Assessment of the microbial diversity at the surface of Livarot cheese using culture-dependent and independent approaches

International audienceThe microbial diversity of the surface of a commercial red-smear cheese, Livarot cheese, sold on the retail market was studied using culture-dependent and independent approaches. Forty yeasts and 40 bacteria from the cheese surface were collected, dereplicated using single-strand conformation polymorphism (SSCP) analysis and identified using rRNA gene sequencing for the culture-dependent approach. The cultureindependent approach involved cloning and sequencing of the 16S rRNA gene and SSCP analysis from total DNA extracted from the cheese. The most dominant bacteria were Microbacterium gubbeenense, Leucobacter komagatae and Gram-negative bacteria from the Gamma-Proteobacteria class. Fluorescence in situ hybridization (FISH) analysis was also used to study the cheese microbial diversity with class-level and specific rRNAtargeted probes for bacteria and yeasts, respectively. FISH analysis confirmed that Gamma-Proteobacteria were important microorganisms in this cheese. Four specific FISH probes targeting the dominant yeasts present in the cheese, Candida catenulata, Candida intermedia, Geotrichum spp. and Yarrowia lipolytica, were also designed and evaluated. These probes allowed the detection of these yeasts directly in cheese. The use of the rRNA gene-based approach combined with FISH analysis was useful to investigate the diversity of a surface microbial consortium from cheese

Susceptibility of neuroblastoma and glioblastoma cell lines to SARS-CoV-2 infection

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Compensation des exportations minérales et remédiations aux dégradations des sols. Compte rendu de l’atelier 3

Les forêts françaises font face aujourd’hui à des pressions extérieures croissantes. Ces contraintes sont d’ordre nutritionnel ou sylvicole ou climatique et risquent d’impacter la durabilité des écosystèmes forestiers. Le sol peut être impacté, entraînant une dégradation de ses composantes chimique ou physique ou biologique. L’objectif de l’atelier était d’apporter des éléments de connaissance et de débat autour des différents types de dégradation, de remédiation et de restauration des sols. Cet atelier a également permis d’échanger autour de différentes approches permettant de soutenir la productivité forestière, par l’utilisation d’intrants de différentes natures (amendements/cendres, boues de stations d’épuration…) ou par l’utilisation des friches industrielles pour produire de la biomasse

Effects of sodium nitrite reduction, removal or replacement on cured and cooked meat for microbiological growth, food safety, colon ecosystem, and colorectal carcinogenesis in Fischer 344 rats

Epidemiological and experimental evidence indicated that processed meat consumption is associated with colorectal cancer risks. Several studies suggest the involvement of nitrite or nitrate additives via N-nitroso-compound formation (NOCs). Compared to the reference level (120 mg/kg of ham), sodium nitrite removal and reduction (90 mg/kg) similarly decreased preneoplastic lesions in F344 rats, but only reduction had an inhibitory effect on Listeria monocytogenes growth comparable to that obtained using the reference nitrite level and an effective lipid peroxidation control. Among the three nitrite salt alternatives tested, none of them led to a significant gain when compared to the reference level: vegetable stock, due to nitrate presence, was very similar to this reference nitrite level, yeast extract induced a strong luminal peroxidation and no decrease in preneoplastic lesions in rats despite the absence of NOCs, and polyphenol rich extract induced the clearest downward trend on preneoplastic lesions in rats but the concomitant presence of nitrosyl iron in feces. Except the vegetable stock, other alternatives were less efficient than sodium nitrite in reducing L. monocytogenes growth

Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs

Life-threatening `breakthrough' cases of critical COVID-19 are attributed to poor or waning antibody response to the SARS- CoV-2 vaccine in individuals already at risk. Pre-existing autoantibodies (auto-Abs) neutralizing type I IFNs underlie at least 15% of critical COVID-19 pneumonia cases in unvaccinated individuals; however, their contribution to hypoxemic breakthrough cases in vaccinated people remains unknown. Here, we studied a cohort of 48 individuals ( age 20-86 years) who received 2 doses of an mRNA vaccine and developed a breakthrough infection with hypoxemic COVID-19 pneumonia 2 weeks to 4 months later. Antibody levels to the vaccine, neutralization of the virus, and auto- Abs to type I IFNs were measured in the plasma. Forty-two individuals had no known deficiency of B cell immunity and a normal antibody response to the vaccine. Among them, ten (24%) had auto-Abs neutralizing type I IFNs (aged 43-86 years). Eight of these ten patients had auto-Abs neutralizing both IFN-a2 and IFN-., while two neutralized IFN-omega only. No patient neutralized IFN-ss. Seven neutralized 10 ng/mL of type I IFNs, and three 100 pg/mL only. Seven patients neutralized SARS-CoV-2 D614G and the Delta variant (B.1.617.2) efficiently, while one patient neutralized Delta slightly less efficiently. Two of the three patients neutralizing only 100 pg/mL of type I IFNs neutralized both D61G and Delta less efficiently. Despite two mRNA vaccine inoculations and the presence of circulating antibodies capable of neutralizing SARS-CoV-2, auto-Abs neutralizing type I IFNs may underlie a significant proportion of hypoxemic COVID-19 pneumonia cases, highlighting the importance of this particularly vulnerable population

A first update on mapping the human genetic architecture of COVID-19

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Extracorporeal Membrane Oxygenation for Severe Acute Respiratory Distress Syndrome associated with COVID-19: An Emulated Target Trial Analysis.

RATIONALE: Whether COVID patients may benefit from extracorporeal membrane oxygenation (ECMO) compared with conventional invasive mechanical ventilation (IMV) remains unknown. OBJECTIVES: To estimate the effect of ECMO on 90-Day mortality vs IMV only Methods: Among 4,244 critically ill adult patients with COVID-19 included in a multicenter cohort study, we emulated a target trial comparing the treatment strategies of initiating ECMO vs. no ECMO within 7 days of IMV in patients with severe acute respiratory distress syndrome (PaO2/FiO2 <80 or PaCO2 ≥60 mmHg). We controlled for confounding using a multivariable Cox model based on predefined variables. MAIN RESULTS: 1,235 patients met the full eligibility criteria for the emulated trial, among whom 164 patients initiated ECMO. The ECMO strategy had a higher survival probability at Day-7 from the onset of eligibility criteria (87% vs 83%, risk difference: 4%, 95% CI 0;9%) which decreased during follow-up (survival at Day-90: 63% vs 65%, risk difference: -2%, 95% CI -10;5%). However, ECMO was associated with higher survival when performed in high-volume ECMO centers or in regions where a specific ECMO network organization was set up to handle high demand, and when initiated within the first 4 days of MV and in profoundly hypoxemic patients. CONCLUSIONS: In an emulated trial based on a nationwide COVID-19 cohort, we found differential survival over time of an ECMO compared with a no-ECMO strategy. However, ECMO was consistently associated with better outcomes when performed in high-volume centers and in regions with ECMO capacities specifically organized to handle high demand. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Modifications et restauration de propriétés physiques et chimiques de deux sols forestiers soumis au passage d'un engin d'exploitation

Les risques de dégradation physique des sols forestiers sous l'effet de contraintes mécaniques externes liées à la mécanisation des opérations forestières, augmentent considérablement. Les mécanismes et le temps nécessaires à la restauration non assistée de la qualité des sols forestiers tassés restent encore peu étudiés, et leur identification nécessite de coupler les approches physiques, chimiques et biologiques. L'objectif de ce travail était d'étudier l'impact de la circulation d'un porteur forestier sur les conditions de l'enracinement (aération, régime hydrique et pénétrabilité) ainsi que son évolution à court terme. Ce travail s'appuie sur l'observation de deux sites expérimentaux mis en place dans le Nord Est de la France, concernant des sols de morphologie similaire (couche limono-argileuse de 50 cm d'épaisseur reposant sur un substrat argileux) et ayant subi des contraintes identiques. Des paramètres physiques (température et humidité du sol, densité apparente et résistance à la pénétration) et chimiques (composition de l'atmosphère du sol) ont été suivis pendant trois à quatre ans, à des fréquences allant d'un pas de temps quotidien à annuel. Le suivi du climat du sol et de la composition de son atmosphère a mis en évidence une diminution forte des conditions aérobies pendant un à un an et demi après le passage du porteur. Cet effet initial sur l'aération du sol a diminué subitement dès l'apparition de la première période de sécheresse édaphique, probablement grâce à la formation de fissures dans l'horizon de surface du sol tassé. Cependant un effet significatif du traitement sur la composition de l'atmosphère du sol pouvait toujours être observé trois à quatre ans après tassement. Pour suivre l'évolution des propriétés physiques du sol après circulation du porteur, il a été nécessaire d'opérer une normalisation par rapport à l'humidité au moment du prélèvement. Trois ou quatre ans après la circulation du porteur, une différence toujours significative existe entre les propriétés physiques des sols témoins et celles des sols tassés. Cependant une évolution de l'impact du porteur peut être mise en évidence dans la couche de surface (0 10 cm) des deux sites. Ce début de restauration se traduit, sur un des deux sites, par une différence entre traitement qui n'est plus significative quand les sols sont humides mais qui l'est encore quand les sols sont secs. Sur le deuxième site, cette différence a diminué quelle que ce soit l'humidité du sol. Ainsi, le début de régénération de la structure du sol perturbé ne s'accompagne pas d'une disparition de son comportement de prise en masse lors de son desséchement sur un des deux sites. Ce travail a permis de mettre en évidence une évolution des conséquences du porteur en surface du sol tassé qui serait liée à des processus physiques (gonflement retrait, gel dégel). Cependant, l'impact sur les conditions de l'enracinement (forte résistance à la pénétration quand les sols sont secs, faible aération quand ils sont humides) reste élevé de même que sur la résilience à long terme du peuplement.Soil compaction belongs to the major treats to soil quality with no exceptions of forest ecosystems where the frequency and intensity of loads application increase since several decades. The mechanisms and the duration of soil quality recovery following heavy traffic in forests remain poorly documented and their study requires multidisciplinary approaches.The aim of this work was to evaluate the impact of forwarder traffic on the potential constraints to roots growth (aeration, water content, and penetrability) growing in two forest soils sensitive to compaction, and the evolution of these consequences in the short-term. This work is based on two experimental sites, set up in the northeast of France, with soils displaying similar morphologies (50 cm thick silt loam layer laying on a clayey layer) and having being loaded with the same forwarder under similar (wet) soil conditions. Soil climate (temperature and moisture), soil air composition, and soil bulk density and resistance to penetration were investigated continuously, monthly and yearly, respectively. Soil climate and air composition monitoring showed a strong initial decrease in aerobic conditions lasting one to one and a half year. The strong initial impact on soil aeration decreased concurrently with the first soil drought experimented at both sites, probably because of soil cracks formation in the disturbed soil. Yet heavy traffic still affected significantly soil air composition 3 to 4 years after compaction at both sites. To monitor changes in soil physical parameters, we had to standardize measures with regards to soil climatic conditions at the time of sampling. Three to four years after soil compaction, the difference in soil physical properties between treatments was still significant. However, changes in the impact of the forwarder traffic on soil physical characteristics could be stated in the surface layer (0 10 cm) of both sites. This beginning of soil restoration results at one of both sites in a difference between treatments that is no longer significant when soils are wet but that is still significant when the soils are dry. At the second site, the difference is still significant whatever soil moisture conditions but it has decreased since the start of the experiment. Consequently, this beginning of soil structure recovery is not accompanied by a disappearance of the hardsetting behaviour (decrease in hydrostructural stability) of the compacted soil at one site. In this study changes in the consequences of the forwarder traffic were stated in the surface soil layers of both sites, these changes may be due to physical processes (wetting drying, freezing thawing). Nevertheless, the impact remains strong on roots growth (high resistance to penetration when dry, poor gas transfer when wet) and on stand resilience to external stresses (drought, storm).PARIS-AgroParisTech Centre Paris (751052302) / SudocSudocFranceF

Corps et souffrances génocidaires, plongée dans l’univers de la déshumanisation

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