Hierarchy and Feedback in the Evolution of the E. coli Transcription Network

The E.coli transcription network has an essentially feedforward structure, with, however, abundant feedback at the level of self-regulations. Here, we investigate how these properties emerged during evolution. An assessment of the role of gene duplication based on protein domain architecture shows that (i) transcriptional autoregulators have mostly arisen through duplication, while (ii) the expected feedback loops stemming from their initial cross-regulation are strongly selected against. This requires a divergent coevolution of the transcription factor DNA-binding sites and their respective DNA cis-regulatory regions. Moreover, we find that the network tends to grow by expansion of the existing hierarchical layers of computation, rather than by addition of new layers. We also argue that rewiring of regulatory links due to mutation/selection of novel transcription factor/DNA binding interactions appears not to significantly affect the network global hierarchy, and that horizontally transferred genes are mainly added at the bottom, as new target nodes. These findings highlight the important evolutionary roles of both duplication and selective deletion of crosstalks between autoregulators in the emergence of the hierarchical transcription network of E.coli.Comment: to appear in PNA

Evidence of light guiding in ion-implanted diamond

We demonstrate the feasibility of fabricating light-waveguiding microstructures in bulk single-crystal diamond by means of direct ion implantation with a scanning microbeam, resulting in the modulation of the refractive index of the ion-beam damaged crystal. Direct evidence of waveguiding through such buried microchannels is obtained with a phase-shift micro-interferometric method allowing the study of the multimodal structure of the propagating electromagnetic field. The possibility of defining optical and photonic structures by direct ion writing opens a range of new possibilities in the design of quantumoptical devices in bulk single-crystal diamond

Fluctuations of a driven membrane in an electrolyte

We develop a model for a driven cell- or artificial membrane in an electrolyte. The system is kept far from equilibrium by the application of a DC electric field or by concentration gradients, which causes ions to flow through specific ion-conducting units (representing pumps, channels or natural pores). We consider the case of planar geometry and Debye-H\"{u}ckel regime, and obtain the membrane equation of motion within Stokes hydrodynamics. At steady state, the applied field causes an accumulation of charges close to the membrane, which, similarly to the equilibrium case, can be described with renormalized membrane tension and bending modulus. However, as opposed to the equilibrium situation, we find new terms in the membrane equation of motion, which arise specifically in the out-of-equilibrium case. We show that these terms lead in certain conditions to instabilities.Comment: 7 pages, 2 figures. submitted to Europhys. Let

Micro-beam and pulsed laser beam techniques for the micro-fabrication of diamond surface and bulk structures

Micro-fabrication in diamond is involved in a wide set of emerging technologies, exploiting the exceptional characteristics of diamond for application in bio-physics, photonics, radiation detection. Micro ion-beam irradiation and pulsed laser irradiation are complementary techniques, which permit the implementation of complex geometries, by modification and functionalization of surface and/or bulk material, modifying the optical, electrical and mechanical characteristics of the material. In this article we summarize the work done in Florence (Italy) concerning ion beam and pulsed laser beam micro-fabrication in diamond.Comment: 14 pages, 5 figure

Evidence For The Production Of Slow Antiprotonic Hydrogen In Vacuum

We present evidence showing how antiprotonic hydrogen, the quasistable antiproton-proton (pbar-p) bound system, has been synthesized following the interaction of antiprotons with the hydrogen molecular ion (H2+) in a nested Penning trap environment. From a careful analysis of the spatial distributions of antiproton annihilation events, evidence is presented for antiprotonic hydrogen production with sub-eV kinetic energies in states around n=70, and with low angular momenta. The slow antiprotonic hydrogen may be studied using laser spectroscopic techniques.Comment: 5 pages with 4 figures. Published as Phys. Rev. Letters 97, 153401 (2006), in slightly different for

Computational core and fixed-point organisation in Boolean networks

In this paper, we analyse large random Boolean networks in terms of a constraint satisfaction problem. We first develop an algorithmic scheme which allows to prune simple logical cascades and under-determined variables, returning thereby the computational core of the network. Second we apply the cavity method to analyse number and organisation of fixed points. We find in particular a phase transition between an easy and a complex regulatory phase, the latter one being characterised by the existence of an exponential number of macroscopically separated fixed-point clusters. The different techniques developed are reinterpreted as algorithms for the analysis of single Boolean networks, and they are applied to analysis and in silico experiments on the gene-regulatory networks of baker's yeast (saccaromices cerevisiae) and the segment-polarity genes of the fruit-fly drosophila melanogaster.Comment: 29 pages, 18 figures, version accepted for publication in JSTA

Reproductive Capacity Evolves in Response to Ecology through Common Changes in Cell Number in Hawaiian Drosophila

© 2019 Elsevier Ltd Lifetime reproductive capacity is a critical fitness component. In insects, female reproductive capacity is largely determined by the number of ovarioles, the egg-producing subunits of the ovary [e.g., 1]. Recent work has provided insights into ovariole number regulation in Drosophila melanogaster. However, whether mechanisms discovered under laboratory conditions explain evolutionary variation in natural populations is an outstanding question. We investigated potential effects of ecology on the developmental processes underlying ovariole number evolution among Hawaiian Drosophila, a large adaptive radiation wherein the highest and lowest ovariole numbers of the family have evolved within 25 million years. Previous studies proposed that ovariole number correlated with oviposition substrate [2–4] but sampled largely one clade of these flies and were limited by a provisional phylogeny and the available comparative methods. We test this hypothesis by applying phylogenetic modeling to an expanded sampling of ovariole numbers and substrate types and show support for these predictions across all major groups of Hawaiian Drosophila, wherein ovariole number variation is best explained by adaptation to specific substrates. Furthermore, we show that oviposition substrate evolution is linked to changes in the allometric relationship between body size and ovariole number. Finally, we provide evidence that the major changes in ovarian cell number that regulate D. melanogaster ovariole number also regulate ovariole number in Hawaiian drosophilids. Thus, we provide evidence that this remarkable adaptive radiation is linked to evolutionary changes in a key reproductive trait regulated at least partly by variation in the same developmental parameters that operate in the model species D. melanogaster. Organisms leaving more offspring likely have higher fitness. Sarikaya et al. use the adaptive radiation of Hawaiian Drosophila to investigate the evolution of fecundity. They find that habitat shifts played a strong role and identify a developmental process that underlies evolutionary change in ovarian development and impacts egg-laying capacity

Coherent Hydrodynamic Coupling for Stochastic Swimmers

A recently developed theory of stochastic swimming is used to study the notion of coherence in active systems that couple via hydrodynamic interactions. It is shown that correlations between various modes of deformation in stochastic systems play the same role as the relative internal phase in deterministic systems. An example is presented where a simple swimmer can use these correlations to hunt a non-swimmer by forming a hydrodynamic bound state of tunable velocity and equilibrium separation. These results highlight the significance of coherence in the collective behavior of nano-scale stochastic swimmers.Comment: 6 pages, 3 figure

Detection of antihydrogen annihilations with a Si-micro-strip and pure CsI detector

In 2002, the ATHENA collaboration reported the creation and detection of cold (~15 K) antihydrogen atoms [1]. The observation was based on the complete reconstruction of antihydrogen annihilations, simultaneous and spatially correlated annihilations of an antiproton and a positron. Annihilation byproducts are measured with a cylindrically symmetric detector system consisting of two layers of double sided Si-micro-strip modules that are surrounded by 16 rows of 12 pure CsI crystals (13 x 17.5 x 17 mm^3). This paper gives a brief overview of the experiment, the detector system, and event reconstruction. Reference 1. M. Amoretti et al., Nature 419, 456 (2002).Comment: 7 pages, 5 figures; Proceedings for the 8th ICATPP Conference on Astroparticle, Particle, Space Physics, Detectors and Medical Physics Applications (Como, Italy October 2003) to be published by World Scientific (style file included

Three Dimensional Annihilation Imaging of Antiprotons in a Penning Trap

We demonstrate three-dimensional annihilation imaging of antiprotons trapped in a Penning trap. Exploiting unusual feature of antiparticles, we investigate a previously unexplored regime in particle transport; the proximity of the trap wall. Particle loss on the wall, the final step of radial transport, is observed to be highly non-uniform, both radially and azimuthally. These observations have considerable implications for the production and detection of antihydrogen atoms.Comment: Invited Talk at NNP03, Workshop on Non-Neutral Plasmas, 200