The RNA Silencing Pathway: The Bits and Pieces That Matter

Cellular pathways are generally proposed on the basis of available experimental knowledge. The proposed pathways, however, may be inadequate to describe the phenomena they are supposed to explain. For instance, by means of concise mathematical models we are able to reveal shortcomings in the current description of the pathway of RNA silencing. The silencing pathway operates by cleaving siRNAs from dsRNA. siRNAs can associate with RISC, leading to the degradation of the target mRNA. We propose and analyze a few small extensions to the pathway: a siRNA degrading RNase, primed amplification of aberrant RNA pieces, and cooperation between aberrant RNA to trigger amplification. These extensions allow for a consistent explanation for various types of silencing phenomena, such as virus induced silencing, transgene and transposon induced silencing, and avoidance of self-reactivity, as well as for differences found between species groups

Root System Architecture from Coupling Cell Shape to Auxin Transport

Lateral organ position along roots and shoots largely determines plant architecture, and depends on auxin distribution patterns. Determination of the underlying patterning mechanisms has hitherto been complicated because they operate during growth and division. Here, we show by experiments and computational modeling that curvature of the Arabidopsis root influences cell sizes, which, together with tissue properties that determine auxin transport, induces higher auxin levels in the pericycle cells on the outside of the curve. The abundance and position of the auxin transporters restricts this response to the zone competent for lateral root formation. The auxin import facilitator, AUX1, is up-regulated by auxin, resulting in additional local auxin import, thus creating a new auxin maximum that triggers organ formation. Longitudinal spacing of lateral roots is modulated by PIN proteins that promote auxin efflux, and pin2,3,7 triple mutants show impaired lateral inhibition. Thus, lateral root patterning combines a trigger, such as cell size difference due to bending, with a self-organizing system that mediates alterations in auxin transport

Landmark detection in 2D bioimages for geometric morphometrics: a multi-resolution tree-based approach

The detection of anatomical landmarks in bioimages is a necessary but tedious step for geometric morphometrics studies in many research domains. We propose variants of a multi-resolution tree-based approach to speed-up the detection of landmarks in bioimages. We extensively evaluate our method variants on three different datasets (cephalometric, zebrafish, and drosophila images). We identify the key method parameters (notably the multi-resolution) and report results with respect to human ground truths and existing methods. Our method achieves recognition performances competitive with current existing approaches while being generic and fast. The algorithms are integrated in the open-source Cytomine software and we provide parameter configuration guidelines so that they can be easily exploited by end-users. Finally, datasets are readily available through a Cytomine server to foster future research

A multiscale hybrid model for pro-angiogenic calcium signals in a vascular endothelial cell

Cytosolic calcium machinery is one of the principal signaling mechanisms by which endothelial cells (ECs) respond to external stimuli during several biological processes, including vascular progression in both physiological and pathological conditions. Low concentrations of angiogenic factors (such as VEGF) activate in fact complex pathways involving, among others, second messengers arachidonic acid (AA) and nitric oxide (NO), which in turn control the activity of plasma membrane calcium channels. The subsequent increase in the intracellular level of the ion regulates fundamental biophysical properties of ECs (such as elasticity, intrinsic motility, and chemical strength), enhancing their migratory capacity. Previously, a number of continuous models have represented cytosolic calcium dynamics, while EC migration in angiogenesis has been separately approached with discrete, lattice-based techniques. These two components are here integrated and interfaced to provide a multiscale and hybrid Cellular Potts Model (CPM), where the phenomenology of a motile EC is realistically mediated by its calcium-dependent subcellular events. The model, based on a realistic 3-D cell morphology with a nuclear and a cytosolic region, is set with known biochemical and electrophysiological data. In particular, the resulting simulations are able to reproduce and describe the polarization process, typical of stimulated vascular cells, in various experimental conditions.Moreover, by analyzing the mutual interactions between multilevel biochemical and biomechanical aspects, our study investigates ways to inhibit cell migration: such strategies have in fact the potential to result in pharmacological interventions useful to disrupt malignant vascular progressio

Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism

Leaves display a remarkable range of forms, from flat sheets with simple outlines to cup-shaped traps. Although much progress has been made in understanding the mechanisms of planar leaf development, it is unclear whether similar or distinctive mechanisms underlie shape transformations during development of more complex curved forms. Here, we use 3D imaging and cellular and clonal analysis, combined with computational modelling, to analyse the development of cup-shaped traps of the carnivorous plant Utricularia gibba. We show that the transformation from a near-spherical form at early developmental stages to an oblate spheroid with a straightened ventral midline in the mature form can be accounted for by spatial variations in rates and orientations of growth. Different hypotheses regarding spatiotemporal control predict distinct patterns of cell shape and size, which were tested experimentally by quantifying cellular and clonal anisotropy. We propose that orientations of growth are specified by a proximodistal polarity field, similar to that hypothesised to account for Arabidopsis leaf development, except that in Utricularia, the field propagates through a highly curved tissue sheet. Independent evidence for the polarity field is provided by the orientation of glandular hairs on the inner surface of the trap. Taken together, our results show that morphogenesis of complex 3D leaf shapes can be accounted for by similar mechanisms to those for planar leaves, suggesting that simple modulations of a common growth framework underlie the shaping of a diverse range of morphologies

Dynamics of defect formation

A dynamic symmetry-breaking transition with noise and inertia is analyzed. Exact solution of the linearized equation that describes the critical region allows precise calculation (exponent and prefactor) of the number of defects produced as a function of the rate of increase of the critical parameter. The procedure is valid in both the overdamped and underdamped limits. In one space dimension, we perform quantitative comparison with numerical simulations of the nonlinear nonautonomous stochastic partial differential equation and report on signatures of underdamped dynamics.Comment: 4 pages, LaTeX, 4 figures. Submitted to Physical Revie

The Roots of Bioinformatics in Theoretical Biology

From the late 1980s onward, the term “bioinformatics” mostly has been used to refer to computational methods for comparative analysis of genome data. However, the term was originally more widely defined as the study of informatic processes in biotic systems. In this essay, I will trace this early history (from a personal point of view) and I will argue that the original meaning of the term is re-emerging

Catalyst composition and impurity-dependent kinetics of nanowire heteroepitaxy.

The mechanisms and kinetics of axial Ge-Si nanowire heteroepitaxial growth based on the tailoring of the Au catalyst composition via Ga alloying are studied by environmental transmission electron microscopy combined with systematic ex situ CVD calibrations. The morphology of the Ge-Si heterojunction, in particular, the extent of a local, asymmetric increase in nanowire diameter, is found to depend on the Ga composition of the catalyst, on the TMGa precursor exposure temperature, and on the presence of dopants. To rationalize the findings, a general nucleation-based model for nanowire heteroepitaxy is established which is anticipated to be relevant to a wide range of material systems and device-enabling heterostructures.S.H. acknowledges funding from ERC grant InsituNANO (No. 279342). A.D.G. acknowledges funding from the Marshall Aid Commemoration Commission and the National Science Foundation. C.D. acknowledges funding from the Royal Society. A portion of the research was also performed using EMSL, a national scientific user facility sponsored by the Department of Energy’s (DOE) Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for the U.S. DOE under Contract DE-AC05-76RL01830. We gratefully acknowledge the use of facilities within the LeRoy Eyring Center for Solid State Science at Arizona State University. This work was performed in part at CINT, a U.S. DOE, Office of Science User Facility. The research was funded in part by the Laboratory Directed Research and Development Program at LANL, an affirmative action equal opportunity employer operated by Los Alamos National Security, LLC, for the National Nuclear Security Administration of the U.S. DOE under Contract DE-AC52-06NA25396.This document is the Accepted Manuscript version of a Published Work that appeared in final form in ACS Nano, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://pubs.acs.org/doi/abs/10.1021/nn402208p. Gamalski AD, Perea DE, Yoo J, Li N, Olszta MJ, Colby R, Schreiber DK, Ducati C, Picraux ST, Hofmann S, ACS Nano 2013, 7 (9), 7689–7697, doi:10.1021/nn402208