Nemo: an evolutionary and population genetics programming framework

Summary: Nemo is an individual-based, genetically explicit and stochastic population computer program for the simulation of population genetics and life-history trait evolution in a metapopulation context. It comes as both a C++ programming framework and an executable program file. Its object-oriented programming design gives it the flexibility and extensibility needed to implement a large variety of forward-time evolutionary models. It provides developers with abstract models allowing them to implement their own life-history traits and life-cycle events. Nemo offers a large panel of population models, from the Island model to lattice models with demographic or environmental stochasticity and a variety of already implemented traits (deleterious mutations, neutral markers and more), life-cycle events (mating, dispersal, aging, selection, etc.) and output operators for saving data and statistics. It runs on all major computer platforms including parallel computing environments. Availability: The source code, binaries and documentation are available under the GNU General Public License at . Contact: [email protected]

DNA microarray data and contextual analysis of correlation graphs

BACKGROUND: DNA microarrays are used to produce large sets of expression measurements from which specific biological information is sought. Their analysis requires efficient and reliable algorithms for dimensional reduction, classification and annotation. RESULTS: We study networks of co-expressed genes obtained from DNA microarray experiments. The mathematical concept of curvature on graphs is used to group genes or samples into clusters to which relevant gene or sample annotations are automatically assigned. Application to publicly available yeast and human lymphoma data demonstrates the reliability of the method in spite of its simplicity, especially with respect to the small number of parameters involved. CONCLUSIONS: We provide a method for automatically determining relevant gene clusters among the many genes monitored with microarrays. The automatic annotations and the graphical interface improve the readability of the data. A C++ implementation, called Trixy, is available from

Few crucial links assure checkpoint efficiency in the yeast cell-cycle network

Motivation: The ability of cells to complete mitosis with high fidelity relies on elaborate checkpoint mechanisms. We study S- and M-phase checkpoint responses in silico in the budding yeast with a stochastic dynamical model for the cell-cycle. We aim to provide an unbiased functional classification of network interactions that reflect the contribution of each link to checkpoint efficiency in the presence of cellular fluctuations. Results: We developed an algorithm BNetDyn to compute stochastic dynamical trajectories for an input gene network and its structural perturbations. User specified output measures like the mutual information between trigger and output nodes are then evaluated on the stationary state of the Markov process. Systematic perturbations of the yeast cell-cycle model by Li et al. classify each link according to its effect on checkpoint efficiencies and stabilities of the main cell-cycle phases. This points to the crosstalk in the cascades downstream of the SBF/MBF transcription activator complexes as determinant for checkpoint optimality; a finding that consistently reflects recent experiments. Finally our stochastic analysis emphasizes how dynamical stability in the yeast cell-cycle network crucially relies on backward inhibitory circuits next to forward induction. Availability: C++ source code and network models can be downloaded at Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

A Rapid Bootstrap Algorithm for the RAxML Web Servers

Despite recent advances achieved by application of high-performance computing methods and novel algorithmic techniques to maximum likelihood (ML)-based inference programs, the major computational bottleneck still consists in the computation of bootstrap support values. Conducting a probably insufficient number of 100 bootstrap (BS) analyses with current ML programs on large datasets—either with respect to the number of taxa or base pairs—can easily require a month of run time. Therefore, we have developed, implemented, and thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated Maximum Likelihood) that are more than an order of magnitude faster than current algorithms. These new heuristics can contribute to resolving the computational bottleneck and improve current methodology in phylogenetic analyses. Computational experiments to assess the performance and relative accuracy of these heuristics were conducted on 22 diverse DNA and AA (amino acid), single gene as well as multigene, real-world alignments containing 125 up to 7764 sequences. The standard BS (SBS) and rapid BS (RBS) values drawn on the best-scoring ML tree are highly correlated and show almost identical average support values. The weighted RF (Robinson-Foulds) distance between SBS- and RBS-based consensus trees was smaller than 6% in all cases (average 4%). More importantly, RBS inferences are between 8 and 20 times faster (average 14.73) than SBS analyses with RAxML and between 18 and 495 times faster than BS analyses with competing programs, such as PHYML or GARLI. Moreover, this performance improvement increases with alignment size. Finally, we have set up two freely accessible Web servers for this significantly improved version of RAxML that provide access to the 200-CPU cluster of the Vital-IT unit at the Swiss Institute of Bioinformatics and the 128-CPU cluster of the CIPRES project at the San Diego Supercomputer Center. These Web servers offer the possibility to conduct large-scale phylogenetic inferences to a large part of the community that does not have access to, or the expertise to use, high-performance computing resource

Collective synchronization in populations of globally coupled phase oscillators with drifting frequencies

We generalize the Kuramoto model for coupled phase oscillators by allowing the frequencies to drift in time according to Ornstein-Uhlenbeck dynamics. Such drifting frequencies were recently measured in cellular populations of circadian oscillator and inspired our work. Linear stability analysis of the Fokker-Planck equation for an infinite population is amenable to exact solution and we show that the incoherent state is unstable passed a critical coupling strength K_c(\ga, \sigf), where \ga is the inverse characteristic drifting time and \sigf the asymptotic frequency dispersion. Expectedly $K_c$ agrees with the noisy Kuramoto model in the large \ga (Schmolukowski) limit but increases slower as \ga decreases. Asymptotic expansion of the solution for \ga\to 0 shows that the noiseless Kuramoto model with Gaussian frequency distribution is recovered in that limit. Thus varying a single parameter allows to interpolate smoothly between two regimes: one dominated by the frequency dispersion and the other by phase diffusion.Comment: 5 pages, 5 figures, accepted in Phys. Rev.

Dynamical signatures of cellular fluctuations and oscillator stability in peripheral circadian clocks

Cell-autonomous and self-sustained molecular oscillators drive circadian behavior and physiology in mammals. From rhythms recorded in cultured fibroblasts we identified the dominant cause for amplitude reduction as desynchronization of self-sustained oscillators. Here, we propose a general framework for quantifying luminescence signals from biochemical oscillators, both in populations and individual cells. Our model combines three essential aspects of circadian clocks: the stability of the limit cycle, fluctuations, and intercellular coupling. From population recordings we can simultaneously estimate the stiffness of individual frequencies, the period dispersion, and the interaction strength. Consistent with previous work, coupling is found to be weak and insufficient to synchronize cells. Moreover, we find that frequency fluctuations remain correlated for longer than one clock cycle, which is confirmed from individual cell recordings. Using genetic models for circadian clocks, we show that this reflects the stability properties of the underlying circadian limit-cycle oscillators, and we identify biochemical parameters that influence oscillator stability in mammals. Our study thus points to stabilizing mechanisms that dampen fluctuations to maintain accurate timing in peripheral circadian oscillators

On Lossless Compression of 1-bit Audio Signals

In this paper we consider the problem of lossless compression of 1-bit audio signals. We study the properties of some existing proposed solutions. We also discuss possible improvements. Other methods have been considered, and the results are reported

High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis

To construct a regulatory map of the genome of the human pathogen, Mycobacterium tuberculosis, we applied two complementary high-resolution approaches: strand-specific RNA-seq, to survey the global transcriptome, and ChIP-seq, to monitor the genome-wide dynamics of RNA polymerase (RNAP) and the anti-terminator NusA. Although NusA does not bind directly to DNA, but rather to RNAP and/or to the nascent transcript, we demonstrate that NusA interacts with RNAP ubiquitously throughout the chromosome, and that its profile mirrors RNAP distribution in both the exponential and stationary phases of growth. Generally, promoter-proximal peaks for RNAP and NusA were observed, followed by a decrease in signal strength reflecting transcriptional polarity. Differential binding of RNAP and NusA in the two growth conditions correlated with transcriptional activity as reflected by RNA abundance. Indeed, a significant association between expression levels and the presence of NusA throughout the gene body was detected, confirming the peculiar transcription-promoting role of NusA. Integration of the data sets pinpointed transcriptional units, mapped promoters and uncovered new anti-sense and non-coding transcripts. Highly expressed transcriptional units were situated mainly on the leading strand, despite the relatively unbiased distribution of genes throughout the genome, thus helping the replicative and transcriptional complexes to alig

"Adrénaline-addiction" et comportements de prises de risques chez les sportifs : quelles réalités ?

Cet article résume les hypothèses psycho-biologiques qui sous-tendent le fait que l'individu s'expose au danger. La question se pose de savoir si certaines formes de sports à risque peuvent être considérées comme une dépendance. En effet, la forte activation de l'axe adrénocorticotrope pourrait agir comme un renforçateur addictogène dans la mesure où elle efface une émotion déplaisante, selon le modèle du coping du stress focalisé sur l'émotion. De plus, un mimétisme pharmacologique semble possible, car l'effet ressenti des catécholamines pourrait imiter certains effets des drogues stimulantes. Enfin, les concepts courants de la réduction des risques et des dommages sont transposés au sport. Ceci correspondrait à l'application de mesures préventives diversifiées à un large continuum de comportements potentiellement dangereux. [Auteurs]]]> Sports ; Behavior, Addictive ; Risk-Taking ; Epinephrine ; Sympathomimetics fre oai:serval.unil.ch:BIB_1175C0480B6A 2022-05-07T01:10:22Z <oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd"> https://serval.unil.ch/notice/serval:BIB_1175C0480B6A Inter-class competition in stage-structured populations: effects of adult density on life-history traits of adult and juvenile common lizards. info:doi:10.1007/s00442-016-3738-7 info:eu-repo/semantics/altIdentifier/doi/10.1007/s00442-016-3738-7 info:eu-repo/semantics/altIdentifier/pmid/27655331 San-Jose, L.M. Peñalver-Alcázar, M. Huyghe, K. Breedveld, M.C. Fitze, P.S. info:eu-repo/semantics/article article 2016-12 Oecologia, vol. 182, no. 4, pp. 1063-1074 info:eu-repo/semantics/altIdentifier/eissn/1432-1939 urn:issn:0029-8549 <![CDATA[Ecological and evolutionary processes in natural populations are largely influenced by the population's stage-structure. Commonly, different classes have different competitive abilities, e.g., due to differences in body size, suggesting that inter-class competition may be important and largely asymmetric. However, experimental evidence states that inter-class competition, which is important, is rare and restricted to marine fish. Here, we manipulated the adult density in six semi-natural populations of the European common lizard, Zootoca vivipara, while holding juvenile density constant. Adult density affected juveniles, but not adults, in line with inter-class competition. High adult density led to lower juvenile survival and growth before hibernation. In contrast, juvenile survival after hibernation was higher in populations with high adult density, pointing to relaxed inter-class competition. As a result, annual survival was not affected by adult density, showing that differences in pre- and post-hibernation survival balanced each other out. The intensity of inter-class competition affected reproduction, performance, and body size in juveniles. Path analyses unravelled direct treatment effects on early growth (pre-hibernation) and no direct treatment effects on the parameters measured after hibernation. This points to allometry of treatment-induced differences in early growth, and it suggests that inter-class competition mainly affects the early growth of the competitively inferior class and thereby their future performance and reproduction. These results are in contrast with previous findings and, together with results in marine fish, suggest that the strength and direction of density dependence may depend on the degree of inter-class competition, and thus on the availability of resources used by the competing classes