Scientific publications

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Transposable element (TE) science has been significantly influenced by the pioneering ideas of David Finnegan near the end of the last century, as well as by the classification systems that were subsequently developed. Today, whole genome TE annotation is mostly done using tools that were developed to aid gene annotation rather than to specifically study TEs. We argue that further progress in the TE field is impeded both by current TE classification schemes and by a failure to recognize that TE biology is fundamentally different from that of multicellular organisms. Novel genome wide TE annotation methods are helping to redefine our understanding of TE sequence origins and evolution. We briefly discuss some of these new methods as well as ideas for possible alternative classification schemes. Our hope is to encourage the formation of a society to organize a larger debate on these questions and to promote the adoption of standards for annotation and an improved TE classification.


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The chicken genome was the third vertebrate to be sequenced. To date, its sequence and feature annotations are used as the reference for avian models in genome sequencing projects developed on birds and other Sauropsida species, and in genetic studies of domesticated birds of economic and evolutionary biology interest. Therefore, an accurate description of this genome model is important to a wide number of scientists. Here, we review the location and features of a very basic element, the centromeres of chromosomes in the galGal5 genome model. Centromeres are elements that are not determined by their DNA sequence but by their epigenetic status, in particular by the accumulation of the histone-like protein CENP-A. Comparison of data from several public sources (primarily marker probes flanking centromeres using fluorescent in situ hybridization done on giant lampbrush chromosomes and CENP-A ChIP-seq datasets) with galGal5 annotations revealed that centromeres are likely inappropriately mapped in 9 of the 16 galGal5 chromosome models in which they are described. Analysis of karyology data confirmed that the location of the main CENP-A peaks in chromosomes is the best means of locating the centromeres in 25 galGal5 chromosome models, the majority of which (16) are fully sequenced and assembled. This data re-analysis reaffirms that several sources of information should be examined to produce accurate genome annotations, particularly for basic structures such as centromeres that are epigenetically determined.


Variations in genome size between wild and domesticated lineages of fowls belonging to the Gallus gallus species


Benoît Piégu, Peter Arensburger, Linda Beauclair, Marie Chabault, Emilie Raynaud, Vincent Coustham, Sophie Brard, Sébastien Guizard, Thierry Burlot, Elisabeth Le Bihan-Duval, Yves Bigot

DOI https://doi.org/10.1016/j.ygeno.2019.10.004
Scientific Field Life & Health Sciences
Fellow Dr Peter Arensburger
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Efforts to elucidate the causes of biological differences between wild fowls and their domesticated relatives, the chicken, have to date mainly focused on the identification of single nucleotide mutations. Other types of genomic variations have however been demonstrated to be important in avian evolution and associated to variations in phenotype. They include several types of sequences duplicated in tandem that can vary in their repetition number. Here we report on genome size differences between the red jungle fowl and several domestic chicken breeds and selected lines. Sequences duplicated in tandem such as rDNA, telomere repeats, satellite DNA and segmental duplications were found to have been significantly re-shaped during domestication and subsequently by human-mediated selection. We discuss the extent to which changes in genome organization that occurred during domestication agree with the hypothesis that domesticated animal genomes have been shaped by evolutionary forces aiming to adapt them to anthropized environments.


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Background:

Previous studies have shown that exposure to high frequency electromagnetic fields induces alterations in simple organic systems such as proteins in bidistilled water solution.

Objective:

The aim of this study was to test the shielding action of sodium chloride in bidistilled water solution against exposure to a high frequency electromagnetic field, in order to evaluate if the addition of NaCl in proteins aqueous solution can be considered a valuable bioprotector against electromagnetic fields.

Method:

Samples of 250 μl of different hemoglobin aqueous solutions, in the absence or presence of sodium-chloride, were exposed for 3 hours to an electromagnetic field at 1750 MHz at a power density around 1 W/m2 emitted by an operational mobile phone. Fourier Transform Infrared Spectroscopy was used to study the effects of exposure on the secondary structure of hemoglobin also in the presence of sodium-chloride.

Results:

Spectral analysis evidenced that significant increase in intensity of the Amide I and II vibration bands in hemoglobin bidistilled water solution occurred after exposure to the electromagnetic field. This result can be due to the increase of dipole moment of the protein due to the alignment of α-helix towards the direction of the field. In contrast, no appreciable change was observed in hemoglobin in sodium-chloride water solution after exposure.

Conclusion:

This protective effect of sodium-chloride can be explained by the orientation of water molecules due to the strong electric field around each ion that reduces the possibility of rotation of the protein in response to an applied electromagnetic field.


Stilbenoid-Enriched Grape Cane Extracts for the Biocontrol of Grapevine Diseases


Kevin Billet, Magdalena Anna Malinowska, Thibaut Munsch, Marianne Unlubayir, Thomas Dugé de Bernonville, Sebastien Besseau, Vincent Courdavault, Audrey Oudin, Olivier Pichon, Marc Clastre, Nathalie Giglioli-Guivarc’h, Arnaud Lanoue

DOI https://doi.org/10.1007/978-3-030-51034-3_9
Scientific Field Life & Health Sciences
Fellow Dr Magdalena Malinowska
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Grape canes are under-valued byproducts of viticulture that accumulate large amounts of stilbenoids. These specialized metabolites are phytoalexins of Vitis vinifera that play a keyrole in defence of Vitis vinifera against pathogens. Since in vitro assays demonstrated the antifungal activity of several pure stilbenoids, grape cane extracts (GCE) have been proposed as eco-friendly alternative to classical fungicides in a context of sustainable viticulture. Following the grape pruning during winter, a storage period associated to an efficient extraction procedure, are determinant to obtain GCE with optimal stilbenoid titration. Stilbenoid-enriched extracts have shown promising protection in vitro against various grape pathogens including downy mildew, powdery mildew, gray mold and wood diseases. Additionally, large-scale studies in vineyards reported a significant partial protection against downy mildew. Protection level is relative to the concentration of stilbenoids contained in the grape cane extract. Therefore, the huge varietal diversity of grape could be explored to select high-producing varieties for future use as biocontrol agent.


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This article presents the report of a research carried out during the postdoctoral program, which focused on the peda-gogical practices used for teaching Design for Social Innovation, with the objective of structuring the course of Ecosocial Design, a class to be taught to undergraduate college students majoring in Design in Brazil. To develop the search in this period, it was initiated a reflection on the creation and application of the Postgraduate Program in Design at the School of Fine Arts of the Federal University of Rio de Janeiro. The research method was based on the combination of the intrinsic and extrinsic aspects of the intermediate objects that are need to the creation of this Program with the ped-agogical instruments developed during its organization, and the potential of these instruments to participate associ-atively in the creation of new Graduate Programs in Brazil. It was determined that the preservation of the autonomy of the knowledge accrued in different contexts, according to the principle of individuation of the Intermediate Objects of Conception, is potentially capable of reducing territorial inequalities by strengthening their associations, and thus performing a coordinating role of associative forms.


Ion traps and the memory effect for periodic gravitational waves


P.-M. Zhang, M. Cariglia, C. Duval , M. Elbistan, G.W. Gibbons, P.A. Horvathy

DOI 10.1103/PhysRevD.98.044037
Scientific Field Computer science, Mathematics and Mathematical physics
Fellow Prof. Gary Gibbons
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The Eisenhart lift of a Paul trap used to store ions in molecular physics is a linearly polarized periodic gravitational wave. A modified version of Dehmelt’s Penning trap is, in turn, related to circularly polarized periodic gravitational waves, sought in inflationary models. Similar equations also govern the Lagrange points in celestial mechanics. The explanation is provided by anisotropic oscillators.


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Most species of moths use a female-produced volatile sex pheromone, typically produced via de novo fatty acid synthesis in a specialized gland, for communication among mates. While de novo biosynthesis of pheromone (DNP) is rapid, suggesting transient precursor acids, substantial amounts of pheromone precursor (and other) acids are stored, predominantly in triacylglycerols in the pheromone gland. Whether these stored acids are converted to pheromone later or not has been the subject of some debate. Using a tracer/tracee approach, in which we fed female Heliothis virescens U-13C-glucose, we were able to distinguish two pools of pheromone, in which precursors were temporally separated (after and before feeding on labeled glucose): DNP synthesized from a mixed tracer/tracee acetyl CoA pool after feeding, and pheromone made from precursor acids primarily synthesized before feeding, which we call recycled precursor fat pheromone (RPP). DNP titer varied from high (during scotophase) to low (photophase) and with presence/absence of pheromone biosynthesis activating neuropeptide (PBAN), in accord with native pheromone titer previously observed. By contrast, RPP was constant throughout the photoperiod and did not change with PBAN presence/absence. The amount of RPP (6.3–10.3 ng/female) was typically much lower than that of DNP, especially during the scotophase (peak DNP, 105 ng/female). We propose an integral role for stored fats in pheromone biosynthesis, in which they are hydrolyzed and re-esterified throughout the photoperiod, with a small proportion of liberated precursor acyl CoAs being converted to pheromone. During the sexually active period, release of PBAN results in increased flux of glucose (from trehalose) and hydrolyzed acids entering the mitochondria, producing acetyl CoA precursor for de novo fat and pheromone biosynthesis.


Promises and challenges in insect–plant interactions


David Giron, Géraldine Dubreuil, Alison Bennett, Franck Dedeine, Marcel Dicke, Lee A. Dyer, Matthias Erb, Marion O. Harris, Elisabeth Huguet, Isgouhi Kaloshian, Atsushi Kawakita, Carlos Lopez-Vaamonde, Todd M. Palmer, Theodora Petanidou, Michael Poulsen, Aurélien Salle, Jean-Christophe Simon, John S. Terblanche, Denis Thiery, Noah K. Whiteman, H. Arthur Woods, Sylvain Pincebourde

DOI 10.1111/eea.12679
Scientific Field Earth, Ecology and Environmental sciences
Fellow Prof. Marion Harris
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There is tremendous diversity of interactions between plants and other species. These relationships range from antagonism to mutualism. Interactions of plants with members of their ecological community can lead to a profound metabolic reconfiguration of the plants’ physiology. This reconfiguration can favour beneficial organisms and deter antagonists like pathogens or herbivores. Determining the cellular and molecular dialogue between plants, microbes, and insects, and its ecological and evolutionary implications is important for understanding the options for each partner to adopt an adaptive response to its biotic environment. Moving forward, understanding how such ecological interactions are shaped by environmental change and how we potentially mitigate deleterious effects will be increasingly important. The development of integrative multidisciplinary approaches may provide new solutions to the major ecological and societal issues ahead of us. The rapid evolution of technology provides valuable tools and opens up novel ways to test hypotheses that were previously unanswerable, but requires that scientists master these tools, understand potential ethical problems flowing from their implementation, and train new generations of biologists with diverse technical skills. Here, we provide brief perspectives and discuss future promise and challenges for research on insect–plant interactions building on the 16th International Symposium on Insect–Plant interactions (SIP) meeting that was held in Tours, France (2–6 July 2017). Talks, posters, and discussions are distilled into key research areas in insect–plant interactions, highlighting the current state of the field and major challenges, and future directions for both applied and basic research.


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The Little Red Schoolbook (1969) was one of the most welltravelled media products for children from ’68 aimed at children, and it was certainly the most notorious. Over the course of a few years (1970–2) it was translated and published in Belgium, Finland, France, Great Britain, the Federal Republic of Germany, Greece, Iceland, Italy, the Netherlands, Norway, Sweden and Switzerland. It also circulated freely in Austria and Luxembourg, and reached beyond Europe to countries including Australia, Japan and Mexico. It led to an obscenity trial in Great Britain, nearly toppled the Australian government, and caused a global publishing scandal. This essay therefore looks at the Scandinavian children’s ’68 in its international context, via a transnational, comparative analysis of the reception of the LRSB, in order to examine how ‘68 counterculture and ideas of childhood clashed and converged in the West around 1970. It asks: what can the publishing history of the LRSB tell us about the distinctive features of children’s media in Scandinavia at this time?