ALBERT

Description: Motivation: Cell growth and division affect the kinetics of internal cellular processes and the phenotype diversity of cell populations. Since the effects are complex, e.g. different cellular components are partitioned differently in cell division, to account for them in silico, one needs to simulate these processes in great detail. Results : We present SGNS2, a simulator of chemical reaction systems according to the Stochastic Simulation Algorithm with multi-delayed reactions within hierarchical, interlinked compartments which can be created, destroyed and divided at runtime. In division, molecules are randomly segregated into the daughter cells following a specified distribution corresponding to one of several partitioning schemes, applicable on a per-molecule-type basis. We exemplify its use with six models including a stochastic model of the disposal mechanism of unwanted protein aggregates in Escherichia coli , a model of phenotypic diversity in populations with different levels of synchrony, a model of a bacteriophage’s infection of a cell population and a model of prokaryotic gene expression at the nucleotide and codon levels. Availability : SGNS2, instructions and examples available at www.cs.tut.fi/~lloydpri/sgns2/ (open source under New BSD license). Contact : jason.lloyd-price@tut.fi Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Single-molecule measurements of live Escherichia coli transcription dynamics suggest that this process ranges from sub- to super-Poissonian, depending on the conditions and on the promoter. For its accurate quantification, we propose a model that accommodates all these settings, and statistical methods to estimate the model parameters and to select the relevant components. Results: The new methodology has improved accuracy and avoids overestimating the transcription rate due to finite measurement time, by exploiting unobserved data and by accounting for the effects of discrete sampling. First, we use Monte Carlo simulations of models based on measurements to show that the methods are reliable and offer substantial improvements over previous methods. Next, we apply the methods on measurements of transcription intervals of different promoters in live E. coli , and show that they produce significantly different results, both in low- and high-noise settings, and that, in the latter case, they even lead to qualitatively different results. Finally, we demonstrate that the methods can be generalized for other similar purposes, such as for estimating gene activation kinetics. In this case, the new methods allow quantifying the inducer uptake dynamics as opposed to just comparing them between cases, which was not previously possible. We expect this new methodology to be a valuable tool for functional analysis of cellular processes using single-molecule or single-event microscopy measurements in live cells. Availability and implementation: Source code is available under Mozilla Public License at http://www.cs.tut.fi/%7Ehakkin22/censored/ . Contact: andre.ribeiro@tut.fi or andre.sanchesribeiro@tut.fi Supplementary information: Supplementary data are available at Bioinformatics online .

Description: Subduction initiation at passive margins plays a central role in the plate tectonics theory. However, the process by which a passive margin becomes active is not well understood. In this paper we use the southwest Iberia margin (SIM) in the Atlantic Ocean to study the process of passive margin reactivation. Currently there are two tectonic mechanisms operating in the SIM: migration of the Gibraltar Arc and Africa-Eurasia convergence. Based on a new tectonic map, we propose that a new subduction zone is forming at the SIM as a result of both propagation of compressive stresses from the Gibraltar Arc and stresses related to the large-scale Africa-Eurasia convergence. The Gibraltar Arc and the SIM appear to be connected and have the potential to develop into a new eastern Atlantic subduction system. Our work suggests that the formation of new subduction zones in Atlantic-type oceans may not require the spontaneous foundering of its passive margins. Instead, subduction can be seen as an invasive process that propagates from ocean to ocean.

Description: We are able to extend the investigation of the colour–morphology–density–radius relations, for bright and faint galaxies, to R 3 x R 200 and to very low density regions, probing the transition region between cluster and field galaxies and finding a smooth variation between these two populations. We investigate the environmental variation of galaxy properties (and their relations), such as colour, spectral type and concentration. Our sample comprises 6415 galaxies that were previously selected as cluster members from 152 systems with z  ≤ 0.100. This sample is further divided in complete subsamples of 5106 galaxies with M r  ≤  M * + 1 (from clusters at z  ≤ 0.100) and 1309 galaxies with M * + 1 〈  M r  ≤  M * + 3 (from objects at z  ≤ 0.045). We characterize the environment as a function of the local galaxy density and global cluster related parameters, such as radial distance, substructure, X-ray luminosity and velocity dispersion. For a sample of field galaxies we also trace their environmental dependence using a local galaxy density estimate. Our main findings are the following. (i) The fraction of discs is generally higher than the ones for blue and star-forming galaxies, indicating a faster transformation of colour and star formation compared to structural parameters. (ii) Regarding the distance to the cluster centre we find a small variation in the galaxy populations outside the virial radius. Once within that radius the fractions of each population change fast, decreasing even faster within R ~ 0.3 R 200 . (iii) We also find a small increase in the fraction of blue faint galaxies within R ~ 0.4 R 200 , before decreasing again to the most central bin. (iv) Our results do not indicate a significant dependence on cluster mass, except for the disc fraction in the core of clusters. (v) The relations between galaxy properties also point to no dependence on cluster mass, except for the scatter of the colour–stellar mass relation. Our results corroborate a scenario on which pre-processing in groups leads to a strong evolution in galaxy properties, before they are accreted by large clusters.

Description: Motivation : MS2-GFP-tagging of RNA is currently the only method to measure intervals between consecutive transcription events in live cells. For this, new transcripts must be accurately detected from intensity time traces. Results : We present a novel method for automatically estimating RNA numbers and production intervals from temporal data of cell fluorescence intensities that reduces uncertainty by exploiting temporal information. We also derive a robust variant, more resistant to outliers caused e.g. by RNAs moving out of focus. Using Monte Carlo simulations, we show that the quantification of RNA numbers and production intervals is generally improved compared with previous methods. Finally, we analyze data from live Escherichia coli and show statistically significant differences to previous methods. The new methods can be used to quantify numbers and production intervals of any fluorescent probes, which are present in low copy numbers, are brighter than the cell background and degrade slowly. Availability : Source code is available under Mozilla Public License at http://www.cs.tut.fi/%7ehakkin22/jumpdet/ . Contact : andre.ribeiro@tut.fi

Description: The monoterpenes are the main constituents of most essential oils and p-cymene is a monoterpene commonly found in various species of aromatic herbs, which has been reported for anti-inflammatory, antinociceptive, and antimicrobial activities. However, there is no report concerning its pharmacological activity on the vascular smooth muscle. The aim of current work was to investigate the effects of p-cymene in isolated rat aorta and also study its mechanism of action. In this work, we show that p-cymene has a relaxant effect, in a dose-dependent way, on the vascular smooth muscle, regardless of the presence of the endothelium. Using a nonselective potassium channel blocker, the CsCl, the relaxant effect of p-cymene was attenuated. In the presence of more selective potassium channels blockers, such as TEA or 4-AP, no change in the relaxant effect of p-cymene was evidenced, indicating that and channels are not involved in that relaxant effect. However, in the presence of glibenclamide or BaCl2, and blockers, respectively, the relaxant effect of p-cymene was attenuated. The data presented indicate that p-cymene has a relaxing effect on rat aorta, regardless of the endothelium, but with the participation of the and channels.

Description: Anopheles darlingi is the principal neotropical malaria vector, responsible for more than a million cases of malaria per year on the American continent. Anopheles darlingi diverged from the African and Asian malaria vectors ~100 million years ago (mya) and successfully adapted to the New World environment. Here we present an annotated reference A. darlingi genome, sequenced from a wild population of males and females collected in the Brazilian Amazon. A total of 10 481 predicted protein-coding genes were annotated, 72% of which have their closest counterpart in Anopheles gambiae and 21% have highest similarity with other mosquito species. In spite of a long period of divergent evolution, conserved gene synteny was observed between A. darlingi and A. gambiae . More than 10 million single nucleotide polymorphisms and short indels with potential use as genetic markers were identified. Transposable elements correspond to 2.3% of the A. darlingi genome. Genes associated with hematophagy, immunity and insecticide resistance, directly involved in vector–human and vector–parasite interactions, were identified and discussed. This study represents the first effort to sequence the genome of a neotropical malaria vector, and opens a new window through which we can contemplate the evolutionary history of anopheline mosquitoes. It also provides valuable information that may lead to novel strategies to reduce malaria transmission on the South American continent. The A. darlingi genome is accessible at www.labinfo.lncc.br/index.php/anopheles-darlingi .

Description: Quartz Crystal Microbalance (QCM) is a widely used technique to characterize adsorption/desorption phenomena at the solid/liquid interface. However, the obtained adsorption/desorption kinetics curves are often not reproducible and present some noise and long term fluctuations. In this work, the accuracy of a commercial QCM to measure the adsorbed amount of polyelectrolytes and biological molecules was evaluated in terms of experimental QCM configurations with respect to quality, stability, and reproducibility of the measured data. Evaluation consisted in comparing the adsorption kinetics curves of the cationic polyelectrolyte poly(ethyleneimine) and the anionic 1,2-dipalmitoyl- sn -glycero-3-phospho-(1′- rac -glycerol) (sodium salt) liposomes, when setting the quartz crystal surface in stationary horizontal open, stationary horizontal closed, stationary vertical open, continuous vertical closed, and stationary vertical closed measuring configuration. For this last configuration, a new cell was designed and implemented. The analysis of the kinetics curves revealed that horizontal modes are more unstable when subjected to fostering noise due to the mechanical vibrations and lead to resonance frequency shift. This shift is caused by the measurement of non-adsorbed molecules which are deposited on the quartz crystal due to gravity force. The vertical modes proved to be more reproducible and reliable.

Description: Photo induced birefringent materials can be used to develop optical and conversion energy devices, and consequently, the study of the variables that influences the creation and relaxation of birefringence should be carefully analyzed. In this work, the parameters of birefringence creation and relaxation kinetics curves obtained on layer-by-layer (LBL) films, prepared from azo-polyectrolyte poly[1-[4-(3-carboxy-4 hydroxyphenylazo) benzene sulfonamido]-1,2-ethanediyl, sodium salt] (PAZO) and poly(allylamine hydrochloride)(PAH), are related with the presence of counterions and the degree of ionization of the polyelectrolytes. Those kinetics curves obtained on PAH/PAZO LBL films, prepared from PAH solutions with different pHs and maintaining the pH of PAZO solution constant at pH = 9, were analyzed taking into account the films composition which was characterized by X-ray photoelectron spectroscopy. The creation and relaxation birefringence curves are justified by two processes: one associated to local mobility of the azobenzene with a characteristic time 30 s and intensity constant and other associated with polymeric chains mobility with the characteristic time and intensity decreasing with pH. These results allow us to conclude that the birefringence creation process, associated to local mobility of azobenzenes is independent of the degree of ionization and of number of counterions or co-ions present while the birefringence creation process associated to mobility of chains have its characteristic time and intensity dependent of both degree of ionization and number of counterions. The birefringence relaxation processes are dependent of the degree of ionization. The analysis of the films composition revealed, in addition, the presence of a protonated secondary or tertiary amine revealing that PAZO may have positive charges and consequently a zwitterionic behavior.