Biological and Soft SystemsResearch areas include biophysics, biomaterials, nanoscience and Physics of Medicine, using techniques and inspirations from classical polymer physics, soft matter physics and the study of condensed matterhttps://www.repository.cam.ac.uk/handle/1810/198337https://www.repository.cam.ac.uk/retrieve/db095c48-fa32-44d6-a467-65098cd72211/biological.jpg2024-03-28T22:45:58Z2024-03-28T22:45:58Z201The role of hydrodynamic forces in synchronisation and alignment of mammalian motile ciliaPellicciotta, Nicolahttps://www.repository.cam.ac.uk/handle/1810/3036402021-04-21T22:43:09Z2020-05-01T00:00:00Zdc.title: The role of hydrodynamic forces in synchronisation and alignment of mammalian motile cilia
dc.contributor.author: Pellicciotta, Nicola
dc.description.abstract: Fluid flow generated by a ciliated epithelium is a fascinating evidence of collective behaviour in nature. In many organs and eukaryotic organisms, thousands of microscale whip-like structures called `motile cilia' beat aligned at the same frequency and in a coordinated fashion. This dynamics, known as `metachronal wave', has fundamental physiological roles in microorganisms and many organs of vertebrates. In the airways, the coordinated beatings of motile cilia generate a fluid flow that pushes mucus to the pharynx, and so protects the lungs from inhaled contaminants. The failure of this collective dynamics can precipitate or exacerbate severe infections and chronic inflammatory conditions such as cystic fibrosis (CF), primary ciliary dyskinesia (PCD) or asthma. In the brain, the multiciliated ependymal cells cover all the ventricles. Their cilia beat in a coordinated fashion to ensure the cerebrospinal fluid circulation necessary for brain homoeostasis, toxin washout and orientation of the migration of newborn neurons. Despite the fundamental role in nature, the mechanism underpinning such collective behaviour is still unknown.
A recent hypothesis, supported by simulations, experiments with microorganisms and with cilia models, proposed that hydrodynamic interactions between cilia could provide a physical mechanism for their coordination. In contrast, others have proposed a role of the cytoskeletal elastic coupling between cilia. While previous works mainly focused on algae and protists, investigating the conditions that are required for the emergence of the metachronal wave in mammalian tissues can provide important progress in the diagnosis and treatment of human medical diseases. Specifically, I tackled this broad topic by studying the hydrodynamic forces necessary for the synchronisation and alignment of motile cilia from brain and airways. This question was addressed experimentally by measuring cilia motility during treatment with oscillatory and constant external fluid flows. We found that synchronisation and alignment of mammalian cilia in the brain is achieved with flows of similar magnitude of the ones generated by cilia themselves. Our results suggest that hydrodynamic forces between cilia are sufficient for the emergence of their collective behaviour.
The first chapter provides basic knowledge on motile cilia structure and functions in microorganisms and humans. Additionally, I introduce the reader to the open questions related to the coordination of a pair and a carpet of cilia, with specific attention on previous works on mammals. This first chapter is followed by a description of a novel microfluidic device that I developed to grow $\textit{in vitro}$ airway and brain cells and apply controlled viscous forces.
In Chapter 3, I describe how we have investigated cilia synchronisation of mammalian cilia. Applying external oscillatory flow on brain cells, we studied the susceptibility of cilia motility to hydrodynamic forces similar to the ones generated by cilia themselves. We found that cells with few cilia (up to five) can be entrained at flows comparable to the cilia-driven flows reported in vivo. We suggest that hydrodynamic forces between mammalian cilia are sufficiently strong to be the mechanism underpinning frequency synchronisation.
In the second part of my thesis, I looked into the hydrodynamic shear forces needed to align permanently the cilia direction of beating. We tackled this problem by using $\textit{in vitro}$ cultures of mouse brain and human airway cells grown in custom flow channels.
We found that cilia from mouse brain do not lock their beating direction after $\emph{ciliogenesis}$, but can respond and align to physiological shear stress found $\emph{in vivo}$ at any time, in contrast with was previously believed. Moreover, we suggest that cilia alignment depends on the density of cilia, in agreement with a hydrodynamic screening effect of the external flow by the nearby cilia that we aim to investigate in the future. These results are described in Chapter 4. Successively in Chapter 5, I report our approach to study whether physiological shear stress can induce cilia alignment in airway cell cultures. The current hypothesis is that these cilia may also be able to align with external hydrodynamic forces - however, experimental evidence is still needed. There is a lack of experiments on this topic mainly because airway cells are cultured in an air-liquid interface, and so shear stress has to be applied with airflows. We developed novel setups for applying long term shear stress with air and fluid flow on this system, leaving further experiments for the future.
2020-05-01T00:00:00ZSuppressed Quenching and Strong-Coupling of Purcell-Enhanced Single-Molecule Emission in Plasmonic NanocavitiesKongsuwan, NDemetriadou, AChikkaraddy, RBenz, FTurek, VAKeyser, UFBaumberg, JJHess, Ohttps://www.repository.cam.ac.uk/handle/1810/2783132023-12-21T07:33:07Z2018-01-17T00:00:00Zdc.title: Suppressed Quenching and Strong-Coupling of Purcell-Enhanced Single-Molecule Emission in Plasmonic Nanocavities
dc.contributor.author: Kongsuwan, N; Demetriadou, A; Chikkaraddy, R; Benz, F; Turek, VA; Keyser, UF; Baumberg, JJ; Hess, O
dc.description.abstract: An emitter in the vicinity of a metal nanostructure is quenched by its decay through nonradiative channels, leading to the belief in a zone of inactivity for emitters placed within <10 nm of a plasmonic nanostructure. Here we demonstrate and explain why in tightly coupled plasmonic resonators forming nanocavities “quenching is quenched” due to plasmon mixing. Unlike isolated nanoparticles, such plasmonic nanocavities show mode hybridization, which can massively enhance emitter excitation and decay via radiative channels, here experimentally confirmed by laterally dependent emitter placement through DNA-origami. We explain why this enhancement of excitation and radiative decay can be strong enough to facilitate single-molecule strong coupling, as evident in dynamic Rabi-oscillations.
2018-01-17T00:00:00ZTrue Molecular Scale Visualization of Variable Clustering Properties of Ryanodine Receptors.Jayasinghe, IzzyClowsley, Alexander HLin, RuishengLutz, TobiasHarrison, CarlGreen, EllenBaddeley, DavidDi Michele, LorenzoSoeller, Christianhttps://www.repository.cam.ac.uk/handle/1810/2776242024-01-07T07:02:59Z2018-01-09T00:00:00Zdc.title: True Molecular Scale Visualization of Variable Clustering Properties of Ryanodine Receptors.
dc.contributor.author: Jayasinghe, Izzy; Clowsley, Alexander H; Lin, Ruisheng; Lutz, Tobias; Harrison, Carl; Green, Ellen; Baddeley, David; Di Michele, Lorenzo; Soeller, Christian
dc.description.abstract: Signaling nanodomains rely on spatial organization of proteins to allow controlled intracellular signaling. Examples include calcium release sites of cardiomyocytes where ryanodine receptors (RyRs) are clustered with their molecular partners. Localization microscopy has been crucial to visualizing these nanodomains but has been limited by brightness of markers, restricting the resolution and quantification of individual proteins clustered within. Harnessing the remarkable localization precision of DNA-PAINT (<10 nm), we visualized punctate labeling within these nanodomains, confirmed as single RyRs. RyR positions within sub-plasmalemmal nanodomains revealed how they are organized randomly into irregular clustering patterns leaving significant gaps occupied by accessory or regulatory proteins. RyR-inhibiting protein junctophilin-2 appeared highly concentrated adjacent to RyR channels. Analyzing these molecular maps showed significant variations in the co-clustering stoichiometry between junctophilin-2 and RyR, even between nearby nanodomains. This constitutes an additional level of complexity in RyR arrangement and regulation of calcium signaling, intrinsically built into the nanodomains.
2018-01-09T00:00:00ZPhysical descriptions of the bacterial nucleoid at large scales, and their biological implications.Benza, Vincenzo GBassetti, BrunoDorfman, Kevin DScolari, Vittore FBromek, KrystynaCicuta, PietroLagomarsino, Marco Cosentinohttps://www.repository.cam.ac.uk/handle/1810/2761962024-01-05T20:16:44Z2012-07-01T00:00:00Zdc.title: Physical descriptions of the bacterial nucleoid at large scales, and their biological implications.
dc.contributor.author: Benza, Vincenzo G; Bassetti, Bruno; Dorfman, Kevin D; Scolari, Vittore F; Bromek, Krystyna; Cicuta, Pietro; Lagomarsino, Marco Cosentino
dc.description.abstract: Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organized at various length scales. This has implications for modulating (when not directly enabling) the core biological processes of replication, transcription and segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. In particular, we highlight the role that statistical and soft condensed matter physics play in describing this system of fundamental biological importance, specifically reviewing classic and more modern tools from the theory of polymers. We also discuss some attempts toward unifying interpretations of the current results, pointing to possible directions for future investigation.
2012-07-01T00:00:00ZEmergence of biaxial nematic phases in solutions of semiflexible dimers.Vaghela, ArvinTeixeira, Paulo ICTerentjev, Eugene Mhttps://www.repository.cam.ac.uk/handle/1810/2703842024-01-07T04:00:14Z2017-10-01T00:00:00Zdc.title: Emergence of biaxial nematic phases in solutions of semiflexible dimers.
dc.contributor.author: Vaghela, Arvin; Teixeira, Paulo IC; Terentjev, Eugene M
dc.description.abstract: We investigate the isotropic, uniaxial nematic and biaxial nematic phases, and the transitions between them, for a model lyotropic mixture of flexible molecules consisting of two rigid rods connected by a spacer with variable bending stiffness. We apply density-functional theory within the Onsager approximation to describe strictly excluded-volume interactions in this athermal model and to self-consistently find the orientational order parameters dictated by its complex symmetry, as functions of the density. Earlier work on lyotropic ordering of rigid bent-rod molecules is reproduced and extended to show explicitly the continuous phase transition at the Landau point, at a critical bend angle of 36^{∘}. For flexible dimers with no intrinsic biaxiality, we find that a biaxial nematic phase can nevertheless form at a sufficiently high density and low bending stiffness. For bending stiffness κ>0.86k_{B}T, this biaxial phase manifests as dimer bending fluctuations occurring preferentially in one plane. When the dimers are more flexible, κ<0.86k_{B}T, the modal shape of the fluctuating dimer is a V with an acute opening angle, and one of the biaxial order parameters changes sign, indicating a rotation of the directors. These two regions are separated by a narrow strip of uniaxial nematic in the phase diagram, which we generate in terms of the spacer stiffness and particle density.
2017-10-01T00:00:00ZPerspective: Differential dynamic microscopy extracts multi-scale activity in complex fluids and biological systemsCicuta, PCerbino, Rhttps://www.repository.cam.ac.uk/handle/1810/2678442024-01-06T00:31:20Z2017-09-21T00:00:00Zdc.title: Perspective: Differential dynamic microscopy extracts multi-scale activity in complex fluids and biological systems
dc.contributor.author: Cicuta, P; Cerbino, R
dc.description.abstract: Differential dynamic microscopy (DDM) is a technique that exploits optical microscopy to obtain local, multi-scale quantitative information about dynamic samples, in most cases without user intervention. It is proving extremely useful in understanding dynamics in liquid suspensions, soft materials, cells, and tissues. In DDM, image sequences are analyzed via a combination of image differences and spatial Fourier transforms to obtain information equivalent to that obtained by means of light scattering techniques. Compared to light scattering, DDM offers obvious advantages, principally (a) simplicity of the setup; (b) possibility of removing static contributions along the optical path; (c) power of simultaneous different microscopy contrast mechanisms; and (d) flexibility of choosing an analysis region, analogous to a scattering volume. For many questions, DDM has also advantages compared to segmentation/tracking approaches and to correlation techniques like particle image velocimetry. The very straightforward DDM approach, originally demonstrated with bright field microscopy of aqueous colloids, has lately been used to probe a variety of other complex fluids and biological systems with many different imaging methods, including dark-field, differential interference contrast, wide-field, light-sheet, and confocal microscopy. The number of adopting groups is rapidly increasing and so are the applications. Here, we briefly recall the working principles of DDM, we highlight its advantages and limitations, we outline recent experimental breakthroughs, and we provide a perspective on future challenges and directions. DDM can become a standard primary tool in every laboratory equipped with a microscope, at the very least as a first bias-free automated evaluation of the dynamics in a system.
2017-09-21T00:00:00ZVersatile Applications of Nanostructured Metal OxidesLi, Lihttps://www.repository.cam.ac.uk/handle/1810/2453032019-02-01T12:05:54Z2014-05-29T00:00:00Zdc.title: Versatile Applications of Nanostructured Metal Oxides
dc.contributor.author: Li, Li
2014-05-29T00:00:00ZSynthesis and Applications of Double-Gyroid-Structured Functional MaterialsScherer, Maikhttps://www.repository.cam.ac.uk/handle/1810/2453022019-02-01T12:05:54Z2014-05-27T00:00:00Zdc.title: Synthesis and Applications of Double-Gyroid-Structured Functional Materials
dc.contributor.author: Scherer, Maik
2014-05-27T00:00:00ZElectrohydrodynamic Patterning of Functional MaterialsGoldberg Oppenheimer, Polahttps://www.repository.cam.ac.uk/handle/1810/2453012019-02-01T12:05:54Z2014-05-27T00:00:00Zdc.title: Electrohydrodynamic Patterning of Functional Materials
dc.contributor.author: Goldberg Oppenheimer, Pola
2014-05-27T00:00:00ZPhotonic Structures Inspired by NatureKolle, Mathiashttps://www.repository.cam.ac.uk/handle/1810/2453002019-02-01T12:05:54Z2014-05-27T00:00:00Zdc.title: Photonic Structures Inspired by Nature
dc.contributor.author: Kolle, Mathias
2014-05-27T00:00:00Z