In vivo Analysis and Modeling Reveals that Transient Interactions of Myosin XI, its Cargo, and Filamentous Actin Overcome Diffusion Limitations to Sustain Polarized Cell Growth

Tip growth is a ubiquitous process throughout the plant kingdom in which a single cell elongates in one direction in a self-similar manner. To sustain tip growth in plants, the cell must regulate the extensibility of the wall to promote growth and avoid turgor-induced rupture. This process is heavily dependent on the cytoskeleton, which is thought to coordinate the delivery and recycling of vesicles containing cell wall materials at the cell tip. Although significant work has been done to elucidate the various molecular players in this process, there remains a need for a more mechanistic understanding of the cytoskeletonÂ’s role in tip growth. For this reason, specific emphasis should be placed on understanding the dynamics of the cytoskeleton, its associated motors, and their cargo. Since the advent of fluorescence fusion technology, various quantitative fluorescence dynamics techniques have emerged. Among the most prominent of these techniques is fluorescence recovery after photobleaching (FRAP). Despite its prominence, it is unclear how to interpret fluorescence recoveries in confined cellular geometries such as tip-growing cells. Here we developed a digital confocal microscope simulation of FRAP in tip-growing cells. With this simulation, we determined that fluorescence recoveries are significantly influenced by cell boundaries. With this FRAP simulation, we then measured the diffusion of VAMP72-labeled vesicles in the moss Physcomitrella patens. Using finite element modeling of polarized cell growth, and the measured VAMP72-labeled vesicle diffusion coefficient, we were able to show that diffusion alone cannot support the required transport of wall materials to the cell tip. This indicates that an actin-based active transport system is necessary for vesicle clustering at the cell tip to support growth. This provides one essential function of the actin cytoskeleton in polarized cell growth. After establishing the requirement for actin-based transport, we then sought to characterize the in vivo binding interactions of myosin XI, vesicles, and filamentous actin. Particle tracking evidence from P. patens protoplasts suggests that myosin XI and VAMP72-labeled vesicles exhibit fast transient interactions. Hidden Markov modeling of particle tracking indicates that myosin XI and VAMP72- labeled vesicles move along actin filaments in short-lived linear trajectories. These fast transient interactions may be necessary to achieve the rapid dynamics of the apical actin, important for growth. This work advances the fieldÂ’s understanding of fluorescence dynamics, elucidates a necessary function of the actin cytoskeleton, and provides insight into how the components of the cytoskeleton interact in vivo

Standardization of sample collection, isolation and analysis methods in extracellular vesicle research

The emergence of publications on extracellular RNA (exRNA) and extracellular vesicles (EV) has highlighted the potential of these molecules and vehicles as biomarkers of disease and therapeutic targets. These findings have created a paradigm shift, most prominently in the field of oncology, prompting expanded interest in the field and dedication of funds for EV research. At the same time, understanding of EV subtypes, biogenesis, cargo and mechanisms of shuttling remains incomplete. The techniques that can be harnessed to address the many gaps in our current knowledge were the subject of a special workshop of the International Society for Extracellular Vesicles (ISEV) in New York City in October 2012. As part of the “ISEV Research Seminar: Analysis and Function of RNA in Extracellular Vesicles (evRNA)”, 6 round-table discussions were held to provide an evidence-based framework for isolation and analysis of EV, purification and analysis of associated RNA molecules, and molecular engineering of EV for therapeutic intervention. This article arises from the discussion of EV isolation and analysis at that meeting. The conclusions of the round table are supplemented with a review of published materials and our experience. Controversies and outstanding questions are identified that may inform future research and funding priorities. While we emphasize the need for standardization of specimen handling, appropriate normative controls, and isolation and analysis techniques to facilitate comparison of results, we also recognize that continual development and evaluation of techniques will be necessary as new knowledge is amassed. On many points, consensus has not yet been achieved and must be built through the reporting of well-controlled experiments

Interactions between the plant Golgi apparatus and the cytoskeleton

In animal cells, the relationship between the Golgi apparatus and cytoskeleton has been well characterised but not much is known in plants. The functions of the Golgi apparatus are conserved amongst eukaryotes. It is one of the main stations in the secretory pathway and is involved in protein processing and sorting to different destinations. In plants, it is also involved in trafficking and positioning of cell wall components. In tobacco epidermal cells, fluorescent labelling with Golgi marker proteins has shown that the Golgi apparatus is made of hundreds of individual units scattered in the cortical cytoplasm and moving on the actin cytoskeleton. The contribution of actin filaments to Golgi body motility in plant has been extensively described, but this actin-centric view has recently been challenged. Emerging evidence suggests that microtubules may contribute to short distance movement and ‘fine tuning’ of Golgi body displacement. Moreover, proteomic studies linking the actin- cytoskeleton to microtubules have demonstrated that these two components of the cytoskeleton are closely related and a role of the microtubules in Golgi movement cannot be excluded. In this thesis, automated tracking of Golgi bodies was used to understand and quantify the contribution of actin filaments and microtubules to the organelle dynamics. The tracking technique is also used to assess how the labelling of the cytoskeleton, with a novel fluorescent nanoprobe, affects the dynamics and stability of the actin filaments and the movement of Golgi bodies; FRAP analysis (fluorescent recovery after photo-bleaching) was also used to investigate the binding properties of the fluorescent nanoprobe to the actin filaments. The nanoprobe was compared with another cytoskeletal marker, Lifeact-GFP, to evaluate their suitability for studying the organelle’s motility in relation to the actin-cytoskeleton. Micromanipulation of Golgi bodies with optical tweezers was used to test if there are physical links between the organelles and the cytoskeleton. The widely accepted model is that organelles move on actin filaments and movement is powered by myosins. The hypothesis that actin filaments slide one of top of the other, and drag the organelles along, was tested using the FRAP technique. Kinesin-13a is the only microtubule motor protein localized on Golgi bodies by immunochemical studies. Its localization was investigated in vivo to evaluate if it is involved in linking Golgi bodies to microtubules

Electrical Lab-on-a-Chip for Ex Vivo Study on the Influence of Electric Fields on Pollen Cells

Pollen tubes are polarly growing plant cells that are able to respond to a combination of chemical, mechanical, and electrical cues during their journey through the flower pistil in order to accomplish fertilization. How signals are perceived and processed in the pollen tube is still poorly understood and evidence for electrical guidance, in particular, is vague and highly contradictory. To generate reproducible experimental conditions for ex vivo pollen cell cultures, here we present a low-cost, reusable Electrical Lab-on-a-Chip (ELoC) for investigating the influence of electric fields on growing cells. Viability of pollen growth using a structured microfluidic network is first investigated and validated. Then the integration of microelectrodes into the device is addressed in detail. Characterization of the pollen growth medium conductivity and simulation of the ELoC electrical configuration were carried out to define the experimental conditions. Reusability of the microdevice is achieved by structuring the design into two separate rebondable modules: a microfluidic module and a microelectrode module. Two experimental approaches were realized: a batch design for exposing simultaneously a large number of cells to a global electric field, and a single-cell design in which a localized electric field is applied to individual cells. Extensive batch results indicate that DC fields were inhibitory above 6 V/cm. However, switching to AC fields re-established pollen tube growth at frequencies above 100 mHz, suggesting a significant role of the medium conductivity in controlling the cellular response. Unlike macroscopic open-assay experimental setups, single-cell tests further indicate no reorientation of pollen tube growth, suggesting that previously reported tropic behavior was caused by ion movement in the substrate rather than by a direct effect of the electric field on the cell

Bridging Single-Particle Characterisation Gaps of Optical Microscopy in the Nano-Submicron Regime

As the practical importance of particles in the nano-submicron size regime continues to increase in both biomedical applications and industrial processes, so does the need for accurate and versatile characterisation methods. Optical scattering microscopy methods are commonly used for single-particle characterisation as they provide quick measurements at physiologically relevant conditions with detection limits reaching down to individual biomolecules. However, quantitative particle characterisation using optical microscopy often rely on assumptions about the surrounding media and theparticle, including solution viscosity, boundary conditions, as well as particle shape and material. Since these assumptions are difficult to evaluate, particle characterisation beyond hydrodynamic radius and/or mass remains challenging.The aim of this thesis is to contribute to bridging the gaps that limit quantitative optical microscopy-based characterisation of individual particles in the nano-submicron regime by both developing new and improving existing microscopy methods. Specifically, in Paper I a method was developed to evaluate the relation between diffusivity and particle size to enable measurements of the hydrodynamic boundary condition. Papers II-V are based around the development of holographic nanoparticle tracking (H-NTA) and extensions thereof, with the intent of using the complex-valued optical field for material sensitive particle characterisation with minimal dependence on the surrounding media. In Paper II, H-NTA by itself was used to characterise suspensions containing nanobubbles and molecular aggregates. In Paper III, the combination of H-NTA with deep learning was used to achieve simultaneous quantification of size and refractive index directly from single microscopy images, which allowed detection of reversible fluctuations in nanoparticle aggregates. In Paper IV, H-NTA augmented with a low frequency attenuation filter, coined twilight holography, was used to investigate the interaction between herpes viruses and functionalised gold nanoparticles in terms of size, bound gold mass, and virus refractive index. In Paper V, the combination of twilight holography and interferometric scattering microscopy (iSCAT) was used to quantify both size and polarizability of individual nanoparticles without the need of detailed knowledge about the surrounding media. Taken together, the presented results in this thesis provide both new insights into heterogenous nanoparticle systems and contributes to narrowing the gap for detailed optical particle characterisation

Lab-On-Chip for Ex-Vivo Study of Bio-Mechanical-Chemical Behavior of Tip Growing Plant Cells

This thesis presents design, modeling, fabrication, and testing of different Lab-on-chip (LOC) devices to study static and dynamic behavior of pollen tubes in bio-mechanical-chemical environments. The main components of microfluidic platform include microfluidic network for manipulation, trapping and growing of a series of pollen tubes in a controlled environment, actuating channels in order to introduce chemicals and drugs toward the pollen tube, microstructural elements such as microgaps and microcantilevers to provide Ex-Vivo environment for characterizing static and dynamic responses of pollen tubes. A Lab-On-Chip (LOC), called, TipChip was developed as a flexible platform that can simplify sophisticated functions such as chemical reactions, drug development, by integrating them within a single micro-device. The configuration of the microfluidic network was developed in such a way that it allows observation under chemical or mechanical manipulation of multiple pollen tubes. The growth of pollen tubes under different flow rates and geometrical dimensions of microfluidic network has been studied and the challenges have been identified. The microfluidic platform design was enhanced to deal with the challenges by adapting the dimensions of the microfluidic network and the inlet flow. It provides identical growth environments for growing pollen tubes along each microchannel and improves the performance of microfluidic device, through varying the dimensions and geometries of the microfluidic network. The thesis identifies the static response of pollen tube to chemical stimulation which was used to determine the role of a few of the growth regulators such as sucrose and calcium ions as they regulate tube turgor pressure and cell wall mechanical properties of pollen tube. New experimental platforms were fabricated to treat locally the pollen tube at the tip in order to characterize its static response to local treatment in reorienting the growth direction. The device is also used to locally stimulate the cylindrical region of pollen tube. Using these LOC devices we attempted to answer some questions regarding the role of regulators in pollen tube growth. The thesis explores in detail the dynamic growth of pollen tube in normal condition and also under chemical stimulation. Waveform analysis is employed in order to extract primary and secondary oscillation frequencies of pollen tube as significant indicators of dynamic growth of pollen tube. The dynamic response of pollen tubes is implemented as a whole-plant cell sensor for toxicity detection in order to detect toxic materials in concentration-based manner. Aluminum ions were tested as the toxic substance. The degree of toxicity was defined by measuring the reduction in growth rate as well as peak oscillation frequencies in the case of static and dynamic response of pollen tube, respectively. The thesis addresses the quantification of mechanical properties of pollen tube cell wall using the Bending LOC (BLOC) platform. The flexural rigidity of the pollen tube and the Young’s modulus of the cell wall are estimated through finite element modeling of the observed fluid-structure interaction. The thesis also explores the feasibility of studying the pollen tube response to the mechanical stimulation. The microfluidic device also enables integrating mechanical force obstructing pollen tube growth in order to characterize the interaction of pollen tube and mechanical structures which are similar to the in-vivo interaction between a pollen tube and the growth matrix during the course of growth toward the ovule. The behavior of the pollen tube while passing through microgap was also explored in detail. The deflection of microgap under growth force and the changes in diameter of the pollen tube under reaction force from microgap were evaluated. This part explores the role of mechanical forces in bursting the pollen tube tip which could explain the contribution of mechanical signal in the bursting of tube near the vicinity of the ovule. In addition, the configuration of microgap enabled the estimation of the maximum invasive force exerted by pollen tube. Thus, the proposed microfluidic platform is highly suitable for cellular analysis, pollen tube biology and detection of toxicity

Characterizing the diffusional behavior and trafficking pathways of Kv2.1 using single particle tracking in live cells

2013 Spring.Includes bibliographical references.Studying the diffusion pattern of membrane components yields valuable information regarding membrane structure, organization, and dynamics. Single particle tracking serves as an excellent tool to probe these events. We are investigating of the dynamics of the voltage gated potassium channel, Kv2.1. Kv2.1 uniquely localizes to stable, micro-domains on the cell surface where it plays a non-conducting role. The work reported here examines the diffusion pattern of Kv2.1 and determines alternate functional roles of surface clusters by investigating recycling pathways using single particle tracking in live cells. The movement of Kv2.1 on the cell surface is found to be best modeled by the combination of a stationary and non-stationary process, namely a continuous time random walk in a fractal geometry. Kv2.1 surface structures are shown to be specialized platforms involved in trafficking of Kv channels to and from the cell surface in hippocampal neurons and transfected HEK cells. Both Kv2.1 and Kv1.4, a non-clustering membrane protein, are inserted and retrieved from the plasma membrane at the perimeter of Kv2.1 clusters. From the distribution of cluster sizes, using a Fokker-Planck formalism, we find there is no evidence of a feedback mechanism controlling Kv2.1 domain size on the cell surface. Interestingly, the sizes of Kv2.1 clusters are rather governed by fluctuations in the endocytic and exocytic machinery. Lastly, we pinpoint the mechanism responsible for inducing Kv2.1 non-ergodic dynamics: the capture of Kv2.1 into growing clathrin-coated pits via transient binding to pit proteins

F-actin rearrangements and analysis of physical environment of invasive hyphal growth.

Invasive growth through a substrate requires a massive amount of penetrative force, and this is generated in the space of a few microns in a growing tip. This process is known to be critical in the root hair, pollen tube, rhizoids, and the topic of this thesis, hyphal growth. However defining the mechanisms underlying the tip growth remains a contentious issue. Shortcomings in control of direction and regulation of growth began to undermine early turgor-based theories, and the cytoskeletal protein actin, ubiquitous in nature and with crucial roles in structure and motility became a target for investigation. A major breakthrough came with the discovery that a characteristic actin depleted zone (ADZ) occurs at the growing tip of hyphae during invasive but not non-invasive hyphal growth. The ADZ is likely to have an important role in generating the greater protrusive force required for invasive growth. However, since its discovery, little has been determined about the characteristics of the ADZ. Uncertainty in the description of the physical environment the hyphae face adds a layer of complexity to interpretation of results. This thesis aims to address this issue, studying the impact of increasing agarose substrate concentration on the presence and dimensions of the ADZ in the oomycete A. bisexualis. Furthermore, agarose is examined by compression and imaging to compare the physical characteristics of the agar samples over the range of concentrations, and determine whether increasing agarose concentration influences agarose gel structure. Results suggest a difference in the number of ADZ observed in non-invasive compared with invasive samples, however no significant differences in the number or dimensions of ADZ were found amongst the 1-4% w/v agarose concentrations. The 0% sample showed 20.7 percent of hyphae exhibited depleted zones, while 1, 2, 3 and 4% samples showed 56.9%, 48.8%, 40.9% and 54.2% respectively. ADZ dimensions did not correlate with agarose concentration. The average ADZ area:hyphal diameter ratio was 0.634, 0.526, 0.430, 1.09, and 0.65 for 0-4% agarose concentrations respectively. Additionally, investigation of gel compression forces revealed gel strength increases with agarose concentration. The force required to compress the agarose increased from 1.85 Psi in 1% agarose to 4.85, 7.09 and 12.22 Psi in 2, 3 and 4% agarose concentrations respectively. SEM imaging, however, suggests heterogeneity of the fibrous interconnected network of agarose gels at a microscopic scale with variable porous structure at all agarose concentrations. This scale is relevant to hyphal tip growth. In combination, these results suggest F-actin depletion may be a response mechanism to provide greater force for invasive growth. Additionally, this response is not dependent on the concentration of the agarose media, possibly due to the variability encountered within the media. These results contribute another important step forward in unraveling the elusive mechanism of tip growth