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Biology subjects

Blondel, L.

Publications and source records attributed to Blondel, L..

8 recordsLinked to original sources

Lineage domains and cytoskeletal cables organize a cellular square grid in a crustacean

To build tissues, and ultimately functional bodies, cells in early embryos must arrange into specific patterns. In most animals, epithelial tissues exhibit a predominantly hexagonal space-packing geometry. However, in many species of the largest group of crustaceans, the Malacostraca, the embryonic epithelium takes on the striking form of a grid made up of predominantly square cells, sequential rows of which establish the adult segmented body plan. After square cells emerge, their organization appears to be maintained by specific cell division patterns. However, the mechanisms that initially generate square cells from hexagonal precursors are unknown. Here we address this problem by combining long-term multiview lightsheet microscopy, immunohistochemistry, laser ablation, and pharmacological perturbation. We show that in the emerging model crustacean Parhyale hawaiensis this highly unusual grid geometry is first initiated from two perpendicular axes that are established sequentially according to different cellular mechanisms. The first axis arises dorso-ventrally at a tensile lineage compartment boundary, while the second emerges at the anterior-posterior axis along the ventral midline through lineage-independent cell intercalation driven by tensile actomyosin cables. We show that these midline cables are necessary for organizing square-cell packing as well as for proper expression of the segmentation gene engrailed. Our findings show that both cell lineage-specific behaviors, as well as lineage-independent supracellular structures, are required to establish square grid epithelial organization and a segmented body plan.

developmental biology↗

Wikipedia as a tool for contemporary history of science: A case study on CRISPR

Rapid developments and methodological divides hinder the study of how scientific knowledge accumulates, consolidates and transfers to the public sphere. Our work proposes using Wikipedia, the online encyclopedia, as a historiographical source for contemporary science. We chose the high-profile field of gene editing as our test case, performing a historical analysis of the English-language Wikipedia articles on CRISPR. Using a mixed method approach, we qualitatively and quantitatively analyzed its text, sections and references, alongside 50 affiliated articles. These, we found, documented CRISPRs maturation from a fundamental scientific discovery to a biotechnological revolution with vast social and cultural implications. We developed automated tools to support such research generically and demonstrated its applicability on two other scientific fields we have previously studied - COVID-19 and Circadian clocks. This method makes use of Wikipedia as a digital and free archive, documenting the incremental growth of knowledge and the manner scientific research accumulates and translates into public discourse. Using Wikipedia in this manner compliments and overcomes some issues with contemporary histories and can also augment existing bibliometric research.

scientific communication and education↗

The pentatricopeptide repeat protein MTSF3 is required for nad2 mRNA stability and embryogenesis in Arabidopsis

Gene expression in plant mitochondria is predominantly governed at the post-transcriptional level and relies mostly on nuclear-encoded proteins. However, the involved protein factors and the underlying molecular mechanisms are still not well understood. In this study, we report the function of the mitochondrial stability factor 3 (MTSF3) protein and we show that it is essential for accumulation of the mitochondrial nad2 transcript in Arabidopsis and not for the splicing of nad2 intron 2, as recently proposed (Marchetti et al., 2020). The MTSF3 gene encodes a pentatricopeptide repeat protein that localizes in the mitochondrion. An MTSF3 null mutation induces embryonic lethality but viable mtsf3 mutant plants could be generated by partial complementation with the developmentally-regulated ABSCISIC ACID INSENSITIVE3 promoter. Genetic analyses reveal that mtsf3 rescued plants display growth retardation due to the specific destabilization of a nad2 precursor transcript bearing exons 3 to 5. Biochemical data demonstrate that MTSF3 protein specifically binds to the 3-terminus of nad2. The destabilization of nad2 mRNA induces a significant decrease in complex I assembly and activity, and an overexpression of the alternative respiratory pathway. Our results support that the MTSF3 protein protects nad2 transcript from degradation by mitochondrial exoribonucleases by binding to its 3 extremity.

plant biology↗

Community review: a robust and scalable selection system for resource allocation within open science and innovation communities

Resource allocation is essential to the selection and implementation of innovative projects in science and technology. With large stakes involved in concentrating large fundings over a few promising projects, current "winner-take-all" models for grant applications are time-intensive endeavours that mobilise significant researcher time in writing extensive project proposals, and rely on the availability of a few time-saturated volunteer experts. Such processes usually carry over several months, resulting in high effective costs compared to expected benefits. Faced with the need for a rapid response to the Covid19 pandemic in 2020, we devised an agile "community review" system to allocate micro-grants for the fast prototyping of innovative solutions. Here we describe and evaluate the implementation of this community review across 147 projects from the "Just One Giant Labs OpenCOVID19 initiative" and "Helpful Engineering" open research communities. The community review process uses granular review forms and requires the participation of grant applicants in the review process. Within a year, we organised 7 rounds of review, resulting in 614 reviews from 201 reviewers, and the attribution of 48 micro-grants of up to 4,000 euros. We show that this system is fast, with a median process duration of 10 days, scalable, with a median of 4 reviewers per project independent of the total number of projects, and fair, with project rankings highly preserved after the synthetic removal of reviewers. We investigate the potential bias introduced by involving applicants in the process, and find that review scores from both applicants and non-applicants have a similar correlation of r=0.28 with other reviews within a project, matching previous observations using traditional approaches. Finally, we find that the ability of projects to apply to several rounds allows to both foster the further implementation of successful early prototypes, as well as provide a pathway to constructively improve an initially failing proposal in an agile manner. Overall, this study quantitatively highlights the benefits of a frugal, community review system acting as a due diligence for rapid and agile resource allocation in open research and innovation programs, with particular implications for decentralised communities.

scientific communication and education↗

Evolution of a cytoplasmic determinant: evidence for the biochemical basis of functional evolution of a novel germ line regulator

Germ line specification is essential in sexually reproducing organisms. Despite their critical role, the evolutionary history of the genes that specify animal germ cells is heterogeneous and dynamic. In many insects, the gene oskar is required for the specification of the germ line. However, the germ line role of oskar is thought to be a derived role resulting from co-option from an ancestral somatic role. To address how evolutionary changes in protein sequence could have led to changes in the function of Oskar protein that enabled it to regulate germ line specification, we searched for oskar orthologs in 1565 publicly available insect genomic and transcriptomic datasets. The earliest-diverging lineage in which we identified an oskar ortholog was the order Zygentoma (silverfish and firebrats), suggesting that oskar originated before the origin of winged insects. We noted some order-specific trends in oskar sequence evolution, including whole gene duplications, clade-specific losses, and rapid divergence. An alignment of all known 379 Oskar sequences revealed new highly conserved residues as candidates that promote dimerization of the LOTUS domain. Moreover, we identified regions of the OSK domain with conserved predicted RNA binding potential. Furthermore, we show that despite a low overall amino acid conservation, the LOTUS domain shows higher conservation of predicted secondary structure than the OSK domain. Finally, we suggest new key amino acids in the LOTUS domain that may be involved in the previously reported Oskar-Vasa physical interaction that is required for its germ line role.

evolutionary biology↗

Topology-driven analysis of protein-protein interaction networks detects functional genetic modules regulating reproductive capacity

Understanding the genetic regulation of organ structure is a fundamental problem in developmental biology. Here, we use egg-producing structures of insect ovaries, called ovarioles, to deduce systems-level gene regulatory relationships from quantitative functional genetic analysis. We previously showed that Hippo signalling, a conserved regulator of animal organ size, regulates ovariole number in Drosophila melanogaster. To comprehensively determine how Hippo signalling interacts with other pathways in this regulation, we screened all known signalling pathway genes, and identified Hpo-dependent and Hpo-independent signalling requirements. Network analysis of known protein-protein interactions among screen results identified independent gene regulatory sub-networks regulating one or both of ovariole number and egg laying. These sub-networks predict involvement of previously uncharacterised genes with higher accuracy than the original candidate screen. This shows that network analysis combining functional genetic and large-scale interaction data can predict function of novel genes regulating development.

developmental biology↗

Ancestral and offspring nutrition interact to affect life history traits in Drosophila melanogaster

Ancestral environmental conditions can impact descendant phenotypes through a variety of epigenetic mechanisms. Previous studies on transgenerational effects in Drosophila melanogaster suggest that parental nutrition may affect the body size, developmental duration, and egg size of the next generation. However, it is unknown whether these effects on phenotype remain stable across generations, or if specific generations have general responses to ancestral diet. In the current study, we examined the effect on multiple life history phenotypes of changing diet quality across three generations. Our analysis revealed unforeseen patterns in how phenotypes respond to dietary restriction. Our generalized linear model showed that when considering only two generations, offspring phenotypes were primarily affected by their own diet, and to a lesser extent by the diet of their parents or the interaction between the two generations. Surprisingly, however, when considering three generations, offspring phenotypes were primarily impacted by their grandparents diet and their own diet. Interactions amongst different generations diets affected development time, egg volume, and pupal mass more than ovariole number or wing length. Further, pairwise comparisons of diet groups from the same generation revealed commonalities in strong responses to rich vs. poor diet: ovariole number, pupal mass, and wing length responded more strongly to poor diet than to rich diet, while development time responded strongly to both rich and poor diets. To improve investigations into the mechanisms and consequences of transgenerational, epigenetic inheritance, future studies should closely examine how phenotypes change across a higher number of generations, and consider responses to broader variability in diet treatments.

physiology↗

Bacterial contribution to genesis of the novel germ line determinant oskar

New cellular functions and developmental processes can evolve by modifying existing genes or creating novel genes. Novel genes can arise not only via duplication or mutation but also by acquiring foreign DNA, also called horizontal gene transfer (HGT). Here we show that HGT likely contributed to the creation of a novel gene indispensable for reproduction in some insects. Long considered a novel gene with unknown origin, oskar has evolved to fulfil a crucial role in insect germ cell formation. Our analysis of over 100 insect Oskar sequences suggests that Oskar arose de novo via fusion of eukaryotic and prokaryotic sequences. This work shows that highly unusual gene origin processes can give rise to novel genes that can facilitate evolution of novel developmental mechanisms. One Sentence SummaryOur research shows that gene origin processes often considered highly unusual, including HGT and de novo coding region evolution, can give rise to novel genes that can both participate in pre-existing gene regulatory networks, and also facilitate the evolution of novel developmental mechanisms.

evolutionary biology↗