Thesis (Ph. D.)--Ohio State University, 2009. / Title from first page of PDF file. Includes vita. Includes bibliographical references (p. 136-142).

Rheology is a discipline of continuum mechanics that is concerned with the mechanical properties of matter as it flows. Key to the study of rheology is the concept that materials do not behave as Newtonian liquids of as heterogenous, homogenous mateirials, but as a combination of the two. This combination and blurring of the line between liquid and solid peoperties is knows as viscosity. Furthermore, the viscosity of a material or liquid will not necessarily remain constant when it is subjected input forces or stresses at different frequencies. This consideration brings with it the idea of viscoelasticity which can account for the variations in the characteristics of a sample medium.Magnetic tweezers are tools that allow examination of and investigation into the viscoelastic properties of a sample on the mesoscopic scale. Magnetic matter can be inserted into and bound onto a sample. This magnetic matter can then be manipulated using an external magnetic or electromagnetic field. Calibrated magnetic tweezers apparatus can be used to investigate the mechanical and viscoelastic properties of a material with the novel application of time-variant forcesand stresses. The resultant behaviour, or response, of the sample can be observed using a microscope and analysed further.Fibrin is the highly extensible, fibre-like protein that makes up blood clots. Its particularly high levels of extensibility combined with interesting material properties such as viscoelasticity can strain-hardening make it an ideal test sample for magnetic tweezers experiments. The high elastic limit of fibrin ensures that plastic deformation does not usually occur under the range of input forces and stresses exerted by magnetic tweezers. This allows non-destructive and repeatable tests to be performed.Magnetic tweezers have been developed and used in a series of experiments on fibrin to produce a viscoelastic characterisation of the fibrous networks. The key results in this work are the design of high-sensitivity apparatus for the experiments and associated techniques for high-frequency analysis, use of the tweezers with a high-speed CCD attached to a microscope and the analysis of the viscoelastic properties of fibrin over a several decades of frequency.

Gong, Xiangjun = 基於磁鑷和全反射顯微鏡的單粒子追踪微流變方法 / 龔湘君. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references. / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese. / Gong, Xiangjun = Ji yu ci nie he quan fan she xian wei jing de dan li zi zhui zong wei liu bian fang fa / Gong Xiangjun.

Mechanical forces regulate biological processes in unique and unexpected ways, but many biochemical methods are unable to reproduce the vectorial stretching experienced by proteins in cells. Force spectroscopy techniques remedy these shortcomings by utilizing microscopic force probes to stretch and relax single protein, DNA, and RNA molecules. The central focus of this thesis is the development and implementation of a custom-built protein magnetic tweezers for unfolding and refolding Ig domains from titin, a critical filament of the sarcomere, and the longest continuous peptide in the human body. Suspended from the Z-disc to the tip of the thick filament, titin sustains the brunt of intracellular forces during muscle elongation. Since the discovery of titin, it has been widely debated whether Ig domain unfolding contributes to muscle mechanics. A combination of single quantum dot tracking in myofibrils extracted from rabbit muscle and single molecule magnetic tweezers experiments on recombinant titin fragments confirms, for the first time, the presence of titin Ig domain unfolding and refolding at physiological sarcomere lengths and stretching forces. The magnetic tweezers experiments show the surprising ability of titin Ig domains to generate piconewton level forces during folding, and we advance the hypothesis that titin folding is an important source of energy during muscle contraction. Muscle elongation recruits Ig domains to the unfolded state, whereby folding is initiated through reduction of force on titin upon actomyosin crossbridges formation. Magnetic tweezers measurements demonstrate that titin Ig folding generates peak work, velocity, and power output of 64 zeptojoules, 1.9 microns per second, and 6,000 zeptowatts, matching or exceeding the equivalent single molecule measurements from single molecule myosin II powerstrokes. The forces generated by protein folding are therefore likely to be an integral part of the contractile process of animal muscle.

No description available.

Les techniques de micromanipulation de molécules d’ADN uniques offrent des perspectives nouvelles pour lire et exploiter l’information contenue dans les génomes. Cela inclut le séquençage, la cartographie, le dénombrement de molécules et l'identification de modifications chimiques de l'ADN. Dans ce contexte, l'Équipe ABCDLab de l'ENS a développé une méthode utilisant l’ouverture et la fermeture mécanique répétée d’une molécule d’ADN en épingle à cheveux par pince magnétique. Cet outil permet de déterminer la position d'hybridation de petits oligonucléotides ainsi que celle d'anticorps révélant la position de marques épigénétiques. Un avantage de cette approche est de pouvoir travailler sur la même molécule pour d’une part identifier les marques épigénétiques et d'autre part réaliser une cartographie de sa position dans le génome. Mon travail de thèse consiste à développer un ensemble de méthodes bio-informatique visant à réaliser cette étape de cartographie. Le signal expérimental consiste en lecture des positions d’hybridation d’un, ou de plusieurs petits oligonucléotides sur la molécule étudiée. Cette mesure permet de construire une signature spécifique de la molécule que l’on peut rechercher dans le génome d’origine. Dans ce travail de thèse, j'ai réalisé des expériences avec sur pinces magnétiques pour acquérir des signatures moléculaires sur des molécules sélectionnées en aveugle dans E. coli. J'ai développé un logiciel capable de faire la recherche de ces signatures dans un génome et ensuite effectué l’ensemble du traitement des données pour tester le logiciel. Après plusieurs étapes d’optimisation, j’ai pu retrouver la position génomique des molécules étudiées, établissant ainsi une preuve de concept de cette stratégie de cartographie. Le travail a concerné l'ensemble de la chaîne de mesure : (1) le choix des sondes utilisées pour constituer la signature d’une molécule observée en optimisant un ensemble de critères liés aux conditions expérimentales et à la combinatoire des motifs de séquence. (2) la mise au point d’algorithmes de cartographie adaptés aux caractéristiques expérimentales des mesures. Enfin, j'ai testé ces algorithmes, à la fois sur des données simulées in silico et in vitro sur de l'ADN d'origine bactérienne. Je discuterais en quoi les performances des solutions de cartographie développées ici sont influencées par, d’une part les limites du montage expérimental actuel, et d’autre part les limites des approches bioinformatiques. Je présenterais les voies d’amélioration possibles de ces dernières. Mes travaux établissent qu'identifier des molécules d’ADN uniques par pinces magnétiques est possible dans le contexte d’application épigénétique et en génomique. / Single molecule micromanipulations technic offer new perspectives to read and unravel genome information. This includes sequencing, mapping, molecule counting and identification of DNA modifications. In this respect, ABCDLab team has developed a cutting edge method using repeated mechanical opening and closing of a DNA molecule with a hairpin shape using magnetic tweezers. This tool allows measuring along the DNA molecule the hybridization positions of oligonucleotides a few bases long and also to locate specific antibodies transiently bound to epigenetic markers. With this approach we can identify with the single molecule level epigenetics markers and localized them on the genome. My PhD work consisted of developing a set of bioinformatics methods to perform DNA mapping using magnetics tweezer signal consisting of hybridization positions along the studied molecule. This measurement may be viewed as a fingerprint of the molecule which can be searched on the reference genome. During my thesis, I have realized an experimental test using magnetic tweezers to acquire a set fingerprint data on a set of blinded selected molecules in the E. coli genome. I have developed a software performing a rapid search of these fingerprints inside the genome. Then I have performed the whole data treatment to check the software on the selected molecules. After several rounds of optimization, I have recovered the genetic position of the studied molecules, establishing a proof of concept of this cartography strategy. The work has addressed the whole measuring chain; (1) by choosing the oligonucleotides best adapted to obtain the molecular signature by optimizing the set of experimental constrains and combinatorial motifs of the sequence. (2) by tuning the cartography algorithm to adapt to the experimental measurement constrains. Finally, I have tested these algorithms, both on simulated data in silico and on experimental fingerprint in vitro. I shall discuss how the performances of these cartography solutions that have been developed here are impacted by the experimental limitations of the present technique, and by the bioinformatics limits. I shall present possible improvements to these methods. My studies constitute a proof of concept for genomic and epigenetic applications.

The process of a single cell evolving into a complex organism results from a series of coordinated movements of cells and tissues, especially during early embryo development. Although a wealth of morphological data characterises the shapes and movements of cells in embryos, how these movements are driven, patterned and controlled, and how this patterning is related to the mechanical properties of tissues remains unknown. Four-pole electromagnetic tweezers have been developed to probe the mechanical properties of living embryonic tissues that are undergoing active morphogenetic development. The device is capable of generating magnetic forces in the order of nano-Newtons on a grafted magnetic bead. The local passive mechanical properties of the tissues can be characterised by measuring the three-dimensional bead movement and analysing cell shape changes and cell rearrangement in response to this externally applied force. The magnetic device is used to probe the rheology in early zebrafish embryos between high stage (3.3 hpf) and the onset of gastrulation (5.3 hpf) when rapid cell cycles give way to a hollow sphere of cells. The tissue response to the applied force is modelled as linear visco- elastic. The embryo becomes stiffer and more viscous during this period of development, showing that a loose collection of cells becomes cohesive tissues. A computational model is used to explore how cells respond to local or global mechanical perturbations in two systems. First, the model simulates the movement of the bead within an embryo, and the results illustrate the generation, patterning and relaxation of the local cell stress around the bead. Second, the model reproduces the autonomous changes in mitotic cells within a stretched monolayer, and the results show that propensity of cells to divide along their long axis facilitates stress relaxation and contributes to tissue homoeostasis.

Eukaryotic genomes are densely compacted into chromatin, so that they can be contained in the nucleus. Despite the tight packaging genes need to be accessible for normal metabolic activities to occur, such as transcription, repair and replication. These processes are regulated by a vast number of proteins but also by the level of compaction of chromatin. The translocation of motor proteins along DNA produces torsional stress which in turn alters chromatin compaction both upstream and downstream. Few single-molecule studies have investigated the behaviour of nucleosomes when subjected to torsion. The inability to measure the applied torque though represented a major limitation to those reports. The implementation of the rotor bead assay, which allows to directly measure the torque applied in magnetic tweezers experiments, has been hindered by a difficult sample preparation procedure. In order to overcome this limitation an efficient protocol for the insertion of chemical or structural modifications in long DNA substrates was developed. This was then further expanded to allow the introduction of labels in multiple loci and/or both strands and has been used successfully in a number of studies. Furthermore this is the first report of tensile experiments performed on nucleosomes with a histone variant. H2AvD nucleosomes were studied due to the interest in the biological role of H2A.Z-family proteins. Interestingly, the variant nucleosomes appear to bind less DNA and to be evicted from the DNA at lower forces than those observed for canonical nucleosomes. These findings show an important role for the H2A-H2B dimers in the mechanical stability of nucleosomes. Furthermore these results are in agreement with recently proposed models of a dynamic nucleosome, in contrast to the long-standing view of nucleosomes as static structures.

Mild Traumatic Brain Injuries (mTBIs) are non-penetrating brain injuries that do not result in gross pathological lesions, yet they may cause a spectrum of cognitive and behavioral deficits. mTBI has been placed in the spotlight because of increased awareness of blast induced and sports-related concussions, but the underlying pathophysiological mechanisms are poorly understood. Several studies have implicated neuronal membrane poration and ion channel dysfunction as the primary mechanism of injury. We hypothesized that injury forces utilize mechanically-sensitive, transmembrane integrin proteins, which are coupled to the neuronal cytoskeleton (CSK) and distribute injury forces within the intracellular space, disrupting CSK organization and reducing intercellular neuronal functionality. To test this, magnetic beads were coated with adhesive protein, allowing them to bind to integrins in the neuronal membrane in vitro. To apply forces to the neurons via the bound beads, we built custom magnetic tweezers and demonstrated that focal adhesions (FACs) formed at the site of bead binding. We showed that the beads were coupled to the CSK via integrins by measuring the disparate adhesion of the soma and neurite to their underlying substrate. The soma also required more force to detach than neurites, correlating with the FAC density between each neuronal microcompartment and substrate. We then utilized the magnetic tweezers to test whether beads bound to integrins injured neurons more than beads that bound to neurons nonspecifically. Integrin-bound beads injured neurons more often and the injury was characterized by the formation of focal swellings along axons, reminiscent of Diffuse Axonal Injury. While integrin-bound beads initiated swellings throughout neurons, beads bound nonspecifically only caused local injury where beads were attached to neurons. To demonstrate the electrical dysfunction of integrin-mediated injury forces, we adapted Magnetic Twisting Cytometry to simultaneously apply injury forces to beads bound to multiple cells within neuronal networks in vitro. The formation of focal swellings resulted in reduced axonal electrical activity and decreased coordinated network activity. These data demonstrate that the mechanical insult associated with mTBI is propagated into neurons via integrins, initiating maladaptive CSK remodeling that is linked to impaired electrical function, providing novel insight into the underlying mechanisms of mTBI. / Engineering and Applied Sciences

Eukaryotic genomes are densely compacted into chromatin, so that they can be contained in the nucleus. Despite the tight packaging genes need to be accessible for normal metabolic activities to occur, such as transcription, repair and replication. These processes are regulated by a vast number of proteins but also by the level of compaction of chromatin. The translocation of motor proteins along DNA produces torsional stress which in turn alters chromatin compaction both upstream and downstream. Few single-molecule studies have investigated the behaviour of nucleosomes when subjected to torsion. The inability to measure the applied torque though represented a major limitation to those reports. The implementation of the rotor bead assay, which allows to directly measure the torque applied in magnetic tweezers experiments, has been hindered by a difficult sample preparation procedure. In order to overcome this limitation an efficient protocol for the insertion of chemical or structural modifications in long DNA substrates was developed. This was then further expanded to allow the introduction of labels in multiple loci and/or both strands and has been used successfully in a number of studies. Furthermore this is the first report of tensile experiments performed on nucleosomes with a histone variant. H2AvD nucleosomes were studied due to the interest in the biological role of H2A.Z-family proteins. Interestingly, the variant nucleosomes appear to bind less DNA and to be evicted from the DNA at lower forces than those observed for canonical nucleosomes. These findings show an important role for the H2A-H2B dimers in the mechanical stability of nucleosomes. Furthermore these results are in agreement with recently proposed models of a dynamic nucleosome, in contrast to the long-standing view of nucleosomes as static structures.:Abstract Table of contents 1 Introduction 1.1 The transforming principle 1.2 Chromatin 1.2.1 Nucleosomes 1.2.2 The 30 nm fibre: a mirage? 1.2.3 Histone code 1.3 Histone variant H2A.Z 1.3.1 H2A.Z and transcription 1.4 Single molecule studies of chromatin 1.4.1 Chromatin under tension 1.4.2 Open nucleosome 1.4.3 Twisted chromatin 1.5 Single molecule techniques 1.5.1 Atomic force microscopy 1.5.2 Foerster resonance energy transfer 1.5.3 Magnetic tweezers 1.5.4 Worm-like chain model 2 Aims of the project 3 Cut and paste method for internal DNA labelling 3.1 Introduction 3.2 Experimental design 3.3 Results 3.3.1 Sequence design and cloning 3.3.2 Labelling and religation efficiency 3.3.3 Structural modifications 3.3.4 Labelling of multiple loci 3.3.5 Opposite-strand labelling 3.4 Discussion 4 Reconstituting chromatin 4.1 Long array of NPSs 4.1.1 Polymer physics applied to molecular cloning 4.1.2 Preventing homologous recombination 4.2 Expression and purification of histone proteins 4.2.1 Protein expression 4.2.2 Inclusions bodies 4.2.3 Histone purification 4.2.4 Octamer reconstitution and isolation 4.2.5 H2AvD 4.3 Reconstitution of nucleosomal arrays and biochemical analysis 4.3.1 Reconstitution procedure 4.3.2 Biochemical analysis 4.4 Tweezers construct with nucleosomes 5 Eviction of nucleosomes 5.1 Nucleosome eviction 5.1.1 A two-stage process 5.1.2 Chromatin fibres 5.1.3 Reassembly of nucleosomes 5.1.4 Distinct populations within nucleosome eviction events 5.1.5 Nicked and supercoilable nucleosomal arrays 5.2 Eviction of H2AvD-nucleosomes 5.2.1 H2AvD-nucleosomes bind less inner turn DNA 5.2.2 H2AvD-nucleosomes evict at lower forces 5.2.3 Likelihood of nucleosome reassembly 5.2.4 Gradual weakening of nucleosomes 5.2.5 Analysis software NucleoStep 5.3 Towards a rotor-bead assay on chromatin 5.4 Discussion 5.4.1 Nucleosome eviction in two stages 5.4.2 The fate of dimers in single molecule experiments 5.4.3 Structural origin and biological relevance of the mechanical properties of H2AvD-nucleosomal core particles 5.4.4 Monolithic or dynamic nucleosomes 6 Conclusions Bibliography Appendix 6.1 Internal labelling Procedure 6.1.1 Cloning 6.1.2 Nicking & cutting 6.1.3 The replace reaction 6.1.4 Purification 6.1.5 Ligation (optional) 6.1.6 Opposite strand labelling 6.1.7 Assessing the results of the labelling reaction 6.2 Chromatin reconstitution 6.2.1 Long array of NPSs 6.2.2 Expression and purification of histone proteins 6.2.3 Reconstitution of nucleosomal arrays and biochemical characterization 6.2.4 Simple Phenol:chloroform isolation of DNA 6.3 Magnetic tweezers experiments 6.3.1 Flow cell assembly 6.3.2 Functionalization of flow cells 6.3.3 Magnetic tweezers and rotor bead measurements 6.3.4 Force calibration List of Figures List of Tables List of publications Acknowledgements Declaration of originality