Image analysis for understanding embryo development: a bridge from microscopy to biological insights.

The digital reconstruction of the embryogenesis of model organisms from 3D+time data is revolutionizing practices in quantitative and integrative Developmental Biology. A manual and fully supervised image analysis of the massive complex data acquired with new microscopy technologies is no longer an option and automated image processing methods are required to fully exploit the potential of imaging data for biological insights. Current developments and challenges in biological image processing include algorithms for microscopy multiview fusion, cell nucleus tracking for quasi-perfect lineage reconstruction, segmentation, and validation methodologies for cell membrane shape identification, single cell gene expression quantification from in situ hybridization data, and multidimensional image registration algorithms for the construction of prototypic models. These tools will be essential to ultimately produce the multilevel in toto reconstruction that combines the cell lineage tree, cells, and tissues structural information and quantitative gene expression data in its spatio-temporal context throughout development.

Comparison of distribution and activity of nanoparticles with short interfering DNA (Dbait) in various living systems.

Introducing small DNA molecules (Dbait) impairs the repair of damaged chromosomes and provides a new method for enhancing the efficiency of radiotherapy in radio-resistant tumors. The radiosensitizing activity is dependent upon the efficient delivery of Dbait molecules into the tumor cells. Different strategies have been compared, to improve this key step. We developed a pipeline of assays to select the most efficient nanoparticles and administration protocols before preclinical assays: (i) molecular analyses of complexes formed with Dbait molecules, (ii) cellular tests for Dbait uptake and activity, (iii) live zebrafish embryo confocal microscopy monitoring for in vivo distribution and biological activity of the nanoparticles and (iv) tumor growth and survival measurement on mice with xenografted tumors. Two classes of nanoparticles were compared, polycationic polymers with linear or branched polyethylenimine (PEI) and covalently attached cholesterol (coDbait). The most efficient Dbait transfection was observed with linear PEI complexes, in vitro and in vivo. Doses of coDbait ten-fold higher than PEI/Dbait nanoparticles, and pretreatment with chloroquine, were required to obtain the same antitumoral effect on xenografted melanoma. However, with a 22-fold lower 'efficacy dose/toxicity dose' ratio as compared with Dbait/PEI, coDbait was selected for clinical trials.

Segmentation of 3D cell membrane images by PDE methods and its applications.

We present a set of techniques that enable us to segment objects from 3D cell membrane images. Particularly, we propose methods for detection of approximate cell nuclei centers, extraction of the inner cell boundaries, the surface of the organism and the intercellular borders--the so called intercellular skeleton. All methods are based on numerical solution of partial differential equations. The center detection problem is represented by a level set equation for advective motion in normal direction with curvature term. In case of the inner cell boundaries and the global surface, we use the generalized subjective surface model. The intercellular borders are segmented by the advective level set equation where the velocity field is given by the gradient of the signed distance function to the segmented inner cell boundaries. The distance function is computed by solving the time relaxed eikonal equation. We describe the mathematical models, explain their numerical approximation and finally we present various possible practical applications on the images of zebrafish embryogenesis--computation of important quantitative characteristics, evaluation of the cell shape, detection of cell divisions and others.

3D early embryogenesis image filtering by nonlinear partial differential equations.

We present nonlinear diffusion equations, numerical schemes to solve them and their application for filtering 3D images obtained from laser scanning microscopy (LSM) of living zebrafish embryos, with a goal to identify the optimal filtering method and its parameters. In the large scale applications dealing with analysis of 3D+time embryogenesis images, an important objective is a correct detection of the number and position of cell nuclei yielding the spatio-temporal cell lineage tree of embryogenesis. The filtering is the first and necessary step of the image analysis chain and must lead to correct results, removing the noise, sharpening the nuclei edges and correcting the acquisition errors related to spuriously connected subregions. In this paper we study such properties for the regularized Perona-Malik model and for the generalized mean curvature flow equations in the level-set formulation. A comparison with other nonlinear diffusion filters, like tensor anisotropic diffusion and Beltrami flow, is also included. All numerical schemes are based on the same discretization principles, i.e. finite volume method in space and semi-implicit scheme in time, for solving nonlinear partial differential equations. These numerical schemes are unconditionally stable, fast and naturally parallelizable. The filtering results are evaluated and compared first using the Mean Hausdorff distance between a gold standard and different isosurfaces of original and filtered data. Then, the number of isosurface connected components in a region of interest (ROI) detected in original and after the filtering is compared with the corresponding correct number of nuclei in the gold standard. Such analysis proves the robustness and reliability of the edge preserving nonlinear diffusion filtering for this type of data and lead to finding the optimal filtering parameters for the studied models and numerical schemes. Further comparisons consist in ability of splitting the very close objects which are artificially connected due to acquisition error intrinsically linked to physics of LSM. In all studied aspects it turned out that the nonlinear diffusion filter which is called geodesic mean curvature flow (GMCF) has the best performance.

An automatic quantification and registration strategy to create a gene expression atlas of zebrafish embryogenesis.

In order to properly understand and model the gene regulatory networks in animals development, it is crucial to obtain detailed measurements, both in time and space, about their gene expression domains. In this paper, we propose a complete computational framework to fulfill this task and create a 3D Atlas of the early zebrafish embryogenesis annotated with both the cellular localizations and the level of expression of different genes at different developmental stages. The strategy to construct such an Atlas is described here with the expression pattern of 5 different genes at 6 hours of development post fertilization.

Cell tracking in fluorescence images of embryogenesis processes with morphological reconstruction by 4D-tubular structuring elements.

We present a simple and parameter-free nuclei tracking method for reconstructing cell dynamics in fluorescence 3D+t images of embryogenesis. The strategy is based on the use of the mathematical morphology operators directly in the 4D image. The morphological reconstruction of a marker -manually or automatically selected- in an initial spatio-temporal position generates a connected path over the time representing the cell migration. Thus, the processing provides a coherent spatiotemporal estimation of cell movement. The algorithm has been validated on in vivo images of early zebrafish and sea urchin embryogenesis acquired with two-photon laser scanning microscopy providing mean tracking rates above 98% per time step.

Combining sea urchin embryo cell lineages by error-tolerant graph matching.

Obtaining the complete cell lineage tree of an embryo's development is a very appealing and ambitious goal, but fortunately recent developments both in optical imaging and digital image processing are bringing it closer. However, when imaging the embryos (sea urchin embryos for this work) with high enough spatial resolution and short enough time-step to make cell segmentation and tracking possible, it is currently not possible to image the specimen throughout its all embryogenesis. For this reason it is interesting to explore how cell lineage trees extracted from two different embryos of the same species and imaged for overlapping periods of time can be concatenated, resulting in a single lineage tree covering both embryos' development time frames. To achieve this we used an error-tolerant graph matching strategy by selecting a time point at which both lineage trees overlap, and representing the information about each embryo at that time point as a graph in which nodes stand for cells and edges for neighborhood relationships among cells. The expected output of the graph matching algorithm is the minimal-cost correspondence between cells of both specimens, allowing us to perform the lineage combination.

Cooperative action of ADMP- and BMP-mediated pathways in regulating cell fates in the zebrafish gastrula.

It was shown in Xenopus and chick that Spemann's organizer activity is regulated through the negative action of Anti-Dorsalizing Morphogenetic Protein (ADMP). We report the characterization and functional properties of admp in zebrafish. admp expression profile is consistent with a role in the organizer, including the tail organizer. We studied admp function through overexpression experiments, with the use of a dominant-negative form (TR-ADMP) and of an antisense morpholino-modified oligonucleotide. Our results indicate that the ADMP pathway causes the restriction of anterior and axial fates and that ADMP, BMP2b, and BMP7 pathways have distinct actions but cooperate in establishing proper dorso-ventral regionalization. This is shown by partial rescue of the dorsalized mutant snailhouse and of the ventralized mutant chordino, upon admp and tr-admp RNA injection, respectively. Moreover, ADMP and BMP7 probably form heterodimers as shown by the ability of TR-ADMP and BMP7 to antagonize each other. We observed that a MYC-tagged ADMP was secreted and detected in the extracellular space, suggesting that admp could act at a distance. Simultaneous local inhibition of bmp function at the blastoderm margin and impairment of ADMP secretion led to the induction of secondary head structures, confirming that the two pathways cooperatively regulate organizer formation and activity.

Conversion of zebrafish blastomeres to an endodermal fate by TGF-beta-related signaling.

The endoderm contributes cells to the gut, and participates in the induction and patterning of the vertebrate head and heart. The mechanisms controlling the formation of endoderm are poorly understood. Commitment of endoderm cells occurs at the onset of gastrulation and requires cell interactions; studies in vitro have implicated transforming growth factor Beta (TGF-beta)-related molecules in this process. TARAM-A is a zebrafish receptor kinase that is related to the type I subunit of the TGF-beta receptor, and is expressed in presumptive endomesodermal cells at gastrulation. We provide here evidence for its involvement in endoderm formation in vivo. Activation of TARAM-A was found to drive blastomeres towards an endodermal fate. The induced endoderm behaved ad endogenous endoderm during gastrulation: it migrated in contact with the yolk and expressed endoderm-specific markers. Loss-of-function mutations in the zebrafish one-eyed-pinhead (OEP) gene lead to defects in heart formation, defects of the ventral central nervous system (CNS) and cyclopia. Mutant embryos also lack endoderm and anterior mesoderm. Endoderm formation in oep mutant embryos was found to be restored by the activation of the TARAM-A signaling pathway. Cardiac and ocular defects, but not midline CNS structures, were rescued non-autonomously, demonstrating that endoderm may provide signals that can pattern the eye anlage, and which are distinct form those specifying the ventral midline of the CNS.

Inhibitory interactions controlling organizer activity in fish.

An experimental system allowing the observation of 2 active organizing centers during zebrafish development is described. It was achieved by injection into a single marginal cell at the 16-cell stage of TARAM-A-D mRNA. TARAM-A-D was previously described as the mutated constitutive form of a type I receptor for transforming growth factor beta. In 80% of the injected embryos, 2 distinct organizers were observed at the onset of gastrulation. At the end of gastrulation, these embryos showed duplicated axial structures. Nevertheless, only 25% of the injected embryos displayed a recognizable axis duplication after 1 day of development. This paradox is taken as an evidence for suppressive effects exerted in a reciprocal manner when more than 1 organizing center is present.

Instability at the W/c-kit locus in mice: analysis of melanocyte cell lines derived from reversion spots.

Mutations at the mouse W/c-kit locus have pleiotropic defects including impaired development of the melanocyte lineage. We have characterized the molecular basis of the Wei mutation. We show here that Wei is the result of a missense mutation in the ATP binding site domain of c-kit proto-oncogene which affects the tyrosine kinase function of the receptor. As a result, few melanoblasts survive during embryogenesis in heterozygous Wei/+ foetuses. Therefore the adult skin is partly devoid of differentiated pigmented cells giving rise to a mottled coat colour phenotype. However, three per cent of Wei/+ mice exhibit spots of wild-type pigmentation on the coat which is otherwise of mutant phenotype. Such areas are known as phenotypic reversions. To dissect the molecular events responsible for the phenotypic instability of the Wei mutation, we have isolated pure cultures of continuously proliferating melanocytes from two independent reversion spots. These melanocyte lines, designated Wei-R1 and Wei-R2, were shown to exhibit none of the characteristics associated with transformed melanocytes. We have used a polymorphic restriction site generated by the Wei mutation to show that both melanocyte lines are still heterozygous at the W focus. Furthermore, Wei-R1 and Wei-R2 melanocytes express both the mutated and the wild-type c-kit RNA. These results indicate that the somatic mutation events responsible for reversion spots are not necessarily associated with loss of heterozygosity at the W/c-kit locus. Together with previous data, this points to the fact that several mechanisms account for the coat colour reversion phenotype.

Glycosylation of gamma-glutamyltransferase is modified by ethanol in H5-6 hepatoma cell line.

The H5-6 cultured rat hepatoma cell line was used to investigate the post-translational maturation of gamma-glutamyltransferase (GGT) and the effects of acute ethanol administration on the expression and glycosylation of this membrane-bound glycoprotein. We found that the two subunits of H5-6 GGT with molecular masses of 55 and 33 kDa were derived from a single glycosylated precursor of 80 kDa. In addition, signals of high molecular mass (more than 90 kDa) were detected. In vitro deglycosylation experiments indicated that N-linked sugars represented about 25% of the molecular weight of the H5-6 enzyme. By use of serial lectin affinity technique, we showed that N-linked sugar chains were mainly of the biantennary complex and hybrid-type, without fucose linkage to the innermost N-acetyl-glucosamine. Ethanol treatment did not seem to affect the expression of GGT and the sialic acid content of the enzyme, but altered its oligosaccharide chain composition both quantitatively and qualitatively.

Inhibited gastrulation in mouse embryos overexpressing the leukemia inhibitory factor.

Leukemia inhibitory factor (LIF) is a cytokine active in vitro on different target cells. It is detected in vivo during mouse gestation in both extraembryonic membranes and maternal tissues. Two isoforms have been described maintaining embryonic stem cells in culture in a pluripotent state. However, overexpression of their cDNAs in chimeric mouse embryos observed between 6.5 and 9.5 days postcoitus gave strikingly different phenotypes. Embryos overexpressing the diffusible form of LIF cDNA looked essentially normal. Chimerae expressing LIF associated with the extracellular matrix cDNA showed an abnormal proliferation of tissues and the absence of differentiated mesoderm. They have not undertaken the normal pathway of gastrulation.

Characterization of antigens recognized by monoclonal and polyclonal antibodies directed against uvomorulin.

Uvomorulin is a cell surface glycoprotein involved in compaction of early mouse embryo. Antibodies, either monoclonal or polyclonal, raised against a purified tryptic fragment of uvomorulin recognize, in a detergent lysate of embryonal carcinoma cells metabolically labeled with 35S, three molecules (120, 100, and 88 kDa) that are not related, as judged by peptide mapping. Only the 120-kDa form is related to the tryptic fragment of uvomorulin and, thus, is considered as the native form of uvomorulin. Although all three products are apparently detectable at the cell surface, only the 120-kDa form is glycosylated. Coimmunoprecipitation of the three different polypeptides is probably due to shared epitopes rather than to their presence in a multimeric complex.

Inhibition of N-linked oligosaccharide trimming does not interfere with surface expression of certain integral membrane proteins.

The effects of 1-deoxynojirimycin (dNM) and 1-deoxymannojirimycin (dMM), inhibitors of oligosaccharide trimming glucosidase I and mannosidase I, respectively, on the biosynthesis of vesicular stomatitis virus G protein, influenza virus hemagglutinin, and human class I histocompatibility antigens were investigated. Although the oligosaccharides of these membrane glycoproteins were greatly altered, neither dNM nor dMM interferred with their surface expression, as determined by a variety of assays, including accessibility to proteases and antibodies; neither did these drugs inhibit production of infectious virus particles.

Uvomorulin: a nonintegral membrane protein of early mouse embryo.

A monoclonal antibody has allowed the characterization of various forms of uvomorulin, a glycoprotein involved in the process of compaction of mouse morula. In addition to various degradation products, uvomorulin exists as a 120-kilodalton exocellular molecule stable at the cell surface. A short-lived 135-kilodalton precursor of uvomorulin has been detected after 10-min pulse labeling. Uvomorulin-like molecules are found on various tissues at various stages of development of the mouse.

Effects of the glucosidase inhibitors nojirimycin and deoxynojirimycin on the biosynthesis of membrane and secretory glycoproteins.

The glucosidase inhibitors nojirimycin (NM) and 1-deoxynojirimycin (dNM) interfere with N-linked glycosylation. The effects of NM and dNM on the biosynthesis of secretory glycoproteins (IgD and IgM) and membrane glycoproteins (HLA-A, B, C and -DR antigens) have been examined. Whereas treatment of IgD- and IgM-producing cells with NM results in the transfer of drastically shortened oligosaccharide side chains, treatment with dNM inhibits trimming, most probably through interaction with glucosidase I and/or II. A comparison of NM and dNM with tunicamycin and the mannosidase inhibitor swainsonine (SW) show that each of the inhibitors interferes with N-linked glycosylation in a distinct manner. For both Ig and HLA antigens, the effects of SW are discernible at the final stages of glycan maturation only, whereas the effects of dNM are observed quite early in the biosynthetic process. The secretion of IgD, but not IgM, was blocked in dNM-treated cells. The HLA-A, B, C heavy chains synthesized by the Daudi cell line were degraded in an accelerated fashion in dNM-treated cells, but no effects were seen on the HLA-DR antigens in these cells. Although both SW and dNM interfere with trimming, further modifications of the oligosaccharide side chains occur, and show that the two processes are not obligately coupled. Glucosidase inhibitors such as NM and dNM, as well as the mannosidase inhibitor SW, allow modification of glycan structure, and may be used to study the biological role of glycoprotein oligosaccharides and their modifications.