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

Rabbit haemorrhagic disease: experimental study of a recent highly pathogenic GI.2/RHDV2/b strain and evaluation of vaccine efficacy

[EN] In 2010, a variant of the rabbit haemorrhagic disease virus (RHDV) belonging to a new GI.2 genotype was identified in France and rapidly spread worldwide. Due to antigenic difference, new vaccines including G1.2 strains have been developed to confer adequate protection. An increase in the pathogenicity of the circulating strains was recently reported. The objective of this experimental study was to characterise the infection with a highly pathogenic GI.2/RHDV2/b isolate (2017) and assess the efficacy of Filavac VHD K C+V vaccine (Filavie) against this strain. Four and 10-wk-old specific pathogen-free rabbits were inoculated with a recommended dose of vaccine. After 7 d, controls and vaccinated rabbits were challenged and clinically monitored for 14 d. All animals were necropsied and blood, organs and urine were sampled for quantitative reverse transcription polymerase chain reaction (RT-qPCR) analysis. In adult groups, regular nasal and rectal swabbing were performed, and faeces were collected after death to monitor RNA shedding. In control groups, the challenge strain induced acute RHD between 31 and 72 h post-inoculation, with a mortality rate of 100% for kits and 89% for adult rabbits. Except for a shorter mean time to death in kits, similar clinical signs and lesions were observed between age groups. The vaccination significantly prevented all mortality, clinical signs, detection of viral RNA in serum and gross lesions in kits and adult rabbits. In adult groups, we also demonstrated that vaccine significantly protected from detectable RNA shedding via naso-conjunctival and rectal routes. Two weeks after challenge, RNA copies were not detected by PCR in the liver, spleen, lungs, kidneys, faeces and urine of vaccinated adult rabbits. The findings for kits were similar, except that very low levels of RNA were present in the liver and spleen of a few rabbits. These data show that immunisation prevented any significant viral multiplication and/or allowed a rapid clearance. We concluded that, despite the quick evolution of GI.2/RHDV2/b strains, the protection conferred by the vaccine remains adequate. In the context of coexistence of both GI.1 and GI.2 genotypes in some countries, with the circulation of multiples recombinant viruses, the vaccination should be based on the association of strains from both genotypes.Le Minor, O.; Boucher, S.; Joudou, L.; Mellet, R.; Sourice, M.; Le Moullec, T.; Nicolier, A.... (2019). Rabbit haemorrhagic disease: experimental study of a recent highly pathogenic GI.2/RHDV2/b strain and evaluation of vaccine efficacy. World Rabbit Science. 27(3):143-156. https://doi.org/10.4995/wrs.2019.11082SWORD143156273Abrantes J., van der Loo W., Le Pendu J., Esteves P.J. 2012. Rabbit haemorrhagic disease (RHD) and rabbit haemorrhagic disease virus (RHDV): a review. Vet. Res., 43: 12. https://doi.org/10.1186/1297-9716-43-12Abrantes J., Lopes A.M., Dalton K.P., Melo P., Correia J.J., Ramada M., Alves P.C., Parra F., Esteves P.J. 2013. New variant of rabbit hemorrhagic disease virus, Portugal, 2012-2013. Emerg. Infect. Dis., 19: 1900-1902. https://doi.org/10.3201/eid1911.130908Calvete C., Sarto P., Calvo A.J., Monroy F., Calvo J.H. 2014. Letter - Could the new rabbit haemorrhagic disease virus variant (RHDVb) be fully replacing classical RHD strains in the Iberian Peninsula?. World Rabbit Sci., 22: 91-91. https://doi.org/10.4995/wrs.2014.1715Calvete C, Mendoza M, Alcaraz A, Sarto M.P., Jiménez-de-Bagüéss M.P., Calvo A.J., Monroy F., Calvo J.H., 2018. Rabbit haemorrhagic disease: Cross-protection and comparative pathogenicity of GI.2/RHDV2/b and GI.1b/RHDV lagoviruses in a challenge trial. Vet. Microbiol., 219: 87-95. https://doi.org/10.1016/j.vetmic.2018.04.018Capucci L., Cavadini P., Schiavitto M., Lombardi G., Lavazza A. 2017. Increased pathogenicity in rabbit haemorrhagic disease virus type 2 (RHDV2). Vet. Rec., 180: 426. https://doi.org/10.1136/vr.104132Carvalho C.L., Duarte E.L., Monteiro M., Botelho A., Albuquerque T., Fevereiro M., Henriques A.M., Barros SS., Duarte MD. 2017. Challenges in the rabbit haemorrhagic disease 2 (RHDV2) molecular diagnosis of vaccinated rabbits. Vet. Microbiol. 198: 43-50. https://doi.org/10.1016/j.vetmic.2016.12.006Dalton K.P., Balseiro A., Juste R.A., Podadera A., Nicieza I., Del Llano D., González R., Martin Alonso J.M., Prieto J.M., Parra F., Casais R. 2018. Clinical course and pathogenicity of variant rabbit haemorrhagic disease virus in experimentally infected adult and kit rabbits: Significance towards control and spread. Vet. Microbiol., 220: 24-32. https://doi.org/10.1016/j.vetmic.2018.04.033Dalton K.P., Nicieza I., Abrantes J., Esteves P.J., Parra F., 2014. Spread of new variant RHDV in domestic rabbits on the Iberian Peninsula. Vet. Microbiol., 169: 67-73. https://doi.org/10.1016/j.vetmic.2013.12.015Dalton K.P., Nicieza I., Balseiro A., Muguerza M.A., Rosell J.M., Casais R., Álvarez Á.L., Parra F. 2012. Variant rabbit hemorrhagic disease virus in young rabbits, Spain. Emerg. Infect. Dis., 18: 2009-2012. https://doi.org/10.3201/eid1812.120341Duarte M., Henriques M., Barros S.C., Fagulha T., Ramos F., Luís T., Fevereiro M., Benevides S., Flor L., Barros S.V., Bernardo S. 2015. Detection of RHDV variant 2 in the Azores. Vet. Rec.,176: 130. https://doi.org/10.1136/vr.h497Forrester N.L., Boag B., Moss S.R., Turner S.L., Trout R.C., White P.J., Hudson P.J., Gould E.A., 2003. Long-term survival of New Zealand rabbit haemorrhagic disease virus RNA in wild rabbits, revealed by RT-PCR and phylogenetic analysis. J. Gen.Virol., 84: 3079-3086. https://doi.org/10.1099/vir.0.19213-0Gall A., Schirrmeier H. 2006. Persistence of rabbit haemorrhagic disease virus genome in vaccinated rabbits after experimental infection. J. Vet. Med. B. Infect. Dis. Vet. Public Health, 53: 358-362. https://doi.org/10.1111/j.1439-0450.2006.00986.xGall A., Hoffmann B., Teifke J.P., Lange B., Schirrmeier H., 2007. Persistence of viral RNA in rabbits which overcome an experimental RHDV infection detected by a highly sensitive multiplex real-time RT-PCR. Vet. Microbiol.,120: 17-32. https://doi.org/10.1016/j.vetmic.2006.10.006Hall R.N., Mahar J.E., Haboury S., Stevens V., Holmes E.C., Strive T. 2015. Emerging Rabbit Hemorrhagic Disease Virus 2 (RHDVb), Australia. Emerg. Infect. Dis., 21: 2276-2278. https://doi.org/10.3201/eid2112.151210Le Gall G., Boilletot E., Morisse J.P. 1992. Viral haemorrhagic disease of rabbit: purification and characterization of a strain isolated in France. Ann. Rech. Vet., 23: 381-387.Le Gall-Reculé G., Zwingelstein F., Boucher S., Le Normand B., Plassiart G., Portejoie Y., Decors A., Bertagnoli S., Guérin J.L., Marchandeau S. 2011. Detection of a new variant of rabbit haemorrhagic disease virus in France. Vet. Rec., 168: 137-138. https://doi.org/10.1136/vr.d697Le Gall-Reculé G., Lavazza A., Marchandeau S., Bertagnoli S., Zwingelstein F., Cavadini, P., Martinelli N., Lombardi G., Guérin J.L., Lemaitre E., Decors A., Boucher S., Le Normand B., Capucci L. 2013. Emergence of a new lagovirus related to Rabbit Haemorrhagic Disease Virus. Vet. Res., 44: 81. https://doi.org/10.1186/1297-9716-44-81Le Gall-Reculé G., Lemaitre E., Bertagnoli S., Hubert C., Top S., Decors A., Marchandeau S., Guitton J.S., 2017. Large-scale lagovirus disease outbreaks in European brown hares (Lepus europaeus) in France caused by RHDV2 strains spatially shared with rabbits (Oryctolagus cuniculus). Vet. Res., 48: 70. https://doi.org/10.1186/s13567-017-0473-yLe Minor O., Beilvert F., Le Moullec T., Djadour D., Martineau J. 2013. Evaluation de l'efficacité d'un nouveau vaccin contre le virus variant de la maladie hémorragique virale du lapin (VHD).15èmes Journées de la Recherche Cunicole, 19-20 novembre, Le Mans, France.Le Minor O., Joudou L., Le Moullec T., Beilvert F. 2017. Innocuité et efficacité de la vaccination à 2 et 3 semaines d'âge contre le virus RHDV2 de la maladie hémorragique virale du lapin (VHD).17èmes Journées de la Recherche Cunicole, 22-13 novembre, Le Mans, France.Le Pendu J., Abrantes J., Bertagnoli S., Guitton J.S., Le Gall-Reculé G., Lopes A.M., Marchandeau S., Alda F., Almeida T., Célio A.P., Bárcena J., Burmakina G., Blanco E., Calvete C., Cavadini P., Cooke B., Dalton K., Delibes Mateos M., Deptula W., Eden J.S., Wang F., Ferreira C.C., Ferreira P., Foronda P., Gonçalves D., Gavier-Widén D., Hall R., Hukowska-Szematowicz B., Kerr P., Kovaliski J., et al. 2017. Proposal for a unified classification system and nomenclature of lagoviruses. J. Gen. Virol., 98:1658-1666. https://doi.org/10.1099/jgv.0.000840Lopes A.M., Correia J., Abrantes J., Melo P., Ramada M., Magalhães M.J., Alves P.C., Esteves P.J. 2015. Is the new variant RHDV replacing genogroup 1 in Portuguese wild rabbit populations? Viruses, 7: 27-36. https://doi.org/10.3390/v7010027Mahar J.E., Hall R.N., Peacock D., Kovaliski J., Piper M., Mourant R., Huang N., Campbell S., Gu X., Read A., Urakova N., Cox T., Holmes E.C., Strive T. 2018. Rabbit haemorrhagic disease virus 2 (GI.2) is replacing endemic strains of RHDV in the Australian landscape within 18 months of its arrival. J. Virol., https://doi.org/10.1128/JVI.01374-17Martin-Alonso A., Martin-Carrillo N., Garcia-livia K., Valladares B., Foronda P. 2016. Emerging rabbit haemorrhagic disease virus 2 (RHDV2) at the gates of the African continent. Infect. Genet. Evol., 44: 46-50. https://doi.org/10.1016/j.meegid.2016.06.034Morin H., Le Minor O., Beilvert F., Le Moullec T. 2015. Durée d'immunité conférée par un vaccin vis-à-vis des calicivirus classique et variant de la maladie virale hémorragique. 16èmes Journées de la Recherche Cunicole, 18-19 novembre, Le mans, France.Neimanis A., Larsson Pettersson U., Huang N., Gavier‑Widén D.,Strive T. 2018. Elucidation of the pathology and tissue distribution of Lagovirus europaeus GI.2/RHDV2 (rabbit haemorrhagic disease virus 2) in young and adult rabbits (Oryctolagus cuniculus). Vet. Res., 49: 46. https://doi.org/10.1186/s13567-018-0540-zOIE, 2017. Manual of Diagnostic Tests and Vaccines for Terrestrial Animals 2017. Chapter 2.6.2. Rabbit Haemorrhagic disease. Available at: (Accessed 8 February 2018): http://www.oie.int/fileadmin/Home/fr/Health_standards/tahm/3.06.02_RHD.pdfOIE, 2016. Rabbit Haemorrhagic disease, Canada-immediate notification report. Available at: http://www.oie.int/wahis_2/public/wahid.php/Reviewreport/Review?page_refer=MapFullEventReport&reportid=20799.Puggioni G., Cavadini P., Maestrale C., Scivoli R., Botti G., Ligios C., Le Gall- Recule G., Lavazza A., Capucci L. 2013. The new French 2010 Rabbit Hemorrhagic Disease Virus causes an RHD-like disease in the Sardinian Cape hare (Lepus capensis mediterraneus). Vet. Res., 44: 96.https://doi.org/10.1186/1297-9716-44-96Read A.J., Kirkland P.D. 2017. Efficacy of a commercial vaccine against different strains of rabbit haemorrhagic disease virus. Aust. Vet. J., 95: 223-226. https://doi.org/10.1111/avj.12600Silvério D., Lopes A.M., Melo-Ferreira J., Magalhães M.J., Monterroso P., Serronha A., Maio E., Alves P.C., Esteves P.J., Abrantes J. 2018. Insights into the evolution of the new variant rabbit haemorrhagic disease virus (GI.2) and the identification of novel recombinant strains. Transbound. Emerg. Dis., 65: 983-992. https://doi.org/10.1111/tbed.12830Shien, J.H., Shieh, H.K., Lee, L.H. 2000. Experimental infections of rabbits with rabbit haemorrhagic disease virus monitored by polymerase chain reaction. Res. Vet. Sci., 68, 255-259. https://doi.org/10.1053/rvsc.1999.0372Spikey N., McCabe V.J., Greenwood N.M., Jack S.C., Sutton D., van der Waart L. 2012. Novel bivalent vectored vaccine for control of myxomatosis and rabbit haemorrhagic disease. Vet. Rec., 170: 309. https://doi.org/10.1136/vr.100366Strive T., Wright J., Kovaliski J., Botti G., Capucci L. 2010. The non-pathogenic Australian lagovirus RCV-A1 causes a prolonged infection and elicits partial crossprotection to rabbit haemorrhagic disease virus. Virology, 398, 125-134. https://doi.org/10.1016/j.virol.2009.11.045Westcott D.G., Frossard J.P., Everest D., Dastjerdi A., Duff J.P., Choudhury B. 2014. Incursion of RHDV2- like variant in Great Britain. Vet. Rec., 174: 333-333. https://doi.org/10.1136/vr.g234

Local Renyi entropic profiles of DNA sequences

<p>Abstract</p> <p>Background</p> <p>In a recent report the authors presented a new measure of continuous entropy for DNA sequences, which allows the estimation of their randomness level. The definition therein explored was based on the Rényi entropy of probability density estimation (pdf) using the Parzen's window method and applied to Chaos Game Representation/Universal Sequence Maps (CGR/USM). Subsequent work proposed a fractal pdf kernel as a more exact solution for the iterated map representation. This report extends the concepts of continuous entropy by defining DNA sequence entropic profiles using the new pdf estimations to refine the density estimation of motifs.</p> <p>Results</p> <p>The new methodology enables two results. On the one hand it shows that the entropic profiles are directly related with the statistical significance of motifs, allowing the study of under and over-representation of segments. On the other hand, by spanning the parameters of the kernel function it is possible to extract important information about the scale of each conserved DNA region. The computational applications, developed in Matlab m-code, the corresponding binary executables and additional material and examples are made publicly available at <url>http://kdbio.inesc-id.pt/~svinga/ep/</url>.</p> <p>Conclusion</p> <p>The ability to detect local conservation from a scale-independent representation of symbolic sequences is particularly relevant for biological applications where conserved motifs occur in multiple, overlapping scales, with significant future applications in the recognition of foreign genomic material and inference of motif structures.</p

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

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

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

Parameters and DOA estimation based on wavelet packets

International audienc

Dual-modulation fiber Fabry-Perot interferometer with double reflection for slowly-varying displacements

This Letter describes a dual-amplitude modulation technique incorporated into a double reflection extrinsic-type fiber Fabry-Perot interferometer to measure periodic, nonperiodic as well as quasi-static displacements. The modulation scheme simultaneously maintains the interference signal pair in quadrature and provides a reference signal for displacements inferior to a quarter of the source wavelength. The control and phase demodulation of the interferometer carried out via software enable quasi-real-time measurement and facilitates sensor alignment. The sensor system can be exploited in the low frequency range from 10−3 to ∼500 Hz and has a resolution better than 2.2 nm, targeting applications in geophysics

Notchless is required for axial skeleton formation in mice.

International audienceMaintenance of cell survival is essential for proper embryonic development. In the mouse, Notchless homolog 1 (Drosophila) (Nle1) is instrumental for survival of cells of the inner cell mass upon implantation. Here, we analyze the function of Nle1 after implantation using the Meox2tm1(cre)Sor mouse that expresses the Cre recombinase specifically in the epiblast at E5.5. First, we find that NLE1 function is required in epiblast cells, as Nle1-deficient cells are rapidly eliminated. In this report, we also show that the Meox2Cre transgene is active in specific tissues during organogenesis. In particular, we detect high Cre expression in the vertebral column, ribs, limbs and tailbud. We took advantage of this dynamic expression profile to analyze the effects of inducing mosaic deletion of Nle1 in the embryo. We show that Nle1 deletion in this context, results in severe developmental anomalies leading to lethality at birth. Mutant embryos display multiple developmental defects in particular during axial skeletal formation. We also provide evidence that axial defects are due to an increase in apoptotic cell death in the somite at E9.5. These data demonstrate an essential role for Nle1 during organogenesis and in particular during axial development