Parameter estimation for the distribution of single cell lag times

In Quantitative Microbial Risk Assessment, it is vital to understand how lag times of individual cells are distributed over a bacterial population. Such identified distributions can be used to predict the time by which, in a growth-supporting environment, a few pathogenic cells can multiply to a poisoning concentration level.We model the lag time of a single cell, inoculated into a new environment, by the delay of the growth function characterizing the generated subpopulation. We introduce an easy-to-implement procedure, based on the method of moments, to estimate the parameters of the distribution of single cell lag times. The advantage of the method is especially apparent for cases where the initial number of cells is small and random, and the culture is detectable only in the exponential growth phase.     

Genome size in wild Pisum species

Genome size was measured in 75 samples of the wild pea species Pisum abyssinicum, P. elatius, P. fulvum and P. humile by ethidium-bromide (EB) flow cytometry (internal standard: Triticum monococcum) and Feulgen densitometry (internal standard: Pisum sativum Kleine Rheinländerin). Total variation of EB-DNA between samples covered 97.7% to 114.9% of the P. sativum value, and Feulgen DNA values were strongly correlated with EB-DNA values (r=0.9317, P < 0.001). Only P. fulvum was homogeneous in genome size (108.9% of P. sativum). Wide variation was observed between samples in P. abyssinicum (100.9–109.7%), P. elatius (97.7–114.9%) and P. humile (98.3–111.1% of P. sativum). In view of the world-wide genome size constancy in P. sativum, the present data are interpreted to show that the pea taxa with variable genome size are genetically inhomogeneous and that the current classification is not sufficient to describe the biological species groups adequately.     

Observing growth and division of large numbers of individual bacteria by image analysis

We describe a method that enabled us to observe large numbers of individual bacterial cells during a long period of cell growth and proliferation. We designed a flow chamber in which the cells attached to a transparent solid surface. The flow chamber was mounted on a microscope equipped with a digital camera. The shear force of the flow removed the daughter cells, making it possible to monitor the consecutive divisions of a single cell. In this way, kinetic parameters and their distributions, as well as some physiological characteristics of the bacteria, could be analyzed based on more than 1,000 single-cell observations. The method which we developed enabled us to study the history effect on the distribution of the lag times of single cells.     

Distribution of turbidity detection times produced by single cell-generated bacterial populations

The distributions of the times to turbidity for wells inoculated with single cells of Listeria innocua were determined in different environmental conditions (pH 4.5 to 7 and with 0.5% to 8% of NaCl at 30 degrees C). It was established by statistical analysis that the main source of the variability of the detection times, T, is the variability of individual lag times. A linear relation dev(T) approximately T was observed between the detection times and their standard deviation. At slow growth, other sources of variability became increasingly significant.     

Animal models of complement-mediated hypersensitivity reactions to liposomes and other lipid-based nanoparticles

Intravenous injection of some liposomal drugs, diagnostic agents, micelles and other lipid-based nanoparticles can cause acute hypersensitivity reactions (HSRs) in a high percentage (up to 45%) of patients, with hemodynamic, respiratory and cutaneous manifestations. The phenomenon can be explained with activation of the complement (C) system on the surface of lipid particles, leading to anaphylatoxin (C5a and C3a) liberation and subsequent release reactions of mast cells, basophils and possibly other inflammatory cells in blood. These reactions can be reproduced and studied in pigs, dogs and rats, animal models which differ from each other in sensitivity and spectrum of symptoms. In the most sensitive pig model, a few miligrams of liposome (phospholipid) can cause anaphylactoid shock, characterized by pulmonary hypertension, systemic hypotension, decreased cardiac output and major cardiac arrhythmias. Pigs also display cutaneous symptoms, such as flushing and rash. The sensitivity of dogs to hemodynamic changes is close to that of pigs, but unlike pigs, dogs also react to micellar lipids (such as Cremophor EL) and their response includes pronounced blood cell and vegetative neural changes (e.g., leukopenia followed by leukocytosis, thrombocytopenia, fluid excretions). Rats are relatively insensitive inasmuch as hypotension, their most prominent response to liposomes, is induced only by one or two orders of magnitude higher phospholipid doses (based on body weight) compared to the reactogenic dose in pigs and dogs. It is suggested that the porcine and dog models are applicable for measuring and predicting the (pseudo)allergic activity of particulate "nanodrugs".     

Transgenic rabbit production with simian immunodeficiency virus-derived lentiviral vector

Transgenic rabbit is the preferred disease model of atherosclerosis, lipoprotein metabolism and cardiovascular diseases since upon introducing genetic mutations of human genes, rabbit models reflect human physiological and pathological states more accurately than mouse models. Beyond that, transgenic rabbits are also used as bioreactors to produce pharmaceutical proteins in their milk. Since in the laboratory rabbit the conventional transgenesis has worked with the same low efficiency in the last twenty five years and truly pluripotent embryonic stem cells are not available to perform targeted mutagenesis, our aim was to adapt lentiviral transgenesis to this species. A simian immunodeficiency virus based replication defective lentiviral vector was used to create transgenic rabbit through perivitelline space injection of fertilized oocytes. The enhanced green fluorescent protein (GFP) gene was placed under the ubiquitous CAG promoter. Transgenic founder rabbits showed mosaic pattern of GFP expression. Transgene integration and expression was revealed in tissues derived from all three primary germ layers. Transgene expression was detected in the developing sperm cells and could get through the germ line without epigenetic silencing, albeit with very low frequency. Our data show for the first time, that lentiviral transgenesis could be a feasible and viable alternative method to create genetically modified laboratory rabbit.     

Soil carbon and nitrogen dynamics along a latitudinal transect in Western Siberia, Russia

An 1800-km South to North transect (N 53°43′ to 69°43′) through Western Siberia was established to study the interaction of nitrogen and carbon cycles. The transect comprised all major vegetation zones from steppe, through taiga to tundra and corresponded to a natural temperature gradient of 9.5°C mean annual temperature (MAT). In order to elucidate changes in the control of C and N cycling along this transect, we analyzed physical and chemical properties of soils and microbial structure and activity in the organic and in the mineral horizons, respectively. The impact of vegetation and climate exerted major controls on soil C and N pools (e.g., soil organic matter, total C and dissolved inorganic nitrogen) and process rates (gross N mineralization and heterotrophic respiration) in the organic horizons. In the mineral horizons, however, the impact of climate and vegetation was less pronounced. Gross N mineralization rates decreased in the organic horizons from south to north, while remaining nearly constant in the mineral horizons. Especially, in the northern taiga and southern tundra gross nitrogen mineralization rates were higher in the mineral compared to organic horizons, pointing to strong N limitation in these biomes. Heterotrophic respiration rates did not exhibit a clear trend along the transect, but were generally higher in the organic horizon compared to mineral horizons. Therefore, C and N mineralization were spatially decoupled at the northern taiga and tundra. The climate change implications of these findings (specifically for the Arctic) are discussed.     

Use of Optical Density Detection Times To Assess the Effect of Acetic Acid on Single-Cell Kinetics

The growth of Listeria innocua at different acetic acid concentrations (0 to 2,000 ppm) was monitored by optical density measurements in a Bioscreen (Labsystems, Vantaa, Finland). The generated populations came from low inocula that were obtained by serial dilution. A new method to estimate both the growth rate and the lag time of single cells from the detection times (time to reach an optical density of 0.11) was developed. It assumes that the single-cell lag times follow a gamma distribution and takes into account the randomness of the inoculation level. (The initial cell number per well was assumed to follow a Poisson distribution.) In this way, relatively small numbers of replicates are sufficient to obtain a robust estimation of the distribution of single-cell lag times. The results were validated with plate count experiments. It was found that logarithms of both the growth rates and of population lag times increased linearly with the acetic acid concentration. The logarithm of the scale parameter of the gamma distribution of the single-cell lag times also increased linearly with the acetic acid concentration irrespective of the phase of the inoculum.     

Complexity of the international agro-food trade network and its impact on food safety

With the world's population now in excess of 7 billion, it is vital to ensure the chemical and microbiological safety of our food, while maintaining the sustainability of its production, distribution and trade. Using UN databases, here we show that the international agro-food trade network (IFTN), with nodes and edges representing countries and import-export fluxes, respectively, has evolved into a highly heterogeneous, complex supply-chain network. Seven countries form the core of the IFTN, with high values of betweenness centrality and each trading with over 77% of all the countries in the world. Graph theoretical analysis and a dynamic food flux model show that the IFTN provides a vehicle suitable for the fast distribution of potential contaminants but unsuitable for tracing their origin. In particular, we show that high values of node betweenness and vulnerability correlate well with recorded large food poisoning outbreaks.     

Single-cell and population lag times as a function of cell age

After inoculation, the times to the first divisions are longer and more widely distributed for those Escherichia coli single cells that spent more time in the stationary phase prior to inoculation. The second generation times are still longer than the typical generation times in the exponential phase, and this extended the apparent lag time of the cell population. The greater the variability of the single-cell interdivision intervals, the shorter are both the lag time and the doubling time of the population.