Anomalous transport in the crowded world of biological cells

A ubiquitous observation in cell biology is that diffusion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarising their densely packed and heterogeneous structures. The most familiar phenomenon is a power-law increase of the MSD, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations, non-gaussian distributions of the displacements, heterogeneous diffusion, and immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarise some widely used theoretical models: gaussian models like FBM and Langevin equations for visco-elastic media, the CTRW model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Emphasis is put on the spatio-temporal properties of the transport in terms of 2-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even for identical MSDs. Then, we review the theory underlying common experimental techniques in the presence of anomalous transport: single-particle tracking, FCS, and FRAP. We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where model systems mimic physiological crowding conditions. Finally, computer simulations play an important role in testing the theoretical models and corroborating the experimental findings. The review is completed by a synthesis of the theoretical and experimental progress identifying open questions for future investigation.Comment: review article, to appear in Rep. Prog. Phy

Unifying the mechanism of mitotic exit control in a spatiotemporal logical model.

The transition from mitosis into the first gap phase of the cell cycle in budding yeast is controlled by the Mitotic Exit Network (MEN). The network interprets spatiotemporal cues about the progression of mitosis and ensures that release of Cdc14 phosphatase occurs only after completion of key mitotic events. The MEN has been studied intensively; however, a unified understanding of how localisation and protein activity function together as a system is lacking. In this paper, we present a compartmental, logical model of the MEN that is capable of representing spatial aspects of regulation in parallel to control of enzymatic activity. We show that our model is capable of correctly predicting the phenotype of the majority of mutants we tested, including mutants that cause proteins to mislocalise. We use a continuous time implementation of the model to demonstrate that Cdc14 Early Anaphase Release (FEAR) ensures robust timing of anaphase, and we verify our findings in living cells. Furthermore, we show that our model can represent measured cell-cell variation in Spindle Position Checkpoint (SPoC) mutants. This work suggests a general approach to incorporate spatial effects into logical models. We anticipate that the model itself will be an important resource to experimental researchers, providing a rigorous platform to test hypotheses about regulation of mitotic exit

Estimating Movement from Mobile Telephony Data

Mobile enabled devices are ubiquitous in modern society. The information gathered by their normal service operations has become one of the primary data sources used in the understanding of human mobility, social connection and information transfer. This thesis investigates techniques that can extract useful information from anonymised call detail records (CDR). CDR consist of mobile subscriber data related to people in connection with the network operators, the nature of their communication activity (voice, SMS, data, etc.), duration of the activity and starting time of the activity and servicing cell identification numbers of both the sender and the receiver when available. The main contributions of the research are a methodology for distance measurements which enables the identification of mobile subscriber travel paths and a methodology for population density estimation based on significant mobile subscriber regions of interest. In addition, insights are given into how a mobile network operator may use geographically located subscriber data to create new revenue streams and improved network performance. A range of novel algorithms and techniques underpin the development of these methodologies. These include, among others, techniques for CDR feature extraction, data visualisation and CDR data cleansing. The primary data source used in this body of work was the CDR of Meteor, a mobile network operator in the Republic of Ireland. The Meteor network under investigation has just over 1 million customers, which represents approximately a quarter of the country’s 4.6 million inhabitants, and operates using both 2G and 3G cellular telephony technologies. Results show that the steady state vector analysis of modified Markov chain mobility models can return population density estimates comparable to population estimates obtained through a census. Evaluated using a test dataset, results of travel path identification showed that developed distance measurements achieved greater accuracy when classifying the routes CDR journey trajectories took compared to traditional trajectory distance measurements. Results from subscriber segmentation indicate that subscribers who have perceived similar relationships to geographical features can be grouped based on weighted steady state mobility vectors. Overall, this thesis proposes novel algorithms and techniques for the estimation of movement from mobile telephony data addressing practical issues related to sampling, privacy and spatial uncertainty

The relationship between MEG and fMRI

In recent years functional neuroimaging techniques such as fMRI, MEG, EEG and PET have provided researchers with a wealth of information on human brain function. However none of these modalities can measure directly either the neuro-electrical or neuro-chemical processes that mediate brain function. This means that metrics directly reflecting brain ‘activity’ must be inferred from other metrics (e.g. magnetic fields (MEG) or haemodynamics (fMRI)). To overcome this limitation, many studies seek to combine multiple complementary modalities and an excellent example of this is the combination of MEG (which has high temporal resolution) with fMRI (which has high spatial resolution). However, the full potential of multi-modal approaches can only be truly realised in cases where the relationship between metrics is known. In this paper, we explore the relationship between measurements made using fMRI and MEG. We describe the origins of the two signals as well as their relationship to electrophysiology. We review multiple studies that have attempted to characterise the spatial relationship between fMRI and MEG, and we also describe studies that exploit the rich information content of MEG to explore differing relationships between MEG and fMRI across neural oscillatory frequency bands. Monitoring the brain at “rest” has become of significant recent interest to the neuroimaging community and we review recent evidence comparing MEG and fMRI metrics of functional connectivity. A brief discussion of the use of magnetic resonance spectroscopy (MRS) to probe the relationship between MEG/fMRI and neurochemistry is also given. Finally, we highlight future areas of interest and offer some recommendations for the parallel use of fMRI and MEG

Development and validation of kinase activity reporters for the dynamic study of cell response modalities by microscopy

Necroptosis is defined as a caspase-independent programmed cell death and relies on a signaling pathway involving two serine-threonine kinases: Receptor-Interacting Protein Kinase 1 and 3 (RIPK1 and RIPK3) and the pseudo-kinase Mixed-Lineage Kinase Like (MLKL). Activation of Extracellular signal-Regulated Kinases 1 and 2 (ERK1/2) was reported to be involved in different modes of programmed cell death. It is now accepted that the regulation of the duration, magnitude and subcellular compartmentalization of ERK1/2 activity by specific spatio-temporal regulators is interpreted by the cell towards cell fate determination. ERK1/2 inhibition delays TNFα-induced necroptosis in L929 cells in a dose dependent manner but did not block it, providing arguments for a pro-necrotic function of ERK1/2. In this context, a compartmentalized biphasic phosphorylation of ERK1/2 was observed. Our results indicate a RIPK1-dependent phosphorylation of ERK1/2. Owing to the importance of ERK1/2 spatio-temporal dynamics in determining cellular responses, we developed a new reporter of ERK2 localization named ERK2-LOC. We observed a transient translocation of ERK2 when necroptosis was triggered in L929 upon TNFα stimulation, followed by progressive ERK2 accumulation in the nucleus. ERK1/2 activities were monitored during necroptosis using a FRET-based kinase biosensor for ERK1/2 (ERK1/2-ACT). Using ERK1/2-ACT, a dedicated spatio-temporal signature of ERK1/2 activity was recorded during necroptosis. Finally, to correlate ERK1/2 activity code with necroptosis occurrence, we also engineered a first generation of FRET biosensors to report on both RIPK1 and RIPK3 activities during necroptosis

Interfacing of neuromorphic vision, auditory and olfactory sensors with digital neuromorphic circuits

The conventional Von Neumann architecture imposes strict constraints on the development of intelligent adaptive systems. The requirements of substantial computing power to process and analyse complex data make such an approach impractical to be used in implementing smart systems. Neuromorphic engineering has produced promising results in applications such as electronic sensing, networking architectures and complex data processing. This interdisciplinary field takes inspiration from neurobiological architecture and emulates these characteristics using analogue Very Large Scale Integration (VLSI). The unconventional approach of exploiting the non-linear current characteristics of transistors has aided in the development of low-power adaptive systems that can be implemented in intelligent systems. The neuromorphic approach is widely applied in electronic sensing, particularly in vision, auditory, tactile and olfactory sensors. While conventional sensors generate a huge amount of redundant output data, neuromorphic sensors implement the biological concept of spike-based output to generate sparse output data that corresponds to a certain sensing event. The operation principle applied in these sensors supports reduced power consumption with operating efficiency comparable to conventional sensors. Although neuromorphic sensors such as Dynamic Vision Sensor (DVS), Dynamic and Active pixel Vision Sensor (DAVIS) and AEREAR2 are steadily expanding their scope of application in real-world systems, the lack of spike-based data processing algorithms and complex interfacing methods restricts its applications in low-cost standalone autonomous systems. This research addresses the issue of interfacing between neuromorphic sensors and digital neuromorphic circuits. Current interfacing methods of these sensors are dependent on computers for output data processing. This approach restricts the portability of these sensors, limits their application in a standalone system and increases the overall cost of such systems. The proposed methodology simplifies the interfacing of these sensors with digital neuromorphic processors by utilizing AER communication protocols and neuromorphic hardware developed under the Convolution AER Vision Architecture for Real-time (CAVIAR) project. The proposed interface is simulated using a JAVA model that emulates a typical spikebased output of a neuromorphic sensor, in this case an olfactory sensor, and functions that process this data based on supervised learning. The successful implementation of this simulation suggests that the methodology is a practical solution and can be implemented in hardware. The JAVA simulation is compared to a similar model developed in Nengo, a standard large-scale neural simulation tool. The successful completion of this research contributes towards expanding the scope of application of neuromorphic sensors in standalone intelligent systems. The easy interfacing method proposed in this thesis promotes the portability of these sensors by eliminating the dependency on computers for output data processing. The inclusion of neuromorphic Field Programmable Gate Array (FPGA) board allows reconfiguration and deployment of learning algorithms to implement adaptable systems. These low-power systems can be widely applied in biosecurity and environmental monitoring. With this thesis, we suggest directions for future research in neuromorphic standalone systems based on neuromorphic olfaction

Imaging functional and structural networks in the human epileptic brain

Epileptic activity in the brain arises from dysfunctional neuronal networks involving cortical and subcortical grey matter as well as their connections via white matter fibres. Physiological brain networks can be affected by the structural abnormalities causing the epileptic activity, or by the epileptic activity itself. A better knowledge of physiological and pathological brain networks in patients with epilepsy is critical for a better understanding the patterns of seizure generation, propagation and termination as well as the alteration of physiological brain networks by a chronic neurological disorder. Moreover, the identification of pathological and physiological networks in an individual subject is critical for the planning of epilepsy surgery aiming at resection or at least interruption of the epileptic network while sparing physiological networks which have potentially been remodelled by the disease. This work describes the combination of neuroimaging methods to study the functional epileptic networks in the brain, structural connectivity changes of the motor networks in patients with localisation-related or generalised epilepsy and finally structural connectivity of the epileptic network. The combination between EEG source imaging and simultaneous EEG-fMRI recordings allowed to distinguish between regions of onset and propagation of interictal epileptic activity and to better map the epileptic network using the continuous activity of the epileptic source. These results are complemented by the first recordings of simultaneous intracranial EEG and fMRI in human. This whole-brain imaging technique revealed regional as well as distant haemodynamic changes related to very focal epileptic activity. The combination of fMRI and DTI tractography showed subtle changes in the structural connectivity of patients with Juvenile Myoclonic Epilepsy, a form of idiopathic generalised epilepsy. Finally, a combination of intracranial EEG and tractography was used to explore the structural connectivity of epileptic networks. Clinical relevance, methodological issues and future perspectives are discussed