Approximate maximum likelihood estimation for stochastic chemical kinetics

Recent experimental imaging techniques are able to tag and count molecular populations in a living cell. From these data mathematical models are inferred and calibrated. If small populations are present, discrete-state stochastic models are widely-used to describe the discreteness and randomness of molecular interactions. Based on time-series data of the molecular populations, the corresponding stochastic reaction rate constants can be estimated. This procedure is computationally very challenging, since the underlying stochastic process has to be solved for different parameters in order to obtain optimal estimates. Here, we focus on the maximum likelihood method and estimate rate constants, initial populations and parameters representing measurement errors.     

Confocal-multilabeling, ultrasensitive TUNEL analysis of DNA breaks in individual cells

OBJECTIVE: To visualize and localize fragmented DNA strands within apoptotic cells by means of fluorescence using TdT-mediated dUTP-biotin nick end labeling (TUNEL) techniques, laser scanning confocal microscopy (CLSM) and factor analysis of biomedical image sequences (FAMIS). STUDY DESIGN: For this experiment, lymphoid reverted cells were used as a model. Characteristic DNA breaks inside apoptotic cells were detected using TUNEL techniques by a reaction involving tetramethyl rhodamin isothyocyanate (TRITC). The DNA from cell nuclei was counterstained using chromomycin A3 (CA3). The tandem TRITC-CA3 in CLSM was applied to investigate the ability to detect DNA breaks in individual cells using TUNEL techniques and its amplified variants (TUNEL-CARD). FAMIS was applied on dynamic sequences of images of TUNEL preparations and on four-dimensional (4-D) sequences of images of TUNEL-CARD preparations. RESULTS: Distribution and amplitude of fluorescent structures were characterized on dynamic sequences of images. Characterization was improved when FAMIS was applied on 4-D sequences of images, taking into account differences in photobleaching and/or spectrum of TRITC and CA3. CONCLUSION: It is possible to discriminate targets from CA3. FAMIS and TUNEL methods can be used to visualize and localize multiple DNA breaks in lymphoid reverted cells in improved methods of experimentation.     

Growth of 19 conifer species is highly sensitive to winter warming,spring frost and summer drought

Background and AimsConifers are key components of many temperate and boreal forests and are important for forestry, but species differences in stem growth responses to climate are still poorly understood and may hinder effective management of these forests in a warmer and drier future.MethodsWe studied 19 Northern Hemisphere conifer species planted in a 50-year-old common garden experiment in the Netherlands to (1) assess the effect of temporal dynamics in climate on stem growth, (2) test for a possible positive relationship between the growth potential and climatic growth sensitivity across species, and (3) evaluate the extent to which stem growth is controlled by phylogeny.Key resultsEighty-nine per cent of the species showed a significant reduction in stem growth to summer drought, 37 % responded negatively to spring frost and 32 % responded positively to higher winter temperatures. Species differed largely in their growth sensitivity to climatic variation and showed, for example, a four-fold difference in growth reduction to summer drought. Remarkably, we did not find a positive relationship between productivity and climatic sensitivity, but instead observed that some species combined a low growth sensitivity to summer drought with high growth potential. Both growth sensitivity to climate and growth potential were partly phylogenetically controlled.ConclusionsA warmer and drier future climate is likely to reduce the productivity of most conifer species. We did not find a relationship between growth potential and growth sensitivity to climate; instead, some species combined high growth potential with low sensitivity to summer drought. This may help forest managers to select productive species that are able to cope with a warmer and drier future.