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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.

Electron tomography is a technique to obtain three-dimensional structural information of samples. However, the technique is limited by shifts occurring during acquisition that need to be corrected before the reconstruction process. In 2009, we proposed an approach for post-acquisition alignment of tilt series images. This approach was marker-free, based on patch tracking and integrated in free software. Here, we present improvements to the method to make it more reliable, stable and accurate. In addition, we modified the image formation model underlying the alignment procedure to include different deformations occurring during acquisition. We propose a new way to correct these computed deformations to obtain reconstructions with reduced artifacts. The new approach has demonstrated to improve the quality of the final 3D reconstruction, giving access to better defined structures for different transmission electron tomography methods: resin embedded STEM-tomography and cryo-TEM tomography. The method is freely available in TomoJ software.

Objectives: The RNA epitranscriptomic modification known as N6 -methyladenosine (m 6 A) represents a novel mechanism of gene regulation that is poorly understood in human autoimmune diseases. Our research explores the role of this RNA m 6 A modification in salivary gland epithelial cells (SGEC) and its impact on the pathogenesis of Sjögren's disease (SjD)., Methods: SGECs from SjD patients and controls were analysed for m 6 A writers METTL3 and METTL14 expression using RNA-seq, quantitative PCR and immunohistochemistry. Functional assays assessed the impact of METTL3 knockdown or pharmacological inhibition on proinflammatory gene expression and immune cell interactions (using transwell and coculture systems). Mechanistic studies examined METTL3-mediated m 6 A modifications in double-stranded RNA (dsRNA) formation through immunofluorescence. Unsupervised clustering identified patterns of interferon activation in salivary glands and their correlation with m 6 A writers., Results: METTL3 and METTL14 were elevated in SGEC from SjD patients in comparison to controls. Paradoxically, inhibiting METTL3 increased proinflammatory gene expression, enhancing SGEC's ability to attract immune cells and activate B cells. Conversely, inhibiting the eraser FTO had the opposite effect. METTL3-mediated m 6 A modifications prevented dsRNA formation and IFN signalling activation. SGEC from SjD showed insufficient METTL3 upregulation compared with controls in response to inflammatory triggers, indicating a limited capacity to regulate the inflammatory response. SjD patients with elevated disease activity and higher interferon signature exhibit reduced METTL3 expression., Conclusions: Impairment of m 6 A modifications in SGEC in response to inflammatory triggers favour the formation of dsRNA, potentially amplifying the interferon loop and contributing to SjD pathogenesis., Competing Interests: Competing interests: XM received an honorarium for consultancy advice on Sjögren’s disease from Argenx, BMS, GSK, Novartis and Otsuka. The rest of the authors declare that they have no relevant conflicts of interest., (© Author(s) (or their employer(s)) 2024. No commercial re-use. See rights and permissions. Published by BMJ on behalf of EULAR.)

Here, we present a protocol for multivariate quantitative-image-based cytometry (QIBC) analysis by fluorescence microscopy of asynchronous adherent cells. We describe steps for the preparation, treatment, and fixation of cells, sample staining, and imaging for QIBC. We then detail image analysis with our open source Fiji script developed for QIBC and present multiparametric data visualization. Our QIBC Fiji script integrates modern artificial-intelligence-based tools, applying deep learning, for robust automated nuclei segmentation with minimal user adjustments, a major asset for efficient QIBC analysis. For complete details on the use and execution of this protocol, please refer to Besse et al. (2023). 1 ., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Motivation: FIB-SEM (Focused Ion Beam-Scanning Electron Microscopy) is a technique to generate 3D images of samples up to several microns in depth. The principle is based on the alternate use of SEM to image the surface of the sample (a few nanometers thickness) and of FIB to mill the surface of the sample a few nanometers at the time. In this way, huge stacks of images can thus be acquired.Although this technique has proven useful in imaging biological systems, the presence of some visual artifacts (stripes due to sample milling, detector saturation, charge effects, focus or sample drift, etc.) still raises some challenges for image interpretation and analyses., Results: With the aim of meeting these challenges, we developed a freeware (SEM3De) that either corrects artifacts with state-of-the-art approaches or, when artifacts are impossible to correct, enables the replacement of artifactual slices by an in-painted image created from adjacent non-artifactual slices. Thus, SEM3De improves the overall usability of FIB-SEM acquisitions., Availability and Implementation: SEM3De can be downloaded from https://sourceforge.net/projects/sem3de/ as a plugin for ImageJ., Competing Interests: None declared., (© The Author(s) 2023. Published by Oxford University Press.)

Background: Postpartum care is crucial for addressing conditions associated with severe maternal morbidity and mortality. Examination of programs that affect these outcomes for women at high risk, including disparate populations, is needed., Objective: This study aimed to examine whether a postpartum navigation program decreases all-cause 30-day postpartum hospitalizations and hospitalizations because of severe maternal morbidity identified using the US Centers for Disease Control and Prevention guidelines. The effect of this program was explored across patient demographics, including race and ethnicity., Study Design: This was a retrospective cohort study that used health records of women who delivered at 3 large hospitals in the New York metropolitan area (Queens and Long Island) between April 2020 and November 2021 and who were at high risk of severe maternal morbidity. The incidence rates of 30-day postpartum all-cause hospitalization and hospitalization because of severe maternal morbidity were compared between women who were and were not enrolled in a novel postpartum transitional care management program. Navigation included standardized assessments, development of care plans, clinical management, and connection to clinical and social services that would extend beyond the postpartum period. Because the program prioritized enrolling women of the greatest risk, the risk-adjusted incidence was estimated using multivariate Poisson regression and stratified across patient demographics., Results: Patient health records of 5819 women were included for analysis. Of note, 5819 of 19,258 deliveries (30.2%) during the study period were identified as having a higher risk of severe maternal morbidity. This was consistent with the incidence of high-risk pregnancies for tertiary hospitals in the New York metropolitan area. The condition most identified for risk of severe maternal morbidity at the time of delivery was hypertension (3171/5819 [54.5%]). The adjusted incidence of all-cause rehospitalization was 20% lower in enrollees than in nonenrollees (incident rate ratio, 0.80; 95% confidence interval, 0.67-0.95). Rehospitalization was decreased the most among Black women (incident rate ratio, 0.57; 95% confidence interval, 0.42-0.80). The adjusted incidence of rehospitalization because of indicators of severe maternal morbidity was 56% lower in enrollees than in nonenrollees (incident rate ratio, 0.44; 95% confidence interval, 0.24-0.77). Furthermore, it decreased most among Black women (incident rate ratio, 0.23; 95% confidence interval, 0.07-0.73)., Conclusion: High-risk medical conditions at the time of delivery increased the risk of postpartum hospitalization, including hospitalizations because of severe maternal morbidity. A postpartum navigation program designed to identify and resolve clinical and social needs reduced postpartum hospitalizations and racial disparities with hospitalizations. Hospitals and healthcare systems should adopt this type of care model for women at high risk of severe maternal morbidity. Cost analyses are needed to evaluate the financial effect of postpartum navigation programs for women at high risk of severe maternal morbidity or mortality, which could influence reimbursement for these types of services. Further evidence and details of novel postpartum interventional models are needed for future studies., (Copyright © 2023 Elsevier Inc. All rights reserved.)

ASC-G4 is an algorithm for the calculation of the advanced structural characteristics of G-quadruplexes (G4). It allows the unambiguous determination of the intramolecular G4 topology, based on the oriented strand numbering. It also resolves the ambiguity in the determination of the guanine glycosidic configuration. With this algorithm, we showed that the use of the C3' or C5' atoms to calculate the groove width in G4 is more appropriate than the P atoms and that the groove width does not always reflect the space available within the groove. For the latter, the minimum groove width is more appropriate. The application of ASC-G4 to 207 G4 structures guided the choices made for the calculations. A website based on ASC-G4 (http://tiny.cc/ASC-G4) was created, where the user uploads his G4 structure and gets its topology, the types of its loops and their lengths, the presence of snapbacks and bulges, the distribution of guanines in the tetrads and strands, the glycosidic configuration of these guanines, their rise, the groove widths, the minimum groove widths, the tilt and twist angles, the backbone dihedral angles, etc. It also provides a large number of atom-atom and atom-plane distances that are relevant to evaluating the quality of the structure., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

A variety of novel disubstituted 2-(alknyl, aryl and arylamine)-6-alkynylpyrazolo[1,5- a ]pyrimidine derivatives was prepared via sequential site-selective cross-coupling reactions from 2,6-dibromopyrazolo[1,5- a ]pyrimidine 3. The regio-controlled Sonogashira-type coupling of 3 with a wide range of terminal alkynes proceeded smoothly with excellent selectivity in favor of the C6-position through careful adjustment of the coupling conditions, followed by the subsequent introduction of alkynyl, aryl or arylamine groups at the C2-position via the Sonogashira, Suzuki-Miyaura and Buchwald-Hartwig coupling reactions, respectively. These promising results allow for further use and diversification of the chemically and biologically interesting pyrazolo[1,5- a ]pyrimidine scaffold. In addition, computational studies were conducted to provide explanations for the origin of regioselectivity.

The MITF transcription factor and the RAS/RAF/MEK/ERK pathway are two interconnected main players in melanoma. Understanding how MITF activity is regulated represents a key question since its dynamic modulation is involved in the phenotypic plasticity of melanoma cells and their resistance to therapy. By investigating the role of ARAF in NRAS-driven mouse melanoma through mass spectrometry experiments followed by a functional siRNA-based screen, we unexpectedly identified MITF as a direct ARAF partner. Interestingly, this interaction is conserved among the RAF protein kinase family since BRAF/MITF and CRAF/MITF complexes were also observed in the cytosol of NRAS-mutated mouse melanoma cells. The interaction occurs through the kinase domain of RAF proteins. Importantly, endogenous BRAF/MITF complexes were also detected in BRAF-mutated human melanoma cells. RAF/MITF complexes modulate MITF nuclear localization by inducing an accumulation of MITF in the cytoplasm, thus negatively controlling its transcriptional activity. Taken together, our study highlights a new level of regulation between two major mediators of melanoma progression, MITF and the MAPK/ERK pathway, which appears more complex than previously anticipated., (© 2022. The Author(s).)

The α-β tubulin heterodimer undergoes subtle conformational changes during microtubule assembly. These can be modulated by external factors, whose effects on microtubule structure can be characterized on 2D views obtained by cryo-electron microscopy. Analysis of microtubule images is facilitated if they are straight enough to interpret and filter their image Fourier transform, which provide useful information concerning the arrangement of tubulin molecules inside the microtubule lattice. Here, we describe the use of the TubuleJ software to straighten microtubules and determine their lattice parameters. Basic 3D reconstructions can be performed to evaluate the relevance of these parameters. This approach can be used to analyze the effects of nucleotide analogues, drugs or MAPs on microtubule structure, or to select microtubule images prior to high-resolution 3D reconstructions., Competing Interests: Competing interestsTubuleJ was deposited to the Agency for the Protection of programs (APP) under the code number IDDN.FR.001.240023.000.S.P.2011.000.21000., (Copyright © The Authors; exclusive licensee Bio-protocol LLC.)

Electron tomography is a technique to obtain three-dimensional structural information of samples. However, the technique is limited by shifts occurring during acquisition that need to be corrected before the reconstruction process. In 2009, we proposed an approach for post-acquisition alignment of tilt series images. This approach was marker-free, based on patch tracking and integrated in free software. Here, we present improvements to the method to make it more reliable, stable and accurate. In addition, we modified the image formation model underlying the alignment procedure to include different deformations occurring during acquisition. We propose a new way to correct these computed deformations to obtain reconstructions with reduced artifacts. The new approach has demonstrated to improve the quality of the final 3D reconstruction, giving access to better defined structures for different transmission electron tomography methods: resin embedded STEM-tomography and cryo-TEM tomography. The method is freely available in TomoJ software., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2020 The Author(s).)

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., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2019 Published by Elsevier Inc.)

Background: Due to the presence of high noise level in tomographic series of energy filtered transmission electron microscopy (EFTEM) images, alignment and 3D reconstruction steps become so difficult. To improve the alignment process which will in turn allow a more accurate and better three dimensional tomography reconstructions, a preprocessing step should be applied to the EFTEM data series., Results: Experiments with real EFTEM data series at low SNR, show the feasibility and the accuracy of the proposed denoising approach being competitive with the best existing methods for Poisson image denoising. The effectiveness of the proposed denoising approach is thanks to the use of a nonparametric Bayesian estimation in the Contourlet Transform with Sharp Frequency Localization Domain (CTSD) and variance stabilizing transformation (VST). Furthermore, the optimal inverse Anscome transformation to obtain the final estimate of the denoised images, has allowed an accurate tomography reconstruction., Conclusion: The proposed approach provides qualitative information on the 3D distribution of individual chemical elements on the considered sample., Competing Interests: Competing interestsThe authors declare that they have no competing interests., (© The Author(s) 2019.)

A central challenge in scanning transmission electron microscopy (STEM) is to reduce the electron radiation dosage required for accurate imaging of 3D biological nano-structures. Methods that permit tomographic reconstruction from a reduced number of STEM acquisitions without introducing significant degradation in the final volume are thus of particular importance. In random-beam STEM (RB-STEM), the projection measurements are acquired by randomly scanning a subset of pixels at every tilt view. In this work, we present a tailored RB-STEM acquisition-reconstruction framework that fully exploits the compressed sensing principles. We first demonstrate that RB-STEM acquisition fulfills the "incoherence" condition when the image is expressed in terms of wavelets. We then propose a regularized tomographic reconstruction framework to recover volumes from RB-STEM measurements. We demonstrate through simulations on synthetic and real projection measurements that the proposed framework reconstructs high-quality volumes from strongly downsampled RB-STEM data and outperforms existing techniques at doing so. This application of compressed sensing principles to STEM paves the way for a practical implementation of RB-STEM and opens new perspectives for high-quality reconstructions in STEM tomography., (Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.)

A new multi-platform freeware has been developed for the processing and reconstruction of scanning multi-technique X-ray imaging and tomography datasets. The software platform aims to treat different scanning imaging techniques: X-ray fluorescence, phase, absorption and dark field and any of their combinations, thus providing an easy-to-use data processing tool for the X-ray imaging user community. A dedicated data input stream copes with the input and management of large datasets (several hundred GB) collected during a typical multi-technique fast scan at the Nanoscopium beamline and even on a standard PC. To the authors' knowledge, this is the first software tool that aims at treating all of the modalities of scanning multi-technique imaging and tomography experiments.

Chemical imaging offers extensive possibilities for better understanding of biological systems by allowing the identification of chemical components at the tissue, cellular, and subcellular levels. In this review, we introduce modern methods for chemical imaging that can be applied to biological samples. This work is mainly addressed to the biological sciences community and includes the bases of different technologies, some examples of its application, as well as an introduction to approaches on combining multimodal data., (Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Since scanning transmission electron microscopy can produce high signal-to-noise ratio bright-field images of thick (≥500 nm) specimens, this tool is emerging as the method of choice to study thick biological samples via tomographic approaches. However, in a convergent-beam configuration, the depth of field is limited because only a thin portion of the specimen (from a few nanometres to tens of nanometres depending on the convergence angle) can be imaged in focus. A method known as through-focal imaging enables recovery of the full depth of information by combining images acquired at different levels of focus. In this work, we compare tomographic reconstruction with the through-focal tilt-series approach (a multifocal series of images per tilt angle) with reconstruction with the classic tilt-series acquisition scheme (one single-focus image per tilt angle). We visualised the base of the flagellum in the protist Trypanosoma brucei via an acquisition and image-processing method tailored to obtain quantitative and qualitative descriptors of reconstruction volumes. Reconstructions using through-focal imaging contained more contrast and more details for thick (≥500 nm) biological samples., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

The characterization of biological and inorganic materials by determining their three-dimensional structure in conditions closer to their native state is a major challenge of technological research. Environmental scanning electron microscopy (ESEM) provides access to the observation of hydrated samples in water environments. Here, we present a specific device for ESEM in the scanning transmission electron microscopy mode, allowing the acquisition of tilt-series suitable for tomographic reconstructions. The resolution which can be obtained with this device is first determined. Then, we demonstrate the feasibility of tomography on wet materials. The example studied here is hydrophilic mesoporous silica (MCM-41). Finally, the minimum thickness of water which can be detected is calculated from Monte Carlo simulations and compared with the resolution expected in the tomograms.

Electron tomography is becoming one of the most used methods for structural analysis at nanometric scale in biological and materials sciences. Combined with chemical mapping, it provides qualitative and semiquantitative information on the distribution of chemical elements on a given sample. Due to the current difficulties in obtaining three-dimensional (3D) maps by energy-filtered transmission electron microscopy (EFTEM), the use of 3D chemical mapping has not been widely adopted by the electron microscopy community. The lack of specialized software further complicates the issue, especially in the case of data with a low signal-to-noise ratio (SNR). Moreover, data interpretation is rendered difficult by the absence of efficient segmentation tools. Thus, specialized software for the computation of 3D maps by EFTEM needs to include optimized methods for image series alignment, algorithms to improve SNR, different background subtraction models, and methods to facilitate map segmentation. Here we present a software package (EFTEM-TomoJ, which can be downloaded from http://u759.curie.fr/fr/download/softwares/EFTEM-TomoJ), specifically dedicated to computation of EFTEM 3D chemical maps including noise filtering by image reconstitution based on multivariate statistical analysis. We also present an algorithm named BgART (for background removing algebraic reconstruction technique) allowing the discrimination between background and signal and improving the reconstructed volume in an iterative way.

We present here the application of the energy-filtered transmission electron microscopy (EFTEM) in the tomographic mode to determine the precise 3D distribution of nitrogen within nitrogen-doped carbon nanotubes (N-CNTs). Several tilt series of energy-filtered images were acquired on the K ionization edges of carbon and nitrogen on a multiwalled N-CNT containing a high amount of nitrogen. Two tilt series of carbon and nitrogen 2D maps were then calculated from the corresponding energy-filtered images by using a proper extraction procedure of the chemical signals. Applying iterative reconstruction algorithms provided two spatially correlated C and N elemental-selective volumes, which were then simultaneously analyzed with the shape-sensitive reconstruction deduced from Zero-Loss recordings. With respect to the previous findings, crucial information obtained by analyzing the 3D chemical maps was that, among the two different kind of arches formed in these nanotubes (transversal or rounded ones depending on their morphology), the transversal arches contain more nitrogen than do the round ones. In addition, a detailed analysis of the shape-sensitive volume allowed the observation of an unexpected change in morphology along the tube axis: close to the round arches (with less N), the tube is roughly cylindrical, whereas near the transversal ones (with more N), its shape changes to a prism. This relatively new technique is very powerful in the material science because it combines the ability of the classical electron tomography to solve 3D structures and the chemical selectivity of the EFTEM imaging.

Membrane proteins are often present in low amounts in cells. Their function can be modulated by interactions with other proteins. Moreover, these complexes can be transiently formed, thus making them difficult to be isolated and to be purified. One way to overcome these difficulties is to visualize these complexes in situ in the cells. For such purpose, electron microscopy coupled to tomography is a promising approach that has been developed over the last decades.Mitochondria are a good example of organelles where many membrane proteins form different functional complexes within the outer and the inner membranes. The latter is either close to the former or projects within the matrix to form cristae. Structure of these cristae involves different proteins and can vary from lamellar to tubular forms in normal mitochondria. In pathological conditions, other mitochondrial morphologies have been described, for instance, vesicular structures for inner boundary membrane have been observed.

Background: Tilt series are commonly used in electron tomography as a means of collecting three-dimensional information from two-dimensional projections. A common problem encountered is the projection alignment prior to 3D reconstruction. Current alignment techniques usually employ gold particles or image derived markers to correctly align the images. When these markers are not present, correlation between adjacent views is used to align them. However, sequential pairwise correlation is prone to bias and the resulting alignment is not always optimal., Results: In this paper we introduce an algorithm to find regions of the tilt series which can be tracked within a subseries of the tilt series. These regions act as landmarks allowing the determination of the alignment parameters. We show our results with synthetic data as well as experimental cryo electron tomography., Conclusion: Our algorithm is able to correctly align a single-tilt tomographic series without the help of fiducial markers thanks to the detection of thousands of small image patches that can be tracked over a short number of images in the series.

Centrioles are components of the centrosome, which is present in most eukaryotic cells (from protozoa to mammals). They organize the microtubule skeleton during interphase and the mitotic spindle during cell division. In ciliate cells, centrioles form basal bodies that are involved in cellular motility. Despite their important roles in biology, the detailed structure of centrioles remains obscure. This work contributes to a more complete model of centriole structure. The authors used electron tomography of isolated centrosomes from the human lymphoblast KE37 to explore the details of subdistal appendages and centriole lumen organization in mother centrioles. Their results reveal that each of the nine subdistal appendages is composed of two halves (20 nm diameter each) fused in a 40 nm tip that extends 100 nm from where it anchors to microtubules. The centriole lumen is filled at the distal domain by a 45 nm periodic stack of rings. Each ring has a 30 nm diameter, is 15 nm thick, and appears to be tilted at 53 degrees perpendicular to the centriole axis. The rings are anchored to microtubules by arms. Based on their results, the authors propose a model of the mother centriole distal structure., (Copyright 2008 Wiley-Liss, Inc.)

Objective: We assessed a new estradiol (E2) immunoassay on the Architect-i2000 (Abbott Laboratories) for monitoring ovulation stimulation for IVF-ET and re-establishing clinical cut-off points. The method has been modified to improve E2 measurements especially at normal and low concentrations., Design and Method: E2 was determined for 552 samples, from 83 women, presenting normal follicular status and undergoing 100 cycles of IVF treatment. We assessed the value of this assay for down-regulation of E2 concentration limit using gonadoliberin-releasing hormone agonist (GnRHa), and monitoring of the ovarian hyperstimulation, expected range of E2 per mature follicle prior to the administration of exogenous hCG and day 3 concentration limit. We compared results with our routine method (E2-6II Advia-Centaur; Siemens-Diagnostics) for which decision-making values were known., Results: Considering E2 concentrations obtained with the new Architect-i2000 assay for patients treated with GnRHa for 2 weeks, the cutoff-point for ovarian down-regulation should be set down at 110 pmol/L to maintain 100% of sensitivity. Considering day 3 concentration limit determination, results were not significantly different from those obtained with our routine method. The mean E2 values per mature follicle fell into the range generally expected., Conclusion: E2 determination with the new E2 Architect-i2000 assay could be used to monitor ovulation, in patients undergoing IVF-ET, in combination with transvaginal ultrasound.

Unlabelled: Cylindroma of the head and neck, known as "cystic adenoid carcinoma", begins more often at the expense of the all glandular structures of ectodermic origin, in particularly at the minor and principal salivary glands. However the laryngeal localization is rare, by way of the low distribution of the accessory glands at this level., Objective: To study the clinical characteristics; anatomo-pathologic, treatment and results together with a review of the literature., Material and Method: We report the case a 49 years old patient, without particular antecedent, and wither a sub-glottis tumour presenting as a dysphonic. A biopsy is realized under general anesthesia, and the histopathologic results has been a laryngeal CAK, a radio therapy was also under taken, because the patient refused the surgery., Results: The patient is free of disease after six months of follow up., Conclusion: The laryngeal cylindroma is rare. The symptomatology does not show a proper characteristic, the diagnosis is a histological finding, and the natural evolution is marked by the very show development of this tumour the onset of cervical lymphatic adenopathy. The local recurrence and metastasis. The surgical exercise, followed by radiotherapy seen to be the best treatment of choice.

Background Information: Transmission electron tomography is becoming a powerful tool for studying subcellular components of cells. Classical approaches for electron tomography consist of recording images along a single-tilt axis. This approach is being improved by dual-axis reconstructions and/or high-tilt devices (tilt angle>+/-60 degrees) on microscopes to compensate part of the information loss due to the 'missing wedge' phenomena., Results: In the present work we have evaluated the extension of the dual-axis technique to a multiple-axis approach, and we demonstrate a freely available plug-in for the Java-based freeware image-analysis software ImageJ. Our results from phantom and experimental data sets from Paramecium tetraurelia epon-embedded sections have shown that multiple-axis tomography achieves results equivalent to those obtained by dual-axis approach without the requirement for high-tilt devices., Conclusions: This new approach allows performance of high-resolution tomography, avoiding the need for high-tilt devices, and therefore will increase the access of electron tomography to a larger community.

Background: Detection of fluorescent probes by fluorescence in situ hybridization in cells with preserved three-dimensional nuclear structures (3D-FISH) is useful for studying the organization of chromatin and localization of genes in interphase nuclei. Fast and reliable measurements of the relative positioning of fluorescent spots specific to subchromosomal regions and genes would improve understanding of cell structure and function., Methods: 3D-FISH protocol, confocal microscopy, and digital image analysis were used., Results: New software (Smart 3D-FISH) has been developed to automate the process of spot segmentation and distance measurements in images from 3D-FISH experiments. It can handle any number of fluorescent spots and incorporate images of 4',6-diamino-2-phenylindole counterstained nuclei to measure the relative positioning of spot loci in the nucleus and inter-spot distance. Results from a pilot experiment using Smart 3D-FISH on ENL, MLL, and AF4 genes in two lymphoblastic cell lines were satisfactory and consistent with data published in the literature., Conclusion: Smart 3D-FISH should greatly facilitate image processing and analysis of 3D-FISH images by providing a useful tool to overcome the laborious task of image segmentation based on user-defined parameters and decrease subjectivity in data analysis. It is available as a set of plugins for ImageJ software., ((c) 2005 Wiley-Liss, Inc.)

Energy-filtering transmission electron microscopy (EFTEM) allows the determination of elemental distributions out of a sequence of energy filtered images. Combined with electron tomography, EFTEM is a powerful tool to obtain three-dimensional chemical maps from sub-cellular structures. However, there is no existing software in the public-domain for the computation and analysis of 3D-chemical maps. Here, we present a Java-based program to compute 3D-elemental distribution. This program is available as a set of plug-ins for the public-domain Java image processing program Image J inspired by NIH Image. Its implemented algorithms have been successfully applied to the three-dimensional localization of iron granules in semi thin (200 nm) epon sections from the vent worm Riftia pachyptalia.

Electron tomography allows computing three-dimensional (3D) reconstructions of objects from their projections recorded at several angles. Combined with transmission electron microscopy, electron tomography has contributed greatly to the understanding of subcellular structures and organelles. Performed on frozen-hydrated samples, electron tomography has yielded useful information about complex biological structures. Combined with energy filtered transmission electron microscopy (EFTEM) it can be used to analyze the spatial distribution of chemical elements in biological or material sciences samples. In the present review, we present an overview of the requirements, applications, and perspectives of electron tomography in structural biology.

Recent advances in electron microscopy and image analysis techniques have resulted in the development of tomography, which makes possible the study of structures neither accessible to X-ray crystallography nor nuclear magnetic resonance. However, the use of tomography to study biological structures, ranging from 100 to 500 nm, requires developments in sample preparation and image analysis. Indeed, cryo-electron tomography present two major drawbacks: the low contrast of recorded images and the sample radiation damage. In the present work we have tested, on T4 bacteriophage samples, the use of a new preparation technique, cryo-negative staining, which reduces the radiation damage while preserving a high signal-to-noise ratio. Our results demonstrate that the combination of cryo-negative staining in tomography with standard cryo-microscopy and single particle analysis results in a methodological approach that could be useful in the study of biological structures ranging in the T4 bacteriophage size.

The chromosomes of Menetes berdmorei (Rodentia, Sciuridae, Sciurinae) were studied by ZOO-FISH using whole human chromosome probes. All homoeologies between M. berdmorei and human chromosomes were determined, except for two small chromosome segments. Twelve human chromosomes are conserved in a unique block of synteny; ten are split into two and one into three blocks. Thus, a small number of interchromosomal rearrangements, about twenty, separates human from this squirrel karyotype. Homoeologies between human and the presumed ancestral chromosomes of Sciurinae could also be deduced, as well as those with the presumed ancestral chromosomes of eutherian mammals. Sciurinae chromosomes appear to be much closer to those of non-rodent mammals than those of Muridae and Cricetidae species studied so far. Thus, they provide an interesting tool to link the rodent genome to those of other mammals.

Inhibition of copper-induced low-density lipoprotein (LDL) oxidation by phenolic acids and their ethyl esters was investigated. LDL oxidation was evaluated by the hydroperoxide concentration and the chromatographic pattern of apoprotein fractions after fast protein liquid chromatography (FPLC). Antiradical properties against 1,1-diphenyl-2-picryl hydrazyl (DPPH) radical and 2,2'-azobis(2-amidinopropane)dihydrochloride (AAPH) were also investigated, and lipophilicity determined by thin-layer chromatography. Caffeic acid at 5 microM and sinapic acid at 10 microM protected LDL against oxidation, inhibiting both hydroperoxide formation and the increase of apoprotein negative charge. Ferulic, gallic and p-hydroxy cinnamic acids were ineffective. Ethyl esterification increased the lipophilicity of the five acids, and enhanced the antioxidant properties of caffeic, sinapic and ferulic acids. Ethyl caffeate was protective at 1 microM. In contrast, gallic and p-hydroxy cinnamic ethyl esters were ineffective. Our results indicate that ethyl esterification of phenolic acids increases lipophilicity of their ethyl esters and may enable a better incorporation into the lipid layer of the LDL particle and the exertion of their antioxidant effect in the true site of lipoperoxidation. However, increasing lipophilicity is not the only mechanism able to potentiate preexisting antioxidant properties of molecules, and probably other mechanisms are implicated.

Using human chromosome painting probes, we looked for homologies between human and mountain zebra (Equus zebra hartmannae, Equidae, Perissodactyla) karyotypes. Except for two very short segments, all euchromatic regions were found to have a human homologous chromosome segment. Conserved syntenies previously described in various mammalian orders were detected. Each synteny corresponded to a chromosomal region homologous to two parts of human chromosomes: HSA3 and HSA21, HSA7 and HSA16, HSA12 and HSA22, and HSA16 and HSA19. Chromosomal segments homologous to a part of HSA11 and HSA19p are found syntenic in zebra, horse and donkey, suggesting that this group of synteny has been inherited from an Equidae or Perissodactyla common ancestor. A synteny of segments homologous to parts of HSA4 and HSA8 was observed in zebra and horse. It also exists in the rabbit (Lagomorpha) and several Carnivora species. A second group of taxa which does not have this region of synteny is composed of primates, Chiroptera and Insectivora, and possibly also Cetacea and Scandantia. Thus, the presence or absence of this region of synteny may separate two groups of eutherian mammals., (Copyright 2001 S. Karger AG, Basel)

1. Since oxygen free radicals are directly involved in a variety of pathologies such as atherosclerosis, diabetes mellitus, inflammation and/or when a deficit of defences of the organism against radicals occurs, we developed a suitable and simple method to determine both the erythrocyte sensitivity to an oxidative stress and plasma antioxidant protective capacity. 2. This test is based on the introduction at 37 degrees C of a radical initiator, 2,2'-azobis (2-amidinopropane) dihydrochloride (AAPH), within an erythrocyte suspension leading to a membrane alteration and ultimately to haemolysis. The latter can be quantified by determining the lacticodeshydrogenase activity released in the medium. The erythrocyte sensitivity to haemolysis and the volume of plasma inhibiting 50% of the haemolysis were determined. 3. Intra-assay CVs were 1.9% for erythrocyte sensitivity to oxidative stress and 3.4% for inhibitory 50% plasma volume. Inter-assay CVs for both erythrocyte sensitivity and inhibitory 50% plasma volume were 4%. 4. The reliability of this method was assessed and applied to test the protective effect of vitamin E, a well known antioxidant agent, in six healthy volunteers. Two weeks after daily administration of 500 mg of vitamin E, the mean plasma vitamin E concentration increased by 41% from 10.7 +/- 2.0 mg l-1 before treatment (P < 0.05). As the vitamin E concentration increased, the mean inhibitory 50% plasma volume and the percentage of haemolysed erythrocytes decreased respectively by 29% from 3.35 +/- 0.5 microliter (P < 0.05) and 18% from 71.5 +/- 3.8% (P < 0.05). No significative variation of these parameters was observed in six adult men without vitamin E supplementation. 5. Thus, this global and simple test permits an antioxidant status evaluation of a patient. It can be applied to various pathologies and allows the potency of new antioxidant molecules to be evaluated.