Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic ...elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems. CRISPRCasFinder can either be used online or as a standalone tool compatible with Linux operating system. All third-party software packages employed by the program are freely available. CRISPRCasFinder is available at https://crisprcas.i2bc.paris-saclay.fr.
Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose.
...Macromolecular System Finder (MacSyFinder) provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway) including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems. Models are used to search for molecular systems in complete genomes or in unstructured data like metagenomes. The components of the systems are searched by sequence similarity using Hidden Markov model (HMM) protein profiles. The assignment of hits to a given system is decided based on compliance with the content and organization of the system model. A graphical interface, MacSyView, facilitates the analysis of the results by showing overviews of component content and genomic context. To exemplify the use of MacSyFinder we built models to detect and class CRISPR-Cas systems following a previously established classification. We show that MacSyFinder allows to easily define an accurate "Cas-finder" using publicly available protein profiles.
MacSyFinder is a standalone application implemented in Python. It requires Python 2.7, Hmmer and makeblastdb (version 2.2.28 or higher). It is freely available with its source code under a GPLv3 license at https://github.com/gem-pasteur/macsyfinder. It is compatible with all platforms supporting Python and Hmmer/makeblastdb. The "Cas-finder" (models and HMM profiles) is distributed as a compressed tarball archive as Supporting Information.
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Integrons recombine gene arrays and favor the spread of antibiotic resistance. Their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a ...program - IntegronFinder - to identify integrons with high accuracy and sensitivity. IntegronFinder is available as a standalone program and as a web application. It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching. We searched for integrons, integron-integrases lacking attC sites, and clusters of attC sites lacking a neighboring integron-integrase in bacterial genomes. All these elements are especially frequent in genomes of intermediate size. They are missing in some key phyla, such as α-Proteobacteria, which might reflect selection against cell lineages that acquire integrons. The similarity between attC sites is proportional to the number of cassettes in the integron, and is particularly low in clusters of attC sites lacking integron-integrases. The latter are unexpectedly abundant in genomes lacking integron-integrases or their remains, and have a large novel pool of cassettes lacking homologs in the databases. They might represent an evolutionary step between the acquisition of genes within integrons and their stabilization in the new genome.
Background The dynamics of phosphorus (P) in the environment is important for regulating nutrient cycles in natural and managed ecosystems and an integral part in assessing biological resilience ...against environmental change. Organic P (Po) compounds play key roles in biological and ecosystems function in the terrestrial environment being critical to cell function, growth and reproduction. Scope We asked a group of experts to consider the global issues associated with Po in the terrestrial environment, methodological strengths and weaknesses, benefits to be gained from understanding the Po cycle, and to set priorities for Po research. Conclusions We identified seven key opportunities for Po research including: the need for integrated, quality controlled and functionally based methodologies; assessment of stoichiometry with other elements in organic matter; understanding the dynamics of Po in natural and managed systems; the role of microorganisms in controlling Po cycles; the implications of nanoparticles in the environment and the need for better modelling and communication of the research. Each priority is discussed and a statement of intent for the Po research community is made that highlights there are key contributions to be made toward understanding biogeochemical cycles, dynamics and function of natural ecosystems and the management of agricultural systems.
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BFBNIB, DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NMLJ, NUK, OBVAL, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Bacteria with two cell membranes (diderms) have evolved complex systems for protein secretion. These systems were extensively studied in some model bacteria, but the characterisation of their ...diversity has lagged behind due to lack of standard annotation tools. We built online and standalone computational tools to accurately predict protein secretion systems and related appendages in bacteria with LPS-containing outer membranes. They consist of models describing the systems' components and genetic organization to be used with MacSyFinder to search for T1SS-T6SS, T9SS, flagella, Type IV pili and Tad pili. We identified ~10,000 candidate systems in bacterial genomes, where T1SS and T5SS were by far the most abundant and widespread. All these data are made available in a public database. The recently described T6SS(iii) and T9SS were restricted to Bacteroidetes, and T6SS(ii) to Francisella. The T2SS, T3SS, and T4SS were frequently encoded in single-copy in one locus, whereas most T1SS were encoded in two loci. The secretion systems of diderm Firmicutes were similar to those found in other diderms. Novel systems may remain to be discovered, since some clades of environmental bacteria lacked all known protein secretion systems. Our models can be fully customized, which should facilitate the identification of novel systems.
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Integrons are flexible gene-exchanging platforms that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons embedded within mobile genetic ...elements often contain multiple antibiotic resistance genes that they spread among nosocomial pathogens and contribute to the current antibiotic resistance crisis. However, most integrons are presumably sedentary and encode a much broader diversity of functions. IntegronFinder is a widely used software to identify novel integrons in bacterial genomes, but has aged and lacks some useful functionalities to handle very large datasets of draft genomes or metagenomes. Here, we present IntegronFinder version 2. We have updated the code, improved its efficiency and usability, adapted the output to incomplete genome data, and added a few novel functions. We describe these changes and illustrate the relevance of the program by analyzing the distribution of integrons across more than 20,000 fully sequenced genomes. We also take full advantage of its novel capabilities to analyze close to 4000
genomes for the presence of integrons and antibiotic resistance genes within them. Our data show that
has a large diversity of integrons and the largest mobile integron in our database of plasmids. The pangenome of these integrons contains a total of 165 different gene families with most of the largest families being related with resistance to numerous types of antibiotics. IntegronFinder is a free and open-source software available on multiple public platforms.
Conjugation of DNA through a type IV secretion system (T4SS) drives horizontal gene transfer. Yet little is known on the diversity of these nanomachines. We previously found that T4SS can be divided ...in eight classes based on the phylogeny of the only ubiquitous protein of T4SS (VirB4). Here, we use an ab initio approach to identify protein families systematically and specifically associated with VirB4 in each class. We built profiles for these proteins and used them to scan 2262 genomes for the presence of T4SS. Our analysis led to the identification of thousands of occurrences of 116 protein families for a total of 1623 T4SS. Importantly, we could identify almost always in our profiles the essential genes of well-studied T4SS. This allowed us to build a database with the largest number of T4SS described to date. Using profile–profile alignments, we reveal many new cases of homology between components of distant classes of T4SS. We mapped these similarities on the T4SS phylogenetic tree and thus obtained the patterns of acquisition and loss of these protein families in the history of T4SS. The identification of the key VirB4-associated proteins paves the way toward experimental analysis of poorly characterized T4SS classes.
Extracellular capsules constitute the outermost layer of many bacteria, are major virulence factors, and affect antimicrobial therapies. They have been used as epidemiological markers and recently ...became vaccination targets. Despite the efforts to biochemically serotype capsules in a few model pathogens, little is known of their taxonomic and environmental distribution. We developed, validated, and made available a computational tool, CapsuleFinder, to identify capsules in genomes. The analysis of over 2500 prokaryotic genomes, accessible in a database, revealed that ca. 50% of them-including Archaea-encode a capsule. The Wzx/Wzy-dependent capsular group was by far the most abundant. Surprisingly, a fifth of the genomes encode more than one capsule system-often from different groups-and their non-random co-occurrence suggests the existence of negative and positive epistatic interactions. To understand the role of multiple capsules, we queried more than 6700 metagenomes for the presence of species encoding capsules and showed that their distribution varied between environmental categories and, within the human microbiome, between body location. Species encoding capsules, and especially those encoding multiple capsules, had larger environmental breadths than the other species. Accordingly, capsules were more frequent in environmental bacteria than in pathogens and, within the latter, they were more frequent among facultative pathogens. Nevertheless, capsules were frequent in clinical samples, and were usually associated with fast-growing bacteria with high infectious doses. Our results suggest that capsules increase the environmental range of bacteria and make them more resilient to environmental perturbations. Capsules might allow opportunistic pathogens to profit from empty ecological niches or environmental perturbations, such as those resulting from antibiotic therapy, to colonize the host. Capsule-associated virulence might thus be a by-product of environmental adaptation. Understanding the role of capsules in natural environments might enlighten their function in pathogenesis.
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This study aims at improving the understanding of fracture genesis in layered carbonate sedimentary sequences, focusing on field analysis of Jurassic to Maastrichtian age carbonates of Provence ...(France). Fracture patterns of 9 outcrops were characterized in 3D: 6 of Urgonian, 1 of Tithonian and 2 of Campanian-Late Maastrichtian ages. Seven sites are located in relatively weakly deformed areas away from larges fault and fold zones where strain partitioning and stress localization effects may take place. Two sites are located in fold flanks for the purpose of relative dating and for comparison with the sites in the weakly deformed areas. Patterns and detailed fracture attributes were compared to host rock sedimentary facies, porosity and P-wave velocities. Fracture chronology was determined with cross-cutting relationships and compared to burial/uplift history reconstructed from subsidence curves and from a regional structural analysis.
Our results show that fractures are clustered in two perpendicular joint sets whatever the host rock age. We observe an average spacing of 20cm and no control of strike, age, facies, or bed thickness on fracture size. There is no mechanical stratigraphy. The fracture sequence compared to subsidence curves indicates that fractures occurred before tectonic inversion, during early and rapid burial, whatever the host rock age and facies. The abundance of burial stylolites does not correlate with maximum burial depth but with fracture frequency, host rock porosity and P-wave velocity.
We conclude that the studied carbonates had early brittle properties controlled by their geographic position rather than by depositional facies types and undergone early diagenesis. The porosity loss/gain and the mechanical differentiation in carbonates of Provence could have been acquired during very early burial and diagenesis and have preserved through time. This study also demonstrates that regional fracturing is not necessarily driven by large scale structural events as it is often assumed in fractured reservoir modelling.
► Fractures initiated very early in the burial history whatever the age of the host rocks. ► No mechanical stratigraphy existed when fractures formed. ► Fracture frequency is related to the rock mechanical properties and porosity and varies from South to North emphasizing the prime role of shallow burial early diagenesis. ► One cannot systematically account for the present-day mechanical stratigraphy to predict fracture stratigraphy in carbonate reservoirs. ► Burial and diagenetic host rock history must be deciphered and considered.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
10.
Alfvén Wave Propagation in the Io Plasma Torus Hinton, P. C.; Bagenal, F.; Bonfond, B.
Geophysical research letters,
16 February 2019, Volume:
46, Issue:
3
Journal Article, Web Resource
Peer reviewed
Open access
Io, the most volcanically active body in the solar system, fuels a plasma torus around Jupiter with dissociation products of SO2 at a rate of ~1,000 kg/s. We use a combination of in situ Voyager 1 ...data and Cassini Ultraviolet Imaging Spectrograph observations to constrain a diffusive equilibrium model of the Io plasma torus. The interaction of the Io plasma torus with Io launches Alfvén waves in both directions along magnetic field lines. We use the recent Juno‐based JRM09 magnetic field model combined with our 3‐D model of the Io plasma torus to simulate the propagation of Alfvén waves from the moon to the ionosphere of Jupiter. We map the location of multiple reflections of iogenic Alfvén waves between the northern and southern hemispheres. The location of the first few bounces of the Alfvén wave pattern match the Io auroral footprints observed by the Hubble Space Telescope.
Plain Language Summary
Jupiter's moon Io is embedded in toroidal cloud of plasma that comes from the ionization of SO2 gas escaping from the volcanic moon. As Jupiter's magnetosphere rotates, it sweeps past Io in its orbit, disturbing the flow of the plasma torus. These disturbances travel along magnetic field lines, exciting electrons that stimulate aurora in Jupiter's atmosphere. We use a model of the plasma torus plus a model of Jupiter's magnetic field derived from recent measurements by the Juno spacecraft to predict the location of Io's auroral footprints. These predictions are compared with observations from the Hubble Space Telescope.
Key Points
A 3‐D plasma torus model is combined with the JRM09 magnetic field model to produce updated Alfvén travel times
One‐way Alfvén travel times range from ~2 to ~12 min when Io is below/above the torus at 20/200 degrees West System III longitudes, respectively
The Alfvén wing locations predicted by the model in Jupiter's ionosphere closely match the location of auroral emissions observed by Hubble Space Telescope
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