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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 10 September 2013, Vol.110(37), pp.E3497-505
    Description: Promiscuous expression of numerous tissue-restricted self-antigens (TRAs) in medullary thymic epithelial cells (mTECs) is essential to safeguard self-tolerance. A distinct feature of promiscuous gene expression is its mosaic pattern (i.e., at a given time, each self-antigen is expressed only in 1-3% of mTECs). How this mosaic pattern is generated at the single-cell level is currently not understood. Here, we show that subsets of human mTECs expressing a particular TRA coexpress distinct sets of genes. We identified three coexpression groups comprising overlapping and complementary gene sets, which preferentially mapped to certain chromosomes and intrachromosomal gene clusters. Coexpressed gene loci tended to colocalize to the same nuclear subdomain. The TRA subsets aligned along progressive differentiation stages within the mature mTEC subset and, in vitro, interconverted along this sequence. Our data suggest that single mTECs shift through distinct gene pools, thus scanning a sizeable fraction of the overall repertoire of promiscuously expressed self-antigens. These findings have implications for the temporal and spatial (re)presentation of self-antigens in the medulla in the context of tolerance induction.
    Keywords: Central Tolerance ; Human Thymic Epithelial Cells ; Promiscuous Gene Expression ; Autoantigens -- Genetics ; Thymus Gland -- Immunology
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 24 May 2011, Vol.108(21), pp.E136-44
    Description: The role of the intranuclear movement of chromatin in gene expression is not well-understood. Herpes simplex virus forms replication compartments (RCs) in infected cell nuclei as sites of viral DNA replication and late gene transcription. These structures develop from small compartments that grow in size, move, and coalesce. Quantitative analysis of RC trajectories, derived from 4D images, shows that most RCs move by directed motion. Directed movement is impaired in the presence of actin and myosin inhibitors as well as a transcription inhibitor. In addition, RCs coalesce at and reorganize nuclear speckles. Lastly, distinct effects of actin and myosin inhibitors on viral gene expression suggest that RC movement is not required for transcription, but rather, movement results in the bridging of transcriptionally active RCs with nuclear speckles to form structures that enhance export of viral late mRNAs.
    Keywords: Active Transport, Cell Nucleus ; Transcription, Genetic ; Virus Replication ; Herpesviridae -- Physiology ; RNA, Viral -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 3
    Language: English
    In: Biophysical Journal, 2011, Vol.100(3), pp.419a-419a
    Keywords: Biology
    ISSN: 0006-3495
    E-ISSN: 1542-0086
    Source: ScienceDirect Journals (Elsevier)
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  • 4
    Language: English
    In: NeuroImage, 01 November 2018, Vol.181, pp.235-251
    Description: To understand the spatial organization as well as long- and short-range connections of the human brain at microscopic resolution, 3D reconstruction of histological sections is important. We approach this challenge by reconstructing series of unstained histological sections of multi-scale ( and ) and multi-modal 3D polarized light imaging (3D-PLI) data. Since spatial coherence is lost during the sectioning procedure, image registration is the major step in 3D reconstruction. We propose a non-rigid registration method which comprises of a novel multi-modal similarity metric and an improved regularization scheme to cope with deformations inevitably introduced during the sectioning procedure, as well as a rigid registration approach using a robust similarity metric for improved initial alignment. We also introduce a multi-scale feature-based localization and registration approach for mapping of sections to sections and a scale-adaptive method that can handle challenging sections with large semi-global deformations due to tissue splits. We have applied our registration method to 126 consecutive sections of the temporal lobe of the human brain with and resolution. Each step of the registration method was quantitatively evaluated using 10 different sections and manually determined ground truth, and a quantitative comparison with previous methods was performed. Visual assessment of the reconstructed volumes and comparison with reference volumes confirmed the high quality of the registration result.
    Keywords: Image Registration ; 3d Reconstruction ; Canonical Correlation Transform ; Polarized Light Imaging ; Human Brain ; Hippocampus ; Medicine
    ISSN: 1053-8119
    E-ISSN: 1095-9572
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  • 5
    Language: English
    In: Biophysical Journal, 01 December 2015, Vol.109(11), pp.2352-2362
    Description: The number of fluorophores within a molecule complex can be revealed by single-molecule photobleaching imaging. A widely applied strategy to analyze intensity traces over time is the quantification of photobleaching step counts. However, several factors can limit and bias the detection of photobleaching steps, including noise, high numbers of fluorophores, and the possibility that several photobleaching events occur almost simultaneously. In this study, we propose a new approach, to our knowledge, to determine the fluorophore number that correlates the intensity decay of a population of molecule complexes with the decay of the number of visible complexes. We validated our approach using single and fourfold Atto-labeled DNA strands. As an example we estimated the subunit stoichiometry of soluble CD95L using GFP fusion proteins. To assess the precision of our method we performed in silico experiments showing that the estimates are not biased for experimentally observed intensity fluctuations and that the relative precision remains constant with increasing number of fluorophores. In case of fractional fluorescent labeling, our simulations predicted that the fluorophore number estimate corresponds to the product of the true fluorophore number with the labeling fraction. Our method, denoted by spot number and intensity correlation (SONIC), is fully automated, robust to noise, and does not require the counting of photobleaching events.
    Keywords: Biology
    ISSN: 0006-3495
    E-ISSN: 1542-0086
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  • 6
    Language: English
    In: International Journal of Computer Vision, Jan 1, Vol.106(1), p.76(17)
    Description: We introduce a new approach for spline-based elastic image registration using both point landmarks and intensity information. With this approach, both types of information as well as a regularization based on the Navier equation are directly integrated in a single energy minimizing functional. For this functional we have derived an analytic solution, which is based on matrix-valued non-radial basis functions. With our approach the full 3D intensity information is exploited, i.e., all voxels are considered and subsampling using a grid is not required. A special case of our hybrid approach is obtained by disregarding the landmark information, which results in a pure intensity-based elastic registration approach. We have successfully applied our approach to 3D synthetic images, 2D MR images of the human brain, 2D gel electrophoresis images, and 3D CT lung images. Keywords Elastic image registration * Hybrid registration * Gaussian elastic body splines * Analytic solution
    Keywords: Three Dimensional ; Landmarks ; Basis Functions ; Two Dimensional ; Image Registration ; Images ; Exact Solutions ; Mathematical Analysis ; Pattern Recognition (Ci);
    ISSN: 0920-5691
    E-ISSN: 15731405
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  • 7
    Language: English
    In: PLoS ONE, 01 January 2016, Vol.11(9), p.e0162516
    Description: PURPOSE:To demonstrate feasibility of automated 3D volumetry of central pulmonary arteries based on magnetic resonance angiography (MRA), to assess pulmonary artery volumes in patients with pulmonary hypertension compared to healthy controls, and to investigate the potential of the technique...
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 8
    Language: English
    In: 2012, Vol.7(12), p.e50988
    Description: Neuroblastoma is the most common extra-cranial solid tumor of early childhood. Standard therapies are not effective in case of poor prognosis and chemotherapy resistance. To improve drug therapy, it is imperative to discover new targets that play a substantial role in tumorigenesis of neuroblastoma. The mitotic machinery is an attractive target for therapeutic interventions and inhibitors can be developed to target mitotic entry, spindle apparatus, spindle activation checkpoint, and mitotic exit. We present an elaborate analysis pipeline to determine cancer specific therapeutic targets by first performing a focused gene expression analysis to select genes followed by a gene knockdown screening assay of live cells. We interrogated gene expression studies of neuroblastoma tumors and selected 240 genes relevant for tumorigenesis and cell cycle. With these genes we performed time-lapse screening of gene knockdowns in neuroblastoma cells. We classified cellular phenotypes and used the temporal context of the perturbation effect to determine the sequence of events, particularly the mitotic entry preceding cell death. Based upon this phenotype kinetics from the gene knockdown screening, we inferred dynamic gene functions in mitosis and cell proliferation. We identified six genes ( DLGAP5 , DSCC1 , SMO , SNRPD1 , SSBP1 , and UBE2C ) with a vital role in mitosis and these are promising therapeutic targets for neuroblastoma. Images and movies of every time point of all screened genes are available at https://ichip.bioquant.uni-heidelberg.de .
    Keywords: Research Article ; Biology ; Medicine ; Genetics And Genomics ; Molecular Biology ; Computational Biology ; Oncology
    E-ISSN: 1932-6203
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  • 9
    Language: English
    In: IEEE Transactions on Image Processing, March 2017, Vol.26(3), pp.1405-1417
    Description: To gain a better understanding of cellular and molecular processes, it is important to quantitatively analyze the motion of subcellular particles in live cell microscopy image sequences. Since, generally, the subcellular particles move and cell nuclei move as well as deform, it is important to decouple the movement of particles from that of the cell nuclei using non-rigid registration methods. We have developed a diffeomorphic multi-frame approach for non-rigid registration of cell nuclei in 2D and 3D live cell fluorescence microscopy images. Our non-rigid registration approach is based on local optic flow estimation, exploits information from multiple consecutive image frames, and determines diffeomorphic transformations in the log-domain, which allows efficient computation of the inverse transformations. To register single images of an image sequence to a reference image, we use a temporally weighted mean image, which is constructed based on inverse transformations and multiple consecutive frames. Using multiple consecutive frames improves the registration accuracy compared to pairwise registration, and using a temporally weighted mean image significantly reduces the computation time compared with previous work. In addition, we use a flow boundary preserving method for regularization of computed deformation vector fields, which prevents from over-smoothing compared to standard Gaussian filtering. Our approach has been successfully applied to 2D and 3D synthetic as well as real live cell microscopy image sequences, and an experimental comparison with non-rigid pairwise, multi-frame, and temporal groupwise registration has been carried out.
    Keywords: Microscopy ; Image Sequences ; Two Dimensional Displays ; Three-Dimensional Displays ; Optical Imaging ; Shape ; Optical Microscopy ; Biomedical Image Processing ; Microscopy ; Image Sequence Analysis ; Diffeomorphic Registration ; Engineering ; Applied Sciences
    ISSN: 1057-7149
    E-ISSN: 1941-0042
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  • 10
    Language: English
    In: Medical Image Analysis, October 2012, Vol.16(7), pp.1436-1444
    Description: ► Cell segmentation using active contours, level sets, and convex energy functionals. ► Reformulation and combination of well-known non-convex energy functionals. ► Efficient numeric computation of the global solution using the Split Bregman method. ► Experimental evaluation based on different fluorescence microscopy images. ► The approach copes well with intensity inhomogeneities and cell clustering. In high-throughput applications, accurate and efficient segmentation of cells in fluorescence microscopy images is of central importance for the quantification of protein expression and the understanding of cell function. We propose an approach for segmenting cell nuclei which is based on active contours using level sets and convex energy functionals. Compared to previous work, our approach determines the global solution. Thus, the approach does not suffer from local minima and the segmentation result does not depend on the initialization. We consider three different well-known energy functionals for active contour-based segmentation and introduce convex formulations of these functionals. We also suggest a numeric approach for efficiently computing the solution. The performance of our approach has been evaluated using fluorescence microscopy images from different experiments comprising different cell types. We have also performed a quantitative comparison with previous segmentation approaches.
    Keywords: Cell Segmentation ; Active Contours ; Level Sets ; Convex Optimization ; Medicine ; Engineering
    ISSN: 1361-8415
    E-ISSN: 1361-8423
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