High richness of non-volant mammals in a seasonal forest fragment in southeastern Brazil

The seasonal forest formations of the Atlantic Forest are a threatened and poorly known habitat. We present here a list of the non-volant mammals occurring in a 515‑ha forest fragment known as Santa Maria and located in the Brazilian state of São Paulo. Our surveys are based on live trap captures, camera traps, and active searches for footprints, as well as secondary data. We list 29 species of non-volant mammals in the fragment, recorded between 1996 and 2021. One species found in the fragment, Leontopithecus chrysopygus, is globally endangered. Two species are classified as "vulnerable" in the global red list: Myrmecophaga tridactyla, and Tapirus terresris. One species, Panthera onca, is classified as "critically endangered" in São Paulo state. The red howler, Alouatta guariba, was not recorded after 1999 and has probably been extirpated in the fragment. We show that the number of non-volant mammal species in Santa Maria fragment is high, in relation to its size. The fragment is also in a strategic position, between the Morro do Diabo state park and the Black Lion Tamarin Ecological station, the two largest protected areas in the region. Considering its high mammal richness and its possible role as stepping stone for the local fauna, we recommend that the fragment become a protected area

Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes.

International audienceLateral gene transfers (LGT), species to species transmission of genes by means other than direct inheritance from a common ancestor, have played significant role in shaping prokaryotic genomes and are involved in gain or transfer of important biological processes. Whether LGT significantly contributed to the composition of an animal genome is currently unclear. In nematodes, multiple LGT are suspected to have favored emergence of plant-parasitism. With the availability of whole genome sequences it is now possible to assess whether LGT have significantly contributed to the composition of an animal genome and to establish a comprehensive list of these events. We generated clusters of homologous genes and automated phylogenetic inference, to detect LGT in the genomes of root-knot nematodes and found that up to 3.34% of the genes originate from LGT of non-metazoan origin. After their acquisition, the majority of genes underwent series of duplications. Compared to the rest of the genes in these species, several predicted functional categories showed a skewed distribution in the set of genes acquired via LGT. Interestingly, functions related to metabolism, degradation or modification of carbohydrates or proteins were substantially more frequent. This suggests that genes involved in these processes, related to a parasitic lifestyle, have been more frequently fixed in these parasites after their acquisition. Genes from soil bacteria, including plant-pathogens were the most frequent closest relatives, suggesting donors were preferentially bacteria from the rhizosphere. Several of these bacterial genes are plasmid-borne, pointing to a possible role of these mobile genetic elements in the transfer mechanism. Our analysis provides the first comprehensive description of the ensemble of genes of non-metazoan origin in an animal genome. Besides being involved in important processes regarding plant-parasitism, genes acquired via LGT now constitute a substantial proportion of protein-coding genes in these nematode genomes

0357: Two-dimensional speckle-tracking imaging for the left atrial and ventricular function in patients undergoing atrial fibrillation ablation

IntroductionLeft atrium (LA) structural remodeling associated with atrial fibrillation (AF) contributes to recurrence after AF catheter ablation (CA). Characterizing LA function may be useful to identify patients with higher risk of recurrence and could guide ablation strategy in term of substrate modification. We aimed to identify predictors of recurrence and atrial remodeling by assessing LA and left ventricle (LV) deformation properties using two-dimensional speckle-tracking imaging before and after AF CA.Methods62 patients (age 54±10 years, 90% male) with AF (45 paroxysmal (PAF), 17 persistent (PsAF)) underwent an echocardiography before CA, 3 and 6 months after CA to assess LA strain (S total (S-tot), positive peak (S-pos), negative peak (S-neg)), LA strain rate (SR positive peak (SRs), early (SRe) and late negative peak (SRa)) and LV strain (LV longitudinal and radial S).ResultsPsAF patients baseline had significantly larger LA volumes (41±8 vs 32±10ml/m2), decreased S-tot (10±5 vs 20±6%; p<0.001), SR-LAs (0.6±0.2 vs 1±0.3s−1; p<0.001) and LV strain (−12±3 vs −16±3%; p<0.001) compared to PAF group. After 6 month follow-up, 69% of the patients remained in sinus rhythm. Baseline LA active emptying, reservoir function and LA S-tot (13.2±6.2 vs 20.1±7%, p<0.001), S-neg (−7.2±3.5 vs –10.6±3.3%, p<0.009), SR-s (0.71±0.3 vs 1.01±0.35 s−1, <0.004), SR-a (–0.89±0.56 vs −1.37±0.48 s−1, p<0.01) and LV strain (−13.5±4.8 vs −17.1±3.5%, p<0.003) were significantly decreased in patients with AF recurrence. At multivariate analysis, the unique independent predictor of sinus rhythm maintenance was LA S-tot (HR 0.819 (0.685–0.979), p=0.028). In the overall cohort, LA volumes decreased from baseline to 3 and 6 months but there was no significant change in LA S, LA SR nor LV strain. At multivariate analysis, the unique independent predictor of LA reverse remodeling after CA was the duration of AF history (HR 0.84 (0.73–0.96), p=0.013).ConclusionsAltered global LA and LV strain before CA is associated with AF recurrence. Echocardiographic LA function characterization before ablation procedures may be helpful to guide AF ablation strategy and drug management after CA

Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

Background: In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability.[br/] Results: In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data.[br/] Conclusions: To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection

The future of road transport

A perfect storm of new technologies and new business models is transforming not only our vehicles, but everything about how we get around, and how we live our lives. The JRC report “The future of road transport - Implications of automated, connected, low-carbon and shared mobility” looks at some main enablers of the transformation of road transport, such as data governance, infrastructures, communication technologies and cybersecurity, and legislation. It discusses the potential impacts on the economy, employment and skills, energy use and emissions, the sustainability of raw materials, democracy, privacy and social fairness, as well as on the urban context. It shows how the massive changes on the horizon represent an opportunity to move towards a transport system that is more efficient, safer, less polluting and more accessible to larger parts of society than the current one centred on car ownership. However, new transport technologies, on their own, won't spontaneously make our lives better without upgrading our transport systems and policies to the 21st century. The improvement of governance and the development of innovative mobility solutions will be crucial to ensure that the future of transport is cleaner and more equitable than its car-centred present.JRC.C.4-Sustainable Transpor

PanACoTA: a modular tool for massive microbial comparative genomics

International audienceThe study of the gene repertoires of microbial species, their pangenomes, has become a key part of microbial evolution and functional genomics. Yet, the increasing number of genomes available complicates the establishment of the basic building blocks of comparative genomics. Here, we present PanA-CoTA (https://github.com/gem-pasteur/PanACoTA), a tool that allows to download all genomes of a species, build a database with those passing quality and redundancy controls, uniformly annotate and then build their pangenome, several variants of core genomes, their alignments and a rapid but accurate phylogenetic tree. While many programs building pangenomes have become available in the last few years, we have focused on a modular method, that tackles all the key steps of the process, from download to phylogenetic inference. While all steps are integrated, they can also be run separately and multiple times to allow rapid and extensive exploration of the parameters of interest. PanACoTA is built in Python3, includes a singularity container and features to facilitate its future development. We believe PanACoTa is an interesting addition to the current set of comparative genomics tools, since it will accelerate and standardize the more routine parts of the work, allowing microbial genomicists to more quickly tackle their specific questions

Selection for the bacterial capsule in the absence of biotic and abiotic aggressions depends on growth conditions

Extracellular capsules protect the cell against both abiotic and biotic stresses such as bacteriophages and the host immune system. Yet, it is unclear if capsules contribute to fitness in the absence of external aggressions, in spite of the cost of production. Here, we enquire if there are conditions favouring the presence of the capsule in Klebsiella , where it is a major virulence factor. We shortly experimentally evolved 19 different strains, and show that small changes in growth media have a strong impact on the maintenance of the capsule. Competitions with capsule mutants in nine different strains showed that capsules provide ∼20% of fitness advantage in nutrient-poor conditions, due to faster growth rates and higher yields. In contrast, the capsule was readily lost in nutrient-rich media. The growth environment, as well as the capsule serotype, strongly influenced the role of the capsule in major virulence traits like hypermucoviscosity and biofilm formation. Our data shows that the capsule is selected for in situations lacking abiotic, but also biotic stresses and further supports that the capsule role in virulence may be a by-product of adaptation outside the host, hinting that it may have important roles in bacterial physiology yet to be discovered

Nutrient conditions are primary drivers of bacterial capsule maintenance in Klebsiella

International audienceThe fitness cost associated with the production of bacterial capsules is considered to be offset by the protection provided by these extracellular structures against biotic aggressions or abiotic stress. However, it is unknown if the capsule contributes to fitness in the absence of these. Here, we explored conditions favouring the maintenance of the capsule in Klebsiella pneumoniae, where the capsule is known to be a major virulence factor. Using short-term experimental evolution on different Klebsiella strains, we showed that small environmental variations have a strong impact on the maintenance of the capsule. Capsule inactivation is frequent in nutrient-rich, but scarce in nutrient-poor media. Competitions between wild-type and capsule mutants in nine different strains confirmed that the capsule is costly in nutrient-rich media. Surprisingly, these results also showed that the presence of a capsule provides a clear fitness advantage in nutrient-poor conditions by increasing both growth rates and population yields. The comparative analyses of the wild-type and capsule mutants reveal complex interactions between the environment, genetic background and serotype even in relation to traits known to be relevant during pathogenesis. In conclusion, our data suggest there are novel roles for bacterial capsules yet to be discovered and further supports the notion that the capsule's role in virulence may be a by-product of its contribution to bacterial adaptation outside the host

Adaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits

International audienceThe extracellular capsule is a major virulence factor, but its ubiquity in free-living bacteria with large environmental breadths suggests that it shapes adaptation to novel niches. Yet, how it does so, remains unexplored. Here, we evolve three Klebsiella strains and their capsule mutants in parallel. Their comparison reveals different phenotypic and genotypic evolutionary changes that alter virulence-associated traits. Non-capsulated populations accumulate mutations that reduce exopolysaccharide production and increase biofilm formation and yield, whereas most capsulated populations become hypermucoviscous, a signature of hypervirulence. Hence, adaptation to novel environments primarily occurs by fine-tuning expression of the capsular locus. The same evolutionary conditions selecting for mutations in the capsular gene wzc leading to hypermucoviscosity also result in increased susceptibility to antibiotics by mutations in the ramA regulon. This implies that general adaptive processes outside the host can affect capsule evolution and its role in virulence and infection outcomes may be a by-product of such adaptation

Latent evolution of biofilm formation depends on life-history and genetic background

Abstract Adaptation to one environment can often generate phenotypic and genotypic changes which impact the future ability of an organism to thrive in other environmental conditions. In the context of host-microbe interactions, biofilm formation can increase survival rates in vivo upon exposure to stresses, like the host’s immune system or antibiotic therapy. However, how the generic process of adaptation impacts the ability to form biofilm and how it may change through time has seldomly been studied. To do so, we used a previous evolution experiment with three strains of the Klebsiella pneumoniae species complex, in which we specifically did not select for biofilm formation. We observed that changes in the ability to form biofilm happened very fast at first and afterwards reverted to ancestral levels in many populations. Biofilm changes were associated to changes in population yield and surface polysaccharide production. Genotypically, mutations in the tip adhesin of type III fimbriae (mrkD) or the fim switch of type I fimbriae were shaped by nutrient availability during evolution, and their impact on biofilm formation was dependent on capsule production. Analyses of natural isolates revealed similar mutations in mrkD, suggesting that such mutations also play an important role in adaptation outside the laboratory. Our work reveals that the latent evolution of biofilm formation, and its temporal dynamics, depend on nutrient availability, the genetic background and other intertwined phenotypic and genotypic changes. Ultimately, it suggests that small differences in the environment can alter an organism’s fate in more complex niches like the host