Minimum Action Path theory reveals the details of stochastic biochemical transitions out of oscillatory cellular states

Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Tran- sitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending non-locally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function

Femtosecond time-resolved phase-change microscopy and ablation threshold calculations to understand ultrafast laser ablation

El trabajo recoge experimentos realizados en una configuración sonda-prueba haciendo uso de un láser de femtosegundos, con el objetivo de comprender los fenómenos de ablación de materiales sólidos ras irradiación con láseres de pulso ultracorto.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

A Statistical Approach Reveals Designs for the Most Robust Stochastic Gene Oscillators

The engineering of transcriptional networks presents many challenges due to the inherent uncertainty in the system structure, changing cellular context, and stochasticity in the governing dynamics. One approach to address these problems is to design and build systems that can function across a range of conditions; that is they are robust to uncertainty in their constituent components. Here we examine the parametric robustness landscape of transcriptional oscillators, which underlie many important processes such as circadian rhythms and the cell cycle, plus also serve as a model for the engineering of complex and emergent phenomena. The central questions that we address are: Can we build genetic oscillators that are more robust than those already constructed? Can we make genetic oscillators arbitrarily robust? These questions are technically challenging due to the large model and parameter spaces that must be efficiently explored. Here we use a measure of robustness that coincides with the Bayesian model evidence, combined with an efficient Monte Carlo method to traverse model space and concentrate on regions of high robustness, which enables the accurate evaluation of the relative robustness of gene network models governed by stochastic dynamics. We report the most robust two and three gene oscillator systems, plus examine how the number of interactions, the presence of autoregulation, and degradation of mRNA and protein affects the frequency, amplitude, and robustness of transcriptional oscillators. We also find that there is a limit to parametric robustness, beyond which there is nothing to be gained by adding additional feedback. Importantly, we provide predictions on new oscillator systems that can be constructed to verify the theory and advance design and modeling approaches to systems and synthetic biology

Deterministic and stochastic study for a microscopic angiogenesis model: applications to the Lewis lung carcinoma

Angiogenesis modelling is an important tool to understand the underlying mechanisms yielding tumour growth. Nevertheless, there is usually a gap between models and experimental data. We propose a model based on the intrinsic microscopic reactions defining the angiogenesis process to link experimental data with previous macroscopic models. The microscopic characterisation can describe the macroscopic behaviour of the tumour, which stability analysis reveals a set of predicted tumour states involving different morphologies. Additionally, the microscopic description also gives a framework to study the intrinsic stochasticity of the reactive system through the resulting Langevin equation. To follow the goal of the paper, we use available experimental information on the Lewis lung carcinoma to infer meaningful parameters for the model that are able to describe the different stages of the tumour growth. Finally we explore the predictive capabilities of the fitted model by showing that fluctuations are determinant for the survival of the tumour during the first week and that available treatments can give raise to new stable tumour dormant states with a reduced vascular network

Time-resolved laser-induced phase change microscopy: understanding laser-matter effects at the femtosecond scale

LA comunicación describe el desarrollo instrumental y las aplicaciones con un microscopio de cambio de fase con resolución de femtosegundos que se ha puesto a punto en el LAboratorio LAser de la UMAUniversidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Fisheries and reproductive biology of Octopus vulgaris (Mollusca: Cephalopoda) in the Gulf of Alicante (Northwestern Mediterranean)

The common octopus Octopus vulgarisCuvier, 1797 is the most fished cephalopod species along the Spanish coasts. Its catches are highly fluctuating due to the short life cycle of the species and to the annual variability of the recruitment pattern, strongly dependent on the environmental conditions affecting the eggs and paralarvae. This study examines the common octopus fishery, the catch composition, and the main features of the reproductive biology of this species in the Gulf of Alicante (Spanish Eastern coast, Western Mediterranean FAO division 37.1.1). The common octopus fishery was studied analysing the monthly landing and effort data by fishing gear from 1994 to 2005. Monthly samplings of the commercial O. vulgarislandings from trawlers and clay pots from January 2004 to December 2005 resulted in the measuring of 1833 specimens to enable analysis of the catch composition, and allowed the biological sampling of 1176 individuals to provide the reproductive parameters of the species in the study area. The length-weight relationship calculated for the species was BW = 0.51 * DML 2.87. The yearly sex ratios (males:females) were 1:1 (trawl, 2004), 1:0.74 (trawl, 2005), and 1:0.88 (clay pots, 2005). The size (dorsal mantle length, DML) at maturity of the species in the study area was 9.67 cm for males and 14.38 cm for females. The gonadosomatic index reached a peak between April and July for males and in July for females. The Fulton condition index was lower in both sexes between June and September, and for males in November-December, whereas for both sexes the values of the digestive gland index were at their maximum between June and December. The energy allocation between somatic and reproductive growth was investigated and the results suggested that the energy spent on reproduction mainly came from feeding, and not from energy stored in the mantle tissues or in the digestive glan

Temporal and energetic scale of solid matter interaction phenomena occurring during femtosecond ablation of solids

Ablation using femtosecond lasers exhibits significant differences with that at the nanosecond timescale, where the concurrence of photochemical and photothermal processes taking place during the photon absorption govern the process. In the ultrashort regime, the several phenomena involved in the laser-matter interaction are markedly different. Thus, a prior comprehension of the processes is required in order to extend the range of current applications and improve the analytical results. Our current studies are facing fundamental and applied studies with the aim of better understanding laser-matter interaction processes in condensed phase using femtosecond lasers. To achieve this goal, we have designed experimental strategies expecting to improve the knowledge of the timescale and onset generation of chemical species and surface alterations during femtosecond ablation of solids. Time-resolved optical emission spectroscopy, time-of-flight mass spectrometry and time-resolved phase-change microscopy are currently implemented. The combined use of the cited techniques is allowing the experimental determination of the energy threshold, temporal regime and macroscopic effects occurring in a variety of materials as a consequence of the interaction with an ultra-short laser pulse. The core of the experiment is a 80 Mhz, 100 nJ, 400 fs Ti-Saphire oscillator that is additionally subjected to chirped pulse amplification to produce an output of 3,5 mJ at 35 fs and a maximum repletion rate of 1 KHz. Different wavelengths (800, 400 and 266 nm) are achievable. An intensified CCD and a dual-state reflectron equipped with a cassegrain reflective optics are used for the analysis of the photons and ion generated after laser irradiation. Additionally, a pump-probe microscope with a temporal resolution better than 500 fs has been designed to allow time-resolved studies of phase-change in the ablated samples.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec