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Parmryd, Ingela
Alternative names
Publications (10 of 44) Show all publications
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, 294A-294A p.Article 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
Fujimoto, T. & Parmryd, I. (2016). Interleaflet Coupling, Pinning, and Leaflet Asymmetry—Major Players in Plasma Membrane Nanodomain Formation. Frontiers in Cell and Developmental Biology, 4, Article ID 155.
Open this publication in new window or tab >>Interleaflet Coupling, Pinning, and Leaflet Asymmetry—Major Players in Plasma Membrane Nanodomain Formation
2016 (English)In: Frontiers in Cell and Developmental Biology, ISSN 2296-634X, Vol. 4, 155Article, review/survey (Refereed) Published
Abstract [en]

The plasma membrane has a highly asymmetric distribution of lipids and contains dynamic nanodomains many of which are liquid entities surrounded by a second, slightly different, liquid environment. Contributing to the dynamics is a continuous repartitioning of components between the two types of liquids and transient links between lipids and proteins, both to extracellular matrix and cytoplasmic components, that temporarily pin membrane constituents. This make plasma membrane nanodomains exceptionally challenging to study and much of what is known about membrane domains has been deduced from studies on model membranes at equilibrium. However, living cells are by definition not at equilibrium and lipids are distributed asymmetrically with inositol phospholipids, phosphatidylethanolamines and phosphatidylserines confined mostly to the inner leaflet and glyco- and sphingolipids to the outer leaflet. Moreover, each phospholipid group encompasses a wealth of species with different acyl chain combinations whose lateral distribution is heterogeneous. It is becoming increasingly clear that asymmetry and pinning play important roles in plasma membrane nanodomain formation and coupling between the two lipid monolayers. How asymmetry, pinning, and interdigitation contribute to the plasma membrane organization is only beginning to be unraveled and here we discuss their roles and interdependence.

National Category
Cell Biology
Research subject
Biology with specialization in Molecular Cell Biology
Identifiers
urn:nbn:se:uu:diva-312766 (URN)10.3389/fcell.2016.00155 (DOI)
Available from: 2017-01-12 Created: 2017-01-12 Last updated: 2017-01-13Bibliographically approved
Mahammad, S. & Parmryd, I. (2015). Cholesterol Depletion Using Methyl-β-cyclodextrin. In: Dylan M. Owen (Ed.), Methods in Membrane Lipids: (pp. 91-102). Springer, 1232.
Open this publication in new window or tab >>Cholesterol Depletion Using Methyl-β-cyclodextrin
2015 (English)In: Methods in Membrane Lipids / [ed] Dylan M. Owen, Springer, 2015, Vol. 1232, 91-102 p.Chapter in book (Refereed)
Abstract [en]

Cholesterol is an essential component of mammalian cells. It is the major lipid constituent of the plasma membrane and is also abundant in most other organelle membranes. In the plasma membrane cholesterol plays critical physical roles in the maintenance of membrane fluidity and membrane permeability. It is also important for membrane trafficking, cell signalling, and lipid as well as protein sorting. Cholesterol is essential for the formation of liquid ordered domains in model membranes, which in cells are known as lipid nanodomains or lipid rafts. Cholesterol depletion is widely used to study the role of cholesterol in cellular processes and can be performed over days using inhibitors of its synthesis or acutely over minutes using chemical reagents. Acute cholesterol depletion by methyl-β-cyclodextrin (MBCD) is the most widely used method and here we describe how it should be performed to avoid the common side-effect cell death.

Place, publisher, year, edition, pages
Springer, 2015
Series
Methods in Molecular Biology : Methods and Protocols, ISSN 1064-3745 ; 1232
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Medical Cell Biology; Molecular Cellbiology
Identifiers
urn:nbn:se:uu:diva-235778 (URN)10.1007/978-1-4939-1752-5_8 (DOI)25331130 (PubMedID)2-s2.0-84954607751 (Scopus ID)9781493917518 (ISBN)9781493917525 (ISBN)
Available from: 2014-11-10 Created: 2014-11-10 Last updated: 2016-12-02Bibliographically approved
Ashrafzadeh, P. & Parmryd, I. (2015). Methods applicable to membrane nanodomain studies?. Essays in Biochemistry, 57, 57-68.
Open this publication in new window or tab >>Methods applicable to membrane nanodomain studies?
2015 (English)In: Essays in Biochemistry, ISSN 0071-1365, E-ISSN 1744-1358, Vol. 57, 57-68 p.Article, review/survey (Refereed) Published
Abstract [en]

Membrane nanodomains are dynamic liquid entities surrounded by another type of dynamic liquid. Diffusion can take place inside, around and in and out of the domains, and membrane components therefore continuously shift between domains and their surroundings. In the plasma membrane, there is the further complexity of links between membrane lipids and proteins both to the extracellular matrix and to intracellular proteins such as actin filaments. In addition, new membrane components are continuously delivered and old ones removed. On top of this, cells move. Taking all of this into account imposes great methodological challenges, and in the present chapter we discuss some methods that are currently used for membrane nanodomain studies, what information they can provide and their weaknesses.

Place, publisher, year, edition, pages
London: Portland Press, 2015
Keyword
cholesterol; detergent-resistant membrane; giant plasma membrane vesicle; laurdan; liquid disorder; liquid order; membrane nanodomain; methyl-beta-cyclodextrin
National Category
Cell Biology Biochemistry and Molecular Biology Biophysics
Identifiers
urn:nbn:se:uu:diva-244445 (URN)10.1042/bse0570057 (DOI)000358260800005 ()25658344 (PubMedID)
Available from: 2015-02-16 Created: 2015-02-16 Last updated: 2017-12-04Bibliographically 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, 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, 98A-98A p.Article 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
Ashrafzadeh, P., Dinic, J. & Parmryd, I. (2014). Actin Filaments Attachment to the Plasma Membrane Cause the Formation of Ordered Lipid Domains in Live Cells. Paper presented at 58th Annual Meeting of the Biophysical-Society, FEB 15-19, 2014, San Francisco, CA. Biophysical Journal, 106(2), 706A-706A.
Open this publication in new window or tab >>Actin Filaments Attachment to the Plasma Membrane Cause the Formation of Ordered Lipid Domains in Live Cells
2014 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, 706A-706A p.Article in journal, Meeting abstract (Other academic) Published
Abstract [en]

The aim of this study was to investigate the relationship between ordered plasma membrane nanodomains and actin filaments using di-4-ANEPPDHQ and laurdan together with the reagents that affect actin filament dynamics in live Jurkat and primary T cells. The degree of lipid packing can be quantified using polarity sensitive membrane dyes such as laurdan and di-4-ANEPPDHQ. These two dyes display a red shift in their emission peaks for membranes in ld phase relative to lo phase. Laurdan is uncharged and can easily flip between two leaflets of the plasma membrane and we demonstrate that it reports equally on the two leaflets of the plasma membrane.

National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-228608 (URN)10.1016/j.bpj.2013.11.3904 (DOI)000337000404033 ()
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). 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, 602A-602A p.Article 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, e111983- p.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
Dinic, J., Ashrafzadeh, P. & Parmryd, I. (2013). Actin filaments attachment at the plasma membrane in live cells cause the formation of ordered lipid domains. Biochimica et Biophysica Acta - Biomembranes, 1828(3), 1102-1111.
Open this publication in new window or tab >>Actin filaments attachment at the plasma membrane in live cells cause the formation of ordered lipid domains
2013 (English)In: Biochimica et Biophysica Acta - Biomembranes, ISSN 0005-2736, E-ISSN 1879-2642, Vol. 1828, no 3, 1102-1111 p.Article in journal (Refereed) Published
Abstract [en]

The relationship between ordered plasma membrane nanodomains, known as lipid rafts, and actin filaments is the focus of this study. Plasma membrane order was followed in live cells at 37°C using laurdan and di-4-ANEPPDHQ to report on lipid packing. Disrupting actin polymerisation decreased the fraction of ordered domains, which strongly argue that unstimulated cells have a basal level of ordered domains. Stabilising actin filaments had the opposite effect and increased the proportion of ordered domains. Decreasing the plasma membrane level of 4-phosphate-inositides lowers the number of attachment points for actin filaments and reduced the proportion of ordered domains. Aggregation of plasma membrane molecules, both lipid raft and non-lipid raft markers, lead to the formation of ordered domains. The increase in ordered domains was correlated with an increase in actin filaments just beneath the plasma membrane. In live cell plasma membrane blebs, which are detached from the underlying actin filaments, the fraction of ordered domains was low and GM1 could not be patched to form ordered domains. We conclude that ordered domains form when actin filaments attach to the plasma membrane. This downplays lipid-lipid interactions as the main driving force behind the formation of ordered membrane domains in vivo, giving greater prominence to membrane-intracellular filament interactions.

National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-196480 (URN)10.1016/j.bbamem.2012.12.004 (DOI)000315473400021 ()23246974 (PubMedID)
Available from: 2013-03-10 Created: 2013-03-10 Last updated: 2018-01-11Bibliographically approved
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