Nathalie Casse

The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments.

Transposable elements (TEs) are present in roughly all genomes. These mobile DNA sequences are able to invade genomes and their impact on genome evolution is substantial. The mobility of TEs can induce the appearance of deleterious mutations, gene disruption and chromosome rearrangements, but transposition activity also has positive aspects and the mutational activities of TEs contribute to the genetic diversity of organisms. This short review aims to give a brief overview of the impact TEs may have on animal and plant genome structure and expression, and the relationship between TEs and the stress response of organisms, including insecticide resistance.

Automatic classification within families of transposable elements: Application to the mariner Family

The higher levels of the classification of transposable elements (TEs) from Classes to Superfamilies or Families, is regularly updated, but the lower levels (below the Family) have received little investigation. In particular, this applies to the Families that include a large number of copies. In this article we propose an automatic classification of DNA sequences. This procedure is based on an aggregation process using a pairwise matrix of distances, allowing us to define several groups characterized by a sphere with a central sequence and a radius. This method was tested on the mariner Family, because this is probably one of the most extensively studied Families. Several Subfamilies had already been defined from phylogenetic analyses based on multiple alignments of complete or partial amino-acid sequences of the transposase. The classification obtained here from DNA sequences of 935 items matches the phylogenies of the transposase. The rate of error from a posteriori re-assignment is relatively low.

Thermoresponsive block copolymers containing reactive azlactone groups and their bioconjugation with lysozyme

Thermoresponsive block copolymers based on poly(ethylene oxide) (PEO) and poly(N-isopropyl acrylamide) (PNIPAM) containing azlactone groups along the backbone and at the chain-end of the macromolecular chain were synthesized by statistically reversible addition–fragmentation chain transfer (RAFT) copolymerization and by using a combination of RAFT polymerization and thiol–ene Michael addition. Well-defined poly(ethylene oxide)-b-poly(2-vinyl-4,4-dimethylazlactone-co-N-isopropyl acrylamide) (PEO-b-P(VDM-co-NIPAM)) block copolymers and azlactone-terminated poly(ethylene oxide)-b-poly(N-isopropyl acrylamide) (PEO-b-PNIPAM-VDM) diblock copolymers with low polydispersity indices (PDIs ≤ 1.10) were prepared and fully characterized by 1H NMR spectroscopy, FT-IR spectroscopy, and SEC. Such PEO-b-P(VDM-co-NIPAM) block copolymers and azlactone-terminated PEO-b-PNIPAM block copolymers present tunable lower critical solution temperature (LCST) depending on PEO, PNIPAM, and PVDM molar ratios. The reactivity of the PEO44-b-P(VDM20-co-NIPAM80) copolymer (Mn,NMR = 14 200 g mol−1, PDI = 1.08) and of the PEO44-b-PNIPAM101-VDM copolymer (Mn,NMR = 13 700 g mol−1, PDI = 1.08) was studied with lysozyme as a model protein. A bioconjugate with a higher apparent molecular weight was obtained with the PEO44-b-P(VDM20-co-NIPAM80) copolymer in comparison with the one obtained using the PEO44-b-PNIPAM101-VDM copolymer as shown by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The results suggest promising applications of azlactone-functionalized polymers within the field of bioconjugation.

Mariner transposons as genetic tools in vertebrate cells

Transposable elements (TEs) are being investigated as potential molecular tools in genetic engineering, for use in procedures such as transgenesis and insertional mutagenesis. Naturally active and reconstructed active TEs are both being studied to develop non-viral delivery vehicles. To date, the active elements being used include three Mariner-Like Elements (MLEs). We review below the studies that have investigated the ability of these MLEs to insert a transgene in vertebrate cells.

Electrochemically Modified Carbon and Chromium Surfaces for AFM Imaging of Double-Strand DNA Interaction with Transposase Protein

Carbon and chromium surfaces were modified by electrochemical reduction of a diazonium salt formed in situ from the sulfanilic acid. The organic layer formed was activated by phosphorus pentachloride (PCl(5)) to form a benzene sulfonil chloride (Ar-SO(2)Cl). An electrochemical study of the blocking effect and the activity of this surface was carried out on a carbon electrode. The chromium surface study was completed by X-ray photoelectron spectroscopy and atomic force microscopy to characterize the formation of a compact monolayer (0.8 nm height and roughness 0.2-0.3 nm). The compactness and the activity of this organic monolayer allowed us to affix a length dsDNA with the aim of analyzing the formation of a complex between dsDNA and a protein. The interaction of a transposase protein with its target dsDNA was investigated. The direct imaging of the nucleoproteic complex considered herein gives new insights in the comprehension of transposase-DNA interaction in agreement with biochemical data.

Strong and stable environmental structuring of the zooplankton communities in interconnected salt ponds

This study investigated assemblages of Copepoda and Artemia in saltern ponds and determined the main environmental factors affecting them. Copepoda and Artemia were collected from four ponds of varying salinity. Community composition was analyzed relative to environmental variables, with a focus on spatial and seasonal changes. We used a method called Costatis, which is particularly suited to analyze species and environmental data collected at the same sites and dates where the relationships between environmental conditions and composition of biological communities are strong and rather stable, which is the case in our system. The major structuring factors identified by Costatis were salinity and N:P ratio. Cyclopoida and Calanoida were associated with low salinity and low N:P ratios; Harpacticoida were associated with high salinity and high N:P ratios; and Artemia were associated with very high salinity and low N:P ratios. The distribution of these groups over the salinity gradient is in accordance with previous results; the influence of N:P ratio had not been identified before and may reflect specific environmental requirements of the taxa.

Innovative well-defined primary amine-based polyacrylates for plasmid DNA complexation

Well-defined quaternized poly(2-aminoethyl acrylate)s (qPAEAs) have been synthesized by RAFT polymerization of N-(tert-butoxycarbonyl)aminoethyl acrylate (t-BocAEA) followed by t-Boc group deprotection. The ability of qPAEAs to act as potential “smart” DNA carriers has been shown by plasmid DNA/qPAEA complexation and qPAEA degradation in water at 37 °C without any trigger.

An introduction to the vast world of transposable elements – what about the diatoms?

Transposable elements (TEs) are DNA sequences that are able to move and replicate within the genomes of virtually all organisms, ranging from animals to plants, and also including protozoans, bacteria and diatoms. Initially considered to be ‘junk DNA’ with no function, TEs are now thought to play a pivotal role in the evolution of genomes and organisms. This review is intended to provide non-specialists with an introduction to the world of TEs by summarizing the information available about these elements, ranging from their impact on genome structure to their potential involvement in the evolution of species. In this review, we propose to bring together what is known about the TEs and provide an overview of recent advances concerning TEs in diatoms.

Tuning the Molar Composition of “Charge-Shifting” Cationic Copolymers Based on 2-(N,N-Dimethylamino)Ethyl Acrylate and 2-(tert-Boc-Amino)Ethyl Acrylate

Copolymers of 2-(N,N-dimethylamino)ethyl acrylate (DMAEA) and 2-(tert-Boc-amino)ethyl acrylate (tBocAEA) are synthesized by reversible addition-fragmentation chain transfer polymerization in a controlled manner with defined molar masses and narrow molar masses distributions (Ð ≤ 1.17). Molar compositions of the P(DMAEA-co-tBocAEA) copolymers are assessed by means of 1 H NMR. A complete screening in molar composition is studied from 0% of DMAEA to 100% of DMAEA. Reactivity ratios of both comonomers are determined by the extended Kelen-Tüdos method (r DMAEA = 0.81 and rtBocAEA = 0.99).

Expression of the retrotransposons Surcouf and Blackbeard in the marine diatom Phaeodactylum tricornutum under thermal stress

Abstract: Transposable elements (TEs) are mobile DNA sequences thought to be involved in the genomic response to environmental stresses of organisms. The thermal stress behaviour of two retrotransposons (Surcouf and Blackbeard ) was investigated in the genome of two strains of the marine diatom Phaeodactylum tricornutum. Using quantitative reverse transcriptase polymerase chain reaction, the retrotransposon expression pattern was investigated after thermal stresses and compared with that of the small heat-shock protein (shsp). While the expression of Blackbeard was not affected by temperature changes, the retroelement Surcouf was markedly overexpressed in response to high temperature in correlation with shsp overexpression. An in silico analysis investigated the presence of regulatory heat-inducible motifs such as heat-shock elements, stress response elements and CCAAT boxes within the promoters of shsp and retrotransposons in the genome of P. tricornutum. The results of mRNA quantification are supported by the presence of heat-shock response motifs found in the promoters of shsp and the retrotransposon Surcouf.