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Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on α/β-mixed or β-structure–rich proteins. The problem arises from the spectral diversity of β-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual β-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the β-sheets account for the observed spectral diversity. We have developed a method called β-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of β-structures. This method can reliably distinguish parallel and antiparallel β-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides. Significance Circular dichroism (CD) spectroscopy is widely used for protein secondary structure analysis. However, quantitative estimation for β-sheet–containing proteins is problematic due to the huge morphological and spectral diversity of β-structures. We show that parallel/antiparallel orientation and twisting of β-sheets account for the observed spectral diversity. Taking into account the twist of β-structures, our method accurately estimates the secondary structure for a broad range of protein folds, particularly for β-sheet–rich proteins and amyloid fibrils. Moreover, the method can predict the protein fold down to the topology level following the CATH classification. We provide a general tool for a quick and reliable structure analysis using conventional or synchrotron radiation CD spectroscopy, which is especially useful when X-ray or NMR techniques fail.

To understand the onset of collective motion, we investigate active systems where particles switch on and off their self-propulsion. We prove that even when the only possible transition is off\\(\\to\\)on, an active 2-state system behaves as an effective 3-state system that exhibits a sharp phase transition in 1D, and critical behavior in 2D, with scale-invariant activity avalanches. The obtained results show how criticality can naturally emerge in active systems, providing insight into the way collectives distribute, process, and respond to local environmental cues.

Despite the need for quantitative measurements of light intensity across many scientific disciplines, existing technologies for measuring light dose at the sample of a fluorescence microscope cannot simultaneously retrieve light intensity along with spatial distribution over a wide range of wavelengths and intensities. To address this limitation, we developed two rapid and straightforward protocols that use organic dyes and fluorescent proteins as actinometers. The first protocol relies on molecular systems whose fluorescence intensity decays and/or rises in a monoexponential fashion when constant light is applied. The second protocol relies on a broad-absorbing photochemically inert fluorophore to back-calculate the light intensity from one wavelength to another. As a demonstration of their use, the protocols are applied to quantitatively characterize the spatial distribution of light of various fluorescence imaging systems, and to calibrate illumination of commercially available instruments and light sources. Two methods for fluorescence-based actinometry using organic dyes and photoconvertible fluorescent proteins enable rapid and precise measurement of light intensity at the sample in fluorescence microscopes.

PurposeTo assess the results of endovascular treatment in a large population of patients suffering from post-thrombotic syndrome (PTS) due to iliocaval occlusive disease.MethodsIn this retrospective multi-center study, 698 patients treated by stenting for PTS in 15 French centers were analyzed. Primary, primary assisted, and secondary patency rates were assessed, and clinical efficacy was evaluated using Villalta and Chronic Venous Insufficiency Questionnaire in 20 questions (CIVIQ-20) scores. Outcomes were compared against pre-operative CT-based severity of the post-thrombotic lesions in the thigh (4 grades).ResultsTechnical success, defined as successful recanalization and stent deployment restoring rapid anterograde flow in the targeted vessel, was obtained in 668 (95.7%) patients with a complication rate of 3.9%. After a mean follow-up of 21.0 months, primary patency, primary assisted patency, and secondary patency were achieved in 537 (80.4%), 566 (84.7%), and 616 (92.2%) of the 668 patients, respectively. Venous patency was strongly correlated to the grade of post-thrombotic changes in the thigh, with secondary patency rates of 96.0%, 92.9%, 88.4%, and 78.9%, respectively, for grades 0 to 3 (p = .0008). The mean improvements of Villalta and CIVIQ-20 scores were 7.0 ± 4.7 points (p < .0001) and 19.1 ± 14.8 points (p < .0001), respectively.ConclusionEndovascular stenting as a treatment option for PTS due to chronic iliocaval venous occlusion generates a high technical success, low morbidity, high midterm patency rate, and clinical improvement. Venous patency was strongly correlated to the severity of post-thrombotic lesions in the thigh.

The growth of plants is a hydromechanical phenomenon in which cells enlarge by absorbing water, while their walls expand and remodel under turgor-induced tension. In multicellular tissues, where cells are mechanically interconnected, morphogenesis results from the combined effect of local cell growths, which reflects the action of heterogeneous mechanical, physical, and chemical fields, each exerting varying degrees of nonlocal influence within the tissue. To describe this process, we propose a physical field theory of plant growth. This theory treats the tissue as a poromorphoelastic body, namely a growing poroelastic medium, where growth arises from pressure-induced deformations and osmotically-driven imbibition of the tissue. From this perspective, growing regions correspond to hydraulic sinks, leading to the possibility of complex non-local regulations, such as water competition and growth-induced water potential gradients. More in general, this work aims to establish foundations for a mechanistic, mechanical field theory of morphogenesis in plants, where growth arises from the interplay of multiple physical fields, and where biochemical regulations are integrated through specific physical parameters.

Understanding the mechanisms regulating development requires a quantitative characterization of cell divisions, rearrangements, cell size and shape changes, and apoptoses. We developed a multiscale formalism that relates the characterizations of each cell process to tissue growth and morphogenesis. Having validated the formalism on computer simulations, we quantified separately all morphogenetic events in the Drosophila dorsal thorax and wing pupal epithelia to obtain comprehensive statistical maps linking cell and tissue scale dynamics. While globally cell shape changes, rearrangements and divisions all significantly participate in tissue morphogenesis, locally, their relative participations display major variations in space and time. By blocking division we analyzed the impact of division on rearrangements, cell shape changes and tissue morphogenesis. Finally, by combining the formalism with mechanical stress measurement, we evidenced unexpected interplays between patterns of tissue elongation, cell division and stress. Our formalism provides a novel and rigorous approach to uncover mechanisms governing tissue development. In animals, the final size and shape of each tissue is determined by the precise control of when, where and how much individual cells grow, divide, move and die. An important challenge in biology is to understand how the behaviors of each individual cell can act together to generate a large and reproducible change at the scale of entire tissues and organs. Here, Guirao et al. have developed a new approach to provide maps that reveal how much each cell process contributes to the development of tissues. A caterpillar becoming a butterfly is a famous example of insect ‘metamorphosis’. The fruit fly offers another example of such tissue development: within five days, a rice grain-like maggot morphs into an adult fly with long antennae, legs and wings. Guirao et al. used a microscope to observe cells over a period of several hours during the metamorphosis of the adult fruit fly wings and thorax (the region between the neck and abdomen). In both regions, Guirao et al. showed that all the cell processes participate in the formation of the adult tissue. Cell division, cell death, and changes in cell size affect the size of the tissue, while cell division, cell rearrangements, and changes in cell shape alter the shape of the tissue. The relative contributions of these cell processes varied a lot in both space and time. Further experiments then used mutant flies with defects in cell division to analyse the impact of cell division on the other cell processes and the eventual shape of the tissue. Finally, Guirao et al. showed that there are unexpected interactions between the patterns of tissue growth, cell division and the mechanical forces in the tissue. These findings provide a new approach to uncover how animals from different species can have such a variety of shapes and sizes, even though they each start life as a single cell. Ultimately, this may also aid efforts to understand how certain diseases affect the development of tissues.

We investigate the measurement of DNA supercoiling density ($σ$) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in bacteria, to the quantitative modeling of binding properties of ParB proteins around their centromere-like site, {\\it parS}. Using this framework, we provide an upper bound for $σ$ in the {\\it Escherichia coli} chromosome, consistent with plasmid values, and offer a proof of concept for a high accuracy measurement. To reach these conclusions, we revisit the problem of the formation of ParB clusters. We predict, in particular, that they result from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., they behave like liquid-like protein condensates with unconventional ``leaky'' boundaries.

Topological defects in active polar fluids can organise spontaneous flows and influence macroscopic density patterns. Both of them play, for example, an important role during animal development. Yet the influence of density on active flows is poorly understood. Motivated by experiments on cell monolayers confined to discs, we study the coupling between density and polar order for a compressible active polar fluid in presence of a +1 topological defect. As in the experiments, we find a density-controlled spiral-to-aster transition. In addition, biphasic orientational phases emerge as a generic outcome of such coupling. Our results highlight the importance of density gradients as a potential mechanism for controlling flow and orientational patterns in biological systems.

We study the spreading of cell aggregates deposited on adhesive substrates decorated with microparticles (MPs). A cell monolayer expands around the aggregate. The cells on the periphery of the monolayer take up the MPs, clearing the substrate as they progress and forming an aureole of cells filled with MPs. We study the dynamics of spreading and determine the width of the aureole and the level of MP internalization in cells as a function of MP size, composition, and density. From the radius and width of the aureole, we quantify the volume fraction of MPs within the cell, which leads to an easy, fast, and inexpensive measurement of the cell – particle internalization.