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Dynamic CpG methylation delineates subregions within super-enhancers selectively decommissioned at the exit from naive pluripotency
No full textSerial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems
No full textMany insects depend on obligate mutualistic bacteria to provide essential nutrients lacking from their diet. Most aphids, whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera aphidicola to supply essential amino acids and B vitamins. However, in some aphid species, provision of these nutrients is partitioned between Buchnera and a younger bacterial partner, whose identity varies across aphid lineages. Little is known about the origin and the evolutionary stability of these di-symbiotic systems. It is also unclear whether the novel symbionts merely compensate for losses in Buchnera or carry new nutritional functions. Using whole-genome endosymbiont sequences of nine Cinara aphids that harbour an Erwinia-related symbiont to complement Buchnera, we show that the Erwinia association arose from a single event of symbiont lifestyle shift, from a free-living to an obligate intracellular one. This event resulted in drastic genome reduction, long-term genome stasis, and co-divergence with aphids. Fluorescence in situ hybridisation reveals that Erwinia inhabits its own bacteriocytes near Buchnera's. Altogether these results depict a scenario for the establishment of Erwinia as an obligate symbiont that mirrors Buchnera's. Additionally, we found that the Erwinia vitamin-biosynthetic genes not only compensate for Buchnera's deficiencies, but also provide a new nutritional function; whose genes have been horizontally acquired from a Sodalis-related bacterium. A subset of these genes have been subsequently transferred to a new Hamiltonella co-obligate symbiont in one specific Cinara lineage. These results show that the establishment and dynamics of multi-partner endosymbioses can be mediated by lateral gene transfers between co-ocurring symbionts
Genome ancestry mosaics reveal multiple and cryptic contributors to cultivated banana
No full textHybridizations between closely related species commonly occur in the domestication process of many crops. Banana cultivars are derived from such hybridizations between species and subspecies of the Musa genus that have diverged in various tropical Southeast Asian regions and archipelagos. Among the diploid and triploid hybrids generated, those with seedless parthenocarpic fruits were selected by humans and thereafter dispersed through vegetative propagation. Musa acuminata subspecies contribute to most of these cultivars. We analyzed sequence data from 14 M. acuminata wild accessions and 10 M. acuminata-based cultivars, including diploids and one triploid, to characterize the ancestral origins along their chromosomes. We used multivariate analysis and single nucleotide polymorphism clustering and identified five ancestral groups as contributors to these cultivars. Four of these corresponded to known M. acuminata subspecies. A fifth group, found only in cultivars, was defined based on the 'Pisang Madu' cultivar and represented two uncharacterized genetic pools. Diverse ancestral contributions along cultivar chromosomes were found, resulting in mosaics with at least three and up to five ancestries. The commercially important triploid Cavendish banana cultivar had contributions from at least one of the uncharacterized genetic pools and three known M. acuminata subspecies. Our results highlighted that cultivated banana origins are more complex than expected - involving multiple hybridization steps - and also that major wild banana ancestors have yet to be identified. This study revealed the extent to which admixture has framed the evolution and domestication of a crop plant
MIFlowCyt-EV: a framework for standardized reporting of extracellular vesicle flow cytometry experiments
No full textExtracellular vesicles (EVs) are small, heterogeneous and difficult to measure. Flow cytometry (FC) is a key technology for the measurement of individual particles, but its application to the analysis of EVs and other submicron particles has presented many challenges and has produced a number of controversial results, in part due to limitations of instrument detection, lack of robust methods and ambiguities in how data should be interpreted. These complications are exacerbated by the field's lack of a robust reporting framework, and many EV-FC manuscripts include incomplete descriptions of methods and results, contain artefacts stemming from an insufficient instrument sensitivity and inappropriate experimental design and lack appropriate calibration and standardization. To address these issues, a working group (WG) of EV-FC researchers from ISEV, ISAC and ISTH, worked together as an EV-FC WG and developed a consensus framework for the minimum information that should be provided regarding EV-FC. This framework incorporates the existing Minimum Information for Studies of EVs (MISEV) guidelines and Minimum Information about a FC experiment (MIFlowCyt) standard in an EV-FC-specific reporting framework (MIFlowCyt-EV) that supports reporting of critical information related to sample staining, EV detection and measurement and experimental design in manuscripts that report EV-FC data. MIFlowCyt-EV provides a structure for sharing EV-FC results, but it does not prescribe specific protocols, as there will continue to be rapid evolution of instruments and methods for the foreseeable future. MIFlowCyt-EV accommodates this evolution, while providing information needed to evaluate and compare different approaches. Because MIFlowCyt-EV will ensure consistency in the manner of reporting of EV-FC studies, over time we expect that adoption of MIFlowCyt-EV as a standard for reporting EV- FC studies will improve the ability to quantitatively compare results from different laboratories and to support the development of new instruments and assays for improved measurement of EVs
Racinator : pour l'extraction de racines et de graines des échantillons de sol
No full textRacinator est un nouvel équipement d’extraction des racines et des graines contenues dans une carotte de sol, permettant de filtrer les éléments jusqu’à 200µm. Le principe de fonctionnement repose sur plusieurs phases successives : trempage, barbotage et tamisage. La carotte de sol préalablement dissoute par trempage dans de l’eau salée est insérée dans l’appareil. Un bocal séparateur est alors alimenté automatiquement par séquences, avec le mélange de terre, de racines et de graines via une vanne pneumatique pilotée par un contrôleur logique programmable. Sous l’effet de barbotage créé par l’injection d’eau et d’air comprimé dans le bocal, les racines et les graines sont séparées de la terre et remontent à la surface de l’eau. Elles sont ensuite récupérées dans un ou plusieurs tamis superposés. La réduction du maillage de chaque tamis permet d’isoler les éléments en fonction de leur tailleRacinator is a new equipment to extract roots and seeds contained in core samples allowing filter elements up to 200 µm. Its functionning is based on successive phases : soaking, paddling and screening. The core sample that was previously disolved by soaking in salted water is inserted in the machine. A separator jar then received automatically sequences with a mix of soil, roots and seeds by a pneumatic valve piloted by a program logic controller. When injecting water and compressed air in the jar a paddling effect is created, roots and seeds are separated from soil and come back up to the surface of water. They are afterwards received in one or several screenings of different meshings. The reduction of the screening meshing allows isolate elements from
smaller parts
Allometries in plants as drivers of forage nutritive value: A review
No full textThe nutritive value of forage for herbivores has been for a long time determined by the concentration in protein and, hence in nitrogen (N), the concentration in different minerals (P, K, Ca, Mg, and oligo-elements), and the in vivo dry matter (DM) digestibility. Forage DM digestibility, the proportion of ingested DM being metabolized by ruminant animals has been related to different components of plant tissue composition such as Neutral Detergent Fiber (NDF) and Acid Detergent Fiber (ADF); the NDF concentration represents an estimate of cell wall content while the ADF concentration is an estimate of the more lignified cell wall content. Forage nutritive value is generally analyzed by relating the attributes of nutritive value to plant phenology, in order to predict the decline of these attributes with plant age. A more functional approach, initially developed for the analysis of N concentration dynamic analysis (Lemaire et al. 2008 and Lemaire et al. 2019), and extended for digestibility for this review, is based on the assumption that above-ground plant mass (W) is composed of two compartments: (i) the metabolic compartment (Wm), associated with plant growth process scaling with leaf area, having a high N concentration (%N), and a high Digestibility (%D); (ii) the structural compartment (Ws) associated with architectural plant development, scaling with plant height and thickness and having low %N and %D. With the postulate that Wm is allometrically related to W (Wm = c x W-alpha with alpha < 1), the ontogenetic decline of both %N and %D as the plant gets bigger and forage mass increases can be explained, and the purely empirical statistical approach of forage quality based on plant phenology can be replaced by a more mechanistic and comprehensive analysis linking forage production and forage quality dynamics within the same functional approach for a better understanding of genotype-environment-management interactions
Spécificités du processus d’internationalisation d’une firme africaine : étude du cas de l’entreprise malgache Vidzar
No full textFrench Abstract: L’objet de notre travail est d’identifier les spécificités du processus d’internationalisation d’une firme africaine à travers l’étude du cas du développement international du groupe malgache Vidzar, un des leaders africains du Rhum. Deux objectifs sont assignés à cette étude de cas : prendre en compte les spécificités contextuelles (Jackson, 2013 et Devine et Kiggundu, 2016) et adapter la démarche méthodologique (Kriauciunas et al., 2011). Les résultats obtenus montrent certaines spécificités en termes de rythme et de séquences du processus ou encore en termes de gestion des représentations commerciales et des intermédiaires, mais témoignent aussi de facteurs de ressemblances avec des cycles génériques d’internationalisation. Nos résultats plaident fortement pour l’analyse contextualisée du développement international des firmes africaines.Our work aims to identify the specificities of the internationalization process of an African firm through a case study of the international development of the Malagasy group Vidzar, one of the African leaders of Rum. Two objectives are assigned to this case study: taking contextual specificities into account (Jackson, 2013 and Devine and Kiggundu, 2016) and adapting the methodological approach (Kriauciunas et al., 2011). Our results show some specificities in terms of rhythm and sequences of the process and also the management of commercial representations and intermediaries. Our analysis also bears witness to factors of similarities with generic cycles of internationalization. Our results strongly support the contextualized analysis of the international development of African firms. ...