Analysis of gene expression patterns in animals

During my PhD, my aim was to provide new tools to increase our capacity to analyse gene expression patterns, and to study on a large-scale basis the evolution of gene expression in animals. Gene expression patterns (when and where a gene is expressed) are a key feature in understanding gene function, notably in development. It appears clear now that the evolution of developmental processes and of phenotypes is shaped both by evolution at the coding sequence level, and at the gene expression level.Studying gene expression evolution in animals, with complex expression patterns over tissues and developmental time, is still challenging. No tools are available to routinely compare expression patterns between different species, with precision, and on a large-scale basis. Studies on gene expression evolution are therefore performed only on small genes datasets, or using imprecise descriptions of expression patterns.The aim of my PhD was thus to develop and use novel bioinformatics resources, to study the evolution of gene expression. To this end, I developed the database Bgee (Base for Gene Expression Evolution). The approach of Bgee is to transform heterogeneous expression data (ESTs, microarrays, and in-situ hybridizations) into present/absent calls, and to annotate them to standard representations of anatomy and development of different species (anatomical ontologies). An extensive mapping between anatomies of species is then developed based on hypothesis of homology. These precise annotations to anatomies, and this extensive mapping between species, are the major assets of Bgee, and have required the involvement of many co-workers over the years. My main personal contribution is the development and the management of both the Bgee database and the web-application.Bgee is now on its ninth release, and includes an important gene expression dataset for 5 species (human, mouse, drosophila, zebrafish, Xenopus), with the most data from mouse, human and zebrafish. Using these three species, I have conducted an analysis of gene expression evolution after duplication in vertebrates.Gene duplication is thought to be a major source of novelty in evolution, and to participate to speciation. It has been suggested that the evolution of gene expression patterns might participate in the retention of duplicate genes. I performed a large-scale comparison of expression patterns of hundreds of duplicated genes to their singleton ortholog in an outgroup, including both small and large-scale duplicates, in three vertebrate species (human, mouse and zebrafish), and using highly accurate descriptions of expression patterns. My results showed unexpectedly high rates of de novo acquisition of expression domains after duplication (neofunctionalization), at least as high or higher than rates of partitioning of expression domains (subfunctionalization). I found differences in the evolution of expression of small- and large-scale duplicates, with small-scale duplicates more prone to neofunctionalization. Duplicates with neofunctionalization seemed to evolve under more relaxed selective pressure on the coding sequence. Finally, even with abundant and precise expression data, the majority fate I recovered was neither neo- nor subfunctionalization of expression domains, suggesting a major role for other mechanisms in duplicate gene retention.

Juvenile arthritis patients report favorable subjective outcomes of hip arthroplasty despite poor standard outcome scores.

We evaluated midterm patient-reported outcomes and satisfaction with total hip arthroplasty in patients who had severe juvenile idiopathic arthritis. Thirty-one patients (49 hips), with a mean age of 29 years (range, 16-43 years), reported low hip pain and stiffness at follow-up (mean, 7 years; range, 3-17 years). Up to 92% were satisfied with their ability to perform various activities; 96% were satisfied with pain relief. A mean postoperative flexion arc of 96° was observed. Final 36-Item Short Form Health Survey, EuroQol in 5 dimensions, Western Ontario and McMaster Universities Arthritis Index, and Harris Hip scores were lower than reference populations, particularly for mobility, physical functioning, and social functioning subscores. Young adults with end-stage hip involvement and severe longstanding juvenile idiopathic arthritis expressed high satisfaction with total hip arthroplasty, which improved range of motion, pain, and stiffness, despite poor performance on widely used outcome measures.

Conditional manipulation of sex ratios by ant workers: A test of kin selection theory

Variable queen mating frequencies provide a unique opportunity to study the resolution of worker-queen conflict over sex ratio in social Hymenoptera, because the conflict is maximal in colonies headed by a singly mated queen and is weak or nonexistent in colonies headed by a multiply mated queen. In the wood ant Formica exsecta, workers in colonies with a singly mated queen, but not those in colonies with a multiply mated queen, altered the sex ratio of queen-laid eggs by eliminating males to preferentially raise queens. By this conditional response to queen mating frequency, workers enhance their inclusive fitness.

Effects of bioaerosol exposure on work-related symptoms among Swiss sawmill workers

Objective Exposure to bioaerosols in the occupational environment of sawmills could be associated with a wide range of health effects, in particular respiratory impairment, allergy and organic dust toxic syndrome. The objective of the study was to assess the frequency of medical respiratory and general symptoms and their relation to bioaerosol exposure. Method Twelve sawmills in the French part of Switzerland were investigated and the relationship between levels of bioaerosols (wood dust, airborne bacteria, airborne fungi and endotoxins), medical symptoms and impaired lung function was explored. A health questionnaire was distributed to 111 sawmill workers. Results The concentration of airborne fungi exceeded the limit recommended by the Swiss National Insurance (SUVA) in the twelve sawmills. This elevated fungi level significantly influenced the occurrence of bronchial syndrome (defined by cough and expectorations). No other health effects (irritations or respiratory effects) could be associated to the measured exposures. We observed that junior workers showed significantly more irritation syndrome (defined by itching/running nose, snoring and itching/red eyes) than senior workers. Lung function tests were not influenced by bioaerosol levels nor dust exposure levels. Conclusion Results suggest that occupational exposure to wood dust in a Swiss sawmill does not promote a clinically relevant decline in lung function. However, the occurrence of bronchial syndrome is strongly influenced by airborne fungi levels. [Authors]

In vivo measurements of atrial repolarization alternans based on standard pacemaker technology

It has been shown that repolarization alternans, a beat-to-beat alternation in action potential duration, enhances dispersion of repolarization above a critical heart rate and promotes susceptibility to ventricular arrhythmias. It is unknown whether repolarization alternans is measurable in the atria using standard pacemakers and whether it plays a role in promoting atrial fibrillation. In this work, atrial repolarization alternans amplitude and periodicity are studied in a sheep model of pacing-induced atrial fibrillation. Two pacemakers, each with one right atrial and ventricular lead, were implanted in 4 male sheep after ablation of the atrioventricular junction. The first one was used to deliver rapid pacing for measurements of right atrial repolarization alternans and the second one to record a unipolar electrogram. Atrial repolarization alternans appeared rate-dependent and its amplitude increased as a function of pacing rate. Repolarization alternans was intermittent but no periodicity was detected. An increase of repolarization alternans preceding episodes of non-sustained atrial fibrillation suggests that repolarization alternans is a promising parameter for assessment of atrial fibrillation susceptibility.

Occupational exposure to beryllium in Switzerland : exposed workers and occupations at risk

Introduction: Beryllium (Be) is increasingly used in various industrial applications. Occupational exposure to Be may lead to chronic beryllium disease (CBD), a pulmonary granulomatous disorder closely similar to sarcoidosis, which develop in 1 to 15% of exposed workers. Although Switzerland is one of the major Be importers worldwide, little information is available about occurrence of exposure and the number of workers exposed in this country. Objectives: 1) evaluate the number of workers potentially exposed to Be in Switzerland; 2) construct a screening tool to allow potential Be exposure detection in a clinical setting. Methods: After identification of industrial sectors involving beryllium exposure based on expert reports and scientific literature, an estimation of the number of workers employed in these relevant industries was made using data from the Swiss federal population census and registries of economic activities. A second analysis was performed to estimate the fraction of workers really exposed to Be in each industrial sector. This adjustment was made according to the results of a French survey (INRS, Institut National de Recherche et de Sécurité) conducted by questionnaire addressed to 4500 companies in relevant industries on their use of beryllium and other issues such as percentage of employees really exposed. These realistic data were used to develop a self-administrated screening questionnaire allowed to identify patients with possible Be exposure. Results: In Switzerland, the number of workers employed in industries using Be was nearly 150 000. The estimated number of workers exposed to beryllium in these industries ranged from 2000 to 4000. Relevant sectors were: microengineering, precision turning, watchmaking and metal waste treatment and recycling. The validation of the self-administrated questionnaire containing a list of jobs and leisure activities associated with potential Be exposure is in progress within the framework of a national study. Conclusions: The number of workers potentially exposed to Be in Switzerland is rather high compared to estimations for other industrialized countries and might constitute an underestimated occupational health problem. Undetected Be exposure in patients with sarcoidosis may occur and result in misdiagnosis. Once validated, the self-administrated questionnaire could be used by clinicians to screen for Be exposure in patients with granulomatous lung disorders.

Is the function of the serratus anterior muscle disturbed following division during a standard thoracotomy?

In a prospective study the functional results after dissection or preservation of the serratus anterior muscle in the postero-lateral standard thoracotomy were evaluated. In 14 patients of our clinic with dissection and suture and in 14 patients with preservation of the serratus muscle the muscle function was assessed and compared preoperatively, within the first two post-operative weeks, and three months after the operation by the same physiotherapists. The two groups were blinded in regard to age, original disease, and mode of intervention. We compared the wing position of the scapula in the sitting position and the positioning of the scapula at fixation of the shoulder joint in the sitting and in the supine position. Using a four-grade function assessment scheme, both groups obtained the same functional results. There was no seroma in either group. After 2.8 (2.5 to 3.0) years all the surviving patients described symmetric functional conditions. We therefore conclude that in order to achieve a better view of the operative field the serratus muscle may be dissected close to the origin if it is then readapted.

La mortalité par tumeur maligne chez les ouvriers d'une fabrique de caoutchouc en Suisse: étude épidémiologique, 1955-1975. [Cancer mortality among the workers of a Swiss rubber goods factory. Epidemiological study, 1955-75].

In an epidemiologic investigation of mortality among workers in a Swiss rubber-goods factory the cancer mortality in the period 1955-1975 has been studied in all male workers active on 1 January 1955 in (a) a rubber-goods factory and (b) a munitions factory, the latter as reference population. The two groups numbered some 1000 each. Both factories were located in the same Central Swiss village where no other industry was present. Mortality in each industry is compared with that in the Swiss population in general (SMR) and the mortalities of the two industries are compared with each other. The results tend to confirm that rubber workers are exposed to a higher risk of cancer mortality. Three particular types of cancer are briefly discussed: cancer of the stomach, of the lower urinary tract, and glioblastoma.

A detailed urinary excretion time course study of captan and folpet biomarkers in workers for the estimation of dose, main route-of-entry and most appropriate sampling and analysis strategies

Captan and folpet are two fungicides largely used in agriculture, but biomonitoring data are mostly limited to measurements of captan metabolite concentrations in spot urine samples of workers, which complicate interpretation of results in terms of internal dose estimation, daily variations according to tasks performed, and most plausible routes of exposure. This study aimed at performing repeated biological measurements of exposure to captan and folpet in field workers (i) to better assess internal dose along with main routes-of-entry according to tasks and (ii) to establish most appropriate sampling and analysis strategies. The detailed urinary excretion time courses of specific and non-specific biomarkers of exposure to captan and folpet were established in tree farmers (n = 2) and grape growers (n = 3) over a typical workweek (seven consecutive days), including spraying and harvest activities. The impact of the expression of urinary measurements [excretion rate values adjusted or not for creatinine or cumulative amounts over given time periods (8, 12, and 24 h)] was evaluated. Absorbed doses and main routes-of-entry were then estimated from the 24-h cumulative urinary amounts through the use of a kinetic model. The time courses showed that exposure levels were higher during spraying than harvest activities. Model simulations also suggest a limited absorption in the studied workers and an exposure mostly through the dermal route. It further pointed out the advantage of expressing biomarker values in terms of body weight-adjusted amounts in repeated 24-h urine collections as compared to concentrations or excretion rates in spot samples, without the necessity for creatinine corrections.

Biomarkers of oxidative stress and its association with the urinary reducing capacity in bus maintenance workers.

BACKGROUND: Exposure to particles (PM) induces adverse health effects (cancer, cardiovascular and pulmonary diseases). A key-role in these adverse effects seems to be played by oxidative stress, which is an excess of reactive oxygen species relative to the amount of reducing species (including antioxidants), the first line of defense against reactive oxygen species. The aim of this study was to document the oxidative stress caused by exposure to respirable particles in vivo, and to test whether exposed workers presented changes in their urinary levels for reducing species.METHODS: Bus depot workers (n = 32) exposed to particles and pollutants (respirable PM4, organic and elemental carbon, particulate metal content, polycyclic aromatic hydrocarbons, NOx, O3) were surveyed over two consecutive days. We collected urine samples before and after each shift, and quantified an oxidative stress biomarker (8-hydroxy-2'-deoxyguanosine), the reducing capacity and a biomarker of PAH exposure (1-hydroxypyrene). We used a linear mixed model to test for associations between the oxidative stress status of the workers and their particle exposure as well as with their urinary level of reducing species.RESULTS: Workers were exposed to low levels of respirable PM4 (range 25-71 μg/m3). However, urinary levels of 8-hydroxy-2'-deoxyguanosine increased significantly within each shift and between both days for non-smokers. The between-day increase was significantly correlated (p < 0.001) with the concentrations of organic carbon, NOx, and the particulate copper content. The within-shift increase in 8OHdG was highly correlated to an increase of the urinary reducing capacity (Spearman ρ = 0.59, p < 0.0001).CONCLUSIONS: These findings confirm that exposure to components associated to respirable particulate matter causes a systemic oxidative stress, as measured with the urinary 8OHdG. The strong association observed between urinary 8OHdG with the reducing capacity is suggestive of protective or other mechanisms, including circadian effects. Additional investigations should be performed to understand these observations.

Exposure to bioaerosols, respiratory health and lung-specific proteins: a prospective study in garbage and wastewater workers.

Objectives To prospectively assess respiratory health in wastewater workers and garbage collectors over 5 years. Methods Exposure, respiratory symptoms and conditions, spirometry and lung-specific proteins were assessed yearly in a cohort of 304 controls, 247 wastewater workers and 52 garbage collectors. Results were analysed with random coefficient models and linear regression taking into account several potential confounders. Results Symptoms, spirometry and lung-specific proteins were not affected by occupational exposure. Conclusions In this population no effects of occupational exposure to bioaerosols were found, probably because of good working conditions.

Load Ratings for Standard Bridges, HR-239 Phase IV, 2008

In this report, sixteen secondary and primary bridge standards for two types of bridges are rated for AASHTO HS20-44 vehicle configuration utilizing Load Factor methodology. The ratings apply only to those bridges which: (1) are built according to the applicable bridge standard plans, (2) have no structural deterioration or damage, and (3) have no added wearing surface in excess of one-half inch integral wearing surface.

Load Ratings for Standard Bridges, HR-239 Phase III, 1998

In this report, 25 secondary bridge standards for three types of bridges are rated for the AASHTO HS20-44 vehicle configuration and five typical Iowa legal vehicles. The ratings apply only to those bridges which: (1) are built according to the applicable bridge standard plans, (2) have no structural deterioration or damage, and (3) have no added wearing surface in excess of 0.5-in. (1.27-cm) integral wearing surface. Appendix A contains the results of the original October 1982 report on load ratings for standard bridges.