An amplicon-based nanopore sequencing workflow for rapid tracking of avian influenza outbreaks, France, 2020-2022

During the recent avian influenza epizootics that occurred in France in 2020/21 and 2021/22, the virus was so contagiousness that it was impossible to control its spread between farms. The preventive slaughter of millions of birds consequently was the only solution available. In an effort to better understand the spread of avian influenza viruses (AIVs) in a rapid and innovative manner, we established an amplicon-based MinION sequencing workflow for the rapid genetic typing of circulating AIV strains. An amplicon-based MinION sequencing workflow based on a set of PCR primers targeting primarily the hemagglutinin gene but also the entire influenza virus genome was developed. Thirty field samples from H5 HPAIV outbreaks in France, including environmental samples, were sequenced using the MinION MK1C. A real-time alignment of the sequences with MinKNOW software allowed the sequencing run to be stopped as soon as enough data were generated. The consensus sequences were then generated and a phylogenetic analysis was conducted to establish links between the outbreaks. The whole sequence of the hemagglutinin gene was obtained for the 30 clinical samples of H5Nx HPAIV belonging to clade 2.3.4.4b. The consensus sequences comparison and the phylogenetic analysis demonstrated links between some outbreaks. While several studies have shown the advantages of MinION for avian influenza virus sequencing, this workflow has been applied exclusively to clinical field samples, without any amplification step on cell cultures or embryonated eggs. As this type of testing pipeline requires only a short amount of time to link outbreaks or demonstrate a new introduction, it could be applied to the real-time management of viral epizootics.

Household Cases Suggest That Cats Belonging to Owners with COVID-19 Have a Limited Role in Virus Transmission

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for COVID-19 and spread rapidly following its emergence in Wuhan in 2019. Although cats are, among other domestic animals, susceptible to SARS-CoV-2 infection, little is known about their epidemiological role in the dynamics of a household infection. In this study, we monitored five cats for viral shedding daily. Each cat was confined with its COVID-19 positive owners in separate households. Low loads of viral nucleic acid were found in two cats, but only one developed anti-SARS-CoV-2 antibodies, which suggests that cats have a limited role in COVID-19 epidemiology.

Endosymbiotic Sinorhizobium meliloti modulate Medicago root susceptibility to secondary infection via ethylene

A complex network of pathways coordinates nodulation and epidermal root hair infection in the symbiotic interaction between rhizobia and legume plants. Whereas nodule formation was known to be autoregulated, it was so far unclear whether a similar control is exerted on the infection process. We assessed the capacity of Medicago plants nodulated by Sinorhizobium meliloti to modulate root susceptibility to secondary bacterial infection or to purified Nod factors in split-root and volatile assays using bacterial and plant mutant combinations. Ethylene implication in this process emerged from gas production measurements, use of a chemical inhibitor of ethylene biosynthesis and of a Medicago mutant affected in ethylene signal transduction. We identified a feedback mechanism that we named AOI (for Autoregulation Of Infection) by which endosymbiotic bacteria control secondary infection thread formation by their rhizospheric peers. AOI involves activation of a cyclic adenosine 3',5'-monophosphate (cAMP) cascade in endosymbiotic bacteria, which decreases both root infectiveness and root susceptibility to bacterial Nod factors. These latter two effects are mediated by ethylene. AOI is a novel component of the complex regulatory network controlling the interaction between Sinorhizobium meliloti and its host plants that emphasizes the implication of endosymbiotic bacteria in fine-tuning the interaction.

Functional Tests for the Characterization of Surfactant Protein B (SP-B) and a Fluorescent SP-B Analog

Surfactant protein B (SP-B) enhances lipid insertion into the alveolar air/liquid interface upon inhalation. The aim of this study was (i) to apply a palette of tests for a detailed biochemical and biophysical characterization of SP-B and (ii) to use these tests to compare native SP-B with a fluorescent (Bodipy) SP-B analog. The method of labeling was fast and resulted in a covalent fluorophore-protein bond. The ability of both proteins to spread a surfactant film on top of a buffer surface was determined in a spreading tray using the Wilhelmy plate technique to allow detection of alterations in surface tension and calculation of spreading velocities. In a captive bubble surfactometer surface tensions of spread films were measured. Similar biophysical properties were found for both native and Bodipy-labeled SP-B. It is concluded that the combination of tests used allows detection of small differences in structure and activity between the two proteins.

Effect of streptolysin O on the microelasticity of human platelets analyzed by atomic force microscopy

Atomic force microscopy (AFM) has been shown to be a suitable tool to probe biophysical properties of cells and cell fragments. We analysed biophysical alterations of human platelets by AFM using streptolysin O (SLO) as a model for pore forming proteins. Permeabilization of platelet membrane by SLO was confirmed by transmission electron and confocal microscopy. Using force volume imaging combined with FIEL analysis we were able to show dynamically the increase in the elasticity of platelets during the pore formation by SLO and could correlate the viscoelasticity to the morphology of platelets. Stabilizing the actin cytoskeleton by phalloidin resulted in partial restoration of the elasticity indicating that loss of stability in platelets by SLO is mediated by alterations of both plasma membrane and cytoskeleton.

Hydrophobic lung surfactant proteins B and C remain associated with surface film during dynamic cyclic area changes

The biophysical activity of lung surfactant depends, to a large extent, on the presence of the hydrophobic surfactant proteins B (SP-B) and C (SP-C). The role of these proteins in lipid adsorption and lipid squeeze-out under dynamic conditions simulating breathing is not yet clear. Therefore, the aim of this study was to investigate the interaction of spread hydrophobic surfactant proteins with phospholipids in a captive-bubble surfactometer during rapid cyclic area changes (6 cycles/min). We found that SP-B and SP-C facilitated the rapid transport of lipids into the air-water interface in a concentration-dependent manner (threshold concentration > or = 0.05:0.5 mol% SP-B/SP-C). Successive rapid cyclic area changes did not affect the concentration-dependent lipid adsorption process, suggesting that SP-B and SP-C remained associated with the surface film.

A spreading technique for forming film in a captive bubble

Mechanisms underlying the surface properties of lung surfactant are extensively studied in in vitro systems such as the captive-bubble surfactometer (CBS), the pulsating-bubble surfactometer, and the Wilhelmy balance. Among these systems, the CBS is advantageous when a leakproof system and high cycling rates are required. However, widespread application of the CBS to mechanistic studies of dynamic surfactant protein-phospholipid interactions of spread film and to comparative studies between spread and adsorbed film is hampered because spreading of film is difficult. In addition, when film is formed by adsorption, the amount of material required is fairly large. We have developed an easy spreading technique that allows routine formation of film by spreading of small amounts of surfactant components at the air-water interface of an air bubble in a CBS. The technique is reliable, precise, and accurate, and the biophysical activity of film formed by spreading is similar to that of film formed by adsorption. This method will be useful for mechanistic studies of surfactant components under dynamic conditions and for comparative studies of spread films and adsorbed films.

Bacterial succession within a biofilm in water supply lines of dental air-water syringes

Biofilms have been implicated as reservoirs for bacterial contamination of water delivered by dental air-water syringes. A 6-month study was done of bacterial colonization and biofilm formation in plastic water supply lines connected to dental air-water syringes. Changes in biofilm flora were observed by both scanning electron microscopy and bacteriologic culture. By day 7, many rod- and spiral-shaped bacteria had colonized the ridged surface of the luminal wall of the tubing, as revealed by scanning electron microscopy. By day 30, individual microcolonies were embedded in extracellular polymeric material. By day 120, these microcolonies had begun to coalesce, and by day 180 the biofilm had developed into a multilayered, heterogeneous mixture of microcolonies. The mean aerobic plate counts of colony-forming units of planktonic and biofilm populations were, in log10 values, 5.9 +/- 0.54/mL and 4.2 +/- 0.82/cm2, respectively. Early colonizers were predominantly Pseudomonas spp., but included Pasteurella, Moraxella, Ochrobactrum, and Aeromonas spp. Flavobacterium and Acinetobacter spp. were observed later. Many of these organisms are opportunistic pathogens. These results demonstrate the longitudinal dynamics of biofilm formation.

Molecular computing for edge-enhanced laser imaging

In order to illustrate the self-assembly capability, we consider a laser imaging experiment on a wet film that is made of bacteriorhodopsin (BR) molecules suspended in a diffusion-limited viscous medium. BR wet film is similar to a wet photograph film but having a finer resolution and adaptive pixel locations due to laser-induced thermal diffusion. The synergism between thermal diffusion of BR molecules (induced externally by a write-laser) and molecular photochromism (generated internally by a read-laser) is exploited naturally for edge-enhanced image applications.

Ammonia Induces Settlement Behavior in Oyster Larvae

Oyster larvae exposed to solutions of NH4Cl exhibit stereotypical settlement behavior similar to that which normally precedes cementation and metamorphosis. Un-ionized ammonia is the active chemical species. At pH = 8.0, the threshold concentration of NH4Cl (pH = 8.0) for newly competent larvae is 2.5 mM; maximum activity is at 7.9 mM, corresponding to calculated NH3 concentrations of 100 {mu}M and 310 {mu}M, respectively. Induction of settlement behavior is rapid, with >90% of larvae exposed to 310 {mu}M NH3 responding within less than 5 min. After 15 to 30 min, larvae become habituated to NH3 and resume swimming so that the percent exhibiting settlement behavior after 30 min is <10%. Other weak bases, such as methylamine and trimethylamine, induce similar behavior suggesting that NH3 acts by increasing intracellular pH. Evidence that NH3 and L-3,4-dihyrodxyphenylalanine (L-DOPA) induce settlement behavior through different mechanisms is presented. Ammonia may be a natural environmental cue that promotes oyster settlement behavior and, ultimately, recruitment.

Factors influencing bacterial production of inducers of settlement behavior of larvae of the oysterCrassostrea gigas

Dissolved chemical inducers of settlement behavior of veliger larvae of the oysterCrassostrea gigas are found in supernatants of both pigmented species of bacteria (Alteromonas colwelliana, Vibrio cholerae strain HTX) as well as nonpigmented bacteria (Excherichia coli, Vibrio cholerae strain 596-B). Usually less than 10% of veligers exhibited settlement behavior in response to supernatants from the early bacterial growth phases, whereas 30-90% of larvae responded when exposed to supernatant from late-log and stationary phase cultures. Percentages of larvae exhibiting settlement behavior were inversely correlated with oxygen levels in the culture. Furthermore, the behavioral response decreased with pigment formation, suggesting that quantities of noxious compounds such as quinones may build up in the supernatants of cultures of pigmented bacteria. Tyrosinase, an enzyme that converts L-tyrosine to L-DOPA in the first step of melanogenesis, was detected both in the bacterial pellet and the supernatant during growth of the pigmented species. The enzyme is not required for the production of settlement inducer as the nonpigmented speciesE. coli andV. cholerae (596-B) also released inducer into the supernatant and had no detectable tyrosinase. The data suggest either that there is more than one inducer of settlement behavior found in bacterial supernatants or that the inducer is not L-DOPA or an L-DOPA-mimetic associated with the melanin biochemical pathway.