Recovery time reduction to decrease experimental duration (R2D2): A simple and universal method to accelerate NMR experiments.

Acceleration techniques for one dimensional Nuclear Magnetic Resonance (1D NMR) are very useful, both for NMR enthusiasts and for chemists that use NMR for structural elucidation. To the latter, such techniques need to be straightforward. Recovery time Reduction to Decrease the experimental Duration (R2D2) relies on the incremental reduction of a pulse sequence's Recycle Time (TR). A pseudo-2D spectrum is acquired and after two Fourier transform, extraction and addition of the central rows, a 1D spectrum is obtained. Not only can it be applied to any pulse sequence that contains a TR, but it also requires only a list of recovery times and 2D processes to operate. With this method, we were able to easily reduce the experimental time by a factor of 2 and up to 4 using single-pulse, APT and DEPT 13C sequences. Moreover, R2D2 has the potential to be used on other low abundance nuclei (such as 15N or 2H) and numerous other pulse sequences.

Radio-frequency pulse calibration using the MISSTEC sequence.

NMR sequences are composed of multiple radio-frequency pulses. Probe adjustment, sample concentration and solvent influence the loading factor, therefore these parameters also impact the validity of flip angles. The commonly used method to calibrate RF pulses is to measure a nutation curve by varying the pulse duration. However, this method is impacted by off-resonance effects, radiation damping and B1 and B0 inhomogeneities. Furthermore, it is important to avoid partial saturation. In this work, the MISSTEC sequence is proposed for pulse calibration. This sequence takes only 8 s or 2 min for 1H or 13C calibration, respectively. High accuracy (with an error below 1%) was obtained for both nuclei. Therefore, the calibrations can be done rapidly and accurately. Furthermore, the MISSTEC measurement could be performed on each sample - in an automated way- before acquisitions, after which the calibration found could be automatically used.

DNA replication fork speed underlies cell fate changes and promotes reprogramming.

Totipotency emerges in early embryogenesis, but its molecular underpinnings remain poorly characterized. In the present study, we employed DNA fiber analysis to investigate how pluripotent stem cells are reprogrammed into totipotent-like 2-cell-like cells (2CLCs). We show that totipotent cells of the early mouse embryo have slow DNA replication fork speed and that 2CLCs recapitulate this feature, suggesting that fork speed underlies the transition to a totipotent-like state. 2CLCs emerge concomitant with DNA replication and display changes in replication timing (RT), particularly during the early S-phase. RT changes occur prior to 2CLC emergence, suggesting that RT may predispose to gene expression changes and consequent reprogramming of cell fate. Slowing down replication fork speed experimentally induces 2CLCs. In vivo, slowing fork speed improves the reprogramming efficiency of somatic cell nuclear transfer. Our data suggest that fork speed regulates cellular plasticity and that remodeling of replication features leads to changes in cell fate and reprogramming.

Publisher Correction: An actin-based viscoplastic lock ensures progressive body-axis elongation.

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

Publisher Correction: An actin-based viscoplastic lock ensures progressive body-axis elongation.

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

An actin-based viscoplastic lock ensures progressive body-axis elongation.

Body-axis elongation constitutes a key step in animal development, laying out the final form of the entire animal. It relies on the interplay between intrinsic forces generated by molecular motors1-3, extrinsic forces exerted by adjacent cells4-7 and mechanical resistance forces due to tissue elasticity or friction8-10. Understanding how mechanical forces influence morphogenesis at the cellular and molecular level remains a challenge1. Recent work has outlined how small incremental steps power cell-autonomous epithelial shape changes1-3, which suggests the existence of specific mechanisms that stabilize cell shapes and counteract cell elasticity. Beyond the twofold stage, embryonic elongation in Caenorhabditis elegans is dependent on both muscle activity7 and the epidermis; the tension generated by muscle activity triggers a mechanotransduction pathway in the epidermis that promotes axis elongation7. Here we identify a network that stabilizes cell shapes in C. elegans embryos at a stage that involves non-autonomous mechanical interactions between epithelia and contractile cells. We searched for factors genetically or molecularly interacting with the p21-activating kinase homologue PAK-1 and acting in this pathway, thereby identifying the α-spectrin SPC-1. Combined absence of PAK-1 and SPC-1 induced complete axis retraction, owing to defective epidermal actin stress fibre. Modelling predicts that a mechanical viscoplastic deformation process can account for embryo shape stabilization. Molecular analysis suggests that the cellular basis for viscoplasticity originates from progressive shortening of epidermal microfilaments that are induced by muscle contractions relayed by actin-severing proteins and from formin homology 2 domain-containing protein 1 (FHOD-1) formin bundling. Our work thus identifies an essential molecular lock acting in a developmental ratchet-like process.

Genome-lamina interactions are established de novo in the early mouse embryo.

In mammals, the emergence of totipotency after fertilization involves extensive rearrangements of the spatial positioning of the genome1,2. However, the contribution of spatial genome organization to the regulation of developmental programs is unclear3. Here we generate high-resolution maps of genomic interactions with the nuclear lamina (a filamentous meshwork that lines the inner nuclear membrane) in mouse pre-implantation embryos. We reveal that nuclear organization is not inherited from the maternal germline but is instead established de novo shortly after fertilization. The two parental genomes establish lamina-associated domains (LADs)4 with different features that converge after the 8-cell stage. We find that the mechanism of LAD establishment is unrelated to DNA replication. Instead, we show that paternal LAD formation in zygotes is prevented by ectopic expression of Kdm5b, which suggests that LAD establishment may be dependent on remodelling of H3K4 methylation. Our data suggest a step-wise assembly model whereby early LAD formation precedes consolidation of topologically associating domains.

Imaging of native transcription factors and histone phosphorylation at high resolution in live cells.

Fluorescent labeling of endogenous proteins for live-cell imaging without exogenous expression of tagged proteins or genetic manipulations has not been routinely possible. We describe a simple versatile antibody-based imaging approach (VANIMA) for the precise localization and tracking of endogenous nuclear factors. Our protocol can be implemented in every laboratory allowing the efficient and nonharmful delivery of organic dye-conjugated antibodies, or antibody fragments, into different metazoan cell types. Live-cell imaging permits following the labeled probes bound to their endogenous targets. By using conventional and super-resolution imaging we show dynamic changes in the distribution of several nuclear transcription factors (i.e., RNA polymerase II or TAF10), and specific phosphorylated histones (γH2AX), upon distinct biological stimuli at the nanometer scale. Hence, considering the large panel of available antibodies and the simplicity of their implementation, VANIMA can be used to uncover novel biological information based on the dynamic behavior of transcription factors or posttranslational modifications in the nucleus of single live cells.

An Arf6- and caveolae-dependent pathway links hemidesmosome remodeling and mechanoresponse.

Hemidesmosomes (HDs) are epithelial-specific cell-matrix adhesions that stably anchor the intracellular keratin network to the extracellular matrix. Although their main role is to protect the epithelial sheet from external mechanical strain, how HDs respond to mechanical stress remains poorly understood. Here we identify a pathway essential for HD remodeling and outline its role with respect to α6ß4 integrin recycling. We find that α6ß4 integrin chains localize to the plasma membrane, caveolae, and ADP-ribosylation factor-6+ (Arf6+) endocytic compartments. Based on fluorescence recovery after photobleaching and endocytosis assays, integrin recycling between both sites requires the small GTPase Arf6 but neither caveolin1 (Cav1) nor Cavin1. Strikingly, when keratinocytes are stretched or hypo-osmotically shocked, α6ß4 integrin accumulates at cell edges, whereas Cav1 disappears from it. This process, which is isotropic relative to the orientation of stretch, depends on Arf6, Cav1, and Cavin1. We propose that mechanically induced HD growth involves the isotropic flattening of caveolae (known for their mechanical buffering role) associated with integrin diffusion and turnover.

LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo.

After fertilization, to initiate development, gametes are reprogramed to become totipotent. Approximately half of the mammalian genome consists of repetitive elements, including retrotransposons, some of which are transcribed after fertilization. Retrotransposon activation is generally assumed to be a side effect of the extensive chromatin remodeling underlying the epigenetic reprogramming of gametes. Here, we used a targeted epigenomic approach to address whether specific retrotransposon families play a direct role in chromatin organization and developmental progression. We demonstrate that premature silencing of LINE-1 elements decreases chromatin accessibility, whereas prolonged activation prevents the gradual chromatin compaction that occurs naturally in developmental progression. Preventing LINE-1 activation and interfering with its silencing decreases developmental rates independently of the coding nature of the LINE-1 transcript, thus suggesting that LINE-1 functions primarily at the chromatin level. Our data suggest that activation of LINE-1 regulates global chromatin accessibility at the beginning of development and indicate that retrotransposon activation is integral to the developmental program.

The interplay of stiffness and force anisotropies drives embryo elongation.

The morphogenesis of tissues, like the deformation of an object, results from the interplay between their material properties and the mechanical forces exerted on them. The importance of mechanical forces in influencing cell behaviour is widely recognized, whereas the importance of tissue material properties, in particular stiffness, has received much less attention. Using Caenorhabditis elegans as a model, we examine how both aspects contribute to embryonic elongation. Measuring the opening shape of the epidermal actin cortex after laser nano-ablation, we assess the spatiotemporal changes of actomyosin-dependent force and stiffness along the antero-posterior and dorso-ventral axis. Experimental data and analytical modelling show that myosin-II-dependent force anisotropy within the lateral epidermis, and stiffness anisotropy within the fiber-reinforced dorso-ventral epidermis are critical in driving embryonic elongation. Together, our results establish a quantitative link between cortical tension, material properties and morphogenesis of an entire embryo.

Non-centrosomal epidermal microtubules act in parallel to LET-502/ROCK to promote C. elegans elongation.

C. elegans embryonic elongation is a morphogenetic event driven by actomyosin contractility and muscle-induced tension transmitted through hemidesmosomes. A role for the microtubule cytoskeleton has also been proposed, but its contribution remains poorly characterized. Here, we investigate the organization of the non-centrosomal microtubule arrays present in the epidermis and assess their function in elongation. We show that the microtubule regulators γ-tubulin and NOCA-1 are recruited to hemidesmosomes and adherens junctions early in elongation. Several parallel approaches suggest that microtubule nucleation occurs from these sites. Disrupting the epidermal microtubule array by overexpressing the microtubule-severing protein Spastin or by inhibiting the C. elegans ninein homolog NOCA-1 in the epidermis mildly affected elongation. However, microtubules were essential for elongation when hemidesmosomes or the activity of the Rho kinase LET-502/ROCK were partially compromised. Imaging of junctional components and genetic analyses suggest that epidermal microtubules function together with Rho kinase to promote the transport of E-cadherin to adherens junctions and myotactin to hemidesmosomes. Our results indicate that the role of LET-502 in junctional remodeling is likely to be independent of its established function as a myosin II activator, but requires a microtubule-dependent pathway involving the syntaxin SYX-5. Hence, we propose that non-centrosomal microtubules organized by epidermal junctions contribute to elongation by transporting junction remodeling factors, rather than having a mechanical role.

Higher chromatin mobility supports totipotency and precedes pluripotency in vivo.

The fusion of the gametes upon fertilization results in the formation of a totipotent cell. Embryonic chromatin is expected to be able to support a large degree of plasticity. However, whether this plasticity relies on a particular conformation of the embryonic chromatin is unknown. Moreover, whether chromatin plasticity is functionally linked to cellular potency has not been addressed. Here, we adapted fluorescence recovery after photobleaching (FRAP) in the developing mouse embryo and show that mobility of the core histones H2A, H3.1, and H3.2 is unusually high in two-cell stage embryos and decreases as development proceeds. The transition toward pluripotency is accompanied by a decrease in histone mobility, and, upon lineage allocation, pluripotent cells retain higher mobility than the differentiated trophectoderm. Importantly, totipotent two-cell-like embryonic stem cells also display high core histone mobility, implying that reprogramming toward totipotency entails changes in chromatin mobility. Our data suggest that changes in chromatin dynamics underlie the transitions in cellular plasticity and that higher chromatin mobility is at the nuclear foundations of totipotency.

BTK: an open-source toolkit for fetal brain MR image processing.

Studies about brain maturation aim at providing a better understanding of brain development and links between brain changes and cognitive development. Such studies are of great interest for diagnosis help and clinical course of development and treatment of illnesses. However, the processing of fetal brain MR images remains complicated which limits the translation from the research to the clinical domain. In this article, we describe an open-source image processing toolkit dedicated to these images. In this toolkit various tools are included such as: denoising, image reconstruction, super-resolution and tractography. The BTK resource program (distributed under CeCILL-B license) is developed in C++ and relies on common medical imaging libraries such as Insight Toolkit (ITK), Visualization Toolkit (VTK) and Open Multi-Processing (OpenMP).

Probabilistic tractography using Q-ball modeling and particle filtering.

By assuming that orientation information of brain white matter fibers can be inferred from Diffusion Weighted Magnetic Resonance Imaging (DWMRI) measurements, tractography algorithms provide an estimation of the brain connectivity in-vivo. The two key ingredients of tractography are the diffusion model (tensor, high-order tensor, Q-ball, etc.) and the way to deal with uncertainty during the tracking process (deterministic vs probabilistic). In this paper, we investigate the use of an analytical Q-ball model for the diffusion data within a well-formalized particle filtering framework. The proposed method is validated and compared to other tracking algorithms on the MICCAI'09 contest Fiber Cup phantom and on in-vivo brain DWMRI data.