scholarly journals Bistability in the synchronization of actuated microfilaments

2017 ◽  
Vol 836 ◽  
pp. 304-323 ◽  
Author(s):  
Hanliang Guo ◽  
Lisa Fauci ◽  
Michael Shelley ◽  
Eva Kanso
Keyword(s):  
Fluid Transport ◽  
Phase Synchronization ◽  
Biological Fluid ◽  
Building Blocks ◽  
Hydrodynamic Interactions ◽  
Cell Type ◽  
Hydrodynamic Coupling ◽  
Cilia And Flagella ◽  
Driving Torque

Cilia and flagella are essential building blocks for biological fluid transport and locomotion at the micrometre scale. They often beat in synchrony and may transition between different synchronization modes in the same cell type. Here, we investigate the behaviour of elastic microfilaments, protruding from a surface and driven at their base by a configuration-dependent torque. We consider full hydrodynamic interactions among and within filaments and no slip at the surface. Isolated filaments exhibit periodic deformations, with increasing waviness and frequency as the magnitude of the driving torque increases. Two nearby but independently driven filaments synchronize their beating in-phase or anti-phase. This synchrony arises autonomously via the interplay between hydrodynamic coupling and filament elasticity. Importantly, in-phase and anti-phase synchronization modes are bistable and coexist for a range of driving torques and separation distances. These findings are consistent with experimental observations of in-phase and anti-phase synchronization in pairs of cilia and flagella and could have important implications on understanding the biophysical mechanisms underlying transitions between multiple synchronization modes.

scholarly journals Coordinated beating of algal flagella is mediated by basal coupling

2016 ◽  
Vol 113 (20) ◽  
pp. E2784-E2793 ◽  
Author(s):  
Kirsty Y. Wan ◽  
Raymond E. Goldstein
Keyword(s):  
Phase Locking ◽  
Flagellar Apparatus ◽  
Hydrodynamic Interactions ◽  
Basal Bodies ◽  
Unicellular Algae ◽  
Naturally Occurring ◽  
Hydrodynamic Coupling ◽  
Respiratory Cilia ◽  
Unicellular Organisms ◽  
Cilia And Flagella

Cilia and flagella often exhibit synchronized behavior; this includes phase locking, as seen inChlamydomonas, and metachronal wave formation in the respiratory cilia of higher organisms. Since the observations by Gray and Rothschild of phase synchrony of nearby swimming spermatozoa, it has been a working hypothesis that synchrony arises from hydrodynamic interactions between beating filaments. Recent work on the dynamics of physically separated pairs of flagella isolated from the multicellular algaVolvoxhas shown that hydrodynamic coupling alone is sufficient to produce synchrony. However, the situation is more complex in unicellular organisms bearing few flagella. We show that flagella ofChlamydomonasmutants deficient in filamentary connections between basal bodies display markedly different synchronization from the wild type. We perform micromanipulation on configurations of flagella and conclude that a mechanism, internal to the cell, must provide an additional flagellar coupling. In naturally occurring species with 4, 8, or even 16 flagella, we find diverse symmetries of basal body positioning and of the flagellar apparatus that are coincident with specific gaits of flagellar actuation, suggesting that it is a competition between intracellular coupling and hydrodynamic interactions that ultimately determines the precise form of flagellar coordination in unicellular algae.

scholarly journals Statistical mechanics and hydrodynamics of bacterial suspensions

2009 ◽  
Vol 106 (37) ◽  
pp. 15567-15572 ◽  
Author(s):  
Aparna Baskaran ◽  
M. Cristina Marchetti
Keyword(s):  
Physical Model ◽  
Large Scale ◽  
Hydrodynamic Interactions ◽  
Nonequilibrium Phenomena ◽  
Active Particles ◽  
Cilia And Flagella ◽  
Living Organisms ◽  
The Individual ◽  
Scale Behavior

Unicellular living organisms, such as bacteria and algae, propel themselves through a medium via cyclic strokes involving the motion of cilia and flagella. Dense populations of such “active particles” or “swimmers” exhibit a rich collective behavior at large scales. Starting with a minimal physical model of a stroke-averaged swimmer in a fluid, we derive a continuum description of a suspension of active organisms that incorporates fluid-mediated, long-range hydrodynamic interactions among the swimmers. Our work demonstrates that hydrodynamic interactions provide a simple, generic origin for several nonequilibrium phenomena predicted or observed in the literature. The continuum model derived here does not depend on the microscopic physical model of the individual swimmer. The details of the large-scale physics do, however, differ for “shakers” (particles that are active but not self-propelled, such as melanocytes) and “movers” (self-propelled particles), “pushers” (most bacteria) and “pullers” (algae like Chlamydomonas). Our work provides a classification of the large-scale behavior of all these systems.

scholarly journals Geometry of unsteady fluid transport during fluid–structure interactions

2007 ◽  
Vol 589 ◽  
pp. 125-145 ◽  
Author(s):  
ELISA FRANCO ◽  
DAVID N. PEKAREK ◽  
JIFENG PENG ◽  
JOHN O. DABIRI
Keyword(s):  
Fluid Transport ◽  
Recirculation Zone ◽  
Biological Fluid ◽  
Canonical System ◽  
Two Dimensional ◽  
Fluid Structure Interactions ◽  
Fluid Exchange ◽  
Fluid Structure ◽  
Ambient Flow ◽  
Unsteady Fluid

We describe the application of tools from dynamical systems to define and quantify the unsteady fluid transport that occurs during fluid–structure interactions and in unsteady recirculating flows. The properties of Lagrangian coherent structures (LCS) are used to enable analysis of flows with arbitrary time-dependence, thereby extending previous analytical results for steady and time-periodic flows. The LCS kinematics are used to formulate a unique, physically motivated definition for fluid exchange surfaces and transport lobes in the flow. The methods are applied to numerical simulations of two-dimensional flow past a circular cylinder at a Reynolds number of 200; and to measurements of a freely swimming organism, the Aurelia aurita jellyfish. The former flow provides a canonical system in which to compare the present geometrical analysis with classical, Eulerian (e.g. vortex shedding) perspectives of fluid–structure interactions. The latter flow is used to deduce the physical coupling that exists between mass and momentum transport during self-propulsion. In both cases, the present methods reveal a well-defined, unsteady recirculation zone that is not apparent in the corresponding velocity or vorticity fields. Transport rates between the ambient flow and the recirculation zone are computed for both flows. Comparison of fluid transport geometry for the cylinder crossflow and the self-propelled swimmer within the context of existing theory for two-dimensional lobe dynamics enables qualitative localization of flow three-dimensionality based on the planar measurements. Benefits and limitations of the implemented methods are discussed, and some potential applications for flow control, unsteady propulsion, and biological fluid dynamics are proposed.

scholarly journals Proteins and Small Molecules for Cellular Regenerative Medicine

2013 ◽  
Vol 93 (1) ◽  
pp. 311-325 ◽  
Author(s):  
Eric M. Green ◽  
Richard T. Lee
Keyword(s):  
Regenerative Medicine ◽  
Small Molecules ◽  
Tissue Regeneration ◽  
Target Cell ◽  
Building Blocks ◽  
Cell Type ◽  
Multipotent Cells ◽  
Fundamental Goal ◽  
Treatment Paradigm ◽  
Ischemic Diseases

Regenerative medicine seeks to understand tissue development and homeostasis and build on that knowledge to enhance regeneration of injured tissues. By replenishing lost functional tissues and cells, regenerative medicine could change the treatment paradigm for a broad range of degenerative and ischemic diseases. Multipotent cells hold promise as potential building blocks for regenerating lost tissues, but successful tissue regeneration will depend on comprehensive control of multipotent cells–differentiation into a target cell type, delivery to a desired tissue, and integration into a durable functional structure. At each step of this process, proteins and small molecules provide essential signals and, in some cases, may themselves act as effective therapies. Identifying these signals is thus a fundamental goal of regenerative medicine. In this review we discuss current progress using proteins and small molecules to regulate tissue regeneration, both in combination with cellular therapies and as monotherapy.

scholarly journals MetaCell: analysis of single cell RNA-seq data using k-NN graph partitions

2018 ◽  
Author(s):  
Yael Baran ◽  
Arnau Sebe-Pedros ◽  
Yaniv Lubling ◽  
Amir Giladi ◽  
Elad Chomsky ◽  
...  
Keyword(s):  
Single Cell ◽  
Software Package ◽  
Building Blocks ◽  
Cell Populations ◽  
Compact Groups ◽  
Sampling Variance ◽  
Statistical Control ◽  
Rna Seq ◽  
Cell Type ◽  
Graph Partitions

ABSTRACTSingle cell RNA-seq (scRNA-seq) has become the method of choice for analyzing mRNA distributions in heterogeneous cell populations. scRNA-seq only partially samples the cells in a tissue and the RNA in each cell, resulting in sparse data that challenge analysis. We develop a methodology that addresses scRNA-seq’s sparsity through partitioning the data into metacells: disjoint, homogenous and highly compact groups of cells, each exhibiting only sampling variance. Metacells constitute local building blocks for clustering and quantitative analysis of gene expression, while not enforcing any global structure on the data, thereby maintaining statistical control and minimizing biases. We illustrate the MetaCell framework by re-analyzing cell type and transcriptional gradients in peripheral blood and whole organism scRNA-seq maps. Our algorithms are implemented in the new MetaCell R/C++ software package.

Membrane polarity in epithelial cells: protein sorting and establishment of polarized domains

1997 ◽  
Vol 272 (4) ◽  
pp. F425-F429 ◽  
Author(s):  
M. J. Caplan
Keyword(s):  
Epithelial Cell ◽  
Epithelial Cells ◽  
Plasma Membranes ◽  
Fluid Transport ◽  
Transport Proteins ◽  
Cell Type ◽  
Physiological Properties ◽  
Polarized Epithelia ◽  
Cellular Pathways ◽  
Surface Domains

Epithelial cells go to great trouble to organize the subdomains of their plasma membranes. The apical and basolateral surfaces of polarized epithelia are equipped with markedly distinct populations of channels, carriers, and pumps. This anisotropy is an absolute prerequisite for vectorial solute and fluid transport. The physiological properties of an individual epithelial cell type are determined not only by its census of transport proteins but also by the manner in which these proteins are segregated between the apical and basolateral portions of the plasmalemma (Curr. Top. Membr. 39: 37-86, 1991). To achieve this asymmetry, an epithelial cell must be able to establish distinct surface domains, to target newly synthesized transport proteins to their appropriate sites of functional residence, and to retain them there following their delivery. Studies of the cellular pathways involved in generating and maintaining the polarized state have begun to illuminate an elegant network of cell biological specializations that may be involved not only in establishing the distributions of transport proteins but in dynamically regulating their function as well.

scholarly journals The role of optimal vortex formation in biological fluid transport

2005 ◽  
Vol 272 (1572) ◽  
pp. 1557-1560 ◽  
Author(s):  
John O Dabiri ◽  
Morteza Gharib
Keyword(s):  
Vortex Ring ◽  
Fluid Transport ◽  
Biological Fluid ◽  
Ring Formation ◽  
Vortex Rings ◽  
Jet Flows ◽  
Vortex Ring Formation ◽  
Biological Studies ◽  
Macro Scale ◽  
Animal Phyla

Animal phyla that require macro-scale fluid transport for functioning have repeatedly and often independently converged on the use of jet flows. During flow initiation these jets form fluid vortex rings, which facilitate mass transfer by stationary pumps (e.g. cardiac chambers) and momentum transfer by mobile systems (e.g. jet-propelled swimmers). Previous research has shown that vortex rings generated in the laboratory can be optimized for efficiency or thrust, based on the jet length-to-diameter ratio ( L / D ), with peak performance occurring at 3.5< L / D <4.5. Attempts to determine if biological jets achieve this optimization have been inconclusive, due to the inability to properly account for the diversity of jet kinematics found across animal phyla. We combine laboratory experiments, in situ observations and a framework that reduces the kinematics to a single parameter in order to quantitatively show that individual animal kinematics can be tuned in correlation with optimal vortex ring formation. This new approach identifies simple rules for effective fluid transport, facilitates comparative biological studies of jet flows across animal phyla irrespective of their specific functions and can be extended to unify theories of optimal jet-based and flapping-based vortex ring formation.

scholarly journals Single-cell transitional dynamics unravel stimulus- and cell type-dependent signaling outputs of distinct p53 regulatory feedback motifs

2021 ◽  
Author(s):  
Jun Xie ◽  
Lichun Zhang ◽  
Yanting Zhu ◽  
Xiao Liang ◽  
Jue Shi
Keyword(s):  
Single Cell ◽  
Network Motif ◽  
Building Blocks ◽  
Cell Types ◽  
Dynamic Responses ◽  
Transitional Dynamics ◽  
Cell Type ◽  
P53 Pathway ◽  
Systemic Analysis ◽  
Context Specific

AbstractDespite myriad of systemic analysis, our quantitative understanding of signaling networks and their differential outputs is still limited, especially at the dynamic level. Here we employed a network motif approach to dissect key regulatory units of p53 pathway and determined how their collective activities generated context-specific dynamic responses. By combining single-cell imaging and mathematical modeling of dose-dependent p53 dynamics induced by three chemotherapeutics of distinct mechanism-of-action, including Etoposide, Nutlin-3a and 5-Fluouracil, and in five cancer cell types, we identified novel p53 dynamic modes and their mechanistic origins with new insight on previously unknown drug mediators and phenotypic heterogeneity of cancer cells. Our results established the functional roles of unique feedback motifs of p53 pathway in generating the stimulus- and cell type-specific signaling responses and demonstrated that transitional dynamics activated at intermediate stimulus levels can be exploited as novel quantitative readouts to uncover and elucidate the key building blocks of bio-networks.

scholarly journals Dzip1 and Fam92 form a ciliary transition zone complex with cell type specific roles in Drosophila

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Jean-André Lapart ◽  
Marco Gottardo ◽  
Elisabeth Cortier ◽  
Jean-Luc Duteyrat ◽  
Céline Augière ◽  
...  
Keyword(s):  
Transition Zone ◽  
Basal Body ◽  
Functional Module ◽  
Complex Structure ◽  
Ciliated Cells ◽  
Cell Type ◽  
Life Threatening ◽  
Cell Type Specific ◽  
Cilia And Flagella ◽  
Conserved Core

Cilia and flagella are conserved eukaryotic organelles essential for cellular signaling and motility. Cilia dysfunctions cause life-threatening ciliopathies, many of which are due to defects in the transition zone (TZ), a complex structure of the ciliary base. Therefore, understanding TZ assembly, which relies on ordered interactions of multiprotein modules, is of critical importance. Here, we show that Drosophila Dzip1 and Fam92 form a functional module which constrains the conserved core TZ protein, Cep290, to the ciliary base. We identify cell type specific roles of this functional module in two different tissues. While it is required for TZ assembly in all Drosophila ciliated cells, it also regulates basal-body growth and docking to the plasma membrane during spermatogenesis. We therefore demonstrate a novel regulatory role for Dzip1 and Fam92 in mediating membrane/basal-body interactions and show that these interactions exhibit cell type specific functions in basal-body maturation and TZ organization.

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