uu.seUppsala universitets publikationer
Ändra sökning
Länk till posten
Permanent länk

Direktlänk
BETA
Adler, Jeremy
Publikationer (10 of 12) Visa alla publikationer
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.
Öppna denna publikation i ny flik eller fönster >>Conventional analysis of movement on non-flat surfaces like the plasma membrane makes Brownian motion appear anomalous
2019 (Engelska)Ingår i: Communications Biology, ISSN 2399-3642, Vol. 2, artikel-id 12Artikel i tidskrift (Refereegranskat) Published
Nationell ämneskategori
Biofysik
Forskningsämne
Datoriserad bildbehandling
Identifikatorer
urn:nbn:se:uu:diva-380506 (URN)10.1038/s42003-018-0240-2 (DOI)000461148000001 ()30652124 (PubMedID)
Tillgänglig från: 2019-01-08 Skapad: 2019-04-15 Senast uppdaterad: 2019-05-07Bibliografiskt granskad
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.
Öppna denna publikation i ny flik eller fönster >>Quantifying colocalization: the MOC is a hybrid coefficient - an uninformative mix of co-occurrence and correlation
2019 (Engelska)Ingår i: Journal of Cell Science, ISSN 0021-9533, E-ISSN 1477-9137, Vol. 132, nr 1, artikel-id UNSP jcs222455Artikel i tidskrift, Letter (Övrigt vetenskapligt) Published
Ort, förlag, år, upplaga, sidor
COMPANY BIOLOGISTS LTD, 2019
Nationell ämneskategori
Cellbiologi
Identifikatorer
urn:nbn:se:uu:diva-376310 (URN)10.1242/jcs.222455 (DOI)000455900700008 ()30626689 (PubMedID)
Forskningsfinansiär
Vetenskapsrådet, 201504764
Tillgänglig från: 2019-02-05 Skapad: 2019-02-05 Senast uppdaterad: 2019-02-05Bibliografiskt granskad
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
Öppna denna publikation i ny flik eller fönster >>Membrane Topography can Cause Apparent Clustering - Identification and Differentiation from Genuine Clustering
2018 (Engelska)Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, nr 3, s. 165A-165AArtikel i tidskrift, Meeting abstract (Övrigt vetenskapligt) Published
Nationell ämneskategori
Biofysik
Identifikatorer
urn:nbn:se:uu:diva-357661 (URN)000430439600076 ()
Konferens
62nd Annual Meeting of the Biophysical-Society, FEB 17-21, 2018, San Francisco, CA.
Tillgänglig från: 2018-08-23 Skapad: 2018-08-23 Senast uppdaterad: 2018-08-23Bibliografiskt granskad
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
Öppna denna publikation i ny flik eller fönster >>Colocalisation - the Tale of Co-Occurrence and Correlation
2017 (Engelska)Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, nr 3, s. 294A-294AArtikel i tidskrift, Meeting abstract (Övrigt vetenskapligt) Published
Ort, förlag, år, upplaga, sidor
CELL PRESS, 2017
Nationell ämneskategori
Biofysik
Identifikatorer
urn:nbn:se:uu:diva-332756 (URN)000402375600456 ()
Konferens
58th Annual Meeting of the Biophysical-Society, FEB 15-19, 2014, San Francisco, CA
Tillgänglig från: 2017-11-06 Skapad: 2017-11-06 Senast uppdaterad: 2017-11-06Bibliografiskt granskad
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.
Öppna denna publikation i ny flik eller fönster >>The T cell receptor resides in ordered plasma membrane nanodomains that aggregate upon patching of the receptor
2015 (Engelska)Ingår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, artikel-id 10082Artikel i tidskrift (Refereegranskat) 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.

Nationell ämneskategori
Övrig annan medicin och hälsovetenskap
Forskningsämne
Biologi med inriktning mot molekylär cellbiologi
Identifikatorer
urn:nbn:se:uu:diva-252756 (URN)10.1038/srep10082 (DOI)000354118300001 ()25955440 (PubMedID)
Tillgänglig från: 2015-05-11 Skapad: 2015-05-11 Senast uppdaterad: 2017-12-04Bibliografiskt granskad
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
Öppna denna publikation i ny flik eller fönster >>The T Cell Receptor Resides in Ordered Plasma Membrane Nanodomains that Aggregate Upon T Cell Activation
2015 (Engelska)Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, nr 2, s. 98A-98AArtikel i tidskrift, Meeting abstract (Övrigt vetenskapligt) Published
Nationell ämneskategori
Medicinsk bioteknologi (med inriktning mot cellbiologi (inklusive stamcellsbiologi), molekylärbiologi, mikrobiologi, biokemi eller biofarmaci)
Identifikatorer
urn:nbn:se:uu:diva-274841 (URN)000359471700496 ()
Tillgänglig från: 2016-01-26 Skapad: 2016-01-26 Senast uppdaterad: 2017-11-30Bibliografiskt granskad
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
Öppna denna publikation i ny flik eller fönster >>Quantification of Colocalisation; Co-Occurrence, Correlation, Empty Voxels, Regions of Interest and Thresholding
2014 (Engelska)Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, nr 2, s. 602A-602AArtikel i tidskrift, Meeting abstract (Övrigt vetenskapligt) 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.

Nationell ämneskategori
Biofysik
Identifikatorer
urn:nbn:se:uu:diva-228605 (URN)10.1016/j.bpj.2013.11.3333 (DOI)000337000403385 ()
Konferens
58th Annual Meeting of the Biophysical-Society, FEB 15-19, 2014, San Francisco, CA
Tillgänglig från: 2014-07-18 Skapad: 2014-07-17 Senast uppdaterad: 2017-12-05Bibliografiskt granskad
Adler, J. & Parmryd, I. (2014). Quantifying colocalization: thresholding, void voxels and the H-coef. PLoS ONE, 9(11), e111983
Öppna denna publikation i ny flik eller fönster >>Quantifying colocalization: thresholding, void voxels and the H-coef
2014 (Engelska)Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, nr 11, s. e111983-Artikel i tidskrift (Refereegranskat) 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.

Nationell ämneskategori
Cellbiologi
Forskningsämne
Biologi med inriktning mot molekylär cellbiologi
Identifikatorer
urn:nbn:se:uu:diva-235777 (URN)10.1371/journal.pone.0111983 (DOI)000344402600086 ()25375829 (PubMedID)
Forskningsfinansiär
Magnus Bergvalls Stiftelse
Tillgänglig från: 2014-11-10 Skapad: 2014-11-10 Senast uppdaterad: 2017-12-05Bibliografiskt granskad
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
Öppna denna publikation i ny flik eller fönster >>Movement on Uneven Surfaces Displays Characteristic Features of Hop Diffusion
2013 (Engelska)Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 104, nr 2, s. 524A-524AArtikel i tidskrift, Meeting abstract (Övrigt vetenskapligt) Published
Nationell ämneskategori
Medicinsk bildbehandling
Identifikatorer
urn:nbn:se:uu:diva-199053 (URN)10.1016/j.bpj.2012.11.2901 (DOI)000316074305176 ()
Konferens
57th Annual Meeting of the Biophysical-Society, FEB 02-06, 2013, Philadelphia, PA
Tillgänglig från: 2013-05-02 Skapad: 2013-05-02 Senast uppdaterad: 2017-12-06Bibliografiskt granskad
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
Öppna denna publikation i ny flik eller fönster >>VE-PTP regulates VEGFR2 activity in stalk cells to establish endothelial cell polarity and lumen formation
Visa övriga...
2013 (Engelska)Ingår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, s. 1672-Artikel i tidskrift (Refereegranskat) 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.

Nationell ämneskategori
Naturvetenskap Medicin och hälsovetenskap
Identifikatorer
urn:nbn:se:uu:diva-202980 (URN)10.1038/ncomms2683 (DOI)000318872100029 ()
Tillgänglig från: 2013-07-01 Skapad: 2013-07-01 Senast uppdaterad: 2017-12-06Bibliografiskt granskad
Organisationer

Sök vidare i DiVA

Visa alla publikationer