Tuning the Elasticity of Biopolymer Gels for Optimal Wound Healing

AbstractSoft polymer networks with large mesh size, not flat rigid surfaces, are the normal environment for most animal cells. Cell structure and function depend on the stiffness of the surfaces on which cells adhere as well as on the type of adhesion complex by which the cell binds its extracellular ligand. Many cell types, including fibroblasts and endothelial cells, switch from a round to spread morphology as stiffness is increased between 1000 and 10,000 Pa. Coincident with the change in morphology are a host of differences in protein phosphorylation levels, expression of integrins, and changes in cytoskeletal protein expression and assembly. In contrast, other cells types such as neutrophils and platelets do not require rigid substrates in order to spread, and neurons extend processes better on soft (50 Pa) materials than on stiffer gels. We compare the stiffness sensing of four cell types: platelets, neurons and astrocytes, a glial cell type derived from embryonic rat brain, and melanoma cells. Astrocytes switch from a round to spread morphology as substrate stiffness increases, but do so over a stiffness range 10 times softer than that over which fibroblasts alter morphology. Stiffness-dependent morphologic changes observed from studies of cells grown on surfaces of protein-laminated polyacrylamide gels that have linear elasticity are also seen when cells are on matrices of natural biopolymers such as fibrin. Biopolymer gels like fibrin can be formed with appropriate stiffness to optimize for neuronal cell survival and patterning, and may have utility for repair of damaged neural tissues. The complex non-linear rheology of fibrin and other gels formed by semi-flexible biopolymers that exhibit strain-stiffening provide additional mechanisms by which cells can respond to and actively remodel the mechanical features of their environment.

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Form and Function in Cells of the Brain

The Neuron ◽

10.1093/med/9780199773893.003.0002 ◽

2015 ◽

pp. 23-38

Author(s):

Irwin B. Levitan ◽

Leonard K. Kaczmarek

Keyword(s):

Axonal Transport ◽

Molecular Motors ◽

Critical Role ◽

Neuronal Cell ◽

Cell Types ◽

Neuronal Cell Body ◽

Long Distance ◽

Form And Function ◽

And Function ◽

The Brain

This chapter examines unique mechanisms that the neuron has evolved to establish and maintain the form required for its specialized signaling functions. Unlike some other organs, the brain contains a variety of cell types including several classes of glial cells, which play a critical role in the formation of the myelin sheath around axons and may be involved in immune responses, synaptic transmission, and long-distance calcium signaling in the brain. Neurons share many features in common with other cells (including glia), but they are distinguished by their highly asymmetrical shapes. The neuronal cytoskeleton is essential for establishing this cell shape during development and for maintaining it in adulthood. The process of axonal transport moves vesicles and other organelles to regions remote from the neuronal cell body. Proteins such as kinesin and dynein, called molecular motors, make use of the energy released by hydrolysis of ATP to drive axonal transport.

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Properties and metabolism of the aqueous cytoplasm and its boundaries

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.1984.246.2.r133 ◽

1984 ◽

Vol 246 (2) ◽

pp. R133-R151 ◽

Cited By ~ 15

Author(s):

J. S. Clegg

Keyword(s):

Cell Biology ◽

Cell Structure ◽

Large Fraction ◽

Pure Water ◽

Cell Ultrastructure ◽

Structure And Function ◽

Cell Water ◽

Animal Cells ◽

Intact Cells ◽

And Function

The nucleoplasm, the interiors of cytoplasmic membrane-bound organelles, and the aqueous cytoplasm make up the aqueous compartments of animal cells. The extent to which these compartments are concentrated solutions of macromolecules, metabolites, ions, and other solutes is a matter of some importance to current thinking about cell structure and function. This paper will focus on the aqueous cytoplasm. It will show that the composition and metabolic activities of the cytosol, obtained by methods of cell disruption and fractionation, bear almost no resemblance to those of the aqueous cytoplasm in intact cells. The consequences of this to contemporary views on cell structure and function are considered. A closely related topic concerns the physical properties of the dominant component of these compartments, water: Are these properties the same as those of water in aqueous solutions, or are they altered as a result of interaction with cell architecture? Available evidence strongly suggests that at least a large fraction of the total cell water exhibits properties that markedly differ from those of pure water. Selected examples of these studies will be reviewed, and the roles of cell water will be discussed, notably as they relate to metabolism and cell ultrastructure. Although dimly perceived at present, it appears that living cells exhibit an organization far greater than the current teachings of cell biology reveal.

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Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids

10.1101/589598 ◽

2019 ◽

Cited By ~ 2

Author(s):

Lisa M. Smits ◽

Stefano Magni ◽

Kamil Grzyb ◽

Paul MA. Antony ◽

Rejko Krüger ◽

...

Keyword(s):

Single Cell ◽

Dopaminergic Neurons ◽

Neuronal Cell ◽

Cell Types ◽

Human Stem Cell ◽

Glutamatergic Neurons ◽

And Function ◽

Excellent Tool

AbstractHuman stem cell-derived organoids have great potential for modelling physiological and pathological processes. They recapitulatein vitrothe organisation and function of a respective organ or part of an organ. Human midbrain organoids (hMOs) have been described to contain midbrain-specific dopaminergic neurons that release the neurotransmitter dopamine. However, the human midbrain contains also additional neuronal cell types, which are functionally interacting with each other. Here, we analysed hMOs at high-resolution by means of single-cell RNA-sequencing (scRNA-seq), imaging and electrophysiology to unravel cell heterogeneity. Our findings demonstrate that hMOs show essential neuronal functional properties as spontaneous electrophysiological activity of different neuronal subtypes, including dopaminergic, GABAergic, and glutamatergic neurons. Recapitulating thesein vivofeatures makes hMOs an excellent tool forin vitrodisease phenotyping and drug discovery.

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Complexity and graded regulation of neuronal cell type-specific alternative splicing revealed by single-cell RNA sequencing

10.1101/2021.01.27.428525 ◽

2021 ◽

Author(s):

Huijuan Feng ◽

Daniel F. Moakley ◽

Shuonan Chen ◽

Melissa G. McKenzie ◽

Vilas Menon ◽

...

Keyword(s):

Alternative Splicing ◽

Rna Binding ◽

Rna Binding Proteins ◽

Neuronal Cell ◽

Cell Types ◽

Mammalian Brain ◽

Differential Splicing ◽

Hierarchical Levels ◽

Neuronal Types ◽

And Function

AbstractThe enormous neuronal cellular diversity in the mammalian brain, which is highly prototypical and organized in a hierarchical manner, is dictated by cell type-specific gene regulatory programs at the molecular level. Although prevalent in the brain, contribution of alternative splicing (AS) to the molecular diversity across neuronal cell types is just starting to emerge. Here we systematically investigated AS regulation across over 100 transcriptomically defined neuronal types of the adult mouse cortex using deep single cell RNA-sequencing (scRNA-seq) data. We found distinct splicing programs between glutamatergic and GABAergic neurons and between subclasses within each neuronal class, consisting of overlapping sets of alternative exons showing differential splicing at multiple hierarchical levels. Using an integrative approach, our analysis suggests that RNA-binding proteins (RBPs) Celf1/2, Mbnl2 and Khdrbs3 are preferentially expressed and more active in glutamatergic neurons, while Elavl2 and Qk are preferentially expressed and more active in GABAergic neurons. Importantly, these and additional RBPs also contribute to differential splicing between neuronal subclasses at multiple hierarchical levels, and some RBPs drive splicing dynamics that do not conform to the hierarchical structure defined by the transcriptional profiles. Thus, our results suggest graded regulation of AS across neuronal cell types, which provides a molecular mechanism orthogonal to, rather than downstream of, transcriptional regulation in specifying neuronal identity and function.SignificanceAlternative splicing (AS) is extensively used in the mammalian brain, but its contribution to the molecular and cellular diversity across neuronal cell types remains poorly understood. Through systematic and integrative analysis of AS regulation across over 100 transcriptomically defined cortical neuronal types, we found neuronal subclass-specific splicing regulatory programs consists of overlapping alternative exons showing differential splicing at multiple hierarchical levels. This graded AS regulation is controlled by unique combinations of RNA-binding proteins (RBPs). Importantly, these RBPs also drive splicing dynamics across neuronal cell types that do not conform to the hierarchical taxonomy established based on transcriptional profiles, suggesting that the graded AS regulation provides a molecular mechanism orthogonal to transcriptional regulation in specifying neuronal identity and function.

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Nuclear transcriptomes of the seven neuronal cell types that constitute the Drosophila mushroom bodies

10.1101/412569 ◽

2018 ◽

Author(s):

Meng-Fu Maxwell Shih ◽

Fred P. Davis ◽

Gilbert Lee Henry ◽

Josh Dubnau

Keyword(s):

Neuronal Cell ◽

Cell Types ◽

Mushroom Bodies ◽

Rna Seq ◽

Memory Processing ◽

Neuropeptide Receptors ◽

Invertebrate Model ◽

And Function ◽

And Storage ◽

Neuroscience Community

ABSTRACTThe insect mushroom body (MB) is a conserved brain structure that plays key roles in a diverse array of behaviors. The Drosophila melanogaster MB is the primary invertebrate model of neural circuits related to memory formation and storage, and its development, morphology, wiring, and function has been extensively studied. MBs consist of intrinsic Kenyon Cells that are divided into three major neuron classes (γ, α’/β’ and α/β) and 7 cell subtypes (γd, γm, α’/β’ap, α’/β’m, α/βp, α/βs and α/βc) based on their birth order, morphology, and connectivity. These subtypes play distinct roles in memory processing, however the underlying transcriptional differences are unknown. Here, we used RNA sequencing (RNA-seq) to profile the nuclear transcriptomes of each MB neuronal cell subtypes. We identified 350 MB class- or subtype-specific genes, including the widely used α/β class marker Fas2 and the α’/β’ class marker trio. Immunostaining corroborates the RNA-seq measurements at the protein level for several cases. Importantly, our data provide a full accounting of the neurotransmitter receptors, transporters, neurotransmitter biosynthetic enzymes, neuropeptides, and neuropeptide receptors expressed within each of these cell types. This high-quality, cell type-level transcriptome catalog for the Drosophila MB provides a valuable resource for the fly neuroscience community.

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“A Cellular Encounter”

The American Biology Teacher ◽

10.1525/abt.2014.76.8.8 ◽

2014 ◽

Vol 76 (8) ◽

pp. 544-549 ◽

Cited By ~ 2

Author(s):

Joel I. Cohen

Keyword(s):

Problem Solving ◽

Cell Structure ◽

Group Learning ◽

Cell Types ◽

System Level ◽

Guided Inquiry ◽

The Subject ◽

Science Standard ◽

And Function ◽

Generation Science Standard

A standard part of biology curricula is a project-based assessment of cell structure and function. However, these are often individual assignments that promote little problem-solving or group learning and avoid the subject of organelle chemical interactions. I evaluate a model-based cell project designed to foster group and individual guided inquiry, and review how the project stimulates problem-solving at a cellular system level. Students begin with four organism cell types, label organelles, describe their structures, and affix chemicals produced or needed for each organelle’s function. Students simulate cell signaling, cell recognition, and transport of molecules through membranes. After describing the project, I present measures of student participation and a rubric, compare individual versus group work, and highlight future modifications, including alignment with the Next Generation Science Standard of “Structure, Function, and Information Processing.”

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EFFECT OF SUBSTRATE STIFFNESS ON THE STRUCTURE AND FUNCTION OF CELLS

Biophysical Reviews and Letters ◽

10.1142/s1793048006000331 ◽

2006 ◽

Vol 01 (04) ◽

pp. 401-410 ◽

Cited By ~ 2

Author(s):

PENELOPE C. GEORGES ◽

ILYA LEVENTAL ◽

WILFREDO De JESúS ROJAS ◽

R. TYLER MILLER ◽

PAUL A. JANMEY

Keyword(s):

Cell Structure ◽

Soft Materials ◽

Cell Types ◽

Biological Tissues ◽

Structure And Function ◽

Substrate Stiffness ◽

Filamin A ◽

Strong Response ◽

Different Response ◽

And Function

Most biological tissues are soft viscoelastic materials with elastic moduli ranging from approximately 100 to 100,000 Pa. Recent studies have examined the effect of substrate rigidity on cell structure and function, and many, but not all cell types exhibit a strong response to substrate stiffness. Some blood cells such as platelets and neutrophils have indistinguishable structures on hard and soft materials as long as they are sufficiently adhesive, whereas many cell types, including fibroblasts and endothelial cells spread much more strongly on rigid compared to soft substrates. A few cell types such as neurons appear to extend better on very soft materials. The different response of astrocytes and neurons to the stiffness of their substrate results in preferential growth of neurons on soft gels and astrocytes on hard gels, and suggests that preventing rigidification of damaged central nervous system tissue after injury may have utility in wound healing. How cells sense substrate stiffness is unknown. One candidate protein, filamin A, which responds to externally derived stresses, was tested in melanoma cells. Cells devoid of filamin A retain the ability to sense substrate stiffness, suggesting that other proteins are required for stiffness sensing.

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Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids

Cell and Tissue Research ◽

10.1007/s00441-020-03249-y ◽

2020 ◽

Vol 382 (3) ◽

pp. 463-476 ◽

Cited By ~ 2

Author(s):

Lisa M. Smits ◽

Stefano Magni ◽

Kaoru Kinugawa ◽

Kamil Grzyb ◽

Joachim Luginbühl ◽

...

Keyword(s):

Single Cell ◽

Dopaminergic Neurons ◽

Neuronal Cell ◽

Cell Types ◽

Human Stem Cell ◽

Electrophysiological Activity ◽

And Function ◽

Excellent Tool

AbstractHuman stem cell-derived organoids have great potential for modelling physiological and pathological processes. They recapitulate in vitro the organization and function of a respective organ or part of an organ. Human midbrain organoids (hMOs) have been described to contain midbrain-specific dopaminergic neurons that release the neurotransmitter dopamine. However, the human midbrain contains also additional neuronal cell types, which are functionally interacting with each other. Here, we analysed hMOs at high-resolution by means of single-cell RNA sequencing (scRNA-seq), imaging and electrophysiology to unravel cell heterogeneity. Our findings demonstrate that hMOs show essential neuronal functional properties as spontaneous electrophysiological activity of different neuronal subtypes, including dopaminergic, GABAergic, glutamatergic and serotonergic neurons. Recapitulating these in vivo features makes hMOs an excellent tool for in vitro disease phenotyping and drug discovery.

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