The Reverse Transcription Signature of N-\u3csub\u3e1\u3c/sub\u3e-Methyladenosine in RNA-Seq is Sequence Dependent

The combination of Reverse Transcription (RT) and high-throughput sequencing has emerged as a powerful combination to detect modified nucleotides in RNA via analysis of either abortive RT-products or of the incorporation of mismatched dNTPs into cDNA. Here we simultaneously analyze both parameters in detail with respect to the occurrence of N-1-methyladenosine (m1A) in the template RNA. This naturally occurring modification is associated with structural effects, but it is also known as a mediator of antibiotic resistance in ribosomal RNA. In structural probing experiments with dimethylsulfate, m1A is routinely detected by RT-arrest. A specifically developed RNA-Seq protocol was tailored to the simultaneous analysis of RT-arrest and misincorporation patterns. By application to a variety of native and synthetic RNA preparations, we found a characteristic signature of m1A, which, in addition to an arrest rate, features misincorporation as a significant component. Detailed analysis suggests that the signature depends on RNA structure and on the nature of the nucleotide 3’ of m1A in the template RNA, meaning it is sequence dependent. The RT-signature ofm1Awas used for inspection and confirmation of suspected modification sites and resulted in the identification of hitherto unknown m1A residues in trypanosomal tRNA

DHX15-independent roles for TFIP11 in U6 snRNA modification, U4/U6.U5 tri-snRNP assembly and pre-mRNA splicing fidelity

International audienceThe U6 snRNA, the core catalytic component of the spliceosome, is extensively modified post-transcriptionally, with 2’-O-methylation being most common. However, how U6 2’-O-methylation is regulated remains largely unknown. Here we report that TFIP11, the human homolog of the yeast spliceosome disassembly factor Ntr1, localizes to nucleoli and Cajal Bodies and is essential for the 2’-O-methylation of U6. Mechanistically, we demonstrate that TFIP11 knockdown reduces the association of U6 snRNA with fibrillarin and associated snoRNAs, therefore altering U6 2′-O-methylation. We show U6 snRNA hypomethylation is associated with changes in assembly of the U4/U6.U5 tri-snRNP leading to defects in spliceosome assembly and alterations in splicing fidelity. Strikingly, this function of TFIP11 is independent of the RNA helicase DHX15, its known partner in yeast. In sum, our study demonstrates an unrecognized function for TFIP11 in U6 snRNP modification and U4/U6.U5 tri-snRNP assembly, identifying TFIP11 as a critical spliceosome assembly regulator

Étude de la fragmentation de métal liquide en chute libre dans un environnement visqueux : application à la formation des planètes

L'accrétion de planètes telluriques comme la Terre se déroule par collisions successives entre proto-planètes déjà différenciées en un manteau de silicate et un noyau de fer. Le résultat de ces impacts est un écoulement diphasique qui est la dernière occasion pour les deux composants principaux des planètes de partiellement se mélanger. Afin d'étudier les conditions des échanges diffusifs de chaleur et d'éléments chimiques dans cet écoulement, nous avons fait des expériences sur un système de fluide analogue. Le fer liquide est représenté par un alliage de gallium et l'océan de magma est représenté par un liquide visqueux. Les vidéos de la chute d'un sphéroïde de métal liquide dans le fluide visqueux sont analysées par ordinateur pour en extraire la dynamique de l'écoulement post-impact .La température du métal liquide avant et après sa chute est mesurée dans le but d'analyser les conditions des échanges diffusifs entre les deux phases intégrées sur toute la chute. Nous montrons que la dilution du diapir produit par l'entrainement de fluide ambiant au cours de sa chute suit l'hypothèse d'entrainement turbulent. La fragmentation du métal liquide est caractérisée par la mesure de la distance de fragmentation, par la mesure du rayon moyen des gouttes produites en fonction du rayon initial du diapir et par la mesure de la distribution des tailles de goutte. La distribution est donnée par une fonction de Bessel. Les données sur la dynamique, sur la fragmentation et sur la température sont ensuite utilisées pour tester les différents modèles d'équilibration entre les deux phasesThe accretion of terrestrial planets like Earth proceeds partly by impacts of proto-planets already differentiated in a silicate mantle and an iron core. Those impacts result in a two phase flow where the two main components of the planets partially mix for the last time. In order to study the conditions of diffusive transfer of heat and elements during this flow, we have performed experiments using an analog system of fluids. A gallium alloy is used to represent the molten iron core and a viscous fluid is used to represent the molten silicatemantle. Video recordings of the fall of liquid metal spheroids through the viscous fluid areanalyzed as a way to study the dynamics of the post impact flow. Measurements of the temperature of the liquid metal before and after its fall are performed in order to probe the conditions of the diffusive transfer between the two phases integrated along the fall.The diapir is found to dilute by entraining ambient fluid during its fall in a manner thatis well described by the entrainment hypothesis. The fragmentation of the liquid metal is quantified in terms of the break up distance, the mean radius of the droplets as a function of the spheroid’s initial radius andthe distribution of sizes of the droplets. The mean radius of the droplets is marked by the large scale falling speed which we interpret as a sign of a continuous break up process. The distribution of sizes is given by a Bessel function. The data on the dynamics, on the fragmentation and on the temperature are then used to test the existing thermal equilibration models between the two phase

Fall and fragmentation of liquid metal in a viscous fluid

International audienceSimulations of the solar system formation as well as the diversity of meteorites chemical composition both point toward a scenario where the late stages of Earth-like planets accretion involved massive impacts of Mars size planets [1]. Due to the combination of the energy release during impact, to the intense radioactive decay of short-lived elements, and to the heat remaining from the conversion of potential energy required to form a planet, these planetary embryos were most likely molten for a large part [2]. This also means that they were differentiated in a liquid iron core covered by a molten silicate mantle, since these two main phases of terrestrial bodies are immiscible and of significantly different densities. Following each impact, a large-scale two-phase flow occurred as the molten iron of the impactor core flowed across the silicate magma ocean to merge with the planetary embryo core. Because of the immense inertia of the process, this flow was characterized by very high Reynolds and Weber numbers, hence prone to rapid fragmentation. The quantification of the exchanges of heat and elements in this dispersed flow is crucial to the knowledge of the initial state of telluric planets

Experiments on fragmentation and thermo-chemical exchanges during planetary core formation

International audienceThe initial thermo-chemical state of telluric planets was largely controlled by mixing following the collision of differentiated proto-planets. Up to now, most models of planet formation simply assume that the iron core of the impactors immediately broke up to form an "iron rain" within a large-scale magma ocean, leading to the rapid equilibration of the whole metal with the whole mantle. Only recent studies have focused on resolving the fluid mechanics of the problem, with the aim to define more relevant diffusion-advection models of thermal and chemical exchanges within and between the two fluids. Furthermore, the influence of the viscosity ratio on this dynamical process is generally neglected, whilst it is known to play a role in the breakup of the initial iron diapirs and in the shape of the resulting droplets. Here we report the results of analog laboratory experiments matching the dynamical regime of the geophysical configuration. High speed video recording allows us to describe and characterize the fluid dynamics of the system, and temperature measurements allow us to quantify the diffusive exchanges integrated during the fall of the liquid metal. We find that the early representation of this flow as an iron rain is far from the experimental results. The equilibration coefficient at a given depth depends both on the initial size of the metal diapir Preprint submitted to Physics of the Earth and Planetary Interiors May 26, 2017 and on the viscosity of the ambient fluid, whereas the falling speed is only controlled by the initial size. Various scalings for the diffusive exchanges coming from the literature are tested. We find good agreement with the turbulent thermal model developed by Deguen et al. (2014)

Invasive Fungal Sinusitis with Ophthalmological Complications: Case Series and Review of the Literature.

Invasive fungal sinusitis can lead to dramatic complications in immunocompromised patients and requires prompt diagnosis. Here we report three cases with ophthalmological complications secondary to invasive fungal sinusitis in immunocompromised patients. From an ophthalmological point of view, these cases illustrate different clinical presentations, evolutions, complications, treatments, prognoses, and highlight different pathophysiological mechanisms. Diagnoses were delayed in all cases. In none of the cases did patients recover better vision than counting fingers at 24 months follow up, and two patients died. This case series highlights key points useful for quickly recognising this highly morbid infection in immunocompromised patients

Laboratory experiments on the breakup of liquid metal diapirs

International audienceThe validity of the iron rain scenario, i.e. the widely accepted model for the dynamics of iron sedimentation through a magma ocean during the latest stage of the Earth's accretion, is explored via a suite of laboratory experiments. Liquid gallium and mixtures of water and glycerol are used as analogs of the iron and the molten silicate respectively. This allows us to investigate the effects of the viscosity ratio between iron and silicate and to reproduce the relevant effects of surface tension on the fragmentation dynamics. While the classical iron rain scenario considers a population of purely spherical drops with a single characteristic radius that fall towards the bottom of the magma ocean at a unique velocity without any further change, our experiments exhibit a variety of stable shapes for liquid metal drops, a large distribution of sizes and velocities, and an intense internal dynamics within the cloud with the superimposition of further fragmentations and merging events. Our results demonstrate that rich and complex dynamics occur in models of molten metal diapir physics. Further, we hypothesize that the inclusion of such flows into state of the art thermochemical equilibration models will generate a similarly broad array of complex, and likely novel, behaviors

Soft tissue recurrence of an osteoid osteoma: an exceptional observation.

We report the observation of the soft tissue recurrence of an osteoid osteoma (OO) in a 26-year-old man initially complaining of post-traumatic pain and swelling of the right ankle. A first arthroscopic resection was performed after the misdiagnosis of "bone irregularities" observed on computed tomography (CT) and magnetic resonance imaging (MRI). The diagnosis of OO was made by histological analysis of the resection material. The patient became asymptomatic for 5 years until the symptoms progressively recurred. Follow-up MRI and CT studies demonstrated a nodular bony focus within the periarticular soft tissues of the ankle. The lesion was removed, and histological analysis confirmed the diagnosis of a whole viable OO. This observation likely resulted from the displacement of the initial lesion during the initial arthroscopic procedure. This case report highlights the possibility of recurrence of OO in the soft tissues

Dynamics of core-mantle separation: Influence of viscosity contrast and metal/silicate partition coefficients on the chemical equilibrium

International audienceThe composition of the Earth's core and mantle is set by the chemical equilibrium between metals and silicates during core/mantle segregation. The metallic core separated from the mantle by gravitational descent in the form of diapirs in a magma ocean, and therefore the dynamics of the diapir's downward movement has an influence on the chemical equilibrium. In this study, we characterize the descent of metallic droplets into a molten silicate using numerical models. By varying the silicate and metal viscosities (between 0.1 and 1000 Pa·s for each phase) as well as the partition coefficient between metal and silicate (Dmet/sil, varying between 1 and 1000), we obtained quantifying parametrizing equations for the degree of equilibrium between molten metal and molten silicate, in a regime characterized by low We (We < 10) and low Re (10−3 < Re<102). We showed that the main parameters controlling the equilibrium for a siderophile element are the viscosity of the silicate and the partition coefficient. We applied our parameterization for Ni and Co in the context of late accretion on Earth so as to quantify the variation of the Ni/Co ratio after a large impact as a function of the magma ocean viscosity, for an iron-rain scenario of metal/silicate segregation. Using previous models (Canup, 2004) of the Moon–forming impact, we showed that the Moon formation had an effect on the current Ni/Co ratio. Depending on the radius of Theia's core and the viscosity of the magma ocean produced after the impact between the proto-Earth and Theia, the Moon formation could account for 0.45% to 3% of the current Ni/Co ratio for magma ocean viscosities of 0.1 to 100 Pa·s, respectively