REAL-TIME METHOD FOR THE DETECTION OF VIABLE MICRO-ORGANISMS

The invention relates to a method for real-time detection of viable microorganisms comprising: a. addition of a cell-permeable, phototautomeric compound to a micro-organism or other living cell; and b. measuring the fluorescent emission of said phototautomeric compound. Preferably the phototautomeric compound is salicylic acid, 2-hydroxy-1-naphtoic acid or 1-hydroxy-2-naphtoic acid. Further, the assay can he used to assess the antibiotic effect of a test compound. This test can be used as a high-throughput screening for compounds with antibiotic activity. Also part of the invention is the use of a cell permeable phototautomeric compound in a method for determining the viability of micro-organisms and for assessing the antibiotic effect of a test compound

Magma Design Automation: Component placement on chips; the "holey cheese" problem.

The costs of the fabrication of a chip is partly determined by the wire length needed by the transistors to respect the wiring scheme. The transistors have to be placed without overlap into a prescribed configuration of blockades, i.e. parts of the chipthat are beforehand excluded from positioning by for example some other functional component, and holes, i.e. the remaining free area on the chip. A method to minimize the wire length when the free area is a simply connected domain has already been implemented by Magma, but the placement problem becomes much more complex when the free area is not a simply connected domain anymore, forming a ``holey cheese''. One of the approaches of the problem in this case is to first cluster the transistors into so-called macro's in such a way that closely interconnected transistors stay together, and that the macro's can be fit into the holes. One way to carry out the clustering is to use a graph clustering algorithm, the so-called Markov Cluster algorithm. Another way is to combine the placement method of Magma on a rectangular area of the same size as the total size of the holes, and a min cut-max flow algorithm to divide that rectangle into more or less rectangular macro's in such a way that as little wires as possible are cut. It is now possible to formulate the Quadratic Assignment Problem that remains after clustering the original problem to one with 100 up to 1000 macros. There exists a lot of literature on finding the global minimum of the costs, but nowadays computational possibilities are still too restrictive to find an optimal solution within a reasonable amount of time and computational memory. however, we believe it is possible to find a solution that leads to a acceptable local minimum of the costs

A comparison of 3D particle, fluid and hybrid simulations for negative streamers

In the high field region at the head of a discharge streamer, the electron energy distribution develops a long tail. In negative streamers, these electrons can run away and contribute to energetic processes such as terrestrial gamma-ray and electron flashes. Moreover, electron density fluctuations can accelerate streamer branching. To track energies and locations of single electrons in relevant regions, we have developed a 3D hybrid model that couples a particle model in the region of high fields and low electron densities with a fluid model in the rest of the domain. Here we validate our 3D hybrid model on a 3D (super-)particle model for negative streamers in overvolted gaps, and we show that it almost reaches the computational efficiency of a 3D fluid model. We also show that the extended fluid model approximates the particle and the hybrid model well until stochastic fluctuations become important, while the classical fluid model underestimates velocities and ionization densities. We compare density fluctuations and the onset of branching between the models, and we compare the front velocities with an analytical approximation

Positive and negative streamers in ambient air: modeling evolution and velocities

We simulate short positive and negative streamers in air at standard temperature and pressure. They evolve in homogeneous electric fields or emerge from needle electrodes with voltages of 10 to 20 kV. The streamer velocity at given streamer length depends only weakly on the initial ionization seed, except in the case of negative streamers in homogeneous fields. We characterize the streamers by length, head radius, head charge and field enhancement. We show that the velocity of positive streamers is mainly determined by their radius and in quantitative agreement with recent experimental results both for radius and velocity. The velocity of negative streamers is dominated by electron drift in the enhanced field; in the low local fields of the present simulations, it is little influenced by photo-ionization. Though negative streamer fronts always move at least with the electron drift velocity in the local field, this drift motion broadens the streamer head, decreases the field enhancement and ultimately leads to slower propagation or even extinction of the negative streamer.Comment: 18 pages, 10 figure

Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data

<p>Abstract</p> <p>Background</p> <p><it>Saccharomyces cerevisiae </it>is the first eukaryotic organism for which a multi-compartment genome-scale metabolic model was constructed. Since then a sequence of improved metabolic reconstructions for yeast has been introduced. These metabolic models have been extensively used to elucidate the organizational principles of yeast metabolism and drive yeast strain engineering strategies for targeted overproductions. They have also served as a starting point and a benchmark for the reconstruction of genome-scale metabolic models for other eukaryotic organisms. In spite of the successive improvements in the details of the described metabolic processes, even the recent yeast model (i.e., <it>i</it>MM904) remains significantly less predictive than the latest <it>E. coli </it>model (i.e., <it>i</it>AF1260). This is manifested by its significantly lower specificity in predicting the outcome of grow/no grow experiments in comparison to the <it>E. coli </it>model.</p> <p>Results</p> <p>In this paper we make use of the automated GrowMatch procedure for restoring consistency with single gene deletion experiments in yeast and extend the procedure to make use of synthetic lethality data using the genome-scale model <it>i</it>MM904 as a basis. We identified and vetted using literature sources 120 distinct model modifications including various regulatory constraints for minimal and YP media. The incorporation of the suggested modifications led to a substantial increase in the fraction of correctly predicted lethal knockouts (i.e., specificity) from 38.84% (87 out of 224) to 53.57% (120 out of 224) for the minimal medium and from 24.73% (45 out of 182) to 40.11% (73 out of 182) for the YP medium. Synthetic lethality predictions improved from 12.03% (16 out of 133) to 23.31% (31 out of 133) for the minimal medium and from 6.96% (8 out of 115) to 13.04% (15 out of 115) for the YP medium.</p> <p>Conclusions</p> <p>Overall, this study provides a roadmap for the computationally driven correction of multi-compartment genome-scale metabolic models and demonstrates the value of synthetic lethals as curation agents.</p

A Genomic Approach for the Identification and Classification of Genes Involved in Cell Wall Formation and its Regulation in Saccharomyces Cerevisiae

Using a hierarchical approach, 620 non-essential single-gene yeast deletants generated by EUROFAN I were systematically screened for cell-wall-related phenotypes. By analyzing for altered sensitivity to the presence of Calcofluor white or SDS in the growth medium, altered sensitivity to sonication, or abnormal morphology, 145 (23%) mutants showing at least one cell wall-related phenotype were selected. These were screened further to identify genes potentially involved in either the biosynthesis, remodeling or coupling of cell wall macromolecules or genes involved in the overall regulation of cell wall construction and to eliminate those genes with a more general, pleiotropic effect. Ninety percent of the mutants selected from the primary tests showed additional cell wall-related phenotypes. When extrapolated to the entire yeast genome, these data indicate that over 1200 genes may directly or indirectly affect cell wall formation and its regulation. Twenty-one mutants with altered levels of β1,3-glucan synthase activity and five Calcofluor white-resistant mutants with altered levels of chitin synthase activities were found, indicating that the corresponding genes affect β1,3-glucan or chitin synthesis. By selecting for increased levels of specific cell wall components in the growth medium, we identified 13 genes that are possibly implicated in different steps of cell wall assembly. Furthermore, 14 mutants showed a constitutive activation of the cell wall integrity pathway, suggesting that they participate in the modulation of the pathway either directly acting as signaling components or by triggering the Slt2-dependent compensatory mechanism. In conclusion, our screening approach represents a comprehensive functional analysis on a genomic scale of gene products involved in various aspects of fungal cell wall formation

Crossmodal duration perception involves perceptual grouping, temporal ventriloquism, and variable internal clock rates

Here, we investigate how audiovisual context affects perceived event duration with experiments in which observers reported which of two stimuli they perceived as longer. Target events were visual and/or auditory and could be accompanied by nontargets in the other modality. Our results demonstrate that the temporal information conveyed by irrelevant sounds is automatically used when the brain estimates visual durations but that irrelevant visual information does not affect perceived auditory duration (Experiment 1). We further show that auditory influences on subjective visual durations occur only when the temporal characteristics of the stimuli promote perceptual grouping (Experiments 1 and 2). Placed in the context of scalar expectancy theory of time perception, our third and fourth experiments have the implication that audiovisual context can lead both to changes in the rate of an internal clock and to temporal ventriloquism-like effects on perceived on- and offsets. Finally, intramodal grouping of auditory stimuli diminished any crossmodal effects, suggesting a strong preference for intramodal over crossmodal perceptual grouping (Experiment 5)

Optimization of interneuron function by direct coupling of cell migration and axonal targeting

Neural circuit assembly relies on the precise synchronization of developmental processes, such as cell migration and axon targeting, but the cell-autonomous mechanisms coordinating these events remain largely unknown. Here we found that different classes of interneurons use distinct routes of migration to reach the embryonic cerebral cortex. Somatostatin-expressing interneurons that migrate through the marginal zone develop into Martinotti cells, one of the most distinctive classes of cortical interneurons. For these cells, migration through the marginal zone is linked to the development of their characteristic layer 1 axonal arborization. Altering the normal migratory route of Martinotti cells by conditional deletion of Mafb—a gene that is preferentially expressed by these cells—cell-autonomously disrupts axonal development and impairs the function of these cells in vivo. Our results suggest that migration and axon targeting programs are coupled to optimize the assembly of inhibitory circuits in the cerebral cortex

Famine food of vegetal origin consumed in the Netherlands during World War II

Background: Periods of extreme food shortages during war force people to eat food that they normally do not consider edible. The last time that countries in Western Europe experienced severe scarcities was during World War II. The so-called Dutch famine or Hunger Winter (1944-1945) made at least 25,000 victims. The Dutch government took action by opening soup kitchens and providing information on wild plants and other famine food sources in "wartime cookbooks." The Dutch wartime diet has never been examined from an ethnobotanical perspective. Methods: We interviewed 78 elderly Dutch citizens to verify what they remembered of the consumption of vegetal and fungal famine food during World War II by them and their close surroundings. We asked whether they experienced any adverse effects from consuming famine food plants and how they knew they were edible. We identified plant species mentioned during interviews by their local Dutch names and illustrated field guides and floras. We hypothesized that people living in rural areas consumed more wild species than urban people. A Welch t test was performed to verify whether the number of wild and cultivated species differed between urban and rural citizens. Results: A total number of 38 emergency food species (14 cultivated and 21 wild plants, three wild fungi) were mentioned during interviews. Sugar beets, tulip bulbs, and potato peels were most frequently consumed. Regularly eaten wild species were common nettle, blackberry, and beechnuts. Almost one third of our interviewees explicitly described to have experienced extreme hunger during the war. People from rural areas listed significantly more wild species than urban people. The number of cultivated species consumed by both groups was similar. Negative effects were limited to sore throats and stomachache from the consumption of sugar beets and tulip bulbs. Knowledge on the edibility of famine food was obtained largely by oral transmission; few people remembered the written recipes in wartime cookbooks. Conclusion: This research shows that 71years after the Second World War, knowledge on famine food species, once crucial for people's survival, is still present in the Dutch society. The information on famine food sources supplied by several institutions was not distributed widely. For the necessary revival of famine food knowledge during the 1940s, people needed to consult a small group of elders. Presumed toxicity was a major reason given by our participants to explain why they did not collect wild plants or mushrooms during the war