Biology subjects

Mortier, J.

Publications and source records attributed to Mortier, J..

3 recordsLinked to original sources

bioRxiv2024

SPArrOW: a flexible, interactive and scalable pipeline for spatial transcriptomics analysis

Current spatial transcriptomics technologies are increasingly able to measure large gene panels at subcellular resolution, but a major bottleneck in this rapidly advancing field is the computational analysis and interpretation of the data. To bridge this gap, here we present SPArrOW, a flexible, modular and scalable pipeline for processing spatial transcriptomics data. SPArrOW improves cell segmentation and leads to better overall data quality, resulting in more accurate cell annotations at the single-cell level. Furthermore, it provides the users with numerous visual quality checks that are crucial for the correct interpretation of the data, offering users more control in processing their data. Our workflow is designed to accommodate the various available spatial transcriptomics platforms. Finally, SPArrOW offers interactive visualization and data exploration, enabling sample-specific pipeline optimization by various tuneable parameters and an efficient comparison of different staining and gene allocation strategies.

bioinformatics↗

bioRxiv2024

A bovine model of rhizomelic chondrodysplasia punctata caused by a deep intronic splicing mutation in the GNPAT gene

BackgroundGenetic defects that occur naturally in livestock species provide valuable models for investigating the molecular mechanisms underlying rare human diseases. Livestock breeds are subject to the regular emergence of recessive genetic defects, due to their low genetic variability, while their large population sizes provide easy access to case and control individuals, as well as massive amounts of pedigree, genomic and phenotypic information recorded for selection purposes. In this study, we investigated a lethal form of recessive chondrodysplasia observed in 21 stillborn calves of the Aubrac breed of beef cattle. ResultsDetailed clinical examinations revealed proximal limb shortening, epiphyseal calcific deposits and other clinical signs consistent with human rhizomelic chondrodysplasia punctata, a rare peroxisomal disorder caused by recessive mutations in one of five genes (AGPS, FAR1, GNPAT, PEX5 and PEX7). Using homozygosity mapping, whole genome sequencing of two affected individuals, and filtering for variants found in 1,867 control genomes, we reduced the list of candidate variants to a single deep intronic substitution in GNPAT (g.4,039,268G>A on Chromosome 28 of the ARS-UCD1.2 bovine genome assembly). For verification, we performed large-scale genotyping of this variant using a custom SNP array and found a perfect genotype-phenotype correlation in 21 cases and 26 of their parents, and a complete absence of homozygotes in 1,195 Aubrac controls. The g.4,039,268A allele segregated at a frequency of 2.6% in this population and was absent in 375,535 additional individuals from 17 breeds. Then, using in vivo and in vitro analyses, we demonstrated that the derived allele activates cryptic splice sites within intron 11 resulting in abnormal transcripts. Finally, by mining the wealth of records available in the French bovine database, we demonstrated that this deep intronic substitution was responsible not only for stillbirth but also for juvenile mortality in homozygotes and had a moderate but significant negative effect on muscle development in heterozygotes. ConclusionsWe report the first spontaneous large animal model of rhizomelic chondrodysplasia punctata and provide both a diagnostic test to counter-select this defect in cattle and interesting insights into the molecular consequences of complete or partial GNPAT insufficiency in mammals.

genetics↗

bioRxiv2023

Phosphate starvation decouples cell differentiation from DNA replication control in the dimorphic bacterium Caulobacter crescentus

Upon nutrient depletion, bacteria stop proliferating and undergo physiological and morphological changes to ensure their survival. Yet, how these processes are coordinated in response to distinct starvation conditions is poorly understood. Here we compare the cellular responses of Caulobacter crescentus to carbon (C), nitrogen (N) and phosphorus (P) starvation conditions. We find that DNA replication initiation and abundance of the replication initiator DnaA are, under all three starvation conditions, regulated by a common mechanism involving the inhibition of DnaA translation. By contrast, cell differentiation from a motile swarmer cell to a sessile stalked cell is regulated differently under the three starvation conditions. During C and N starvation, production of the signaling molecules (p)ppGpp is required to arrest cell development in the motile swarmer stage. By contrast, our data suggest that low (p)ppGpp levels under P starvation allow P-starved swarmer cells to differentiate into sessile stalked cells. Further, we show that limited DnaA abundance, and consequently absence of DNA replication initiation, is the main reason that prevents P-starved stalked cells from completing the cell cycle. Together, our findings demonstrate that C. crescentus decouples cell differentiation from DNA replication initiation under certain starvation conditions, two otherwise intimately coupled processes. We hypothesize that arresting the developmental program either as motile swarmer cells or as sessile stalked cells improves the chances of survival of C. crescentus during the different starvation conditions. Author SummaryBacteria frequently encounter periods of nutrient limitation. To ensure their survival, they dynamically modulate their own proliferation and cellular behaviors in response to nutrient availability. In many Alphaproteobacteria, progression through the cell cycle is tightly coupled to morphological transitions generating distinct cell types. Here, we show how starvation for either of the major nutrients carbon, nitrogen, or phosphorus affects this coupling between key cell cycle events and cell differentiation in the model bacterium Caulobacter crescentus. All three starvation conditions prevent cell proliferation by blocking DNA replication initiation. However, while carbon and nitrogen exhaustion cause cells to arrest the cell cycle as non-replicating motile cells, phosphorus starvation leads to accumulation of non-replicating sessile stalked cells. Our data demonstrate that starvation-dependent differences in (p)ppGpp signaling account for these different starvation responses. Together, our work provides insights into the mechanisms that allow bacteria to modulate their developmental program in response to changing environmental conditions.

microbiology↗