Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect.

Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli) where protein aggregates accumulate at the old pole region of the aging bacterium. Because of the potential of E. coli as a model organism, elucidating aging and protein aggregation in this bacterium may pave the way to significant advances in our global understanding of aging. A first obstacle along this path is to decipher the mechanisms by which protein aggregates are targeted to specific intercellular locations. Here, using an integrated approach based on individual-based modeling, time-lapse fluorescence microscopy and automated image analysis, we show that the movement of aging-related protein aggregates in E. coli is purely diffusive (Brownian). Using single-particle tracking of protein aggregates in live E. coli cells, we estimated the average size and diffusion constant of the aggregates. Our results provide evidence that the aggregates passively diffuse within the cell, with diffusion constants that depend on their size in agreement with the Stokes-Einstein law. However, the aggregate displacements along the cell long axis are confined to a region that roughly corresponds to the nucleoid-free space in the cell pole, thus confirming the importance of increased macromolecular crowding in the nucleoids. We thus used 3D individual-based modeling to show that these three ingredients (diffusion, aggregation and diffusion hindrance in the nucleoids) are sufficient and necessary to reproduce the available experimental data on aggregate localization in the cells. Taken together, our results strongly support the hypothesis that the localization of aging-related protein aggregates in the poles of E. coli results from the coupling of passive diffusion-aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of "soft" intracellular structuring (based on macromolecular crowding) in diffusion-based protein localization in E. coli.

Synthesis of fluorinated catharanthine analogues and investigation of their biomimetic coupling with vindoline.

The syntheses of 20,20-difluorocatharanthine and congeners, starting from the naturally occurring catharanthine, are reported. The fluorinated catharanthine analogues were investigated as potential precursors to dimeric Vinca alkaloids of the vinflunine family. However, the biomimetic coupling of the fluorinated catharanthine derivatives with vindoline led to unexpected alkaloid structures, the formation of which was rationalized.

The Reissner fiber under tension in vivo shows dynamic interaction with ciliated cells contacting the cerebrospinal fluid.

The Reissner fiber (RF) is an acellular thread positioned in the midline of the central canal that aggregates thanks to the beating of numerous cilia from ependymal radial glial cells (ERGs) generating flow in the central canal of the spinal cord. RF together with cerebrospinal fluid (CSF)-contacting neurons (CSF-cNs) form an axial sensory system detecting curvature. How RF, CSF-cNs and the multitude of motile cilia from ERGs interact in vivo appears critical for maintenance of RF and sensory functions of CSF-cNs to keep a straight body axis, but is not well-understood. Using in vivo imaging in larval zebrafish, we show that RF is under tension and resonates dorsoventrally. Focal RF ablations trigger retraction and relaxation of the fiber's cut ends, with larger retraction speeds for rostral ablations. We built a mechanical model that estimates RF stress diffusion coefficient D at 5 mm2/s and reveals that tension builds up rostrally along the fiber. After RF ablation, spontaneous CSF-cN activity decreased and ciliary motility changed, suggesting physical interactions between RF and cilia projecting into the central canal. We observed that motile cilia were caudally-tilted and frequently interacted with RF. We propose that the numerous ependymal motile monocilia contribute to RF's heterogenous tension via weak interactions. Our work demonstrates that under tension, the Reissner fiber dynamically interacts with motile cilia generating CSF flow and spinal sensory neurons.

A small molecule that mimics the BB-loop in the Toll interleukin-1 (IL-1) receptor domain of MyD88 attenuates staphylococcal enterotoxin B-induced pro-inflammatory cytokine production and toxicity in mice.

Toxic shock syndrome (TSS) is a clinical consequence of the profound amplification of host pro-inflammatory cytokine signaling that results from staphylococcal enterotoxin (SE) exposure. We recently reported that MyD88(-/-) mice were resistant to SEA or SEB toxic shock and displayed reduced levels of pro-inflammatory cytokines in their serum. Here we report that SEB stimulation of total mononuclear cells up-regulated MyD88 in monocytes and T cells. Further, MyD88 gene silencing in primary human cells using siRNA prevented SEB or SEB plus lipopolysaccharide (LPS) induction of interleukin-1ß (IL-1ß) transcriptional activation, suggesting that MyD88-mediated signaling is an essential component of SEB toxicity. We synthesized small molecules that mimic the conserved BB-loop in the Toll/IL-1 receptor (TIR) domain of MyD88. In primary human cells, these mimetics attenuated SEB-induced pro-inflammatory cytokine production. SEB stimulation of primary cells with mimetic affected newly synthesized MyD88 and downstream signaling components. Furthermore, LPS-induced MyD88 signaling was likewise inhibited in a cell-based reporter assay. More importantly, administration of mimetic reduced cytokine responses and increased survivability in a murine SEB challenge model. Collectively, these results suggest that MyD88 BB-loop mimetics interfere with SEB-induced pro-inflammatory signaling and toxicity, thus offering a potential approach in the therapy of toxic shock.

Synthesis of pyridazine-based scaffolds as alpha-helix mimetics.

The synthesis of several amphiphilic, nonpeptidic scaffolds that mimic the presentation of i, i + 3 or i + 4, and i + 7 residues of a peptide alpha-helix is described. The approach uses a pyridazine core, and the synthesis involves only a few steps and minimizes the number of C-C bond-forming reactions. The versatility of the synthesis makes it suitable for the preparation of small libraries of low molecular weight alpha-helix mimetics that could be targeted to certain protein/protein interactions.

In the golden age of organocatalysis.

The term "organocatalysis" describes the acceleration of chemical reactions through the addition of a substoichiometric quantity of an organic compound. The interest in this field has increased spectacularly in the last few years as result of both the novelty of the concept and, more importantly, the fact that the efficiency and selectivity of many organocatalytic reactions meet the standards of established organic reactions. Organocatalytic reactions are becoming powerful tools in the construction of complex molecular skeletons. The diverse examples show that in recent years organocatalysis has developed within organic chemistry into its own subdiscipline, whose "Golden Age" has already dawned.

Computational gestalts and perception thresholds.

In 1923, Max Wertheimer proposed a research programme and method in visual perception. He conjectured the existence of a small set of geometric grouping laws governing the perceptual synthesis of phenomenal objects, or "gestalt" from the atomic retina input. In this paper, we review this set of geometric grouping laws, using the works of Metzger, Kanizsa and their schools. In continuation, we explain why the Gestalt theory research programme can be translated into a Computer Vision programme. This translation is not straightforward, since Gestalt theory never addressed two fundamental matters: image sampling and image information measurements. Using these advances, we shall show that gestalt grouping laws can be translated into quantitative laws allowing the automatic computation of gestalts in digital images. From the psychophysical viewpoint, a main issue is raised: the computer vision gestalt detection methods deliver predictable perception thresholds. Thus, we are set in a position where we can build artificial images and check whether some kind of agreement can be found between the computationally predicted thresholds and the psychophysical ones. We describe and discuss two preliminary sets of experiments, where we compared the gestalt detection performance of several subjects with the predictable detection curve. In our opinion, the results of this experimental comparison support the idea of a much more systematic interaction between computational predictions in Computer Vision and psychophysical experiments.

Dequantizing image orientation.

We address the problem of computing a local orientation map in a digital image. We show that standard image gray level quantization causes a strong bias in the repartition of orientations, hindering any accurate geometric analysis of the image. In continuation, a simple dequantization algorithm is proposed, which maintains all of the image information and transforms the quantization noise in a nearby Gaussian white noise (we actually prove that only Gaussian noise can maintain isotropy of orientations). Mathematical arguments are used to show that this results in the restoration of a high quality image isotropy. In contrast with other classical methods, it turns out that this property can be obtained without smoothing the image or increasing the signal-to-noise ratio (SNR). As an application, it is shown in the experimental section that, thanks to this dequantization of orientations, such geometric algorithms as the detection of nonlocal alignments can be performed efficiently. We also point out similar improvements of orientation quality when our dequantization method is applied to aliased images.

Enantioselective Organocatalysis.

The last few years have witnessed a spectacular advancement in new catalytic methods based on metal-free organic molecules. In many cases, these small compounds give rise to extremely high enantioselectivities. Preparative advantages are notable: usually the reactions can be performed under an aerobic atmosphere with wet solvents. The catalysts are inexpensive and they are often more stable than enzymes or other bioorganic catalysts. Also, these small organic molecules can be anchored to a solid support and reused more conveniently than organometallic/bioorganic analogues, and show promising adaptability to high-throughput screening and process chemistry. Herein we focus on four different domains in which organocatalysis has made major advances: 1) The activation of the reaction based on the nucleophilic/electrophilic properties of the catalysts. This type of catalysis has much in common with conventional Lewis acid/base activation by metal complexes. 2) Transformations in which the organic catalyst forms a reactive intermediate: the chiral catalyst is consumed in the reaction and requires regeneration in a parallel catalytic cycle. 3) Phase-transfer reactions: The chiral catalyst forms a host-guest complex with the substrate and shuttles between the standard organic solvent and the second phase (i.e. a solid, aqueous, or fluorous phase in which the organic transformation takes place). 4) Molecular-cavity-accelerated asymmetric transformations: the catalyst can select between competing substrates, depending on size and structure criteria. The rate acceleration of a given reaction is similar to the Lewis acid/base activation and is the consequence of the simultaneous action of different polar functions. Herein it is shown that organocatalysis complements rather than competes with current methods. It offers something conceptually novel and opens new horizons in synthesis.

Conical diffraction illumination opens the way for low phototoxicity super-resolution imaging.

We present a new technology for super-resolution fluorescence imaging, based on conical diffraction. Conical diffraction is a linear, singular phenomenon, taking place when a laser beam is diffracted through a biaxial crystal. We use conical diffraction in a thin biaxial crystal to generate illumination patterns that are more compact than the classical Gaussian beam, and use them to generate a super-resolution imaging modality. While there already exist several super-resolution modalities, our technology (biaxial super-resolution: BSR) is distinguished by the unique combination of several performance features. Using BSR super-resolution data are achieved using low light illumination significantly less than required for classical confocal imaging, which makes BSR ideal for live-cell, long-term time-lapse super-resolution imaging. Furthermore, no specific sample preparation is required, and any fluorophore can be used. Perhaps most exciting, improved resolution BSR-imaging resolution enhancement can be achieved with any type of objective no matter the magnification, numerical aperture, working distance, or the absence or presence of immersion medium. In this article, we present the first implementation of BSR modality on a commercial confocal microscope. We acquire and analyze validation data, showing high quality super-resolved images of biological objects, and demonstrate the wide applicability of the technology. We report live-cell super-resolution imaging over a long period, and show that the light dose required for super-resolution imaging is far below the threshold likely to generate phototoxicity.

A dictionary learning approach for Poisson image deblurring.

The restoration of images corrupted by blur and Poisson noise is a key issue in medical and biological image processing. While most existing methods are based on variational models, generally derived from a maximum a posteriori (MAP) formulation, recently sparse representations of images have shown to be efficient approaches for image recovery. Following this idea, we propose in this paper a model containing three terms: a patch-based sparse representation prior over a learned dictionary, the pixel-based total variation regularization term and a data-fidelity term capturing the statistics of Poisson noise. The resulting optimization problem can be solved by an alternating minimization technique combined with variable splitting. Extensive experimental results suggest that in terms of visual quality, peak signal-to-noise ratio value and the method noise, the proposed algorithm outperforms state-of-the-art methods.

Multiplicative noise removal via a learned dictionary.

Multiplicative noise removal is a challenging image processing problem, and most existing methods are based on the maximum a posteriori formulation and the logarithmic transformation of multiplicative denoising problems into additive denoising problems. Sparse representations of images have shown to be efficient approaches for image recovery. Following this idea, in this paper, we propose to learn a dictionary from the logarithmic transformed image, and then to use it in a variational model built for noise removal. Extensive experimental results suggest that in terms of visual quality, peak signal-to-noise ratio, and mean absolute deviation error, the proposed algorithm outperforms state-of-the-art methods.

Multiparametric analyses reveal the pH-dependence of silicon biomineralization in diatoms.

Diatoms, the major contributors of the global biogenic silica cycle in modern oceans, account for about 40% of global marine primary productivity. They are an important component of the biological pump in the ocean, and their assemblage can be used as useful climate proxies; it is therefore critical to better understand the changes induced by environmental pH on their physiology, silicification capability and morphology. Here, we show that external pH influences cell growth of the ubiquitous diatom Thalassiosira weissflogii, and modifies intracellular silicic acid and biogenic silica contents per cell. Measurements at the single-cell level reveal that extracellular pH modifications lead to intracellular acidosis. To further understand how variations of the acid-base balance affect silicon metabolism and theca formation, we developed novel imaging techniques to measure the dynamics of valve formation. We demonstrate that the kinetics of valve morphogenesis, at least in the early stages, depends on pH. Analytical modeling results suggest that acidic conditions alter the dynamics of the expansion of the vesicles within which silica polymerization occurs, and probably its internal pH. Morphological analysis of valve patterns reveals that acidification also reduces the dimension of the nanometric pores present on the valves, and concurrently overall valve porosity. Variations in the valve silica network seem to be more correlated to the dynamics and the regulation of the morphogenesis process than the silicon incorporation rate. These multiparametric analyses from single-cell to cell-population levels demonstrate that several higher-level processes are sensitive to the acid-base balance in diatoms, and its regulation is a key factor for the control of pattern formation and silicon metabolism.

On the elucidation of the mechanism of Vinca alkaloid fluorination in superacidic medium.

Detailed investigations on one of the key steps of the superacidic fluorination of Vinca alkaloids that is the origin of C20' activation are reported. While two different pathways can be envisioned for the emergence of the transient secondary carbocationic intermediate, isotopic labeling experiments unambiguously revealed the involvement of a 1,2-hydride shift mechanism.

An a-contrario approach for subpixel change detection in satellite imagery.

This paper presents a new method for unsupervised subpixel change detection using image series. The method is based on the definition of a probabilistic criterion capable of assessing the level of coherence of an image series relative to a reference classification with a finer resolution. In opposition to approaches based on an a priori model of the data, the model developed here is based on the rejection of a nonstructured model-called a-contrario model-by the observation of structured data. This coherence measure is the core of a stochastic algorithm which automatically selects the image subdomain representing the most likely changes. A theoretical analysis of this model is led to predict its performances, in particular regarding the contrast level of the image as well as the number of change pixels in the image. Numerical simulations are also presented that confirm the high robustness of the method and its capacity to detect changes impacting more than 25 percent of a considered pixel under average conditions. An application to land-cover change detection is then provided using time series of satellite images.

Heterocyclic alpha-helix mimetics for targeting protein-protein interactions.

The design and synthesis of alpha-helix peptidomimetics using inverse electron demand Diels-Alder reactions is described. The potency of the resulting pyridazine-based library to disrupt the Bak/Bcl-X(L) interaction was tested using an in vitro fluorescence polarization assay.

Catharanthinol and dihydrocatharanthinol: two Iboga-class alkaloids.

The title compounds are indole alkaloids of the Iboga class. In both compounds, viz. catharanthinol methanol solvate, C(20)H(24)N(2)O.CH(4)O, (I), and dihydrocatharanthinol monohydrate, C(20)H(26)N(2)O.H(2)O, (II), a nitrogen-containing seven-membered ring is fused to the indole system and shares two sides with a tricyclic isoquinuclidine group. The main difference between (I) and (II) is the presence of a C=C bond in the isoquinuclidine ring in (I). The presence of amine and hydroxy groups in these molecules and of methanol [in (I)] or water [in (II)] solvent molecules results in intra- and/or intermolecular hydrogen bonding.

An ion pair formed by protonated Fe(cp*py)2 and the octanuclear cluster U8Cl24O4(cp*py)2 [cp*py is tetramethyl-5-(2-pyridyl)cyclopentadiene].

In bis[1,1',2,2',3,3',4,4'-octamethyl-5-(2-pyridinio)-5'-(2-pyridyl)ferrocene] di-mu(3)-chloro-hexadeca-mu(2)-chloro-hexachlorodi-mu(4)-oxo-di-mu(3)-oxo-bis[(eta(5),kappaN)-1,2,3,4-tetramethyl-5-(2-pyridyl)cyclopentadienyl]octauranium(IV) dichloromethane tetrasolvate, [Fe(C(14)H(17)N)(C(14)H(16)N)](2)[U(8)Cl(24)O(4)(C(14)H(16)N)(2)].4CH(2)Cl(2), (I), two protonated Fe(cp*py)(2) units [cp*py is tetramethyl-5-(2-pyridyl)cyclopentadiene] form an ion pair with the dianionic centrosymmetric cluster U(8)Cl(24)O(4)(cp*py)(2). The latter is the highest nuclearity assemblage in the chemistry of uranium (non-uranyl) compounds reported to date.