach contents, and predator-prey spatiotemporal overlap and predation indices, using the Baltic Sea as a case study. We use three decades of spatially resolved biomass and stomach content data on Atlantic cod (Gadus morhua), and biomass data on three of its key prey: herring (Clupea harengus), the isopod Saduria entomon, and sprat (Sprattus sprattus). Using geostatistical generalized linear mixed effects models fitted to relative biomass density and prey-weight-per-predator-weight, we estimate spatiotemporal trends and annual indices of biomass weighted and area-expanded per-capita and population-level predation, predator-prey overlap, and the correlation between these indices. Range shifts have resulted in reduced predator-prey overlap over time, which is now the lowest in three decades. For Saduria, we find an association between prey availability and stomach contents, but not for herring or sprat. Similarly, only in Saduria do we find a positive correlation between population-level predation indices and the spatiotemporal overlap. Although behavioral interactions with pelagic prey are challenging to infer from stomach content and acoustic data due to high mobility leading to fine-scale spatiotemporal mismatch, the weak connection with local-scale availability, and low correlation between population-level predation and spatial overlap, could imply weaker coupling between pelagic prey and cod than previously thought. These findings provide key information on the strength of species interactions, which is crucial for the continued development of multispecies models and ecosystem-based fisheries management.

ecology↗

bioRxiv2025

Sex-related gut microbiota in three geographically separated Norway lobster (Nephrops norvegicus) populations

Despite the ecological and economic interest of the Norway lobster (Nephrops norvegicus), its gut microbiota remains largely understudied. The current study aimed at investigating the gut bacterial microbiota in three geographically separated N. norvegicus populations from the Mediterranean and the North Sea and detecting any potential sex-related microbiota differences, by high-throughput sequencing of the V3-V4 16S rRNA gene diversity of the gut tissue. From the Greek population, egg-bearing females were also caught. A total of 2,385 operational taxonomic units (OTUs) were identified and between 417 and 1290 occurred in each population/sex group. The dominant OTUs belonged to the Fusobacteriia and Bacteroidia (Sweden), Bacilli and Gammaproteobacteria (Italy) and Spirochaetia and Bacilli (Greece) bacterial classes. In the eggs, the Actinobacteria, Alphaproteobacteria and Gammproteobacteria prevailed. Four OTUs related to the Oceanispirochaeta, Kordiimonas, Desulfovibrio, Carboxylicivirga genera and one unafilliated OTU were positively correlated (p values between 0.001 and 0.04) to body size indicating their potential role in the animals nutrition and growth. No statistically significant differences were found between males-females in each of the three populations. However, statistically significant differences between populations for each sex, were found for all females (p values between 0.008 and 0.032) and for the males between the most distant populations, i.e. Italy-Sweden (p=0.021) and Greece-Sweden (p=0.015). The eggs microbiota was statistically different from both the adult females (p=0.027) and males (p=0.046) gut microbiota. Overall, this study showed that N. norvegicus gut microbiota are differentiated between geographically distant populations and that sex-related differences are not significant.

microbiology↗

bioRxiv2024

Quantifying competition between two demersal fish species from spatiotemporal stomach content data

Inference on competition is often made on indirect patterns of potential competition, such as population trends and spatiotemporal overlap in diet and distribution. However, these indicators do not test if the contested resources are limited in supply, nor if they decline as competitor biomass increases. Using stomach content and biomass data, we evaluate food competition between Atlantic cod (Gadus morhua) and flounder (Platichthys spp.) in the Baltic Sea. We quantify diet overlap and fit geostatistical mixed models to evaluate effects of local-scale covariates on stomach contents. The dietary overlap is low and does not decline with predator density. We find that cod feed less on the isopod Saduria entomon at high flounder densities. However, the total prey weight in cod is not affected by flounder densities. This suggests interspecific food competition is not limiting the overall feeding of cod, but affects its diet composition. In addition, we find support for intraspecific food competition in large cod and flounder. Our study illustrates the importance of local-scale processes when inferring competition from stomach content data.

ecology↗

bioRxiv2023

Assessing the overlap between fishing activities and chondrichthyans distribution exposes high-risk areas for bycatch of threatened species

Sharks, rays, and chimaeras (chondrichthyans) play a crucial role in marine ecosystem functioning but are highly vulnerable to fishing. Hence, understanding the spatial overlap between chondrichthyans and fishing effort is essential for effective conservation and management. Here, we propose an integrated approach that combines Vessel Monitoring System data with geostatistical species distribution models to assess the potential impact of fishing on chondrichthyan populations in the western Adriatic Sea. By mapping the overlap between model-based chondrichthyan distribution, species richness, and the proportion of threathened species with bottom trawl fishing activities, we identify areas at high risk for chondrichthyan bycatch. Our findings show that many of these species are at risk across a large part of their distribution within the study area. Notably, there is a substantial spatial overlap between regions where threatened chondrichthyans are found and species-rich areas with locations of intensive bottom trawl fishing in the northern and central offshore regions of the western Adriatic, emphasizing the vulnerability of these species to fishing pressure. Furthermore, differences in overlap between distinct fishing gears highlight the importance of considering specific fishing practices when formulating management strategies. While our work provides novel insights to potential bycatch hotspots, limitations related to data sources, spatial resolution, and the inability to directly quantify fishing impacts should be considered. Nonetheless, our findings contribute to the development of targeted conservation and spatial management measures, offering a general approach to study model-based spatial hotspots aimed at protecting and sustaining chondrichthyan populations in the heavily exploited Adriatic Sea.

ecology↗

bioRxiv2023

Spatio-temporal patterns of whiting (Merlangius merlangus) in the Adriatic Sea under environmental forcing

Understanding how environmental factors affect species distribution is crucial for the conservation and management of marine organisms, especially in the face of global changes. Whiting (Merlangius merlangus) is a demersal temperate fish, considered a relict species in the Adriatic Sea. Despite its significance to commercial fisheries in the region, the specific drivers behind its spatial and temporal patterns have not been thoroughly examined. Here, we fitted a set of Generalized Linear Mixed Effects Models to data collected in the Northern and Central Adriatic from 1999 to 2019 during the Mediterranean International Trawl Survey to investigate the potential influence of depth, seafloor temperature and bottom dissolved oxygen on the annual biomass density and spatial distribution of whiting. Our results showed that depth, and to a lesser degree temperature and oxygen, are important predictors of whiting distribution in spring-summer, with preferences for depths of [~] 45 m, temperature of [~] 15.4 {degrees}C and dissolved oxygen > 5.5 ml L-1. We predicted a persistent core area of distribution in front of the Po River Delta, in the Northern Adriatic Sea, while the density progressively declined towards the Central and Southern Adriatic Sea along the Italian coast. Additionally, the temporal trend exhibited high fluctuations over the years, occurring in cycles of 3 to 4 years. Finally, by comparing the biomass density estimates obtained under optimum conditions with those derived from the actual values for each variable, our analysis revealed that temperature had a pronounced and general impact on biomass density in the northern survey area (prediction revealed a ratio of density reduction of approximatively a half), while oxygen displayed a minor and more localized influence. This work deepens the current knowledge about the ecology of whiting in the Adriatic Sea and provides support for the conservation and management of this species.

ecology↗

bioRxiv2023

Declining food availability and habitat shifts drive community responses to marine hypoxia

Worsening marine hypoxia has had severe negative consequences for fish communities across the globe. While individual{-} and population{-}level impacts of deoxygenation have been identified, it is unknown how they interact to drive changes in food webs. To address this, we incorporated several major impacts of hypoxia, including declines in benthic re{-} sources, habitat shifts, increasing mortality, and changes to rates of feeding, assimilation, and reproductive efficiency, into an existing size spectrum food web modeling framework. We used this structure to ask the following questions: which of these direct effects are most critical to capturing population and community dynamics in a representative hypoxic system, how do they interact to result in community responses to deoxygenation, and what are the potential consequences of these effects in the context of accelerating deoxygenation? We tested the effect of different combinations of oxygen{-}dependent processes, driven by observed oxygen levels, on the food web models ability to explain time series of observed somatic growth, diets, biomass, and fishery yields of commercially relevant species in the Baltic Sea. Model results suggest that food availability is most critical to capturing observed dynamics. There is also some evidence for oxygen{-}dependent habitat use and physological rates as drivers of observed dynamics. Deoxygenation results in declining growth both of benthic and benthopelagic fish species, as the latter are unable to compensate for the loss of benthic resources by consuming more pelagic fish and resources. Analysis of scenarios of ideal, declining, and degraded oxygen conditions show that deoxygenation results in a decline in somatic growth of predators, an altered habitat occupancy resulting in changing species interactions, and a shift in energy flow to benthopelagic predators from benthic to pelagic resources. This may have important implications for management as oxygen declines or improves.

ecology↗

bioRxiv2022

Evaluating drivers of spatiotemporal individual condition of a bottom-associated marine fish

An organisms body condition describes its mass given its length and is often positively associated with fitness. The condition of Atlantic cod (Gadus morhua) in the Baltic Sea has declined dramatically since the early 1990s, possibly due to increased competition, food limitation, and hypoxia. However, the effect of biotic and abiotic variables on body condition have not been evaluated at local scales, which is important given spatial heterogeneity. We evaluate changes in distribution, experienced environmental conditions, and individual-level condition of cod in relation to covariates at different spatial scales using geostatistical models with spatial and spatiotemporal random effects. Oxygen, sprat biomass, and temperature were positively related to condition, and depth negatively associated, but the effect sizes of these variables were small--spatial and spatiotemporal latent variables explained almost five times more variation than fixed effects. We also show that accounting for the heterogenous distribution of cod leads to both lover levels and steeper trends over time in experienced oxygen compared to those in the environment. Understanding the drivers of spatiotemporal variation in body condition is critical for predicting responses to environmental change and to effective fishery management; yet low explanatory power of covariates on individual condition constitutes a major challenge.

ecology↗

bioRxiv2020

The genetic architecture underlying ecological adaptation in Atlantic herring is not consistent with the infinitesimal model

Atlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic adaptation due to minute genetic differentiation at selectively neutral loci. Here we report hundreds of loci underlying ecological adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying ecological adaptation in the herring is in conflict with the infinitesimal model for complex traits because of the large shifts in allele frequencies at hundreds of loci under selection.

evolutionary biology↗

bioRxiv2017

Improved management facilitates return of an iconic fish species

Species declines and losses of biota are often associated with shifting baselines in perceived historical abundances, and/or neglect or abandonment of recovery actions aimed at ecological restoration. Such declines are frequently accompanied by contractions in the geographical distribution of the species, with associated negative ecological impacts and diminishing socio-economic benefits. Here we show using citizen science and other data that after 50-60 years of near total absence, the iconic top predator and highly migratory species bluefin tuna, Thunnus thynnus, returned by the hundreds if not thousands in waters near Denmark, Norway and Sweden during August-October 2015-2017. The re-utilisation of this former habitat is part of a geographically more widespread expansion of the summer foraging area to the northern part of the northeast Atlantic Ocean, encompassing waters from east Greenland to west Sweden. The remarkable return to the Skagerrak, Kattegat and North Sea has been facilitated by improved fishery management for bluefin tuna and its prey. Bluefin tuna biomass in the northeast Atlantic and Mediterranean has been increasing since a recovery plan was implemented in the late 2000s, and biomasses of two key prey species (herring, Clupea harengus; mackerel, Scomber scombrus) recovered during the late 1980s-1990s. The reappearance of bluefin tuna in the Skagerrak-Kattegat and other waters of northern Europe, despite a recent history of mismanagement and illegal fishing in the northeast Atlantic and Mediterranean which led to a critical population decline, offers hope that other marine ecological recoveries are possible under improved management of fisheries and ecosystems. One Sentence SummaryImproved management promotes the return of an ocean icon to northern Europe. Significance StatementCommercial fisheries are often perceived being in a state of decline and collapse, putting food and economic security at risk. Such declines are frequently accompanied by contractions in stock distribution, negative ecological impacts and diminishing socio-economic benefits. Here we present an example based on one of the worlds most valuable and iconic fish species, bluefin tuna, which demonstrates that effective management of both bluefin tuna and its prey has been a key factor leading to a remarkable reoccupation of formerly lost habitat. This reappearance, following decades of absence, occurred despite the bluefin tuna stock having had a recent, long history of unsustainable and illegal exploitation. Marine ecological recovery actions can be successful, even in situations which may initially appear intractable.

ecology↗

bioRxiv2017

Moderate Nucleotide Diversity In The Atlantic Herring Is Associated With A Low Mutation Rate

The Atlantic herring (Clupea harengus) is one of the most abundant vertebrates on earth but its nucleotide diversity is moderate ({pi}=0.3%), only three-fold higher than in human. The expected nucleotide diversity for selectively neutral alleles is a function of population size and the mutation rate, and it is strongly affected by demographic history. Here, we present a pedigree-based estimation of the mutation rate in the Atlantic herring. Based on whole-genome sequencing of four parents and 12 offspring, the estimated mutation rate is 1.7 x 10-9 per base per generation. There was no significant difference in the frequency of paternal and maternal mutations (8 and 7, respectively). Furthermore, we observed a high degree of parental mosaicism indicating that a large fraction of these de novo mutations occurred during early germ cell development when we do not expect a strong gender effect. The now estimated mutation rate - the lowest among vertebrates analyzed to date - partially explains the discrepancy between the rather low nucleotide diversity in herring and its huge census population size (>1011). But our analysis indicates that a species like the herring will never reach its expected nucleotide diversity for selectively neutral alleles primarily because of fluctuations in population size due to climate variation during the millions of years it takes to build up a high nucleotide diversity. In addition, background selection and selective sweeps lead to reductions in nucleotide diversity at linked neutral sites.

genomics↗