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Biology subjects

Cardenas, P.

Publications and source records attributed to Cardenas, P..

6 recordsLinked to original sources

Image-based ecological assessment of deep-sea sponge, coral and other cnidarian assemblages through a morpho-functional approach

AO_SCPLOWBSTRACTC_SCPLOWPorifera and Cnidaria are key phyla of marine ecosystem functioning. Slow-growing and long-lived, they show limited resilience to human disturbances and are therefore commonly used as indicator taxa of Vulnerable Marine Ecosystems. Their diversity and distribution largely rely on seafloor images, but image-based identification (ID) of sponges and cnidarians beyond class/order ranks is hindered by morphological plasticity and convergence, and the need of microscopic diagnostic characters or molecular markers that are not accessible on images. Higher-rank taxonomy also poorly reflects their morphological and functional diversity. To address this issue, we applied an image-based classification relying on multiple macro-morphological traits to define statistically morpho-functional groups (MFGs) based on these traits, then used as response variables in ecological analyses, instead of taxa. We applied this framework to seamounts and island slopes in the Mozambique Channel, a poorly sampled region where taxonomic limitations are acute. We aimed to evaluate the relevance of a sponge/cnidarian morpho-functional approach to characterise their diversity and distribution at multiscales, responses to environmental gradients and structuring roles on the megabenthic community. We identified 37 sponge and 34 cnidarian MFGs with varying distributions among sites. MFGs richness and beta diversity varied among seamounts, and between seamounts and island slopes. Hydrology explained 26% of the sponge MFG spatial structure at the channel scale, while topography and substrate played a main role at a smaller scale in the northern part of the channel (17-23%). Some sponge/cnidarian MFGs co-structured with other megabenthic taxa (e.g., sea urchins, comatulids, ophiuroids). This morpho-functional approach, especially effective for sponges, allowed quantifying morphological variation of habitat-forming taxa using qualitative traits, identifying environmental drivers shaping the spatial distribution of these traits, and characterising potential biogenic habitats they provide for other megabenthic organisms. The framework proposes metrics to detect and quantify the heterogeneity and spatial variability of potentially vulnerable biogenic habitats in imagery-based studies.

ecology↗

ARTIC RSV amplicon sequencing reveals global RSV genotype dynamics.

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections (LTRIs) in young children and adults over 65, contributing significantly to global healthcare burdens. With the recent approval of multiple pharmacological interventions for RSV, there is an increased demand for efficient, high-throughput sequencing methods to monitor RSV genetic diversity and any potential impact these interventions may have. Here we introduce two novel amplicon-based sequencing schemes designed for RSV A and B, optimised for integration with widespread existing ARTIC sequencing workflows. We demonstrate that these primer schemes can produce high quality genomes from RSV samples across the globe, with eight laboratories in five countries generating complete genomes on both Nanopore and Illumina sequencing platforms. The ability to effectively multiplex these RSV A and B primer schemes, enables streamlined, high-throughput sequencing without prior subtyping. Furthermore, these results provide a snapshot of the circulating diversity of RSV. Phylogenetic analysis of the 882 samples sequenced for this study suggests only minimal geographic clustering of RSV sequences, underscoring the global nature of RSV spread. It also highlights the distinct lineage dynamics seen between RSV A and B. This study represents an advancement in RSV genomics, providing robust tools for global sequencing efforts aimed at tracking RSV evolution and assessing the efficacy of new therapeutic interventions both rapidly and at scale.

genomics↗

Independent origins of spicules reconcile the evolutionary history of sponges

Sponges (Porifera) play a critical role in global biogeochemical processes. However, their evolutionary timeline remains unclear hampering our understanding of Neoproterozoic paleoecology. Molecular data suggest a Tonian or Cryogenian origin, while the oldest confirmed sponge fossils, represented by siliceous spicules, date to the Ediacaran. To understand this 150-million-year discrepancy, we compiled a new phylogenomic dataset, revised fossil evidence, derived a new dated sponge phylogeny, and tested whether ancestral sponges were aspiculated or not. We infer the last common sponge ancestor to have been early Ediacaran in age and aspiculated. Siliceous spicules evolved independently at least four times, and calcareous spicules at least two times in crown sponges. We performed a diversification rate analysis showing that siliceous spicules did not drive species radiations. Our study reconciles molecular and fossil evidence, indicating that while sponges emerged in the early Ediacaran, they are largely absent from the Neoproterozoic fossil record because they had not yet evolved spicules. TeaserSponges emerged in the Precambrian, were soft-bodied and did not produce mineralized spicules, which emerged multiple times independently.

evolutionary biology↗

Genomic epidemiological models describe pathogen evolution across fitness valleys

Genomics is fundamentally changing epidemiological research. However, systematically exploring hypotheses in pathogen evolution requires new modeling tools. Models intertwining pathogen epidemiology and genomic evolution can help understand processes such as the emergence of novel pathogen genotypes with higher transmissibility or resistance to treatment. In this work, we present Opqua, a flexible simulation framework that explicitly links epidemiology to sequence evolution and selection. We use Opqua to study determinants of evolution across fitness valleys. We confirm that competition can limit evolution in high transmission environments and find that low transmission, host mobility, and complex pathogen life cycles facilitate reaching new adaptive peaks through population bottlenecks and decoupling of selective pressures. The results show the potential of genomic epidemiological modeling as a tool in infectious disease research.

evolutionary biology↗

Characterization of the immune resistance of SARS-CoV-2 Mu variant and the immunity induced by Mu infection

We have revealed that the SARS-CoV-2 Mu variant is highly resistant to COVID-19 convalescent sera and vaccine sera.1 However, it remains unclear how the immune resistance of the Mu variant is determined. Also, although the Mu variant is highly resistant to the sera obtained from COVID-19 convalescent during early pandemic (i.e., infected with prototypic virus) and vaccinated individuals (i.e., immunized based on prototypic virus), it was unaddressed how the convalescent sera from Mu-infected individuals function. In this study, we revealed that the two mutations in the spike protein of Mu variant, YY144-145TSN and E484K, are responsible for the potent immune resistance of Mu variant. Additionally, we showed that the convalescent sera obtained from the Mu-infected individuals can be broadly antiviral against the Mu variant as well as other SARS-CoV-2 variants of concern/interest. Our findings suggest that developing novel vaccines based on the Mu variant can be more effective against a broad range of SARS-CoV-2 variants.

microbiology↗

dCas9 regulator to neutralize competition in CRISPRi circuits

CRISPRi-mediated gene repression allows simultaneous control of many genes. However, despite highly specific sgRNA-promoter binding, multiple sgRNAs still interfere with one another by competing for dCas9. We created a dCas9 regulator that adjusts dCas9 concentration based on sgRNAs demand, mitigating competition in CRISPRi-based logic gates. The regulators performance is demonstrated on both single-stage and layered CRISPRi logic gates and in two common E. coli strains. When a competitor sgRNA causes between two and ~25 fold-change in a logic gates input/output response without dCas9 regulator, the response is essentially unchanged when the regulator is used. The dCas9 regulator thus enables concurrent and independent operation of multiple sgRNAs, thereby supporting independent control of multiple genes.

synthetic biology↗