UV wavelengths experienced during development affect larval newt visual sensitivity and predation efficiency

We experimentally investigated the influence of developmental plasticity of ultraviolet (UV) visual sensitivity on predation efficiency of the larval smooth newt, Lissotriton vulgaris. We quantified expression of SWS1 opsin gene (UV-sensitive protein of photoreceptor cells) in the retinas of individuals who had developed in the presence (UV+) or absence (UV-) of UV light (developmental treatments), and tested their predation efficiency under UV+ and UV- light (testing treatments). We found that both SWS1 opsin expression and predation efficiency were significantly reduced in the UV- developmental group. Larvae in the UV- testing environment displayed consistently lower predation efficiency regardless of their developmental treatment. These results prove for the first time, we believe, functional UV vision and developmental plasticity of UV sensitivity in an amphibian at the larval stage. They also demonstrate that UV wavelengths enhance predation efficiency and suggest that the magnitude of the behavioural response depends on retinal properties induced by the developmental lighting environment

Radio emission of extensive air shower at CODALEMA: Polarization of the radio emission along the v*B vector

Cosmic rays extensive air showers (EAS) are associated with transient radio emission, which could provide an efficient new detection method of high energy cosmic rays, combining a calorimetric measurement with a high duty cycle. The CODALEMA experiment, installed at the Radio Observatory in Nancay, France, is investigating this phenomenon in the 10^17 eV region. One challenging point is the understanding of the radio emission mechanism. A first observation indicating a linear relation between the electric field produced and the cross product of the shower axis with the geomagnetic field direction has been presented (B. Revenu, this conference). We will present here other strong evidences for this linear relationship, and some hints on its physical origin.Comment: Contribution to the 31st International Cosmic Ray Conference, Lodz, Poland, July 2009. 4 pages, 8 figures. v2: Typo fixed, arxiv references adde

Membrane-Targeted HrpN Ea Can Modulate Apple Defense Gene Expression

Fire blight caused by Erwinia amylovora is the major bacterial disease of tribe Maleae, including apple. Among the proteins secreted by this bacterium, HrpNEa, also called harpin, is known to induce hypersensitive response in nonhost plants and to form amyloid oligomers leading to pore opening in the plasma membrane and alteration of membrane homeostasis. To better understand the physiological effects of HrpNEa in the host plant, we produced transgenic apple plants expressing HrpNEa with or without a secretion signal peptide (SP). HrpNEa expressed with a SP was found to be associated within the membrane fraction, in accordance with amyloidogenic properties and the presence of transmembrane domains revealed by in silico analysis. Expression analysis of 28 apple defense-related genes revealed gene modulations in the transgenic line expressing membrane-targeted HrpNEa. While apple transgenic trees displaying a high constitutive expression level of SP-HrpNEa showed a slight reduction of infection frequency after E. amylovora inoculation, there was no decrease in the disease severity. Thus HrpNEa seems to act as an elicitor of host defenses, when localized in the host membrane

Geomagnetic origin of the radio emission from cosmic ray induced air showers observed by CODALEMA

The new setup of the CODALEMA experiment installed at the Radio Observatory in Nancay, France, is described. It includes broadband active dipole antennas and an extended and upgraded particle detector array. The latter gives access to the air shower energy, allowing us to compute the efficiency of the radio array as a function of energy. We also observe a large asymmetry in counting rates between showers coming from the North and the South in spite of the symmetry of the detector. The observed asymmetry can be interpreted as a signature of the geomagnetic origin of the air shower radio emission. A simple linear dependence of the electric field with respect to vxB is used which reproduces the angular dependencies of the number of radio events and their electric polarity.Comment: 9 pages, 15 figures, 1 tabl

Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data

<p>Abstract</p> <p>Background</p> <p>In bioinformatics it is common to search for a pattern of interest in a potentially large set of rather short sequences (upstream gene regions, proteins, exons, etc.). Although many methodological approaches allow practitioners to compute the distribution of a pattern count in a random sequence generated by a Markov source, no specific developments have taken into account the counting of occurrences in a set of independent sequences. We aim to address this problem by deriving efficient approaches and algorithms to perform these computations both for low and high complexity patterns in the framework of homogeneous or heterogeneous Markov models.</p> <p>Results</p> <p>The latest advances in the field allowed us to use a technique of optimal Markov chain embedding based on deterministic finite automata to introduce three innovative algorithms. Algorithm 1 is the only one able to deal with heterogeneous models. It also permits to avoid any product of convolution of the pattern distribution in individual sequences. When working with homogeneous models, Algorithm 2 yields a dramatic reduction in the complexity by taking advantage of previous computations to obtain moment generating functions efficiently. In the particular case of low or moderate complexity patterns, Algorithm 3 exploits power computation and binary decomposition to further reduce the time complexity to a logarithmic scale. All these algorithms and their relative interest in comparison with existing ones were then tested and discussed on a toy-example and three biological data sets: structural patterns in protein loop structures, PROSITE signatures in a bacterial proteome, and transcription factors in upstream gene regions. On these data sets, we also compared our exact approaches to the tempting approximation that consists in concatenating the sequences in the data set into a single sequence.</p> <p>Conclusions</p> <p>Our algorithms prove to be effective and able to handle real data sets with multiple sequences, as well as biological patterns of interest, even when the latter display a high complexity (PROSITE signatures for example). In addition, these exact algorithms allow us to avoid the edge effect observed under the single sequence approximation, which leads to erroneous results, especially when the marginal distribution of the model displays a slow convergence toward the stationary distribution. We end up with a discussion on our method and on its potential improvements.</p

Mining protein loops using a structural alphabet and statistical exceptionality

<p>Abstract</p> <p>Background</p> <p>Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied.</p> <p>Results</p> <p>We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 Å). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints.</p> <p>Conclusions</p> <p>We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at <url>http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/</url>.</p

Bone Regeneration Using Porous Titanium Particles versus Bovine Hydroxyapatite: A Sinus Lift Study in Rabbits.

Aim: The first objective of this study was to qualitatively and quantitatively assess the bone formation process, particularly the long-term behavior and three-dimensional volume stability of subsinusal bone regeneration, using titanium (Ti) or bovine hydroxyapatite (BHA) granules, in a rabbit model. The second objective was to evaluate the effect of the hydration of the BHA particles with a therapeutic concentration of doxycycline solution on the osteogenesis and biomaterial resorption. Materials and Methods: Rabbits underwent a double sinus lift procedure using one of three materials: grade 1 porous Ti particles, BHA, or BHA hydrated with doxycycline solution (0.1 mg/ml) (BHATTC). Animals were sacrificed after 1 week, 5 weeks, or 6 months. Samples were analyzed using µCT and nondecalcified histology. Results: The materials used in each of the three groups allowed an optimal bone formation; bone quantities and densities were not statistically different between the three groups. At 6 months, more stable three-dimensional volume stability was found with Ti and BHATTC (p = .0033). At 5 weeks and 6 months, bone to material contact corroborating osteoconduction was significantly higher with BHA and BHATTC than with Ti (p < .0001). Conclusions and Clinical Implications: Even though the studied biomaterials displayed different architectures, they are relevant candidates for sinus lift bone augmentation prior to dental implants because they allow adequate three-dimensional stability and osteogenesis. However, to recommend the clinical use of Ti, both an observation on the drilling effects of Ti particles and clinical trials are needed

Influence of space-filling materials in subantral bone augmentation: blood clot vs. autogenous bone chips vs. bovine hydroxyapatite

Aim: The first objective of the present study was to compare the short- and long-term 3D volume stability of sub-sinusal bone regeneration in rabbits using different space fillers. The second objective was to assess qualitatively and quantitatively the early bone formation process and long-term behavior of the regenerated bone. Materials and methods: Fifteen rabbits underwent a double sinus lift procedure using: blood clot (Clot), autogenous bone chips (Auto) and bovine hydroxyapatite (BHA). Animals were euthanized at 1 week, 5 weeks and 6 months. Samples were subjected to X-ray microtomography and histology. Variations in the volume of bone augmentations were calculated at different time points. Qualitative analysis was performed using 7 μm sections and quantitative histomorphometric analyses were carried out using scanning electron microscopy. Results: From baseline (100%) to 5 weeks, the augmented volumes declined to 17.3% (Clot), 57.6% (Auto) and 90.6% (BHA). After 6 months, only 19.4% (Clot) and 31.4% (Auto) of initial volumes were found, while it remained more stable in the BHA group (84%). At 1 week, an initial osteogenesis process could be observed in the three groups along the bone walls. At 5 weeks, despite a significant decline in the volume, newly formed bone density was higher with Clot and Auto than with BHA. At 6 months, bone densities were statistically similar in the three groups. However, after 6 months, the surface invaded by newly formed bone (regenerated area) was significantly higher when BHA was used as space filler. In the BHA group, the biomaterial area slightly decreased from 42.7% (1 week) to 40% (5 weeks) and 34.9% (6 months) and the density of the composite regenerated tissue (bone+BHA) reached >50% at 6 months. Conclusions and clinical implications: The three space fillers allowed bone formation to occur. Nevertheless, augmented volumes declined in the Clot and Auto groups, while they remained stable with BHA. A slowly resorbable biomaterial might be suitable in sub-sinusal bone augmentation for preventing the re-expansion process and for augmenting the density of the regenerated tissues

Re: Agarwal et al Stylomandibular fusion that complicates recurrent bilateral ankylosis of the temporomandibular joint

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