A staging scheme for the development of the moth midge Clogmia albipunctata.

Published onlineJournal ArticleResearch Support, Non-U.S. Gov'tThis is the final version of the article. Available from Public Library of Science via the DOI in this record.Model organisms, such as Drosophila melanogaster, allow us to address a wide range of biological questions with experimental rigour. However, studies in model species need to be complemented by comparative studies if we are to fully understand the functional properties and evolutionary history of developmental processes. The establishment of new model organisms is crucial for this purpose. One of the first essential steps to establish a species as an experimental model is to carefully describe its life cycle and development. The resulting staging scheme serves as a framework for molecular studies, and allows us to homologise developmental processes between species. In this paper, we have characterised the life cycle and development of an emerging non-drosophilid dipteran model system: the moth midge Clogmia albipunctata. In particular, we focus on early embryogenesis (cleavage and blastoderm cycles before gastrulation), on formation and retraction of extraembryonic tissues, and on formation of the germ line. Considering the large evolutionary distance between the two species (approximately 250 million years), we find that the development of C. albipunctata is remarkably conserved compared to D. melanogaster. On the other hand, we detect significant differences in morphology and timing affecting the development of extraembryonic tissues and the germ line. Moreover, C. albipunctata shows several heterochronic shifts, and lacks head involution and associated processes during late stages of development.The laboratory of Johannes Jaeger and this study in particular was funded by the MEC-EMBL agreement for the EMBL/CRG Research Unit in Systems Biology, by SGR grant 406 from the Catalan funding agency AGAUR, by grants BFU2009-10184 & BFU2012-33775 from the Spanish Ministry of Science (MICINN, now called MINECO), and by ERANet: ERASysBio+ grant EUI2009-04045 (MODHEART). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Demonstration of the Complementarity of One- and Two-Photon Interference

The visibilities of second-order (single-photon) and fourth-order (two-photon) interference have been observed in a Young's double-slit experiment using light generated by spontaneous parametric down-conversion and a photon-counting intensified CCD camera. Coherence and entanglement underlie one-and two-photon interference, respectively. As the effective source size is increased, coherence is diminished while entanglement is enhanced, so that the visibility of single-photon interference decreases while that of two-photon interference increases. This is the first experimental demonstration of the complementarity between single- and two-photon interference (coherence and entanglement) in the spatial domain.Comment: 21 pages, 7 figure

A staging scheme for the development of the scuttle fly Megaselia abdita

This is the final version of the article. Available from the publisher via the DOI in this record.Model organisms, such as Drosophila melanogaster, provide powerful experimental tools for the study of development. However, approaches using model systems need to be complemented by comparative studies for us to gain a deeper understanding of the functional properties and evolution of developmental processes. New model organisms need to be established to enable such comparative work. The establishment of new model system requires a detailed description of its life cycle and development. The resulting staging scheme is essential for providing morphological context for molecular studies, and allows us to homologise developmental processes between species. In this paper, we provide a staging scheme and morphological characterisation of the life cycle for an emerging non-drosophilid dipteran model system: the scuttle fly Megaselia abdita. We pay particular attention to early embryogenesis (cleavage and blastoderm stages up to gastrulation), the formation and retraction of extraembryonic tissues, and the determination and formation of germ (pole) cells. Despite the large evolutionary distance between the two species (approximately 150 million years), we find that M. abdita development is remarkably similar to D. melanogaster in terms of developmental landmarks and their relative timing.Funding: The laboratory of Johannes Jaeger and this study in particular was funded by the MEC-EMBL agreement for the EMBL/CRG Research Unit in Systems Biology, by SGR grant 406 from the Catalan funding agency AGAUR, by grants BFU2009-10184 & BFU2012-33775 from the Spanish Ministry of Science (MICINN, now called MINECO), and by ERANet: ERASysBio+ grant EUI2009-04045 (MODHEART). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Logarithmic Relaxations in a Random Field Lattice Gas Subject to Gravity

A simple lattice gas model with random fields and gravity is introduced to describe a system of grains moving in a disordered environment. Off equilibrium relaxations of bulk density and its two time correlation functions are numerically found to show logarithmic time dependences and "aging" effects. Similitudes with dry granular media are stressed. The connections with off equilibrium dynamics in others kinds of "frustrated" lattice models in presence of a directional driving force (gravity) are discussed to single out the appearance of universal features in the relaxation process.Comment: 15 pages, latex, 7 figures include

Heap Formation in Granular Media

Using molecular dynamics (MD) simulations, we find the formation of heaps in a system of granular particles contained in a box with oscillating bottom and fixed sidewalls. The simulation includes the effect of static friction, which is found to be crucial in maintaining a stable heap. We also find another mechanism for heap formation in systems under constant vertical shear. In both systems, heaps are formed due to a net downward shear by the sidewalls. We discuss the origin of net downward shear for the vibration induced heap.Comment: 11 pages, 4 figures available upon request, Plain TeX, HLRZ-101/9

Aging and multiscaling in out of equilibrium dynamical processes in granular media

In the framework of recently introduced frustrated lattice gas models, we study the out of equilibrium dynamical processes during the compaction process in granular media. We find irreversible-reversible cycles in agreement with recent experimental observations. Moreover in analogy with the phenomenology of the glass transition we find aging effects during the compaction process In particular we find that the two time density correlation function $C(t,t')$ asymptotically scales as a function of the single variable $\ln(t')/\ln(t)$. This result is interpreted in terms of multiscaling properties of the system.Comment: 4 page

A Model for Force Fluctuations in Bead Packs

We study theoretically the complex network of forces that is responsible for the static structure and properties of granular materials. We present detailed calculations for a model in which the fluctuations in the force distribution arise because of variations in the contact angles and the constraints imposed by the force balance on each bead of the pile. We compare our results for force distribution function for this model, including exact results for certain contact angle probability distributions, with numerical simulations of force distributions in random sphere packings. This model reproduces many aspects of the force distribution observed both in experiment and in numerical simulations of sphere packings

Estimating good discrete partitions from observed data: symbolic false nearest neighbors

A symbolic analysis of observed time series data requires making a discrete partition of a continuous state space containing observations of the dynamics. A particular kind of partition, called ``generating'', preserves all dynamical information of a deterministic map in the symbolic representation, but such partitions are not obvious beyond one dimension, and existing methods to find them require significant knowledge of the dynamical evolution operator or the spectrum of unstable periodic orbits. We introduce a statistic and algorithm to refine empirical partitions for symbolic state reconstruction. This method optimizes an essential property of a generating partition: avoiding topological degeneracies. It requires only the observed time series and is sensible even in the presence of noise when no truly generating partition is possible. Because of its resemblance to a geometrical statistic frequently used for reconstructing valid time-delay embeddings, we call the algorithm ``symbolic false nearest neighbors''