Premature thoughts on writing disorders

Three papers appeared in the 19th century describing the dissociation between speech and writing: Marce (1856), Ogle (1867) and Pitres (1884). An account of the convincing evidence of dissociations put forward in these papers is presented. Three explanations are proposed as to the reason why the observations reported by these authors were overlooked or rejected by their contemporaries, namely: (a) in the first half of the century it seems that very little knowledge of the processes underlying writing (as opposed to speech) was available, (b) the debates focussed on the independence of speech versus motor control and language versus the intellect, (c) parallelisms between phylogeny, ontogeny and aphasia impeded the application of the principle of double dissociations, including the dissociations between speech and writing. It is argued that this phenomenon in the history of aphasia is best captured by the concept of prematurity in scientific discovery proposed by Stent (1972, 2003)

Experimental study on grooved Si and Ge crystals for Laue lens application

An experimental study on the method of indentations for bent crystals to realize a hard X-ray Laue lens has been done. We tested the diffraction properties of indented Si and Ge crystalline plates at European Synchrotron Radiation Facility (Grenoble, France). The samples were analyzed by diffraction of their (111) planes with hard X-rays from 150 to 600 keV. Crystals have shown significantly high diffraction efficiency, i.e. a Si crystal has exhibited up to 80% at 300 keV. A Ge crystal has confirmed the observation for a Si one, though the diffraction efficiency was about 60%. In both cases rocking curves showed flat-toped rectangular shapes, which demonstrates that the method of indentations evenly bends the crystals. Moreover, measured angular spread was always very close to the morphological curvature of the sample under investigation, showing that this method offers high reproducibility and, thus, easy control of diffraction properties of the crystals

Planar subgraphs without low-degree nodes

We study the following problem: given a geometric graph G and an integer k, determine if G has a planar spanning subgraph (with the original embedding and straight-line edges) such that all nodes have degree at least k. If G is a unit disk graph, the problem is trivial to solve for k = 1. We show that even the slightest deviation from the trivial case (e.g., quasi unit disk graphs or k = 1) leads to NP-hard problems.Peer reviewe

Networks become navigable as nodes move and forget

We propose a dynamical process for network evolution, aiming at explaining the emergence of the small world phenomenon, i.e., the statistical observation that any pair of individuals are linked by a short chain of acquaintances computable by a simple decentralized routing algorithm, known as greedy routing. Previously proposed dynamical processes enabled to demonstrate experimentally (by simulations) that the small world phenomenon can emerge from local dynamics. However, the analysis of greedy routing using the probability distributions arising from these dynamics is quite complex because of mutual dependencies. In contrast, our process enables complete formal analysis. It is based on the combination of two simple processes: a random walk process, and an harmonic forgetting process. Both processes reflect natural behaviors of the individuals, viewed as nodes in the network of inter-individual acquaintances. We prove that, in k-dimensional lattices, the combination of these two processes generates long-range links mutually independently distributed as a k-harmonic distribution. We analyze the performances of greedy routing at the stationary regime of our process, and prove that the expected number of steps for routing from any source to any target in any multidimensional lattice is a polylogarithmic function of the distance between the two nodes in the lattice. Up to our knowledge, these results are the first formal proof that navigability in small worlds can emerge from a dynamical process for network evolution. Our dynamical process can find practical applications to the design of spatial gossip and resource location protocols.Comment: 21 pages, 1 figur

Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict

Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated

Role of the Single-Stranded DNA–Binding Protein SsbB in Pneumococcal Transformation: Maintenance of a Reservoir for Genetic Plasticity

Bacteria encode a single-stranded DNA (ssDNA) binding protein (SSB) crucial for genome maintenance. In Bacillus subtilis and Streptococcus pneumoniae, an alternative SSB, SsbB, is expressed uniquely during competence for genetic transformation, but its precise role has been disappointingly obscure. Here, we report our investigations involving comparison of a null mutant (ssbB−) and a C-ter truncation (ssbBΔ7) of SsbB of S. pneumoniae, the latter constructed because SSBs' acidic tail has emerged as a key site for interactions with partner proteins. We provide evidence that SsbB directly protects internalized ssDNA. We show that SsbB is highly abundant, potentially allowing the binding of ∼1.15 Mb ssDNA (half a genome equivalent); that it participates in the processing of ssDNA into recombinants; and that, at high DNA concentration, it is of crucial importance for chromosomal transformation whilst antagonizing plasmid transformation. While the latter observation explains a long-standing observation that plasmid transformation is very inefficient in S. pneumoniae (compared to chromosomal transformation), the former supports our previous suggestion that SsbB creates a reservoir of ssDNA, allowing successive recombination cycles. SsbBΔ7 fulfils the reservoir function, suggesting that SsbB C-ter is not necessary for processing protein(s) to access stored ssDNA. We propose that the evolutionary raison d'être of SsbB and its abundance is maintenance of this reservoir, which contributes to the genetic plasticity of S. pneumoniae by increasing the likelihood of multiple transformation events in the same cell

Macro-level Modeling of the Response of C. elegans Reproduction to Chronic Heat Stress

A major goal of systems biology is to understand how organism-level behavior arises from a myriad of molecular interactions. Often this involves complex sets of rules describing interactions among a large number of components. As an alternative, we have developed a simple, macro-level model to describe how chronic temperature stress affects reproduction in C. elegans. Our approach uses fundamental engineering principles, together with a limited set of experimentally derived facts, and provides quantitatively accurate predictions of performance under a range of physiologically relevant conditions. We generated detailed time-resolved experimental data to evaluate the ability of our model to describe the dynamics of C. elegans reproduction. We find considerable heterogeneity in responses of individual animals to heat stress, which can be understood as modulation of a few processes and may represent a strategy for coping with the ever-changing environment. Our experimental results and model provide quantitative insight into the breakdown of a robust biological system under stress and suggest, surprisingly, that the behavior of complex biological systems may be determined by a small number of key components

Distinct Functional Constraints Partition Sequence Conservation in a cis-Regulatory Element

Different functional constraints contribute to different evolutionary rates across genomes. To understand why some sequences evolve faster than others in a single cis-regulatory locus, we investigated function and evolutionary dynamics of the promoter of the Caenorhabditis elegans unc-47 gene. We found that this promoter consists of two distinct domains. The proximal promoter is conserved and is largely sufficient to direct appropriate spatial expression. The distal promoter displays little if any conservation between several closely related nematodes. Despite this divergence, sequences from all species confer robustness of expression, arguing that this function does not require substantial sequence conservation. We showed that even unrelated sequences have the ability to promote robust expression. A prominent feature shared by all of these robustness-promoting sequences is an AT-enriched nucleotide composition consistent with nucleosome depletion. Because general sequence composition can be maintained despite sequence turnover, our results explain how different functional constraints can lead to vastly disparate rates of sequence divergence within a promoter