Characterization of Multiple Groups of Data

In this paper we propose a new approach for computing characterizations of sets of data by means of partially defined Boolean functions. The main objective is to provide minimal sets of characters that allows the user to discriminate groups of Boolean data representing individuals described by means of presence or absence of characters. Compared to previous approaches, our algorithms are more efficient and are able to compute complete sets of solutions, which may be useful according to our underlying application domain in plant biology

Two-dimensional simulations of internal gravity waves in a 5 M⊙M_{\odot} Zero-Age-Main-Sequence model

Main-sequence intermediate-mass stars present a radiative envelope that supports internal gravity waves (IGWs). Excited at the boundary with the convective core, IGWs propagate towards the stellar surface and are suspected to impact physical processes such as rotation and chemical mixing. Using the fully compressible time-implicit code MUSIC, we study IGWs in two-dimensional simulations of a zero-age-main-sequence 5 solar mass star model up to 91\% of the stellar radius with different luminosity and radiative diffusivity enhancements. Our results show that low frequency waves excited by core convection are strongly impacted by radiative effects as they propagate. This impact depends on the radial profile of radiative diffusivity which increases by almost 5 orders of magnitude between the centre of the star and the top of the simulation domain. In the upper layers of the simulation domain, we observe an increase of the temperature. Our study suggests that this is due to heat added in these layers by IGWs damped by radiative diffusion. We show that non-linear effects linked to large amplitude IGWs may be relevant just above the convective core. Both these effects are intensified by the artificial enhancement of the luminosity and radiative diffusivity, with enhancement factors up to $10^4$ times the realistic values. Our results also highlight that direct comparison between numerical simulations with enhanced luminosity and observations must be made with caution. Finally, our work suggests that thermal effects linked to the damping of IGWs could have a non-negligible impact on stellar structure.Comment: 15 pages, 10 figures, accepted for publication in MNRA

Comparative Genomics of Pathogenic and Nonpathogenic Strains of Xanthomonas arboricola Unveil Molecular and Evolutionary Events Linked to Pathoadaptation

The bacterial species Xanthomonas arboricola contains plant pathogenic and nonpathogenic strains. It includes the pathogen X. arboricola pv. juglandis, causing the bacterial blight of Juglans regia. The emergence of a new bacterial disease of J, regia in France called vertical oozing canker (VOC) was previously described and the causal agent was identified as a distinct genetic lineage within the pathovar Symptoms on walnut leaves and fruits are similar to those of a bacterial blight but VOC includes also cankers on trunk and branches. In this work, we used comparative genomics and physiological tests to detect differences between four X. arboricola strains isolated from walnut tree: strain CFBP 2528 causing walnut blight (WB), strain CFBP 7179 causing VOC and two nonpathogenic strains, CFBP 7634 and CFBP 7651, isolated from healthy walnut buds. Whole genome sequence comparisons revealed that pathogenic strains possess a larger and wider range of mobile genetic elements than nonpathogenic strains. One pathogenic strain, CFBP 7179, possessed a specific integrative and conjugative element (ICE) of 95 kb encoding genes involved in copper resistance, transport and regulation. The type three effector repertoire was larger in pathogenic strains than in nonpathogenic strains. Moreover, CFBP 7634 strain lacked the type three secretion system encoding genes. The flagellar system appeared incomplete and nonfunctional in the pathogenic strain CFBP 2528. Differential sets of chemoreceptor and different repertoires of genes coding adhesins were identified between pathogenic and nonpathogenic strains. Besides these differences, some strain-specific differences were also observed. Altogether, this study provides valuable insights to highlight the mechanisms involved in ecology, environment perception, plant adhesion and interaction, leading to the emergence of new strains in a dynamic environment

Recombination-prone bacterial strains form a reservoir from which epidemic clones emerge in agroecosystems

The acquisition of virulence-related genes through horizontal gene transfer can modify the pathogenic profiles of strains and lead to the emergence of new diseases. Xanthomonas arboricola is a bacterial species largely known for the damage it causes to stone and nut fruit trees worldwide. In addition to these host-specific populations called pathovars, many nonpathogenic strains have been identified in this species. Their evolutionary significance in the context of pathogen emergence is unknown. We looked at seven housekeeping genes amplified from 187 pathogenic and nonpathogenic strains isolated from various plants worldwide to analyze population genetics and recombination dynamics. We also examined the dynamics of the gains and losses of genes associated with life history traits (LHTs) during X. arboricola evolution. We discovered that X. arboricola presents an epidemic population structure. Successful pathovars of trees (i.e. pruni, corylina and juglandis) are epidemic clones whose emergence appears to be linked to the acquisition of eight genes coding for Type III effectors. The other strains of this species are part of a recombinant network, within which LHT-associated genes might have been lost. We suggest that nonpathogenic strains, because of their high genetic diversity and propensity for recombination, may promote the emergence of pathogenic strains

A study of convective core overshooting as a function of stellar mass based on two-dimensional hydrodynamical simulations

This is the final version. Available from Oxford University Press via the DOI in this record. We perform two-dimensional (2D) numerical simulations of core convection for zero-age main-sequence stars covering a mass range from 3 to 20 M. The simulations are performed with the fully compressible time-implicit code MUSIC. We study the efficiency of overshooting, which describes the ballistic process of convective flows crossing a convective boundary, as a function of stellar mass and luminosity. We also study the impact of artificially increasing the stellar luminosity for 3 M models. The simulations cover hundreds to thousands of convective turnover time-scales. Applying the framework of extreme plume events previously developed for convective envelopes, we derive overshooting lengths as a function of stellar masses. We find that the overshooting distance (dov) scales with the stellar luminosity (L) and the convective core radius (rconv). We derive a scaling law dov ∝ L1/3r1/2 conv, which isimplemented in a one-dimensionalstellar evolution code and the resulting stellar models are compared to observations. The scaling predicts values for the overshooting distance that significantly increase with stellar mass, in qualitative agreement with observations. Quantitatively, however, the predicted values are underestimated for masses 10 M. Our 2D simulations show the formation of a nearly adiabatic layer just above the Schwarzschild boundary of the convective core, as exhibited in recent three-dimensionalsimulations of convection. The most luminous modelsshow a growth in size with time of the nearly adiabatic layer. This growth seemsto slow down asthe upper edge of the nearly adiabatic layer gets closer to the maximum overshooting length and as the simulation time exceeds the typical thermal diffusive time-scale in the overshooting layer.Science and Technology Facilities CouncilEuropean Commissio

Integration of various stacking processes in carrier ampholyte-based capillary electrophoresis

Field-enhanced sample stacking, field-enhanced sample injection as well as electrokinetic supercharging have been successfully integrated in carrier ampholyte-based capillary electrophoresis. Through the analysis of different test sample mixtures, it has been shown that the carrier ampholyte-based background electrolytes, in spite of their very low conductivity, allow efficient online preconcentration of analytes by fieldamplified techniques. Sensitivity enhancement factors of the same magnitude as those usually encountered with classical conductive background electrolytes have been obtained in such carrier ampholyte-based buffers. Depending on the online preconcentration method that has been integrated, sensitivity enhancement factors between 50 and several thousands have been reached

Two-dimensional simulations of solar-like models with artificially enhanced luminosity. II. Impact on internal gravity waves

This is the final version. Available from EDP Sciences via the DOI in this recordArtificially increasing the luminosity and the thermal diffusivity of a model is a common tactic adopted in hydrodynamical simulations of stellar convection. In this work, we analyse the impact of these artificial modifications on the physical properties of stellar interiors and specifically on internal gravity waves. We perform two-dimensional simulations of solar-like stars with the MUSIC code. We compare three models with different luminosity enhancement factors to a reference model. The results confirm that properties of the waves are impacted by the artificial enhancement of the luminosity and thermal diffusivity. We find that an increase in the stellar luminosity yields a decrease in the bulk convective turnover timescale and an increase in the characteristic frequency of excitation of the internal waves. We also show that a higher energy input in a model, corresponding to a larger luminosity, results in higher energy in high frequency waves. Across our tests with the luminosity and thermal diffusivity enhanced together by up to a factor of 104, our results are consistent with theoretical predictions of radiative damping. Increasing the luminosity also has an impact on the amplitude of oscillatory motions across the convective boundary. One must use caution when interpreting studies of internal gravity waves based on hydrodynamical simulations with artificially enhanced luminosity.Science and Technology Facilities Council (STFC)European Research Council (ERC

Expression and In Vivo Rescue of Human ABCC6 Disease-Causing Mutants in Mouse Liver

Loss-of-function mutations in ABCC6 can cause chronic or acute forms of dystrophic mineralization described in disease models such as pseudoxanthoma elasticum (OMIM 26480) in human and dystrophic cardiac calcification in mice. The ABCC6 protein is a large membrane-embedded organic anion transporter primarily found in the plasma membrane of hepatocytes. We have established a complex experimental strategy to determine the structural and functional consequences of disease-causing mutations in the human ABCC6. The major aim of our study was to identify mutants with preserved transport activity but failure in intracellular targeting. Five missense mutations were investigated: R1138Q, V1298F, R1314W, G1321S and R1339C. Using in vitro assays, we have identified two variants; R1138Q and R1314W that retained significant transport activity. All mutants were transiently expressed in vivo, in mouse liver via hydrodynamic tail vein injections. The inactive V1298F was the only mutant that showed normal cellular localization in liver hepatocytes while the other mutants showed mostly intracellular accumulation indicating abnormal trafficking. As both R1138Q and R1314W displayed endoplasmic reticulum localization, we tested whether 4-phenylbutyrate (4-PBA), a drug approved for clinical use, could restore their intracellular trafficking to the plasma membrane in MDCKII and mouse liver. The cellular localization of R1314W was significantly improved by 4-PBA treatment, thus potentially rescuing its physiological function. Our work demonstrates the feasibility of the in vivo rescue of cellular maturation of some ABCC6 mutants in physiological conditions very similar to the biology of the fully differentiated human liver and could have future human therapeutic application

H4K20me1 and H3K27me3 are concurrently loaded onto the inactive X chromosome but dispensabe for inducing gene silencing

© 2021 EMBO. This is an open access article under the terms of the Creative Commons Attribution License,which permits use, distribution and reproduction in any medium, provided the original work is properly cited.During X chromosome inactivation (XCI), in female placental mammals, gene silencing is initiated by the Xist long non-coding RNA. Xist accumulation at the X leads to enrichment of specific chromatin marks, including PRC2-dependent H3K27me3 and SETD8-dependent H4K20me1. However, the dynamics of this process in relation to Xist RNA accumulation remains unknown as is the involvement of H4K20me1 in initiating gene silencing. To follow XCI dynamics in living cells, we developed a genetically encoded, H3K27me3-specific intracellular antibody or H3K27me3-mintbody. By combining live-cell imaging of H3K27me3, H4K20me1, the X chromosome and Xist RNA, with ChIP-seq analysis we uncover concurrent accumulation of both marks during XCI, albeit with distinct genomic distributions. Furthermore, using a Xist B and C repeat mutant, which still shows gene silencing on the X but not H3K27me3 deposition, we also find a complete lack of H4K20me1 enrichment. This demonstrates that H4K20me1 is dispensable for the initiation of gene silencing, although it may have a role in the chromatin compaction that characterises facultative heterochromatin.This work was supported by Fundação para a Ciência e Tecnologia (S.T.d.R), project grants PTDC/BIA‐ MOL/29320/2017 IC&DT (A. C. R. & S.T.d.R), CEECUIND/01234/207 (S.T.d.R), and SFRH/BD/137099/2018 (A.C.R.), by an ERC Advanced Investigator award ERC‐ADG‐2014 671027 attributed to E.H., Sir Henry Wellcome Postdoctoral Fellowship (J.J.Z.), Japan Society for the Promotion of Science KAKENHI grants (JP17KK0143 and JP20K06484 to Y.S., JP19H04970, JP19H03158 and JP20H05393 to K.M., JP17K17719 to T.H., JP18H05534 to H.Ku, JP18H05527 and JP20H00456 to Y.O., JP17H01417 and JP18H05527 to H.Ki), and Japan Science and Technology Agency (JST) CREST JPMJCR16G1 to T.K., H.Ku, Y.O. and H.Ki, PREST JPMJPR2026 to K.M., and ERATO JPMJER1901 to H.Ku. J.J.Z. is supported by core funding of The Novo Nordisk Foundation Center for Stem Cell Biology (Novo Nordisk Foundation grant number NNF17CC0027852). Open Access funding enabled and organized by Projekt DEAL.info:eu-repo/semantics/publishedVersio

Evolutionary History of the Plant Pathogenic Bacterium Xanthomonas axonopodis

Deciphering mechanisms shaping bacterial diversity should help to build tools to predict the emergence of infectious diseases. Xanthomonads are plant pathogenic bacteria found worldwide. Xanthomonas axonopodis is a genetically heterogeneous species clustering, into six groups, strains that are collectively pathogenic on a large number of plants. However, each strain displays a narrow host range. We address the question of the nature of the evolutionary processes – geographical and ecological speciation – that shaped this diversity. We assembled a large collection of X. axonopodis strains that were isolated over a long period, over continents, and from various hosts. Based on the sequence analysis of seven housekeeping genes, we found that recombination occurred as frequently as point mutation in the evolutionary history of X. axonopodis. However, the impact of recombination was about three times greater than the impact of mutation on the diversity observed in the whole dataset. We then reconstructed the clonal genealogy of the strains using coalescent and genealogy approaches and we studied the diversification of the pathogen using a model of divergence with migration. The suggested scenario involves a first step of generalist diversification that spanned over the last 25 000 years. A second step of ecology-driven specialization occurred during the past two centuries. Eventually, secondary contacts between host-specialized strains probably occurred as a result of agricultural development and intensification, allowing genetic exchanges of virulence-associated genes. These transfers may have favored the emergence of novel pathotypes. Finally, we argue that the largest ecological entity within X. axonopodis is the pathovar