Biology subjects

Catala, P.

Publications and source records attributed to Catala, P..

6 recordsLinked to original sources

bioRxiv2026

Dose-dependent transcriptional responses of marine prokaryotes to Fe-rich colloids of glacial and non-glacial origin in the Kerguelen region (Southern Ocean)

The trace metal iron (Fe) plays a key role in regulating microbial carbon metabolism through complex processes. In ocean regions where Fe is potentially limiting, new Fe sources can significantly influence prokaryotic activity and growth, stimulating the microbially-mediated cycling of carbon. The accelerated melting of glaciers delivers large quantities of Fe-rich material to the ocean, but the bioavailability of the diverse glacial Fe species remains poorly understood. Here, we investigated the response of marine prokaryotes to Fe contained in the colloidal fraction (20 - 200 nm size fraction) originating from the Cook Ice Cap on Kerguelen Island (Southern Ocean). We assessed growth and gene transcriptional responses to dose-additions of Fe-rich colloids from two sources, glacial meltwater and a non-glacial origin. The two colloid types resulted both in dose-dependent, but contrasting growth responses. While non-glacial colloids stimulated prokaryotic growth, the opposite pattern was observed with glacial colloids. The transcriptional profiles revealed an increasing trend in Fe-limitation, as evidenced by transcripts of the glyoxylate shunt, as a function of the addition of either colloid type. However, only non-glacial colloids induced a dose-dependent increase in transcripts of aromatic compound degradation, suggesting that these Fe-rich colloids could also provide C. These results point to the key role of C regulating the prokaryotic growth in response to Fe-rich colloids. The clear trends in the expression of genes in response to dose addition allowed to map transcript abundances to nutritional stress and specific metabolic pathways. Dose additions of limiting nutrients in incubation experiments induce quantitative transcriptional responses, thereby offering insights to the nutritional status of prokaryotes and to the mechanisms leading to Fe and C co-limitation.

microbiology↗

bioRxiv2026

TonB-dependent Transporters of Fe-petrobactin in Marinobacter nauticus and Southern Ocean bacteria

TonB-dependent transporters (TBDTs) play a central role in siderophore-mediated iron acquisition in the marine environment. However, assigning substrate specificity to TBDTs remains a major bottleneck in understanding the ecological and mechanistic roles of siderophore production and uptake. Here, we identify in Marinobacter nauticus two TBDTs, OptA and OptB, that share low sequence identity yet both mediate Fe-petrobactin uptake. Despite this functional overlap, they underlie distinct regulatory mechanisms, suggesting differential utilization under specific environmental conditions. Phylogenetic analyses indicate that OptA likely co-evolved with the petrobactin biosynthetic gene cluster, whereas OptB appears to have followed a distinct evolutionary trajectory, acquiring the capacity to import petrobactin as a xenosiderophore. Using resuscitated communities from the Southern Ocean, we further show that Fe-petrobactin stimulated prokaryotic growth. Based on amino acid similarity, we identified OptB-like transporters encoded in metagenomes and MAGs and show that taxa harbouring these transporters, such as Pseudoaltermonas, respond specifically to Fe-petrobactin addition. OptB-like transporters were also detected in environmental metagenomes from the Southern Ocean, whereas the petrobactin biosynthetic gene clusters were not, indicating that petrobactin primarily functions as a xenosiderophore in natural communities.

microbiology↗

bioRxiv2026

Spatial control of light-responsive proteins and optogenetics within hydrogels via volumetric bioprinting

Spatiotemporal control over cell fate and behaviour within bioprinted constructs remains a key challenge in tissue engineering. Optogenetics offers versatile potential for non-invasive regulation of biological processes. Yet, its integration within large-scale, cell-laden bioprinted materials is still limited, especially considering spatial constraints of existing light delivery methods. In this study, we introduce a novel approach that repurposes tomographic volumetric bioprinting to enable post-printing stimulation of photosensitive protein-switches and optogenetic circuits in cells deep within hydrogel constructs. By converging different bioprinting approaches, computer vision, context-aware model generation, and synthetic biology and cell engineering, we demonstrated selective activation of a fluorescent, light-responsive protein probe within multi-material centimeter-scale constructs. Moreover, leveraging a multi-wavelength volumetric bioprinter, we further demonstrate this concept by selectively stimulating cells expressing a near-infrared optogenetic system that triggers gene expression and the induction of pancreas-specific transcription factors. The described methods provide platforms for remote, repeatable, and localized control of biological events in volumetric constructs, opening new possibilities for advanced tissue models, and dynamic tuning of cell-mediated protein production in engineered living systems.

bioengineering↗

bioRxiv2023

Tagging of water masses with covariance of trace metals and prokaryotic taxa in the Southern Ocean

Marine microbes are strongly interrelated to trace metals in the ocean. How the availability of trace metals selects for prokaryotic taxa and the potential feedbacks of microbial processes on the trace metal distribution in the ocean remains poorly understood. We investigate here the potential reciprocal links between diverse prokaryotic taxa and iron (Fe), manganese (Mn), copper (Cu), Nickel (Ni) as well as apparent oxygen utilization (AOU) across 12 well-defined water masses in the Southern Indian Ocean (SWINGS-South West Indian Ocean GEOTRACES GS02 Section cruise). Applying Partial Least Square Regression (PLSR) analysis we show that the water masses are associated with particular latent vectors that are a combination of the spatial distribution of prokaryotic taxa, trace elements and AOU. This approach provides novel insights on the potential interactions between prokaryotic taxa and trace metals in relation to organic matter remineralization in distinct water masses of the ocean.

microbiology↗

bioRxiv2023

A Single-Cell RNA-Seq Analysis Unravels The Heterogeniety Of Primary Cultured Human Corneal Endothelial Cells

The primary culture of donor-derived human corneal endothelial cells (CECs) is a promising cell therapy. It confers the potential to treat multiple patients from a single donor, alleviating the global donor shortage. Nevertheless, this approach has limitations preventing its adoption, particularly culture protocols allow limited expansion of CECs and there is a lack of clear parameters to identify therapy-grade CECs. To address this limitation, a better understanding of the molecular changes arising from the primary culture of CECs is required. Using single- cell RNA sequencing on primary cultured CECs, we identify their variable transcriptomic fingerprint at the single cell level, provide a pseudo temporal reconstruction of the changes arising from primary culture, and suggest markers to assess the quality of primary CEC cultures. This research depicts a deep transcriptomic understanding of the cellular heterogeneity arising from the primary expansion of CECs and sets the basis for further improvement of culture protocols and therapies.

cell biology↗

bioRxiv2021

A single cell transcriptome atlas reveals the heterogeneity of the healthy human cornea and identifies novel markers of the corneal limbus and stroma

The cornea is the clear window that lets light into the eye. It is composed of five layers: epithelium, Bowmans layer, stroma, Descemets membrane and endothelium. The maintenance of its structure and transparency are determined by the functions of the different cell types populating each layer. Attempts to regenerate corneal tissue and understand disease conditions requires knowledge of how cell profiles vary across this heterogeneous tissue. We performed a single cell transcriptomic profiling of 19,472 cells isolated from eight healthy donor corneas. Our analysis delineates the heterogeneity of the corneal layers by identifying cell populations and revealing cell states that contribute in preserving corneal homeostasis. We identified that the expression of CAV1, CXCL14, HOMER3 and CPVL were exclusive to the corneal epithelial limbal stem cell niche, CKS2, STMN1 and UBE2C were exclusively expressed in highly proliferative transit amplifying cells, and NNMT was exclusively expressed by stromal keratocytes. Overall, this research provides a basis to improve current primary cell expansion protocols, for future profiling of corneal disease states, to help guide pluripotent stem cells into different corneal lineages, and to understand how engineered substrates affect corneal cells to improve regenerative therapies.

cell biology↗