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Curic, Vladimir
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Publications (10 of 16) Show all publications
Kipper, K., Lundius, E. G., Ćurić, V., Nikic, I., Wiessler, M., Lemke, E. A. & Elf, J. (2017). Application of Noncanonical Amino Acids for Protein Labeling in a Genomically Recoded Escherichia coli. ACS Photonics, 6(2), 233-255
Open this publication in new window or tab >>Application of Noncanonical Amino Acids for Protein Labeling in a Genomically Recoded Escherichia coli
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2017 (English)In: ACS Photonics, E-ISSN 2330-4022, Vol. 6, no 2, p. 233-255Article in journal (Refereed) Published
Abstract [en]

Small synthetic fluorophores are in many ways superior to fluorescent proteins as labels for imaging. A major challenge is to use them for a protein-specific labeling in living cells. Here, we report on our use of noncanonical amino acids that are genetically encoded via the pyrrolysyl-tRNA/pyrrolysyl-RNA synthetase pair at artificially introduced TAG codons in a recoded E. coli strain. The strain is lacking endogenous TAG codons and the TAG-specific release factor RF1. The amino acids contain bioorthogonal groups that can be clicked to externally supplied dyes, thus enabling protein-specific labeling in live cells. We find that the noncanonical amino acid incorporation into the target protein is robust for diverse amino acids and that the usefulness of the recoded E. coli strain mainly derives from the absence of release factor RF1. However, the membrane permeable dyes display high nonspecific binding in intracellular environment and the electroporation of hydrophilic nonmembrane permeable dyes severely impairs growth of the recoded strain. In contrast, proteins exposed on the outer membrane of E. coli can be labeled with hydrophilic dyes with a high specificity as demonstrated by labeling of the osmoporin OmpC. Here, labeling can be made sufficiently specific to enable single molecule studies as exemplified by OmpC single particle tracking.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2017
Keywords
noncanonical amino acid, tetrazine, recoded E. coli, in vivo fluorescence labeling, OmpC, single particle tracking
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-320513 (URN)10.1021/acssynbio.6b00138 (DOI)000394736400009 ()27775882 (PubMedID)
Funder
EU, European Research CouncilSwedish Research CouncilKnut and Alice Wallenberg FoundationGerman Research Foundation (DFG), SPP1623
Available from: 2017-04-20 Created: 2017-04-20 Last updated: 2018-06-14Bibliographically approved
Jones, D., Leroy, P., Unoson, C., Fange, D., Curic, V., Lawson, M. J. & Elf, J. (2017). Kinetics of dCas9 target search in Escherichia coli. Science, 357(6358), 1420-1423
Open this publication in new window or tab >>Kinetics of dCas9 target search in Escherichia coli
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2017 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 357, no 6358, p. 1420-1423Article in journal (Refereed) Published
Abstract [en]

How fast can a cell locate a specific chromosomal DNA sequence specified by a single-stranded oligonucleotide? To address this question, we investigate the intracellular search processes of the Cas9 protein, which can be programmed by a guide RNA to bind essentially any DNA sequence. This targeting flexibility requires Cas9 to unwind the DNA double helix to test for correct base pairing to the guide RNA. Here we study the search mechanisms of the catalytically inactive Cas9 (dCas9) in living Escherichia coli by combining single-molecule fluorescence microscopy and bulk restriction-protection assays. We find that it takes a single fluorescently labeled dCas9 6 hours to find the correct target sequence, which implies that each potential target is bound for less than 30 milliseconds. Once bound, dCas9 remains associated until replication. To achieve fast targeting, both Cas9 and its guide RNA have to be present at high concentrations.

Place, publisher, year, edition, pages
AMER ASSOC ADVANCEMENT SCIENCE, 2017
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-337092 (URN)10.1126/science.aah7084 (DOI)000411880800052 ()28963258 (PubMedID)
Funder
EU, European Research CouncilSwedish Research CouncilKnut and Alice Wallenberg Foundation
Available from: 2018-01-25 Created: 2018-01-25 Last updated: 2018-01-25Bibliographically approved
Lindén, M., Curic, V., Amselem, E. & Elf, J. (2017). Pointwise error estimates in localization microscopy. Nature Communications, 8, Article ID 15115.
Open this publication in new window or tab >>Pointwise error estimates in localization microscopy
2017 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 15115Article in journal (Refereed) Published
Abstract [en]

Pointwise localization of individual fluorophores is a critical step in super-resolution localization microscopy and single particle tracking. Although the methods are limited by the localization errors of individual fluorophores, the pointwise localization precision has so far been estimated using theoretical best case approximations that disregard, for example, motion blur, defocus effects and variations in fluorescence intensity. Here, we show that pointwise localization precision can be accurately estimated directly from imaging data using the Bayesian posterior density constrained by simple microscope properties. We further demonstrate that the estimated localization precision can be used to improve downstream quantitative analysis, such as estimation of diffusion constants and detection of changes in molecular motion patterns. Finally, the quality of actual point localizations in live cell super-resolution microscopy can be improved beyond the information theoretic lower bound for localization errors in individual images, by modelling the movement of fluorophores and accounting for their pointwise localization uncertainty.

Place, publisher, year, edition, pages
Nature Publishing Group, 2017
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-322671 (URN)10.1038/ncomms15115 (DOI)000400487500002 ()28466844 (PubMedID)
Available from: 2017-05-29 Created: 2017-05-29 Last updated: 2018-01-13Bibliographically approved
Curic, V., Lefèvre, S. & Luengo Hendriks, C. L. (2015). Adaptive hit or miss transform. In: Mathematical Morphology and Its Applications to Signal and Image Processing: . Paper presented at ISMM 2015, May 27–29, Reykjavik, Iceland (pp. 741-752). Springer
Open this publication in new window or tab >>Adaptive hit or miss transform
2015 (English)In: Mathematical Morphology and Its Applications to Signal and Image Processing, Springer, 2015, p. 741-752Conference paper, Published paper (Refereed)
Abstract [en]

The Hit or Miss Transform is a fundamental morphological operator, and can be used for template matching. In this paper, we present a framework for adaptive Hit or Miss Transform, where structuring elements are adaptive with respect to the input image itself. We illustrate the difference between the new adaptive Hit or Miss Transform and the classical Hit or Miss Transform. As an example of its usefulness, we show how the new adaptive Hit or Miss Transform can detect particles in single molecule imaging.

Place, publisher, year, edition, pages
Springer, 2015
Series
Lecture Notes in Computer Science ; 9082
National Category
Computer Vision and Robotics (Autonomous Systems)
Research subject
Computerized Image Processing
Identifiers
urn:nbn:se:uu:diva-254744 (URN)10.1007/978-3-319-18720-4_62 (DOI)000362366800062 ()978-3-319-18719-8 (ISBN)
Conference
ISMM 2015, May 27–29, Reykjavik, Iceland
Available from: 2015-06-10 Created: 2015-06-10 Last updated: 2018-01-11Bibliographically approved
Curic, V., Lindblad, J., Sladoje, N., Sarve, H. & Borgefors, G. (2014). A new set distance and its application to shape registration. Pattern Analysis and Applications, 17(1), 141-152
Open this publication in new window or tab >>A new set distance and its application to shape registration
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2014 (English)In: Pattern Analysis and Applications, ISSN 1433-7541, E-ISSN 1433-755X, Vol. 17, no 1, p. 141-152Article in journal (Refereed) Published
National Category
Discrete Mathematics
Identifiers
urn:nbn:se:uu:diva-220413 (URN)10.1007/s10044-012-0290-x (DOI)000330839400011 ()
Available from: 2012-08-23 Created: 2014-03-13 Last updated: 2018-12-18Bibliographically approved
Curic, V., Landström, A., Thurley, M. J. & Luengo Hendriks, C. L. (2014). Adaptive Mathematical Morphology: a survey of the field. Pattern Recognition Letters, 47, 18-28
Open this publication in new window or tab >>Adaptive Mathematical Morphology: a survey of the field
2014 (English)In: Pattern Recognition Letters, ISSN 0167-8655, E-ISSN 1872-7344, Vol. 47, p. 18-28Article in journal (Refereed) Published
Abstract [en]

We present an up-to-date survey on the topic of adaptive mathematical morphology. A broad review of research performed within the field is provided, as well as an in-depth summary of the theoretical advances within the field. Adaptivity can come in many different ways, based on different attributes, measures, and parameters. Similarities and differences between a few selected methods for adaptive structuring elements are considered, providing perspective on the consequences of different types of adaptivity. We also provide a brief analysis of perspectives and trends within the field, discussing possible directions for future studies.

Keywords
Overview, Mathematical morphology, Adaptive morphology, Adaptive structuring elements, Adjunction property
National Category
Computer Vision and Robotics (Autonomous Systems)
Identifiers
urn:nbn:se:uu:diva-221159 (URN)10.1016/j.patrec.2014.02.022 (DOI)000339999200003 ()
Available from: 2014-03-18 Created: 2014-03-25 Last updated: 2018-01-11Bibliographically approved
Ćurić, V. (2014). Distance Functions and Their Use in Adaptive Mathematical Morphology. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>Distance Functions and Their Use in Adaptive Mathematical Morphology
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

One of the main problems in image analysis is a comparison of different shapes in images. It is often desirable to determine the extent to which one shape differs from another. This is usually a difficult task because shapes vary in size, length, contrast, texture, orientation, etc. Shapes can be described using sets of points, crisp of fuzzy. Hence, distance functions between sets have been used for comparing different shapes.

Mathematical morphology is a non-linear theory related to the shape or morphology of features in the image, and morphological operators are defined by the interaction between an image and a small set called a structuring element. Although morphological operators have been extensively used to differentiate shapes by their size, it is not an easy task to differentiate shapes with respect to other features such as contrast or orientation. One approach for differentiation on these type of features is to use data-dependent structuring elements.

In this thesis, we investigate the usefulness of various distance functions for: (i) shape registration and recognition; and (ii) construction of adaptive structuring elements and functions.

We examine existing distance functions between sets, and propose a new one, called the Complement weighted sum of minimal distances, where the contribution of each point to the distance function is determined by the position of the point within the set. The usefulness of the new distance function is shown for different image registration and shape recognition problems. Furthermore, we extend the new distance function to fuzzy sets and show its applicability to classification of fuzzy objects.

We propose two different types of adaptive structuring elements from the salience map of the edge strength: (i) the shape of a structuring element is predefined, and its size is determined from the salience map; (ii) the shape and size of a structuring element are dependent on the salience map. Using this salience map, we also define adaptive structuring functions. We also present the applicability of adaptive mathematical morphology to image regularization. The connection between adaptive mathematical morphology and Lasry-Lions regularization of non-smooth functions provides an elegant tool for image regularization.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2014. p. 88
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1137
Keywords
Image analysis, Distance functions, Mathematical morphology, Adaptive mathematical morphology, Image regularization
National Category
Computer Vision and Robotics (Autonomous Systems)
Research subject
Computerized Image Processing
Identifiers
urn:nbn:se:uu:diva-221568 (URN)978-91-554-8923-6 (ISBN)
Public defence
2014-05-23, Room 2347, Polacksbacken, Lägerhyddsvägen 2, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2014-04-28 Created: 2014-04-01 Last updated: 2018-01-11
Gonzalez-Castro, V., Debayle, J. & Curic, V. (2014). Pixel Classification Using General Adaptive Neighborhood-Based Features. In: Proceedings 22nd International Conference on Pattern Recognition (ICPR) 2014: . Paper presented at 22nd International Conference on Pattern Recognition, Stockholm, Sweden, August 24-28, 2014 (pp. 3750-3755).
Open this publication in new window or tab >>Pixel Classification Using General Adaptive Neighborhood-Based Features
2014 (English)In: Proceedings 22nd International Conference on Pattern Recognition (ICPR) 2014, 2014, p. 3750-3755Conference paper, Published paper (Refereed)
Abstract [en]

This paper introduces a new descriptor for characterizing and classifying the pixels of texture images by means of General Adaptive Neighborhoods (GANs). The GAN of a pixel is a spatial region surrounding it and fitting its local image structure. The features describing each pixel are then region-based and intensity-based measurements of its corresponding GAN. In addition, these features are combined with the gray-level values of adaptive mathematical morphology operators using GANs as structuring elements. The classification of each pixel of images belonging to five different textures of the VisTex database has been carried out to test the performance of this descriptor. For the sake of comparison, other adaptive neighborhoods introduced in the literature have also been used to extract these features from: the Morphological Amoebas (MA), adaptive geodesic neighborhoods (AGN) and salience adaptive structuring elements (SASE). Experimental results show that the GAN-based method outperforms the others for the performed classification task, achieving an overall accuracy of 97.25% in the five-way classifications, and area under curve values close to 1 in all the five "one class vs. all classes" binary classification problems.

Series
International Conference on Pattern Recognition, ISSN 1051-4651
National Category
Computational Mathematics
Identifiers
urn:nbn:se:uu:diva-238692 (URN)10.1109/ICPR.2014.644 (DOI)000359818003148 ()978-1-4799-5208-3 (ISBN)
Conference
22nd International Conference on Pattern Recognition, Stockholm, Sweden, August 24-28, 2014
Available from: 2014-12-15 Created: 2014-12-15 Last updated: 2015-10-13Bibliographically approved
Curic, V. & Luengo Hendriks, C. L. (2013). Salience-Based Parabolic Structuring Functions. In: Mathematical Morphology and Its Applications to Signal and Image Processing: . Paper presented at 11th International Symposium on Mathematical Morphology (pp. 183-194). Springer Berlin/Heidelberg
Open this publication in new window or tab >>Salience-Based Parabolic Structuring Functions
2013 (English)In: Mathematical Morphology and Its Applications to Signal and Image Processing, Springer Berlin/Heidelberg, 2013, p. 183-194Conference paper, Published paper (Refereed)
Abstract [en]

It has been shown that the use of the salience map based on the salience distance transform can be useful for the construction of spatially adaptive structuring elements. In this paper, we propose salience-based parabolic structuring functions that are defined for a fixed, predefined spatial support, and have low computational complexity. In addition, we discuss how to properly define adjunct morphological operators using the new spatially adaptive structuring functions. It is also possible to obtain flat adaptive structuring elements by thresholding the salience-based parabolic structuring functions.

Place, publisher, year, edition, pages
Springer Berlin/Heidelberg, 2013
Series
Lecture Notes in Computer Science, ISSN 0302-9743 ; 7883
National Category
Other Mathematics
Research subject
Mathematics with specialization in Applied Mathematics; Computerized Image Analysis
Identifiers
urn:nbn:se:uu:diva-204715 (URN)10.1007/978-3-642-38294-9_16 (DOI)978-3-642-38293-2 (ISBN)
Conference
11th International Symposium on Mathematical Morphology
Available from: 2013-08-09 Created: 2013-08-09 Last updated: 2014-04-29Bibliographically approved
Curic, V., Luengo Hendriks, C. L. & Borgefors, G. (2012). Adaptive structuring elements based on salience distance transform. In: In Proceedings of Swedish Society for Image Analysis, SSBA 2012. Paper presented at SSBA 2012. KTH, Stockholm
Open this publication in new window or tab >>Adaptive structuring elements based on salience distance transform
2012 (English)In: In Proceedings of Swedish Society for Image Analysis, SSBA 2012, KTH, Stockholm, 2012Conference paper, Oral presentation only (Other academic)
Abstract [en]

Spatially adaptive structuring elements adjust their shape to the local structures in the image, and are often defined by a ball in a geodesic distance or gray-weighted distance metric space. This paper introduces salience adaptive structuring elements as spatially variant structuring elements that modify not only their shape, but also their size according to the salience of the edges in the image. Consequently they have good properties for filtering.

Place, publisher, year, edition, pages
KTH, Stockholm: , 2012
National Category
Discrete Mathematics
Identifiers
urn:nbn:se:uu:diva-175578 (URN)
Conference
SSBA 2012
Available from: 2012-06-10 Created: 2012-06-10 Last updated: 2012-06-25
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