scholarly journals Automated analysis of invadopodia dynamics in live cells

2014 ◽  
Author(s):  
Matthew E Berginski ◽  
Sarah J Creed ◽  
Shelly Cochran ◽  
David W Roadcap ◽  
James E Bear ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Metastatic Cancer ◽  
Automated Analysis ◽  
Time Lapse ◽  
Cell Types ◽  
Live Cells ◽  
Imaging Data ◽  
The Matrix ◽  
Invadopodia Formation

Multiple cell types form specialized protein complexes, podosomes or invadopodia and collectively referred to as invadosomes, which are used by the cell to actively degrade the surrounding extracellular matrix. Due to their potential importance in both healthy physiology as well as in pathological conditions such as cancer, the characterization of these structures has been of increasing interest. Following early descriptions of invadopodia, assays were developed which labelled the matrix underneath metastatic cancer cells allowing for the assessment of invadopodia activity in motile cells. However, characterization of invadopodia using these methods has traditionally been done manually with time-consuming and potentially biased quantification methods, limiting the number of experiments and the quantity of data that can be analysed. We have developed a system to automate the segmentation, tracking and quantification of invadopodia in time-lapse fluorescence image sets at both the single invadopodia level and whole cell level. We rigorously tested the ability of the method to detect changes in invadopodia formation and dynamics through the use of well-characterized small molecule inhibitors, with known effects on invadopodia. Our results demonstrate the ability of this analysis method to quantify changes in invadopodia formation from live cell imaging data in a high throughput, automated manner.

scholarly journals Automated analysis of invadopodia dynamics in live cells

2014 ◽  
Author(s):  
Matthew E Berginski ◽  
Sarah J Creed ◽  
Shelly Cochran ◽  
David W Roadcap ◽  
James E Bear ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Metastatic Cancer ◽  
Automated Analysis ◽  
Time Lapse ◽  
Cell Types ◽  
Live Cells ◽  
Imaging Data ◽  
The Matrix ◽  
Invadopodia Formation

Multiple cell types form specialized protein complexes, podosomes or invadopodia and collectively referred to as invadosomes, which are used by the cell to actively degrade the surrounding extracellular matrix. Due to their potential importance in both healthy physiology as well as in pathological conditions such as cancer, the characterization of these structures has been of increasing interest. Following early descriptions of invadopodia, assays were developed which labelled the matrix underneath metastatic cancer cells allowing for the assessment of invadopodia activity in motile cells. However, characterization of invadopodia using these methods has traditionally been done manually with time-consuming and potentially biased quantification methods, limiting the number of experiments and the quantity of data that can be analysed. We have developed a system to automate the segmentation, tracking and quantification of invadopodia in time-lapse fluorescence image sets at both the single invadopodia level and whole cell level. We rigorously tested the ability of the method to detect changes in invadopodia formation and dynamics through the use of well-characterized small molecule inhibitors, with known effects on invadopodia. Our results demonstrate the ability of this analysis method to quantify changes in invadopodia formation from live cell imaging data in a high throughput, automated manner.

scholarly journals Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase

2015 ◽  
Vol 112 (39) ◽  
pp. 12093-12098 ◽  
Author(s):  
Chiao-Lin Chen ◽  
Yanhui Hu ◽  
Namrata D. Udeshi ◽  
Thomas Y. Lau ◽  
Frederik Wirtz-Peitz ◽  
...  
Keyword(s):  
Ascorbate Peroxidase ◽  
Protein Interactions ◽  
Protein Complexes ◽  
Cell Types ◽  
Live Cells ◽  
Specific Cell ◽  
Physiological Conditions ◽  
Subcellular Domains ◽  
Endogenous Proteins

Characterization of the proteome of organelles and subcellular domains is essential for understanding cellular organization and identifying protein complexes as well as networks of protein interactions. We established a proteomic mapping platform in live Drosophila tissues using an engineered ascorbate peroxidase (APEX). Upon activation, the APEX enzyme catalyzes the biotinylation of neighboring endogenous proteins that can then be isolated and identified by mass spectrometry. We demonstrate that APEX labeling functions effectively in multiple fly tissues for different subcellular compartments and maps the mitochondrial matrix proteome of Drosophila muscle to demonstrate the power of APEX for characterizing subcellular proteomes in live cells. Further, we generate “MitoMax,” a database that provides an inventory of Drosophila mitochondrial proteins with subcompartmental annotation. Altogether, APEX labeling in live Drosophila tissues provides an opportunity to characterize the organelle proteome of specific cell types in different physiological conditions.

scholarly journals Interphase Nuclei of Many Mammalian Cell Types Contain Deep, Dynamic, Tubular Membrane-bound Invaginations of the Nuclear Envelope

1997 ◽  
Vol 136 (3) ◽  
pp. 531-544 ◽  
Author(s):  
Mark Fricker ◽  
Michael Hollinshead ◽  
Nick White ◽  
David Vaux
Keyword(s):  
Nuclear Envelope ◽  
Time Lapse ◽  
Cell Types ◽  
Live Cells ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Nuclear Surface ◽  
Topological Features ◽  
Cytoplasmic Transport ◽  
Pore Complexes

The nuclear envelope consists of a doublemembraned extension of the rough endoplasmic reticulum. In this report we describe long, dynamic tubular channels, derived from the nuclear envelope, that extend deep into the nucleoplasm. These channels show cell-type specific morphologies ranging from single short stubs to multiple, complex, branched structures. Some channels transect the nucleus entirely, opening at two separate points on the nuclear surface, while others terminate at or close to nucleoli. These channels are distinct from other topological features of the nuclear envelope, such as lobes or folds. The channel wall consists of two membranes continuous with the nuclear envelope, studded with features indistinguishable from nuclear pore complexes, and decorated on the nucleoplasmic surface with lamins. The enclosed core is continuous with the cytoplasm, and the lumenal space between the membranes contains soluble ER-resident proteins (protein disulphide isomerase and glucose-6-phosphatase). Nuclear channels are also found in live cells labeled with the lipophilic dye DiOC6. Time-lapse imaging of DiOC6-labeled cells shows that the channels undergo changes in morphology and spatial distribution within the interphase nucleus on a timescale of minutes. The presence of a cytoplasmic core and nuclear pore complexes in the channel walls suggests a possible role for these structures in nucleo–cytoplasmic transport. The clear association of a subset of these structures with nucleoli would also be consistent with such a transport role.

Polygonal networks in living chick embryonic cells

1981 ◽  
Vol 52 (1) ◽  
pp. 55-69
Author(s):  
G.W. Ireland ◽  
F.C. Voon
Keyword(s):  
Dorsal Surface ◽  
Time Lapse ◽  
Cell Types ◽  
Outer Edge ◽  
Live Cells ◽  
Embryonic Cells ◽  
Embryo Cells ◽  
Dissociated Cells ◽  
The Relationship ◽  
Free Edges

Regular polygonal networks have been found in explants and dissociated cells of early chick embryos. These networks are readily observable in live cells with phase-contrast optics thus allowing time-lapse cinemicroscopy. They consisted of a regular pattern of nodes and radiating struts found predominantly in the lamelliplasm of the free edges of the cells bordering explants. At the outer edge, the network was terminated by radial struts associated with substrate-attached retraction processes whilst toward the centre of the cells it faded out. The network was also associated with stress fibres running across the cell and with microextensions on the dorsal surface. Even within one cell the network varied in size. Time-lapse films showed that microvilli were protruded from the dorsal surface over the nodes. Although the cells containing the networks were poorly motile the network itself was a mobile structure. Many explants from regions differing in prospective fates developed these networks after 2–4 days in culture. They appeared earlier in the smaller less yolky cells of definitive endoblast and epiblast. Experiments with dissociated and reaggregated cells confirmed their occurrence mainly in free edges of cells. The relationship between these networks seen in living chick embryo cells and those seen in other cell types using immunofluorescent techniques is discussed and a mechanism is proposed for their formation.

scholarly journals Quantification of proteins, protein complexes and mRNA in single cells by proximity-sequencing

2020 ◽  
Author(s):  
Luke Vistain ◽  
Hoang Van Phan ◽  
Christian Jordi ◽  
Mengjie Chen ◽  
Sai T. Reddy ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
Single Cells ◽  
Cell Types ◽  
Cellular Behaviors ◽  
Functional States ◽  
Drug Studies ◽  
New Protein

Multiplexed analysis of single-cells enables accurate modeling of cellular behaviors, classification of new cell types, and characterization of their functional states. Here we present proximity-sequencing (Prox-seq), a method for simultaneous measurement of an individual cell’s proteins, protein complexes and mRNA. Prox-seq utilizes deep sequencing and barcoded proximity assays to measure proteins and their complexes from all pairwise combinations of targeted proteins, in thousands of single-cells. The number of measured protein complexes scales quadratically with the number of targeted proteins, providing unparalleled multiplexing capacity. We developed a high-throughput experimental and computational pipeline and demonstrated the potential of Prox-Seq for multi-omic analysis with a panel of 13 barcoded proximity probes, enabling the measurement of 91 protein complexes, along with thousands of mRNA molecules in single T-cells and B-cells. Prox-seq provides access to an untapped yet powerful measurement modality for single-cell phenotyping and can discover new protein interactions in signaling and drug studies.

scholarly journals Characterization of Individual Projections Reveal That Neuromasts of the Zebrafish Lateral Line are Innervated by Multiple Inhibitory Efferent Cells

2021 ◽  
Vol 15 ◽  
Author(s):  
Remy Manuel ◽  
Ana Belen Iglesias Gonzalez ◽  
Judith Habicher ◽  
Harmen Kornelis Koning ◽  
Henrik Boije
Keyword(s):  
Lateral Line ◽  
Sensory System ◽  
Time Lapse ◽  
Cell Types ◽  
The Body ◽  
Posterior Lateral Line ◽  
Distinct Cell ◽  
Efferent Neurons ◽  
Time Lapse Imaging

The zebrafish lateral line is a sensory system used to detect changes in water flow. It is comprized of clusters of superficial hair cells called neuromasts. Modulation occurs via excitatory and inhibitory efferent neurons located in the brain. Using mosaic transgenic labeling we provide an anatomical overview of the lateral line projections made by individual inhibitory efferent neurons in 5-day old zebrafish larvae. For each hemisphere we estimate there to be six inhibitory efferent neurons located in two different nuclei. Three distinct cell types were classified based on their projections; to the anterior lateral line around the head, to the posterior lateral line along the body, or to both. Our analyses corroborate previous studies employing back-fills, but our transgenic labeling allowed a more thorough characterization of their morphology. We found that individual inhibitory efferent cells connect to multiple neuromasts and that a single neuromast is connected by multiple inhibitory efferent cells. The efferent axons project to the sensory ganglia and follow the sensory axon tract along the lateral line. Time-lapse imaging revealed that inhibitory efferent axons do not migrate with the primordium as the primary sensory afferent does, but follow with an 8–14 h lag. These data bring new insights into the formation of a sensory circuit and support the hypothesis that different classes of inhibitory efferent cells have different functions. Our findings provide a foundation for future studies focussed toward unraveling how and when sensory perception is modulated by different efferent cells.

scholarly journals Crosstalk between astrocytes and microglia results in increased degradation of α-synuclein and amyloid-β aggregates

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Jinar Rostami ◽  
Tobias Mothes ◽  
Mahshad Kolahdouzan ◽  
Olle Eriksson ◽  
Mohsen Moslem ◽  
...  
Keyword(s):  
Amyloid Β ◽  
Protein Aggregates ◽  
Time Lapse ◽  
Cell Types ◽  
Alpha Synuclein ◽  
Culture Chamber ◽  
Imaging Data ◽  
Intracellular Protein ◽  
Membrane Structures ◽  
Tunneling Nanotubes

Abstract Background Alzheimer’s disease (AD) and Parkinson’s disease (PD) are characterized by brain accumulation of aggregated amyloid-beta (Aβ) and alpha-synuclein (αSYN), respectively. In order to develop effective therapies, it is crucial to understand how the Aβ/αSYN aggregates can be cleared. Compelling data indicate that neuroinflammatory cells, including astrocytes and microglia, play a central role in the pathogenesis of AD and PD. However, how the interplay between the two cell types affects their clearing capacity and consequently the disease progression remains unclear. Methods The aim of the present study was to investigate in which way glial crosstalk influences αSYN and Aβ pathology, focusing on accumulation and degradation. For this purpose, human-induced pluripotent cell (hiPSC)-derived astrocytes and microglia were exposed to sonicated fibrils of αSYN or Aβ and analyzed over time. The capacity of the two cell types to clear extracellular and intracellular protein aggregates when either cultured separately or in co-culture was studied using immunocytochemistry and ELISA. Moreover, the capacity of cells to interact with and process protein aggregates was tracked using time-lapse microscopy and a customized “close-culture” chamber, in which the apical surfaces of astrocyte and microglia monocultures were separated by a <1 mm space. Results Our data show that intracellular deposits of αSYN and Aβ are significantly reduced in co-cultures of astrocytes and microglia, compared to monocultures of either cell type. Analysis of conditioned medium and imaging data from the “close-culture” chamber experiments indicate that astrocytes secrete a high proportion of their internalized protein aggregates, while microglia do not. Moreover, co-cultured astrocytes and microglia are in constant contact with each other via tunneling nanotubes and other membrane structures. Notably, our live cell imaging data demonstrate that microglia, when attached to the cell membrane of an astrocyte, can attract and clear intracellular protein deposits from the astrocyte. Conclusions Taken together, our data demonstrate the importance of astrocyte and microglia interactions in Aβ/αSYN clearance, highlighting the relevance of glial cellular crosstalk in the progression of AD- and PD-related brain pathology.

scholarly journals Label-free three-dimensional analyses of live cells with deep-learning-based segmentation exploiting refractive index distributions

2021 ◽  
Author(s):  
Jinho Choi ◽  
Hye-Jin Kim ◽  
Gyuhyeon Sim ◽  
Sumin Lee ◽  
Wei Sun Park ◽  
...  
Keyword(s):  
Cell Biology ◽  
Lipid Droplets ◽  
Three Dimensional ◽  
Time Lapse ◽  
Cell Types ◽  
Live Cells ◽  
Label Free ◽  
Subcellular Organelles ◽  
Long Time ◽  
Three Dimensional Segmentation

Visualisations and analyses of cellular and subcellular organelles in biological cells is crucial for the study of cell biology. However, existing imaging methods require the use of exogenous labelling agents, which prevents the long-time assessments of live cells in their native states. Here we propose and experimentally demonstrate three-dimensional segmentation of subcellular organelles in unlabelled live cells, exploiting a 3D U-Net-based architecture. We present the high-precision three-dimensional segmentation of cell membrane, nucleus membrane, nucleoli, and lipid droplets of various cell types. Time-lapse analyses of dynamics of activated immune cells are also analysed using label-free segmentation.

scholarly journals Quantitative behavior of protein complexes in human cells

2018 ◽  
Author(s):  
Morteza H Chalabi ◽  
Vasileios Tsiamis ◽  
Lukas Käll ◽  
Fabio Vandin ◽  
Veit Schwämmle
Keyword(s):  
Web Service ◽  
Human Cell ◽  
Protein Complexes ◽  
Complex Function ◽  
Cell Types ◽  
Human Cells ◽  
Control Mechanisms ◽  
Complex Behavior ◽  
Link Type

AbstractTranslational and post-translational control mechanisms in the cell result in widely observable differences between measured gene transcription and protein abundances. Herein, protein complexes are among the most tightly controlled entities by selective degradation of their individual proteins. They furthermore act as control hubs that regulate highly important processes in the cell and exhibit a high functional diversity due to their ability to change their composition and their structure. To better understand and predict these functional states, extensive characterization of complex composition, behavior, and abundance is necessary. Mass spectrometry provides an unbiased approach to directly determine protein abundances across cell populations and thus to profile a comprehensive abundance map of proteins. We investigated the behavior of protein subunits in known complexes by comparing their abundance profiles across up to 140 cell types available in ProteomicsDB. After thorough assessment of different randomization methods and statistical scoring algorithms, we developed a computational tool to quantify the significance of concurrent profiles within a complex, therefore providing insights into the conservation of their composition across human cell types. We identified the intrinsic structures in complex behavior that allow to determine which proteins orchestrate complex function. This analysis can be extended to investigate common profiles within arbitrary protein groups. With the CoExpresso web service, we offer a potent scoring scheme to assess proteins for their co-regulation and thereby offer insight into their potential for forming functional groups like protein complexes. CoExpresso can be accessed through http://computproteomics/Apps/CoExpresso. Source code and R scripts for database generation are available at https://bitbucket.org/veitveit/coexpresso.Author summaryMany proteins form multi-functional assemblies called protein complexes instead of working as singly units. These complexes control most processes in the cell making the full characterization of their behavior inevitable to understand cellular control mechanisms. Detailed knowledge about complex behavior will elucidate biomarkers and drug targets that exhibit and correct aberrant cell states, respectively. We investigated abundance changes of the protein complex components over more than 100 different human cell types. By using statistical scoring models, we estimated the evidence for the co-regulation of the proteins and revealed which proteins form subunits with impact on complex function and composition. By providing the interactive web service CoExpresso, any combination of proteins can be tested for their co-regulation in human cells.

Assembly of a chondrocyte-like pericellular matrix on non-chondrogenic cells. Role of the cell surface hyaluronan receptors in the assembly of a pericellular matrix

1991 ◽  
Vol 99 (2) ◽  
pp. 227-235 ◽  
Author(s):  
W. Knudson ◽  
C.B. Knudson
Keyword(s):  
Cell Surface ◽  
Plasma Membranes ◽  
Cell Types ◽  
Competitive Inhibitor ◽  
Live Cells ◽  
Pericellular Matrix ◽  
The Matrix ◽  
Express Cell ◽  
Hyaluronan Receptors

In this study, we have examined the capacity of various cell types, which express cell surface hyaluronan receptors, to organize a chondrocyte-like pericellular matrix when given chondrocyte-derived extracellular matrix macromolecules exogenously. The assembly of a pericellular matrix was visualized by a particle exclusion assay. Without the addition of exogenous macromolecular components, none of the cell types studied exhibited significant pericellular matrices extending from their plasma membranes. However, upon the addition of high molecular weight hyaluronan in combination with aggregating cartilage proteoglycan monomers, large pericellular matrices were formed within two hours of incubation. No pericellular matrices were formed if these macromolecular components were added separately at equivalent concentrations or if the components were added in the presence of hyaluronan hexasaccharide, a competitive inhibitor of hyaluronan interaction with cell surface hyaluronan receptors. Fully assembled pericellular matrices could also be displaced by the subsequent addition of hyaluronan hexasaccharides. Nonliving, glutaraldehyde-fixed cells, which retained functional hyaluronan receptors, maintained the capacity to assembly pericellular matrices with exogenous components, in serum-containing or serum-free medium. Cells that were incubated with exogenous matrix macromolecules for 24 h, followed by a chase incubation in medium minus the exogenous macromolecules, continued to maintain the matrix for up to 6 h on live cells and more than 24 h on glutaraldehyde-fixed cells. Cell types that did not express hyaluronan receptors were not capable of organizing such pericellular matrices when incubated with these exogenous components. These findings suggest that cells expressing hyaluronan receptors have a significant capacity to organize their immediate extracellular environment via hyaluronan-hyaluronan receptor interactions. Possible physiological functions for this type of matrix organizing capacity are discussed.

Sign in / Sign up

Export Citation Format

Share Document