A cross-species genome-wide analysis of sequences similar to those involved in DNA uptake bias in the Pastuerellaceae and Neisseriaceae families of pathogenic bacteria.

Acquiring new DNA allows the emergence of drug resistance in bacteria. Some Pasteurellaceae and Neisseriaceae species preferentially take up specific sequence tags. The study of such sequences is therefore relevant. They are over-represented in the genomes of the corresponding species. I found similar sequences to be present only in, but not in all, the genomes of the Pasteurellaceae and Neisseriaceae families. The genomic densities of these sequences are different both between species and between families. Interestingly, the family whose genomes harbor more of such sequences also shows more sequence types. A phylogenetic analysis allowed inferring the possible ancestral Neisseriacean sequence and a nucleotide-by-nucleotide analysis allowed inferring the potential ancestral Pasteurellacean sequence based on its genomic footprint. The method used for this work could be applied to other sequences, including transcription factor binding and repeated DNAs.

Culture-Based Methods and Molecular Tools for Azole-Resistant Aspergillus fumigatus Detection in a Belgian University Hospital.

Azole-resistant Aspergillus fumigatus is an increasing worldwide problem with major clinical implications. Surveillance is warranted to guide clinicians to provide optimal treatment to patients. To investigate azole resistance in clinical Aspergillus isolates in our institution, a Belgian university hospital, we conducted a laboratory-based surveillance between June 2015 and October 2016. Two different approaches were used: a prospective culture-based surveillance using VIPcheck on unselected A. fumigatus (n = 109 patients, including 19 patients with proven or probable invasive aspergillosis [IA]), followed by molecular detection of mutations conferring azole resistance, and a retrospective detection of azole-resistant A. fumigatus in bronchoalveolar lavage fluid using the commercially available AsperGenius PCR (n = 100 patients, including 29 patients with proven or probable IA). By VIPcheck, 25 azole-resistant A. fumigatus specimens were isolated from 14 patients (12.8%). Of these 14 patients, only 2 had proven or probable IA (10.5%). Mutations at the cyp51A gene were observed in 23 of the 25 A. fumigatus isolates; TR34/L98H was the most prevalent mutation (46.7%), followed by TR46/Y121F/T289A (26.7%). Twenty-seven (27%) patients were positive for the presence of Aspergillus species by AsperGenius PCR. A. fumigatus was detected by AsperGenius in 20 patients, and 3 of these patients carried cyp51A mutations. Two patients had proven or probable IA and cyp51A mutation (11.7%). Our study has shown that the detection of azole-resistant A. fumigatus in clinical isolates was a frequent finding in our institution. Hence, a rapid method for resistance detection may be useful to improve patient management. Centers that care for immunocompromised patients should perform routine surveillance to determine their local epidemiology.

A step to the gigantic genome of the desert locust: chromosome sizes and repeated DNAs.

The desert locust (Schistocerca gregaria) has been used as material for numerous cytogenetic studies. Its genome size is estimated to be 8.55 Gb of DNA comprised in 11 autosomes and the X chromosome. Its X0/XX sex chromosome determinism therefore results in females having 24 chromosomes whereas males have 23. Surprisingly, little is known about the DNA content of this locust's huge chromosomes. Here, we use the Feulgen Image Analysis Densitometry and C-banding techniques to respectively estimate the DNA quantity and heterochromatin content of each chromosome. We also identify three satellite DNAs using both restriction endonucleases and next-generation sequencing. We then use fluorescent in situ hybridization to determine the chromosomal location of these satellite DNAs as well as that of six tandem repeat DNA gene families. The combination of the results obtained in this work allows distinguishing between the different chromosomes not only by size, but also by the kind of repetitive DNAs that they contain. The recent publication of the draft genome of the migratory locust (Locusta migratoria), the largest animal genome hitherto sequenced, invites for sequencing even larger genomes. S. gregaria is a pest that causes high economic losses. It is thus among the primary candidates for genome sequencing. But this species genome is about 50 % larger than that of L. migratoria, and although next-generation sequencing currently allows sequencing large genomes, sequencing it would mean a greater challenge. The chromosome sizes and markers provided here should not only help planning the sequencing project and guide the assembly but would also facilitate assigning assembled linkage groups to actual chromosomes.

Non-random expression of ribosomal DNA units in a grasshopper showing high intragenomic variation for the ITS2 region.

We analyse intragenomic variation of the ITS2 internal transcribed spacer of ribosomal DNA (rDNA) in the grasshopper Eyprepocnemis plorans, by means of tagged PCR 454 amplicon sequencing performed on both genomic DNA (gDNA) and RNA-derived complementary DNA (cDNA), using part of the ITS2 flanking coding regions (5.8S and 28S rDNA) as an internal control for sequencing errors. Six different ITS2 haplotypes (i.e. variants for at least one nucleotide in the complete ITS2 sequence) were found in a single population, one of them (Hap4) being specific to a supernumerary (B) chromosome. The analysis of both gDNA and cDNA from the same individuals provided an estimate of the expression efficiency of the different haplotypes. We found random expression (i.e. about similar recovery in gDNA and cDNA) for three haplotypes (Hap1, Hap2 and Hap5), but significant underexpression for three others (Hap3, Hap4 and Hap6). Hap4 was the most extremely underexpressed and, remarkably, it showed the lowest sequence conservation for the flanking 5.8-28S coding regions in the gDNA reads but the highest conservation (100%) in the cDNA ones, suggesting the preferential expression of mutation-free rDNA units carrying this ITS2 haplotype. These results indicate that the ITS2 region of rDNA is far from complete homogenization in this species, and that the different rDNA units are not expressed at random, with some of them being severely downregulated.

Could DNA uptake be a side effect of bacterial adhesion and twitching motility?

DNA acquisition promotes the spread of resistance to antibiotics and virulence among bacteria. It is also linked to several natural phenomena including recombination, genome dynamics, adaptation and speciation. Horizontal DNA transfer between bacteria occurs via conjugation, transduction or competence for natural transformation by DNA uptake. Among these, competence is the only mechanism of transformation initiated and entirely controlled by the chromosome of the recipient bacteria. While the molecular mechanisms allowing the uptake of extracellular DNA are increasingly characterized, the function of competence for natural transformation by DNA uptake, the selective advantage maintaining it and the reasons why bacteria take up DNA in the first place are still debated. In this synthesis, I review some of the literature and discuss the four hypotheses on how and why do bacteria take up DNA. I argue that DNA uptake by bacteria is an accidental by-product of bacterial adhesion and twitching motility. Adhesion and motility are generally increased in stressful conditions, which may explain why bacteria increase DNA uptake in these conditions. In addition to its fundamental scientific relevance, the new hypothesis suggested here has significant clinical implications and finds further support from the fact that antibiotics sometimes fail to eliminate the targeted bacterium while inevitably causing stress to others. The widespread misuse of antibiotics may thus not only be selecting for resistant strains, but may also be causing bacteria to take up more DNA with the consequent increase in the chances of acquiring drug resistance and virulence-a scenario in full concordance with the previously reported induction of competence genes by antibiotics in Streptococcus pneumoniae and Legionella pneumophila.

RNA-Seq reveals large quantitative differences between the transcriptomes of outbreak and non-outbreak locusts.

Outbreaks of locust populations repeatedly devastate economies and ecosystems in large parts of the world. The consequent behavioural shift from solitarious to gregarious and the concomitant changes in the locusts' biology are of relevant scientific interest. Yet, research on the main locust species has not benefitted from recent advances in genomics. In this first RNA-Seq study on Schistocerca gregaria, we report two transcriptomes, including many novel genes, as well as differential gene expression results. In line with the large biological differences between solitarious and gregarious locusts, almost half of the transcripts are differentially expressed between their central nervous systems. Most of these transcripts are over-expressed in the gregarious locusts, suggesting positive correlations between the levels of activity at the population, individual, tissue and gene expression levels. We group these differentially expressed transcripts by gene function and highlight those that are most likely to be associated with locusts' phase change either in a species-specific or general manner. Finally, we discuss our findings in the context of population-level and physiological events leading to gregariousness.

Evolution, expression and association of the chemosensory protein genes with the outbreak phase of the two main pest locusts.

We analyze the evolutionary relationships and expression patterns of the large set of genes for chemosensory proteins (CSPs) in the two main pest locusts. We used the available transcriptome and genome data to infer the number of genes using BLAST searches and sequence similarity matrices. Maximum likelihood phylogenies revealed the relationships between these CSPs and CSPs from several arthropods. RNAseq and qPCR allowed associating CSPs to locust phases. Crossing the phylogenetic and expression data allowed us to deduce homologies and conservation of the involvement in the phase change. We confirm that Locusta migratoria has at least 58 CSP gene copies, only five of which lack evidence of expression, and we reveal that Schistocerca gregaria has at least 42 expressed CSP genes. Both species share 21 orthologs, whereas 33 L. migratoria and 15 S. gregaria CSPs seem species-specific. Additional six S. gregaria and four L. migratoria CSPs seem duplications. Although the expression profiles are not especially conserved, seven orthologous CSP pairs share a gregarious over-expression pattern in adult locusts. We thus confirm that the number of locusts' CSPs is large, due to gene duplications during the evolution of Orthoptera, we establish sequence and potential functional homologies, and we highlight specific CSPs that appear to be involved in locust gregariousness either in general or in a species-specific manner.

The B chromosome polymorphism of the grasshopper Eyprepocnemis plorans in North Africa. IV. Transmission of rare B chromosome variants.

In addition to the principal B chromosome (B(1)) in Moroccan populations of the grasshopper Eyprepocnemis plorans, nine B chromosome variants appeared at low frequency. The transmission of five of these rare B chromosome variants through females was analysed in three natural populations. Sixteen controlled crosses provided useful information on the transmission of B(M2), B(M6) and B(M7) in Smir, B(M3) and B(M6) in SO.DE.A. (Société de Développement Agricole lands near Ksar-el-Kebir city), and B(M2) and B(M10) in Mechra, all located in Morocco. Since six female parents carried two different B variants, a total of 22 progeny analyses could be studied. Intraindividual variation in B transmission rate (k(B)) was observed among the successive egg pods in 26.7 % of the females, but this variation did not show a consistent temporal pattern. Only the B(M2) and B(M6) variants in Smir showed net drive, although variation was high among crosses, especially for B(M2). These two variants are thus good candidates for future regenerations (the replacement of a neutralized B, B(1) in this case, by a new driving variant, B(M2) or B(M6)) in Smir, the northern population where the B polymorphism is presumably older. The analysis of all crosses performed in the three populations, including those reported previously for the analysis of B(1) transmission, showed that the largest variance in k(B) among crosses stands at the individual level, and not at population or type of B levels. The implications of these findings for the occurrence of possible regeneration processes in Moroccan populations are discussed.

Rapid suppression of drive for a parasitic B chromosome.

The persistence of parasitic B chromosomes in natural populations depends on both B ability to drive and host response to counteracting it. In the grasshopper Eyprepocnemis plorans, the B24 chromosome is the most widespread B chromosome variant in the Torrox area (Málaga, Spain). Its evolutionary success, replacing its ancestral neutralized B variant, B2, was based on meiotic drive in females, as we showed in a sample caught in 1992. In females collected six years later, mean B24 transmission ratio (k(B)) was 0.523, implying a very rapid decrease from the 0.696 observed in 1992. This shows that B24 neutralization is running very fast and suggests that it might most likely be based on a single gene of major effect.

Host recombination is dependent on the degree of parasitism.

Parasites and hosts are involved in a continuous coevolutionary process leading to genetic changes in both counterparts. To understand this process, it is necessary to track host responses, one of which could be an increase in sex and recombination, such as is proposed by the Red Queen hypothesis. In this theoretical framework, the inducible recombination hypothesis states that B-chromosomes (genome parasites that prosper in natural populations of many living beings) elicit an increase in host chiasma frequency that is favoured by natural selection because it increases the proportion of recombinant progeny, some of which could be resistant to both B-chromosome effects and B-accumulation in the germline. We have found a clear parallelism between host recombination and the evolutionary status of the B-chromosome polymorphism, which provides explicit evidence for inducible recombination and strong support for the Red Queen hypothesis.

The B chromosome polymorphism of the grasshopper eyprepocnemis plorans in north africa. I. B variants and frequency

Polymorphism for B chromosomes has been detected in all nine populations of the grasshopper Eyprepocnemis plorans ssp. plorans sampled in Morocco. The most frequent B chromosome in all populations showed a C-banding pattern and size similar to those of the B1 variant found in the Iberian Peninsula. In addition, other B chromosome variants (B1iso1, B1iso2, B1d1, B1di1, B3 and B1dd1) were discovered in these populations, although at a very low frequency. No significant differences in B chromosome frequency were found either in the nine populations or, for some of them, in up to three consecutive years. These results are discussed in the light of current hypotheses on the evolution of this B chromosome polymorphism in the Iberian Peninsula.

Common origin of B chromosome variants in the grasshopper eyprepocnemis plorans

Nine B chromosome variants, from seven different populations of Eyprepocnemis plorans collected at four localities in Spain and three in Morocco, have been shown to be mainly composed of two DNA sequences, i.e. a 180-bp tandem repeat and ribosomal DNA. B types, however, differ in the relative amounts of the two sequences. The most widespread one (B1) bears about the same amount of rDNA and 180 bp repeat, but three other variants that have reached a polymorphism by replacing B1 in smaller areas (B2, B5 and B24) carry a conspicuously larger amount of the 180 bp repeat. In Morocco, the most widespread B variant is also B1, and a rare variant that appeared in a single individual is also built with the same two DNA sequences. All these data point to a common origin for these B chromosomes, with B1 probably being the original one. The origin of the different B types and the possible relationship of the relative amount of 180 bp DNA repeat with B drive are discussed.

[Enucleations: epidemiologic investigation in Morocco. presentation of 183 cases]. / Enucléations: enquêté épidémiologique marocaine. A propos de 183 cas.

INTRODUCTION: The authors report the results of an epidemiological study concerning 183 enucleated eyeballs. MATERIAL AND METHODS: [corrected] The study is realized over a 12-year period (1988-2000) in the department of Ophthalmology "B" (University Hospital--Rabat) on 183 enucleated eyes, only 90% having an histological examination. RESULTS: The aetiologies are: trauma (40%), malignant tumours (30%), atrophies and glaucoma (17%), panophthalmitis (9%) and corneal lesions (4%). The authors compare their results with those of the literature. CONCLUSION: The causes of enucleation are the same throughout the world. The frequency has lately decreased due to the development of early diagnosis and to the use of more conservative treatments.

[Epidemiology of orbital processes in children. 54 cases]. / Epidémiologie des processus orbitaires chez l'enfant. A propos de 54 cas.

PURPOSE: The aim of this work was to study epidemiological aspect of orbital processes occurring in childhood. PATIENTS AND METHODS: Fifty-four cases of orbital processes treated between January 1990 and January 1997 were retrospectively reviewed. RESULTS: Mean patient age was 4.2 years (range 1 to 15), 36 were males and 18 were females. Proptosis was the first manifestation in 34 cases, other manifestations were low vision (8 cases), ocular pain (14 cases), inflammatory signs (11 cases), ocular palsy (14 cases). The first cause of these processes was secondary tumors, especially retinoblastoma (13 cases). Other causes were rhabdomyosarcoma (9 cases), orbital hydatic cyst (8 cases), inflammatory pseudotumors (7 cases), capillary hemanigoma (4 cases) chloroma (3 cases), glioma (1 case), lymphangioma (8 cases), and mucocele (1 case). DISCUSSION: We emphasize the particular epidemiological aspect of orbital processes in Moroccan children where retinoblastoma predominates and compare our findings with data in the literature.

[Tumor of the lacrimal sac. Dangers of simple excision biopsy]. / Tumeur du sac lacrymal. Dangers de la biopsie exérèse simple.

Lacrimal sac tumors are relatively uncommon tumors which recur readily and have poor prognosis if adequate care is not provided early. We report here a case of lacrimal sac tumor in a 56-year-old patient with bilateral pseudophakia and an atypical chronic dacryocystisis aspect of the left eye. After clinical and paraclinical investigations, the patient underwent surgical excision of the tumor followed by external radiotherapy. During follow-up, the patient developed a local recurrence which required surgical removal and radiotherapy. Despite early and adapted management, the prognosis of this tumor remains poor.

[Severe toxic optic neuropathies caused by isoniazid. Apropos of 3 cases]. / Neuropathies optiques toxiques graves induites par l'isoniazide. A propos de trois cas.

Three cases of isoniazid-induced toxic optic neuropathy are reported. These severe forms of the disease lead in all cases to bilateral blindness despite drug withdrawal. The epidemiological, clinical and therapeutic aspects of the disease are discussed. Further emphasis is placed on the importance of systematic screening of patients at risk using regular ophthalmological examinations before and after treatment.

[Value of ultrasonography in persistent hyperplastic primary vitreous body. Apropos of 4 cases]. / Intérêt de l'échographie dans la persistance et l'hyperplasie du vitré primitif. A propos de 4 cas.

The authors report 4 patients with complicated persistent hyperplastic primary vitreous. The complications observed are cataract (2 eyes) and retinal detachment (2 eyes). The affection is bilateral in two cases and unilateral in the two other cases. After a short embryologic vitreous recall, the authors present clinical and paraclinical aspects of the condition. The authors focus on the importance of echographic data.

[Tuberculous uveitis]. / Uvéite tuberculeuse.

Ocular tuberculosis is relatively rare; however, the most common ocular lesion during ocular tuberculosis is uveitis. The recrudescence of this disease is probably caused by human immunodeficiency virus or long-term corticotherapy. The authors report a of chronic unilateral tuberculosis-related uveitis complicated by panophthalmia with subconjunctival abcesess and scleral fistula. A histopathological study revealed a granulomatous inflammation with caseous material. An extensive work-up revealed no extraocular lesion. A systemic bactericidal treatement associated with topical steroids decreased the local inflammation with phthisis bulbi, and with no spread of the infection. The authors discuss the etiopathogenic, clinical, and therapeutic aspects of tuberculosis-related uveitis.

[Orbital lymphangioma. A case report]. / Lymphangiome orbitaire. A propos d'un cas.

The diffuse form of orbital lymphangioma is well known for its difficult surgical treatment. A diffuse orbital lymphangioma was diagnosed in a 6-year-old girl, revealed by unilateral recurrent proptosis. The imaging procedure discovered a mass presumed to be vascular in nature. The initial incompleted surgical removal was followed by 3 recurrences motivating 3 reoperations. Finally, the tumor was removed incompletely, with an acceptable reduction of the proptosis. The pathologic analyses indicated lymphangioma. Some vascular orbital tumors such as lymphangioma, may be very difficult to manage because of local spreading and frequent recurrence.