| 1. |
- Bongini, Lorenzo, et al.
(author)
-
Resolving the geometry of biomolecules imaged by cryo electron tomography
- 2007
-
In: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 228:2, s. 174-184
-
Journal article (peer-reviewed)abstract
- In this paper, we describe two methods for computerized analysis of cryo electron tomography reconstructions of biomolecules. Both methods aim at quantifying the degree of structural flexibility of macromolecules and eventually resolving the inner dynamics through automatized protocols. The first method performs a Brownian dynamics evolution of a simplified molecular model into a fictitious force field generated by the tomograms. This procedure enables us to dock the simplified model into the experimental profiles. The second uses a fuzzy framework to delineate the subparts of the proteins and subsequently determine their interdomain relations. The two methods are discussed and their complementarities highlighted with reference to the case of the immunoglobulin antibody. Both artificial maps, constructed from immunoglobulin G entries in the Protein Data Bank and real tomograms are analyzed. Robustness issues and agreement with previously reported measurements are discussed.
|
|
| 2. |
- Essand, Magnus, et al.
(author)
-
Identification and characterization of a novel splicing variant of vesicular monoamine transporter 1
- 2005
-
In: Journal of Molecular Endocrinology. - : Bioscientifica. - 0952-5041 .- 1479-6813. ; 35:3, s. 489-501
-
Journal article (peer-reviewed)abstract
- Vesicular monoamine transporter 1 (VMAT1) is an integral protein in the membrane of secretory vesicles of neuroendocrine and endocrine cells that allows the transport of biogenic monoamines, such as serotonin, from the cytoplasm into the secretory vesicles. The full-length VMAT1 transcript is produced from 16 exons. We have identified and characterized an alternatively spliced form of VMAT1 that lacks exon 15, the next to last exon of VMAT1. The new form was therefore denoted VMAT1Delta15. Exon 15 does not contain an even multiple of three nucleotides. As a consequence, there is a shift of reading frame, and exon 16 is translated in an alternative reading frame, yielding a novel protein with a shorter and unrelated C-terminus compared with the native VMAT1 protein. VMAT1 and VMAT1Delta15 mRNAs are simultaneously expressed in normal and neoplastic neuroendocrine cells of the GI tract. However, VMAT1 expression is always higher than VMAT1Delta15 expression. We prove that VMAT1Delta15 is not localized in large, dense core vesicles as the native form but in the endoplasmic reticulum. Furthermore, while VMAT1 can take up serotonin, VMAT1Delta15 cannot, indicating different functions for the two forms of VMAT1.
|
|
| 3. |
- Fouard, Celine, et al.
(author)
-
An Objective Comparison between Gray Weighted Distance Transforms and Weighted Distance Transforms On Curved Spaces
- 2006
-
In: Discrete Geometry for Computer Imagery. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783540476511 ; , s. 259-270
-
Conference paper (peer-reviewed)abstract
- In this paper, we compare two different definitions of distance transform for gray level images: the Gray Weighted Distance Transform (GWDT), and the Weighted Distance Transform On Curved Space (WDTOCS). We show through theoretical and experimental comparisons the differences, the strengths and the weaknesses of these two distances.
|
|
| 4. |
|
|
| 5. |
- Gedda, Magnus
(author)
-
Clustering of Objects in 3D Electron Tomography Reconstructions of Protein Solutions Based on Shape Measurements
- 2005
-
In: Pattern Recognition and Image Analysis. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 3540288333 ; , s. 809-
-
Conference paper (peer-reviewed)abstract
- This paper evaluates whether shape features can be used for clustering objects in Sidec (tm), Electron Tomography (SET) reconstructions. SET reconstructions contain a large number of objects, and only a few of them are of interest. It is desired to limit the analysis to contain as few uninteresting objects as possible. Unsupervised hierarchical clustering is used to group objects into classes. Experiments are done on one synthetic data set and two data sets from a SET reconstruction of a human growth hormone (1hwg) in solution. The experiments indicate that clustering of objects in SET reconstructions based on shape features is useful for finding structural classes.
|
|
| 6. |
- Gedda, Magnus, et al.
(author)
-
Flexibility Description of the MET Protein Stalk Based on the Use of Non-Uniform B-Splines
- 2007
-
In: 12th International Conference on Computer Analysis of Images and Patterns. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783540742715 ; , s. 173-180
-
Conference paper (peer-reviewed)abstract
- The MET protein controls growth, invasion, and metastasis in cancer cells and is thereby of interest to study, for example from a structural point of view. For individual particle imaging by Cryo-Electron Tomography of the MET protein, or other proteins, dedicated image analysis methods are required to extract information in a robust way as the images have low contrast and resolution (with respect to the size of the imaged structure). We present a method to identify the two parts of the MET protein, Beta-propeller and stalk, using a fuzzy framework. Furthermore, we describe how a representation of the MET stalk, denoted stalk curve, can be identified based on the use of non-uniform B-splines. The stalk curve is used to extract relevant geometrical information about the stalk, e.g., to facilitate curvature and length measurements.
|
|
| 7. |
- Gedda, Magnus, et al.
(author)
-
Fuzzy Distance Based Hierarchical Clustering Calculated Using the A* Algorithm
- 2006
-
In: Combinatorial Image Analysis. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 3540351531 ; , s. 101-115
-
Conference paper (peer-reviewed)abstract
- We present a method for calculating fuzzy distances between pairs of points in an image using the A* algorithm and, furthermore, apply this method for fuzzy distance based hierarchical clustering. The method is general and can be of use in numerous applications. In our case we intend to use the clustering in an algorithm for delineation of objects corresponding to parts of proteins in 3D images. The image is defined as a fuzzy object and represented as a graph, enabling a path finding approach for distance calculations. The fuzzy distance between two adjacent points is used as edge weight and a heuristic is defined for fuzzy sets. A* is applied to the calculation of fuzzy distance between pair of points and hierarchical clustering is used to group the points. The normalised Hubert's statistic is used as validity index to determine the number of clusters. The method is tested on three 2D images; two synthetic images and one fuzzy distance transformed microscopy image of stem cells. All experiments show promising initial results.
|
|
| 8. |
- Gedda, Magnus, et al.
(author)
-
Separation of blob-like structures using fuzzy distance based hierarchical clustering
- 2006
-
In: Symposium on Image Analysis.
-
Conference paper (other academic/artistic)abstract
- We present a method for separation of clustered biomedical blob-like structures in 2D and 3D images. The local maxima found on the fuzzy distance transform of the image are grouped by fuzzy distance based hierarchical clustering and used as seeds in a seeded watershed segmentation to delineate each individual blob. The method shows good initial results and is illustrated on two types of images: bright field microscopy (2D) images of in vitro stem cells and cryo electron tomography (3D) images of the antibody immunoglobulin G.
|
|
| 9. |
- Sintorn, Ida-Maria, et al.
(author)
-
Medial grey-level based representation for proteins in volume images
- 2005
-
In: Pattern Recognition and Image Analysis. - 3540261540 ; , s. 421-428
-
Conference paper (peer-reviewed)abstract
- We present an algorithm to extract a medial representation of proteins in volume images. The representation (MGR) takes into account the internal grey-level distribution of the protein and can be extracted without first segmenting the image into object and background. We show how MGR can facilitate the analysis of the structure of the proteins and thereby also classification. Results are shown on two types of protein images.
|
|
| 10. |
- Svensson, Stina, et al.
(author)
-
Using a fuzzy framework for delineation and decomposition of immunoglobulin G in cryo electron tomographic images
- 2006
-
In: Proceedings The 18th International Conference on Pattern Recognition (ICPR 2006). - 0769525210 ; , s. 961-
-
Conference paper (peer-reviewed)abstract
- In structural studies of proteins, the first task is to identify the different parts of the protein. We present a robust method using a fuzzy framework for delineating a protein and to identify its parts. The method is used in a study of the immunoglobulin G antibody, individually imaged using cryo electron tomography, with satisfactory results.
|
|
