Biology subjects

Theodorou, I.

Publications and source records attributed to Theodorou, I..

4 recordsLinked to original sources

bioRxiv2024

The human blood harbors a phageome which differs in Crohn's disease

Increasing evidence suggests that the human blood hosts microbes including bacteria and eukaryotic viruses, which could have important implications for health. Bacteriophages of the blood are challenging to study and have been overlooked, but could translocate to this environment from different body-sites. We thus developed specific virome protocols and analysis methods to study the viral communities of blood samples obtained from healthy individuals and Crohns disease (CD) patients. We uncovered a diverse viral community in the human blood, dominated by phages infecting Pseudomonadota bacteria. We found that an important fraction of those phages overlaps with the gut virome, consolidating the idea that gut phages can translocate to the blood. Strikingly, viral communities of the blood were different between CD patients and healthy individuals, revealing a new signature of disease. This was not the case for fecal viral communities. Collectively, these results advance our knowledge of the microorganisms present in the human blood and pave the way for further studies of this environment in the context of disease.

microbiology↗

bioRxiv2024

MUM, a maternal unknown message, inhibits early establishment of the mediolateral axis in the embryo of the kelp Saccharina latissima

Brown algae are multicellular photosynthetic organisms that have evolved independently of plants and other algae. Apart from studies on the polarisation of the Fucus zygote in the 1990s, little is known about the mechanisms controlling the embryogenesis of these organisms. Here, we studied the determinism of embryogenesis in the kelp Saccharina latissima, focusing on the formation of its body axes. This alga initially develops an oblong embryo formed of a cell monolayer, which subsequently thickens; growth axes are then established in temporally distinct stages, starting with the formation of a dominant apico-basal axis. Our experiments focused on the role of the stalk, an empty cell that retains the embryo attached to the maternal tissue, in the development of the growth axes in mature embryos. In response to the removal of the stalk, the embryos developed as a monolayered disc rather than an elongated blade, demonstrating that attachment to the stalk inhibits the formation of the medio-lateral axis at the onset of embryogenesis. In addition, compared with embryos attached to the stalk, the cells of detached embryos were smaller and displayed an altered shape. The topology of the tissue was also disrupted, as cells had a higher number of cell neighbours. Observation of cell division patterns just after removal of the stalk showed that the stalk represses longitudinal cell divisions, thereby reinforcing the establishment of the main apico-basal axis. This unique quantitative study of brown algal embryogenesis revealed that, in kelps, a signal from maternal tissue (MUM for maternal unknown message) is necessary for the establishment of growth axes at the onset of embryogenesis and of the organisation of growing embryonic tissues. In addition, we discovered that, although the stalk persists for several weeks until the embryo reaches at least 500 cells, MUM is emitted in the first 4 days after fertilisation only, before the embryo reaches the 8-cell stage. Finally, transplantation experiments indicated that MUM does not diffuse in seawater, but requires contact between the embryo and the stalk. The potential chemical or mechanical nature of MUM is discussed.

developmental biology↗

bioRxiv2022

An alternative method to multiple displacement amplification for preparing virome DNA in a way adapted for the sequencing of both double-strand and single-strand DNA viruses

Background: Bulk microbiome, as well as virome-enriched shotgun sequencing only reveals the double-stranded DNA (dsDNA) content of a given sample, unless specific treatments are applied. However, genomes of viruses often consist of a circular single-stranded DNA (ssDNA) molecule. Pre- treatment and amplification of DNA using the multiple displacement amplification (MDA) method enables conversion of ssDNA to dsDNA, but this process can lead to over-representation of these circular ssDNA genomes. A more recent alternative permits to bypass the amplification step, as library adapters are ligated to sheared and denatured DNA, after an end-modification step (xGen kit). However, the sonication step might shear ssDNA more efficiently than dsDNA, therefore introducing another bias in virome sequencing. These limitations prompted us to explore an alternative method of DNA preparation for sequencing mixed ssDNA and dsDNA viromes. Results: Using a synthetic mix of viral particles, we made use of the T7 DNA polymerase (T7pol) to convert viral circular ssDNA molecules to dsDNA, while preventing over-replication of such molecules, as is the case with the Phi29 DNA polymerase. Our findings indicate that using T7pol and a mix of degenerated primers to convert ssDNA to dsDNA prior library preparation is a good alternative to the currently used methods. It better represents the original synthetic mixtures compared to MDA or direct application of the xGen kit. Furthermore, when applied to two complex virome samples, the T7pol treatment improved both the richness and abundance in the Microviridae fraction. Conclusion: We conclude that T7pol pretreatment is preferable to MDA for the shotgun sequencing of viromes, which is easy to implement and inexpensive.

genomics↗

bioRxiv2021

Tip growth in the brown alga Ectocarpus is controlled by a RHO-GAP-BAR domain protein independently from F-actin organisation

The brown alga Ectocarpus is a filamentous seaweed that grows by tip growth and branching. In the morphometric mutant etoile, tip growth is slower than in the WT and eventually stops. In this paper, we show that the causal etoile mutation is a null mutation in a bi-domain BAR-RhoGAP gene. By quantitative RT-PCR, we showed that ETOILE is ubiquitously expressed in prostrate filaments of the Ectocarpus sporophyte, and is downregulated in the etoile mutant. We immunolocalised both domains of the protein in WT and etoile, as well as RAC1, the known target of Rho-GAP enzymes. Thus, ETOILE would be localised at the apical cell dome where it would control the localisation of EsRAC1 to the plasma membrane. Actin staining showed that the mutant is not affected in F-actin structures. Overall, these results suggest that in Ectocarpus, BAR-RhoGAP controls tip growth by controlling RAC1 localization and through an actin-independent mechanism.

developmental biology↗