Biology subjects

Dubin, A.

Publications and source records attributed to Dubin, A..

7 recordsLinked to original sources

bioRxiv2024

Evaluating bacteriophage impact on gut microbiome composition in broad-nosed pipefish (Syngnathus typhle)

Bacteriophages play a crucial role in shaping microbial community dynamics in marine systems and have the potential to stimulate surges in pathogenic bacteria facilitating disease outbreaks. Notwithstanding, bacteriophages also serve as valuable biocontrol agents, underscoring their huge potential for aquaculture therapy treatments. Insights into the intricate tripartite interplay upon an infection with a virulent bacterium, its specific phages and the eukaryotic microbiome could improve our understanding of how bacteria-phage interactions behave in a natural microbial system. This investigation assessed the influence of a virulent Vibrio alginolyticus (K01M1) infection, in tandem with lytic ([fe]St2) and filamentous ([fe]K04M1) Vibrio-specific phages, on the broad-nosed pipefish (Syngnathus typhle) gut microbiome using 16S rRNA amplicon sequencing and non-intrusive gastric swabbing. Microbial communities and diversity metrics were not permanently impacted by Vibrio and phage introductions, while the different infection regimes shaped Vibrio-specific dynamics. In the filamentous phage and Vibrio-only treatments, V. alginolyticus abundances spiked 12 hours post-ingestion. In contrast, V. alginolyticus numbers in the lytic phage and control treatment were significantly reduced, suggesting phage activity and specific elimination of the introduced bacteria. Assisted by relative true-gut tissue samples, a newly implemented non-intrusive swabbing method was successful at discerning the activity of two contrasting phages and supports previous work that encourages the use of [fe]St2 in bacteriophage treatments. Identifying Vibrio-specific phages with similar positive characteristics could be beneficial for the aquaculture trade, which is currently heavily impacted by the antibiotic crisis.

microbiology↗

bioRxiv2024

Parent-specific transgenerational immune priming enhances offspring defense - unless heat-stress negates it all

Trans-generational immune priming (TGIP) adjusts offspring immune responses based on parental immunological experiences - a form of trans-generational plasticity predicted to be adaptive when parent-offspring environmental conditions match. In contrast, mis-matches between environmental conditions negate those advantages, rendering TGIP costly when mismatched immunological offspring phenotypes are induced. Particularly maternal TGIP was thought to shape offspring immunological preparedness: mothers eggs contain more substance than sperm and, in viviparous species, pregnancy provides additional avenues for immune priming of developing offspring. The syngnathids (pipefishes and seahorses) unique male pregnancy provides an unusual perspective to the ecological relevance of TGIP in a system where egg production and pregnancy occur in different sexes. We simulated parental bacteria exposure in broad nosed pipefish, Syngnathus typhle, through vaccinations with heat-killed Vibrio aestuarianus before mating the fish to each other or control individuals. Resulting offspring were raised, and some exposed to V. aestuarianus, in a control or heat-stress environment, after which transcriptome and microbiome compositions were investigated. Transcriptomic TGIP effects were only observed in Vibrio-exposed offspring at control temperatures, arguing for low costs of TGIP in non-matching environments. Transcriptomic phenotypes elicited by maternal and paternal TGIP had only limited overlap and were not additive. Both transcriptomic responses were significantly associated to immune functions, and specifically the paternal response to the innate immune branch. TGIP of both parents reduced the relative abundance of the experimental Vibrio in exposed offspring, showcasing its ecological effectiveness. Despite its significance in matching biotic environments, no TGIP-associated phenotypes were observed for heat-treated offspring. Heat-spikes caused by climate change thus threaten TGIP benefits, potentially increasing susceptibility to emerging marine diseases. This highlights the urgent need to understand how animals will cope with climate-induced changes in microbial assemblages by illustrating the importance - and limits - of TGIP in mitigating the impacts of environmental stressors on offspring vulnerability.

evolutionary biology↗

bioRxiv2023

Digital twinning of cardiac electrophysiology for congenital heart disease

In recent years, blending mechanistic knowledge with machine learning has had a major impact in digital healthcare. In this work, we introduce a computational pipeline to build certified digital replicas of cardiac electrophysiology in pediatric patients with congenital heart disease. We construct the patient-specific geometry by means of semi-automatic segmentation and meshing tools. We generate a dataset of electrophysiology simulations covering cell-to-organ level model parameters and utilizing rigorous mathematical models based on differential equations. We previously proposed Branched Latent Neural Maps (BLNMs) as an accurate and efficient means to recapitulate complex physical processes in a neural network. Here, we employ BLNMs to encode the parametrized temporal dynamics of in silico 12-lead electrocardiograms (ECGs). BLNMs act as a geometry-specific surrogate model of cardiac function for fast and robust parameter estimation to match clinical ECGs in pediatric patients. Identifiability and trustworthiness of calibrated model parameters are assessed by sensitivity analysis and uncertainty quantification.

bioengineering↗

bioRxiv2023

Sexual antagonism and sex determination in three syngnathid species alongside male pregnancy gradient and varying sex roles.

The allocation of energy towards gamete production, parental care, mate choice, sex roles, and sexual dimorphism generates divergence in selection pressures between the sexes, leading to opposing fitness strategies and sexual antagonism (SA). Due to the shared genetic makeup, a single genomic locus can contain a gene or allele with differing fitness impacts on each sex. This intralocus sexual conflict can be resolved via intersex bias in gene expression and/or formation of sex-linked genomic regions, that may also regulate sex determination. Sex determination (SD) encompasses environmental SD (ESD), monogenic SD, and polygenic SD. Occasionally, shifts from one SD locus to another can occur. While the precise mechanisms driving these shifts are unknown, SA is believed to be a major contributor. To investigate the link between SA and SD, we selected three syngnathid species along the gradient of male pregnancy that evolved with different sex roles and intensities of sexual dimorphism. By looking at intersex genetic divergence (Fst) and sex-biased expression patterns, we uncovered that sex role and mate competition, rather than male pregnancy, primarily drive SA. Furthermore, we identified processes related to non-coding RNAs and biased allele expression as mediators of SA. Most notably, we discovered intraspecies sex chromosome polymorphism in Hippocampus erectus. Overall, we report important details on the interplay between SA and SD, and suggest that understanding SA and its resolution mechanisms is crucial for unraveling the evolution of SD in diverse species.

evolutionary biology↗

bioRxiv2023

The effect of parental age on the quantity and quality of offspring in Syngnathus typhle, a species with male pregnancy.

Offspring quantity and quality are known to vary according to parental age, with most studies focusing on the mothers age, who produces costly eggs and often carries out pregnancy, hampering to distinction between trans-generational age effects due to egg quality or physiological deterioration. We investigated the ramification of parental age on the offspring in the broad-nosed pipefish Syngnathus typhle, a fish species with male pregnancy, allowing us to separate these two female traits. By mating parents of different sizes we examined the impact of parental age on offspring number, size and gene expression. Our results show that older parents produced more and larger-sized offspring. However, we revealed intriguing insights into the differential gene expression patterns in offspring, strongly influenced by the paternal lineage but minimally affected by maternal age. Offspring from old fathers exhibited notable changes in gene expression profiles, particularly related to cell cycle regulation, metabolism, protein synthesis, stress response, DNA repair and neurogenesis. Our findings provide valuable insights into the role of pregnancy in shaping offspring physiology. Moreover, we recognize the value of assessing a broader range of species that have evolved with sex-specific differences in parental investment vs. gamete provisioning, as the age of either the mother or father may hold greater significance than the other in influencing offspring fitness.

evolutionary biology↗

bioRxiv2023

Sex or sex role - unravelling the evolutionary route of sex-specific senescence

Sexual dimorphism, the divergence in morphological traits between males and females of the same species, is often accompanied by sex-biased gene expression. However, the majority of research has focused on species with conventional sex roles, where females have the highest energy burden with both egg production and parental care, neglecting the diversity of reproductive roles found in nature. We investigated sex-biased gene expression in the broadnosed pipefish (Syngnathus typhle), a sex-role reversed species with male pregnancy, allowing us to separate these two female traits. Employing RNA sequencing, we examined gene expression across organs (brain, head kidney, gonads) at various life stages, encompassing differences in age, sex, and reproductive status. While some gene groups were more strongly associated with sex roles, such as stress resistance and immune defence, others were driven by biological sex, such as energy and lipid storage regulation in an organ- and age-specific manner. By investigating how genes regulate and are regulated by changing reproductive roles and resource allocation in a model system with unconventional life-history strategy, we aim to enhance our understanding of the importance of sex and sex role in regulating gene expression patterns, broadening the scope of this discussion to encompass a wide range of organisms.

evolutionary biology↗

bioRxiv2018

OSCA/TMEM63 are an Evolutionarily Conserved Family of Mechanically Activated Ion Channels

IntroductionMechanotransduction, the conversion of mechanical cues into biochemical signals, is crucial for many biological processes in plants and animals1,2. In mammals, some mechanosensory processes such as touch sensation and vascular development are mediated by the PIEZO family of mechanically activated (MA) ion channels3-5. In plants, the impact of gravity or soil properties on root development, wind on stem growth, and turgor pressure on plant-cell size and shape are proposed to involve activation of MA ion channels6,7. Homologues of the bacterial MA channel MscS (MSLs) exist in plants, and MSL8 is shown to be involved in pollen hydration8; however, the identity of the MA channels required for most mechanotransduction processes in plants have remained elusive9. Here, we identify various members of the 15 OSCA proteins from Arabidopsis thaliana (previously reported as hyperosmolarity sensors10,11) as MA ion channels. Purification and reconstitution of OSCA1.2 in liposomes induced stretch-activated currents, suggesting that OSCAs are inherently mechanosensitive, pore-forming ion channels. This conclusion is confirmed by a high-resolution electron microscopy structure of OSCA1.2 described in a companion paper12. Beyond plants, we present evidence that fruit fly, mouse, and human TMEM63 family of proteins, homologues of OSCAs, induce MA currents when expressed in naive cells. Our results suggest that OSCA/TMEM63 proteins are the largest family of MA ion channels identified, and are conserved across eukaryotes. We anticipate that further characterization of OSCA isoforms which have diverse biophysical properties, will help gain substantial insight on the molecular mechanism of MA ion channel gating and permeation. OSCA1.1 mutant plants have impaired leaf and root growth under stress, potentially linking this ion channel to a mechanosensory role11. We expect future studies to uncover novel roles of OSCA/TMEM63 channels in mechanosensory processes across plants and animals.

biophysics↗