TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy

<p>Abstract</p> <p>Background</p> <p>Transmission electron tomography is an increasingly common three-dimensional electron microscopy approach that can provide new insights into the structure of subcellular components. Transmission electron tomography fills the gap between high resolution structural methods (X-ray diffraction or nuclear magnetic resonance) and optical microscopy. We developed new software for transmission electron tomography, TomoJ. TomoJ is a plug-in for the now standard image analysis and processing software for optical microscopy, ImageJ.</p> <p>Results</p> <p>TomoJ provides a user-friendly interface for alignment, reconstruction, and combination of multiple tomographic volumes and includes the most recent algorithms for volume reconstructions used in three-dimensional electron microscopy (the algebraic reconstruction technique and simultaneous iterative reconstruction technique) as well as the commonly used approach of weighted back-projection.</p> <p>Conclusion</p> <p>The software presented in this work is specifically designed for electron tomography. It has been written in Java as a plug-in for ImageJ and is distributed as freeware.</p

A generic classification-based method for segmentation of nuclei in 3D images of early embryos

BACKGROUND: Studying how individual cells spatially and temporally organize within the embryo is a fundamental issue in modern developmental biology to better understand the first stages of embryogenesis. In order to perform high-throughput analyses in three-dimensional microscopic images, it is essential to be able to automatically segment, classify and track cell nuclei. Many 3D/4D segmentation and tracking algorithms have been reported in the literature. Most of them are specific to particular models or acquisition systems and often require the fine tuning of parameters. RESULTS: We present a new automatic algorithm to segment and simultaneously classify cell nuclei in 3D/4D images. Segmentation relies on training samples that are interactively provided by the user and on an iterative thresholding process. This algorithm can correctly segment nuclei even when they are touching, and remains effective under temporal and spatial intensity variations. The segmentation is coupled to a classification of nuclei according to cell cycle phases, allowing biologists to quantify the effect of genetic perturbations and drug treatments. Robust 3D geometrical shape descriptors are used as training features for classification. Segmentation and classification results of three complete datasets are presented. In our working dataset of the Caenorhabditis elegans embryo, only 21 nuclei out of 3,585 were not detected, the overall F-score for segmentation reached 0.99, and more than 95% of the nuclei were classified in the correct cell cycle phase. No merging of nuclei was found. CONCLUSION: We developed a novel generic algorithm for segmentation and classification in 3D images. The method, referred to as Adaptive Generic Iterative Thresholding Algorithm (AGITA), is freely available as an ImageJ plug-in

Dynamique de l'organisation nucléaire des séquences d'ADN répétées centromériques humaines au cours du cycle cellulaire

Le noyau des cellules est une structure très organisée, dont l'organisation joue un rôle important dans la régulation de l'expression des gènes. La compréhension des mécanismes à l'origine de cette organisation est donc essentielle à la compréhension du fonctionnement des génomes. De nombreuses expériences conduites chez la souris ont montré que les régions centromériques (RC) des chromosomes jouent un rôle dans l'organisation du noyau. L'organisation spatiale des RCs humaines est beaucoup moins étudiée, principalement à cause de la complexité des séquences qui les composent, qui rend plus difficile leur détection. Nous avons développé des outils de traitement et d'analyse quantitative d'image, qui, combinés à des nouveaux marqueurs des RCs humaines, nous ont permis de mieux décrire deux aspects de leur organisation spatiale. D'une part nous avons montré qu'elles se positionnent préférentiellement en périphérie du noyau ou aux bords des nucléoles, avec des fréquences qui dépendent des chromosomes. D'autre part nous avons montré qu'elles s'agrègent dans le noyau pour former un compartiment d'hétérochromatine, qui présente des caractéristiques similaires à celui observé dans d'autres espèces telles que la souris. Ces deux aspects sont tous deux inter-dépendants et varient au cours du cycle cellulaire. Cette description nouvelle met sur la piste de mécanismes responsables de l'organisation particulière des RCs, qui pourront être étudiés grâce à la méthode d'analyse et aux observables que nous avons développées. L'étude de ces mécanismes permettra de mieux comprendre la fonction des RCs humaines dans l'organisation du noyau.The cell nucleus is a highly organized structure, playing an important role in gene regulation. Understanding the underlying mechanisms is therefore essential for understanding genome function. Numerous studies conducted in mouse cells have shown that centromeric regions (RC) of chromosomes play a role in nuclear organization. The spatial organization of human RCs is less studied, mainly because of the complexity of the underlying DNA sequences that make them hard to detect. We have developed image processing and analysis tools, that, combined with new markers for human RCs, have allowed us to draw a better description of two features of their spatial organization. On the one hand, we have shown that they are preferentially located close to the nuclear periphery or nucleoli borders, with chromosome-dependent frequencies. On the other hand, we have shown that they cluster to form a heterochromatic compartment that displays similar properties as the one observed in other species such as mouse. Both features are inter-dependent, and vary throughout the cell-cycle. This new description puts on the track of mechanisms responsible for the peculiar organization of RCs. Those mechanisms could be studied using the methodology and the observables we have developed. The study of those mechanisms will provide a better understanding of human RC function in nuclear organization.PARIS-JUSSIEU-Bib.électronique (751059901) / SudocSudocFranceF

The architecture of Rhodobacter sphaeroides chromatophores

International audienceThe chromatophores of Rhodobacter (Rb.) sphaeroides represent a minimal bio-energetic system, which efficiently converts light energy into usable chemical energy. Despite extensive studies, several issues pertaining to the morphology and molecular architecture of this elemental energy conversion system remain controversial or unknown. To tackle these issues, we combined electron microscope tomography, immuno-electron microscopy and atomic force microscopy. We found that the intracellular Rb. sphaeroides chromatophores form a continuous reticulum rather than existing as discrete vesicles. We also found that the cytochrome bc 1 complex localizes to fragile chromatophore regions, which most likely constitute the tubular structures that interconnect the vesicles in the reticulum. In contrast, the peripheral light-harvesting complex 2 (LH2) is preferentially hexagonally packed within the convex vesicular regions of the membrane network. Based on these observations, we propose that the bc 1 complexes are in the inter-vesicular regions and surrounded by reaction center (RC) core complexes, which in turn are bounded by arrays of peripheral antenna complexes. This arrangement affords rapid cycling of electrons between the core and bc 1 complexes while maintaining efficient excitation energy transfer from LH2 domains to the RCs

Tomography of bacteria–mineral associations within the deep-sea hydrothermal vent shrimp <i>Rimicaris exoculata</i>

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Simultaneous localization of MLL, AF4 and ENL genes in interphase nuclei by 3D-FISH: MLL translocation revisited

BACKGROUND: Haematological cancer is characterised by chromosomal translocation (e.g. MLL translocation in acute leukaemia) and two models have been proposed to explain the origins of recurrent reciprocal translocation. The first, established from pairs of translocated genes (such as BCR and ABL), considers the spatial proximity of loci in interphase nuclei (static "contact first" model). The second model is based on the dynamics of double strand break ends during repair processes (dynamic "breakage first" model). Since the MLL gene involved in 11q23 translocation has more than 40 partners, the study of the relative positions of the MLL gene with both the most frequent partner gene (AF4) and a less frequent partner gene (ENL), should elucidate the MLL translocation mechanism. METHODS: Using triple labeling 3D FISH experiments, we have determined the relative positions of MLL, AF4 and ENL genes, in two lymphoblastic and two myeloid human cell lines. RESULTS: In all cell lines, the ENL gene is significantly closer to the MLL gene than the AF4 gene (with P value < 0.0001). According to the static "contact first" model of the translocation mechanism, a minimal distance between loci would indicate a greater probability of the occurrence of t(11;19)(q23;p13.3) compared to t(4;11)(q21;q23). However this is in contradiction to the epidemiology of 11q23 translocation. CONCLUSION: The simultaneous multi-probe hybridization in 3D-FISH is a new approach in addressing the correlation between spatial proximity and occurrence of translocation. Our observations are not consistent with the static "contact first" model of translocation. The recently proposed dynamic "breakage first" model offers an attractive alternative explanation

Structural insights into the cTAR DNA recognition by the HIV-1 nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC

An essential step of the reverse transcription of the HIV-1 genome is the first strand transfer that requires the annealing of the TAR RNA hairpin to the cTAR DNA hairpin. HIV-1 nucleocapsid protein (NC) plays a crucial role by facilitating annealing of the complementary hairpins. Using nuclear magnetic resonance and gel retardation assays, we investigated the interaction between NC and the top half of the cTAR DNA (mini-cTAR). We show that NC(11-55) binds the TGG sequence in the lower stem that is destabilized by the adjacent internal loop. The 5′ thymine interacts with residues of the N-terminal zinc knuckle and the 3′ guanine is inserted in the hydrophobic plateau of the C-terminal zinc knuckle. The TGG sequence is preferred relative to the apical and internal loops containing unpaired guanines. Investigation of the DNA–protein contacts shows the major role of hydrophobic interactions involving nucleobases and deoxyribose sugars. A similar network of hydrophobic contacts is observed in the published NC:DNA complexes, whereas NC contacts ribose differently in NC:RNA complexes. We propose that the binding polarity of NC is related to these contacts that could be responsible for the preferential binding to single-stranded nucleic acids

Cardiovascular end points and mortality are not closer associated with central than peripheral pulsatile blood pressure components

none32Pulsatile blood pressure (BP) confers cardiovascular risk. Whether associations of cardiovascular end points are tighter for central systolic BP (cSBP) than peripheral systolic BP (pSBP) or central pulse pressure (cPP) than peripheral pulse pressure (pPP) is uncertain. Among 5608 participants (54.1% women; mean age, 54.2 years) enrolled in nine studies, median follow-up was 4.1 years. cSBP and cPP, estimated tonometrically from the radial waveform, averaged 123.7 and 42.5 mm Hg, and pSBP and pPP 134.1 and 53.9 mm Hg. The primary composite cardiovascular end point occurred in 255 participants (4.5%). Across fourths of the cPP distribution, rates increased exponentially (4.1, 5.0, 7.3, and 22.0 per 1000 person-years) with comparable estimates for cSBP, pSBP, and pPP. The multivariable-adjusted hazard ratios, expressing the risk per 1-SD increment in BP, were 1.50 (95% CI, 1.33-1.70) for cSBP, 1.36 (95% CI, 1.19-1.54) for cPP, 1.49 (95% CI, 1.33-1.67) for pSBP, and 1.34 (95% CI, 1.19-1.51) for pPP (P<0.001). Further adjustment of cSBP and cPP, respectively, for pSBP and pPP, and vice versa, removed the significance of all hazard ratios. Adding cSBP, cPP, pSBP, pPP to a base model including covariables increased the model fit (P<0.001) with generalized R2 increments ranging from 0.37% to 0.74% but adding a second BP to a model including already one did not. Analyses of the secondary end points, including total mortality (204 deaths), coronary end points (109) and strokes (89), and various sensitivity analyses produced consistent results. In conclusion, associations of the primary and secondary end points with SBP and pulse pressure were not stronger if BP was measured centrally compared with peripherally.noneHuang, Qi-Fang; Aparicio, Lucas S; Thijs, Lutgarde; Wei, Fang-Fei; Melgarejo, Jesus D; Cheng, Yi-Bang; Sheng, Chang-Sheng; Yang, Wen-Yi; Gilis-Malinowska, Natasza; Boggia, José; Niiranen, Teemu J; Wojciechowska, Wiktoria; Stolarz-Skrzypek, Katarzyna; Barochiner, Jessica; Ackermann, Daniel; Tikhonoff, Valérie; Ponte, Belen; Pruijm, Menno; Casiglia, Edoardo; Narkiewicz, Krzysztof; Filipovský, Jan; Czarnecka, Danuta; Kawecka-Jaszcz, Kalina; Jula, Antti M; Bochud, Murielle; Vanassche, Thomas; Verhamme, Peter; Struijker-Boudier, Harry A J; Wang, Ji-Guang; Zhang, Zhen-Yu; Li, Yan; Staessen, Jan AHuang, Qi-Fang; Aparicio, Lucas S; Thijs, Lutgarde; Wei, Fang-Fei; Melgarejo, Jesus D; Cheng, Yi-Bang; Sheng, Chang-Sheng; Yang, Wen-Yi; Gilis-Malinowska, Natasza; Boggia, José; Niiranen, Teemu J; Wojciechowska, Wiktoria; Stolarz-Skrzypek, Katarzyna; Barochiner, Jessica; Ackermann, Daniel; Tikhonoff, Valérie; Ponte, Belen; Pruijm, Menno; Casiglia, Edoardo; Narkiewicz, Krzysztof; Filipovský, Jan; Czarnecka, Danuta; Kawecka-Jaszcz, Kalina; Jula, Antti M; Bochud, Murielle; Vanassche, Thomas; Verhamme, Peter; Struijker-Boudier, Harry A J; Wang, Ji-Guang; Zhang, Zhen-Yu; Li, Yan; Staessen, Jan

A novel generic dictionary-based denoising method for improving noisy and densely packed nuclei segmentation in 3D time-lapse fluorescence microscopy images

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