Biology subjects

Paredes, E.

Publications and source records attributed to Paredes, E..

9 recordsLinked to original sources

bioRxiv2026

Experimental evidence for antagonistic effects of sperm competition in two sea urchin species

Sperm competition can occur when sperm from two or more males compete for fertilization of a batch of eggs. While it has been extensively studied in internal fertilizers, it remains poorly under-stood in external fertilizers. To investigate how sperm competition affects fertilization under sperm limitation, we conducted controlled experiments on two sea urchin species: Paracentrotus lividus and Dendraster excentricus. Eggs from a single female were exposed to sperm from three individ-ual males separately (non-competitive treatment) or to a pooled sample from three males (competi-tive treatment). We measured fertilization success as proportion of eggs fertilized after two hours and assessed sperm motility as percentage of motile sperm and curvilinear velocity. For P. lividus , we estimated the sperm concentrations where fertilization success was 50% of maximum observed fertilization success (F50), and the fertilization efficiency of the sperm (Fe), i.e. the likelihood that a sperm - egg encounter results in a fertilizing contact, using the fertilization kinetics model of Styan (1998). For D. excentricus, fertilization success was measured at a sperm concentration expected to produce 50% fertilization success. Sperm competition reduced fertilization success and increased F50 compared to non-competitive treatments, suggesting antagonistic effects that may compromise fertilization under sperm-limited conditions in external fertilizers.

evolutionary biology↗

bioRxiv2025

Korean Natural Farming practices are dominated by a limited number of microbes and decrease fungal diversity

Korean Natural Farming (KNF) practices claim to cultivate and transfer "indigenous micro-organisms" (IMOs) to donor soils as a method of probiotic soil enhancement. We investigated whether IMO cultivation can propagate unique microbiomes and maintain microbial diversity through successive IMO stages for restoration of flood contaminated soils. Employing a balanced study design using soil samples from salt marsh, deciduous forest, and urban greenspace (plus sterilized controls), samples underwent the first two IMO cultivation steps followed by 16S rRNA and ITS metagenomic sequencing. Notably, IMO cultivation was dominated by limited bacterial taxa (Enterobacterales, Pseudomonadales, Bacillales) and fungal taxa (Rhizopodaceae, particularly R. oryzae). While bacterial diversity was maintained or increased during two IMO stages, fungal diversity consistently decreased. Principal Coordinates Analysis also revealed distinct clustering by inoculum source (i.e. human-altered, human- transported (HAHT) vs. natural vs. sterile) that persisted throughout cultivation. Our evidence suggests that the IMO process enriches for specific taxa likely adapted to cultivated conditions and fails to maintain fungal diversity, contrasting greatly with KNFs proposed benefit of propagating locale-specific, fungal-dominated indigenous microbiomes. However, our results demonstrate that early IMO cultures may capture and sustain bacterial diversity in soil, opening the door for future studies of KNF efficacy and sustainability. Sustainability StatementThis work is primarily associated with UN Sustainable Development Goal SDG 15 (Life on Land). By scientifically evaluating Korean Natural Farming "indigenous Microorganism" (IMO) practices through metagenomic sequencing, this study provides evidence-based insights into microbial community dynamics relevant to soil restoration and terrestrial ecosystem health. The findings inform low-cost bioremediation strategies for flood- contaminated urban soils, which is of growing importance as climate-driven extreme precipitation events intensify. Additional relevant SDGs include: SDG 13 (Climate Action), SDG 11 (Sustainable Cities and Communities), SDG 2 (Zero Hunger), and SDG 3 (Good Health and Well-being).

microbiology↗

bioRxiv2025

Cryopreservation of Platynereis dumerilii larvae

The marine annelid Platynereis dumerilii is a functional molecular model organism for developmental, evolutionary and chronobiological studies. Research on Platynereis is rapidly growing, and with it, the number of genetic variants that laboratories isolate or generate and must subsequently maintain and propagate. Therefore, there is an urgent need to alleviate the burden of live culture maintenance by developing cryopreservation techniques for this species. We report the first cryopreservation protocol for P. dumerilii larvae, which combined with a careful post-thawing culturing regime, allowed us to obtain animals that survived to adulthood and successfully reproduced. Our experiments show highest survival rate in 6 - 8 day-old larvae. Equilibration with cryoprotecting agents takes 1h in 5% (v/v) Me2SO + 0.1%(v/w) sucrose, followed by transfer to 0.25ml straws. The protocol cools larvae at 2,5{degrees}C/min from 20{o}C to -35{degrees}C using a programmable freezer, followed by a rapid transfer to liquid N2. Larvae are thawed in a water bath at 18{degrees}C. The post-thaw larvae feeding regime consisted of 50% Tetraselmis + 50 % diatom strains mixture (Grammatophora marina and Nitzschia laevis). The maximum survival obtained with this protocol so far produced 34% survival after [~]5 months.

zoology↗

bioRxiv2025

Cryopreservation of Juvenile Mytilus galloprovincialis: Safeguarding Mollusk Biodiversity and Aquaculture

Mytilus galloprovincialis Lamarck, 1819, is a globally significant aquaculture species, contributing 25% of fresh seafood landings and leading EU mussel production. In Spain, it accounted for 255,218 tonnes in 2022, around 60% of the global harvest. This study introduces groundbreaking cryopreservation, being the first to successfully cryopreserve the juvenile stage of a marine organism, the largest marine organism ever cryopreserved. By optimizing feeding strategies, equilibration times, and cryoprotectant concentrations, we extended our initial protocol for young larvae to include complex larval stages (72h-26 days post-fertilization) and juveniles (40-45 days, up to 1 mm). These protocols mark a significant step in biodiversity conservation, seedstock preservation, genetic line maintenance, and sustainability of overexploited mollusk populations.

zoology↗

bioRxiv2024

Comprehensive Proteomic, Ultrastructural and Functional Analysis of Cryopreservation Effects on Marine Mussel Oocytes

Cryopreservation is a valuable tool for preserving marine genetic diversity and supporting selective breeding in aquaculture. The blue mussel (Mytilus galloprovincialis) is an important species for the aquaculture industry and a useful model for studying cryopreservation in marine invertebrates. Declining mussel seed availability over the past decade, combined with the growing demand for year-round hatchery production, has increased interest in developing effective cryopreservation methods for gametes and embryos. However, cryopreservation remains challenging, particularly for marine invertebrate oocytes, as it requires balancing cryoprotectant cytotoxicity with sufficient cell protection during freezing and thawing. Moreover, the molecular, structural, and functional changes associated with oocyte cryopreservation in invertebrates are still poorly understood. This study examines the effects of two commonly used cryoprotectants, dimethyl sulfoxide (DMSO) and ethylene glycol (EG), on M. galloprovincialis oocytes under a monitored slow freezing (MSF) protocol. Using an integrative analytical approach combining proteomics, functional assessments, and ultrastructural analyses, we provide a comprehensive understanding of cryoprotectant-induced changes. Our findings reveal that cryoprotectants cause significant proteomic alterations, with DMSO having more pronounced effects. These alterations are associated with increased oxidative stress, an insufficient antioxidant response, and disruptions in meiosis restart mechanisms, ultimately delaying larval development. Cryoprotectant-induced oxidative stress may also weaken the oocyte membrane, leading to rupture during the MSF protocol and subsequent fertilisation failure post-thawing. These results provide evidence that EG is less cytotoxic than DMSO and suggest that supplementing cryoprotectants with antioxidants and membrane stabilizers could enhance success rates in the cryopreservation of oocytes from mussels and other marine invertebrate species.

developmental biology↗

bioRxiv2024

A long-term ecological research data set from the marine genetic monitoring programme ARMS-MBON 2018-2020

Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document biodiversity of complex communities over large spatio-temporal scales. We established an international Marine Biodiversity Observation Network (ARMS-MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard-bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018-2019 and retrieved in 2018-2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open-access data set (image, genetic, and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to [~]5,500 amplicon sequence variants and [~]1,800 operational taxonomic units, and up to [~]250 and [~]50 species per observatory using the cytochrome c oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non-indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least three to six months during the main growth season to use resources as efficiently as possible and that post-sequencing curation is applied to enable statistical comparison of spatio-temporal entities. We suggest that ARMS should be used in biological monitoring programmes and long-term ecological research and encourage the adoption of our ARMS-MBON protocols.

ecology↗

bioRxiv2024

Cryopreservation Enables Long-Term Studies of Octopus vulgaris Hemocyte Immune Functions

As with their nervous system and other physiological traits, the immune system of cephalopods, in general, and of the common octopus, Octopus vulgaris, in particular, could also present highly evolved characteristics compared to other classes of molluscs. However, to date, there is not much information about it, and studying the defense mechanisms is a key step in understanding their response system to external aggressions and, thus, having the tools to anticipate animal health problems and ensure their welfare. The lack of cell cultures in molluscs is a major problem when carrying out in vitro assays that help to deepen the knowledge of the main immune cells of this species. Cryopreservation becomes an alternative to maintain viable and functional cells after freezing/thawing processes, allowing a larger repertoire of studies to be performed with the same sample or to perform time courses. Having access to good quality cells for long periods will allow to cover a larger repertoire of studies with the same sample or to perform time courses, avoiding logistic bottlenecks that could arise due to the loss of viability and/or functionality of the cells on the lab bench, the lack of time to develop all the desired assays in the same day or the possible losses derived from transporting the samples between different laboratories. Additionally, high-quality suspensions of viable and functional cells are required for successful massive sequencing studies, such as single-cell analysis, where these aspects are the key to an optimal identification. We show here the first functional results from cryopreserved octopus hemocytes, where the cells were able to maintain viability above 80% after two months post cryopreservation and storage at -80{degrees}C and their functional ability to phagocytose bacteria similar to fresh cells. Our data revealed that the acclimation process after thawing was essential to recovering the functional activity of the cells. The results presented here will facilitate the study of the functions of the most important immune cells of this species and will provide tools for cell preservation in other molluscs species.

immunology↗

bioRxiv2022

Osmotic, temperature, and cytotoxic damage in sea urchin oocytes

Sea urchin (Paracentrotus lividus) oocytes are an important species for aquaculture and as a model species for multiple scientific fields. Despite their importance, methods of cryopreserved biobanking of oocytes are currently not possible. Optimized cryoprotectant loading may enable vitrification methods of cryopreservation and thus long-term storage of oocytes. Determining an optimized protocol requires membrane characteristics and models of damage associated with the vitrification loading protocol, namely osmotic, temperature, and cytotoxic damage. We present and experimentally evaluated state-of-the-art models alongside our novel models. We experimentally verify the damage models throughout time at difference treatment intensities. Osmotic damage experiments consisted of hypertonic solutions composed of seawater supplemented with NaCl or sucrose and hypotonic solutions composed of seawater diluted with deionized water. Treatment times ranged from 2 to 30 minutes. To test temperature damage (in particular chill injury), oocytes were exposed to 1.7 {degrees}C, 10 {degrees}C, and 20 {degrees}C (control) for exposure times ranging from 2 to 90 minutes. Cytotoxicity was investigated by exposing oocytes to solutions of Me2SO for exposure times ranging from 2 to 30 minutes. We identify appropriate models and use these to search for an optimal loading protocol, namely the time dependent osmotic damage model (for osmotic damage), the temperature dependent model (for temperature damage), and the external molality Arrhenius power model (for cytotoxicity). We combined these models to estimate total damage during a cryopreservation loading protocol and performed a exhaustive grid search for optimal loading for a given goal intracellular cryoprotectant concentration. Given our fitted models, we find sea urchin oocytes can only be loaded to 0.13 Me2SO v/v with a 50% survival, For reference, levels for vitrification are approximately 0.45 v/v. Our synthesis of damages is the first of its kind, and enables a fundamentally novel approach to modelling survival for cells in general.

cell biology↗

bioRxiv2020

Cytoplasmic aggregation of uranium in human dopaminergic cells after continuous exposure to soluble uranyl at non-cytotoxic concentrations

Uranium exposure can lead to neurobehavioral alterations in particular of the monoaminergic system, even at non-cytotoxic concentrations. However, the mechanisms of uranium neurotoxicity after non-cytotoxic exposure are still poorly understood. In particular, imaging uranium in neurons at low intracellular concentration is still very challenging. We investigated uranium intracellular localization by means of synchrotron X-ray fluorescence imaging with high spatial resolution (< 300 nm) and high analytical sensitivity (< 1 g.g-1 per 300 nm pixel). Neuron-like SH-SY5Y human cells differentiated into a dopaminergic phenotype were continuously exposed, for seven days, to a non-cytotoxic concentration (10 M) of soluble natural uranyl. Cytoplasmic submicron uranium aggregates were observed accounting on average for 62% of the intracellular uranium content. In some aggregates, uranium and iron were co-localized suggesting common metabolic pathways between uranium and iron storage. Uranium aggregates contained no calcium or phosphorous indicating that detoxification mechanisms in neuron-like cells are different from those described in bone or kidney cells. Uranium intracellular distribution was compared to fluorescently labeled organelles (lysosomes, early and late endosomes) and to fetuin-A, a high affinity uranium-binding protein. A strict correlation could not be evidenced between uranium and the labelled organelles, or with vesicles containing fetuin-A. Our results indicate a new mechanism of uranium cytoplasmic aggregation after non-cytotoxic uranyl exposure that could be involved in neuronal defense through uranium sequestration into less reactive species. The remaining soluble fraction of uranium would be responsible for protein binding and the resulting neurotoxic effects.

pharmacology and toxicology↗