Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Implications of Fine-Grained Habitat Fragmentation and Road Mortality for Jaguar Conservation in the Atlantic Forest, Brazil

<div><p>Jaguar (<i>Panthera onca</i>) populations in the Upper Paraná River, in the Brazilian Atlantic Forest region, live in a landscape that includes highly fragmented areas as well as relatively intact ones. We developed a model of jaguar habitat suitability in this region, and based on this habitat model, we developed a spatially structured metapopulation model of the jaguar populations in this area to analyze their viability, the potential impact of road mortality on the populations' persistence, and the interaction between road mortality and habitat fragmentation. In more highly fragmented populations, density of jaguars per unit area is lower and density of roads per jaguar is higher. The populations with the most fragmented habitat were predicted to have much lower persistence in the next 100 years when the model included no dispersal, indicating that the persistence of these populations are dependent to a large extent on dispersal from other populations. This, in turn, indicates that the interaction between road mortality and habitat fragmentation may lead to source-sink dynamics, whereby populations with highly fragmented habitat are maintained only by dispersal from populations with less fragmented habitat. This study demonstrates the utility of linking habitat and demographic models in assessing impacts on species living in fragmented landscapes.</p></div

Effects of road mortality rate for jaguar population.

Effects of road mortality rate for jaguar population.</p

Density dependence function used in this model (solid line) and its uncertainty limits used in the sensitivity analysis (dashed lines).

<p>In all models, the proportion of females that are breeding is 50% when population size (N) is small relative to carrying capacity. At carrying capacity, the proportion breeding is 32.9% (which gives an eigenvalue of 1.0; see text for details). The percent breeding declines as N increases, dropping to zero when N = 1.5∙K (1.25 to 1.75 used in the sensitivity analysis).</p

Properties of jaguar populations in the upper Paraná-Paranapanema, Brazil.

<p>Populations were identified by RAMAS GIS (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167372#pone.0167372.g004" target="_blank">Fig 4</a>).</p