Genomics and the renaissance of generalism

A meeting report of the sessions on human, eukaryotic and bacterial genome sequencing at the American Society for Microbiology and Institut Pasteur joint conference: Genomes 2000 International Conference on Microbial and Model Genomes, Paris, April 11-15, 2000     

Sensitivity Analysis of Variable-Size Group Testing and its Related Continuous Models

Parallels between the discrete group-testing model and some closely-related continuous models are elucidated. It is shown that in both the discrete and continuous cases, the maximum likelihood estimators may suffer from similar lack of robustness. Isotonic regression and maximum likelihood estimation were therefore compared for a modified group testing model.     

Drag-Based ‘Hovering’ in Ducks: The Hydrodynamics and Energetic Cost of Bottom Feeding

Diving ducks use their webbed feet to provide the propulsive force that moves them underwater. To hold position near the bottom while feeding, ducks paddle constantly to resist the buoyant force of the body. Using video sequences from two orthogonal cameras we reconstructed the 3-dimensional motion of the feet through water and estimated the forces involved with a quasi-steady blade-element model. We found that during station holding, near the bottom, ducks use drag based propulsion with the webbed area of the foot moving perpendicular to the trajectory of the foot. The body was pitched at 76±3.47° below the horizon and the propulsive force was directed 26±1.9° ventral to the body so that 98% of the propulsive force in the sagittal plane of the duck worked to oppose buoyancy. The mechanical work done by moving both feet through a paddling cycle was 1.1±0.2 J which was equivalent to an energy expenditure of 3.7±0.5 W to hold position while feeding at 1.5 m depth. We conclude that in shallow water the high energetic cost of feeding in ducks is due to the need to paddle constantly against buoyancy even after reaching the bottom. The mechanical energy spent on holding position near the bottom, while feeding, is approximately 2 fold higher than previous estimates that were made for similar bottom depths but based on the presumed motion of the body instead of motion of the feet.     

One-electron reduction of adriamycin: Properties of the semiquinone

Pulse radiolysis of aqueous solutions containing adriamycin and redox indicators of known one-electron reduction potential (E¹) shows that its E¹ at pH 7 is ?328 mV (vs NHE). The variation E¹ with pH in the range 6–12 shows that the net charge on the semiquinone at pH 7 is zero. As well as the pK_a values of 2.9 and ≥ 14 established independently, the semiquinone has a pK_a close to 9.2. The new data enable the structure and likely reactivity of the semiquinone to be specified.     

The −14010*C variant associated with lactase persistence is located between an Oct-1 and HNF1α binding site and increases lactase promoter activity

In most people worldwide intestinal lactase expression declines in childhood. In many others, particularly in Europeans, lactase expression persists into adult life. The lactase persistence phenotype is in Europe associated with the −13910*T single nucleotide variant located 13,910 bp upstream the lactase gene in an enhancer region that affects lactase promoter activity. This variant falls in an Oct-1 binding site and shows greater Oct-1 binding than the ancestral variant and increases enhancer activity. Several other variants have been identified very close to the −13910 position, which are associated with lactase persistence in the Middle East and Africa. One of them, the −14010*C, is associated with lactase persistence in Africa. Here we show by deletion analysis that the −14010 position is located in a 144 bp region that reduces the enhancer activity. In transfections the −14010*C allele shows a stronger enhancer effect than the ancestral −14010*G allele. Binding sites for Oct-1 and HNF1α surrounding the −14010 position were identified by gel shift assays, which indicated that −14010*C has greater binding affinity to Oct-1 than −14010*G.     

<Emphasis Type="Italic">Caenorhabditis elegans</Emphasis>: a model to monitor bacterial air quality

Background

Low environmental air quality is a significant cause of mortality and morbidity and this question is now emerging as a main concern of governmental authorities. Airborne pollution results from the combination of chemicals, fine particles, and micro-organisms quantitatively or qualitatively dangerous for health or for the environment. Increasing regulations and limitations for outdoor air quality have been decreed in regards to chemicals and particles contrary to micro-organisms. Indeed, pertinent and reliable tests to evaluate this biohazard are scarce. In this work, our purpose was to evaluate the Caenorhaditis elegans killing test, a model considered as an equivalent to the mouse acute toxicity test in pharmaceutical industry, in order to monitor air bacterial quality.

Findings

The present study investigates the bacterial population in dust clouds generated during crop ship loading in harbor installations (Rouen harbor, Normandy, France). With a biocollector, airborne bacteria were impacted onto the surface of agar medium. After incubation, a replicate of the colonies on a fresh agar medium was done using a velvet. All the replicated colonies were pooled creating the "Total Air Sample". Meanwhile, all the colonies on the original plate were isolated. Among which, five representative bacterial strains were chosen. The virulence of these representatives was compared to that of the "Total Air Sample" using the Caenorhaditis elegans killing test. The survival kinetic of nematodes fed with the "Total Air Sample" is consistent with the kinetics obtained using the five different representatives strains.

Conclusions

Bacterial air quality can now be monitored in a one shot test using the Caenorhaditis elegans killing test.