FLIM-FRET Measurements of Protein-Protein Interactions in Live Bacteria

Protein-protein interactions (PPIs) control various key processes in cells. Fluorescence lifetime imaging microscopy (FLIM) combined with Förster resonance energy transfer (FRET) provide accurate information about PPIs in live cells. FLIM-FRET relies on measuring the fluorescence lifetime decay of a FRET donor at each pixel of the FLIM image, providing quantitative and accurate information about PPIs and their spatial cellular organizations. We propose here a detailed protocol for FLIM-FRET measurements that we applied to monitor PPIs in live Pseudomonas aeruginosa in the particular case of two interacting proteins expressed with highly different copy numbers to demonstrate the quality and robustness of the technique at revealing critical features of PPIs. This protocol describes in detail all the necessary steps for PPI characterization - starting from bacterial mutant constructions up to the final analysis using recently developed tools providing advanced visualization possibilities for a straightforward interpretation of complex FLIM-FRET data.

[Medical biostatistics with GMRC Shiny Stats - learning by doing]

Biostatistics are omnipresent in the scientific and medical literature and are an essential skill for any health student. We have developed a practical training tool - GMRC Shiny stats - an interactive application specifically dedicated to medical data statistical analysis. The application has been designed to provide an analysis workflow corresponding to the usual progression of an experienced statistician during data analysis. The most common statistical analyses can be performed (descriptive statistics, inferences according to frequentist methods, survival analyses, correlation, agreement measurements, etc.). GMRC Shiny stats is intuitive and user-friendly and assists students in choosing the most appropriate statistical tests. With all these functionalities, students can learn statistical analysis by doing. Getting involved in the statistical analysis and processing of their own data is likely to improve their biostatistics skills.

Machine learning application for incident prostate adenocarcinomas automatic registration in a French regional cancer registry

Cancer registries are collections of curated data about malignant tumor diseases. The amount of data processed by cancer registries increases every year, making manual registration more and more tedious.

OBJECTIVE

We sought to develop an automatic analysis pipeline that would be able to identify and preprocess registry input for incident prostate adenocarcinomas in a French regional cancer registry.

METHODS

Notifications from different sources submitted to the Bas-Rhin cancer registry were used here: pathology data and, ICD 10 diagnosis codes from hospital discharge data and healthcare insurance data. We trained a Support Vector Machine model (machine learning) to predict whether patient's data must be considered or not as a prostate adenocarcinoma incident case that should therefore be registered. The final registration of all identified cases was manually confirmed by a specialized technician. Text mining tools (regular expressions) were used to extract clinical and biological data from non-structured pathology reports.

RESULTS

We performed two successive analyses. First, we used 982 cases manually labeled by registrars from the 2014 dataset to predict the registration of 785 cases submitted in 2015. Then, we repeated the procedure using the 2089 cases labeled by registrars from the 2014 and 2015 datasets to predict the registration of 926 cases submitted in the 2016 data. The algorithm identified 663 cases of prostate adenocarcinoma in 2015, and 610 in 2016. From these findings, 663 and 531 cases were respectively added to the registry; and 641 and 512 cases were confirmed by the specialized technician. This registration process has achieved a precision level above 96 %. The algorithm obtained an overall precision of 99 % (99.5 % in 2015 and 98.5 % in 2016) and a recall of 97 % (97.8 % in 2015 and 96.9 % in 2016). When the information was found in pathology report, text mining was more than 90 % accuracy for major indicators: PSA test, Gleason score, and incidence date). For both PSA and tumor side, information was not detected in the majority of cases."

CONCLUSION

Machine learning was able to identify new cases of prostate cancer, and text mining was able to prefill the data about incident cases. Machine-learning-based automation of the registration process could reduce delays in data production and allow investigators to devote more time to complex tasks and analysis.

An overview of siderophore biosynthesis among fluorescent Pseudomonads and new insights into their complex cellular organization

Siderophores are iron-chelating molecules produced by bacteria to access iron, a key nutrient. These compounds have highly diverse chemical structures, with various chelating groups. They are released by bacteria into their environment to scavenge iron and bring it back into the cells. The biosynthesis of siderophores requires complex enzymatic processes and expression of the enzymes involved is very finely regulated by iron availability and diverse transcriptional regulators. Recent data have also highlighted the organization of the enzymes involved in siderophore biosynthesis into siderosomes, multi-enzymatic complexes involved in siderophore synthesis. An understanding of siderophore biosynthesis is of great importance, as these compounds have many potential biotechnological applications because of their metal-chelating properties and their key role in bacterial growth and virulence. This review focuses on the biosynthesis of siderophores produced by fluorescent Pseudomonads, bacteria capable of colonizing a large variety of ecological niches. They are characterized by the production of chromopeptide siderophores, called pyoverdines, which give the typical green colour characteristic of fluorescent pseudomonad cultures. Secondary siderophores are also produced by these strains and can have highly diverse structures (such as pyochelins, pseudomonine, yersiniabactin, corrugatin, achromobactin and quinolobactin).

Exploring protein-protein interactions with large differences in protein expression levels using FLIM-FRET

Many molecular processes within a cell are carried out by molecular machines built from a large number of proteins organized by their protein-protein interactions (PPIs). Exploring PPIs in their cellular context is critical to better understand the proteins functions. Förster resonance energy transfer measured by fluorescence lifetime imaging (FLIM-FRET) enables to monitor PPIs and to map their spatial organization in a living cell with high spatial and temporal specificity. But both the accurate measurement and the interpretation of multi-exponential FLIM-FRET data associated to mixtures of interacting and non-interacting proteins are difficult. Here we show that a simple diagram plot can find interesting visualization properties by clustering pixels with similar decay signatures. FLIM diagram plot can be used to provide valuable information about stoichiometry and binding mode in PPIs, even in the presence of large differences in protein expression levels of the different interacting partners. The proposed FLIM diagram plot is a useful visual approach for a more straightforward interpretation of complex lifetime data. This approach was applied for revealing critical features of PPIs in live Pseudomonas aeruginosa.

Phenotyping Occupational Asthma Caused by Acrylates in a Multicenter Cohort Study

BACKGROUND

While acrylates are well-known skin sensitizers, they are not classified as respiratory sensitizers although several cases of acrylate-induced occupational asthma (OA) have been reported.

OBJECTIVE

To evaluate the characteristics of acrylate-induced OA in a large series of cases and compare those with OA induced by other low-molecular-weight (LMW) agents.

METHODS

Jobs and exposures, clinical and functional characteristics, and markers of airway inflammation were analyzed in an international, multicenter, retrospective cohort of subjects with OA ascertained by a positive inhalation challenge to acrylates (n = 55) or other LMW agents (n = 418) including isocyanates (n = 125).

RESULTS

Acrylate-containing glues were the most prevalent products, and industrial manufacturing, dental work, and beauty care were typical occupations causing OA. Work-related rhinitis was more common in acrylate-than in isocyanate-induced asthma (P < .001). The increase in postchallenge fractional exhaled nitric oxide was significantly greater in acrylate-induced OA (26.0; 8.2 to 38.0 parts per billion [ppb]) than in OA induced by other LMW agents (3.0; -1.0 to 10.0 ppb; P < .001) or isocyanates (5.0; 2.0 to 16.0 ppb; P = .010). Multivariable models confirmed that OA induced by acrylates was significantly and independently associated with a postchallenge increase in fractional exhaled nitric oxide (≥17.5 ppb).

CONCLUSIONS

Acrylate-induced OA shows specific characteristics, concomitant work-related rhinitis, and exposure-related increases in fractional exhaled nitric oxide, suggesting that acrylates may induce asthma through different immunologic mechanisms compared with mechanisms through which other LMW agents may induce asthma. Our findings reinforce the need for a reevaluation of the hazard classification of acrylates, and further investigation of the pathophysiological mechanisms underlying their respiratory sensitizing potential.

Cluster analysis of indoor environmental factors associated with symptoms of mite allergy

BACKGROUND

The clinical efficacy of controlling environmental allergens as a component of allergic asthma treatment remains controversial. Multifaceted allergen reductions appeared to be the most efficient methods. However, they require home visits with indoor technicians.

OBJECTIVE

To examine the characteristics of indoor environments that might be related to symptoms of children and adult patients with mite allergic rhinitis and/or asthma.

METHODS

We included 315 patients allergic to house dust mites with rhinitis and/or asthma who had been visited at home by 2 medical indoor environment counselors (MIECs) from the Strasbourg University Hospital between January 2007 and June 2015. In a cluster analysis, we analyzed 42 characteristics of respiratory symptoms, dwelling characteristics, and indoor pollutants in this population.

RESULTS

Three clusters were defined among the patients. Cluster 1 included 55 patients, all with rhinitis, 32% with asthma, and all living in an urban area. Clusters 2 and 3 included 86 and 174 patients, respectively. The important factors in these 2 clusters were asthma incidence and exposure to different indoor pollutants, such as indoor perfumes, cleaning products, and tobacco smoke.

CONCLUSION

Our results underlined the variability of indoor environments and the importance of MIEC home visits to investigate individual patient environments and propose an appropriate avoidance management plan. Our results showed that sensitization to mite and exposure to indoor chemical pollutants were associated with severe asthma.

Severe Occupational Asthma: Insights From a Multicenter European Cohort

BACKGROUND

Although sensitizer-induced occupational asthma (OA) accounts for an appreciable fraction of adult asthma, the severity of OA has received little attention.

OBJECTIVE

The aim of this study was to characterize the burden and determinants of severe OA in a large multicenter cohort of subjects with OA.

METHODS

This retrospective study included 997 subjects with OA ascertained by a positive specific inhalation challenge completed in 20 tertiary centers in 11 European countries during the period 2006 to 2015. Severe asthma was defined by a high level of treatment and any 1 of the following criteria: (1) daily need for a reliever medication, (2) 2 or more severe exacerbations in the previous year, or (3) airflow obstruction.

RESULTS

Overall, 162 (16.2%; 95% CI, 14.0%-18.7%) subjects were classified as having severe OA. Multivariable logistic regression analysis revealed that severe OA was associated with persistent (vs reduced) exposure to the causal agent at work (odds ratio [OR], 2.78; 95% CI, 1.50-5.60); a longer duration of the disease (OR, 1.04; 95% CI, 1.00-1.07); a low level of education (OR, 2.69; 95% CI, 1.73-4.18); childhood asthma (OR, 2.92; 95% CI, 1.13-7.36); and sputum production (OR, 2.86; 95% CI, 1.87-4.38). In subjects removed from exposure, severe OA was associated only with sputum production (OR, 3.68; 95% CI, 1.87-7.40); a low education level (OR, 3.41; 95% CI, 1.72-6.80); and obesity (OR, 1.98; 95% CI, 0.97-3.97).

CONCLUSIONS

This study indicates that a substantial proportion of subjects with OA experience severe asthma and identifies potentially modifiable risk factors for severe OA that should be targeted to reduce the adverse impacts of the disease.

Are high- and low-molecular-weight sensitizing agents associated with different clinical phenotypes of occupational asthma?

BACKGROUND

High-molecular-weight (HMW) proteins and low-molecular-weight (LMW) chemicals can cause occupational asthma (OA) although few studies have thoroughly compared the clinical, physiological, and inflammatory patterns associated with these different types of agents. The aim of this study was to determine whether OA induced by HMW and LMW agents shows distinct phenotypic profiles.

METHODS

Clinical and functional characteristics, and markers of airway inflammation were analyzed in an international, multicenter, retrospective cohort of subjects with OA ascertained by a positive inhalation challenge response to HMW (n = 544) and LMW (n = 635) agents.

RESULTS

Multivariate logistic regression analysis showed significant associations between OA caused by HMW agents and work-related rhinitis (OR [95% CI]: 4.79 [3.28-7.12]), conjunctivitis (2.13 [1.52-2.98]), atopy (1.49 [1.09-2.05]), and early asthmatic reactions (2.86 [1.98-4.16]). By contrast, OA due to LMW agents was associated with chest tightness at work (2.22 [1.59-3.03]), daily sputum (1.69 [1.19-2.38]), and late asthmatic reactions (1.52 [1.09-2.08]). Furthermore, OA caused by HMW agents showed a higher risk of airflow limitation (1.76 [1.07-2.91]), whereas OA due to LMW agents exhibited a higher risk of severe exacerbations (1.32 [1.01-1.69]). There were no differences between the two types of agents in the baseline sputum inflammatory profiles, but OA caused by HMW agents showed higher baseline blood eosinophilia and a greater postchallenge increase in fractional nitric oxide.

CONCLUSION

This large cohort study describes distinct phenotypic profiles in OA caused by HMW and LMW agents. There is a need to further explore differences in underlying pathophysiological pathways and outcome after environmental interventions.

Finding Adequate Information: A Major Challenge for Policy-Makers in the Field of Cancer

Background and context: A global cancer epidemic is developing (GLOBOCAN 2012). In the case of low- and-middle-income countries, difficulties are cumulative: inadequate health systems, lack of training for professionals. Drastic decisions have to be taken in a very complex field. Good decision needs good information. What about information dedicated to policy-makers: to decide a question, they need specific information, marked by these features: synthetic, clear, scientifically validated. Actually, this is not easy to find. Moreover policy-makers can't really benefit from: 1. Information for health professionals which is complex and overabundant (the request “cancer” on PubMed “out” nearly 1.5 millions references). 2. Documents or testimonials for patients. Written by scientific societies or patients' associations, they mostly focus on 2 topics “understand your disease” and “how to cope with”. 3. Information from the Web, not always reliable in terms of quality. Strategy/Tactics: While policy advisors and international organizations provide appropriate studies and reports, mostly focused on “what should be done”, we believe that knowledge of basic cancer data are necessary to understand the proposals. We talk about issues like “what is cancer”, “what exactly cover radiotherapy, oncological surgery…”. Regarding French speaking Africa, Alliance Ligues Africaines and Méditérranéennes (ALIAM) and The French League have produced targeted information for decision-makers. The document was presented in Brazzaville in June 2017. Access to this book is free: www.livre-cancer.aliam.org . The editorial method was discussed and we made the choice to write short sheets, to quickly understand the useful definitions and problems. Rather than comprehensiveness, a pedagogical will and a desire for clarity guided the writing. Diagrams and photos had to be abundant to facilitate understanding. Moreover, this format allows a permanent update of the subjects and the introduction of new topics as needed. What was learned: On the basis of this experience, ALIAM and the league are convinced that a pedagogic document with an international vocation would be useful for all policy makers. Proposal for action: UICC would be the perfect organizer of a working group to produce such a document. The goal would be to develop a consensus text which resume essential data on all common themes of cancer. About 25 themes could be identified, e.g., definition and mechanisms of development of cancers, risk factors, screening and early diagnosis, anatomic pathology and telepathology, molecular biology, imaging and interventional radiology, surgery, radiotherapy, chemotherapy and innovative therapies, palliative care etc. Moreover, focus on specific location of cancer (breast, cervix, lung…) and pediatric cancers should be developed. Then, it would be easier for any world regions to supplement this validated information with additional specific data describing the local situation. Hierarchizing action priorities would be facilitated.

A Key Role for the Periplasmic PfeE Esterase in Iron Acquisition via the Siderophore Enterobactin in Pseudomonas aeruginosa

Enterobactin (ENT) is a siderophore (iron-chelating compound) produced by Escherichia coli to gain access to iron, an indispensable nutrient for bacterial growth. ENT is used as an exosiderophore by Pseudomonas aeruginosa with transport of ferri-ENT across the outer membrane by the PfeA transporter. Next to the pfeA gene on the chromosome is localized a gene encoding for an esterase, PfeE, whose transcription is regulated, as for pfeA, by the presence of ENT in bacterial environment. Purified PfeE hydrolyzed ferri-ENT into three molecules of 2,3-DHBS (2,3-dihydroxybenzoylserine) still complexed with ferric iron, and complete dissociation of iron from ENT chelating groups was only possible in the presence of both PfeE and an iron reducer, such as DTT. The crystal structure of PfeE and an inactive PfeE mutant complexed with ferri-ENT or a nonhydrolyzable ferri-catechol complex allowed identification of the enzyme binding site and the catalytic triad. Finally, cell fractionation and fluorescence microscopy showed periplasmic localization of PfeE in P. aeruginosa cells. Thus, the molecular mechanism of iron dissociation from ENT in P. aeruginosa differs from that previously described in E. coli. In P. aeruginosa, siderophore hydrolysis occurs in the periplasm, with ENT never reaching the bacterial cytoplasm. In E. coli, ferri-ENT crosses the inner membrane via the ABC transporter FepBCD and ferri-ENT is hydrolyzed by the esterase Fes only once it is in the cytoplasm.

The RNA Complement of Outer Membrane Vesicles From Salmonella enterica Serovar Typhimurium Under Distinct Culture Conditions

Bacterial outer membrane vesicles (OMVs), as well as OMV-associated small RNAs, have been demonstrated to play a role in host-pathogen interactions. The presence of larger RNA transcripts in OMVs has been less studied and their potential role in host-pathogen interactions remains largely unknown. Here we analyze RNA from OMVs secreted by Salmonella enterica serovar Typhimurium (S. Typhimurium) cultured under different conditions, which mimic host-pathogen interactions. S. Typhimurium was grown to exponential and stationary growth phases in minimal growth control medium (phosphate-carbon-nitrogen, PCN), as well as in acidic and phosphate-depleted PCN, comparable to the macrophage environment and inducing therefore the expression of Salmonella pathogenicity island 2 (SPI-2) genes. Moreover, Salmonella pathogenicity island 1 (SPI-1), which is required for virulence during the intestinal phase of infection, was induced by culturing S. Typhimurium to the stationary phase in Lysogeny Broth (LB). For each condition, we identified OMV-associated RNAs that are enriched in the extracellular environment relative to the intracellular space. All RNA classes could be observed, but a vast majority of rRNA was exported in all conditions in variable proportions with a notable decrease in LB SPI-1 inducing media. Several mRNAs and ncRNAs were specifically enriched in/on OMVs dependent on the growth conditions. Important to note is that some RNAs showed identical read coverage profiles intracellularly and extracellularly, whereas distinct coverage patterns were observed for other transcripts, suggesting a specific processing or degradation. Moreover, PCR experiments confirmed that distinct RNAs were present in or on OMVs as full-length transcripts (IsrB-1/2; IsrA; ffs; SsrS; CsrC; pSLT035; 10Sa; rnpB; STM0277; sseB; STM0972; STM2606), whereas others seemed to be rather present in a processed or degraded form. Finally, we show by a digestion protection assay that OMVs are able to prevent enzymatic degradation of given full-length transcripts (SsrS, CsrC, 10Sa, and rnpB). In summary, we show that OMV-associated RNA is clearly different in distinct culture conditions and that at least a fraction of the extracellular RNA is associated as a full-length transcripts with OMVs, indicating that some RNAs are protected by OMVs and thereby leaving open the possibility that those might be functionally active.

Critical shoulder angle: Measurement reproducibility and correlation with rotator cuff tendon tears

BACKGROUND

Associations have been reported linking rotator cuff tears (RCTs) to both greater lateral extension of the acromion and greater inclination of the glenoid cavity. These two factors combined can be assessed using a recently introduced parameter, the critical shoulder angle (CSA). The primary objective of this study was to confirm the association linking a high CSA value to RCTs, and the secondary objective was to assess the reproducibility of CSA measurement using a goniometer.

HYPOTHESIS

The null hypothesis was that the CSA value in a group of patients with RCTs was not significantly different from that in patients with anterior shoulder instability and a Bankart lesion, taken as the general population for this study.

METHODS

After a power estimation, we retrospectively included 28 patients with a mean age of 55.5 years who had surgery for RCTs and 27 patients with a mean age of 27.2 years who underwent anterior labral repair. Two surgeons used a goniometer to measure the CSA in each patient. Reproducibility was assessed based on Bland-Altman plots and Pearson's correlation coefficient.

RESULTS

The mean CSA was significantly higher (P=0.02) in the RCT group (36.4°±4.4°; range: 30°-46°) than in the labral-repair group (33.3°±3.8°; range: 25°-41°). Intra-observer reproducibility was 96.7% and inter-observer reproducibility was 95.5%.

CONCLUSION

Our results support previously published evidence that the CSA is significantly greater in patients with RCTs. Thus, an anatomical difference seems to exist between patients with RCTs and the general population. The CSA measured on a standard radiograph using a goniometer provides a reproducible assessment of this anatomical difference.

LEVEL OF EVIDENCE

IV, case-control epidemiological study with a power estimation.

Can the presence of an infection be predicted before a revision total hip arthroplasty? Preliminary study to establish an infection score

INTRODUCTION

The diagnosis of periprosthetic joint infection can be challenging, in part because there is no universal diagnostic test. Current recommendations include several diagnostic criteria, and are mainly based on the results of deep microbiological samples; however, these only provide a diagnosis after surgery. A predictive infection score would improve the management of revision arthroplasty cases. The purpose of this study was to define a composite infection score using standard clinical, radiological and laboratory data that can be used to predict whether an infection is present before a total hip arthroplasty (THA) revision procedure.

HYPOTHESIS

The infection score will make it possible to differentiate correctly between infected and non-infected patients in 75% of cases.

MATERIAL AND METHODS

One hundred and four records from patients who underwent THA revision for any reason were analysed retrospectively: 43 with infection and 61 without infection. There were 54 men and 50 women with an average age of 70±12 years (range 30-90). A univariate analysis was performed to look for individual discriminating factors between the data in the medical records of infected and non-infected patients. A multivariate analysis subsequently integrated these factors together. A composite score was defined and its diagnostic effectiveness was evaluated as the percentage of correctly classified records, along with its sensitivity and specificity.

RESULTS

The score consisted of the following individually weighed factors: body mass index, presence of diabetes, mechanical complication, wound healing disturbance and fever. This composite infection score was able to distinguish correctly between the infected patients (positive score) and non-infected patients (negative score) in 78% of cases; the sensitivity was 57% and the specificity 93%.

DISCUSSION

Once this score is evaluated prospectively, it could be an important tool for defining the medical - surgical strategy during THA revision, no matter the reason for revision.

LEVEL OF EVIDENCE

Level IV - retrospective study.

Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy

Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies.

Structural Insights into the HIV-1 Minus-strand Strong-stop DNA

An essential step of human immunodeficiency virus type 1 (HIV-1) reverse transcription is the first strand transfer that requires base pairing of the R region at the 3'-end of the genomic RNA with the complementary r region at the 3'-end of minus-strand strong-stop DNA (ssDNA). HIV-1 nucleocapsid protein (NC) facilitates this annealing process. Determination of the ssDNA structure is needed to understand the molecular basis of NC-mediated genomic RNA-ssDNA annealing. For this purpose, we investigated ssDNA using structural probes (nucleases and potassium permanganate). This study is the first to determine the secondary structure of the full-length HIV-1 ssDNA in the absence or presence of NC. The probing data and phylogenetic analysis support the folding of ssDNA into three stem-loop structures and the presence of four high-affinity binding sites for NC. Our results support a model for the NC-mediated annealing process in which the preferential binding of NC to four sites triggers unfolding of the three-dimensional structure of ssDNA, thus facilitating interaction of the r sequence of ssDNA with the R sequence of the genomic RNA. In addition, using gel retardation assays and ssDNA mutants, we show that the NC-mediated annealing process does not rely on a single pathway (zipper intermediate or kissing complex).

FRET-based assay to screen inhibitors of HIV-1 reverse transcriptase and nucleocapsid protein

During HIV-1 reverse transcription, the single-stranded RNA genome is converted into proviral double stranded DNA by Reverse Transcriptase (RT) within a reverse transcription complex composed of the genomic RNA and a number of HIV-1 encoded proteins, including the nucleocapsid protein NCp7. Here, we developed a one-step and one-pot RT polymerization assay. In this in vitro assay, RT polymerization is monitored in real-time by Förster resonance energy transfer (FRET) using a commercially available doubly-labeled primer/template DNA. The assay can monitor and quantify RT polymerization activity as well as its promotion by NCp7. Z-factor values as high as 0.89 were obtained, indicating that the assay is suitable for high-throughput drug screening. Using Nevirapine and AZT as prototypical RT inhibitors, reliable IC50 values were obtained from the changes in the RT polymerization kinetics. Interestingly, the assay can also detect NCp7 inhibitors, making it suitable for high-throughput screening of drugs targeting RT, NCp7 or simultaneously, both proteins.

Development and multi-centre evaluation of a method for assessing the severity of potential harm of medication reconciliation errors at hospital admission in elderly

BACKGROUND

Medication reconciliation is a powerful process to correct medication errors (ME) resulting from miscommunicated information at transitions of care. This study aims to develop and evaluate a scoring method for assessing the severity of potential harm of ME intercepted by medication reconciliation at hospital admission in elderly.

METHODS

The development of the scoring method was based on a literature search and the creation of a list of high-risk drugs used in outpatient care. The evaluation of the method was carried out in 7 French hospitals and was based on two criteria: the inter-rater reliability and acceptability. The assessment of the inter-rater reliability was based on intra-class correlation coefficient (ICC) calculations. Each hospital prospectively enrolled the 10 first patients aged 65 or older presenting with at least one ME. Seven blocks of 10 patients were formed. After randomization, each block was rated by practitioners from 3 hospitals. The assessment of the acceptability was based on a satisfaction questionnaire.

RESULTS

A clinical algorithm was developed. The inter-rater reliability of the method was validated by the overall agreement of the 7 hospitals ratings. The agreement was at least substantial (ICC>0.60) and in most of cases almost perfect (ICC>0.80). The acceptability of the method was judged as satisfactory.

CONCLUSION

This multi-centre project has validated an instrument for assessing the severity of potential harm of ME intercepted by medication reconciliation. This will allow studies to be conducted with large cohorts of patients in order to develop epidemiological databases of ME of potential clinical significance.

A new, faster, and safe nasal provocation test method for diagnosing mite allergic rhinitis

BACKGROUND

Diagnosing house dust mite (HDM) allergic rhinitis is difficult. The nasal provocation test (NPT) has been shown to be the most pertinent, but several methods are available. According to guidelines, the NPT requires a skin end-point titration and an objective measurement of nasal patency. Hence, NPT is time consuming and its use is limited.

OBJECTIVE

To evaluate the sensitivity, specificity, and safety of a new, more rapid, and simple alternative NPT (NPT-R) to HDM.

METHODS

Eighty-eight patients with from rhinitis (49 allergic to HDM and 39 controls with and without atopy) were included. Allergic rhinitis to HDM was confirmed by a "classic" NPT based on the Lebel score and rhinomanometry. After a period of 4 weeks, NPT-R was performed and only the clinical score was measured.

RESULTS

The study population was young (mean ± SD, 27.7 ± 8.5 years old), composed mostly of women (61 vs 27 men), and 24% reported asthma. The sensitivity and specificity of NPT-R were 83.7% and 100%, respectively. The correlation between the NPTs was statistically significant (0.833, P < .0001, n = 88) and the 2 NPTs were completely safe. Performing NPT-R was more rapid (mean ± SD, 22 ± 8 minutes) than the classic NPT (97 ± 20 minutes).

CONCLUSION

The NPT-R is safe and easier and faster than the classic NPT. This new method appears to be a very useful tool in the diagnosis of HDM allergic rhinitis when the diagnosis is uncertain or before initiating immunotherapy.

TRIAL REGISTRATION

ClinicalTrials.gov, identifier NCT01485523.

Reverse Transcriptase in Action: FRET-Based Assay for Monitoring Flipping and Polymerase Activity in Real Time

Reverse transcriptase (RT) of human immunodeficiency virus-1 (HIV-1) is a multifunctional enzyme that catalyzes the conversion of the single stranded viral RNA genome into double-stranded DNA, competent for host-cell integration. RT is endowed with RNA- and DNA-dependent DNA polymerase activity and DNA-directed RNA hydrolysis (RNase H activity). As a key enzyme of reverse transcription, RT is a key target of currently used highly active antiretroviral therapy (HAART), though RT inhibitors offer generally a poor resistance profile, urging new RT inhibitors to be developed. Using single molecule fluorescence approaches, it has been recently shown that RT binding orientation and dynamics on its substrate play a critical role in its activity. Currently, most in vitro RT activity assays, inherently end-point measurements, are based on the detection of reaction products by using radio-labeled or chemically modified nucleotides. Here, we propose a simple and continuous real-time Förster resonance energy transfer (FRET) based-assay for the direct measurement of RT's binding orientation and polymerase activity, with the use of conventional steady-state fluorescence spectroscopy. Under our working conditions, the change in binding orientation and the primer elongation step can be visualized separately on the basis of their opposite fluorescence changes and their different kinetics. The assay presented can easily discriminate non-nucleoside RT inhibitors from nucleoside RT inhibitors and determine reliably their potency. This one-step and one-pot assay constitutes an improved alternative to the currently used screening assays to disclose new anti-RT drugs and identify at the same time the class to which they belong.

Posterior surgery in high-grade spondylolisthesis

INTRODUCTION

High-grade L5-S1 spondylolisthesis alters sagittal spinopelvic balance, which can cause low back pain and progressive neurologic disorder. The present study assessed spondylolisthesis reduction and maintenance over time with L4-S1 versus L5-S1 fusion using a lever-arm system and posterior fusion combined with lumbosacral graft.

MATERIALS AND METHODS

Forty patients were operated on for symptomatic high-grade spondylolisthesis, 34 of whom had full pre- and post-operative radiological analysis, with a mean follow-up of 5.4years. There were 9 L5-S1 and 25 L4-S1 instrumentations. Analysis of spinopelvic and slipping parameters and the evolution of segmental lordosis compared results between L5-S1 and L4-S1 instrumentation.

RESULTS

Mean Taillard spondylolisthesis index decreased from 64% to 37% (P=0.0001). Overall sagittal spinopelvic balance was not significantly changed. Overall L1-S1 and segmental L4-L5 lordosis were not affected by instrumentation. Mean L5-S1 segmental lordosis increased from 11° to 18°. There was loss of reduction from 19° to 14° with L5-S1 instrumentation, in contrast to maintained reduction with L4-S1 instrumentation (P=0.006).

CONCLUSION

The lever-arm system provided anterior-posterior reduction of spondylolisthesis and corrected slippage. Postoperative change in overall sagittal spinopelvic balance was slight and constant. Posterior L4-S1 fusion provided better long-term control of L5-S1 lordosis reduction than the shorter L5-S1 fusion. Retrospective study of level IV.