Хирургическое лечение эпидермоидных кист около стволовой локализации

КИСТА ЭПИДЕРМОИДНАЯ /ХИ

More Filtering on SNP Calling Does Not Remove Evidence of Inter-Nucleus Recombination in Dikaryotic Arbuscular Mycorrhizal Fungi

Evidence for the existence of dikaryote-like strains, low nuclear sequence diversity and inter-nuclear recombination in arbuscular mycorrhizal fungi has been recently reported based on single nucleus sequencing data. Here, we aimed to support evidence of inter-nuclear recombination using an approach that filters SNP calls more conservatively, keeping only positions that are exclusively single copy and homozygous, and with at least five reads supporting a given SNP. This methodology recovers hundreds of putative inter-nucleus recombination events across publicly available sequence data from individual nuclei. Challenges related to the acquisition and analysis of sequence data from individual nuclei are highlighted and discussed, and ways to address these issues in future studies are presented

Domestication of different varieties in the cheese-making fungus Geotrichum candidum

Domestication is an excellent model for studying adaptation processes, involving recent adaptation and diversification, convergence following adaptation to similar conditions, as well as degeneration of unused functions. Geotrichum candidum is a fungus used for cheese making and is also found in other environments such as soil and plants. By analyzing whole-genome data from 98 strains, we found that all strains isolated from cheese formed a monophyletic clade. Within the cheese clade, we identified three genetically differentiated populations and we detected footprints of recombination and admixture. The genetic diversity in the cheese clade was similar as that in the wild clade, suggesting the lack of strong bottlenecks. Commercial starter strains were scattered across the cheese clade, thus not constituting a single clonal lineage. The cheese populations were phenotypically differentiated from other populations, with a slower growth on all media, even cheese, a prominent production of typical cheese volatiles and a lower proteolytic activity. One of the cheese clusters encompassed all soft goat cheese strains, suggesting an effect of cheese-making practices on differentiation. Another of the cheese populations seemed to represent a more advanced stage of domestication, with stronger phenotypic differentiation from the wild clade, harboring much lower genetic diversity, and phenotypes more typical of cheese fungi, with denser and fluffier colonies and a greater ability of excluding cheese spoiler fungi. Cheese populations lacked two beta lactamase-like genes present in the wild clade, involved in xenobiotic clearance, and displayed higher contents of transposable elements, likely due to relaxed selection. Our findings suggest the existence of genuine domestication in G. candidum, which led to diversification into different varieties with contrasted phenotypes. Some of the traits acquired by cheese strains indicate convergence with other, distantly related fungi used for cheese maturation

A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society

Microbes are all pervasive in their distribution and influence on the functioning and well-being of humans, life in general and the planet. Microbially-based technologies contribute hugely to the supply of important goods and services we depend upon, such as the provision of food, medicines and clean water. They also offer mechanisms and strategies to mitigate and solve a wide range of problems and crises facing humanity at all levels, including those encapsulated in the sustainable development goals (SDGs) formulated by the United Nations. For example, microbial technologies can contribute in multiple ways to decarbonisation and hence confronting global warming, provide sanitation and clean water to the billions of people lacking them, improve soil fertility and hence food production and develop vaccines and other medicines to reduce and in some cases eliminate deadly infections. They are the foundation of biotechnology, an increasingly important and growing business sector and source of employment, and the centre of the bioeconomy, Green Deal, etc. But, because microbes are largely invisible, they are not familiar to most people, so opportunities they offer to effectively prevent and solve problems are often missed by decision-makers, with the negative consequences this entrains. To correct this lack of vital knowledge, the International Microbiology Literacy Initiative–the IMiLI–is recruiting from the global microbiology community and making freely available, teaching resources for a curriculum in societally relevant microbiology that can be used at all levels of learning. Its goal is the development of a society that is literate in relevant microbiology and, as a consequence, able to take full advantage of the potential of microbes and minimise the consequences of their negative activities. In addition to teaching about microbes, almost every lesson discusses the influence they have on sustainability and the SDGs and their ability to solve pressing problems of societal inequalities. The curriculum thus teaches about sustainability, societal needs and global citizenship. The lessons also reveal the impacts microbes and their activities have on our daily lives at the personal, family, community, national and global levels and their relevance for decisions at all levels. And, because effective, evidence-based decisions require not only relevant information but also critical and systems thinking, the resources also teach about these key generic aspects of deliberation. The IMiLI teaching resources are learner-centric, not academic microbiology-centric and deal with the microbiology of everyday issues. These span topics as diverse as owning and caring for a companion animal, the vast range of everyday foods that are produced via microbial processes, impressive geological formations created by microbes, childhood illnesses and how they are managed and how to reduce waste and pollution. They also leverage the exceptional excitement of exploration and discovery that typifies much progress in microbiology to capture the interest, inspire and motivate educators and learners alike. The IMiLI is establishing Regional Centres to translate the teaching resources into regional languages and adapt them to regional cultures, and to promote their use and assist educators employing them. Two of these are now operational. The Regional Centres constitute the interface between resource creators and educators–learners. As such, they will collect and analyse feedback from the end-users and transmit this to the resource creators so that teaching materials can be improved and refined, and new resources added in response to demand: educators and learners will thereby be directly involved in evolution of the teaching resources. The interactions between educators–learners and resource creators mediated by the Regional Centres will establish dynamic and synergistic relationships–a global societally relevant microbiology education ecosystem–in which creators also become learners, teaching resources are optimised and all players/stakeholders are empowered and their motivation increased. The IMiLI concept thus embraces the principle of teaching societally relevant microbiology embedded in the wider context of societal, biosphere and planetary needs, inequalities, the range of crises that confront us and the need for improved decisioning, which should ultimately lead to better citizenship and a humanity that is more sustainable and resilient. The biosphere of planet Earth is a microbial world: a vast reactor of countless microbially driven chemical transformations and energy transfers that push and pull many planetary geochemical processes, including the cycling of the elements of life, mitigate or amplify climate change (e.g., Nature Reviews Microbiology, 2019, 17, 569) and impact the well-being and activities of all organisms, including humans. Microbes are both our ancestors and creators of the planetary chemistry that allowed us to evolve (e.g., Life's engines: How microbes made earth habitable, 2023). To understand how the biosphere functions, how humans can influence its development and live more sustainably with the other organisms sharing it, we need to understand the microbes. In a recent editorial (Environmental Microbiology, 2019, 21, 1513), we advocated for improved microbiology literacy in society. Our concept of microbiology literacy is not based on knowledge of the academic subject of microbiology, with its multitude of component topics, plus the growing number of additional topics from other disciplines that become vitally important elements of current microbiology. Rather it is focused on microbial activities that impact us–individuals/communities/nations/the human world–and the biosphere and that are key to reaching informed decisions on a multitude of issues that regularly confront us, ranging from personal issues to crises of global importance. In other words, it is knowledge and understanding essential for adulthood and the transition to it, knowledge and understanding that must be acquired early in life in school. The 2019 Editorial marked the launch of the International Microbiology Literacy Initiative, the IMiLI. HERE, WE PRESENT our concept of how microbiology literacy may be achieved and the rationale underpinning it; the type of teaching resources being created to realise the concept and the framing of microbial activities treated in these resources in the context of sustainability, societal needs and responsibilities and decision-making; and the key role of Regional Centres that will translate the teaching resources into local languages, adapt them according to local cultural needs, interface with regional educators and develop and serve as hubs of microbiology literacy education networks. The topics featuring in teaching resources are learner-centric and have been selected for their inherent relevance, interest and ability to excite and engage. Importantly, the resources coherently integrate and emphasise the overarching issues of sustainability, stewardship and critical thinking and the pervasive interdependencies of processes. More broadly, the concept emphasises how the multifarious applications of microbial activities can be leveraged to promote human/animal, plant, environmental and planetary health, improve social equity, alleviate humanitarian deficits and causes of conflicts among peoples and increase understanding between peoples (Microbial Biotechnology, 2023, 16(6), 1091–1111). Importantly, although the primary target of the freely available (CC BY-NC 4.0) IMiLI teaching resources is schoolchildren and their educators, they and the teaching philosophy are intended for all ages, abilities and cultural spectra of learners worldwide: in university education, lifelong learning, curiosity-driven, web-based knowledge acquisition and public outreach. The IMiLI teaching resources aim to promote development of a global microbiology education ecosystem that democratises microbiology knowledge.http://www.wileyonlinelibrary.com/journal/mbt2hj2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-01:No povertySDG-02:Zero HungerSDG-03:Good heatlh and well-beingSDG-04:Quality EducationSDG-06:Clean water and sanitationSDG-07:Affordable and clean energySDG-08:Decent work and economic growthSDG-12:Responsible consumption and productionSDG-13:Climate actionSDG-14:Life below wate

Parallel adaptation of cheese fungi

Since the beginning of my scientific career, I have been interested in understanding the genomic processes involved in the adaptation of populations to various environments, using fungi as models. During both my phD thesis and first postdoc, I looked at the mechanisms involved in cheese adaptation within two cheese ripening species, Penicillium camemberti and P. roqueforti. I was also interested in the evolution of the reproduction mode of P. roqueforti, and in its genetic diversity and population structure. During my second postdoc in Canada, I discovered mating-type genes in the mycorrhizal fungus Rhizophagus irregularis, which was yet considered a typical example of an asexual species. During my third postdoc at the Institut Pasteur, I demonstrated the occurrence of gene flows between populations of the human fungal pathogen Candida albicans. Since 2018 as a CNRS permanent researcher, I have been studying parallel adaptation using several fungi thriving in the cheese environment, combining genome analyses, phenotypic, sociological and historical data, and laboratory experiments. By studying parallel adaptations of phylogenetically distant species to the same ecological niche, my project aims to test if there are convergent adaptations, that is if the same genomic mechanisms and/or the same characters/genes have been the targets of selection. Cheese fungi are prime models to study parallel adaptation because multiple phylogenetically distant species thrive in the same ecological niche, cheese, and this adaptation is the result of strong and recent selection (less than 8000 years ago). My project aims at answering the following questions: 1) do cheese specieshave populations adapted to the cheese environment, genetically differentiated from those present in other environments? 2) how were gene flows reduced? 3) what are the genomic processes involved in adaptive divergence? 4) are these processes the same between species?Depuis le début de ma carrière scientifique, je m’intéresse à comprendre les processus génomiques impliqués dans l’adaptation des populations à des environnements variés, en utilisant les champignons comme modèles. Pendant ma thèse et mon premier post-doctorat, j’ai recherché les mécanismes évolutifs impliqués dans l’adaptation au fromage des espèces Penicillium camemberti et P. roqueforti utilisées pour l’affinage. Je me suis aussi intéressée à l’évolution du mode de reproduction de P. roqueforti, et à sa diversité génétique et structure des populations. Pendant mon deuxième post-doctorat au Canada, j’ai découvert les gènes de types sexuels chez le champignon mycorhizien Rhizophagus irregularis, qui était pourtant considéré comme un exemple type d’espèce asexuée. Durant mon troisième post-doctorat à l’Institut Pasteur, j’ai mis en évidence des flux de gènes entre populations du champignon pathogène humain Candida albicans. Depuis ma prise de fonction en tant que chargée de recherche en 2018, j’étudie l’adaptation parallèle en utilisant plusieurs champignons de l’environnement fromager, et en combinant des analyses de génomes, des données phénotypiques, sociologiques et historiques, et des expérimentations au laboratoire. Grâce à l’étude d’adaptations parallèles d’espèces phylogénétiquement éloignées à la même niche écologique, mon projet vise à tester s’il existe des adaptations convergentes, si les mécanismes génomiques sont les mêmes et/ou si les mêmes caractères/gènes ont été les cibles de la sélection. Les champignons du fromage sont des modèles de choix pour étudier l’adaptation parallèle car de multiples espèces phylogénétiquement éloignées vivent dans cette même niche écologique, le fromage, et cette adaptation est le résultat d’une sélection forte et récente (moins de 8000 ans). Mon projet s’articule autour des questions suivantes : 1) est-ce que les espèces du fromage présentent des populations adaptées à ce milieu, et différenciées génétiquement de celles d’autres environnements ? 2) comment les flux de gènes ont-ils été réduits ? 3) quels sont les processus génomiques impliqués dans la divergence adaptative ? 4) ces processus sont-ils les mêmes entre espèces

Massive gene swamping among cheese-making Penicillium fungi

International audienceHorizontal gene transfers (HGT), i.e., the transmission of genetic material between species not directly attributable to meiotic gene exchange, have long been acknowledged as a major driver of prokaryotic evolution and is increasingly recognized as an important source of adaptation in eukaryotes. In fungi in particular , many convincing examples of HGT have been reported to confer selective advantages on the recipient fungal host, either promoting fungal pathogenicity on plants or increasing their toxicity by the acquisition of secondary metabolic clusters, resulting in adaptation to new niches and in some cases eventually even in speciation. These horizontal gene transfers involve single genes, complete metabolic pathways or even entire chromosomes. A recent study has uncovered multiple recent horizontal transfers of a 575 kb ge-nomic island in cheese Penicillium fungi, representing ca. 2% of the Penicillium roqueforti's genome, that may confer selective advantage in the competing cheese environment where bacteria and fungi occur. Novel phylogenomic methods are being developed, revealing massive HGT among fungi. Altogether, these recent studies indicate that HGT is a crucial mechanism of rapid adaptation, even among eukaryotes. A well-documented example of pathogenicity acquisition in fungi involves the recent transfer of the toxin-coding gene ToxA, from Stagonospora nodorum, a fungus pathogen of wheat, to Pyrenophora tritici-repentis, a distant fungal species having thereby acquired the ability to infect wheat. Pyrenophora has also acquired numerous virulence factor

Comptes Rendus Biologies

International audiencemodel for studying adaptation since Charles Darwin. Here we review recent studies on thegenomics of adaptation and domestication syndrome in two cheese-making fungal lineages, Penicilliumroquefortiused for maturing blue cheeses, and the Penicilliumcamemberti species complex usedfor making soft cheeses such as Camembert and Brie. Comparative genomics have revealed horizontalgene transfers involved in convergent adaptation to cheese. Population genomics have identified differentiatedpopulations with contrasted traits, several populations having independently been domesticatedfor cheese making in both P. roqueforti and the Penicillium camemberti species complex, and having undergone bottlenecks. The different cheese populations have acquired traits beneficial forcheese making in comparison to non-cheese populations, regarding color, spore production, growthrates on cheese, salt tolerance, lipolysis, proteolysis, volatile compound or toxin production and/orcompetitive ability. The cheese populations also show degeneration for some unused functions suchas decreased ability of sexual reproduction or of growth under harsh conditions. These recent findingshave fundamental importance for our understanding of adaptation and have applied interest forstrain improvement