Exploration of the potential for the production of biosurfactants by fungi and their use in the fight against marine pollution

Le XXème siècle a fait face à un grand nombre d’accidents maritimes, ayant conduit à des déversements d’hydrocarbures en mer. Une technique de lutte pouvant être utilisée pour faire face à ces pollutions est la dispersion. Elle permet la formation de micelles grâce aux tensioactifs constituant les dispersants. Ces micelles vont s’épandre dans la colonne d’eau et leur biodégradation par des microorganismes hydrocarbonoclastes sera facilitée. Les tensioactifs, largement utilisés de nos jours tendent néanmoins à être remplacés par des bio-tensioactifs, qui sont eux synthétisés par des microorganismes comme les champignons et qui s’avèrent moins toxiques pour la faune et la flore marines et potentiellement tout autant efficaces que leurs homologues pétrochimiques. Dans ce contexte, l’objectif de cette thèse a été d’explorer le potentiel de production de biotensioactifs par des champignons. Dans un premier temps, ce potentiel de production a été démontré chez des champignons appartenant au phylum des Mucoromycota. Ensuite, la diversité fongique retrouvée dans 4 sites contaminés aux hydrocarbures en Bretagne et la capacité de certains champignons à produire des bio-tensioactifs ont été révélées. Enfin, une souche de Trichoderma citrinoviride ayant révélé un réel potentiel a été sélectionnée. Après optimisation du milieu de culture, son activité surfactante a été caractérisée et l’efficacité de dispersion du pétrole d’extraits issus de cette souche a été évaluée à une échelle laboratoire. Ces travaux ont confirmé que les champignons peuvent constituer une source potentielle de bio-tensioactifs.During the 20th century, a large number of maritime accidents has occurred, leading to significant oil spills at sea. Dispersion is one of the technique used to face oil spills, allowing to the formation of micelles, thanks to the surfactants present in the dispersants. These micelles spread in the water column and theirbiodegradation by hydrocarbonoclastic microorganisms is then facilitated. Surfactants, which are widely used nowadays, could be replaced by biosurfactants, which are synthesized by microorganisms such as fungi and are less toxic for marine fauna and flora and yet still as effective as the petrochemical ones.In this context, the objective of this PhD. Thesis was to explore biosurfactant production in fungi.First, their production potential was demonstrated in fungi from the Mucoromycota phylum. Then, the fungal diversity present in oilcontaminated sites in Brittany and the ability of certain members of these communities to produce such compounds were revealed.Finally, a promising strain of Trichoderma citrinoviride was selected to further study its potential. After optimizing culture medium composition, its surfactant activity was characterized and the dispersion efficiency of crude extracts from this strain was evaluated at a laboratory scale. Overall, this study confirmed that fungi can be source of biosurfactants

Exploration du potentiel de production de bio-tensioactifs par des champignons et valorisation dans la lutte contre les pollutions marines

During the 20th century, a large number of maritime accidents has occurred, leading to significant oil spills at sea. Dispersion is one of the technique used to face oil spills, allowing to the formation of micelles, thanks to the surfactants present in the dispersants. These micelles spread in the water column and theirbiodegradation by hydrocarbonoclastic microorganisms is then facilitated. Surfactants, which are widely used nowadays, could be replaced by biosurfactants, which are synthesized by microorganisms such as fungi and are less toxic for marine fauna and flora and yet still as effective as the petrochemical ones.In this context, the objective of this PhD. Thesis was to explore biosurfactant production in fungi.First, their production potential was demonstrated in fungi from the Mucoromycota phylum. Then, the fungal diversity present in oilcontaminated sites in Brittany and the ability of certain members of these communities to produce such compounds were revealed.Finally, a promising strain of Trichoderma citrinoviride was selected to further study its potential. After optimizing culture medium composition, its surfactant activity was characterized and the dispersion efficiency of crude extracts from this strain was evaluated at a laboratory scale. Overall, this study confirmed that fungi can be source of biosurfactants.Le XXème siècle a fait face à un grand nombre d’accidents maritimes, ayant conduit à des déversements d’hydrocarbures en mer. Une technique de lutte pouvant être utilisée pour faire face à ces pollutions est la dispersion. Elle permet la formation de micelles grâce aux tensioactifs constituant les dispersants. Ces micelles vont s’épandre dans la colonne d’eau et leur biodégradation par des microorganismes hydrocarbonoclastes sera facilitée. Les tensioactifs, largement utilisés de nos jours tendent néanmoins à être remplacés par des bio-tensioactifs, qui sont eux synthétisés par des microorganismes comme les champignons et qui s’avèrent moins toxiques pour la faune et la flore marines et potentiellement tout autant efficaces que leurs homologues pétrochimiques. Dans ce contexte, l’objectif de cette thèse a été d’explorer le potentiel de production de biotensioactifs par des champignons. Dans un premier temps, ce potentiel de production a été démontré chez des champignons appartenant au phylum des Mucoromycota. Ensuite, la diversité fongique retrouvée dans 4 sites contaminés aux hydrocarbures en Bretagne et la capacité de certains champignons à produire des bio-tensioactifs ont été révélées. Enfin, une souche de Trichoderma citrinoviride ayant révélé un réel potentiel a été sélectionnée. Après optimisation du milieu de culture, son activité surfactante a été caractérisée et l’efficacité de dispersion du pétrole d’extraits issus de cette souche a été évaluée à une échelle laboratoire. Ces travaux ont confirmé que les champignons peuvent constituer une source potentielle de bio-tensioactifs

Exploration du potentiel de production de bio-tensioactifs par des champignons et valorisation dans la lutte contre les pollutions marines

During the 20th century, a large number of maritime accidents has occurred, leading to significant oil spills at sea. Dispersion is one of the technique used to face oil spills, allowing to the formation of micelles, thanks to the surfactants present in the dispersants. These micelles spread in the water column and theirbiodegradation by hydrocarbonoclastic microorganisms is then facilitated. Surfactants, which are widely used nowadays, could be replaced by biosurfactants, which are synthesized by microorganisms such as fungi and are less toxic for marine fauna and flora and yet still as effective as the petrochemical ones.In this context, the objective of this PhD. Thesis was to explore biosurfactant production in fungi.First, their production potential was demonstrated in fungi from the Mucoromycota phylum. Then, the fungal diversity present in oilcontaminated sites in Brittany and the ability of certain members of these communities to produce such compounds were revealed.Finally, a promising strain of Trichoderma citrinoviride was selected to further study its potential. After optimizing culture medium composition, its surfactant activity was characterized and the dispersion efficiency of crude extracts from this strain was evaluated at a laboratory scale. Overall, this study confirmed that fungi can be source of biosurfactants.Le XXème siècle a fait face à un grand nombre d’accidents maritimes, ayant conduit à des déversements d’hydrocarbures en mer. Une technique de lutte pouvant être utilisée pour faire face à ces pollutions est la dispersion. Elle permet la formation de micelles grâce aux tensioactifs constituant les dispersants. Ces micelles vont s’épandre dans la colonne d’eau et leur biodégradation par des microorganismes hydrocarbonoclastes sera facilitée. Les tensioactifs, largement utilisés de nos jours tendent néanmoins à être remplacés par des bio-tensioactifs, qui sont eux synthétisés par des microorganismes comme les champignons et qui s’avèrent moins toxiques pour la faune et la flore marines et potentiellement tout autant efficaces que leurs homologues pétrochimiques. Dans ce contexte, l’objectif de cette thèse a été d’explorer le potentiel de production de biotensioactifs par des champignons. Dans un premier temps, ce potentiel de production a été démontré chez des champignons appartenant au phylum des Mucoromycota. Ensuite, la diversité fongique retrouvée dans 4 sites contaminés aux hydrocarbures en Bretagne et la capacité de certains champignons à produire des bio-tensioactifs ont été révélées. Enfin, une souche de Trichoderma citrinoviride ayant révélé un réel potentiel a été sélectionnée. Après optimisation du milieu de culture, son activité surfactante a été caractérisée et l’efficacité de dispersion du pétrole d’extraits issus de cette souche a été évaluée à une échelle laboratoire. Ces travaux ont confirmé que les champignons peuvent constituer une source potentielle de bio-tensioactifs

A Deep Learning System Using Optical Coherence Tomography Angiography to Detect Glaucoma and Anterior Ischemic Optic Neuropathy

Introduction. Glaucoma and non-arteritic anterior ischemic optic neuropathy (NAION) are optic neuropathies that can both lead to irreversible blindness. Several studies have compared optical coherence tomography angiography (OCTA) findings in glaucoma and NAION in the presence of similar functional and structural damages with contradictory results. The goal of this study was to use a deep learning system to differentiate OCTA in glaucoma and NAION. Material and methods. Sixty eyes with glaucoma (including primary open angle glaucoma, angle-closure glaucoma, normal tension glaucoma, pigmentary glaucoma, pseudoexfoliative glaucoma and juvenile glaucoma), thirty eyes with atrophic NAION and forty control eyes (NC) were included. All patients underwent OCTA imaging and automatic segmentation was used to analyze the macular superficial capillary plexus (SCP) and the radial peripapillary capillary (RPC) plexus. We used the classic convolutional neural network (CNN) architecture of ResNet50. Attribution maps were obtained using the “Integrated Gradients” method. Results. The best performances were obtained with the SCP + RPC model achieving a mean area under the receiver operating characteristics curve (ROC AUC) of 0.94 (95% CI 0.92–0.96) for glaucoma, 0.90 (95% CI 0.86–0.94) for NAION and 0.96 (95% CI 0.96–0.97) for NC. Conclusion. This study shows that deep learning architecture can classify NAION, glaucoma and normal OCTA images with a good diagnostic performance and may outperform the specialist assessment

Biosurfactant-Producing Mucor Strains: Selection, Screening, and Chemical Characterization

Biosurfactants are amphiphilic molecules with surface tension reducing activities. Among biosurfactant producers, fungi have been identified as promising organisms. While many studies have investigated biosurfactant production in fungal species from the Ascomycota and Basidiomycota phyla, less is known concerning species from the Mucoromycota phylum. In this context, the aim of this study was to screen and optimize biosurfactant production in 24 fungal strains, including seven Mucor, three Lichtheimia, and one Absidia species. After cultivation in a medium stimulating surfactant production, the surface activity of cell-free supernatants was measured using both oil spreading and parafilm M tests. Among them, five Mucor strain cell-free supernatants belonging to M. circinelloides, M. lanceolatus, M. mucedo, M. racemosus, and M. plumbeus, showed oil repulsion. Then, the impact of the medium composition on surfactant production was evaluated for eight strains. Three of them, i.e., Mucor circinelloides UBOCC-A-109190, Mucor plumbeus UBOCC-A-111133, and Mucor mucedo UBOCC-A-101353 showed an interesting surfactant production potential, reducing the medium surface tension to 36, 31, and 32 mN/m, respectively. A preliminary characterization of the surfactant molecules produced by these strains was performed and showed that these compounds belonged to the glycolipid family

Severity of COVID-19 and survival in patients with rheumatic and inflammatory diseases: data from the French RMD COVID-19 cohort of 694 patients

International audienceObjectives: There is little known about the impact of SARS-CoV-2 on patients with inflammatory rheumatic and musculoskeletal diseases (iRMD). We examined epidemiological characteristics associated with severe disease, then with death. We also compared mortality between patients hospitalised for COVID-19 with and without iRMD.Methods: Individuals with suspected iRMD-COVID-19 were included in this French cohort. Logistic regression models adjusted for age and sex were used to estimate adjusted ORs and 95% CIs of severe COVID-19. The most significant clinically relevant factors were analysed by multivariable penalised logistic regression models, using a forward selection method. The death rate of hospitalised patients with iRMD-COVID-19 (moderate-severe) was compared with a subset of patients with non-iRMD-COVID-19 from a French hospital matched for age, sex, and comorbidities.Results: Of 694 adults, 438 (63%) developed mild (not hospitalised), 169 (24%) moderate (hospitalised out of the intensive care unit (ICU) and 87 (13%) severe (patients in ICU/deceased) disease. In multivariable imputed analyses, the variables associated with severe infection were age (OR=1.08, 95% CI: 1.05-1.10), female gender (OR=0.45, 95% CI: 0.25-0.80), body mass index (OR=1.07, 95% CI: 1.02-1.12), hypertension (OR=1.86, 95% CI: 1.01-3.42), and use of corticosteroids (OR=1.97, 95% CI: 1.09-3.54), mycophenolate mofetil (OR=6.6, 95% CI: 1.47-29.62) and rituximab (OR=4.21, 95% CI: 1.61-10.98). Fifty-eight patients died (8% (total) and 23% (hospitalised)). Compared with 175 matched hospitalised patients with non-iRMD-COVID-19, the OR of mortality associated with hospitalised patients with iRMD-COVID-19 was 1.45 (95% CI: 0.87-2.42) (n=175 each group).Conclusions: In the French RMD COVID-19 cohort, as already identified in the general population, older age, male gender, obesity, and hypertension were found to be associated with severe COVID-19. Patients with iRMD on corticosteroids, but not methotrexate, or tumour necrosis factor alpha and interleukin-6 inhibitors, should be considered as more likely to develop severe COVID-19. Unlike common comorbidities such as obesity, and cardiovascular or lung diseases, the risk of death is not significantly increased in patients with iRMD

Severity of COVID-19 and survival in patients with rheumatic and inflammatory diseases: data from the French RMD COVID-19 cohort of 694 patients

International audienceObjectives: There is little known about the impact of SARS-CoV-2 on patients with inflammatory rheumatic and musculoskeletal diseases (iRMD). We examined epidemiological characteristics associated with severe disease, then with death. We also compared mortality between patients hospitalised for COVID-19 with and without iRMD.Methods: Individuals with suspected iRMD-COVID-19 were included in this French cohort. Logistic regression models adjusted for age and sex were used to estimate adjusted ORs and 95% CIs of severe COVID-19. The most significant clinically relevant factors were analysed by multivariable penalised logistic regression models, using a forward selection method. The death rate of hospitalised patients with iRMD-COVID-19 (moderate-severe) was compared with a subset of patients with non-iRMD-COVID-19 from a French hospital matched for age, sex, and comorbidities.Results: Of 694 adults, 438 (63%) developed mild (not hospitalised), 169 (24%) moderate (hospitalised out of the intensive care unit (ICU) and 87 (13%) severe (patients in ICU/deceased) disease. In multivariable imputed analyses, the variables associated with severe infection were age (OR=1.08, 95% CI: 1.05-1.10), female gender (OR=0.45, 95% CI: 0.25-0.80), body mass index (OR=1.07, 95% CI: 1.02-1.12), hypertension (OR=1.86, 95% CI: 1.01-3.42), and use of corticosteroids (OR=1.97, 95% CI: 1.09-3.54), mycophenolate mofetil (OR=6.6, 95% CI: 1.47-29.62) and rituximab (OR=4.21, 95% CI: 1.61-10.98). Fifty-eight patients died (8% (total) and 23% (hospitalised)). Compared with 175 matched hospitalised patients with non-iRMD-COVID-19, the OR of mortality associated with hospitalised patients with iRMD-COVID-19 was 1.45 (95% CI: 0.87-2.42) (n=175 each group).Conclusions: In the French RMD COVID-19 cohort, as already identified in the general population, older age, male gender, obesity, and hypertension were found to be associated with severe COVID-19. Patients with iRMD on corticosteroids, but not methotrexate, or tumour necrosis factor alpha and interleukin-6 inhibitors, should be considered as more likely to develop severe COVID-19. Unlike common comorbidities such as obesity, and cardiovascular or lung diseases, the risk of death is not significantly increased in patients with iRMD

COVID-19 outcomes in patients with inflammatory rheumatic and musculoskeletal diseases treated with rituximab: a cohort study

International audienceBackground: Various observations have suggested that the course of COVID-19 might be less favourable in patients with inflammatory rheumatic and musculoskeletal diseases receiving rituximab compared with those not receiving rituximab. We aimed to investigate whether treatment with rituximab is associated with severe COVID-19 outcomes in patients with inflammatory rheumatic and musculoskeletal diseases.Methods: In this cohort study, we analysed data from the French RMD COVID-19 cohort, which included patients aged 18 years or older with inflammatory rheumatic and musculoskeletal diseases and highly suspected or confirmed COVID-19. The primary endpoint was the severity of COVID-19 in patients treated with rituximab (rituximab group) compared with patients who did not receive rituximab (no rituximab group). Severe disease was defined as that requiring admission to an intensive care unit or leading to death. Secondary objectives were to analyse deaths and duration of hospital stay. The inverse probability of treatment weighting propensity score method was used to adjust for potential confounding factors (age, sex, arterial hypertension, diabetes, smoking status, body-mass index, interstitial lung disease, cardiovascular diseases, cancer, corticosteroid use, chronic renal failure, and the underlying disease [rheumatoid arthritis vs others]). Odds ratios and hazard ratios and their 95% CIs were calculated as effect size, by dividing the two population mean differences by their SD. This study is registered with ClinicalTrials.gov, NCT04353609.Findings: Between April 15, 2020, and Nov 20, 2020, data were collected for 1090 patients (mean age 55·2 years [SD 16·4]); 734 (67%) were female and 356 (33%) were male. Of the 1090 patients, 137 (13%) developed severe COVID-19 and 89 (8%) died. After adjusting for potential confounding factors, severe disease was observed more frequently (effect size 3·26, 95% CI 1·66-6·40, p=0·0006) and the duration of hospital stay was markedly longer (0·62, 0·46-0·85, p=0·0024) in the 63 patients in the rituximab group than in the 1027 patients in the no rituximab group. 13 (21%) of 63 patients in the rituximab group died compared with 76 (7%) of 1027 patients in the no rituximab group, but the adjusted risk of death was not significantly increased in the rituximab group (effect size 1·32, 95% CI 0·55-3·19, p=0·53).Interpretation: Rituximab therapy is associated with more severe COVID-19. Rituximab will have to be prescribed with particular caution in patients with inflammatory rheumatic and musculoskeletal diseases