On modeling chronic detachment of periphyton in artificial rough, open channel flow

Periphyton communities, which are native to river beds, serve as a functional indicator of river health but remain one of the least-studied communities despite the significant increase in the examination of aquatic microbial communities in recent years. In this study, we tested the relevance of three formulations of the chronic detachment term in a simple model for the biomass dynamics of periphyton. Numerical simulations of the periphyton biomass dynamics were performed by using three different descriptors for the flow conditions: the discharge Q, the friction velocity u⁄, and the roughness Reynolds number k+ = u⁄ks/m (where m is water kinetic viscosity and ks is the Nikuradse equivalent sand roughness). Comparisons of numerical simulation results with experimental data from literature revealed chronic detachment to be better simulated by taking the roughness Reynolds number as the external variable of detachment. These results support the idea that transport phenomena that occur in the nearbed layer, e.g. chronic detachment of periphyton matter or vertical transport of nutrients and pollutants in submerged aquatic canopies, are not related to a single turbulence descriptor such as the friction velocity u⁄. Its description requires at least two descriptors, here the friction velocity u⁄ and the Nikuradse equivalent sand roughness ks, which depend on the initial form and dimensions of the colonized substratum, and its changes owing to the thickness, resistance, and composition of the epilithic matter

Effect of near‐bed turbulence on chronic detachment of epilithic biofilm: Experimental and modeling approaches.

The biomass dynamics of epilithic biofilm, a collective term for a complex microorganism community that grows on gravel bed rivers, was investigated by coupling experimental and numerical approaches focusing on epilithic biofilm‐flow interactions. The experiment was conducted during 65 days in an artificial rough open‐channel flow, where filtered river water circulated at a constant discharge. To characterize the effect of near‐bed turbulence on the chronic detachment process in the dynamics of epilithic biofilm, local hydrodynamic conditions were measured by laser Doppler anemometry and turbulent boundary layer parameters inferred from double‐averaged quantities. Numerical simulations of the EB biomass dynamics were performed using three different models of chronic detachment based upon three different descriptors for the flow conditions: Discharge Q, friction velocity u*, and roughness Reynolds number k+. Comparisons of numerical simulation results with experimental data revealed chronic detachment to be better simulated by taking the roughness Reynolds number as the external physical variable forcing chronic detachment. Indeed, the loss of epilithic matter through the chronic detachment process is related not only to hydrodynamic conditions, but also to change in bottom roughness. This suggests that changes in the behavior and dimensions of river bed roughness must be considered when checking the dynamics of epilithic biofilm in running waters

Surveillance, epidemiological, and virological detection of highly pathogenic H5N1 avian influenza viruses in duck and poultry from Bangladesh

Avian influenza viruses (AIVs) continue to pose a global threat. Waterfowl are the main reservoir and are responsible for the spillover of AIVs to other hosts. This study was conducted as part of routine surveillance activities in Bangladesh and it reports on the serological and molecular detection of H5N1 AIV subtype. A total of 2169 cloacal and 2191 oropharyngeal swabs as well as 1725 sera samples were collected from live birds including duck and chicken in different locations in Bangladesh between the years of 2013 and 2014. Samples were tested using virus isolation, serological tests and molecular methods of RT-PCR. Influenza A viruses were detected using reverse transcription PCR targeting the virus matrix (M) gene in 41/4360 (0.94%) samples including both cloacal and oropharyngeal swab samples, 31 of which were subtyped as H5N1 using subtype-specific primers. Twenty-one live H5N1 virus isolates were recovered from those 31 samples. Screening of 1,868 blood samples collected from the same birds using H5-specific ELISA identified 545/1603 (34%) positive samples. Disconcertingly, an analysis of 221 serum samples collected from vaccinated layer chicken in four districts revealed that only 18 samples (8.1%) were seropositive for anti H5 antibodies, compared to unvaccinated birds (n=105), where 8 samples (7.6%) were seropositive. Our result indicates that the vaccination program as currently implemented should be reviewed and updated. In addition, surveillance programs are crucial for monitoring the efficacy of the current poultry vaccinations programs, and to monitor the circulating AIV strains and emergence of AIV subtypes in Bangladesh

Erratum to: Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) (Autophagy, 12, 1, 1-222, 10.1080/15548627.2015.1100356

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