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Using long-read sequencing, we assembled and unzipped the polyploid genomes of Meloidogyne incognita, M. javanica and M. arenaria, three of the most devastating plant-parasitic nematodes. We found the canonical nematode telomeric repeat to be missing in these and other Meloidogyne genomes. In addition, we find no evidence for the enzyme telomerase or for orthologs of C. elegans telomere-associated proteins, suggesting alternative lengthening of telomeres. Instead, analyzing our assembled genomes, we identify species-specific composite repeats enriched mostly at one extremity of contigs. These repeats are G-rich, oriented, and transcribed, similarly to canonical telomeric repeats. We confirm them as telomeric using fluorescent in situ hybridization. These repeats are mostly found at one single end of chromosomes in these species. The discovery of unusual and specific complex telomeric repeats opens a plethora of perspectives and highlights the evolutionary diversity of telomeres despite their central roles in senescence, aging, and chromosome integrity., (© 2024. The Author(s).)

The soil bacterium Sinorhizobium meliloti can establish a nitrogen-fixing symbiosis with the model legume Medicago truncatula. The rhizobia induce the formation of a specialized root organ called nodule, where they differentiate into bacteroids and reduce atmospheric nitrogen into ammonia. Little is known on the mechanisms involved in nodule senescence onset and in bacteroid survival inside the infected plant cells. Although toxin-antitoxin (TA) systems have been shown to promote intracellular survival within host cells in human pathogenic bacteria, their role in symbiotic bacteria was rarely investigated. S. meliloti encodes several TA systems, mainly of the VapBC family. Here we present the functional characterization, through a multidisciplinary approach, of the VapBC10 TA system of S. meliloti. Following a mapping by overexpression of an RNase in Escherichia coli (MORE) RNA-seq analysis, we demonstrated that the VapC10 toxin is an RNase that cleaves the anticodon loop of two tRNASer. Thereafter, a bioinformatics approach was used to predict VapC10 targets in bacteroids. This analysis suggests that toxin activation triggers a specific proteome reprogramming that could limit nitrogen fixation capability and viability of bacteroids. Accordingly, a vapC10 mutant induces a delayed senescence in nodules, associated to an enhanced bacteroid survival. VapBC10 TA system could contribute to S. meliloti adaptation to symbiotic lifestyle, in response to plant nitrogen status., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Horizontal gene transfer (HGT) is the transfer of genes between species outside the transmission from parent to offspring. Due to their impact on the genome and biology of various species, HGTs have gained broader attention, but high-throughput methods to robustly identify them are lacking. One rapid method to identify HGT candidates is to calculate the difference in similarity between the most similar gene in closely related species and the most similar gene in distantly related species. Although metrics on similarity associated with taxonomic information can rapidly detect putative HGTs, these methods are hampered by false positives that are difficult to track. Furthermore, they do not inform on the evolutionary trajectory and events such as duplications. Hence, phylogenetic analysis is necessary to confirm HGT candidates and provide a more comprehensive view of their origin and evolutionary history. However, phylogenetic reconstruction requires several time-consuming manual steps to retrieve the homologous sequences, produce a multiple alignment, construct the phylogeny and analyze the topology to assess whether it supports the HGT hypothesis. Here, we present AvP which automatically performs all these steps and detects candidate HGTs within a phylogenetic framework., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2022 Koutsovoulos et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

During the last decades, metagenomics has highlighted the diversity of microorganisms from environmental or host-associated samples. Most metagenomics public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs. Consequently, eukaryotic contigs with intrinsically different gene features, are not optimally annotated. Using a bioinformatics pipeline, we have filtered 7.9 billion contigs from 6,872 soil metagenomes in the JGI's IMG/M database to identify eukaryotic contigs. We have re-annotated genes using eukaryote-tailored methods, yielding 8 million eukaryotic proteins and over 300,000 orphan proteins lacking homology in public databases. Comparing the gene predictions we made with initial JGI ones on the same contigs, we confirmed our pipeline improves eukaryotic proteins completeness and contiguity in soil metagenomes. The improved quality of eukaryotic proteins combined with a more comprehensive assignment method yielded more reliable taxonomic annotation. This dataset of eukaryotic soil proteins with improved completeness, quality and taxonomic annotation reliability is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes., (© 2022. The Author(s).)

Surfactin, one of the best lipopeptide surfactants, was first isolated from Bacillus sp. in 1969. Since then, Bacillus sp. has been a remarkable source of bioactive lipopeptides, with a huge natural biodiversity. Lipopeptides from Bacillus sp. are now divided into three main families: surfactin, fengycin, and iturin. The peptide moiety of these lipopeptides is synthesised by huge multi-enzymatic proteins called nonribosomal peptide synthetases, which are responsible for the peptide biodiversity of these lipopeptides. Moreover, the fatty acid chain also encompasses a high diversity with different β-hydroxy or β-amino fatty acid chains of different lengths, isomery, or saturation, which can be incorporated. After describing the mode of synthesis of the different families of lipopeptides produced by Bacillus sp. and their biodiversity, this chapter describes how this lipopeptide biodiversity can be increased using genetic engineering and how the lipopeptides can be overproduced and purified. The high biodiversity of lipopeptides induces a broad range of physicochemical properties, which can be linked to multiple biological activities with many applications in different sectors. The increasing understanding of the mode of biosynthesis of these lipopeptides should lead to the development of novel compounds with increased properties and applications., (© 2021. Springer Nature Switzerland AG.)

The Méditerranée Infection University Hospital Institute (IHU) is located in a recent building, which includes experts on a wide range of infectious disease. The IHU strategy is to develop innovative tools, including epidemiological monitoring, point-of-care laboratories, and the ability to mass screen the population. In this study, we review the strategy and guidelines proposed by the IHU and its application to the COVID-19 pandemic and summarise the various challenges it raises. Early diagnosis enables contagious patients to be isolated and treatment to be initiated at an early stage to reduce the microbial load and contagiousness. In the context of the COVID-19 pandemic, we had to deal with a shortage of personal protective equipment and reagents and a massive influx of patients. Between 27 January 2020 and 5 January 2021, 434,925 nasopharyngeal samples were tested for the presence of SARS-CoV-2. Of them, 12,055 patients with COVID-19 were followed up in our out-patient clinic, and 1888 patients were hospitalised in the Institute. By constantly adapting our strategy to the ongoing situation, the IHU has succeeded in expanding and upgrading its equipment and improving circuits and flows to better manage infected patients.

Root-knot nematodes (genus Meloidogyne ) are the major contributor to crop losses caused by nematodes. These nematodes secrete effector proteins into the plant, derived from two sets of pharyngeal gland cells, to manipulate host physiology and immunity. Successful completion of the life cycle, involving successive molts from egg to adult, covers morphologically and functionally distinct stages and will require precise control of gene expression, including effector genes. The details of how root-knot nematodes regulate transcription remain sparse. Here, we report a life stage-specific transcriptome of Meloidogyne incognita . Combined with an available annotated genome, we explore the spatio-temporal regulation of gene expression. We reveal gene expression clusters and predicted functions that accompany the major developmental transitions. Focusing on effectors, we identify a putative cis-regulatory motif associated with expression in the dorsal glands, providing an insight into effector regulation. We combine the presence of this motif with several other criteria to predict a novel set of putative dorsal gland effectors. Finally, we show this motif, and thereby its utility, is broadly conserved across the Meloidogyne genus, and we name it Mel-DOG. Taken together, we provide the first genome-wide analysis of spatio-temporal gene expression in a root-knot nematode and identify a new set of candidate effector genes that will guide future functional analyses.

Despite reproducing without sexual recombination, Meloidogyne incognita is an adaptive and versatile phytoparasitic nematode. This species displays a global distribution, can parasitize a large range of plants, and can overcome plant resistance in a few generations. The mechanisms underlying this adaptability remain poorly known. At the whole-genome level, only a few single nucleotide variations have been observed across different geographical isolates with distinct ranges of compatible hosts. Exploring other factors possibly involved in genomic plasticity is thus important. Transposable elements (TEs), by their repetitive nature and mobility, can passively and actively impact the genome dynamics. This is particularly expected in polyploid hybrid genomes such as the one of M .  incognita . Here, we have annotated the TE content of M .  incognita , analyzed the statistical properties of this TE landscape, and used whole-genome pool-seq data to estimate the mobility of these TEs across twelve geographical isolates, presenting variations in ranges of compatible host plants. DNA transposons are more abundant than retrotransposons, and the high similarity of TE copies to their consensus sequences suggests they have been at least recently active. We have identified loci in the genome where the frequencies of presence of a TE showed substantial variations across the different isolates. Overall, variations in TE frequencies across isolates followed their phylogenetic divergence, suggesting TEs participate in the species diversification. Compared with the M .  incognita reference genome, we detected isolate and lineage-specific de novo insertion of some TEs, including within genic regions or in the upstream regulatory regions. We validated by PCR the insertion of some of these TEs inside genic regions, confirming TE movements have possible functional impacts. Overall, we show DNA transposons can drive genomic plasticity in M .  incognita and their role in genome evolution of other parthenogenetic animal deserves further investigation., Competing Interests: The authors of this paper declare that they have no financial conflict of interest with the content of this article., (© 2021 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Great white pelicans (Pelecanus onocrotalus) exhibit life-history parameters and ecological traits thought to be associated with social learning, and advanced cognitive processing more generally. In this study we investigated whether this species can acquire novel behavior socially in a foraging context. Birds from the test group watched a trained conspecific opening an opaque box containing a food reward by using its beak, whereas the control group had no demonstrator but saw the box for an equivalent time span. Individuals from both groups were subsequently allowed access to the box. Subjects of the test group performed significantly better than the control group. This is the first experimental evidence of social learning in a cooperatively hunting bird. Further studies are needed in order to shed light on the factors favoring the evolution of this capacity, by testing different pelican species that vary in their ecology.

Indian fruit bats, flying fox Pteropus medius was identified as an asymptomatic natural host of recently emerged Nipah virus, which is known to induce a severe infectious disease in humans. The absence of P. medius genome sequence presents an important obstacle for further studies of virus-host interactions and better understanding of mechanisms of zoonotic viral emergence. Generation of the high-quality genome sequence is often linked to a considerable effort associated to elevated costs. Although secondary scaffolding methods have reduced sequencing expenses, they imply the development of new tools for the integration of different data sources to achieve more reliable sequencing results. We initially sequenced the P. medius genome using the combination of Illumina paired-end and Nanopore sequencing, with a depth of 57.4x and 6.1x, respectively. Then, we introduced the novel scaff2link software to integrate multiple sources of information for secondary scaffolding, allowing to remove the association with discordant information among two sources. Different quality metrics were next produced to validate the benefits from secondary scaffolding. The P. medius genome, assembled by this method, has a length of 1,985 Mb and consists of 33,613 contigs and 16,113 scaffolds with an NG50 of 19 Mb. At least 22.5% of the assembled sequences is covered by interspersed repeats already described in other species and 19,823 coding genes are annotated. Phylogenetic analysis demonstrated the clustering of P. medius genome with two other Pteropus bat species, P. alecto and P. vampyrus , for which genome sequences are currently available. SARS-CoV entry receptor ACE2 sequence of P. medius was 82.7% identical with ACE2 of Rhinolophus sinicus bats, thought to be the natural host of SARS-CoV. Altogether, our results confirm that a lower depth of sequencing is enough to obtain a valuable genome sequence, using secondary scaffolding approaches and demonstrate the benefits of the scaff2link application. The genome sequence is now available to the scientific community to (i) proceed with further genomic analysis of P. medius , (ii) to characterize the underlying mechanism allowing Nipah virus maintenance and perpetuation in its bat host, and (iii) to monitor their evolutionary pathways toward a better understanding of bats' ability to control viral infections., (Copyright © 2020 Fouret, Brunet, Binet, Aurine, Enchéry, Croze, Guinier, Goumaidi, Preininger, Volff, Bailly-Bechet, Lachuer, Horvat and Legras-Lachuer.)

The root-knot nematodes are the most devastating worms to worldwide agriculture with Meloidogyne incognita being the most widely distributed and damaging species. This parasitic and ecological success seems surprising given its supposed obligatory clonal reproduction. Clonal reproduction has been suspected based on cytological observations but, so far, never confirmed by population genomics data. As a species, M. incognita is highly polyphagous with thousands of host plants. However, different M. incognita isolates present distinct and overlapping patterns of host compatibilities. Historically, four "host races" had been defined as a function of ranges of compatible and incompatible plants. In this study, we used population genomics to assess whether (a) reproduction is actually clonal in this species, (b) the host races follow an underlying phylogenetic signal or, rather represent multiple independent transitions, and (c) how genome variations associate with other important biological traits such as the affected crops and geographical distribution. We sequenced the genomes of 11 M. incognita isolates across Brazil that covered the four host races in replicates. By aligning the genomic reads of these isolates to the M. incognita reference genome assembly, we identified point variations. Analysis of linkage disequilibrium and 4-gametes test showed no evidence for recombination, corroborating the clonal reproduction of M. incognita . The few point variations between the isolates showed no significant association with the host races, the geographical origin of the samples, or the crop on which they have been collected. Addition of isolates from other locations around the world confirmed this lack of underlying phylogenetic signal. This suggests multiple gains and losses of parasitic abilities and adaptations to different environments account for the broad host spectrum and wide geographical distribution of M. incognita and thus to its high economic impact. This surprising adaptability without sex poses both evolutionary and agro-economic challenges., Competing Interests: The authors declare that they have no financial conflict of interest with the content of this article., (© 2019 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

L1 retrotransposons are transposable elements and major contributors of genetic variation in humans. Where L1 integrates into the genome can directly impact human evolution and disease. Here, we experimentally induced L1 retrotransposition in cells and mapped integration sites at nucleotide resolution. At local scales, L1 integration is mostly restricted by genome sequence biases and the specificity of the L1 machinery. At regional scales, L1 shows a broad capacity for integration into all chromatin states, in contrast to other known mobile genetic elements. However, integration is influenced by the replication timing of target regions, suggesting a link to host DNA replication. The distribution of new L1 integrations differs from those of preexisting L1 copies, which are significantly reshaped by natural selection. Our findings reveal that the L1 machinery has evolved to efficiently target all genomic regions and underline a predominant role for post-integrative processes on the distribution of endogenous L1 elements., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Adaptation to changing environmental conditions represents a challenge to parthenogenetic organisms, and until now, how phenotypic variants are generated in clones in response to the selection pressure of their environment remains poorly known. The obligatory parthenogenetic root-knot nematode species Meloidogyne incognita has a worldwide distribution and is the most devastating plant-parasitic nematode. Despite its asexual reproduction, this species exhibits an unexpected capacity of adaptation to environmental constraints, for example, resistant hosts. Here, we used a genomewide comparative hybridization strategy to evaluate variations in gene copy numbers between genotypes of M. incognita resulting from two parallel experimental evolution assays on a susceptible vs. resistant host plant. We detected gene copy number variations (CNVs) associated with the ability of the nematodes to overcome resistance of the host plant, and this genetic variation may reflect an adaptive response to host resistance in this parthenogenetic species. The CNV distribution throughout the nematode genome is not random and suggests the occurrence of genomic regions more prone to undergo duplications and losses in response to the selection pressure of the host resistance. Furthermore, our analysis revealed an outstanding level of gene loss events in nematode genotypes that have overcome the resistance. Overall, our results support the view that gene loss could be a common class of adaptive genetic mechanism in response to a challenging new biotic environment in clonal animals., (© 2019 John Wiley & Sons Ltd.)

Root-knot nematodes (genus Meloidogyne) exhibit a diversity of reproductive modes ranging from obligatory sexual to fully asexual reproduction. Intriguingly, the most widespread and devastating species to global agriculture are those that reproduce asexually, without meiosis. To disentangle this surprising parasitic success despite the absence of sex and genetic exchanges, we have sequenced and assembled the genomes of three obligatory ameiotic and asexual Meloidogyne. We have compared them to those of relatives able to perform meiosis and sexual reproduction. We show that the genomes of ameiotic asexual Meloidogyne are large, polyploid and made of duplicated regions with a high within-species average nucleotide divergence of ~8%. Phylogenomic analysis of the genes present in these duplicated regions suggests that they originated from multiple hybridization events and are thus homoeologs. We found that up to 22% of homoeologous gene pairs were under positive selection and these genes covered a wide spectrum of predicted functional categories. To biologically assess functional divergence, we compared expression patterns of homoeologous gene pairs across developmental life stages using an RNAseq approach in the most economically important asexually-reproducing nematode. We showed that >60% of homoeologous gene pairs display diverged expression patterns. These results suggest a substantial functional impact of the genome structure. Contrasting with high within-species nuclear genome divergence, mitochondrial genome divergence between the three ameiotic asexuals was very low, signifying that these putative hybrids share a recent common maternal ancestor. Transposable elements (TE) cover a ~1.7 times higher proportion of the genomes of the ameiotic asexual Meloidogyne compared to the sexual relative and might also participate in their plasticity. The intriguing parasitic success of asexually-reproducing Meloidogyne species could be partly explained by their TE-rich composite genomes, resulting from allopolyploidization events, and promoting plasticity and functional divergence between gene copies in the absence of sex and meiosis.

Wolbachia bacteria infect about half of all arthropods, with diverse and extreme consequences ranging from sex-ratio distortion and mating incompatibilities to protection against viruses. These phenotypic effects, combined with efficient vertical transmission from mothers to offspring, satisfactorily explain the invasion dynamics of Wolbachia within species. However, beyond the species level, the lack of congruence between the host and symbiont phylogenetic trees indicates that Wolbachia horizontal transfers and extinctions do happen and underlie its global distribution. But how often do they occur? And has the Wolbachia pandemic reached its equilibrium? Here, we address these questions by inferring recent acquisition/loss events from the distribution of Wolbachia lineages across the mitochondrial DNA tree of 3,600 arthropod specimens, spanning 1,100 species from Tahiti and surrounding islands. We show that most events occurred within the last million years, but are likely attributable to individual level variation (e.g., imperfect maternal transmission) rather than population level variation (e.g., Wolbachia extinction). At the population level, we estimate that mitochondria typically accumulate 4.7% substitutions per site during an infected episode, and 7.1% substitutions per site during the uninfected phase. Using a Bayesian time calibration of the mitochondrial tree, these numbers translate into infected and uninfected phases of approximately 7 and 9 million years. Infected species thus lose Wolbachia slightly more often than uninfected species acquire it, supporting the view that its present incidence, estimated here slightly below 0.5, represents an epidemiological equilibrium., (© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

There is a huge abundance of viruses and membrane vesicles in seawater. We describe a new full-field, incoherently illuminated, shot-noise limited, common-path interferometric detection method that we couple with the analysis of Brownian motion to detect, quantify, and differentiate biotic nanoparticles. We validated the method with calibrated nanoparticles and homogeneous DNA or RNA viruses. The smallest virus size that we characterized with a suitable signal-to-noise ratio was around 30 nm in diameter. Analysis of Brownian motions revealed anisotropic trajectories for myoviruses.We further applied the method for vesicles detection and for analysis of coastal and oligotrophic samples from Tara Oceans circumnavigation.

Gene sequences are the target of evolution operating at different levels, including the nucleotide, codon, and amino acid levels. Disentangling the impact of those different levels on gene sequences requires developing a probabilistic model with three layers. Here we present SENCA (site evolution of nucleotides, codons, and amino acids), a codon substitution model that separately describes 1) nucleotide processes which apply on all sites of a sequence such as the mutational bias, 2) preferences between synonymous codons, and 3) preferences among amino acids. We argue that most synonymous substitutions are not neutral and that SENCA provides more accurate estimates of selection compared with more classical codon sequence models. We study the forces that drive the genomic content evolution, intraspecifically in the core genome of 21 prokaryotes and interspecifically for five Enterobacteria. We retrieve the existence of a universal mutational bias toward AT, and that taking into account selection on synonymous codon usage has consequences on the measurement of selection on nonsynonymous substitutions. We also confirm that codon usage bias is mostly driven by selection on preferred codons. We propose new summary statistics to measure the relative importance of the different evolutionary processes acting on sequences., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

The immune system is able to identify foreign pathogens via different pathways. In the case of viral infection, recognition of the viral RNA is a crucial step, and many efforts have been made to understand which features of viral RNA are detected by the immune system. The biased viral RNA composition, measured as host-virus nucleotidic divergence, or CpG enrichment, has been proposed as salient signal. Peculiar structural features of these RNA could also be related to the immune system activation. Here, we gather multiple datasets and proceed to a meta-analysis to uncover the best predictors of immune system activation by viral RNA. "A" nucleotide content and Minimum Folding Energy are good predictors, and are more easily generalized than more complex indicators suggested previously. As RNA composition and structure are highly correlated, we suggest further experiments on synthetic sequences to identify the viral RNA sensing mechanisms by immune system receptors., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Background: Medication errors (ME) could lead to severe adverse events. Hospital staff have to gain practical knowledge and ME preventing methods. Simulation is a teaching method more and more used in health system. The aim of this study was to create an error patient room which represents a factitious patient room with ME for health professionals of the hospital., Method: Chosen according 3 criteria (errors already observed, "never events" related errors, errors associated with frequent issues), 21 ME were designed concerning the different steps of the medication process (prescribing, dispensing and administration) and took place in a patient room reserved for training. Seven sessions were proposed from april to june 2014. All health professionals were invited to participate on a voluntary basis. Training session was not time limit. An individual debriefing was done after each session., Results: Forty-six health professional participated of 13 different hospitals' departments: 7 medicine residents, 26 nurses and 13 persons of the pharmacy staff (8 pharmacy technicians, 3 pharmacy students and 2 pharmacists). EM rate ranged of 33% (medicine residents), 50% (nurses) to 47% (pharmacy staff)., Discussion - Conclusion: The training ME room represents an easy, useful and reusable simulating tool, to train health professional and to improve their knowledge's and practical methods. This learning tool is developed in order to provide patient safety. This successful study will be evaluated by satisfaction questionnaire. Future sessions will be programmed.

Unlabelled: Lentiviral RNA genomes present a strong bias in their nucleotide composition with extremely high frequencies of A nucleotide in human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV). Based on the observation that human optimization of RNA virus gene fragments may abolish their ability to stimulate the type I interferon (IFN-I) response, we identified the most biased sequences along the SIV genome and showed that they are the most potent IFN-I stimulators. With the aim of designing an attenuated SIV genome based on a reduced capacity to activate the IFN-I response, we synthesized artificial SIV genomes whose biased sequences were optimized toward macaque average nucleotide composition without altering their regulatory elements or amino acid sequences. A synthetic SIV optimized with 169 synonymous mutations in gag and pol genes showed a 100-fold decrease in replicative capacity. Interestingly, a synthetic SIV optimized with 70 synonymous mutations in pol had a normal replicative capacity. Its ability to stimulate IFN-I was reduced when infected cells were cocultured with reporter cells. IFN regulatory factor 3 (IRF3) transcription factor was required for IFN-I stimulation, implicating cytosolic sensors in the detection of SIV-biased RNA in infected cells. No reversion of introduced mutations was observed for either of the optimized viruses after 10 serial passages. In conclusion, we have designed large-scale nucleotide-modified SIVs that may display attenuated pathogenic potential., Importance: In this study, we synthesized artificial SIV genomes in which the most hyperbiased sequences were optimized to bring them closer to the nucleotide composition of the macaque SIV host. Interestingly, we generated a stable synthetic SIV optimized with 70 synonymous mutations in pol gene, which had a normal replicative capacity but a reduced ability to stimulate type I IFN. This demonstrates the possibility to rationally change viral nucleotide composition to design replicative and genetically stable lentiviruses with attenuated pathogenic potentials.

Ovarian granulosa cell tumors (OGCT) are the most frequent kind of sex cord-stromal tumors, and represent ∼2-5% of all ovarian malignancies. OGCTs exist as two entities, juvenile and adult types, with specific clinical and pathological characteristics. The molecular pathogenesis of these tumors has just begun to be unraveled. Indeed, recent studies have indicated that mutation and/or misregulation of the key ovarian transcription factor FOXL2 has a role in OGCT formation, although the mechanisms remain unclear. To better understand the molecular characteristics of OGCT, we studied the transcriptomic profiles of ten human adult-type OGCT samples, as well as ethnically matched granulosa cell (GC) controls. We find that the OGCT samples analyzed herein exhibit several hallmarks of cancer, including increased expression of genes linked to cell proliferation, but decreased expression of those conferring sensitivity to cell death. Moreover, genes differentially expressed in OGCTs are significantly enriched for known FOXL2 target genes, consistently with the prevalence of FOXL2 somatic mutation in these tumors. Expression of these targets is altered in a way expected to promote malignant transformation, for instance, through induction of genes associated with faster cell cycling and downregulation of genes associated with cell death. Over time, such defects may be responsible at least partly for the malignant transformation of healthy GCs into OGCT. These insights into the molecular pathogenesis of OGCTs may open the way to new efforts in the development of more targeted therapeutic strategies for OGCT patients.

How and why female somatic X-chromosome inactivation (XCI) evolved in mammals remains poorly understood. It has been proposed that XCI is a dosage-compensation mechanism that evolved to equalize expression levels of X-linked genes in females (2X) and males (1X), with a prior twofold increase in expression of X-linked genes in both sexes ("Ohno's hypothesis"). Whereas the parity of X chromosome expression between the sexes has been clearly demonstrated, tests for the doubling of expression levels globally along the X chromosome have returned contradictory results. However, changes in gene dosage during sex-chromosome evolution are not expected to impact on all genes equally, and should have greater consequences for dosage-sensitive genes. We show that, for genes encoding components of large protein complexes (≥ 7 members)--a class of genes that is expected to be dosage-sensitive--expression of X-linked genes is similar to that of autosomal genes within the complex. These data support Ohno's hypothesis that XCI acts as a dosage-compensation mechanism, and allow us to refine Ohno's model of XCI evolution. We also explore the contribution of dosage-sensitive genes to X aneuploidy phenotypes in humans, such as Turner (X0) and Klinefelter (XXY) syndromes. X aneuploidy in humans is common and is known to have mild effects because most of the supernumerary X genes are inactivated and not affected by aneuploidy. Only genes escaping XCI experience dosage changes in X-aneuploidy patients. We combined data on dosage sensitivity and XCI to compute a list of candidate genes for X-aneuploidy syndromes.

The genome of human immunodeficiency virus (HIV) has an average nucleotide composition strongly biased as compared to the human genome. The consequence of such nucleotide composition on HIV pathogenicity has not been investigated yet. To address this question, we analyzed the role of nucleotide bias of HIV-derived nucleic acids in stimulating type-I interferon response in vitro. We found that the biased nucleotide composition of HIV is detected in human cells as compared to humanized sequences, and triggers a strong innate immune response, suggesting the existence of cellular immune mechanisms able to discriminate RNA sequences according to their nucleotide composition or to detect specific secondary structures or linear motifs within biased RNA sequences. We then extended our analysis to the entire genome scale by testing more than 1300 HIV-1 complete genomes to look for an association between nucleotide composition of HIV-1 group M subtypes and their pathogenicity. We found that subtype D, which has an increased pathogenicity compared to the other subtypes, has the most divergent nucleotide composition relative to the human genome. These data support the hypothesis that the biased nucleotide composition of HIV-1 may be related to its pathogenicity.

In this work we consider the regulation system present on the SPI1 pathogenicity island of Salmonella enterica serovar Typhimurium. It is well-known that HilA is the central regulator in the overall scheme of SPI1 regulation and directly binds to virulence operons and activates their expression. The regulation of the expression of HilA is via a complex feed-forward loop involving three transcriptional activators: HilC, HilD and RtsA, and the negative regulator HilE. Our aim is to model this regulation network and study its dynamical behavior. We show that this regulatory system can display a bistable behavior relevant to the biology of Salmonella, and that noise can be a driving force in this system.

External information propagates in the cell mainly through signaling cascades and transcriptional activation, allowing it to react to a wide spectrum of environmental changes. High-throughput experiments identify numerous molecular components of such cascades that may, however, interact through unknown partners. Some of them may be detected using data coming from the integration of a protein-protein interaction network and mRNA expression profiles. This inference problem can be mapped onto the problem of finding appropriate optimal connected subgraphs of a network defined by these datasets. The optimization procedure turns out to be computationally intractable in general. Here we present a new distributed algorithm for this task, inspired from statistical physics, and apply this scheme to alpha factor and drug perturbations data in yeast. We identify the role of the COS8 protein, a member of a gene family of previously unknown function, and validate the results by genetic experiments. The algorithm we present is specially suited for very large datasets, can run in parallel, and can be adapted to other problems in systems biology. On renowned benchmarks it outperforms other algorithms in the field.

Background: Transcriptional gene regulation is one of the most important mechanisms in controlling many essential cellular processes, including cell development, cell-cycle control, and the cellular response to variations in environmental conditions. Genes are regulated by transcription factors and other genes/proteins via a complex interconnection network. Such regulatory links may be predicted using microarray expression data, but most regulation models suppose transcription factor independence, which leads to spurious links when many genes have highly correlated expression levels., Results: We propose a new algorithm to infer combinatorial control networks from gene-expression data. Based on a simple model of combinatorial gene regulation, it includes a message-passing approach which avoids explicit sampling over putative gene-regulatory networks. This algorithm is shown to recover the structure of a simple artificial cell-cycle network model for baker's yeast. It is then applied to a large-scale yeast gene expression dataset in order to identify combinatorial regulations, and to a data set of direct medical interest, namely the Pleiotropic Drug Resistance (PDR) network., Conclusions: The algorithm we designed is able to recover biologically meaningful interactions, as shown by recent experimental results 1. Moreover, new cases of combinatorial control are predicted, showing how simple models taking this phenomenon into account can lead to informative predictions and allow to extract more putative regulatory interactions from microarray databases.

Background: No data are available regarding the utility of fractional exhaled nitric oxide (FeNO) level in guiding therapy in smoking asthmatic patients. Identification of the effect of smoking in a large sample is needed., Objective: To study the association between smoking and FeNO level according to current asthma and atopy status in adults from the French EGEA (Epidemiological study on the Genetics and Environment of Asthma, bronchial hyperresponsiveness and atopy)., Methods: Levels of FeNO were measured at 50 mL/s in 654 adults (268 asthmatic participants). Active smoking and environmental tobacco smoke (ETS) exposure at home, at work, and during leisure activities were recorded. Participants were categorized as having no exposure to ETS, mild exposure (ETS <2 h/d), and noticeable exposure (ETS > or = 2 h/d). Multivariate analyses were performed, with adjustment for age, sex, height, and center., Results: Mean adjusted FeNO values increased with asthma (15.1 vs 19.5 ppb), atopy (14.2 vs 18.9 ppb), and eosinophilia (15.8 vs 24.8 ppb) (P < .001 for all). Mean FeNO levels decreased with smoking (18.4, 17.5, and 14.5 ppb in nonsmokers, ex-smokers, and current smokers, respectively; P for trend = .001). The association with smoking was observed in nonasthmatic and asthmatic participants, especially in atopic asthmatic participants. Multivariate analyses showed that ETS exposure of at least 2 h/d and active smoking were negatively and significantly associated with FeNO levels independent of age, sex, height, and center in nonasthmatic participants (mean [SE], -0.13 [0.06], P = .03 and -0.10 [0.03], P < .001) and in asthmatic participants (mean [SE], -0.18 [0.07], P = .01 and -0.14 [0.04], P = .02)., Conclusions: Active and passive smoking decreased FeNO levels in adults. Careful consideration of asthma, atopy, and active and passive smoking are needed to interpret FeNO values.

Deep-sea hydrothermal vent animal communities along oceanic ridges are both patchy and transient. Larval dispersal is a key factor in understanding how these communities function and are maintained over generations. To date, numerical approaches simulating larval dispersal considered the effect of oceanic currents on larval transportation over hundreds of kilometers but very seldom looked at the effect of local conditions within meters around chimneys. However, small scale significant variations in the hydrodynamics may influence larval fate in its early stages after release, and hence have a knock-on effect on both dispersal and colonization processes. Here we present a new numerical approach to the study of larval dispersal, considering small scales within the range of the biological communities, called "bio-hydrodynamical" scale, and ranging from a few centimeters to a few meters around hydrothermal sources. We use a physical model for the vent based on jet theory and compute the turbulent velocity field around the smoker. Larvae are considered as passive particles whose trajectories are affected by hydrodynamics, topography of the vent chimney and larval biological properties. Our model predicts that bottom currents often dominate all other factors either by entraining all larvae away from the vent or enforcing strong colonization rates. When bottom currents are very slow (<1 mms(-1)), general larvae motion is upwards due to entrainment by the main smoker jet. In this context, smokers with vertical slopes favor retention of larvae because larval initial trajectory is nearly parallel to the smoker wall, which increases the chances to settle. This retention phenomenon is intensified with increasing velocity of the main smoker jet because entrainment in the high velocity plume is preceded by a phase when larvae are attracted towards the smoker wall, which occurs earlier with higher velocity of the main jet. Finally, the buoyancy rate of the larvae, measured to be in the range of 0.01 mms(-1), is generally irrelevant unless hydrodynamic conditions are balanced, i.e. if the buoyancy rate is comparable to both the bottom current speed and the local water velocity due to entrainment by close smokers. Overall, our model evidences the strong effect of the release point of larvae on their future entrainment within local fluxes. Larvae released from smoker walls might have an entirely different fate than those released further away in the water column. The latter are not, or less, affected by near-chimney hydrodynamics.

The Forkhead transcription factor FOXL2 plays a crucial role in ovarian development and maintenance. In humans, its mutations lead to craniofacial abnormalities, isolated or associated with ovarian dysfunction. Using a combinatorial approach, we identified and characterized a FoxL2 response element (FLRE) and showed that it is highly specific and that it diverges from that of other Forkhead transcription factors. This specificity should prevent aberrant regulation of FOXL2 targets by other members of the family and should prevent ectopic activation of the ovarian differentiation program in testes. We provide evidence that the FLRE is used in naturally occurring promoters. We show that polyAlanine expansions of FOXL2, which are the most frequent pathogenic mutations, induce a length-dependent loss of response on different artificial promoter reporters depending on the number and sequence of the FLREs that they contain. Thus, we provide clear mechanistic evidence explaining how the architecture of promoters influences their sensitivity to decreased transcription factor availability. Furthermore, we speculate that the generally absent ovarian phenotype of patients carrying the most frequent polyAlanine expansion should come from its ability to properly regulate high-affinity ovarian targets. The existence of critical high-affinity ovarian targets would be compatible with the role of FOXL2 in reproduction and ensure developmental and functional robustness. Taken together, our results give mechanistic insights on the molecular pathogenesis of FOXL2 polyAlanine expansions.

Phages have highly compact genomes with sizes reflecting their capacity to exploit the host resources. Here, we investigate the reasons for tRNAs being the only translation-associated genes frequently found in phages. We were able to unravel the selective processes shaping the tRNA distribution in phages by analyzing their genomes and those of their hosts. We found ample evidence against tRNAs being selected to facilitate phage integration in the prokaryotic chromosomes. Conversely, there is a significant association between tRNA distribution and codon usage. We support this observation by introducing a master equation model, where tRNAs are randomly gained from their hosts and then lost either neutrally or according to a set of different selection mechanisms. Those tRNAs present in phages tend to correspond to codons that are simultaneously highly used by the phage genes, while rare in the host genome. Accordingly, we propose that a selective recruitment of tRNAs compensates for the compositional differences between the phage and the host genomes. To further understand the importance of these results in phage biology, we analyzed the differences between temperate and virulent phages. Virulent phages contain more tRNAs than temperate ones, higher codon usage biases, and more important compositional differences with respect to the host genome. These differences are thus in perfect agreement with the results of our master equation model and further suggest that tRNA acquisition may contribute to higher virulence. Thus, even though phages use most of the cell's translation machinery, they can complement it with their own genetic information to attain higher fitness. These results suggest that similar selection pressures may act upon other cellular essential genes that are being found in the recently uncovered large viruses.

The geography of codon bias distributions over prokaryotic genomes and its impact upon chromosomal organization are analyzed. To this aim, we introduce a clustering method based on information theory, specifically designed to cluster genes according to their codon usage and apply it to the coding sequences of Escherichia coli and Bacillus subtilis. One of the clusters identified in each of the organisms is found to be related to expression levels, as expected, but other groups feature an over-representation of genes belonging to different functional groups, namely horizontally transferred genes, motility, and intermediary metabolism. Furthermore, we show that genes with a similar bias tend to be close to each other on the chromosome and organized in coherent domains, more extended than operons, demonstrating a role of translation in structuring bacterial chromosomes. It is argued that a sizeable contribution to this effect comes from the dynamical compartimentalization induced by the recycling of tRNAs, leading to gene expression rates dependent on their genomic and expression context.

With the Gömöri technique, lead precipitates have been found in thyroid follicle cells in unusual localizations such as apical hyaloplasm and microvilli; it has been established that they were actually significant for acid phosphatase activity: constant results in spite of repeated controls and several variations from the original cytochemical technique, allow to think that lead precipitates were not merely artefactual, but actually significant of enzymatic activity. However it is pointed to the fact that the origin of the enzyme has to be questioned; it is assumed that most likely acid phosphatase has diffused from its original lysosomal site. Such diffusion implies variations of the selective permeability of lysosomal membranes; inappropriate relation between the quantity of enzyme present in these organelles and the quantity of substrate used might also be considered, though changes in the amount (resp. concentration) of substrate remained ineffective and induced no modification in the localization of observed enzymatic activity. In addition, one point of interest is an obvious relation between the observed enzyme diffusion and the state of activity resp. rest of the cell; in the present state of investigations, this remains unexplained and likely related to factors escaping control during processing; moreover, no explanation can be provided for the fact that it revealed impossible to avoid such diffusion even by means of variations of the numerous parameters involved in the Gömöri technique. So that it finally appears necessary to remain on a critical position regarding the results at the ultrastructural level of this standardized technique, and there is no doubt it would reveal useful that several assumptions in the literature about extra lysosomal acid phosphatase activity should be reinvestigated with a similar critical purpose.

By using the hybridoma technology, a monoclonal human thyroid cell line was obtained by fusing fresh normal human thyroid cells with a human lymphoblastoid cell line. The resultant cell line, called GEJ, has been selected for its expression of thyrotropin (TSH) receptors and has morphological and functional characteristics of normal human thyroid cells. In the presence or absence of human TSH, the GEJ cell line accumulates iodide, produces thyroid hormones, expresses thyroid membrane antigens, and binds approximately equal to 600 molecules of TSH per cell. The binding site for TSH has all the characteristics of specific receptor (i.e., temperature and time dependencies, dissociation of bound TSH only by high amounts of TSH, and a glycoprotein nature). Scatchard analysis described a curvilinear graph with two dissociation constants (Kd = 0.12 X 10(-9) M and 1.6 X 10(-9) M) with, respectively, 1.2 X 10(3) and 7.2 X 10(3) binding sites per cell. This human thyroid cell line that expresses TSH receptors could be a useful tool for the study of human thyroid disorders.

The morphological and physiological changes induced by organ culture and thyroid-stimulating hormone (TSH) stimulation in the rat fetal thyroid gland were studied. Organ culture increased Golgi activity which was further enhanced by TSH, subsequently facilitating the formation of intracellular lumina. TSH also raised the intracellular cAMP level. The intracellular lumina observed during follicular morphogenesis are structurally comparable to typical intracellular cavities formed in adult thyroid cells, which are considered as being the result of increased Golgi activity. The intracellular lumen, therefore, is probably not a physiologically significant step in thyroid morphogenesis.

Incubation in a culture medium with and without TSH of 16 day-old foetal thyroid glands induces hypertrophy of the Golgi apparatus which may be correlated with a considerable increase in the number of secretory vesicles. A stereological study performed during the first 6 hr of incubation showed that: vesicle secretion was biphasic; vesicle secretion was heterogeneous with two different populations of vesicles; When TSH (20 mU and 80 mU) was added to the medium, the volume density of the follicular lumina increased; at least during the first 6 hr TSH seemed to be necessary to the formation of follicular lumina.

When cultured in polystyrene dishes subjected to previous treatment and supplied with a serum-containing medium, hog thyroid cells form monolayers displaying dome-like arrangements after three to four days. Cells involved in formation of "domes" are morphologically polarized; the apical microvilli of these cells point toward the culture medium. When the tissue is cultured in untreated polystyrene dishes, thyroid cells remain in suspension; their aggregates swell progressively and form hollow spheres encompassed by a single layer of cells. The polarity of the cells forming such spheres is inverse in comparison to the condition characteristic of the intact thyroid gland. When culture medium is supplemented with TSH, PGE1, PGE2 or dBC, structures resembling true follicles are formed in both types of cultures. Gelatin, added to suspension cultures, is also capable of promoting follicle formation. Cultured thyroid cells regularly form an epithelial layer as a result of the interaction of cellular processes. However, the polarization of this layer depends on culture conditions. Thus, structures with either a normal follicle-like polarization of their cells or showing an inverted type of polarization can be obtained.

Porcine thyroid and embryo skin cells were isolated and cultured. Cultures from each kind of cells, as well as cocultures were fixed twice a week for electron microscopy. On day 8th a basal lamina like material appears only in the cocultures, along the basal plasmalemma of the reassociated thyroid cells. This amorphous material increases up to day 17th.

Endogenous peroxidase is associated with thyroglobulin iodination. It first appears at 17 day of pregnancy in rat fetal thyroid and seems to be synthesized within the perinuclear cistern and the rough endoplasmic reticulum. Then, the enzyme is transferred by vesicles up to the follicular lumen where thyroglobulin iodination takes place. The different steps of this process can occur within a very short time, since peroxidase activity is already located in the apical plasma membrane of follicles formed as early as 17 days of pregnancy, which is consistent with autoradiographic data showing iodinated thyroglobulin at 17 days. It can be concluded that the follicle is functional as soon as it is formed.

A human thyroid tumor is described which, on light microscopy, exhibited the features of medullary carcinoma of the thyroid (MCT). The cells were arranged in solid lobules or trabeculae, and the stroma was abundant and gave positive reaction for amyloid as assessed by congo red, crystal violet and thioflavin T stains. However, there was microfollicular differentiation in certain portions of the tumor even where the tumor was invasively growing. On electron microscopy, numerous microfollicles were identified even where unsuspected by light microscopy. There were junctional complexes, the cells possessed well developed rough endoplasmic reticulum, prominent Golgi and numerous dense bodies obviously derived from the Golgi vesicles, which were of the same morphology as "secretory" granules described previously by some authors in MCT. However, we find this kind of cytology typically in microfollicular thyroid carcinomas. Presence of about 100 A thick fibrils in the stroma was consistent with histochemically positive amyloid. The biochemical data were compatible with the differentiated follicular cell origin of the tissue. The homogenate contained poorly iodinated thyroglobulin, and thyroid peroxidase activity. Calcitonin was undetectable by a sensitive radioimmunoassay. It is concluded that this tumor was follicular thyroid carcinoma with amyloid rich stroma. The presence of amyloid and dense bodies with homogenous electron dense contents is insufficient for making conclusions about histogenesis of thyroid tumors. The so called MCT with amyloid stroma probably represents a heterogenous group of thyroid tumors, at least some of them derived from follicular epithelium.

Thyroid glands from 15 day-old rat foetuses were incubated in Eagle's medium containing Na 125I and supplemented, or not, with TSH for 4 or 24 hours. Electron microscopic radioautographic study shows silver grains mainly in follicular cavities only in the thyroids submitted to TSH during 24 hr. A functional differentiation must therefore take place in thyroid cells under TSH stimulation.

A study of the differentiation of the thyroid follicles was carried out in rat fetuses between day 14 of pregnancy, when cellular polarization begins and day 18, when completely formed follicular lumina are differentiated. After day 18, only the shape and the size of the lumina undergo modifications. The mechanism of folliculogenesis involves the participation of several structures. At 14 days of pregnancy, adherens type contact zones with membrane densification appear between the cells. These junctional zones spread out and form infoldings which deeply penetrate the cytoplasm. Golgi vesicles migrate to these zones and they fuse among themselves and with the contact membranes : follicular cavities result which can be recognized as soon as day 16 of pregnancy. A radioautographic study showed the beginning of iodide organification at 17 days 11 hours of pregnancy. From this time onward silver grains were seen over the follicular cavity, even it is still incompletely formed.

Five cases are reported of embryonal carcinoma with a vitelline structure more or less predominating. The presentation was of an anterior mediastinal tumour occurring in young men and in three cases there was mediastinal obstruction. The clinical examination, in particular testicular examination, was negative. In each case the level of the alpha-fetoprotein was greater than 1,000 micrograms/l, even post-operatively. The alpha-fetoprotein and HCG-beta should be measured systematically in all cases of anterior mediastinal tumour occurring in young subjects, and would enable a more frequent identification of tumours with difficult histology. The serum levels reflected the changes noted clinically and radiologically. Polychemotherapy bases around cis platinum led to a significant but transitory regression of the tumours. Radiotherapy was ineffective. Surgery was never totally curative.

Forskolin, a diterpen stimulating the adenylcyclase induces in vitro an accumulation of cAMP in thyroid glands explanted from 17 day-old rat fetuses. Thyroid glands from 15 day-old fetuses exposed to forskolin exhibit, within 24 hr, an active folliculogenesis and 125I fixation in follicular cavities. The results indicate that cAMP probably activates the onset of both morphological and physiological maturation in the fetal rat thyroid.

Seven effective (nitrogen-fixing) strains of Rhizobium meliloti have been studied. By sedimentation analysis of their alkaline lysates in alkaline sucrose gradients, a plasmid was found in four strains. In a strain (2011 str 3) which gave no result with this method, supercoiled DNA was detected by CsCl-dye buoyant density gradient centrifugation. That result was confirmed by analytical Cs2SO4-Ag+ density gradients, which showed a heterogeneity in the average base composition of the DNA extracted from three strains, including the 2011 str 3 strain. Two of those last strains seemed to contain an extrachromosomal DNA of very high molecular weight.

Follicles from adult rat thyroid glands were isolated by digestion with collagenase followed by sieving. Electron microscopic studies have shown that basement membrane was present around each one of the isolated follicles. Follicles were cultured in vitro with or without thyrotropin and fibronectin. When cultured in a medium free of thyrotropin, basement membrane remained around them, while it was lacking in presence of this hormone.

The authors report one case of sinus histiocytosis with massive lymphadenopathy which occurred in a 70 years old woman. They remind the main features of this pseudolymphomatous benign disorder with three key microscopic findings : massive sinus histiocytosis, lymphophagocytosis, proliferation of mature plasma cells. There is no effective therapy and nothing definite about the etiology.

The expression of the major histocompatibility complex antigens (K, D, and Ia) and thyroglobulin was studied on both freshly dissociated and in vitro cultured murine thyroid cells. Methods used for antigen detection included direct cytotoxicity, fluorescence and electron microscopic studies. Results obtained showed that the K-end, the D-end and thyroglobulin antigens are expressed exclusively on the apical cell surface of thyroid epithelial cells, while Ia antigens are found on the basal part of the cell.