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Adler, Jeremy
Publications (10 of 12) Show all publications
Adler, J., Sintorn, I.-M., Strand, R. & Parmryd, I. (2019). Conventional analysis of movement on non-flat surfaces like the plasma membrane makes Brownian motion appear anomalous. Communications Biology, 2, Article ID 12.
Open this publication in new window or tab >>Conventional analysis of movement on non-flat surfaces like the plasma membrane makes Brownian motion appear anomalous
2019 (English)In: Communications Biology, ISSN 2399-3642, Vol. 2, article id 12Article in journal (Refereed) Published
National Category
Biophysics
Research subject
Computerized Image Processing
Identifiers
urn:nbn:se:uu:diva-380506 (URN)10.1038/s42003-018-0240-2 (DOI)000461148000001 ()30652124 (PubMedID)
Available from: 2019-01-08 Created: 2019-04-15 Last updated: 2019-05-07Bibliographically approved
Adler, J. & Parmryd, I. (2019). Quantifying colocalization: the MOC is a hybrid coefficient - an uninformative mix of co-occurrence and correlation [Letter to the editor]. Journal of Cell Science, 132(1), Article ID UNSP jcs222455.
Open this publication in new window or tab >>Quantifying colocalization: the MOC is a hybrid coefficient - an uninformative mix of co-occurrence and correlation
2019 (English)In: Journal of Cell Science, ISSN 0021-9533, E-ISSN 1477-9137, Vol. 132, no 1, article id UNSP jcs222455Article in journal, Letter (Other academic) Published
Place, publisher, year, edition, pages
COMPANY BIOLOGISTS LTD, 2019
National Category
Cell Biology
Identifiers
urn:nbn:se:uu:diva-376310 (URN)10.1242/jcs.222455 (DOI)000455900700008 ()30626689 (PubMedID)
Funder
Swedish Research Council, 201504764
Available from: 2019-02-05 Created: 2019-02-05 Last updated: 2019-02-05Bibliographically approved
Parmryd, I., Adler, J. & Bernhem, K. (2018). Membrane Topography can Cause Apparent Clustering - Identification and Differentiation from Genuine Clustering. Paper presented at 62nd Annual Meeting of the Biophysical-Society, FEB 17-21, 2018, San Francisco, CA.. Biophysical Journal, 114(3), 165A-165A
Open this publication in new window or tab >>Membrane Topography can Cause Apparent Clustering - Identification and Differentiation from Genuine Clustering
2018 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, no 3, p. 165A-165AArticle in journal, Meeting abstract (Other academic) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-357661 (URN)000430439600076 ()
Conference
62nd Annual Meeting of the Biophysical-Society, FEB 17-21, 2018, San Francisco, CA.
Available from: 2018-08-23 Created: 2018-08-23 Last updated: 2018-08-23Bibliographically approved
Parmryd, I. & Adler, J. (2017). Colocalisation - the Tale of Co-Occurrence and Correlation. Paper presented at 58th Annual Meeting of the Biophysical-Society, FEB 15-19, 2014, San Francisco, CA. Biophysical Journal, 112(3), 294A-294A
Open this publication in new window or tab >>Colocalisation - the Tale of Co-Occurrence and Correlation
2017 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, no 3, p. 294A-294AArticle in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
CELL PRESS, 2017
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-332756 (URN)000402375600456 ()
Conference
58th Annual Meeting of the Biophysical-Society, FEB 15-19, 2014, San Francisco, CA
Available from: 2017-11-06 Created: 2017-11-06 Last updated: 2017-11-06Bibliographically approved
Dinic, J., Riehl, A., Adler, J. & Parmryd, I. (2015). The T cell receptor resides in ordered plasma membrane nanodomains that aggregate upon patching of the receptor. Scientific Reports, 5, Article ID 10082.
Open this publication in new window or tab >>The T cell receptor resides in ordered plasma membrane nanodomains that aggregate upon patching of the receptor
2015 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 10082Article in journal (Refereed) Published
Abstract [en]

Two related models for T cell signalling initiation suggest either that T cell receptor (TCR) engagement leads to its recruitment to ordered membrane domains, often referred to as lipid rafts, where signalling molecules are enriched or that ordered TCR-containing membrane nanodomains coalesce upon TCR engagement. That ordered domains form upon TCR engagement, as they do upon lipid raft marker patching, has not been considered. The target of this study was to differentiate between those three options. Plasma membrane order was followed in live T cells at 37 °C using laurdan to report on lipid packing. Patching of the TCR that elicits a signalling response resulted in aggregation, not formation, of ordered plasma membrane domains in both Jurkat and primary T cells. The TCR colocalised with actin filaments at the plasma membrane in unstimulated Jurkat T cells, consistent with it being localised to ordered membrane domains. The colocalisation was most prominent in cells in G1 phase when the cells are ready to commit to proliferation. At other cell cycle phases the TCR was mainly found at perinuclear membranes. Our study suggests that the TCR resides in ordered plasma membrane domains that are linked to actin filaments and aggregate upon TCR engagement.

National Category
Other Medical Sciences not elsewhere specified
Research subject
Biology with specialization in Molecular Cell Biology
Identifiers
urn:nbn:se:uu:diva-252756 (URN)10.1038/srep10082 (DOI)000354118300001 ()25955440 (PubMedID)
Available from: 2015-05-11 Created: 2015-05-11 Last updated: 2017-12-04Bibliographically approved
Parmryd, I., Riehl, A., Dinic, J. & Adler, J. (2015). The T Cell Receptor Resides in Ordered Plasma Membrane Nanodomains that Aggregate Upon T Cell Activation. Biophysical Journal, 108(2), 98A-98A
Open this publication in new window or tab >>The T Cell Receptor Resides in Ordered Plasma Membrane Nanodomains that Aggregate Upon T Cell Activation
2015 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, no 2, p. 98A-98AArticle in journal, Meeting abstract (Other academic) Published
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-274841 (URN)000359471700496 ()
Available from: 2016-01-26 Created: 2016-01-26 Last updated: 2017-11-30Bibliographically approved
Adler, J. & Parmryd, I. (2014). Quantification of Colocalisation; Co-Occurrence, Correlation, Empty Voxels, Regions of Interest and Thresholding. Paper presented at 58th Annual Meeting of the Biophysical-Society, FEB 15-19, 2014, San Francisco, CA. Biophysical Journal, 106(2), 602A-602A
Open this publication in new window or tab >>Quantification of Colocalisation; Co-Occurrence, Correlation, Empty Voxels, Regions of Interest and Thresholding
2014 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 602A-602AArticle in journal, Meeting abstract (Other academic) Published
Abstract [en]

Measuring colocalisation is not straightforward with a plethora of coefficients that encapsulate different definitions. Measurements may also be implemented differently. Not only do measurements differ; interconversion is impossible making comparisons challenging. There is a need to cull coefficients and for clear definitions of what precisely is meant by colocalisation in individual studies. Colocalisation can be considered to have two components; co-occurrence which reports whether the fluorophores are found together and correlation which reports on the similarity in their patterns of intensity.

National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-228605 (URN)10.1016/j.bpj.2013.11.3333 (DOI)000337000403385 ()
Conference
58th Annual Meeting of the Biophysical-Society, FEB 15-19, 2014, San Francisco, CA
Available from: 2014-07-18 Created: 2014-07-17 Last updated: 2017-12-05Bibliographically approved
Adler, J. & Parmryd, I. (2014). Quantifying colocalization: thresholding, void voxels and the H-coef. PLoS ONE, 9(11), e111983
Open this publication in new window or tab >>Quantifying colocalization: thresholding, void voxels and the H-coef
2014 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 11, p. e111983-Article in journal (Refereed) Published
Abstract [en]

A critical step in the analysis of images is identifying the area of interest e.g. nuclei. When the nuclei are brighter than the remainder of the image an intensity can be chosen to identify the nuclei. Intensity thresholding is complicated by variations in the intensity of individual nuclei and their intensity relative to their surroundings. To compensate thresholds can be based on local rather than global intensities. By testing local thresholding methods we found that the local mean performed poorly while the Phansalkar method and a new method based on identifying the local background were superior. A new colocalization coefficient, the Hcoef, highlights a number of controversial issues. (i) Are molecular interactions measurable (ii) whether to include voxels without fluorophores in calculations, and (iii) the meaning of negative correlations. Negative correlations can arise biologically (a) because the two fluorophores are in different places or (b) when high intensities of one fluorophore coincide with low intensities of a second. The cases are distinct and we argue that it is only relevant to measure correlation using pixels that contain both fluorophores and, when the fluorophores are in different places, to just report the lack of co-occurrence and omit these uninformative negative correlation. The Hcoef could report molecular interactions in a homogenous medium. But biology is not homogenous and distributions also reflect physico-chemical properties, targeted delivery and retention. The Hcoef actually measures a mix of correlation and co-occurrence, which makes its interpretation problematic and in the absence of a convincing demonstration we advise caution, favouring separate measurements of correlation and of co-occurrence.

National Category
Cell Biology
Research subject
Biology with specialization in Molecular Cell Biology
Identifiers
urn:nbn:se:uu:diva-235777 (URN)10.1371/journal.pone.0111983 (DOI)000344402600086 ()25375829 (PubMedID)
Funder
Magnus Bergvall Foundation
Available from: 2014-11-10 Created: 2014-11-10 Last updated: 2017-12-05Bibliographically approved
Parmryd, I., Adler, J., Sintorn, I.-M. & Strand, R. (2013). Movement on Uneven Surfaces Displays Characteristic Features of Hop Diffusion. Paper presented at 57th Annual Meeting of the Biophysical-Society, FEB 02-06, 2013, Philadelphia, PA. Biophysical Journal, 104(2), 524A-524A
Open this publication in new window or tab >>Movement on Uneven Surfaces Displays Characteristic Features of Hop Diffusion
2013 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 104, no 2, p. 524A-524AArticle in journal, Meeting abstract (Other academic) Published
National Category
Medical Image Processing
Identifiers
urn:nbn:se:uu:diva-199053 (URN)10.1016/j.bpj.2012.11.2901 (DOI)000316074305176 ()
Conference
57th Annual Meeting of the Biophysical-Society, FEB 02-06, 2013, Philadelphia, PA
Available from: 2013-05-02 Created: 2013-05-02 Last updated: 2017-12-06Bibliographically approved
Hayashi, M., Majumdar, A., Li, X., Adler, J., Sun, Z., Vertuani, S., . . . Claesson-Welsh, L. (2013). VE-PTP regulates VEGFR2 activity in stalk cells to establish endothelial cell polarity and lumen formation. Nature Communications, 4, 1672
Open this publication in new window or tab >>VE-PTP regulates VEGFR2 activity in stalk cells to establish endothelial cell polarity and lumen formation
Show others...
2013 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, p. 1672-Article in journal (Refereed) Published
Abstract [en]

Vascular endothelial growth factor (VEGF) guides the path of new vessel sprouts by inducing VEGF receptor-2 activity in the sprout tip. In the stalk cells of the sprout, VEGF receptor-2 activity is downregulated. Here, we show that VEGF receptor-2 in stalk cells is dephosphorylated by the endothelium-specific vascular endothelial-phosphotyrosine phosphatase (VE-PTP). VE-PTP acts on VEGF receptor-2 located in endothelial junctions indirectly, via the Angiopoietin-1 receptor Tie2. VE-PTP inactivation in mouse embryoid bodies leads to excess VEGF receptor-2 activity in stalk cells, increased tyrosine phosphorylation of VE-cadherin and loss of cell polarity and lumen formation. Vessels in ve-ptp(-/-) teratomas also show increased VEGF receptor-2 activity and loss of endothelial polarization. Moreover, the zebrafish VE-PTP orthologue ptp-rb is essential for polarization and lumen formation in intersomitic vessels. We conclude that the role of Tie2 in maintenance of vascular quiescence involves VE-PTP-dependent dephosphorylation of VEGF receptor-2, and that VEGF receptor-2 activity regulates VE-cadherin tyrosine phosphorylation, endothelial cell polarity and lumen formation.

National Category
Natural Sciences Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-202980 (URN)10.1038/ncomms2683 (DOI)000318872100029 ()
Available from: 2013-07-01 Created: 2013-07-01 Last updated: 2017-12-06Bibliographically approved
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