Characterisation of T cell receptor repertoires in coeliac disease

AIMS

Characterise T-cell receptor gene (TR) repertoires of small intestinal T cells of patients with newly diagnosed (active) coeliac disease (ACD), refractory CD type I (RCD I) and patients with CD on a gluten-free diet (GFD).

METHODS

Next-generation sequencing of complementarity-determining region 3 (CDR3) of rearranged T cell receptor β (TRB) and γ (TRG) genes was performed using DNA extracted from intraepithelial cell (IEC) and lamina propria cell (LPC) fractions and a small subset of peripheral blood mononuclear cell (PBMC) samples obtained from CD and non-CD (control) patients. Several parameters were assessed, including relative abundance and enrichment.

RESULTS

TRB and TRG repertoires of CD IEC and LPC samples demonstrated lower clonality but higher frequency of rearranged TRs compared with controls. No CD-related differences were detected in the limited number of PBMC samples. Previously published LP gliadin-specific TRB sequences were more frequently detected in LPC samples from patients with CD compared with non-CD controls. TRG repertoires of IECs from both ACD and GFD patients demonstrated increased abundance of certain CDR3 amino acid (AA) motifs compared with controls, which were encoded by multiple nucleotide variants, including one motif that was enriched in duodenal IECs versus the PBMCs of CD patients.

CONCLUSIONS

Small intestinal TRB and TRG repertoires of patients with CD are more diverse than individuals without CD, likely due to mucosal recruitment and accumulation of T cells because of protracted inflammation. Enrichment of the unique TRG CDR3 AA sequence in the mucosa of patients with CD may suggest disease-associated changes in the TCRγδ IE lymphocyte (IEL) landscape.

Infection and inflammation stimulate expansion of a CD74+ Paneth cell subset to regulate disease progression

Paneth cells (PCs), a specialized secretory cell type in the small intestine, are increasingly recognized as having an essential role in host responses to microbiome and environmental stresses. Whether and how commensal and pathogenic microbes modify PC composition to modulate inflammation remain unclear. Using newly developed PC-reporter mice under conventional and gnotobiotic conditions, we determined PC transcriptomic heterogeneity in response to commensal and invasive microbes at single cell level. Infection expands the pool of CD74+ PCs, whose number correlates with auto or allogeneic inflammatory disease progressions in mice. Similar correlation was found in human inflammatory disease tissues. Infection-stimulated cytokines increase production of reactive oxygen species (ROS) and expression of a PC-specific mucosal pentraxin (Mptx2) in activated PCs. A PC-specific ablation of MyD88 reduced CD74+ PC population, thus ameliorating pathogen-induced systemic disease. A similar phenotype was also observed in mice lacking Mptx2. Thus, infection stimulates expansion of a PC subset that influences disease progression.

Gluten induces rapid reprogramming of natural memory αβ and γδ intraepithelial T cells to induce cytotoxicity in celiac disease

Celiac disease (CD) is an autoimmune disease in which intestinal inflammation is induced by dietary gluten. The means through which gluten-specific CD4+ T cell activation culminates in intraepithelial T cell (T-IEL)-mediated intestinal damage remain unclear. Here, we performed multiplexed single-cell analysis of intestinal and gluten-induced peripheral blood T cells from patients in different CD states and healthy controls. Untreated, active, and potential CD were associated with an enrichment of activated intestinal T cell populations, including CD4+ follicular T helper (TFH) cells, regulatory T cells (Tregs), and natural CD8+ αβ and γδ T-IELs. Natural CD8+ αβ and γδ T-IELs expressing activating natural killer cell receptors (NKRs) exhibited a distinct TCR repertoire in CD and persisted in patients on a gluten-free diet without intestinal inflammation. Our data further show that NKR-expressing cytotoxic cells, which appear to mediate intestinal damage in CD, arise from a distinct NKR-expressing memory population of T-IELs. After gluten ingestion, both αβ and γδ T cell clones from this memory population of T-IELs circulated systemically along with gluten-specific CD4+ T cells and assumed a cytotoxic and activating NKR-expressing phenotype. Collectively, these findings suggest that cytotoxic T cells in CD are rapidly mobilized in parallel with gluten-specific CD4+ T cells after gluten ingestion.

Image processing tools for the validation of CryoEM maps

The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded.

Proton Distribution Radii of ^{16-24}O: Signatures of New Shell Closures and Neutron Skin

The root mean square radii of the proton density distribution in ^{16-24}O derived from measurements of charge changing cross sections with a carbon target at ∼900A  MeV together with the matter radii portray thick neutron skin for ^{22-24}O despite ^{22,24}O being doubly magic. Imprints of the shell closures at N=14 and 16 are reflected in local minima of their proton radii that provide evidence for the tensor interaction causing them. The radii agree with ab initio calculations employing the chiral NNLO_{sat} interaction, though skin thickness predictions are challenged. Shell model predictions agree well with the data.

Hierarchical autoclassification of cryo-EM samples and macromolecular energy landscape determination

BACKGROUND AND OBJECTIVE

Cryo-electron microscopy using single particle analysis is a powerful technique for obtaining 3D reconstructions of macromolecules in near native conditions. One of its major advances is its capacity to reveal conformations of dynamic molecular complexes. Most popular and successful current approaches to analyzing heterogeneous complexes are founded on Bayesian inference. However, these 3D classification methods require the tuning of specific parameters by the user and the use of complicated 3D re-classification procedures for samples affected by extensive heterogeneity. Thus, the success of these approaches highly depends on the user experience. We introduce a robust approach to identify many different conformations presented in a cryo-EM dataset based on Bayesian inference through Relion classification methods that does not require tuning of parameters and reclassification strategies.

METHODS

The algorithm allows both 2D and 3D classification and is based on a hierarchical clustering approach that runs automatically without requiring typical inputs, such as the number of conformations present in the dataset or the required classification iterations. This approach is applied to robustly determine the energy landscapes of macromolecules.

RESULTS

We tested the performance of the methods proposed here using four different datasets, comprising structurally homogeneous and highly heterogeneous cases. In all cases, the approach provided excellent results. The routines are publicly available as part of the CryoMethods plugin included in the Scipion package.

CONCLUSIONS

Our results show that the proposed method can be used to align and classify homogeneous and heterogeneous datasets without requiring previous alignment information or any prior knowledge about the number of co-existing conformations. The approach can be used for both 2D and 3D autoclassification and only requires an initial volume. In addition, the approach is robust to the "attractor" problem providing many different conformations/views for samples affected by extensive heterogeneity. The obtained 3D classes can render high resolution 3D structures, while the obtained energy landscapes can be used to determine structural trajectories.

[COVID-19 and lockdown: Impact on pregnancy complications]

Introduction

L’apparition de la COVID-19 a entraîné la mise en place d’un confinement en France du 17 mars au 11 mai 2020. Notre étude a pour but d’évaluer l’impact du confinement sur le taux d’hospitalisation pour menace d’accouchement prématuré et sur le taux d’accouchement prématuré.

Méthodes

Étude épidémiologique rétrospective multicentrique réalisée sur la période du confinement du 15 mars au 31 mai 2020, comparée à la même période au cours des deux années précédentes (2018 et 2019) dans les hôpitaux de Picardie (Centre Hospitalier Universitaire Amiens Picardie, Centres Hospitaliers de Beauvais, Compiègne et Saint-Quentin).

Résultats

Au total, 608 patientes ont été incluses. Nous retrouvons une réduction significative du taux de rupture prématuré des membranes (16,9 % [73/432] en 2018/2019 vs 9,7 % [17/176] en 2020 ; p = 0,02), ainsi que du taux d’accouchement prématuré (9,3 % [276/2961] en 2018/2019 vs 6,8 % [96/1416] en 2020 ; p < 0,05) sur l’ensemble des hôpitaux. Notre étude met également en évidence une diminution des hospitalisations (207 en 2019 vs 176 en 2020).

Conclusion

Il est observé, au cours de la première période de confinement, une réduction du taux d’accouchement prématuré. Il serait, par ailleurs, intéressant d’évaluer l’impact psychologique du confinement.

Orbital Many-Body Dynamics of Bosons in the Second Bloch Band of an Optical Lattice

We explore Josephson-like dynamics of a Bose-Einstein condensate of rubidium atoms in the second Bloch band of an optical square lattice providing a double well structure with two inequivalent, degenerate energy minima. This oscillation is a direct signature of the orbital changing collisions predicted to arise in this system in addition to the conventional on-site collisions. The observed oscillation frequency scales with the relative strength of these collisional interactions, which can be readily tuned via a distortion of the unit cell. The observations are compared to a quantum model of two single-particle modes and to a semiclassical multiband tight-binding simulation of 12×12 tubular sites of the lattice. Both models reproduce the observed oscillatory dynamics and show the correct dependence of the oscillation frequency on the ratio between the strengths of the on-site and orbital changing collision processes.

ENRICH: A fast method to improve the quality of flexible macromolecular reconstructions

Cryo-electron microscopy using single particle analysis requires the computational averaging of thousands of projection images captured from identical macromolecules. However, macromolecules usually present some degree of flexibility showing different conformations. Computational approaches are then required to classify heterogeneous single particle images into homogeneous sets corresponding to different structural states. Nonetheless, sometimes the attainable resolution of reconstructions obtained from these smaller homogeneous sets is compromised because of reduced number of particles or lack of images at certain macromolecular orientations. In these situations, the current solution to improve map resolution is returning to the electron microscope and collect more data. In this work, we present a fast approach to partially overcome this limitation for heterogeneous data sets. Our method is based on deforming and then moving particles between different conformations using an optical flow approach. Particles are then merged into a unique conformation obtaining reconstructions with improved resolution, contrast and signal-to-noise ratio. We present experimental results that show clear improvements in the quality of obtained 3D maps, however, there are also limits to this approach, i.e., the method is restricted to small deformations and cannot determine local patterns of flexibility of small elements, such as secondary structures, which we discuss in the manuscript.

Innate Lymphoid Cells and Celiac Disease: Current Perspective

Celiac disease (CD) is a common autoimmune disorder triggered by the ingestion of gluten in genetically susceptible individuals. Although the mechanisms underlying gliadin-mediated activation of adaptive immunity in CD have been well-characterized, regulation of innate immune responses and the functions of certain immune cell populations within the epithelium and lamina propria are not well-understood at present. Innate lymphoid cells (ILCs) are types of innate immune cells that have lymphoid morphology, lack antigen-specific receptors, and play important roles in tissue homeostasis, inflammation, and protective immune responses against pathogens. Information regarding the diversity and functions of ILCs in lymphoid organs and at mucosal sites has grown over the past decade, and roles of different ILC subsets in the pathogenesis of some inflammatory intestinal diseases have been proposed. However, our understanding of the contribution of ILCs toward the initiation and progression of CD is still limited. In this review, we discuss current pathophysiological aspects of ILCs within the gastrointestinal tract, findings of recent investigations characterizing ILC alterations in CD and refractory CD, and suggest avenues for future research.

Evidence for a New Compact Symmetric Fission Mode in Light Thorium Isotopes

Taking benefit of the R3B/SOFIA setup to measure the mass and the nuclear charge of both fission fragments in coincidence with the total prompt-neutron multiplicity, the scission configurations are inferred along the thorium chain, from the asymmetric fission in the heavier isotopes to the symmetric fission in the neutron-deficient thorium. Against all expectations, the symmetric scission in the light thorium isotopes shows a compact configuration, which is in total contrast to what is known in the fission of the heavier thorium isotopes and heavier actinides. This new main symmetric scission mode is characterized by a significant drop in deformation energy of the fission fragments of about 19 MeV, compared to the well-known symmetric scission in the uranium-plutonium region.

ScribeMD: Mixed-methods analysis of a pen pal program in undergraduate medical education

Introduction: A growing emphasis on humanistic medical care has led to the development of programs to imbue more humanistic values into training physicians. The ScribeMD intra-class pen pal program is a narrative medicine tool designed to meet this need with a focus on the journey through medical education. This study intends to evaluate the efficacy of this novel program on the participants' professional identity formation (PIF), emotional intelligence development (EID), and narrative competency improvement (NCI).Methods: This program evaluation involved quantitative and qualitative survey solicitations from first and second-year medical student participants and controls. An efficacy-triangulation model was developed as a quantitative outcome-measuring tool linking objective, writing prompts, and survey data.Results: The quantitative results showed statistically significant improvements in line with the Efficacy Triangulation Model in the participant group. Qualitatively, reflective and insight-driven gains were elicited, as were notable themes of personal and community improvements.Conclusion: ScribeMD poses a unique avenue for the development of more humanistic physicians during their medical education. We recommend additional development of the Efficacy Triangulation Model as well as the program design itself. We also recommend the piloting of this program in other healthcare-education settings both with medical education and other health professions.

Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening

The analysis of structure factors in 3D cryo-EM Coulomb potential maps and their "enhancement" at the end of the reconstruction process is a well-established practice, normally referred to as sharpening. The aim is to increase contrast and, in this way, to help tracing the atomic model. The most common way to accomplish this enhancement is by means of the so-called B-factor correction, which applies a global filter to boost high frequencies with some dampening considerations related to noise amplification. The results are maps with a better visual aspect and a quasiflat spectrum at medium and high frequencies. This practice is so widespread that most map depositions in the Electron Microscopy Data Base (EMDB) only contain sharpened maps. Here, the use in cryoEM of global B-factor corrections is theoretically and experimentally analyzed. Results clearly illustrate that protein spectra present a falloff. Thus, spectral quasi-flattening may produce protein spectra with distortions when compared with experimental ones, this fact, combined with the practice of reporting only sharpened maps, generates a sub-optimal situation in terms of data preservation, reuse and reproducibility. Now that the field is more advanced, we put forward two suggestions: (1) to use methods which keep more faithfully the original experimental signal properties of macromolecules when "enhancing" the map, and (2) to further stress the need to deposit the original experimental maps without any postprocessing or sharpening, not only the enhanced maps. In the absence of access to these original maps data is lost, preventing their future analysis with new methods.

Measurement of local resolution in electron tomography

Resolution (global and local) is one of the most reported metrics of quality measurement in Single Particle Analysis (SPA). However, in electron tomography, the situation is different and its computation is not straightforward. Typically, resolution estimation is global and, therefore, reduces the assessment of a whole tomogram to a single number. However, it is known that tomogram quality is spatially variant. Still, up to our knowledge, a method to estimate local quality metrics in tomography is lacking. This work introduces MonoTomo, a method developed to estimate locally in a tomogram the highest reliable frequency component, expressed as a form of local resolution. The fundamentals lie in a local analysis of the density map via monogenic signals, which, in analogy to MonoRes, allows for local estimations. Results with experimental data show that the local resolution range that MonoTomo casts agrees with reported resolution values for experimental data sets, with the advantage of providing a local estimation. A range of applications of MonoTomo are suggested for further exploration.

Semen quality of young men in Switzerland: a nationwide cross-sectional population-based study

BACKGROUND

Sperm counts have been steadily decreasing over the past five decades with regional differences in the Western world. The reasons behind these trends are complex, but numerous insights indicate that environmental and lifestyle factors are important players.

OBJECTIVE

To evaluate semen quality and male reproductive health in Switzerland.

MATERIALS AND METHODS

A nationwide cross-sectional study was conducted on 2523 young men coming from all regions of Switzerland, recruited during military conscription. Semen volume, sperm concentration, motility, and morphology were analyzed. Anatomy of the genital area and testicular volume was recorded. Testicular cancer incidence rates in the general population were retrieved from Swiss regional registries.

RESULTS

Median sperm concentration adjusted for period of sexual abstinence was 48 million/mL. Comparing with the 5th percentile of the WHO reference values for fertile men, 17% of men had sperm concentration below 15 million/mL, 25% had less than 40% motile spermatozoa, and 43% had less than 4% normal forms. Disparities in semen quality among geographic regions, urbanization rates, and linguistic areas were limited. A larger proportion of men with poor semen quality had been exposed in utero to maternal smoking. Furthermore, testicular cancer incidence rates in the Swiss general population increased significantly between 1980 and 2014.

DISCUSSION

For the first time, a systematic sampling among young men has confirmed that semen quality is affected on a national level. The median sperm concentration measured is among the lowest observed in Europe. No specific geographical differences could be identified. Further studies are needed to determine to what extent the fertility of Swiss men is compromised and to evaluate the impact of environmental and lifestyle factors.

CONCLUSION

A significant proportion of Swiss young men display suboptimal semen quality with only 38% having sperm concentration, motility, and morphology values that met WHO semen reference criteria.

A robust approach to ab initio cryo-electron microscopy initial volume determination

Structural information from macromolecules provides key insights into the way complexes perform their biological functions. The reconstruction process leading to the final three-dimensional (3D) map is iterative and requires an initial volume to prime the refinement procedure. Particle images are aligned to this first reference and subsequently a new map is calculated from these particles. The accurate determination of an ab initio initial volume is still a challenging and open problem in cryo-electron microscopy (cryo-EM). Different algorithms are available to estimate an initial volume from the dataset. Some of these methods provide multiple candidate initial maps and users looking for robustness typically run different approaches. In this case, users arbitrarily evaluate the different obtained candidate maps, as we lack robust methods to objectively assess the accuracy of initial references. This workflow is subjective and error-prone preventing implementation of high-throughput data processing procedures. In this work, we present a robust method to determine the best initial map or maps from a set of ab initio initial volumes obtained from one or multiple different approaches. The method is based on evaluating multiple small subsets of candidate initial volumes and particle images through reference-based 3D classifications. Obtained 3D classes of accurate initial maps will result majoritarian and the respective attracted particles will be aligned with high angular accuracies. We have tested the proposed approach with structurally homogeneous and heterogeneous datasets providing satisfactory results with both type of data.

Image Processing Protocol for the Analysis of the Diffusion and Cluster Size of Membrane Receptors by Fluorescence Microscopy

Particle tracking on a video sequence and the posterior analysis of their trajectories is nowadays a common operation in many biological studies. Using the analysis of cell membrane receptor clusters as a model, we present a detailed protocol for this image analysis task using Fiji (ImageJ) and Matlab routines to: 1) define regions of interest and design masks adapted to these regions; 2) track the particles in fluorescence microscopy videos; 3) analyze the diffusion and intensity characteristics of selected tracks. The quantitative analysis of the diffusion coefficients, types of motion, and cluster size obtained by fluorescence microscopy and image processing provides a valuable tool to objectively determine particle dynamics and the consequences of modifying environmental conditions. In this article we present detailed protocols for the analysis of these features. The method described here not only allows single-molecule tracking detection, but also automates the estimation of lateral diffusion parameters at the cell membrane, classifies the type of trajectory and allows complete analysis thus overcoming the difficulties in quantifying spot size over its entire trajectory at the cell membrane.

Abstract P6-01-05: Detection of HER2 positive tumor cells using functionalized iron oxide nanoparticles

Background: Iron oxide nanoparticles (NPs) have been used for a variety of in-vivo and ex-vivo applications within the biomedical sciences. Moreover, when intended for clinical in-vivo applications, NPs need to meet rigorous requirements to ensure safety as well as bio-functionality including blood circulation time and specificity for cellular targets. PrecisonMRX® NPs are extensively characterized superparamagnetic NPs composed of a 25nm magnetite cores that are currently employed in a variety of in-vivo applications including non-invasive/in vivo diagnosis of cancer, Magnetic Particle Imaging, MRI, and magnetic hyperthermia.

Objective: Here we report on the extensive pre-clinical development and functionality of antibody (Herceptin)-conjugated NPs for in-vivo and ex-vivo detection of HER2+ tumor cells by Magnetic Relaxometry (MRX).

Results: We observed: 1) specific binding and detection of HER2 positive tumor cells in-vitro; 2) specific detection of HER2+ tumors in mice; 3) binding and amplitude of magnetic signal to be proportional to the level of HER2 expression in-vitro and in-vivo; 4) the nanoconstruct remains stable in circulation; 5) the particles do not induce a pro-inflammatory response nor activate complement; 6) the particles are biodegradable; and do not induce acute or delayed signs of morbidity in mice.

Conclusion: Precision MRX® nanoparticles offer great clinical promise including the in- vivo detection of tumor cells by magnetic relaxometry. Given the stability and safety of these NPs, our pre-clinical results support progressing to clinical testing. A first-in human ex-vivo clinical research study design and strategy will be discussed.

Citation Format: Bischoff FZ, Mathieu K, Vargas J, Pang L, Kulp AM, Dewing A, Liu X, Bast RC, Hazle J, Zhang M. Detection of HER2 positive tumor cells using functionalized iron oxide nanoparticles [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-01-05.

Serotonin induces or inhibits neuritic regeneration of leech CNS neurons depending on neuronal identity

Recovery of motor function after central nervous system (CNS) injury is dependent on the regeneration capacity of the nervous system, which is a multifactorial process influenced, among other things, by the role of neuromodulators such as serotonin. The neurotransmitter serotonin can promote neuronal regeneration but there are also reports of it causing restriction, so it is important to clarify these divergent findings in order to understand the direct scope and side effects of potential pharmacological treatments. We evaluated the effect of serotonin on the extent of neuritic outgrowth and morphology of three different neuronal types in the leech Haementeria officinalis during their regeneration in vitro: Retzius interneurons (Rz), annulus erector (AE) motoneurons, and anterolateral number 1 (AL1) CNS neurons. Neurons were isolated and cultured in L15 medium, with or without serotonin. Growth parameters were registered and quantified, and observed differences were analyzed. The addition of serotonin was found to induce AL1 neurons to increase their average growth dramatically by 8.3-fold (P=0.02; n=5), and to have no clear effect on AE motoneurons (P=0.44; n=5). For Rz interneurons, which normally do not regenerate their neurites, the addition of concanavaline-A causes substantial growth, which serotonin was found to inhibit on average by 98% (P=0.02; n=5). The number of primary neurites and their branches were also affected. These results reveal that depending on the neuronal type, serotonin can promote, inhibit, or have no effect on neuronal regeneration. This suggests that after CNS injury, non-specific pharmacological treatments affecting serotonin may have different effects on different neuronal populations.

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed.

Blind estimation of DED camera gain in Electron Microscopy

The introduction of Direct Electron Detector (DED) videos in the Electron Microscope field has boosted Single Particle Analysis to a point in which it is currently considered to be a key technique in Structural Biology. In this article we introduce an approach to estimate the DED camera gain at each pixel from the movies themselves. This gain is needed to have the set of recorded frames into a coherent gray level range, homogeneous over the whole image. The algorithm does not need any other input than the DED movie itself, being capable of providing an estimate of the camera gain image, helping to identify dead pixels and cases of incorrectly calibrated cameras. We propose the algorithm to be used either to validate the experimentally acquired gain image (for instance, to follow its possible change over time) or to verify that there is no residual gain image after experimentally correcting for the camera gain. We show results for a number of DED camera models currently in use (DE, Falcon II, Falcon 3, and K2).

PGE2 induces apoptosis of hepatic stellate cells and attenuates liver fibrosis in mice by downregulating miR-23a-5p and miR-28a-5p

MicroRNAs (miRNAs), small noncoding RNAs modulating messenger RNA (mRNA) and protein expression, have emerged as key regulatory molecules in chronic liver diseases, whose end stage is hepatic fibrosis, a major global health burden. Pharmacological strategies for prevention or treatment of hepatic fibrosis are still limited, what makes it necessary to establish a better understanding of the molecular mechanisms underlying its pathogenesis. In this context, we have recently shown that cyclooxygenase-2 (COX-2) expression in hepatocytes restricts activation of hepatic stellate cells (HSCs), a pivotal event in the initiation and progression of hepatic fibrosis. Here, we evaluated the role of COX-2 in the regulation of a specific set of miRNAs on a mouse model of CCl₄ and bile duct ligation (BDL)-induced liver fibrosis. Our results provide evidence that COX-2 represses miR-23a-5p and miR-28-5p expression in HSC. The decrease of miR-23a-5p and miR-28-5p expression promotes protection against fibrosis by decreasing the levels of pro-fibrogenic markers α-SMA and COL1A1 and increasing apoptosis of HSC. Moreover, we demonstrate that serum levels of miR-28-5p are decreased in patients with chronic liver disease. These results suggest a protective effect exerted by COX-2-derived prostanoids in the process of hepatofibrogenesis.

Foil-hole and data image quality assessment in 3DEM: Towards high-throughput image acquisition in the electron microscope

Automatic or semiautomatic data collection approaches on a transmission electron microscope (TEM) for Single Particle Analysis, capable of acquiring large datasets composed of only high quality images, are of great importance to obtain 3D density maps with the highest resolution possible. Typically, this task is performed by an experienced microscopist, who manually decides to keep or discard images according to subjective criteria. Therefore, this methodology is slow, intensive in human work and subjective. In this work, we propose a method to automatically or semiautomatically perform this image selection task. The approach is based on some simple, fast and effective image quality descriptors, which can be computed during acquisition, to characterize foil-hole and data images. The proposed approach has been used to evaluate the quality of different datasets consisting of foil-hole and data images obtained with a FEI Titan Krios electron microscope. The results show that the proposed method is very effective evaluating the quality of foil-hole and data images, as well as predicting the quality of the data images from the foil-hole images.

Proton Distribution Radii of ^{12-19}C Illuminate Features of Neutron Halos

Proton radii of ^{12-19}C densities derived from first accurate charge changing cross section measurements at 900A  MeV with a carbon target are reported. A thick neutron surface evolves from ∼0.5  fm in ^{15}C to ∼1  fm in ^{19}C. The halo radius in ^{19}C is found to be 6.4±0.7  fm as large as ^{11}Li. Ab initio calculations based on chiral nucleon-nucleon and three-nucleon forces reproduce the radii well.

Local analysis of strains and rotations for macromolecular electron microscopy maps

Macromolecular complexes perform their physiological functions by local rearrangements of their constituents and biochemically interacting with their reaction partners. These rearrangements may involve local rotations and the induction of local strains causing different mechanical efforts and stretches at the different areas of the protein. The analysis of these local deformations may reveal important insight into the way proteins perform their tasks. In this paper we introduce a method to perform this kind of local analysis using Electron Microscopy volumes in a fully objective and automatic manner. For doing so, we exploit the continuous nature of the result of an elastic image registration using B-splines as its basis functions. We show that the results obtained by the new automatic method are consistent with previous observations on these macromolecules.

Denoising of high-resolution single-particle electron-microscopy density maps by their approximation using three-dimensional Gaussian functions

Cryo-electron microscopy (cryo-EM) of frozen-hydrated preparations of isolated macromolecular complexes is the method of choice to obtain the structure of complexes that cannot be easily studied by other experimental methods due to their flexibility or large size. An increasing number of macromolecular structures are currently being obtained at subnanometer resolution but the interpretation of structural details in such EM-derived maps is often difficult because of noise at these high-frequency signal components that reduces their contrast. In this paper, we show that the method for EM density-map approximation using Gaussian functions can be used for denoising of single-particle EM maps of high (typically subnanometer) resolution. We show its denoising performance using simulated and experimental EM density maps of several complexes.

Particle alignment reliability in single particle electron cryomicroscopy: a general approach

Electron Microscopy is reaching new capabilities thanks to the combined effect of new technologies and new image processing methods. However, the reconstruction process is still complex, requiring many steps and elaborated optimization procedures. Therefore, the possibility to reach a wrong structure exists, justifying the need of robust statistical tests. In this work, we present a conceptually simple alignment test, which does not require tilt-pair images, to evaluate the alignment consistency between a set of projection images with respect to a given 3D density map. We test the approach on a number of problems in 3DEM, especially the ranking and evaluation of initial 3D volumes and high resolution 3D maps, where we show its usefulness in providing an objective evaluation for maps that have recently been subject to a strong controversy in the field. Additionally, this alignment statistical test can be linked to the early stages of structure solving of new complexes, streamlining the whole process.

First Report of Bacterial Panicle Blight of Rice Caused by Burkholderia gladioli in Ecuador

Burkholderia gladioli is one of the causal agents of bacterial panicle blight of rice (BPB). Although B. glumae is considered the main pathogen responsible of BPB, B. gladioli can also cause this disease in rice (3). B. gladioli is also of clinical importance because of the ability of some strains to cause respiratory infections in humans (2). Symptoms in rice plantations of Palestina city, like upright panicles with grayish-straw color, grain rot, and vain grains were observed in July 2013, although similar symptoms were first noticed as early as 2012 in other regions of Ecuador. Since then, similar symptomatology has been reported by farmers in coastal provinces, possibly affecting 75% of the crops. One of the causal agents was recently identified as B. glumae but other bacteria were observed in infected rice (1). Plants showing BPB symptoms were collected from Palestina and bacteria were isolated from panicle twigs using the semi selective SPG agar (KH₂PO₄ 1.3 g, Na₂HPO₄ 1.2 g, (NH₄)₂SO₄ 5 g, MgSO₄·7H₂O 0.25 g, Na₂MoO₄·2H₂O 24 mg, EDTA-Fe 10 mg, L-cystine 10 μg, D-sorbitol 10 g, pheneticillin potassium 50 mg, ampicillin sodium 10 mg, cetrimide 10 mg, methyl violet 1 mg, phenol red 20 mg, agar 15 g/liter distilled water). Colonies were then transferred to PDA. Presumptive B. gladioli colonies were classified into two groups according to their color on PDA. Colonies from group one (six strains) were dull yellow, whereas those from group two (two strains) were olive colored. Both groups produced fluorescent colonies with smooth, shiny surfaces on PDA. All cells were gram-negative rods with the following dimensions: 0.8 to 2.0 × 0.4 to 0.6 μm (group one) or 1.5 to 2.5 × 0.4 to 0.7 μm (group two). All colonies were subjected to biochemical tests (API 20NE) and shared a 99% or higher similarity (APIWEB) with B. gladioli. To confirm identity, genomic DNA was extracted (gDNA extraction kit from Invitrogen) and a portion of the 16s rDNA was amplified by PCR using the primers 536F: 5'-GTGCCAGCMGCCGCGGTAATAC-3' and 1492R: 5'-GGTTACCTTGTTACGACTT-3' followed by sequencing. Sequences of group one strains shared 100% similarity with B. gladioli strain OM1 (GenBank Accession No. EU678361) while the sequences from group two strains were 100% similar to B. gladioli strain BgHL-01 (JX566503). Sequences of the Ecuadorian strains were deposited into NCBI GenBank (group one: KF669879 to KF669882, KF669884, and KF669885; group two: KF669883 and KF669886). Pathogenicity was confirmed by submerging rice seeds in a cell suspension with 10⁸ CFU of the pathogen for 24 h. Seeds were germinated at 28°C and about 70% RH on autoclaved peat. Inoculated seeds yielded plants with BPB symptoms 6 days after planting. Re-isolated strains shared a 99.9% similarity with B. gladioli by APIWEB. To the best of our knowledge, this is the first report of B. gladioli as a rice pathogen in Ecuador. References: (1) C. Riera-Ruiz et al. Plant Dis. 98:988, 2014. (2) C. Segonds et al. J. Clin. Microbiol. 47:1510, 2009. (3) H. Ura et al. J. Gen. Plant Pathol. 72:98, 2006.

Proton radii of (12-17)B define a thick neutron surface in ¹⁷B

The first determination of radii of point proton distribution (proton radii) of (12-17)B from charge-changing cross sections (σ(CC)) measurements at the FRS, GSI, Darmstadt is reported. The proton radii are deduced from a finite-range Glauber model analysis of the σ(CC). The radii show an increase from ¹³B to ¹⁷B and are consistent with predictions from the antisymmetrized molecular dynamics model for the neutron-rich nuclei. The measurements show the existence of a thick neutron surface with neutron-proton radius difference of 0.51(0.11) fm in ¹⁷B.