Expression profiles of growth-related genes in two Nile tilapia strains and their crossbred provide insights into introgressive breeding effects.

The Nile tilapia (Oreochromis niloticus) is a prominent farmed fish in aquaculture worldwide. Crossbreeding has recently been carried out between the Red-Stirling and the wt Chitralada strains of Nile tilapia, producing a heterotic hybrid (7/8 Chitralada and 1/8 Red-Stirling) that combines the superior growth performance of the Chitralada with the reddish coloration of the Red-Stirling strain. While classical selective breeding and crossbreeding strategies are well known, the molecular mechanisms underlying the phenotypic expression of economically advantageous traits in tilapia remain largely unknown. Molecular investigations have shown that variable expression of growth hormone (gh), insulin-like growth factors (igf1 and 2) and somatolactin (smtla) - components of the growth hormone/insulin-like growth factor (GH/IGF) axis - and myostatin (mstn) genes can affect traits of economic relevance in farmed animals. The aim of this study was to assess and compare the gene expression signature among Chitralada, Red-Stirling and their backcross hybrid in order to gain insights into the effects of introgressive breeding in modulation of the GH/IGF axis. Gene expression analyses in distinct tissues showed that most genes of the GH/IGF axis were up-regulated and mstn was down-regulated in backcross animals in comparison with Red-Stirling and Chitralada animals. These gene expression profiles revealed that backcross animals displayed a distinctive expression signature, which attests to the effectiveness of the introgressive breeding technique. Our findings also suggest that the GH/IGF axis and mstn genes might be candidate markers for fish performance and prove useful within genetic improvement programs aimed at the production of superior-quality tilapia strains using introgressive breeding.

Optimal non-invasive diagnosis of fetal achondroplasia combining ultrasonography with circulating cell-free fetal DNA analysis.

OBJECTIVES: To assess the performance of non-invasive prenatal testing (NIPT) for achondroplasia using high-resolution melting (HRM) analysis, and to propose an optimal diagnostic strategy combining ultrasound examination and cell-free fetal DNA (cffDNA) analysis. METHODS: In this prospective multicenter study, cffDNA was extracted from blood of pregnant women at risk for fetal achondroplasia (owing to paternal achondroplasia, previous affected child or suspected rhizomelic shortening) and of pregnant low-risk controls. The presence of either one of the two main fibroblast growth factor receptor 3 gene (FGFR3) mutations was determined using HRM combined with confirmation by SNaPshot minisequencing. Results were compared with phenotypes obtained using three-dimensional computed tomography or postnatal examination, and/or molecular diagnosis by an invasive procedure. Fetal biometry (head circumference and femur length) was analyzed in order to develop a strategy in which cffDNA analysis for diagnosis of achondroplasia is offered only in selected cases. RESULTS: Eighty-six blood samples from women at risk for fetal achondroplasia and 65 from controls were collected. The overall sensitivity and specificity of NIPT were 1.00 (95% CI, 0.87-1.00) and 1.00 (95% CI, 0.96-1.00), respectively. Critical reduction in femur length of affected fetuses could be observed from 26 weeks' gestation. CONCLUSIONS: HRM combined with SNaPshot minisequencing is a reliable method for NIPT for achondroplasia. Its implementation in routine clinical care combined with ultrasonography is an efficient strategy for the non-invasive diagnosis of achondroplasia. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.

Species Identification and In Vitro Antifungal Susceptibility of Aspergillus terreus Species Complex Clinical Isolates from a French Multicenter Study.

Aspergillus section Terrei is a species complex currently comprised of 14 cryptic species whose prevalence in clinical samples as well as antifungal susceptibility are poorly known. The aims of this study were to investigate A. Terrei clinical isolates at the species level and to perform antifungal susceptibility analyses by reference and commercial methods. Eighty-two clinical A. Terrei isolates were collected from 8 French university hospitals. Molecular identification was performed by sequencing parts of beta-tubulin and calmodulin genes. MICs or minimum effective concentrations (MECs) were determined for 8 antifungal drugs using both EUCAST broth microdilution (BMD) methods and concentration gradient strips (CGS). Among the 79 A. Terrei isolates, A. terreus stricto sensu (n = 61), A. citrinoterreus (n = 13), A. hortai (n = 3), and A. alabamensis (n = 2) were identified. All strains had MICs of ≥1 mg/liter for amphotericin B, except for two isolates (both A. hortai) that had MICs of 0.25 mg/liter. Four A. terreus isolates were resistant to at least one azole drug, including one with pan-azole resistance, yet no mutation in the CYP51A gene was found. All strains had low MECs for the three echinocandins. The essential agreements (EAs) between BMD and CGS were >90%, except for those of amphotericin B (79.7%) and itraconazole (73.4%). Isolates belonging to the A section Terrei identified in clinical samples show wider species diversity beyond the known A. terreus sensu stricto Azole resistance inside the section Terrei is uncommon and is not related to CYP51A mutations here. Finally, CGS is an interesting alternative for routine antifungal susceptibility testing.

Occurrence and species distribution of pathogenic Mucorales in unselected soil samples from France.

Mucormycosis is a life-threatening invasive fungal disease that affects a variety of patient groups. Although Mucorales are mostly opportunistic pathogens originating from soil or decaying vegetation, there are currently few data on prevalence of this group of fungi in the environment. The aim of the present study was to assess the prevalence and diversity of species of Mucorales from soil samples collected in France. Two grams of soil were homogenized in sterile saline and plated on Sabouraud dextrose agar and RPMI agar supplemented with itraconazole or voriconazole. Both media contained chloramphenicol and gentamicin. The plates were incubated at 35 ± 2 °C and checked daily for fungal growth for a maximum of 7 d. Mucorales were subcultured for purity. Each isolate was identified phenotypically and molecular identification was performed by ITS sequencing. A total of 170 soil samples were analyzed. Forty-one isolates of Mucorales were retrieved from 38 culture-positive samples. Among the recovered isolates, 27 Rhizopus arrhizus, 11 Mucor circinelloides, one Lichtheimia corymbifera, one Rhizopus microsporus and one Cunninghamella bertholletiae were found. Positive soil samples came from cultivated fields but also from other types of soil such as flower beds. Mucorales were retrieved from samples obtained in different geographical regions of France. Voriconazole-containing medium improved the recovery of Mucorales compared with other media. The present study showed that pathogenic Mucorales are frequently recovered from soil samples in France. Species diversity should be further analyzed on a larger number of soil samples from different geographic areas in France and in other countries.

Cell-free fetal DNA analysis in maternal plasma as screening test for trisomies 21, 18 and 13 in twin pregnancy.

OBJECTIVES: To evaluate in twin pregnancy the utility of non-invasive prenatal testing using circulating cell-free fetal DNA (cfDNA) in screening for the three main autosomal fetal trisomies. METHODS: cfDNA testing was offered to 492 patients with a twin pregnancy without ultrasound anomaly as a first-line screening test or after routine serum screening. Data were collected prospectively and a retrospective analysis was performed. cfDNA analysis was performed by massively parallel sequencing. The fetal-fraction threshold used for test evaluation was 8%. Regression analysis was performed to investigate the effect on the test failure rate of maternal and pregnancy characteristics, and the performance of the test was also reported. RESULTS: cfDNA analysis was performed as a first-line test (after the first-trimester scan) in 377 patients and following serum screening in 115. Of the 420 pregnancies for which outcome was available and cfDNA screening was assessed, 78.7% were dichorionic-diamniotic. The test failed on the first attempt in 12 (2.9%) pregnancies, and regression analysis demonstrated that only maternal weight was a significant independent predictor of test failure. A result was subsequently achieved in the 10 cases for which a second sample was obtained. cfDNA analysis identified all three cases of trisomy 21 and the only case of trisomy 18. For trisomy 21, the specificity was 99.8% (95% CI, 98.7-100.0%). When considering pregnancies according to whether they were conceived spontaneously or after assisted reproductive technology, there were no significant differences in terms of maternal weight or no-result rate for cfDNA screening between these two groups. CONCLUSIONS: In twin pregnancy without fetal ultrasound abnormality, cfDNA screening for trisomies 21, 18 and 13 had a high success rate and good performance. Therefore, in routine practice, cfDNA analysis could be considered as a first- or second-line screening test. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.

Metabolic tumor burden quantified on [18F]FDG PET/CT improves TNM staging of lung cancer patients.

PURPOSE: The purpose of our study was to test a new staging algorithm, combining clinical TNM staging (cTNM) with whole-body metabolic active tumor volume (MATV-WB), with the goal of improving prognostic ability and stratification power. METHODS: Initial staging [18F]FDG PET/CT of 278 non-small cell lung cancer (NSCLC) patients, performed between January/2011 and April/2016, 74(26.6%) women, 204(73.4%) men; aged 34-88 years (mean ± SD:66 ± 10), was retrospectively evaluated, and MATV-WB was quantified. Each patient's follow-up time was recorded: 0.7-83.6 months (mean ± SD:25.1 ± 20.3). RESULTS: MATV-WB was an independent and statistically-significant predictor of overall survival (p < 0.001). The overall survival predictive ability of MATV-WB (C index: mean ± SD = 0.7071 ± 0.0009) was not worse than cTNM (C index: mean ± SD = 0.7031 ± 0.007) (Z = -0.143, p = 0.773). Estimated mean survival times of 56.3 ± 3.0 (95%CI:50.40-62.23) and 21.7 ± 2.2 months (95%CI:17.34-25.98) (Log-Rank = 77.48, p < 0.001), one-year survival rate of 86.8% and of 52.8%, and five-year survival rate of 53.6% and no survivors, were determined, respectively, for patients with MATV-WB < 49.5 and MATV-WB ≥ 49.5. Patients with MATV-WB ≥ 49.5 had a mortality risk 2.9-5.8 times higher than those with MATV-WB < 49.5 (HR = 4.12, p < 0.001). MATV-WB cutoff points were also determined for each cTNM stage: 23.7(I), 49.5(II), 52(III), 48.8(IV) (p = 0.029, p = 0.227, p = 0.025 and p = 0.001, respectively). At stages I, III and IV there was a statistically-significant difference in the estimated mean overall survival time between groups of patients defined by the cutoff points (p = 0.007, p = 0.004 and p < 0.001, respectively). At stage II (p = 0.365), there was a clinically-significant difference of about 12 months between the groups. In all cTNM stages, patients with MATV-WB ≥ cutoff points had lower survival rates. Combined clinical TNM-PET staging (cTNM-P) was then tested: Stage I < 23.7; Stage I ≥ 23.7; Stage II < 49.5; Stage II ≥ 49.5; Stage III < 52; Stage III ≥ 52; Stage IV < 48.8; Stage IV ≥ 48.8. cTNM-P staging presented a superior overall survival predictive ability (C index = 0.730) compared with conventional cTNM staging (C index = 0.699) (Z = -4.49, p < 0.001). CONCLUSION: cTNM-P staging has superior prognostic value compared with conventional cTNM staging, and allows better stratification of NSCLC patients.

Prospective evaluation of azole resistance in Aspergillus fumigatus clinical isolates in France.

OBJECTIVES: Several studies, especially in Europe, have recently reported the emerging phenomenon of azole resistance in Aspergillus fumigatus, but very few data are available in France. Our study aimed to determine the resistance prevalence in A. fumigatus isolates recovered from clinical samples over a 1-year period in two university hospital centers. METHODS: All A. fumigatus isolates were screened for azole resistance using RPMI agar plates supplemented with itraconazole and voriconazole. Resistance was then confirmed by the EUCAST method. A part of the beta-tubulin gene was amplified for resistant isolates to confirm the A. fumigatus species, and the Cyp51A gene and its promoter were afterward sequenced to detect mutations potentially responsible for this resistance. RESULTS: One hundred sixty-five A. fumigatus isolates were recovered from 134 patients. Three isolates recovered from three patients were found resistant with MICs of >8 mg/l, 4 mg/l, and 1 mg/l for itraconazole, voriconazole, and posaconazole, respectively. The TR34/L98H mutation, previously and largely described in other countries, was detected in the three isolates. CONCLUSION: Our study demonstrated the occurrence of azole resistance among unselected A. fumigatus clinical isolates, with an overall prevalence of 1.8%.

Food web structure in oil sands reclaimed wetlands.

Boreal wetlands play an important role in global carbon balance. However, their ecosystem function is threatened by direct anthropogenic disturbance and climate change. Oil sands surface mining in the boreal regions of Western Canada denudes tracts of land of organic materials, leaves large areas in need of reclamation, and generates considerable quantities of extraction process-affected materials. Knowledge and validation of reclamation techniques that lead to self-sustaining wetlands has lagged behind development of protocols for reclaiming terrestrial systems. It is important to know whether wetlands reclaimed with oil sands process materials can be restored to levels equivalent to their original ecosystem function. We approached this question by assessing carbon flows and food web structure in naturally formed and oil sands-affected wetlands constructed in 1970-2004 in the postmining landscape. We evaluated whether a prescribed reclamation strategy, involving organic matter amendment, accelerated reclaimed wetland development, leading to wetlands that were more similar to their natural marsh counterparts than wetlands that were not supplemented with organic matter. We measured compartment standing stocks for bacterioplankton, microbial biofilm, macrophytes, detritus, and zoobenthos; concentrations of dissolved organic carbon and residual naphthenic acids; and microbial production, gas fluxes, and aquatic-terrestrial exports (i.e., aquatic insect emergence). The total biomass of several biotic compartments differed significantly between oil sands and reference wetlands. Submerged macrophyte biomass, macroinvertebrate trophic diversity, and predator biomass and richness were lower in oil sands-affected wetlands than in reference wetlands. There was insufficient evidence to conclude that wetland age and wetland amendment with peat-mineral mix mitigate effects of oil sands waste materials on the fully aquatic biota. Although high variability was observed within most compartments, our data show that 20-year-old wetlands containing oil sands material have not yet reached the same level of function as their reference counterparts.

Guidelines for the genetic diagnosis of hereditary recurrent fevers.

Hereditary recurrent fevers (HRFs) are a group of monogenic autoinflammatory diseases characterised by recurrent bouts of fever and serosal inflammation that are caused by pathogenic variants in genes important for the regulation of innate immunity. Discovery of the molecular defects responsible for these diseases has initiated genetic diagnostics in many countries around the world, including the Middle East, Europe, USA, Japan and Australia. However, diverse testing methods and reporting practices are employed and there is a clear need for consensus guidelines for HRF genetic testing. Draft guidelines were prepared based on current practice deduced from previous HRF external quality assurance schemes and data from the literature. The draft document was disseminated through the European Molecular Genetics Quality Network for broader consultation and amendment. A workshop was held in Bruges (Belgium) on 18 and 19 September 2011 to ratify the draft and obtain a final consensus document. An agreed set of best practice guidelines was proposed for genetic diagnostic testing of HRFs, for reporting the genetic results and for defining their clinical significance.

Grapevine under deficit irrigation: hints from physiological and molecular data.

BACKGROUND: A large proportion of vineyards are located in regions with seasonal drought (e.g. Mediterranean-type climates) where soil and atmospheric water deficits, together with high temperatures, exert large constraints on yield and quality. The increasing demand for vineyard irrigation requires an improvement in the efficiency of water use. Deficit irrigation has emerged as a potential strategy to allow crops to withstand mild water stress with little or no decreases of yield, and potentially a positive impact on fruit quality. Understanding the physiological and molecular bases of grapevine responses to mild to moderate water deficits is fundamental to optimize deficit irrigation management and identify the most suitable varieties to those conditions. SCOPE: How the whole plant acclimatizes to water scarcity and how short- and long-distance chemical and hydraulic signals intervene are reviewed. Chemical compounds synthesized in drying roots are shown to act as long-distance signals inducing leaf stomatal closure and/or restricting leaf growth. This explains why some plants endure soil drying without significant changes in shoot water status. The control of plant water potential by stomatal aperture via feed-forward mechanisms is associated with 'isohydric' behaviour in contrast to 'anysohydric' behaviour in which lower plant water potentials are attained. This review discusses differences in this respect between grapevines varieties and experimental conditions. Mild water deficits also exert direct and/or indirect (via the light environment around grape clusters) effects on berry development and composition; a higher content of skin-based constituents (e.g. tannins and anthocyanins) has generally being reported. Regulation under water deficit of genes and proteins of the various metabolic pathways responsible for berry composition and therefore wine quality are reviewed.

HPV infection as a risk factor for atherosclerosis: A connecting hypothesis.

Atheromatous plaques occurring in large arteries are common and life-threatening lesions. Multiple factors are involved in the pathogenesis of atheromatous plaques, such as hyperlipidaemia and hypercholesterolaemia, high blood pressure and chronic systemic inflammation. Recent findings have suggested that infection with high-risk human papillomavirus (HPV) may increase the risk of developing atheromatous plaques. However, HPV is considered a tissue-specific virus with a strong tropism towards squamous epithelial cells, and the mechanisms whereby it may promote the development of atheromas remain unclear. Here, we propose a connecting hypothesis to explain the possible causative role of HPV on atheroma development. We hypothesize that HPV infection may promote atheroma formation in infected patients by enhancing systemic inflammation or by directly targeting blood vessels via nucleic acids carried by extracellular vesicles such as exosomes. The pro-inflammatory effects of HPV and the release of extracellular vesicles by HPV-transformed cells are well documented in scientific literature. Possible experimental approaches to test this hypothesis are also discussed, especially experiments employing transgenic mice bearing HPV16 transgenes. If correct, this hypothesis would have major implications for the prevention of cardiovascular diseases, especially due to the preventable nature of HPV infection through vaccination.

Diagnosis of invasive aspergillosis using bronchoalveolar lavage in haematology patients: influence of bronchoalveolar lavage human DNA content on real-time PCR performance.

In order to improve invasive pulmonary aspergillosis (IPA) diagnosis, a real-time polymerase chain reaction (PCR) assay detecting Aspergillus spp. was developed. Its detection limit reached 2-20 conidia. The retrospective evaluation on 64 bronchoalveolar lavage (BAL) fluids from 57 patients at risk for IPA, including 20 probable and five proven IPA patients, revealed a 88% or 38% sensitivity in direct examination (DE)/culture-positive or culture-negative BAL, respectively, whereas galactomannan (GM) sensitivity reached 88% or 58%, respectively. Influence on the Aspergillus-PCR yield of BAL fluid volume, cellular count and DNA content (evaluated by human beta-globin quantification) was assessed. Significantly higher beta-globin levels were detected in Aspergillus PCR-positive (median 5,112 pg/microl) than negative (median 1,332 pg/microl) BAL fluids, suggesting that the beta-globin level could reflect BAL yields and DNA extraction. Using beta-globin for the interpretation of fungal PCR could improve the negative predictive value of this test.

Schistosoma haematobium and Schistosomiasis mansoni: production of an estradiol-related compound detected by ELISA.

Estradiol is a steroid hormone secreted principally by the ovarian follicles in vertebrate animals. We have identified the production of an estradiol-related molecule in the trematodes Schistosoma haematobium and Schistosomiasis mansoni. We show in this work that this molecule related to estradiol is present in schistosome worm extracts. The detection method ELISA specific for estradiol, revealed the expression of this estradiol-related molecule in schistosome worm extracts, but not in Fasciola hepatica worm extracts. Our results demonstrate for the first time the production of an estradiol-related compound by a human parasite of the genus Schistosoma.

Task-Based Automatic Evaluation of People with Intellectual Disabilities Performed on a Robotic Table Soccer.

This paper is concerned with the automatic evaluation of selected tasks performed by people with intellectual Disabilities. According to the International Classification of Functioning, Disability and Health (ICF) system, subjects must be divided into two groups: group with no difficulty (N) and group with difficulty (D) being this classification based on performances obtained in a conventional table (CT) soccer. Three tasks, with different levels of difficulty, were proposed for performance evaluation. Experimental results were obtained on the basis of the task execution in both a CT and a robotics table (RT) soccer. All participants were able to perform tasks with the joystick on the RT soccer and the automatic evaluation system identified differences in reaction times with and without red color flag in the participants, on RT soccer. One of the tasks was completely performed by all the participants by using the RT soccer.

Two unusual occurrences of trichomoniasis: rapid species identification by PCR.

PCR analysis in two unusual occurrences of trichomoniasis, trichomonal empyema due to Trichomonas tenax and Trichomonas vaginalis in an infant urine sample, allowed us to obtain rapid and accurate trichomonad species identification. The weak sensitivity of wet preparations and the low viability of the flagellates can be remedied by the PCR method.

Factor VIII genotype and inhibitor development in patients with haemophilia A: highest risk in patients with splice site mutations.

The appearance of inhibitory antibodies against factor VIII (FVIII) is the most severe and costly complication of replacement therapy in patients with haemophilia A (HA). To determine the relationship between FVIII genotype and inhibitor development, baseline FVIII activity, genotype and inhibitor development were reviewed in 1104 patients with HA. In patients with severe HA, splicing errors present the highest frequency of inhibitors, ahead of inversion of intron 1 and of intron 22, nonsense mutations and large deletions. The lowest inhibitor frequency in severe HA is found in patients with missense mutations and small deletions/insertions. Subanalyses indicate that nonsense mutations and small deletions/insertions leading to a frameshift in the light chain are associated with a significant higher risk of inhibitor formation than similar mutations occurring in the heavy chain (27% vs. 14%). These mutation types also have a higher frequency of inhibitors when occurring in exons 23-26, where a second FVIII transcript originates, compared with similar mutations in exons 1-22 (28% vs. 17%). These results suggest that complete absence of FVIII because of null mutations, including splice site mutations, or the absence of a second transcript result in an increased risk of inhibitor development.