Custom human endogenous retroviruses dedicated microarray identifies self-induced HERV-W family elements reactivated in testicular cancer upon methylation control

Endogenous retroviruses (ERVs) are an inherited part of the eukaryotic genomes, and represent ∼400 000 loci in the human genome. Human endogenous retroviruses (HERVs) can be divided into distinct families, composed of phylogenetically related but structurally heterogeneous elements. The majority of HERVs are silent in most physiological contexts, whereas a significant expression is observed in pathological contexts, such as cancers. Owing to their repetitive nature, few of the active HERV elements have been accurately identified. In addition, there are no criteria defining the active promoters among HERV long-terminal repeats (LTRs). Hence, it is difficult to understand the HERV (de)regulation mechanisms and their implication on the physiopathology of the host. We developed a microarray to specifically detect the LTR-containing transcripts from the HERV-H, HERV-E, HERV-W and HERV-K(HML-2) families. HERV transcriptome was analyzed in the placenta and seven normal/tumoral match-pair samples. We identified six HERV-W loci overexpressed in testicular cancer, including a usually placenta-restricted transcript of ERVWE1. For each locus, specific overexpression was confirmed by quantitative RT-PCR, and comparison of the activity of U3 versus U5 regions suggested a U3-promoted transcription coupled with 5′R initiation. The analysis of DNA from tumoral versus normal tissue revealed that hypomethylation of U3 promoters in tumors is a prerequisite for their activation

Microarray-Based Sketches of the HERV Transcriptome Landscape

Human endogenous retroviruses (HERVs) are spread throughout the genome and their long terminal repeats (LTRs) constitute a wide collection of putative regulatory sequences. Phylogenetic similarities and the profusion of integration sites, two inherent characteristics of transposable elements, make it difficult to study individual locus expression in a large-scale approach, and historically apart from some placental and testis-regulated elements, it was generally accepted that HERVs are silent due to epigenetic control. Herein, we have introduced a generic method aiming to optimally characterize individual loci associated with 25-mer probes by minimizing cross-hybridization risks. We therefore set up a microarray dedicated to a collection of 5,573 HERVs that can reasonably be assigned to a unique genomic position. We obtained a first view of the HERV transcriptome by using a composite panel of 40 normal and 39 tumor samples. The experiment showed that almost one third of the HERV repertoire is indeed transcribed. The HERV transcriptome follows tropism rules, is sensitive to the state of differentiation and, unexpectedly, seems not to correlate with the age of the HERV families. The probeset definition within the U3 and U5 regions was used to assign a function to some LTRs (i.e. promoter or polyA) and revealed that (i) autonomous active LTRs are broadly subjected to operational determinism (ii) the cellular gene density is substantially higher in the surrounding environment of active LTRs compared to silent LTRs and (iii) the configuration of neighboring cellular genes differs between active and silent LTRs, showing an approximately 8 kb zone upstream of promoter LTRs characterized by a drastic reduction in sense cellular genes. These gathered observations are discussed in terms of virus/host adaptive strategies, and together with the methods and tools developed for this purpose, this work paves the way for further HERV transcriptome projects

Spatial SPION localization in liposome membranes

Nanocarriers, including liposomes, offer great opportunities for targeted and controlled therapy. The development in this field has led to a large panel of drug delivery systems, which can be classified into 3 different nanovector generations. However, the success of such smart materials requires the control of a large variety of properties and parameters. Unfortunately, characterization at the nanoscale is often cumbersome and many methods are still being developed. Liposomes have been characterized by cryogenic electron microscopy (CryoTEM) for quite some time, also in combination with nanoparticles, in particular with superparamagnetic iron oxide nanoparticles (SPIONs) incorporated inside the liposomal membrane. CryoTEM, unlike classical TEM, maintains the native state of the liposomes. The quick freezing of the sample immobilizes particles and liposomes exactly at their position in the suspension. Therefore, localization information can be extracted from the images. However, data must be treated extremely carefully keeping in mind that 2-D projections of a 3-D object are observed. In this paper, we discuss the analysis of cryoTEM images of liposome-particle hybrids, including the estimation of the contrast transfer function (CTF) and electron dose, as well as the correct positioning of the sample holder and tomography for accurate localization

From individual communication to social networks: evolution of a technical platform for the elderly

International audienceOne of the biggest challenges we currently face is to keep elderly people immersed in their social environment when they leave their home and enter a retirement home. Many of them feel isolated. The TV stands as their favorite media, and our first experiments showed that listening to vocalized local news and receiving TV messages and photos from family helped in fighting these feelings of isolation. With online social networks, we wish to involve the elderly in new types of interactions, more various and frequent. They will be more active and included in micro-conversations around multimedia contents. The retirement homes will benefit also from social networking capabilities. They will participate to the local news dedicated to the elderly people. In addition, the remote family will be informed of activities through an agenda and various publications

Role of hydrodynamism in compositional heterogeneities in acid gas reservoir

International audienceAcid gases (H2S and CO2) compositional heterogeneities have been noticed in many sour gas reservoirs. Their occurrence is an important factor of economic depreciation. Thus, the knowledge of the acid gases distribution is a critical parameter for the design of field development. The mechanisms to explain compositional heterogeneities of acid gas in a reservoir are various. The paper aims at exploring the role of an active aquifer in contact with an initial high H2S content reservoir. The major mechanisms may be controlled by: * Differential solubility of gases which can change the relative amounts of each gas near the contact; * Active aquifer solubilization and transport which can export dissolved gases thus enhancing dissolution on the long-term; * Diffusional transport in the gas phase which can transfer the compositional anomalies farther from the gas-water contact. To test the influence of several parameters on the efficiency of the acid gases leaching, simulations on basic geometries have been performed with the diphasic transport and geochemical software Hytec. The simulation results show a major role of the occurrence of horizontal impermeable barriers yields to sharp heterogeneities, including a decrease in acid gas near the contact, while farther areas H2S concentration remain unaffected

Comparison of intra- and inter-host genetic diversity in rabies virus during experimental cross-species transmission

International audienceThe development of high-throughput genome sequencing enables accurate measurements of levels of sub-consensus intra-host virus genetic diversity and analysis of the role played by natural selection during cross-species transmission. We analysed the natural and experimental evolution of rabies virus (RABV), an important example of a virus that is able to make multiple host jumps. In particular, we (i) analyzed RABV evolution during experimental host switching with the goal of identifying possible genetic markers of host adaptation, (ii) compared the mutational changes observed during passage with those observed in natura, and (iii) determined whether the colonization of new hosts or tissues requires adaptive evolution in the virus. To address these aims, animal infection models (dog and fox) and primary cell culture models (embryo brain cells of dog and fox) were developed and viral variation was studied in detail through deep genome sequencing. Our analysis revealed a strong unidirectional host evolutionary effect, as dog-adapted rabies virus was able to replicate in fox and fox cells relatively easily, while dogs or neuronal dog cells were not easily susceptible to fox adapted-RABV. This suggests that dog RABV may be able to adapt to some hosts more easily than other host variants, or that when RABV switched from dogs to red foxes it lost its ability to adapt easily to other species. Although no difference in patterns of mutation variation between different host organs was observed, mutations were common following both in vitro and in vivo passage. However, only a small number of these mutations also appeared in natura, suggesting that adaptation during successful cross-species virus transmission is a complex, multifactorial evolutionary process

Insertion of Nanoparticle Clusters into Vesicle Bilayers

A major contemporary concern in developing effective liposome–nanoparticle hybrids is the present inclusion size limitation of nanoparticles between vesicle bilayers, which is considered to be around 6.5 nm in diameter. In this article, we present experimental observations backed by theoretical considerations which show that greater structures can be incorporated within vesicle membranes by promoting the clustering of nanoparticles before liposome formation. Cryo-transmission electron microscopy and cryo-electron tomography confirm these observations at unprecedented detail and underpin that the liposome membranes can accommodate flexible structures of up to 60 nm in size. These results imply that this material is more versatile in terms of inclusion capabilities and consequently widens the opportunities in developing multivalent vesicles for nanobiotechnology applications