Chan-Vese based method to segment mouse brain MRI images: application to cerebral malformation analysis in trisomy 21

International audienceIn this paper, a semi automatic active contour method based on Chan-Vese model is proposed for the segmentation of mouse brain MR images. First, a 2 ½ D strategy is applied on the axial images to segment the 3D volume of interest. The method takes into account the special shape of the object to segment. Moreover, the user defines the limits where to search these contours and also provides an initial contour. This semi automatic method makes that human intervention is limited and the tedious manual handling is greatly reduced. Results have shown that the brain volumes estimated by the method are identical to expert manually estimated volumes. Last but not least, the new method was used in the analysis of the cerebral malformations linked to Trisomy 21: no significant difference of the brain volumes between Tri-somy 21 mice and the control ones were found

Interstrand Crosslinking Reaction in Transplatin-Modified Oligo-2‵-O-Methyl Ribonucleotide-RNA Hybrids

International audienceIn the context of developing an approach to irreversibly and specifically link oligonucleotides to RNA, the purpose of this work was to determine the factors interfering with the rate of the rearrangement of the transplatin 1,3-intrastrand crosslinks into interstrand crosslinks, rearrangement triggered by the formation of a double helix between platinated oligo-2'-O-methyl-ribonucleotides and their complementary strands. The rate of the rearrangement has been studied as a function of the length of the hybrids, the location of the intrastrand crosslinks, the nature of the oligonucleotide backbone, and the nature of the doublet replacing the triplet complementary to the intrastrand crosslinks. The thermal stability of the platinated hybrids has been determined in various salt conditions. The results are discussed in relation to the mechanism of the rearrangement. It is shown that the cellular proteins present weaker nonspecific interactions with single-stranded platinated oligo-2'-O-methyl-nucleotides than with the isosequential oligodeoxyribonucleotides

The role of oxides in the shallow vesiculation of ascending magmas

Accepted manuscript version, licensed CC BY-NC-ND 4.0. Despite their generally low volume fraction, Fesingle bondTi oxides have the potential to greatly influence the eruptive style because they lower the supersaturation pressure for heterogeneous bubble nucleation. Once nucleated, bubbles respond fast to pressure changes, fostering rapid expansion and explosive behavior. Yet, oxide microlite quantifications are often absent from data of explosive products. We used new, re-analyzed, and published data to build a compilation of oxide number densities (ONDs) and vesicle number densities (VNDs) of trachytic and calc-alkaline products. Four eruptive styles were selected: 1) Vulcanian explosions from Soufrière Hills volcano, Montserrat, Lascar volcano, Chile, and Kilian volcano, France, 2) blasts from Mt. Pelée volcano, Lesser Antilles, Mount St. Helens, USA, and Merapi volcano, Indonesia, 3) a sub-Plinian explosion from Merapi volcano, and 4) lava dome effusions with intermittent collapse from Soufrière Hills and Mt. Pelée volcanoes. Natural samples were separated into two groups according to the dominant texture of the products of each event: 1) vesicular pumice clasts from explosions with a strong vertical component and 2) dense clasts with diktytaxitic textures from dome collapse event and lateral blast. Group 1 samples are either distributed alongside the 1:1 trend between VND and OND that spans from 1015 to 1017 m−3, or have a constant VND of 1016–16.5 m−3 regardless of OND. A large proportion of oxides (55–100%) touch vesicles. A more variable proportion of vesicles (16–72%) are in contact with oxides because of syn-explosive growth and coalescence. Group 2 samples have ONDs in the same broad range as group 1 samples. We also used new and published data to build a compilation of ONDs and VNDs of five series of experimental decompression of rhyolitic and phonolitic melts. In samples with OND ≈ VND, most bubbles are in contact with more than one oxide and 64–88% of the oxides are in contact with bubbles. Such high levels of connectivity suggest that the role of oxides in controlling bubble nucleation has been underestimated. When VND ≥ OND, nucleation densities of experimental vesicles can be reproduced by heterogeneous nucleation models, which we used to calculate syn-explosive decompression rates from VNDs at Merapi, Soufrière Hills, and Kilian. These rates and textural evidence suggest that the decompression front accompanying these Vulcanian and sub-Plinian explosions is responsible for syn-explosive bubble nucleation. We calculated the average pre-explosive ascent rates necessary to yield the observed ONDs at Soufrière Hills and Merapi volcanoes. The resulting rates, 0.005–20 m/s, overlap considerably with the range of critical ascent rate inferred for the effusive–explosive transition, supporting the hypothesis that this transition is primarily controlled by oxide microlites in the conduit because oxides are a primer for explosive behavior when present in sufficiently high number densities. Focusing on the older eruption of Kilian, for which no observation is available, we infer that pre-explosive ascent rates of >7 × 10−3 m/s were necessary for explosive behavior to occur

NOTO Transcription Factor Directs Human Induced Pluripotent Stem Cell-Derived Mesendoderm Progenitors to a Notochordal Fate

International audienceThe founder cells of the Nucleus pulposus, the centre of the intervertebral disc, originate in the embryonic notochord. After birth, mature notochordal cells (NC) are identified as key regulators of disc homeostasis. Better understanding of their biology has great potential in delaying the onset of disc degeneration or as a regenerative-cell source for disc repair. Using human pluripotent stem cells, we developed a two-step method to generate a stable NC-like population with a distinct molecular signature. Time-course analysis of lineage-specific markers shows that WNT pathway activation and transfection of the notochord-related transcription factor NOTO are sufficient to induce high levels of mesendoderm progenitors and favour their commitment toward the notochordal lineage instead of paraxial and lateral mesodermal or endodermal lineages. This study results in the identification of NOTO-regulated genes including some that are found expressed in human healthy disc tissue and highlights NOTO function in coordinating the gene network to human notochord differentiation

MEMRI for the morphological and functional study of mouse brain: application to the Down syndrome

International audienceIn the transgenic research era, the understanding of the functional consequences of the genes deletions or mutations in order to investigate the origin of human transgenic disease, requires the development of non invasive study methods on murine models. Our aim is to develop new Down syndrome models and a 3D reconstruction software using MEMRI at 9.4T. To improve contrast and spatial resolution at high magnetic field, the Mn2+ contrast agent shows powerful paramagnetic properties leading to a significant increase of MRI signal [1]. Mn2+ is a unique marker for neuroarchitecture, neuronal connections and functions therefore particularly interesting for neuropathological studies in vivo. In order to investigate the morphological and structural consequences on the central nervous system development in new mice models of human chromosome 21 aneuploïdies, we used MEMRI and. we also developed a powerful tool in order to perform an automatic segmentation and 3D reconstruction of three brain structures

Challenges to quantifying glass eel abundance from large and dynamic estuaries

European eel Anguilla anguilla recruitment into the rivers of the northeastern Atlantic has declined substantially since the 1980s. Monitoring of recruiting juveniles, or glass eels, is usually undertaken in small estuaries and rivers. Sampling of large-scale estuaries is rare, due to the size of the sampling area and the resources needed to provide adequate sampling levels. Here we describe surveys for glass eels in the UK's largest estuarine system, the Severn Estuary/Bristol Channel. We sampled across a 20 km-wide stretch of the estuary in 2012 and 2013, using a small-meshed net deployed from a commercial fishing trawler, and the surveys yielded over 2500 glass eels. Eels were more abundant in the surface layer (0-1.4 m depth) than at depth (down to 8.4 m depth), were more abundant close to the south shore than along the north shore or middle of the estuary, and were more abundant in lower salinity water. Numbers were higher in the second year than in the first and eels were more abundant in February than April. The difficulties and logistics of sampling in such a large estuary are discussed, along with the level of resources required to provide robust estimates of glass eel abundance