mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding.

Macromolecular crowding has a profound impact on reaction rates and the physical properties of the cell interior, but the mechanisms that regulate crowding are poorly understood. We developed genetically encoded multimeric nanoparticles (GEMs) to dissect these mechanisms. GEMs are homomultimeric scaffolds fused to a fluorescent protein that self-assemble into bright, stable particles of defined size and shape. By combining tracking of GEMs with genetic and pharmacological approaches, we discovered that the mTORC1 pathway can modulate the effective diffusion coefficient of particles ≥20 nm in diameter more than 2-fold by tuning ribosome concentration, without any discernable effect on the motion of molecules ≤5 nm. This change in ribosome concentration affected phase separation both in vitro and in vivo. Together, these results establish a role for mTORC1 in controlling both the mesoscale biophysical properties of the cytoplasm and biomolecular condensation.

Brain charts for the human lifespan.

Over the past few decades, neuroimaging has become a ubiquitous tool in basic research and clinical studies of the human brain. However, no reference standards currently exist to quantify individual differences in neuroimaging metrics over time, in contrast to growth charts for anthropometric traits such as height and weight1. Here we assemble an interactive open resource to benchmark brain morphology derived from any current or future sample of MRI data ( http://www.brainchart.io/ ). With the goal of basing these reference charts on the largest and most inclusive dataset available, acknowledging limitations due to known biases of MRI studies relative to the diversity of the global population, we aggregated 123,984 MRI scans, across more than 100 primary studies, from 101,457 human participants between 115 days post-conception to 100 years of age. MRI metrics were quantified by centile scores, relative to non-linear trajectories2 of brain structural changes, and rates of change, over the lifespan. Brain charts identified previously unreported neurodevelopmental milestones3, showed high stability of individuals across longitudinal assessments, and demonstrated robustness to technical and methodological differences between primary studies. Centile scores showed increased heritability compared with non-centiled MRI phenotypes, and provided a standardized measure of atypical brain structure that revealed patterns of neuroanatomical variation across neurological and psychiatric disorders. In summary, brain charts are an essential step towards robust quantification of individual variation benchmarked to normative trajectories in multiple, commonly used neuroimaging phenotypes.

PI3K functions as a hub in mechanotransduction.

Mammalian cells integrate different types of stimuli that govern their fate. These stimuli encompass biochemical as well as biomechanical cues (shear, tensile, and compressive stresses) that are usually studied separately. The phosphatidylinositol 3-kinase (PI3K) enzymes, producing signaling phosphoinositides at plasma and intracellular membranes, are key in intracellular signaling and vesicular trafficking pathways. Recent evidence in cancer research demonstrates that these enzymes are essential in mechanotransduction. Despite this, the importance of the integration of biomechanical cues and PI3K-driven biochemical signals is underestimated. In this opinion article, we make the hypothesis that modeling of biomechanical cues is critical to understand PI3K oncogenicity. We also identify known/missing knowledge in terms of isoform specificity and molecular pathways of activation, knowledge that is needed for clinical applications.

[Children with psoriasis in secondary care: Clinical aspects and comorbidities diverge from the generally published data]. / Psoriasis de l'enfant vu en milieu libéral : les aspects cliniques et épidémiologiques diffèrent des données habituellement publiées.

BACKGROUND: Psoriasis affects 0.2-0.7 % of children and is associated with obesity. Published studies have been conducted in hospital settings (tertiary care). The PsoLib study evaluated childhood psoriasis in private practice (secondary care) in terms of epidemiology, clinical aspects and comorbidities. PATIENTS AND METHODS: This was a non-interventional, cross-sectional, multicenter study of children with psoriasis performed by 41 dermatologists working in private practice. The clinical and therapeutic aspects and comorbidities were systemically evaluated. We compared data to the χ-Psocar study performed in hospitals using the same methodology. RESULTS: In all, 207 children (girls: 60.4 %; mean age: 10.5±4.2 years) were included. Scalp psoriasis (40.6 %) was the most frequent clinical type, while plaque psoriasis represented 26 % of cases. Nail, tongue, and arthritic involvement were rare. Less than 1 % of children suffered from hypertension, diabetes or dyslipidemia, but 16.4 % were overweight and 7.0 % were obese. Severity (PG≥4 at peak) was associated with excess weight (P=0.01). CONCLUSION: Scalp psoriasis is the most frequent clinical type of psoriasis in childhood. Comorbidities and extracutaneous localization are rare. Even in private practice, the severity of the disease is associated with excess weight.

Plant programmed cell death from a chromatin point of view.

Programmed cell death (PCD) is a ubiquitous genetically regulated process consisting of the activation of finely controlled signalling pathways that lead to cellular suicide. PCD can be part of a developmental programme (dPCD) or be triggered by environmental conditions (ePCD). In plant cells, as in animal cells, extensive chromatin condensation and degradation of the nuclear DNA are among the most conspicuous features of cells undergoing PCD. Changes in chromatin condensation could either reflect the structural changes required for internucleosomal fragmentation of nuclear DNA or relate to large-scale chromatin rearrangements associated with a major transcriptional switch occurring during cell death. The aim of this review is to give an update on plant PCD processes from a chromatin point of view. The first part will be dedicated to chromatin conformational changes associated with cell death observed in various developmental and physiological conditions, whereas the second part will be devoted to histone dynamics and DNA modifications associated with critical changes in genome expression during the cell death process.

Oxybutynin as a treatment for generalized hyperhidrosis: a randomized, placebo-controlled trial.

BACKGROUND: Hyperhidrosis is a disorder that can impair quality of life. Localized treatments may be cumbersome and ineffective, and no systemic treatments have proven to be significantly beneficial. OBJECTIVES: To evaluate the effectiveness and tolerance of low-dose oxybutynin for hyperhidrosis. METHODS: We conducted a prospective, randomized, placebo-controlled trial. From June 2013 to January 2014, 62 patients with localized or generalized hyperhidrosis were enrolled. Oxybutynin was started at a dose of 2·5 mg per day and increased gradually to 7·5 mg per day. The primary outcome was defined as improvement of at least one point on the Hyperhidrosis Disease Severity Scale (HDSS). Dermatology Life Quality Index (DLQI) and tolerance were also reported. RESULTS: Most patients (83%) in our study had generalized hyperhidrosis. Oxybutynin was superior to placebo in improving the HDSS: 60% of patients treated with oxybutynin, compared with 27% of patients treated with placebo, improved at least one point on the HDSS (P = 0·009). The mean improvement in quality of life measured by DLQI was significantly better in the oxybutynin arm (6·9) than in the placebo arm (2·3). The most frequent side-effect was dry mouth, which was observed in 43% of the patients in the oxybutynin arm, compared with 11% in the placebo arm. CONCLUSIONS: Treatment with low-dose oxybutynin is effective in reducing symptoms of hyperhidrosis in generalized or localized forms. Side-effects were frequent but minor and mainly involved dry mouth.

MAGIX, a new software for the analysis of complex gamma spectra.

The MAGIX code (a French acronym standing for Automatic Gamma and X-ray Measurement) is a software developed to analyze γ/X spectra on the topic of severe accident diagnosis. Indeed, the gamma spectra obtained after a severe reactor core accident are complex because they are composed of hundreds of lines of short-lived fission products and Fukushima accident demonstrated a lack in robustness of data interpretation during a crisis. MAGIX allows a complete and entirely automatic analysis of the spectra, with identification of radionuclides and calculation of activities. It can analyze spectra measured by detectors with excellent resolution such as HPGe detectors as well as detectors with medium resolution (e.g. CZT and LaBr3). For most detectors, the analysis of the spectra can be done without a detection efficiency curve because its process can include the calculation of a relative detection efficiency. MAGIX accepts spectra corresponding to any experimental setup (energy slope, energy range, resolution, absorber, etc.). However, these experimental conditions can have an impact on the quality of the results. Results on spectra simulated in different configurations showed that the analysis of the HPGe spectrum with the user defined efficiency and with the MAGIX detection efficiency were close. Furthermore, they also showed that the accuracy of activities was similar with increasing energy slopes but decreased with resolution degradation, with fewer correctly identified radionuclides in this case.

Calponin modulates the exclusion of Otx-expressing cells from convergence extension movements.

Otx2, a vertebrate homologue of the Drosophila orthodenticle gene, coordinates two processes in early embryonic development. Not only does it specify cell fate in the anterior regions of the embryo, it also prevents the cells that express it from participating in the convergence extension movements that shape the rest of the body axis. Here we show that, in Xenopus, this latter function is mediated by XclpH3, transcription of which is directly stimulated by Xotx2. XclpH3 is a Xenopus homologue of the mammalian calponin gene, the product of which binds both actin and myosin and prevents the generation of contractile force by actin filaments.

[Brachioradial pruritus revealing an ependymoma]. / Prurit brachioradial révélant un épendymome.

BACKGROUND: Brachioradial pruritus is a rare form of pruritus localised to one or more brachioradial dermatomes, initially classified as a photodermatosis but which in fact is generally brought on by nervous compression. We report a case of a brachioradial pruritus revealing an intramedullary tumour. PATIENTS AND METHODS: A 53-year-old man had presented pruritus for seven years under the left clavicle, then on the left forearm followed by the right forearm. Finally cervicodynia appeared associated with dysaesthesia of the two upper limbs, fulgurating pains and paresis of the left cubital region. The examination revealed suspended bilateral hypoaesthesia (C4, C5, C6, C7), proprioceptive disorders of the left upper limb, mild motor deficit in the left C8 area and tetrapyramidal syndrome. Cervical radiography did not show cervical osteoarthritis. The MRI revealed a bulky cervical intramedullary tumour extending from C2 to C6. After ruling out cavernoma by medullary angiography, surgery was performed and histopathological analysis of the complete lesion revealed a benign ependymoma. Four months later, this patient complained about residual pains requiring treatment with gabapentin and class 2 analgesics. DISCUSSION: The case presented underlines the possibility of a brachioradial pruritus revealing an intramedullary tumour. Ependymomas are usually seen in children and are frequently evoked in the presence of dysaesthesia. We report the third case of brachioradial pruritus revealing a medullary tumour. The two other cases involved syringomyelia revealed by pruritus in C5 and ependymoma revealed by pruritus in C5-C6. The patient with ependymoma had refused surgical treatment. CONCLUSION: Atypical brachioradial pruritus complicated by neuropathic pains and disorders should prompt screening for a medullary tumour.

[The value of allergy survey in a retrospective series of 40 patients with burning-mouth syndrome (stomatodynia)]. / Stomatodynies: intérêt de l'enquête allergologique dans une série rétrospective de 40 malades.

BACKGROUND: By definition, stomatodynia or burning-mouth syndrome involves oral pain with no causes being found on history taking or examination. An allergic origin is often suspected by doctors and patients alike. In this study, we attempted to assess the value of epicutaneous tests in demonstrating allergic causes for patients presenting stomatodynia. PATIENTS AND METHODS: This was a single-centre retrospective study of patients undergoing epicutaneous tests between 1996 and 2003 to screen for allergic causes of mouth pain not accounted for by any abnormalities seen during examination performed at consultations for mouth disease. RESULTS: Forty patients were included (11 male, 29 female; mean age: 58 years), and 39 were excluded. Sixteen patients presented at least one positive test, with a total of 35 positive tests in all. In decreasing order of frequency, the causes were metals, mercury derivatives (nickel salts: n=5; chrome salts: n=3; palladium salts: n=2; phenylmercuric acetate: n=2; thiomersal: n=2; cobalt salts: n=1; gold salts: n=1; mercury: n=1) and resins (acrylates: n=4). The relevance of these test results was considered probable in three cases and possible in five cases, associated with the existence of metals or resins in patients' mouths. The Peru balm test was positive in four cases but was not relevant. Tests for personal products were negative in all cases, with the exception of one case of resin from a prosthesis and one case of tixocortol pivalate. COMMENTS: Type I stomatodynia (daily occurrence with gradually increase in discomfort throughout the day) and type II stomatodynia (permanent) are not normally attributable to allergies. However, for type III stomatodynia (non-permanent, with acute episodes followed by remission), an allergy survey guided by questioning may be undertaken to determine the cause, primarily prostheses or diet. The relevance of positive test results must be interpreted with caution in view of the incidence of positive epicutaneous tests for metals and Peru balm among the general population studied.

Mechano-chemostats to study the effects of compressive stress on yeast.

Cells need to act upon the elastic extracellular matrix and against steric constraints when proliferating in a confined environment, leading to the build-up, at the population level, of a compressive, growth-induced, mechanical stress. Compressive mechanical stresses are ubiquitous to any cell population growing in a spatially-constrained environment, such as microbes or most solid tumors. They remain understudied, in particular in microbial populations, due to the lack of tools available to researchers. Here, we present various mechano-chemostats: microfluidic devices developed to study microbes under pressure. A mechano-chemostat permits researchers to control the intensity of growth-induced pressure through the control of cell confinement, while keeping cells in a defined chemical environment. These versatile devices enable the interrogation of physiological parameters influenced by mechanical compression at the single cell level and set a standard for the study of growth-induced compressive stress.

Aminoacyl-tRNA synthetases.

Detailed mechanisms for each step of the reaction catalyzed by both class I and class II aminoacyl-tRNA synthetases have been proposed on the basis of crystallographic data of aminoacyl-tRNA synthetases in complex with their different substrates. Despite the very different topologies of the two classes, there are striking and unanticipated chemical similarities between their active sites and proposed mechanisms.

Mean-field minimization methods for biological macromolecules.

Simulations of macromolecular structures involve the minimization of a potential-energy function that presents many local minima. Mean-field theory provides a tool that enables us to escape these minima, by enhancing sampling in conformational space. The number of applications of this technique has increased significantly over the past year, enabling problems with protein-homology modelling and inverted protein structure prediction to be solved.

[Diagnostic image (330). A woman with lower abdominal pain 3 years after abdominal hysterectomy]. / Diagnose in beeld (330). Een vrouw met onderbuikpijn 3 jaar na abdominale hysterectomie.

A 45-year-old woman developed 3 years after abdominal hysterectomy a prolapse of the left fimbrial end of the uterine tube through a small defect in the vaginal vault with pelvic peritonitis and abscess.

Cell-like pressure sensors reveal increase of mechanical stress towards the core of multicellular spheroids under compression.

The surrounding microenvironment limits tumour expansion, imposing a compressive stress on the tumour, but little is known how pressure propagates inside the tumour. Here we present non-destructive cell-like microsensors to locally quantify mechanical stress distribution in three-dimensional tissue. Our sensors are polyacrylamide microbeads of well-defined elasticity, size and surface coating to enable internalization within the cellular environment. By isotropically compressing multicellular spheroids (MCS), which are spherical aggregates of cells mimicking a tumour, we show that the pressure is transmitted in a non-trivial manner inside the MCS, with a pressure rise towards the core. This observed pressure profile is explained by the anisotropic arrangement of cells and our results suggest that such anisotropy alone is sufficient to explain the pressure rise inside MCS composed of a single cell type. Furthermore, such pressure distribution suggests a direct link between increased mechanical stress and previously observed lack of proliferation within the spheroids core.

Atomic environment energies in proteins defined from statistics of accessible and contact surface areas.

Atomic contact potentials are derived by statistical analysis of atomic surface contact areas versus atom type in a database of non-homologous protein structures. The atomic environment is characterized by the surface area accessible to solvent and the surface of contacts with polar and non-polar atoms. Four types of atoms are considered, namely neutral polar atoms from protein backbones and from protein side-chains, non-polar atoms and charged atoms. Potential energies delta Ej(E) are defined from the preference for an atom of type j to be in a given environment E compared to the expected value if everything was random; Boltzmann's law is then used to transform these preferences into energies. These new potentials very clearly discriminate misfolded from correct structural models. The performance of these potentials are critically assessed by monitoring the recognition of the native fold among a large number of alternative structural folding types (the hide-and-seek procedure), as well as by testing if the native sequence can be recovered from a large number of randomly shuffled sequences for a given 3D fold (a procedure similar to the inverse folding problem). We suggest that these potentials reflect the atomic short range non-local interactions in proteins. To characterise atomic solvation alone, similar potentials were derived as a function of the percentage of solvent-accessible area alone. These energies were found to agree reasonably well with the solvation formalism of Eisenberg and McLachlan.

Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy.

Understanding the relations between the conformation of the side-chains and the backbone geometry is crucial for structure prediction as well as for homology modelling. To attempt to unravel these rules, we have developed a method which allows us to predict the position of the side-chains from the co-ordinates of the main-chain atoms. This method is based on a rotamer library and refines iteratively a conformational matrix of the side-chains of a protein, CM, such that its current element at each cycle CM (ij) gives the probability that side-chain i of the protein adopts the conformation of its possible rotamer j. Each residue feels the average of all possible environments, weighted by their respective probabilities. The method converges in only a few cycles, thereby deserving the name of self consistent mean field method. Using the rotamer with the highest probability in the optimized conformational matrix to define the conformation of the side-chain leads to the result that on average 72% of chi 1, 75% of chi 2 and 62% of chi 1 + 2 are correctly predicted for a set of 30 proteins. Tests with six pairs of homologous proteins have shown that the method is quite successful even when the protein backbone deviates from the correct conformation. The second application of the optimized conformational matrix was to provide estimates of the conformational entropy of the side-chains in the folded state of the protein. The relevance of this entropy is discussed.

Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model.

The Elastic Network Model is used to investigate the open/closed transition in all DNA-dependent polymerases whose structure is known in both forms. For each structure the model accounts well for experimental crystallographic B-factors. It is found in all cases that the transition can be well described with just a handful of the normal modes. Usually, only the lowest and/or the second lowest frequency normal modes deduced from the open form give rise to calculated displacement vectors that have a correlation coefficient larger than 0.50 with the observed difference vectors between the two forms. This is true for every structural class of DNA-dependent polymerases where a direct comparison with experimental structural data is available. In cases where only one form has been observed by X-ray crystallography, it is possible to make predictions concerning the possible existence of another form in solution by carefully examining the vector displacements predicted for the lowest frequency normal modes. This simple model, which has the advantage to be computationally inexpensive, could be used to design novel kind of drugs directed against polymerases, namely drugs preventing the open/closed transition from occurring in bacterial or viral DNA-dependent polymerases.

Solution structural studies and low-resolution model of the Schizosaccharomyces pombe sap1 protein.

Sap1 is a DNA-binding protein involved in controlling the mating type switch in fission yeast Schizosaccharomyces pombe. In the absence of any significant sequence similarity with any structurally known protein, a variety of biophysical techniques has been used to probe the solution low-resolution structure of the sap1 protein. First, sap1 is demonstrated to be an unusually elongated dimer in solution by measuring the translational diffusion coefficient with two independent techniques: dynamic light-scattering and ultracentrifugation. Second, sequence analysis revealed the existence of a long coiled-coil region, which is responsible for dimerization. The length of the predicted coiled-coil matches estimates drawn from the hydrodynamic experimental behaviour of the molecule. In addition, the same measurements done on a shorter construct with a coiled-coil region shortened by roughly one-half confirmed the localization of the long coiled-coil region. A crude T-shape model incorporating all these information was built. Third, small-angle X-ray scattering (SAXS) of the free molecule provided additional evidence for the model. In particular, the P(r) curve strikingly demonstrates the existence of long intramolecular distances. Using a novel 3D reconstruction algorithm, a low resolution 3D model of the protein has been independently constructed that matches the SAXS experimental data. It also fits the translation diffusion coefficients measurements and agrees with the first T-shaped model. This low-resolution model has clearly biologically relevant new functional implications, suggesting that sap1 is a bifunctional protein, with the two active sites being separated by as much as 120 A; a tetrapeptide repeated four times at the C terminus of the molecule is postulated to be of utmost functional importance.