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Cohesin cleavage is insufficient for centriole disengagement in Drosophila
Get PDFMedical Research Council; Wellcome Trust; European Research Council
Filling the gaps of dinosaur eggshell phylogeny: Late Jurassic Theropod clutch with embryos from Portugal
Get PDFThe non-avian saurischians that have associated eggshells and embryos are represented only by the sauropodomorph Massospondylus and Coelurosauria (derived theropods), thus missing the basal theropod representatives. We report a dinosaur clutch containing several crushed eggs and embryonic material ascribed to the megalosaurid theropod Torvosaurus. It represents the first associated eggshells and embryos of megalosauroids, thus filling an important phylogenetic gap between two distantly related groups of saurischians. These fossils represent the only unequivocal basal theropod embryos found to date. The assemblage was found in early Tithonian fluvial overbank deposits of the Lourinhã Formation in West Portugal. The morphological, microstructural and chemical characterization results of the eggshell fragments indicate very mild diagenesis. Furthermore, these fossils allow unambiguous association of basal theropod osteology with a specific and unique new eggshell morphology.Jurassic Foundation financial support under the project: (Dinosaur Eggs and Embryos of the Lourinha˜ Formation [Upper Jurassic, Portugal]), DESY grants: (I-20110184 EC, I-20110229 EC projects), FCT/MCE grant: (PEst-OE/FIS/UI0275/2011), FCT scholarship: (SFRH/BD/62979/2009), European Science Foundation
Majority rules with random tie-breaking in Boolean gene regulatory networks
Get PDFWe consider threshold boolean gene regulatory networks, where the update function of each gene is described as a majority rule evaluated among the regulators of that gene: it is turned ON when the sum of its regulator contributions is positive (activators contribute positively whereas repressors contribute negatively) and turned OFF when this sum is negative. In case of a tie (when contributions cancel each other out), it is often assumed that the gene keeps it current state. This framework has been successfully used to model cell cycle control in yeast. Moreover, several studies consider stochastic extensions to assess the robustness of such a model. Here, we introduce a novel, natural stochastic extension of the majority rule. It consists in randomly choosing the next value of a gene only in case of a tie. Hence, the resulting model includes deterministic and probabilistic updates. We present variants of the majority rule, including alternate treatments of the tie situation. Impact of these variants on the corresponding dynamical behaviours is discussed. After a thorough study of a class of two-node networks, we illustrate the interest of our stochastic extension using a published cell cycle model. In particular, we demonstrate that steady state analysis can be rigorously performed and can lead to effective predictions; these relate for example to the identification of interactions whose addition would ensure that a specific state is absorbing
Canalization and control in automata networks: body segmentation in Drosophila melanogaster
Get PDFWe present schema redescription as a methodology to characterize canalization
in automata networks used to model biochemical regulation and signalling. In
our formulation, canalization becomes synonymous with redundancy present in the
logic of automata. This results in straightforward measures to quantify
canalization in an automaton (micro-level), which is in turn integrated into a
highly scalable framework to characterize the collective dynamics of
large-scale automata networks (macro-level). This way, our approach provides a
method to link micro- to macro-level dynamics -- a crux of complexity. Several
new results ensue from this methodology: uncovering of dynamical modularity
(modules in the dynamics rather than in the structure of networks),
identification of minimal conditions and critical nodes to control the
convergence to attractors, simulation of dynamical behaviour from incomplete
information about initial conditions, and measures of macro-level canalization
and robustness to perturbations. We exemplify our methodology with a well-known
model of the intra- and inter cellular genetic regulation of body segmentation
in Drosophila melanogaster. We use this model to show that our analysis does
not contradict any previous findings. But we also obtain new knowledge about
its behaviour: a better understanding of the size of its wild-type attractor
basin (larger than previously thought), the identification of novel minimal
conditions and critical nodes that control wild-type behaviour, and the
resilience of these to stochastic interventions. Our methodology is applicable
to any complex network that can be modelled using automata, but we focus on
biochemical regulation and signalling, towards a better understanding of the
(decentralized) control that orchestrates cellular activity -- with the
ultimate goal of explaining how do cells and tissues 'compute'
Mind the fish: zebrafish as a model in cognitive social neuroscience
Get PDFUnderstanding how the brain implements social behavior on one hand, and how social processes feedback on the brain to promote fine-tuning of behavioral output according to changes in the social environment is a major challenge in contemporary neuroscience. A critical step to take this challenge successfully is finding the appropriate level of analysis when relating social to biological phenomena. Given the enormous complexity of both the neural networks of the brain and social systems, the use of a cognitive level of analysis (in an information processing perspective) is proposed here as an explanatory interface between brain and behavior. A conceptual framework for a cognitive approach to comparative social neuroscience is proposed, consisting of the following steps to be taken across different species with varying social systems: (1) identification of the functional building blocks of social skills; (2) identification of the cognitive mechanisms underlying the previously identified social skills; and (3) mapping these information processing mechanisms onto the brain. Teleost fish are presented here as a group of choice to develop this approach, given the diversity of social systems present in closely related species that allows for planned phylogenetic comparisons, and the availability of neurogenetic tools that allows the visualization and manipulation of selected neural circuits in model species such as the zebrafish. Finally, the state-of-the art of zebrafish social cognition and of the tools available to map social cognitive abilities to neural circuits in zebrafish are reviewed.FCT Eco-Ethology R&D Unit: (PEst-OE/MAR/UI0331/2011)
Survey of the critically endangered Perrier’s sifaka (Propithecus Perrieri) across most if its distribution range.
Get PDFPropithecus perrieri (Perrier’s sifaka) is one of the most endangered lemur species due to its small and fragmented distribution range. Despite a Critically Endangered (CR) conservation and flagship species status, there are still many uncertainties regarding its actual distribution and its presence in some forests of its putative distribution range. We report the results of diurnal and nocturnal surveys carried out in 2012 across most forest fragments of its putative distribution range, namely the Ankarana National Park, the
Analamerana Special Reserve and Andrafiamena-Andava-koera Protected Area. During our surveys the species was only observed in Andrafiamena and Analamerana protected areas.FCT fellowship: (SFRH/BD/64875/2009), Institut Français de la Biodiversité, the GDRI Madagascar, the “Laboratoire d'Excellence” (LABEX) entitled TULIP (ANR-10-LABX-41), Instituto Gulbenkian de Ciência, “Optimus Alive!” Biodiversity grant, The Rufford Small Grant for Nature Conservation: (ref. 10941-1), Département de Biologie Animale et Ecologie (D.B.A.E.), Faculté des Sciences, University of Mahajanga, the University of Antsiranana, and the Fanamby NGO (in particular S. Rajaobelina), Madagascar National Park, Analamerana Special Reserve, Ankarana National Park
The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data
Get PDFPopulation structure can significantly affect genetic-based demographic inferences, generating spurious bottleneck-like signals. Previous studies have typically assumed island or stepping-stone models, which are characterized by symmetric gene flow. However, many organisms are characterized by asymmetric gene flow. Here, we combined simulated and empirical data to test whether asymmetric gene flow affects the inference of past demographic changes. Through the analysis of simulated genetic data with three methods (i.e. bottleneck, M-ratio and msvar), we demonstrated that asymmetric gene flow biases past demographic changes. Most biases were towards spurious signals of expansion, albeit their strength depended on values of effective population size and migration rate. It is noteworthy that the spurious signals of demographic changes also depended on the statistical approach underlying each of the three methods. For one of the three methods, biases induced by asymmetric gene flow were confirmed in an empirical multispecific data set involving four freshwater fish species (Squalius cephalus, Leuciscus burdigalensis, Gobio gobio and Phoxinus phoxinus). However, for the two other methods, strong signals of bottlenecks were detected for all species and across two rivers. This suggests that, although potentially biased by asymmetric gene flow, some of these methods were able to bypass this bias when a bottleneck actually occurred. Our results show that population structure and dispersal patterns have to be considered for proper inference of demographic changes from genetic data.Agence de l'Eau Adour-Garonne; Génopole Toulouse; Ministère de l'Enseignement Supérieur et de la Recherche; Laboratoire d’Excellence (LABEX) entitled TULIP (ANR -10-LABX- 41)
Placental Malaria: From Infection to Malfunction
Get PDFMalaria during pregnancy is a major factor in infant morbidity and mortality. In this issue of Cell Host and Microbe, Conroy et al. (2013) propose that C5a, a product of complement cascade activation, counteracts the placental vascular remodeling response induced by Plasmodium infection and contributes to fetal growth restriction.Fundação para a Ciência e Tecnologia
How two become one: HJURP dimerization drives CENP-A assembly
Get PDFCENP‐A containing nucleosomes epigenetically specify centromere position on chromosomes. Deposition of CENP‐A into chromatin is mediated by HJURP, a specific CENP‐A chaperone. Paradoxically, HJURP binding sterically prevents dimerization of CENP‐A, which is critical to form functional centromeric nucleosomes. A recent publication in The EMBO Journal (Zasadzińska et al, 2013) demonstrates that HJURP itself dimerizes through a C‐terminal repeat region, which is essential for centromeric assembly of nascent CENP‐A.FCT fellowship: (SFRH/BD/74284/2010); FCT grants: (BIA-BCM/100557/2008, BIAPRO/100537/2008); EMBO Installation Grant
Dynamical Scenarios for Chromosome Bi-orientation
Get PDFChromosome bi-orientation at the metaphase spindle is essential for precise segregation of the genetic material. The process is error-prone, and error-correction mechanisms exist to switch misaligned chromosomes to the correct, bi-oriented configuration. Here, we analyze several possible dynamical scenarios to explore how cells might achieve correct bi-orientation in an efficient and robust manner. We first illustrate that tension-mediated feedback between the sister kinetochores can give rise to a bistable switch, which allows robust distinction between a loose attachment with low tension and a strong attachment with high tension. However, this mechanism has difficulties in explaining how bi-orientation is initiated starting from unattached kinetochores. We propose four possible mechanisms to overcome this problem (exploiting molecular noise; allowing an efficient attachment of kinetochores already in the absence of tension; a trial-and-error oscillation; and a stochastic bistable switch), and assess their impact on the bi-orientation process. Based on our results and supported by experimental data, we put forward a trial-and-error oscillation and a stochastic bistable switch as two elegant mechanisms with the potential to promote bi-orientation both efficiently and robustly.Kavli Institute for Theoretical Physics grant: (NSF PHY11-25915)