A 3-year prognostic score for adults with cystic fibrosis.

BACKGROUND: Therapeutic progress in patients with cystic fibrosis (CF) has resulted in improved prognosis over the past decades. We aim to reevaluate prognostic factors of CF and provide a prognostic score to predict the risk of death or lung transplantation (LT) within a 3-year period in adult patients. METHODS: We developed a logistic model using data from the French CF Registry and combined the coefficients into a prognostic score. The discriminative abilities of the model and the prognostic score were assessed by c-statistic. The prognostic score was validated using a 10-fold cross-validation. RESULTS: The risk of death or LT within 3years was related to eight characteristics. The development and the validation provided excellent results for the prognostic score; the c-statistic was 0.91 and 0.90 respectively. CONCLUSION: The score developed to predict 3-year death or LT in adults with CF might be useful for clinicians to identify patients requiring specialized evaluation for LT.

Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT.

Acute GvHD (aGvHD) is the main complication of hematopoietic SCT (HSCT) during the treatment of hematological disorders. We carried out the first longitudinal study to follow the gut microbiota trajectory, from both the phylogenetic and functional points of view, in pediatric patients undergoing HSCT. Gut microbiota trajectories and short-chain fatty acid production profiles were followed starting from before HSCT and through the 3-4 months after transplant in children developing and not developing aGvHD. According to our findings, HSCT procedures temporarily cause a structural and functional disruption of the gut microbial ecosystem, describing a trajectory of recovery during the following 100 days. The onset of aGvHD is associated with specific gut microbiota signatures both along the course of gut microbiota reconstruction immediately after transplant and, most interestingly, prior to HSCT. Indeed, in pre-HSCT samples, non-aGvHD patients showed higher abundances of propionate-producing Bacteroidetes, highly adaptable microbiome mutualists that showed to persist during the HSCT-induced ecosystem disruption. Our data indicate that structure and temporal dynamics of the gut microbial ecosystem can be a relevant factor for the success of HSCT and opens the perspective to the manipulation of the pre-HSCT gut microbiota configuration to favor mutualistic persisters with immunomodulatory properties in the gut.

Bionomics of temperate and tropical Culicoides midges: knowledge gaps and consequences for transmission of Culicoides-borne viruses.

Culicoides midges are abundant hematophagous flies that vector arboviruses of veterinary and medical importance. Dramatic changes in the epidemiology of Culicoides-borne arboviruses have occurred since 1998, including the emergence of exotic viruses in northern temperate regions, increases in global disease incidence, and enhanced virus diversity in tropical zones. Drivers may include changes in climate, land use, trade, and animal husbandry. New Culicoides species and new wild reservoir hosts have been implicated in transmission, highlighting the dynamic nature of pathogen-vector-host interactions. Focusing on potential vector species worldwide and key elements of vectorial capacity, we review the sensitivity of Culicoides life cycles to abiotic and biotic factors. We consider implications for designing control measures and understanding impacts of environmental change in different ecological contexts. Critical geographical, biological, and taxonomic knowledge gaps are prioritized. Recent developments in genomics and mathematical modeling may enhance ecological understanding of these complex arbovirus systems.

Culicoides Latreille (Diptera: Ceratopogonidae) taxonomy: current challenges and future directions.

Culicoides Latreille biting midges (Diptera: Ceratopogonidae) cause a significant biting nuisance to humans, livestock and equines, and are the biological vectors of a range of internationally important pathogens of both veterinary and medical importance. Despite their economic significance, the delimitation and identification of species and evolutionary relationships between species within this genus remains at best problematic. To date no phylogenetic study has attempted to validate the subgeneric classification of the genus and the monophyly of many of the subgenera remains doubtful. Many informal species groupings are also known to exist but few are adequately described, further complicating accurate identification. Recent contributions to Culicoides taxonomy at the species level have revealed a high correlation between morphological and molecular analyses although molecular analyses are revealing the existence of cryptic species. This review considers the methods for studying the systematics of Culicoides using both morphological and genetic techniques, with a view to understanding the factors limiting our current understanding of Culicoides biology and hence arbovirus epidemiology. In addition, we examine the global status of Culicoides identification, highlighting areas that are poorly addressed, including the potential implementation of emerging technologies.

Draft Genome Sequence of the Host-Restricted Salmonella enterica Serovar Abortusovis Strain SS44.

Salmonella enterica serovar Abortusovis is a pathogen strictly adapted to ovines, in which it causes abortion. To enhance our understanding of this pathogen, we assembled the first draft sequence of an S. Abortusovis genome (strain SS44). The obtained genomic data might facilitate the study of S. enterica evolution and host adaptation.

The piezoresistive effect in graphene-based polymeric composites.

The strain-dependent electrical resistance of polyvinyl ester-based composites filled with different weight fractions of graphene nanoplatelets (GNPs) has been experimentally investigated. The GNP synthesis and nanocomposite fabrication process have been optimized in order to obtain highly homogeneous filler dispersion and outstanding electrical properties. The produced nanocomposites showed a low percolation threshold of 0.226 wt% and electrical conductivity of nearly 10 S m(-1) at only 4 wt% of GNPs. The piezoresistive response of thin nanocomposite laminae has been assessed by measuring the variation of the electrical resistance as a function of the flexural strain in three-point bending tests under both quasi-static monotonic and dynamic cyclic loading conditions. The obtained results showed higher strain sensitivity than traditional metal foil strain gauges or recently investigated carbon-based nanocomposite films.

Expression profiling of genes involved in the formation of aroma in two peach genotypes.

The expression profile of flavour-related genes during ripening was investigated in two peach genotypes, Bolero and OroA, which have been selected for their contrasting aroma/ripening behaviour. A new peach microarray containing 4776 oligonucleotide probes corresponding to a set of ESTs specifically enriched in secondary metabolism (µPEACH2.0) was designed to investigate transcriptome changes during three fruit ripening stages, revealing 1807 transcripts differentially expressed within and between the two genotypes. Differences in the expression of genes involved in the biosynthesis of aroma compounds were detected during the ripening process within and between the two genotypes. In particular, a subset of 12 transcripts involved in metabolism of esters, norisoprenoids, phenylpropanoids and lactones, varied in expression during ripening and between Bolero and OroA.

Non-classic cystic fibrosis associated with D1152H CFTR mutation.

BACKGROUND: Limited knowledge exists on phenotypes associated with the D1152H cystic fibrosis transmembrane conductance regulator (CFTR) mutation. METHODS: Subjects with a D1152H allele in trans with another CFTR mutation were identified using the French Cystic Fibrosis Registry. Phenotypic characteristics were compared with those of pancreatic insufficient (PI) and pancreatic sufficient (PS) cystic fibrosis (CF) subjects in the Registry (CF cohort). RESULTS: Forty-two subjects with D1152H alleles were identified. Features leading to diagnosis included chronic sinopulmonary disease (n = 25), congenital absence of the vas deferens (n = 11), systematic neonatal screening (n = 4), and genetic counseling (n = 2). Median age at diagnosis was 33 [interquartile range (IQR, 24-41)] years in D1152H subjects. Median sweat chloride concentrations were 43.5 (39-63) mmol/l in D1152H subjects and were markedly lower than in PI and PS CF subjects (p < 0.05). Bronchiectasis was present in 67% of D1152H subjects, but Pseudomonas aeruginosa colonization and pancreatic insufficiency were present in <30% of subjects. Estimated rates of decline in forced expiratory volume in 1 s (FEV(1)) were lower in D1152H subjects vs PI CF subjects (p < 0.05). None of the D1152H subjects identified since 1999 had died or required lung transplantation. CONCLUSIONS: When present in trans with a CF-causing mutation, D1152H causes significant pulmonary disease, but all subjects had prolonged survival.

The very low penetrance of cystic fibrosis for the R117H mutation: a reappraisal for genetic counselling and newborn screening.

BACKGROUND: Cystic fibrosis (CF) is caused by compound heterozygosity or homozygosity of CF transmembrane conductance regulator gene (CFTR) mutations. Phenotypic variability associated with certain mutations makes genetic counselling difficult, notably for R117H, whose disease phenotype varies from asymptomatic to classical CF. The high frequency of R117H observed in CF newborn screening has also introduced diagnostic dilemmas. The aim of this study was to evaluate the disease penetrance for R117H in order to improve clinical practice. METHODS: The phenotypes in all individuals identified in France as compound heterozygous for R117H and F508del, the most frequent CF mutation, were described. The allelic prevalences of R117H (p(R117H)), on either intron 8 T5 or T7 background, and F508del (p(F508del)) were determined in the French population, to permit an evaluation of the penetrance of CF for the [R117H]+[F508del] genotype. RESULTS: Clinical details were documented for 184 [R117H]+[F508del] individuals, including 72 newborns. The disease phenotype was predominantly mild; one child had classical CF, and three adults' severe pulmonary symptoms. In 5245 healthy adults, p(F508del) was 1.06%, p(R117H;T7) 0.27% and p(R117H;T5)<0.01%. The theoretical number of [R117H;T7]+[F508del] individuals in the French population was estimated at 3650, whereas only 112 were known with CF related symptoms (3.1%). The penetrance of classical CF for [R117H;T7]+[F508del] was estimated at 0.03% and that of severe CF in adulthood at 0.06%. CONCLUSIONS: These results suggest that R117H should be withdrawn from CF mutation panels used for screening programmes. The real impact of so-called disease mutations should be assessed before including them in newborn or preconceptional carrier screening programmes.

Disposable plastic microreactors for genomic analyses.

We show the design, development and assessment of disposable, biocompatible, fully plastic microreactors, which are demonstrated to be highly efficient for genomic analyses, such as amplification of DNA, quantitative analyses in real time, multiplex PCR (both in terms of efficiency and selectivity), as compared to conventional laboratory equipment for PCR. The plastic microreactors can easily be coupled to reusable hardware, enabling heating/cooling processes and, in the case of qPCR applications, the real-time detection of the signal from a suitable fluorescent reporter present in the reaction mixture during the analysis. The low cost production of these polymeric microreactors, along with their applicability to a wide range of biochemical targets, may open new perspectives towards practical applications of biochips for point of care diagnostics.

A comparison of trapping methods for Tabanidae (Diptera) in North Queensland, Australia.

The ability to monitor the abundance and diversity of tabanid flies over wide areas requires effective and low-cost surveillance methods. Such monitoring activities help to quantify the risk of transmission of pathogens by tabanids. Here we examine the effectiveness and practicality of two types of trap (canopy traps and Nzi traps) and two types of attractant (octenol and carbon dioxide) for monitoring tabanid flies in tropical Australia. The Nzi trap consistently caught more tabanids and more species of tabanids than the canopy trap. It was also more robust and therefore required less maintenance in remote locations. The use of attractants substantially increased capture rates, both of individuals and species, and traps using both attractants were consistently the most effective. However, in remote locations, where it is not possible to check traps frequently, the use of attractants may not be feasible. When attractants were not used, the canopy trap caught very few tabanids, but the Nzi trap remained effective enough to be useful as a monitoring device. In addition, the number of tabanid species caught by the Nzi traps remained high, and included those that were most abundant. We therefore conclude that, in this region, Nzi traps are preferable for tabanid monitoring and that attractants greatly improve their effectiveness. However, for longterm monitoring, especially in remote locations, Nzi traps without attractants are a satisfactory option.

Algorithm for automatic genotype calling of single nucleotide polymorphisms using the full course of TaqMan real-time data.

Single nucleotide polymorphisms (SNPs) are often determined using TaqMan real-time PCR assays (Applied Biosystems) and commercial software that assigns genotypes based on reporter probe signals at the end of amplification. Limitations to the large-scale application of this approach include the need for positive controls or operator intervention to set signal thresholds when one allele is rare. In the interest of optimizing real-time PCR genotyping, we developed an algorithm for automatic genotype calling based on the full course of real-time PCR data. Best cycle genotyping algorithm (BCGA), written in the open source language R, is based on the assumptions that classification depends on the time (cycle) of amplification and that it is possible to identify a best discriminating cycle for each SNP assay. The algorithm is unique in that it classifies samples according to the behavior of blanks (no DNA samples), which cluster with heterozygous samples. This method of classification eliminates the need for positive controls and permits accurate genotyping even in the absence of a genotype class, for example when one allele is rare. Here, we describe the algorithm and test its validity, compared to the standard end-point method and to DNA sequencing.

Multiplex polymerase chain reaction and ligation detection reaction/universal array technology for the traceability of genetically modified organisms in foods.

A multiplex polymerase chain reaction (PCR) system was developed for the simultaneous detection of target sequences in genetically modified soybean (Roundup Ready) and maize (MON810, Bt176, Bt11, and GA21). Primer pairs were designed to amplify the junction regions of the transgenic constructs analyzed and the endogenous genes of soybean (lectin) and maize (zein) were included as internal control targets to assess the efficiency of all reactions. This multiplex PCR has constituted the basis for an efficient platform for genetically modified organism traceability based on microarray technology. In particular, the ligation detection reaction combined to a universal array approach, using the multiplex PCR as target, was applied. High specificity and sensitivity were obtained.

Phenotype and genotype of French cystic fibrosis patients with long survival and follow-up.

Background: The aim of this study was to assess the clinical features and the genotype characteristics of French patients diagnosed with cystic fibrosis (CF) before their fifth year and who were still alive after 30 years. It is the first descriptive study of 114 CF patients with long survival and follow-up. We compared this subgroup of French CF patients with the overall French CF population and with French adult (> 18 years) CF patients regardless of their age at diagnosis. Methods: Data were obtained from the French CF registry. Results: The 67 men and 47 women studied were 30-59 years old. Some 56% of the patients had DeltaF508 homozygous genotype, 90% had a pancreatic insufficiency, and 81% were colonized with Pseudomonas aeruginosa. The mean body mass index (BMI) was 19.5 for both female and male patients. Mean forced expiratory volume in 1 s was 46% (S.D. 29.2) of the predicted value for men and 53% (S.D. 20.6) for women. Eleven patients underwent a lung transplantation. Conclusions: The data on the patients with long survival and long follow-up were very similar to the data of the overall CF adult population in terms of clinical status. Therefore, criteria such as DeltaF508 homozygous genotype, pancreatic insufficiency, and P. aeruginosa colonization are not sufficient to serve as prognostic criteria for life expectancy in CF patients.

Protection of cattle from Culicoides spp. in Australia by shelter and chemical treatments.

Trials were conducted in three regions of Australia to investigate the potential for improvised shelters and chemical treatments to reduce feeding by Culicoides on cattle and thereby minimise the risk of bluetongue transmission during transport of cattle to ports. Various designs and combinations of roofs and walls were placed around penned cattle. Chemical treatments were applied to other penned cattle. Culicoides were collected from the cattle by vacuum samplers or by light traps in the pens. Roofs alone did not consistently reduce the numbers of Culicoides brevitarsis or C. fulvus and increased the numbers of C. actoni collected. Walls alone reduced the numbers of C. wadai but not C. brevitarsis. Roofs and walls in combination reduced the numbers of C. brevitarsis and C. wadai. The chemical treatments 'Flyaway' (a blend of repellents) and fenvalerate reduced the numbers of C. brevitarsis and C. wadai up to 52 h post treatment.

Temporal activity of biting midges (Diptera: Ceratopogonidae) on cattle near Darwin, Northern Territory, Australia.

The activity of nine species of biting midges aspirated from cattle was recorded in the late afternoon, evening and early morning at a site near Darwin, Northern Territory, between March and June in 1999 and 2001. There were no significant differences between the temporal activity patterns for nulliparous and parous females of any species. Nulliparous females dominated collections of all species except Culicoides marksi. C. actoni and Forcipomyia (Lasiohelea) sp., were mostly active during daylight hours while C. peregrinus, C. bundyensis and C. brevipalpis, were nocturnal. Differences in the peak activity of C. brevitarsis were noted between years and occurred slightly earlier than that observed at other sites. C. fulvus, C. marksi and C. oxystoma were generally crepuscular but differed in the length and peak period of activity. C. actoni was four times more active in the evening than in the morning while C. marksi and C. peregrinus, were respectively 2.6 and 3.4 times more active in the morning than in the evening. Numbers of the other six species were not significantly different in the evening and morning. All nine species were collected at least once from cattle shortly after dawn.

Collection of wind-borne haematophagous insects in the Torres Strait, Australia.

Circumstantial evidence has implicated wind-borne mosquitoes (Diptera: Culicidae) in the introduction of Japanese encephalitis (JE) virus into Australia from the New Guinea mainland. A study was initiated on Saibai Island in the northern Torres Strait, during January and February 2000, to identify the potential source of insects collected in aerial (kytoon) and surface-level traps. Wind speed and direction were recorded to determine wind profiles during insect sampling. Northerly winds capable of carrying insects from New Guinea to Saibai Island were only present on three out of 18 nights sampled. Only three male mosquitoes, comprising two Verrallina funerea (Theobald) and one Ochlerotatus vigilax (Skuse), were collected in aerial samples, and were most likely of local origin. Culicoides midges were also collected in aerial nets and included gravid/parous C. bundyensis Lee and Reye, and one parous C. histrio Johannsen. Highest densities of arthropods (up to 1562/million m3) were on 30 January 2000 when NW winds, sustained for six hours, probably introduced midges from the New Guinea mainland. Adult mosquitoes (including three female Ve. funerea and a single female Ficalbia) and Culicoides (including two gravid C. bundyensis and one parous C. cordiger Macfie) were also collected in 2 m high mast nets during northerly surface winds. Although the results do not provide evidence that wind-blown mosquitoes introduced JE from New Guinea into Australia, they do not preclude that strong N winds associated with low pressure systems SW of the Torres Strait could have done so. However, results suggest that Culicoides were more likely than mosquitoes to reach high altitude and travel long distances during the light N winds experienced during the study.

HCV and cancer: a case-control study in a high-endemic area.

BACKGROUND/AIMS: HCV is a RNA virus that cannot be integrated with the host genome; it can, however, exert its oncogenic potential indirectly by contributing to the modulatory effects of the host immune system, probably through a capacity to elude the immune system. We have carried out a case-controlled study on the different oncological pathologies which have, to date, been shown to have a relationship with HCV. METHODS: We screened 495 patients with different types of cancer: 114 cases of liver cancer, 41 of multiple myeloma, 111 non-Hodgkin's lymphomas, 130 thyroid cancers, 63 cases of Hodgkin's disease. The controls were 226 patients with no history of cancer. The relationship between each cancer and HCV infection was assessed by means of odds ratios (OR) and corresponding 95% confidence intervals. RESULTS: Risks were greater for liver cancer (OR=32.9 95% CI 16.5-65.4, p<0.0001), multiple myeloma (OR=4.5 95% CI 1.9-10.7, p=0.0004) and B-cell non-Hodgkin's lymphoma (OR=3.7 95% CI 1.9-7.4, p=0.0001). For Hodgkin's disease there was no significant association (p=0.3). An association between HCV and thyroid cancer was noted (OR=2.8 95% CI 1.2-6.3, p=0.01). CONCLUSION: Our study is particularly important for public health since the high prevalence of HCV in the South of Italy gives reason to expect increases in not only liver cancer, but also tumors associated with the immune system and thyroid cancer in years to come.

An assessment of delays in obtaining definitive breast cancer treatment in Southern Italy.

Female population is medically underserved in Southern Italy (in comparison with other Italian regions). In a recent systematic review of published studies, delays of 3-6 months between symptom onset and treatment have been clearly associated with lower survival rates for breast cancer patients. The aim of this study was to examine breast cancer delays in medically underserved patients in Southern Italy, in order to recognize their determinating factors so as to provide women with a better opportunity for survival. The variables examined were age, education, symptom status at first presentation: symptomatic and asymptomatic, date of first symptom presentation, date of first consultation with a health provider, consulted provider, tumor size and nodal status, according to the pTNM system. Time intervals were categorized into: < 1 month, 1-3 months and > 3 months for patient and medical delay; 1-3 months, 3-6 months, > 6 months for overall delay. Patient delay was associated with education: a higher risk was found for women with < or = 5 years school attendance (OR = 3.3, 95%, CI 2.0-5.6). Medical delay was seen to be associated with the professional figure: significant differences were found between senologists (oncologist exclusively dedicated to breast cancer) and other specialists (OR 3.5, 95%, CI 1.5-8.4). Age and symptomatic presentation were found to be high risk factors. Concerning tumor size in overall delay in cases > 2 cm had OR values were of 2.4 (95%, CI 1.5-3.7). In conclusion our study suggests that diagnostic delay is associated with medically underserved status and can be reduced by educating younger and less educated women, as suggested in other studies and by providing training programs for members in the medical profession.