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BACKGROUND: New records of alien land planarians are regularly reported worldwide, and some correspond to undescribed species of unknown geographic origin. The description of new species of land planarians (Geoplanidae) should classically be based on both external morphology and histology of anatomical structures, especially the copulatory organs, ideally with the addition of molecular data. METHODS: Here, we describe the morphology and reproductive anatomy of a species previously reported as Diversibipalium "black", and the morphology of a species previously reported as Diversibipalium "blue". Based on next generation sequencing, we obtained the complete mitogenome of five species of Bipaliinae, including these two species. RESULTS: The new species Humbertium covidum n. sp. (syn: Diversibipalium "black" of Justine et al., 2018) is formally described on the basis of morphology, histology and mitogenome, and is assigned to Humbertium on the basis of its reproductive anatomy. The type-locality is Casier, Italy, and other localities are in the Department of Pyrénées-Atlantiques, France; some published or unpublished records suggest that this species might also be present in Russia, China, and Japan. The mitogenomic polymorphism of two geographically distinct specimens (Italy vs France) is described; the cox1 gene displayed 2.25% difference. The new species Diversibipalium mayottensis n. sp. (syn: Diversibipalium "blue" of Justine et al., 2018) is formally described on the basis of external morphology and complete mitogenome and is assigned to Diversibipalium on the basis of an absence of information on its reproductive anatomy. The type- and only known locality is the island of Mayotte in the Mozambique Channel off Africa. Phylogenies of bipaliine geoplanids were constructed on the basis of SSU, LSU, mitochondrial proteins and concatenated sequences of cox1, SSU and LSU. In all four phylogenies, D. mayottensis was the sister-group to all the other bipaliines. With the exception of D. multilineatum which could not be circularised, the complete mitogenomes of B. kewense, B. vagum, B. adventitium, H. covidum and D. mayottensis were colinear. The 16S gene in all bipaliine species was problematic because usual tools were unable to locate its exact position. CONCLUSION: Next generation sequencing, which can provide complete mitochondrial genomes as well as traditionally used genes such as SSU, LSU and cox1, is a powerful tool for delineating and describing species of Bipaliinae when the reproductive structure cannot be studied, which is sometimes the case of asexually reproducing invasive species. The unexpected position of the new species D. mayottensis as sister-group to all other Bipaliinae in all phylogenetic analyses suggests that the species could belong to a new genus, yet to be described.

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BACKGROUND: Obama nungara is a species of land flatworm originating from South America; the species was recently described and distinguished from a similar species, Obama marmorata. Obama nungara has invaded several countries of Europe, but the extent of the invasion has not been thoroughly mapped. METHODS: In this article, based on a five and a half-year survey undertaken by citizen science, which yielded 530 records from 2013 to 2018, we analysed information about the invasion of Metropolitan France by O. nungara. We also investigated the variability of newly obtained cytochrome c oxidase 1 (COI) sequences of specimens from France, Italy and Switzerland. RESULTS: Obama nungara was recorded from 72 of the 96 Departments of Metropolitan France. The species is especially abundant along the Atlantic coast, from the Spanish border to Brittany, and along the Mediterranean coast, from the Spanish border to the Italian border. More than half of the records were from an altitude below 50 m, and no record was from above 500 m; mountainous regions such as the Alps, Pyrenees and Massif Central are not invaded. Local abundance can be impressive, with 100 of specimens found in a small garden. An analysis of our new COI sequences, combined with published sequences of specimens from several countries, confirmed that three clades comprise the species. The first clade, 'Brazil', is currently confined to this country in South America; the second clade, 'Argentina 2', was found in Argentina and in Europe, only in Spain; and the third, 'Argentina 1', was found in Argentina and in Europe, in Spain, Portugal, France, UK, Italy, Belgium, and Switzerland. This suggests that two clades of O. nungara from Argentina have invaded Europe, with one widely spread. DISCUSSION: The present findings strongly suggest that O. nungara is a highly invasive species and that the population which has invaded several countries in Europe comes from Argentina. The wide dispersion of the species and its reported local abundance, combined with the predatory character of the species, make O. nungara a potential threat to the biodiversity and ecology of the native soil fauna in Europe, and probably the most threatening species of all invasive land planarians present in Europe.

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BACKGROUND: Inference of gene regulatory networks from gene expression data has been a long-standing and notoriously difficult task in systems biology. Recently, single-cell transcriptomic data have been massively used for gene regulatory network inference, with both successes and limitations. RESULTS: In the present work we propose an iterative algorithm called WASABI, dedicated to inferring a causal dynamical network from time-stamped single-cell data, which tackles some of the limitations associated with current approaches. We first introduce the concept of waves, which posits that the information provided by an external stimulus will affect genes one-by-one through a cascade, like waves spreading through a network. This concept allows us to infer the network one gene at a time, after genes have been ordered regarding their time of regulation. We then demonstrate the ability of WASABI to correctly infer small networks, which have been simulated in silico using a mechanistic model consisting of coupled piecewise-deterministic Markov processes for the proper description of gene expression at the single-cell level. We finally apply WASABI on in vitro generated data on an avian model of erythroid differentiation. The structure of the resulting gene regulatory network sheds a new light on the molecular mechanisms controlling this process. In particular, we find no evidence for hub genes and a much more distributed network structure than expected. Interestingly, we find that a majority of genes are under the direct control of the differentiation-inducing stimulus. CONCLUSIONS: Together, these results demonstrate WASABI versatility and ability to tackle some general gene regulatory networks inference issues. It is our hope that WASABI will prove useful in helping biologists to fully exploit the power of time-stamped single-cell data.

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BACKGROUND: Species of the genera Bipalium and Diversibipalium, or bipaliines, are giants among land planarians (family Geoplanidae), reaching length of 1 m; they are also easily distinguished from other land flatworms by the characteristic hammer shape of their head. Bipaliines, which have their origin in warm parts of Asia, are invasive species, now widespread worldwide. However, the scientific literature is very scarce about the widespread repartition of these species, and their invasion in European countries has not been studied. METHODS: In this paper, on the basis of a four year survey based on citizen science, which yielded observations from 1999 to 2017 and a total of 111 records, we provide information about the five species present in Metropolitan France and French overseas territories. We also investigated the molecular variability of cytochrome-oxidase 1 (COI) sequences of specimens. RESULTS: Three species are reported from Metropolitan France: Bipalium kewense, Diversibipalium multilineatum, and an unnamed Diversibipalium 'black' species. We also report the presence of B. kewense from overseas territories, such as French Polynesia (Oceania), French Guiana (South America), the Caribbean French islands of Martinique, Guadeloupe, Saint Martin and Saint Barthélemy, and Montserrat (Central America), and La Réunion island (off South-East Africa). For B. vagum, observations include French Guiana, Guadeloupe, Martinique, Saint Barthélemy, Saint Martin, Montserrat, La Réunion, and Florida (USA). A probable new species, Diversibipalium sp. 'blue,' is reported from Mayotte Island (off South-East Africa). B. kewense, B. vagum and D. multilineatum each showed 0% variability in their COI sequences, whatever their origin, suggesting that the specimens are clonal, and that sexual reproduction is probably absent. COI barcoding was efficient in identifying species, with differences over 10% between species; this suggests that barcoding can be used in the future for identifying these invasive species. In Metropolitan south-west France, a small area located in the Department of Pyrénées-Atlantiques was found to be a hot-spot of bipaliine biodiversity and abundance for more than 20 years, probably because of the local mild weather. DISCUSSION: The present findings strongly suggest that the species present in Metropolitan France and overseas territories should be considered invasive alien species. Our numerous records in the open in Metropolitan France raise questions: as scientists, we were amazed that these long and brightly coloured worms could escape the attention of scientists and authorities in a European developed country for such a long time; improved awareness about land planarians is certainly necessary.

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Interferon regulatory factor-8 (IRF-8) is critical for Th1 cell differentiation and negatively regulates myeloid cell development including myeloid-derived suppressor cells (MDSC). MDSC expand during infection with various pathogens including the gastrointestinal (GI) nematode Heligmosomoides polygyrus bakeri (Hpb). We investigated if IRF-8 contributes to Th2 immunity to Hpb infection. Irf8 expression was down-regulated in MDSC from Hpb-infected C57BL/6 (B6) mice. IRF-8 deficient Irf8-/- and BXH-2 mice had significantly higher adult worm burdens than B6 mice after primary or challenge Hpb infection. During primary infection, MDSC expanded to a significantly greater extent in mesenteric lymph nodes (MLN) and spleens of Irf8-/- and BXH-2 than B6 mice. CD4+GATA3+ T cells numbers were comparable in MLN of infected B6 and IRF-8 deficient mice, but MLN cells from infected IRF-8 deficient mice secreted significantly less parasite-specific IL-4 ex vivo. The numbers of alternatively activated macrophages in MLN and serum levels of Hpb-specific IgG1 and IgE were also significantly less in infected Irf8-/- than B6 mice. The frequencies of antigen-experienced CD4+CD11ahiCD49dhi cells that were CD44hiCD62L- were similar in MLN of infected Irf8-/- and B6 mice, but the proportions of CD4+GATA3+ and CD4+IL-4+ T cells were lower in infected Irf8-/- mice. CD11b+Gr1+ cells from naïve or infected Irf8-/- mice suppressed CD4+ T cell proliferation and parasite-specific IL-4 secretion in vitro albeit less efficiently than B6 mice. Surprisingly, there were significantly more CD4+ T cells in infected Irf8-/- mice, with a higher frequency of CD4+CD25+Foxp3+ T (Tregs) cells and significantly higher numbers of Tregs than B6 mice. In vivo depletion of MDSC and/or Tregs in Irf8-/- mice did not affect adult worm burdens, but Treg depletion resulted in higher egg production and enhanced parasite-specific IL-5, IL-13, and IL-6 secretion ex vivo. Our data thus provide a previously unrecognized role for IRF-8 in Th2 immunity to a GI nematode.

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Gold nanoparticles (AuNPs) were deposited on a glassy carbon (GC) substrate by constant potential electrolysis and characterized by cyclic voltammetry in H2SO4 and field emission gun scanning electron microscopy (FEG-SEM). The modified AuNPs-GC electrode was used for low Hg(II) concentration detection using a Square Wave Anodic Stripping Voltammetry (SWASV) procedure which included a chloride desorption step. The comparison of the obtained results with our previous work in which no desorption step was used showed that this latter step significantly improved the analytical performances, providing a three time higher sensitivity and a limit of detection of 80pM for 300s preconcentration, as well as a lower average standard deviation. The influence of chloride concentration on the AuNPs-GC electrode response to Hg(II) trace amounts was also studied and its optimal value confirmed to be in the 10(-2)M range. Finally, the AuNPs-GC electrode was used for the determination of Hg(II) in a natural groundwater sample from south of France. By using a preconcentration time of 3000s, a Hg(II) concentration of 19±3pM was found, which compared well with the result obtained by cold vapor atomic fluorescence spectroscopy (22±2pM).

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A great challenge in the area of heavy metal trace detection is the development of electrochemical techniques and devices which are user-friendly, robust, selective, with low detection limits and allowing fast analyses. This review presents the major contribution of the French scientific academic community in the field of electrochemical sensors and electroanalytical methods within the last 20 years. From the well-known polarography to the up-to-date generation of functionalized interfaces, the different strategies dedicated to analytical performances improvement are exposed: stripping voltammetry, solid mercury-free electrode, ion selective sensor, carbon based materials, chemically modified electrodes, nano-structured surfaces. The paper particularly emphasizes their advantages and limits face to the last Water Frame Directive devoted to the Environmental Quality Standards for heavy metals. Recent trends on trace metal speciation as well as on automatic "on line" monitoring devices are also evoked.

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Non-indigenous terrestrial flatworms (Platyhelminthes) have been recorded in thirteen European countries. They include Bipalium kewense and Dolichoplana striata that are largely restricted to hothouses and may be regarded as non-invasive species. In addition there are species from the southern hemisphere such as the invasive New Zealand flatworm Arthurdendyus triangulatus in the United Kingdom, Eire and the Faroe Islands, the Australian flatworm Australoplana sanguinea alba in Eire and the United Kingdom, and the Australian Blue Garden flatworm Caenoplana coerulea in France, Menorca and the United Kingdom. The United Kingdom has some twelve or more non-indigenous species most of which are Australian and New Zealand species. These species may move to an invasive stage when optimum environmental and other conditions occur, and the flatworms then have the potential to cause economic or environmental harm. In this paper, we report the identification (from morphology and molecular analysis of COI sequences) of non-indigenous terrestrial flatworms found in a hothouse in Caen (France) as the New Guinea flatworm Platydemus manokwari de Beauchamp, 1963 (Platyhelminthes, Continenticola, Geoplanidae, Rhynchodeminae). Platydemus manokwari is among the "100 World's Worst Invader Alien Species". Lists of World geographic records, prey in the field and prey in laboratories of P. manokwari are provided. This species is considered a threat to native snails wherever it is introduced. The recent discovery of P. manokwari in France represents a significant extension of distribution of this Invasive Alien Species from the Indo-Pacific region to Europe. If it escaped the hothouse, the flatworm might survive winters and become established in temperate countries. The existence of this species in France requires an early warning of this incursion to State and European Union authorities, followed by the eradication of the flatworm in its locality, tightening of internal quarantine measures to prevent further spread of the flatworm to and from this site, identifying if possible the likely primary source of the flatworm, and tracing other possible incursions that may have resulted from accidental dispersal of plants and soil from the site.

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Adaptation proceeds through the selection of mutations. The distribution of mutant fitness effect and the forces shaping this distribution are therefore keys to predict the evolutionary fate of organisms and their constituents such as enzymes. Here, by producing and sequencing a comprehensive collection of 10,000 mutants, we explore the mutational landscape of one enzyme involved in the spread of antibiotic resistance, the beta-lactamase TEM-1. We measured mutation impact on the enzyme activity through the estimation of amoxicillin minimum inhibitory concentration on a subset of 990 mutants carrying a unique missense mutation, representing 64% of possible amino acid changes in that protein reachable by point mutation. We established that mutation type, solvent accessibility of residues, and the predicted effect of mutations on protein stability primarily determined alone or in combination changes in minimum inhibitory concentration of mutants. Moreover, we were able to capture the drastic modification of the mutational landscape induced by a single stabilizing point mutation (M182T) by a simple model of protein stability. This work thereby provides an integrated framework to study mutation effects and a tool to understand/define better the epistatic interactions.

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The extraintestinal virulence of Escherichia coli is dependent on numerous virulence genes. However, there is growing evidence for a role of the metabolic properties and stress responses of strains in pathogenesis. We assessed the respective roles of these factors in strain virulence by developing phenotypic assays for measuring in vitro individual and competitive fitness and the general stress response, which we applied to 82 commensal and extraintestinal pathogenic E. coli strains previously tested in a mouse model of sepsis. Individual fitness properties, in terms of maximum growth rates in various media (Luria-Bertani broth with and without iron chelator, minimal medium supplemented with gluconate, and human urine) and competitive fitness properties, estimated as the mean relative growth rate per generation in mixed cultures with a reference fluorescent E. coli strain, were highly diverse between strains. The activity of the main general stress response regulator, RpoS, as determined by iodine staining of the colonies, H2O2 resistance, and rpoS sequencing, was also highly variable. No correlation between strain fitness and stress resistance and virulence in the mouse model was found, except that the maximum growth rate in urine was higher for virulent strains. Multivariate analysis showed that the number of virulence factors was the only independent factor explaining the virulence in mice. At the species level, growth capacity and stress resistance are heterogeneous properties that do not contribute significantly to the intrinsic virulence of the strains.

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An electrochemical microsensor has been developed for the simultaneous assay of ascorbate (AA) and urate (UA) antioxidants in human blood serum. The electrode surface was modified by means of electropolymerized conductive poly(3,4-ethylenedioxythiophene) PEDOT organic films. Highly selective responses (detection potential difference more than 250 mV) were obtained for both biomarkers by optimizing the PEDOT thickness. Contrary to most previous studies the analytical performances were recorded by testing the microsensor directly in blood serum without any pretreatment of the samples. Using differential pulse voltammetry (DPV) the sensitivity and detection limit were 0.481 µA µM(-1) cm(-2) and 4.2 µmol L(-1) for AA and 1.815 µA µM(-1) cm(-2) and 2.0 µmol L(-1) for UA. The calibration curves were linear in the concentration range 5-200 µmol L(-1) for AA and 3-700 µmol L-1 for UA. The accuracy of the sensor was satisfactorily compared with the reference analytical methods provided that the synergic effect between both antioxidants was considered. The sensor response was unmodified in the presence of the major biochemical interfering species.

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The murine parasite Heligmosomoides polygyrus is a convenient experimental model to study immune responses and pathology associated with gastrointestinal nematode infections. The excretory-secretory products (ESP) produced by this parasite have potent immunomodulatory activity, but the protein(s) responsible has not been defined. Identification of the protein composition of ESP derived from H. polygyrus and other relevant nematode species has been hampered by the lack of genomic sequence information required for proteomic analysis based on database searches. To overcome this, a transcriptome next generation sequencing (RNA-seq) de novo assembly containing 33,641 transcripts was generated, annotated, and used to interrogate mass spectrometry (MS) data derived from 1D-SDS PAGE and LC-MS/MS analysis of ESP. Using the database generated from the 6 open reading frames deduced from the RNA-seq assembly and conventional identification programs, 209 proteins were identified in ESP including homologues of vitellogenins, retinol- and fatty acid-binding proteins, globins, and the allergen V5/Tpx-1-related family of proteins. Several potential immunomodulators, such as macrophage migration inhibitory factor, cysteine protease inhibitors, galectins, C-type lectins, peroxiredoxin, and glutathione S-transferase, were also identified. Comparative analysis of protein annotations based on the RNA-seq assembly and proteomics revealed processes and proteins that may contribute to the functional specialization of ESP, including proteins involved in signalling pathways and in nutrient transport and/or uptake. Together, these findings provide important information that will help to illuminate molecular, biochemical, and in particular immunomodulatory aspects of host-H. polygyrus biology. In addition, the methods and analyses presented here are applicable to study biochemical and molecular aspects of the host-parasite relationship in species for which sequence information is not available.

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The epistatic interactions among mutations have a large effect on the evolution of populations. In this article we provide a formalism under which epistatic interactions among pairs of mutations have a distribution whose mean can be modulated. We find that the mean epistasis is correlated to the effect of mutations or genetic robustness, which suggests that such formalism is in good agreement with most in silico models of evolution where the same pattern is observed. We further show that the evolution of epistasis is highly dependant on the intensity of drift and of how complex the organisms are, and that either positive or negative epistasis could be selected for, depending on the balance between the efficiency of selection and the intensity of drift.

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Genetic robustness is defined as the constancy of a phenotype in the face of deleterious mutations. Overexpression of chaperones, to assist the folding of proteins carrying deleterious mutations, is so far one of the most accepted molecular mechanisms enhancing genetic robustness. Most theories on the evolution of robustness have focused on the implications of high mutation rate. Here we show that genetic drift, which is modulated by population size, organism complexity, and epistasis, can be a sufficient force to select for chaperone-mediated genetic robustness. Using an exact analytical solution, we also show that selection for costly genetic robustness leads to a paradox: the decrease of population fitness on long timescales and the long-term dependency on robustness mechanisms. We suggest that selection for genetic robustness could be universal and not restricted to high mutation rate organisms such as RNA viruses. The evolution of the endosymbiont Buchnera illustrates this selection mechanism and its paradox: the increased dependency on chaperones mediating genetic robustness. Our model explains why most chaperones might have become essential even in optimal growth conditions.

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The prpZ gene cluster consists of three ORFs coding for proteins with homology to eukaryotic-type Ser/Thr protein phosphatases 2C (prpZ) and Ser/Thr protein kinases (prkY and prkX). This cluster is present in the sequenced genomes of Salmonella enterica serovar Typhi (S. Typhi) strains Ty2 and CT18. This study investigated the genetic organization of this gene cluster, its regulation and its putative involvement in virulence. The three genes are transcribed as a polycistronic mRNA as demonstrated by reverse transcriptase (RT)-PCR. Analysis of a prpZ::lacZ transcriptional fusion showed that the prpZ locus is expressed throughout the growth phase. LacZ activity and real-time RT-PCR showed that transcription of the mRNA is negatively regulated upon exposure of cells to HOCl and, to a lesser extent, hydrogen peroxide. A deletion mutant of the prpZ gene cluster showed a significantly lower level of survival than the parental strain Ty2 in human macrophages at 48 h postinfection. Together these data suggest that prpZ, prkY and prkX are virulence genes that may be part of a signaling pathway controlling long-term survival of S. Typhi in host cells.

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Most of biologists work on textual DNA sequences that are limited to the linear representation of DNA. In this paper, we address the potential offered by Virtual Reality for 3D modeling and immersive visualization of large genomic sequences. The representation of the 3D structure of naked DNA allows biologists to observe and analyze genomes in an interactive way at different levels. We developed a powerful software platform that provides a new point of view for sequences analysis: ADNViewer. Nevertheless, a classical eukaryotic chromosome of 40 million base pairs requires about 6 Gbytes of 3D data. In order to manage these huge amounts of data in real-time, we designed various scene management algorithms and immersive human-computer interaction for user-friendly data exploration. In addition, one bioinformatics study scenario is proposed.

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Cyclic voltammetry is proposed as a new method for evaluating the antioxidant capacity of skin based on the reducing properties of low molecular weight antioxidants (LMWA). Experiments were performed simply by recording the anodic current at 0.9 V/SCE of a platinum microelectrode placed directly on the epidermis surface without any gel or water. This method ensured a direct, rapid (less than 1 min), reliable (accuracy 12%) and non-invasive measurement of the global antioxidant capacity of the stratum corneum with a high spatiotemporal resolution. At the same time, the pH of the skin surface was determined by recording the cathodic current at 0 V/SCE. Based on an exploratory study involving nine volunteer subjects, the evolution of the amperometric response of the microelectrode with time revealed a periodic modification of the redox properties.

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Ferricyanide ions were immobilized on a platinum electrode surface by means of an electrochemically grown polypyrrole film. The entrapped Fe(CN)6(3-)/Fe(CN)6(4-) redox system displayed a high heterogeneous electron transfer rate. The resulting modified electrode was efficient for the ferricyanide-mediated NADH oxidation catalyzed by a diaphorase. The bioelectrochemical interface was applied to the design of a reagentless amperometric D-lactate biosensor. A weakly polarized two polypyrrole-containing Fe(CN)6(3-) modified electrode system was involved without any reference. An enzymatic solution containing D-lactate dehydrogenase, diaphorase and NAD-dextran was further confined on the sensing electrode using a semi-permeable membrane. The sensitivity and the response time of the reagentless biosensor were similar to those of the analogous sensor working with soluble mediator and cofactor, i.e. 25 microA mM(-1) cm(-2) and 120 s, respectively. The other analytical performances were less satisfactorily: the detection limit was 5 x 10 mmol L(-1) and the linearity range was comprised between 0.1 and 0.5 mmol L(-1).

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