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Studies of fungal communities through amplicon metagenomics in aquatic environments, particularly in freshwater ecosystems, are still relatively recent. Unfortunately, many of these water bodies are facing growing threats from human expansion, such as effluent discharge from various human activities. As a result, these effluents have the potential to significantly alter the characteristics of water bodies and, subsequently, impact the diversity of their resident microorganisms. In this context, our objective was to investigate whether the fungal community structure varies according to the presence of different anthropic disturbances. We expect (i) the diversity of fungi will be greater and (ii) more specific unique operational taxonomic units (OTUs) related to each ecotonal system will be found compared to other sites of a lagoon. The study was conducted in the Tramandaí Lagoon (subtropical southern Brazil) at four distinct sampling points (estuary, middle of the lagoon, crop field area, and near a residential area where the Tramandaí River flows into the lagoon). As expected, the estuary and residential zones, which are ecotones, exhibited greater fungal diversity and more specific OTUs compared to the middle of the lagoon and crop field area. Moreover, a substantial proportion of fungal taxa could not be identified at the genus level, with many only classified at the phylum level, indicating potential new lineages. These findings underscore our limited understanding of the subtropical freshwater mycobiota.

On s’est beaucoup moqué des banquets politiques, de « cette éloquence d’automne semée autour de tables bourgeoises et arrosée de vins du cru » (Lamennais). Comment prendre au sérieux en effet ces agapes, à nos yeux si prosaïques en pleine exaltation romantique, mais aussi ridiculement effusives dans une époque qui vouait un culte à la rationalité politique ? Et pourtant, aujourd’hui encore, chacun sait que la cause immédiate de la révolution de Février 1848 fut l’interdiction par Guizot d’un banquet réformiste, celui du XIIe arrondissement de la capitale. Bon nombre de contemporains en restèrent perplexes : comme nous, ils n’arrivaient pas à comprendre comment une décision apparemment anodine avait pu avoir de telles conséquences. Aussi fallait-il reconstituer une histoire qui n’a jamais été écrite, celle d’une forme disparue du répertoire politique. Le banquet n’est si étrange à nos yeux que parce que nous avons indûment valorisé Gavroche et Tocqueville, la barri­cade et le parlement. Décrire les banquets, pour d’abord mieux comprendre la sociabilité du premier xixe siècle, et reconstituer la culture politique de toute une génération, qui savait jouer des symboles et de l’implicite, et qui, après la Révolution et le despotisme napoléonien, cherchait sa voie dans une période décisive pour l’apprentissage de la liberté et de la démocratie. Puis faire toute sa place à un imaginaire dont nous avons oublié la richesse et les multiples enjeux. C’est, en définitive, s’interroger sur la nature même du lien politique, au-delà des discours et des institutions.

© 2016 IEEE. The microwave radiometer technology acceleration (MiRaTA) is a 3U CubeSat mission sponsored by the NASA Earth Science Technology Office. The science payload on MiRaTA consists of a triband microwave radiometer and global positioning system (GPS) radio occultation (GPSRO) sensor. The microwave radiometer takes measurements of all-weather temperature (V-band, 50-57 GHz), water vapor (G-band, 175-191 GHz), and cloud ice (G-band, 205 GHz) to provide observations used to improve weather forecasting. The Aerospace Corporation's GPSRO experiment, called the compact total electron content and atmospheric GPS sensor (CTAGS), measures profiles of temperature and pressure in the upper troposphere/lower stratosphere (∼20 km) and electron density in the ionosphere (over 100 km). The MiRaTA mission will validate new technologies in both passive microwave radiometry and GPSRO: 1) new ultracompact and low-power technology for multichannel and multiband passive microwave radiometers, 2) the application of a commercial off-the-shelf GPS receiver and custom patch antenna array technology to obtain neutral atmospheric GPSRO retrieval from a nanosatellite, and 3) a new approach to space-borne microwave radiometer calibration using adjacent GPSRO measurements. In this paper, we focus on objective 3, developing operational models to meet a mission goal of 100 concurrent radiometer and GPSRO measurements, and estimating the temperature measurement precision for the CTAGS instrument based on thermal noise Based on an analysis of thermal noise of the CTAGS instrument, the expected temperature retrieval precision is between 0.17 and 1.4 K, which supports the improvement of radiometric calibration to 0.25 K.

Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the "big picture" of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic pro

Background: The control and prevention of vector-borne and zoonotic diseases is often based on the reduction of host or vector populations, involving but not limited to preventative culling and use of insecticides. Yet, destructive interventions such as these have shown several limitations including ineffectiveness on arthropods and negative impacts on ecosystems. An alternative strategy would be to rely on the natural ecosystem functions and their careful management to regulate such diseases. The goal of our work was to evaluate existing scientific evidence on potential links between ecosystem components/functions and 14 vector-borne and zoonotic diseases impacting human health and answer the question: “What evidence exists on the impact of specific ecosystem components and functions on infectious diseases?”. Methods: We searched for scientific articles published in English and French and screened them in a 3-round process (title, abstract and full-text). Articles were retained, without any geographical limitation, if they matched the following eligibility criteria: an exposure/intervention linked to changes in biological communities, habitats, or landscapes; an outcome consisting of any measure of infection in vector, animal or human hosts; and the presence of a comparator, in time and/or in space. The results are presented as a systematic map, followed by a narrative review where the amount of papers allowed for synthesis. Results: Searches in 5 scientific publication databases allowed to retrieve 9723 unique articles, among which 207 were retained after the screening process. The amount of relevant literature was highly variable depending on diseases, and the types of exposures also varied greatly among studies focusing on the same disease. A hundred articles presented in the map were unique in their “disease x exposure” combination and thus not eligible for further narrative description. The remaining 107 articles were organized in 34 “disease x exposure” group

The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be trac

Fungal species delimitation was traditionally carried out with multicopy ribosomal RNA (rRNA) genes, principally for their ease of amplification. Since the efficacy of these markers has been questioned, single-copy protein-encoding genes have been proposed alone or in combination for Multi-Locus Sequence Typing (MLST). In this context, the role of the many sequences obtained with Next-Generation Sequencing (NGS) techniques, in both genomics and metagenomics, further pushes toward an analysis of the efficacy of NGS-derived markers and of the metrics to evaluate the marker efficacy in discriminating fungal species. This paper aims at proposing MeTRe (Mean Taxonomic Resolution), a novel index that could be used both for measuring marker efficacy and for assessing the actual resolution (i.e., the level of separation) between species obtained with different markers or their combinations. In this paper, we described and then employed this index to compare the efficacy of two rRNAs and four single-copy markers obtained from public databases as both an amplicon-based approach and genome-derived sequences. Two different groups of species were used, one with a pathogenic species of Candida that was characterized by relatively well-separated taxa, whereas the other, comprising some relevant species of the sensu stricto group of the genus Saccharomyces, included close species and interspecific hybrids. The results showed the ability of MeTRe to evaluate marker efficacy in general and genome-derived markers specifically.

BACKGROUND: biofilm formation on biotic and abiotic surfaces is finely regulated by genetic factors but also by oxygen concentration, pH, temperature and other environmental factors, already extensively explored for bacterial biofilms. Much less is known about fungal biofilm, that is considered a virulence factor for Candida pathogenic species among the few fungal species able to grow and survive at high temperatures such as 37°C as well as those induced by fever. The resistance to high temperatures coupled with the ability to form biofilm are threatening factors of these fungal species that could severely impact at an epidemiological level.OBJECTIVES: in this framework, we decided to study the thermal tolerance of biofilms formed by three medical relevant species such as Candida albicans and two non-Candida-albicans-Candida species.METHODS: Thirty nosocomial strains were investigated for their ability to adhere and grow in proximity and over body temperature (from 31°C to 43°C), mimicking different environmental conditions or severe febrile-like reactions.RESULTS: Candida sessile cells reacted to different temperatures showing a strain-specific response. It was observed that the attachment and growth respond differently to the temperature and that mechanism of adhesion has different outputs at high temperature than the growth.CONCLUSIONS: This strain-dependent response is probably instrumental to guarantee the best success to cells for the infection, attachment and growth to occur. These observations reinforce the concept of temperature as a major trigger in the evolution of these species especially in this period of increasing environmental temperatures and excessive domestic heating.

Homoplasy is a sort of noise in phylogenetic reconstructions, due to the accumulation of backmutations, convergent evolution and horizontal gene transfer (HGT), which is considered the major trigger of homoplasy in microorganism for its massive presence. It is also known that homoplasy increases with the complexity of the tree with both real and simulated data. In this paper, we analyzed the variation of homoplasy with the two widely used taxonomic markers ITS and LSU in four taxonomic models characterized by differences in the intra-specific distances. An algorithm (HomoDist) was developed to analyze the homoplasy index (HI) variation upon addition of a single element (strain or species) in increasing distance from a starting element. This algorithm allows to follow changes of the consistency index (CI), complementary to the HI, with the increase of the number of taxa and with the increase of the distance among elements. Results show that homoplasy increases-as expected-with the number of taxa, but also as a function of the overall distance among species, often with an almost linear relationship between distance and HI. No HI change was observed in trees with few taxa spanning through short distances, indicating that this noise is not prohibitive in this context, although the analysis of the ratio between HI and distance can be recommended as a criterion for tree acceptance. The absence of large changes of the HI within the species, and its increase when new species are added by HomoDist, suggest that homoplasy variation can be used as an auxiliary test in distance-based species delimitation with any type of marker.

The identification and proper naming of microfungi, in particular plant, animal and human pathogens, remains challenging. Molecular identification is becoming the default approach for many fungal groups, and environmental metabarcoding is contributing an increasing amount of sequence data documenting fungal diversity on a global scale. This includes lineages represented only by sequence data. At present, these taxa cannot be formally described under the current nomenclature rules. By considering approaches used in bacterial taxonomy, we propose solutions for the nomenclature of taxa known only from sequences to facilitate consistent reporting and communication in the literature and public sequence repositories.

Ribosomal RNA in fungi is encoded by a series of genes and spacers included in a large operon present in 100 tandem repeats, normally in a single locus. The multigene nature of this locus was somehow masked by Sanger sequencing, which produces a single sequence reporting the prevalent nucleotide of each site. The introduction of next generation sequencing led to deeper knowledge of the individual sequences (reads) and therefore of the variants between the same DNA sequences located in different tandem repeats. In this framework, NGS sequencing of the rDNA region was used to elucidate the extent of intra- and inter-genomic variation at both the strain and species level. Specifically, the use of an innovative NGS technique allowed the high-throughput high-depth sequencing of the ITS1-LSU D1/D2 amplicons of 252 strains belonging to four opportunistic yeast species of the genus Candida. Results showed the presence of a large extent of variability among strains and species. These variants were differently distributed throughout the analyzed regions with a higher concentration within the Internally Transcribed Spacer (ITS) region, suggesting that concerted evolution was not able to totally homogenize these sequences. Both the internal variability and the SNPs between strain can be used for a deep typing of the strains and to study their ecology.

Global warming was proposed to be a contributing cause for the nearly simultaneous emergence of different clades of Candida auris as a nosocomial pathogen in different continents. The global warming emergence hypothesis posits that C. auris existed in the environment prior to its clinical recognition and became pathogenic for humans because of thermal adaptation in response to climate change. The isolation of C. auris from two sites in the remote Andaman Islands establishes it as an environmental organism, a necessary condition for the hypothesis. The observation that one environmental isolate grew slower at mammalian temperatures than clinical strains is consistent with the notion that their ancestor recently adapted to higher temperatures. The knowledge that C. auris can be recovered from the environment should prompt additional searches to define its ecological niches, and the analysis of future environmental isolates will provide evidence for validating or refuting the global warming emergence hypothesis.

The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced

Background: The control and prevention of vector-borne and zoonotic diseases is often based on the reduction of host or vector populations, involving but not limited to preventative culling and use of insecticides. Yet, destructive interventions such as these have shown several limitations including ineffectiveness on arthropods and negative impacts on ecosystems. An alternative strategy would be to rely on the natural ecosystem functions and their careful management to regulate such diseases. The goal of our work was to evaluate existing scientific evidence on potential links between ecosystem components/functions and 14 vector-borne and zoonotic diseases impacting human health and answer the question: “What evidence exists on the impact of specific ecosystem components and functions on infectious diseases?”. Methods: We searched for scientific articles published in English and French and screened them in a 3-round process (title, abstract and full-text). Articles were retained, without any geographical limitation, if they matched the following eligibility criteria: an exposure/intervention linked to changes in biological communities, habitats, or landscapes; an outcome consisting of any measure of infection in vector, animal or human hosts; and the presence of a comparator, in time and/or in space. The results are presented as a systematic map, followed by a narrative review where the amount of papers allowed for synthesis. Results: Searches in 5 scientific publication databases allowed to retrieve 9723 unique articles, among which 207 were retained after the screening process. The amount of relevant literature was highly variable depending on diseases, and the types of exposures also varied greatly among studies focusing on the same disease. A hundred articles presented in the map were unique in their “disease x exposure” combination and thus not eligible for further narrative description. The remaining 107 articles were organized in 34 “disease x exposure” group

Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the "big picture" of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic pro

The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be trac

Fungal species delimitation was traditionally carried out with multicopy ribosomal RNA (rRNA) genes, principally for their ease of amplification. Since the efficacy of these markers has been questioned, single-copy protein-encoding genes have been proposed alone or in combination for Multi-Locus Sequence Typing (MLST). In this context, the role of the many sequences obtained with Next-Generation Sequencing (NGS) techniques, in both genomics and metagenomics, further pushes toward an analysis of the efficacy of NGS-derived markers and of the metrics to evaluate the marker efficacy in discriminating fungal species. This paper aims at proposing MeTRe (Mean Taxonomic Resolution), a novel index that could be used both for measuring marker efficacy and for assessing the actual resolution (i.e., the level of separation) between species obtained with different markers or their combinations. In this paper, we described and then employed this index to compare the efficacy of two rRNAs and four single-copy markers obtained from public databases as both an amplicon-based approach and genome-derived sequences. Two different groups of species were used, one with a pathogenic species of Candida that was characterized by relatively well-separated taxa, whereas the other, comprising some relevant species of the sensu stricto group of the genus Saccharomyces, included close species and interspecific hybrids. The results showed the ability of MeTRe to evaluate marker efficacy in general and genome-derived markers specifically.

Global warming was proposed to be a contributing cause for the nearly simultaneous emergence of different clades of Candida auris as a nosocomial pathogen in different continents. The global warming emergence hypothesis posits that C. auris existed in the environment prior to its clinical recognition and became pathogenic for humans because of thermal adaptation in response to climate change. The isolation of C. auris from two sites in the remote Andaman Islands establishes it as an environmental organism, a necessary condition for the hypothesis. The observation that one environmental isolate grew slower at mammalian temperatures than clinical strains is consistent with the notion that their ancestor recently adapted to higher temperatures. The knowledge that C. auris can be recovered from the environment should prompt additional searches to define its ecological niches, and the analysis of future environmental isolates will provide evidence for validating or refuting the global warming emergence hypothesis.

Homoplasy is a sort of noise in phylogenetic reconstructions, due to the accumulation of backmutations, convergent evolution and horizontal gene transfer (HGT), which is considered the major trigger of homoplasy in microorganism for its massive presence. It is also known that homoplasy increases with the complexity of the tree with both real and simulated data. In this paper, we analyzed the variation of homoplasy with the two widely used taxonomic markers ITS and LSU in four taxonomic models characterized by differences in the intra-specific distances. An algorithm (HomoDist) was developed to analyze the homoplasy index (HI) variation upon addition of a single element (strain or species) in increasing distance from a starting element. This algorithm allows to follow changes of the consistency index (CI), complementary to the HI, with the increase of the number of taxa and with the increase of the distance among elements. Results show that homoplasy increases-as expected-with the number of taxa, but also as a function of the overall distance among species, often with an almost linear relationship between distance and HI. No HI change was observed in trees with few taxa spanning through short distances, indicating that this noise is not prohibitive in this context, although the analysis of the ratio between HI and distance can be recommended as a criterion for tree acceptance. The absence of large changes of the HI within the species, and its increase when new species are added by HomoDist, suggest that homoplasy variation can be used as an auxiliary test in distance-based species delimitation with any type of marker.

BACKGROUND: biofilm formation on biotic and abiotic surfaces is finely regulated by genetic factors but also by oxygen concentration, pH, temperature and other environmental factors, already extensively explored for bacterial biofilms. Much less is known about fungal biofilm, that is considered a virulence factor for Candida pathogenic species among the few fungal species able to grow and survive at high temperatures such as 37°C as well as those induced by fever. The resistance to high temperatures coupled with the ability to form biofilm are threatening factors of these fungal species that could severely impact at an epidemiological level.OBJECTIVES: in this framework, we decided to study the thermal tolerance of biofilms formed by three medical relevant species such as Candida albicans and two non-Candida-albicans-Candida species.METHODS: Thirty nosocomial strains were investigated for their ability to adhere and grow in proximity and over body temperature (from 31°C to 43°C), mimicking different environmental conditions or severe febrile-like reactions.RESULTS: Candida sessile cells reacted to different temperatures showing a strain-specific response. It was observed that the attachment and growth respond differently to the temperature and that mechanism of adhesion has different outputs at high temperature than the growth.CONCLUSIONS: This strain-dependent response is probably instrumental to guarantee the best success to cells for the infection, attachment and growth to occur. These observations reinforce the concept of temperature as a major trigger in the evolution of these species especially in this period of increasing environmental temperatures and excessive domestic heating.

The identification and proper naming of microfungi, in particular plant, animal and human pathogens, remains challenging. Molecular identification is becoming the default approach for many fungal groups, and environmental metabarcoding is contributing an increasing amount of sequence data documenting fungal diversity on a global scale. This includes lineages represented only by sequence data. At present, these taxa cannot be formally described under the current nomenclature rules. By considering approaches used in bacterial taxonomy, we propose solutions for the nomenclature of taxa known only from sequences to facilitate consistent reporting and communication in the literature and public sequence repositories.

Ribosomal RNA in fungi is encoded by a series of genes and spacers included in a large operon present in 100 tandem repeats, normally in a single locus. The multigene nature of this locus was somehow masked by Sanger sequencing, which produces a single sequence reporting the prevalent nucleotide of each site. The introduction of next generation sequencing led to deeper knowledge of the individual sequences (reads) and therefore of the variants between the same DNA sequences located in different tandem repeats. In this framework, NGS sequencing of the rDNA region was used to elucidate the extent of intra- and inter-genomic variation at both the strain and species level. Specifically, the use of an innovative NGS technique allowed the high-throughput high-depth sequencing of the ITS1-LSU D1/D2 amplicons of 252 strains belonging to four opportunistic yeast species of the genus Candida. Results showed the presence of a large extent of variability among strains and species. These variants were differently distributed throughout the analyzed regions with a higher concentration within the Internally Transcribed Spacer (ITS) region, suggesting that concerted evolution was not able to totally homogenize these sequences. Both the internal variability and the SNPs between strain can be used for a deep typing of the strains and to study their ecology.

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In th

© 2016 IEEE. The microwave radiometer technology acceleration (MiRaTA) is a 3U CubeSat mission sponsored by the NASA Earth Science Technology Office. The science payload on MiRaTA consists of a triband microwave radiometer and global positioning system (GPS) radio occultation (GPSRO) sensor. The microwave radiometer takes measurements of all-weather temperature (V-band, 50-57 GHz), water vapor (G-band, 175-191 GHz), and cloud ice (G-band, 205 GHz) to provide observations used to improve weather forecasting. The Aerospace Corporation's GPSRO experiment, called the compact total electron content and atmospheric GPS sensor (CTAGS), measures profiles of temperature and pressure in the upper troposphere/lower stratosphere (∼20 km) and electron density in the ionosphere (over 100 km). The MiRaTA mission will validate new technologies in both passive microwave radiometry and GPSRO: 1) new ultracompact and low-power technology for multichannel and multiband passive microwave radiometers, 2) the application of a commercial off-the-shelf GPS receiver and custom patch antenna array technology to obtain neutral atmospheric GPSRO retrieval from a nanosatellite, and 3) a new approach to space-borne microwave radiometer calibration using adjacent GPSRO measurements. In this paper, we focus on objective 3, developing operational models to meet a mission goal of 100 concurrent radiometer and GPSRO measurements, and estimating the temperature measurement precision for the CTAGS instrument based on thermal noise Based on an analysis of thermal noise of the CTAGS instrument, the expected temperature retrieval precision is between 0.17 and 1.4 K, which supports the improvement of radiometric calibration to 0.25 K.

IEEE CubeSats with miniaturized microwave radiometers are now demonstrating the potential to provide science-quality weather measurements. For example, the Micro-Sized Microwave Atmospheric Satellite-2A (MicroMAS-2A) and Temporal Experiment for Storms and Tropical Systems-Demonstration (TEMPEST-D) CubeSats are both launched in 2018 and have demonstrated microwave atmospheric sounder data from orbit. The NASA Time-Resolved Observations of Precipitation structure and storm Intensity with a Constellation of Smallsats (TROPICS) mission is a follow-on constellation of six 3U CubeSats based on the MicroMAS-2 design that is scheduled for launch no sooner than 2021. The TROPICS sensors use internal noise diodes (NDs) for calibration. Although the NDs on TROPICS are similar to technology flown on GMI, they have not been tested on-orbit at TROPICS frequencies. In order to track and correct ND drift, we develop a novel method of calibration for CubeSat constellations, such as TROPICS, by incorporating periodic solar and lunar intrusions as an additional source of information to counter ND drift. These lunar intrusions also occur for existing satellites hosting microwave radiometers in sun-synchronous polar orbits but are much more infrequent than for the TROPICS constellation's scanning payload. In this work, we develop a solar/lunar calibration correction algorithm and test it using advanced technology microwave sounder (ATMS) lunar intrusion data. The mean bias and standard deviation between the solar/lunar calibration correction algorithm and actual ATMS data fall within the expected ATMS error budget of 0.6-3.9 K, validating our model., NASA (Award NNX16AM73H)

The Micro-Sized Microwave Atmospheric Satellite (MicroMAS-2A) is a 3U CubeSat that launched in January 2018 as a technology demonstration for future microwave sounding constellation missions, such as the NASA Time-Resolved Observations of Precipitation structure and storm Intensity with a Constellation of Smallsats (TROPICS) mission now in development. MicroMAS-2A has a miniaturized 1U 10-channel passive microwave radiometer with channels near 90, 118, 183, and 206 GHz for moisture and temperature profiling and precipitation imaging [4]. MicroMAS-2A provided the first CubeSat atmospheric vertical sounding data from orbit and to date is the only CubeSat to provide temperature and moisture sounding and surface imaging. In this paper, we analyze six segments of data collected from MicroMAS-2A in April 2018 and compare them to ERA5 reanalysis fields coupled with the Community Radiative Transfer Model (CRTM). This initial assessment of CubeSat radiometric accuracy shows biases relative to ERA5 with magnitudes ranging from 0.4 to 2.2 K (with standard deviations ranging from 0.7 to 1.2 K) for the four mid-tropospheric temperature channels and biases of 2.2 and 2.8 K (standard deviations 1.8 and 2.6 K) for the two lower tropospheric water vapor channels., NASA (Award NNX16AM73H)

Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the 'big picture' of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic proces

Les progrès des connaissances, de la médecine et le développement des insecticides ont durant un temps laissé penser qu'on viendrait à bout des nuisances occasionnées par les moustiques, les tiques et les mouches, ainsi que des maladies comme le paludisme, la dengue, la maladie de Chagas, la fièvre catarrhale ovine et bien d'autres maladies infectieuses transmises par voie vectorielle. Mais en ce début de xxie siècle, la réalité s'avère tout autre. Écrit par un collectif de spécialistes, cet ouvrage présente un état actualisé des connaissances sur tous les groupes d'arthropodes d'intérêt médical et vétérinaire. Il s'appuie sur les recherches les plus récentes en systématique, écologie, génétique, anthropologie, histoire, médecine, santé publique et génie sanitaire. Pragmatique et opérationnel, il décrit les techniques d'identification et de lutte à mettre en place pour limiter les nuisances et les effets pathogènes consécutifs à la transmission vectorielle de virus, bactéries, protozoaires et filaires. Véritable voyage au cœur de l'entomologie médicale et vétérinaire, ce livre permettra aux enseignants, aux étudiants, aux personnels de santé, aux chercheurs et aux décideurs en santé publique d'avoir une vision complète, mise à jour et fonctionnelle du contexte, des enjeux et des solutions à mettre en œuvre dans un domaine majeur de la santé humaine et animale.

Les progrès des connaissances, de la médecine et le développement des insecticides ont durant un temps laissé penser qu'on viendrait à bout des nuisances occasionnées par les moustiques, les tiques et les mouches, ainsi que des maladies comme le paludisme, la dengue, la maladie de Chagas, la fièvre catarrhale ovine et bien d'autres maladies infectieuses transmises par voie vectorielle. Mais en ce début de xxie siècle, la réalité s'avère tout autre. Écrit par un collectif de spécialistes, cet ouvrage présente un état actualisé des connaissances sur tous les groupes d'arthropodes d'intérêt médical et vétérinaire. Il s'appuie sur les recherches les plus récentes en systématique, écologie, génétique, anthropologie, histoire, médecine, santé publique et génie sanitaire. Pragmatique et opérationnel, il décrit les techniques d'identification et de lutte à mettre en place pour limiter les nuisances et les effets pathogènes consécutifs à la transmission vectorielle de virus, bactéries, protozoaires et filaires. Véritable voyage au cœur de l'entomologie médicale et vétérinaire, ce livre permettra aux enseignants, aux étudiants, aux personnels de santé, aux chercheurs et aux décideurs en santé publique d'avoir une vision complète, mise à jour et fonctionnelle du contexte, des enjeux et des solutions à mettre en œuvre dans un domaine majeur de la santé humaine et animale.

Les progrès des connaissances, de la médecine et le développement des insecticides ont durant un temps laissé penser qu'on viendrait à bout des nuisances occasionnées par les moustiques, les tiques et les mouches, ainsi que des maladies comme le paludisme, la dengue, la maladie de Chagas, la fièvre catarrhale ovine et bien d'autres maladies infectieuses transmises par voie vectorielle. Mais en ce début de xxie siècle, la réalité s'avère tout autre. Écrit par un collectif de spécialistes, cet ouvrage présente un état actualisé des connaissances sur tous les groupes d'arthropodes d'intérêt médical et vétérinaire. Il s'appuie sur les recherches les plus récentes en systématique, écologie, génétique, anthropologie, histoire, médecine, santé publique et génie sanitaire. Pragmatique et opérationnel, il décrit les techniques d'identification et de lutte à mettre en place pour limiter les nuisances et les effets pathogènes consécutifs à la transmission vectorielle de virus, bactéries, protozoaires et filaires. Véritable voyage au cœur de l'entomologie médicale et vétérinaire, ce livre permettra aux enseignants, aux étudiants, aux personnels de santé, aux chercheurs et aux décideurs en santé publique d'avoir une vision complète, mise à jour et fonctionnelle du contexte, des enjeux et des solutions à mettre en œuvre dans un domaine majeur de la santé humaine et animale.

Les progrès des connaissances, de la médecine et le développement des insecticides ont durant un temps laissé penser qu'on viendrait à bout des nuisances occasionnées par les moustiques, les tiques et les mouches, ainsi que des maladies comme le paludisme, la dengue, la maladie de Chagas, la fièvre catarrhale ovine et bien d'autres maladies infectieuses transmises par voie vectorielle. Mais en ce début de xxie siècle, la réalité s'avère tout autre. Écrit par un collectif de spécialistes, cet ouvrage présente un état actualisé des connaissances sur tous les groupes d'arthropodes d'intérêt médical et vétérinaire. Il s'appuie sur les recherches les plus récentes en systématique, écologie, génétique, anthropologie, histoire, médecine, santé publique et génie sanitaire. Pragmatique et opérationnel, il décrit les techniques d'identification et de lutte à mettre en place pour limiter les nuisances et les effets pathogènes consécutifs à la transmission vectorielle de virus, bactéries, protozoaires et filaires. Véritable voyage au cœur de l'entomologie médicale et vétérinaire, ce livre permettra aux enseignants, aux étudiants, aux personnels de santé, aux chercheurs et aux décideurs en santé publique d'avoir une vision complète, mise à jour et fonctionnelle du contexte, des enjeux et des solutions à mettre en œuvre dans un domaine majeur de la santé humaine et animale.

Les progrès des connaissances, de la médecine et le développement des insecticides ont durant un temps laissé penser qu'on viendrait à bout des nuisances occasionnées par les moustiques, les tiques et les mouches, ainsi que des maladies comme le paludisme, la dengue, la maladie de Chagas, la fièvre catarrhale ovine et bien d'autres maladies infectieuses transmises par voie vectorielle. Mais en ce début de xxie siècle, la réalité s'avère tout autre. Écrit par un collectif de spécialistes, cet ouvrage présente un état actualisé des connaissances sur tous les groupes d'arthropodes d'intérêt médical et vétérinaire. Il s'appuie sur les recherches les plus récentes en systématique, écologie, génétique, anthropologie, histoire, médecine, santé publique et génie sanitaire. Pragmatique et opérationnel, il décrit les techniques d'identification et de lutte à mettre en place pour limiter les nuisances et les effets pathogènes consécutifs à la transmission vectorielle de virus, bactéries, protozoaires et filaires. Véritable voyage au cœur de l'entomologie médicale et vétérinaire, ce livre permettra aux enseignants, aux étudiants, aux personnels de santé, aux chercheurs et aux décideurs en santé publique d'avoir une vision complète, mise à jour et fonctionnelle du contexte, des enjeux et des solutions à mettre en œuvre dans un domaine majeur de la santé humaine et animale.

Les progrès des connaissances, de la médecine et le développement des insecticides ont durant un temps laissé penser qu'on viendrait à bout des nuisances occasionnées par les moustiques, les tiques et les mouches, ainsi que des maladies comme le paludisme, la dengue, la maladie de Chagas, la fièvre catarrhale ovine et bien d'autres maladies infectieuses transmises par voie vectorielle. Mais en ce début de xxie siècle, la réalité s'avère tout autre. Écrit par un collectif de spécialistes, cet ouvrage présente un état actualisé des connaissances sur tous les groupes d'arthropodes d'intérêt médical et vétérinaire. Il s'appuie sur les recherches les plus récentes en systématique, écologie, génétique, anthropologie, histoire, médecine, santé publique et génie sanitaire. Pragmatique et opérationnel, il décrit les techniques d'identification et de lutte à mettre en place pour limiter les nuisances et les effets pathogènes consécutifs à la transmission vectorielle de virus, bactéries, protozoaires et filaires. Véritable voyage au cœur de l'entomologie médicale et vétérinaire, ce livre permettra aux enseignants, aux étudiants, aux personnels de santé, aux chercheurs et aux décideurs en santé publique d'avoir une vision complète, mise à jour et fonctionnelle du contexte, des enjeux et des solutions à mettre en œuvre dans un domaine majeur de la santé humaine et animale.

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve

Tidal effects in planetary systems are the main driver in the orbital migration of natural satellites. They result from physical processes occurring deep inside celestial bodies, whose effects are rarely observable from surface imaging. For giant planet systems, the tidal migration rate is determined by poorly understood dissipative processes in the planet, and standard theories suggest an orbital expansion rate inversely proportional to the power 11/2 in distance, implying little migration for outer moons such as Saturn's largest moon, Titan. Here, we use two independent measurements obtained with the Cassini spacecraft to measure Titan's orbital expansion rate. We find Titan migrates away from Saturn at 11.3 $\pm$ 2.0 cm/year, corresponding to a tidal quality factor of Saturn of Q $\simeq$ 100, and a migration timescale of roughly 10 Gyr. This rapid orbital expansion suggests Titan formed significantly closer to Saturn and has migrated outward to its current position. Our results for Titan and five other moons agree with the predictions of a resonance locking tidal theory, sustained by excitation of inertial waves inside the planet. The associated tidal expansion is only weakly sensitive to orbital distance, motivating a revision of the evolutionary history of Saturn's moon system. The resonance locking mechanism could operate in other systems such as stellar binaries and exoplanet systems, and it may allow for tidal dissipation to occur at larger orbital separations than previously believed., Comment: Published in Nature Astronomy, SharedIt link: https://rdcu.be/b4I3Q

Yeast taxonomy was introduced based on the idea that physiological properties would help discriminate species, thus assuming a strong link between physiology and taxonomy. However, the instability of physiological characteristics within species configured them as not ideal markers for species delimitation, shading the importance of physiology and paving the way to the DNA-based taxonomy. The hypothesis of reconnecting taxonomy with specific traits from phylogenies has been successfully explored for Bacteria and Archaea, suggesting that a similar route can be traveled for yeasts. In this framework, thirteen single copy loci were used to investigate the predictability of complex Fourier Transform InfaRed spectroscopy (FTIR) and High-performance Liquid Chromatography–Mass Spectrometry (LC-MS) profiles of the four historical species of the Saccharomyces sensu stricto group, both on resting cells and under short-term ethanol stress. Our data show a significant connection between the taxonomy and physiology of these strains. Eight markers out of the thirteen tested displayed high correlation values with LC-MS profiles of cells in resting condition, confirming the low efficacy of FTIR in the identification of strains of closely related species. Conversely, most genetic markers displayed increasing trends of correlation with FTIR profiles as the ethanol concentration increased, according to their role in the cellular response to different type of stress.

The construction of powerful cell factories requires intensive and extensive remodelling of microbial genomes. Considering the rapidly increasing number of these synthetic biology endeavors, there is an increasing need for DNA watermarking strategies that enable the discrimination between synthetic and native gene copies. While it is well documented that codon usage can affect translation, and most likely mRNA stability in eukaryotes, remarkably few quantitative studies explore the impact of watermarking on transcription, protein expression, and physiology in the popular model and industrial yeast Saccharomyces cerevisiae. The present study, using S. cerevisiae as eukaryotic paradigm, designed, implemented, and experimentally validated a systematic strategy to watermark DNA with minimal alteration of yeast physiology. The 13 genes encoding proteins involved in the major pathway for sugar utilization (i.e., glycolysis and alcoholic fermentation) were simultaneously watermarked in a yeast strain using the previously published pathway swapping strategy. Carefully swapping codons of these naturally codon optimized, highly expressed genes, did not affect yeast physiology and did not alter transcript abundance, protein abundance, and protein activity besides a mild effect on Gpm1. The markerQuant bioinformatics method could reliably discriminate native from watermarked genes and transcripts. Furthermore, presence of watermarks enabled selective CRISPR/Cas genome editing, specifically targeting the native gene copy while leaving the synthetic, watermarked variant intact. This study offers a validated strategy to simply watermark genes in S. cerevisiae., BT/Industrial Microbiology, OLD BT/Cell Systems Engineering, Pattern Recognition and Bioinformatics

The construction of powerful cell factories requires intensive and extensive remodelling of microbial genomes. Considering the rapidly increasing number of these synthetic biology endeavors, there is an increasing need for DNA watermarking strategies that enable the discrimination between synthetic and native gene copies. While it is well documented that codon usage can affect translation, and most likely mRNA stability in eukaryotes, remarkably few quantitative studies explore the impact of watermarking on transcription, protein expression, and physiology in the popular model and industrial yeast Saccharomyces cerevisiae. The present study, using S. cerevisiae as eukaryotic paradigm, designed, implemented, and experimentally validated a systematic strategy to watermark DNA with minimal alteration of yeast physiology. The 13 genes encoding proteins involved in the major pathway for sugar utilization (i.e., glycolysis and alcoholic fermentation) were simultaneously watermarked in a yeast strain using the previously published pathway swapping strategy. Carefully swapping codons of these naturally codon optimized, highly expressed genes, did not affect yeast physiology and did not alter transcript abundance, protein abundance, and protein activity besides a mild effect on Gpm1. The markerQuant bioinformatics method could reliably discriminate native from watermarked genes and transcripts. Furthermore, presence of watermarks enabled selective CRISPR/Cas genome editing, specifically targeting the native gene copy while leaving the synthetic, watermarked variant intact. This study offers a validated strategy to simply watermark genes in S. cerevisiae.

Although AD hybrids within the Cryptococcus neoformans species complex represent about 20% of the isolates identified in Europe, phylogenetic and population genetic studies are lacking due to the inability to use the standardized typing method. The aim of the present study was to design new molecular type specific primers in order to apply the standard ISHAM consensus multilocus sequence typing (MLST) scheme to AD hybrids. The new primers are able to specifically amplify VNI and VNIV alleles of the seven MLST loci in both haploid and diploid or aneuploid hybrid strains. This study forms the basis for future molecular epidemiology studies of AD hybrids.LAY ABSTRACT: We designed and tested new specific primers to amplify the two alleles of each of the seven MLST loci in C. neoformans species complex hybrids. The sequences obtained from hybrids can be compared with those present in the Cryptococcus global MLST database for future molecular epidemiology studies.

Yeast taxonomy was introduced based on the idea that physiological properties would help discriminate species, thus assuming a strong link between physiology and taxonomy. However, the instability of physiological characteristics within species configured them as not ideal markers for species delimitation, shading the importance of physiology and paving the way to the DNA-based taxonomy. The hypothesis of reconnecting taxonomy with specific traits from phylogenies has been successfully explored for Bacteria and Archaea, suggesting that a similar route can be traveled for yeasts. In this framework, thirteen single copy loci were used to investigate the predictability of complex Fourier Transform InfaRed spectroscopy (FTIR) and High-performance Liquid Chromatography–Mass Spectrometry (LC-MS) profiles of the four historical species of the Saccharomyces sensu stricto group, both on resting cells and under short-term ethanol stress. Our data show a significant connection between the taxonomy and physiology of these strains. Eight markers out of the thirteen tested displayed high correlation values with LC-MS profiles of cells in resting condition, confirming the low efficacy of FTIR in the identification of strains of closely related species. Conversely, most genetic markers displayed increasing trends of correlation with FTIR profiles as the ethanol concentration increased, according to their role in the cellular response to different type of stress.