The proteasome lid triggers COP9 signalosome activity during the transition of Saccharomyces cerevisiae cells into quiescence.

The class of Cullin–RING E3 ligases (CRLs) selectively ubiquitinate a large portion of proteins targeted for proteolysis by the 26S proteasome. Before degradation, ubiquitin molecules are removed from their conjugated proteins by deubiquitinating enzymes, a handful of which are associated with the proteasome. The CRL activity is triggered by modification of the Cullin subunit with the ubiquitin-like protein, NEDD8 (also known as Rub1 in Saccharomyces cerevisiae). Cullin modification is then reversed by hydrolytic action of the COP9 signalosome (CSN). As the NEDD8– Rub1 catalytic cycle is not essential for the viability of S. cerevisiae, this organism is a useful model system to study the alteration of Rub1–CRL conjugation patterns. In this study, we describe two distinct mutants of Rpn11, a proteasome-associated deubiquitinating enzyme, both of which exhibit a biochemical phenotype characterized by high accumulation of Rub1-modified Cdc53–Cullin1 (yCul1) upon entry into quiescence in S. cerevisiae. Further characterization revealed proteasome 19S-lid-associated deubiquitination activity that authorizes the hydrolysis of Rub1 from yCul1 by the CSN complex. Thus, our results suggest a negative feedback mechanism via proteasome capacity on upstream ubiquitinating enzymes

Synchronization of Coupled and Periodically Forced Chemical Oscillators

Physiological rhythms are essential in all living organisms. Such rhythms are regulated through the interactions of many cells. Deviation of a biological system from its normal rhythms can lead to physiological maladies. The tremor and symptoms associated with Parkinson\u27s disease are thought to emerge from abnormal synchrony of neuronal activity within the neural network of the brain. Deep brain stimulation is a therapeutic technique that can remove this pathological synchronization by the application of a periodic desynchronizing signal. Herein, we used the photosensitive Belousov--Zhabotinsky (BZ) chemical reaction to test the mechanism of deep brain stimulation. A collection of oscillators are initially synchronized using a regular light signal. Desynchronization is then attempted using an appropriately chosen desynchronizing signal based on information found in the phase response curve.;Coupled oscillators in various network topologies form the most common prototypical systems for studying networks of dynamical elements. In the present study, we couple discrete BZ photochemical oscillators in a network configuration. Different behaviors are observed on varying the coupling strength and the frequency heterogeneity, including incoherent oscillations to partial and full frequency entrainment. Phase clusters are organized symmetrically or non-symmetrically in phase-lag synchronization structures, a novel phase wave entrainment behavior in non-continuous media. The behavior is observed over a range of moderate coupling strengths and a broad frequency distribution of the oscillators

Synchronization Behavior in Coupled Chemical Oscillators

Synchronization is a collective phenomenon emerging from the interactions of different dynamical systems. Systems with different characteristics adjust their behavior to a common behavior of the group. This collective behavior is observed in many biological, chemical, and physical systems. Examples from different fields include pacemaker heart cells, synchronization of neurons during epilepsy seizures, arrays of microwave oscillators, and robot manipulators. Studies of coupled oscillators have revealed different mechanisms by which discrete oscillators interact and organize to a uniform synchronized state from an incoherent state. The discovery of a new type of synchronization state, called the chimera state has further broadened the field of synchronization. A chimera state is made up of coexisting subpopulations of oscillators, each with same coupling structure, but with one exhibiting synchronous behavior and the other asynchronous behavior. The phenomena has been the focus of much theoretical and experimental research in the past decade. In this thesis, experimental and simulation studies of chimera states in populations of coupled chemical oscillators will be described and their relation to other synchronization states will be characterized. Experiments were carried out with the photosensitive Belousov-Zhabotinsky (BZ) chemical oscillators and a light feedback scheme. The dimensionless two-variable Zhabotinsky-Buchholtz-Kiyatin-Epstein (ZBKE) model of the BZ chemical system was used in simulations.;A two-group coupling model, which splits the oscillators into two subpopulations, was used in the first part of the study. The subpopulations are globally coupled, both within and between the subpopulations. The coupling of every oscillator with members of the other subpopulation is weaker than the coupling with members of its own subpopulation. In-phase, out-of-phase, and phase-cluster synchronized states, as well as the chimera state, were found in both experiments and simulations. The probability of finding a chimera state decreases with increasing intra-group coupling strength. The study also revealed that heterogeneity in the frequencies of the oscillators in the system decreases the lifetime of a chimera. This was evidenced by the collapse of the chimera state to a synchronized state in both experiments and simulations with heterogeneous oscillators.;Synchronized and mixed-state behaviors are observed in populations of nonlocally coupled chemical oscillators in a ring configuration. With nonlocal coupling, the nearest neighbors are strongly coupled and the coupling strength decreases exponentially with distance. Experimental studies show stable chimera states, phase cluster states and phase waves coexisting with unsychronized groups of oscillators. These are spontaneously formed from quasi-random initial phase distributions in the experiments and random initial phase distributions in simulations. Simulations with homogeneous and heterogeneous oscillators revealed that a finite spread of frequencies increases the probability of initiating a synchronized group, leading to chimera states. The effects of group size and coupling strength on chimera states, phase waves, phase clusters, and traveling waves are discussed. Complex behaviors in coexisting states were analyzed, consisting of periodic phase slips with identical oscillators and periodic switching with nonidentical oscillators. Fourier transform analysis was used to distinguish between states exhibiting high periodicity and chimera states, which show similar average behavior

Chroma Key wthout Color Restrictions based on Asynchronous Amplitude Modulation of Background Illumination on Retroreflective Screens

A simple technique to avoid color limitations in image capture systems based on chroma key video composition using retroreflective screens and light-emitting diodes (LED) rings is proposed and demonstrated. The combination of an asynchronous temporal modulation onto the background illumination and simple image processing removes the usual restrictions on foreground colors in the scene. The technique removes technical constraints in stage composition, allowing its design to be purely based on artistic grounds. Since it only requires adding a very simple electronic circuit to widely used chroma keying hardware based on retroreflective screens, the technique is easily applicable to TV and filming studios.Vidal Rodriguez, B.; Lafuente, JA. (2016). Chroma Key wthout Color Restrictions based on Asynchronous Amplitude Modulation of Background Illumination on Retroreflective Screens. Journal of Electronic Imaging. 25(2):230091-230095. doi:10.1117/1.JEI.25.2.023009S23009123009525

Physics of Microswimmers - Single Particle Motion and Collective Behavior

Locomotion and transport of microorganisms in fluids is an essential aspect of life. Search for food, orientation toward light, spreading of off-spring, and the formation of colonies are only possible due to locomotion. Swimming at the microscale occurs at low Reynolds numbers, where fluid friction and viscosity dominates over inertia. Here, evolution achieved propulsion mechanisms, which overcome and even exploit drag. Prominent propulsion mechanisms are rotating helical flagella, exploited by many bacteria, and snake-like or whip-like motion of eukaryotic flagella, utilized by sperm and algae. For artificial microswimmers, alternative concepts to convert chemical energy or heat into directed motion can be employed, which are potentially more efficient. The dynamics of microswimmers comprises many facets, which are all required to achieve locomotion. In this article, we review the physics of locomotion of biological and synthetic microswimmers, and the collective behavior of their assemblies. Starting from individual microswimmers, we describe the various propulsion mechanism of biological and synthetic systems and address the hydrodynamic aspects of swimming. This comprises synchronization and the concerted beating of flagella and cilia. In addition, the swimming behavior next to surfaces is examined. Finally, collective and cooperate phenomena of various types of isotropic and anisotropic swimmers with and without hydrodynamic interactions are discussed.Comment: 54 pages, 59 figures, review article, Reports of Progress in Physics (to appear

Weak Chimeras in Modular Electrochemical Oscillator Networks

This is the final version. Available on open access from Frontiers Media via the DOI in this recordWe investigate the formation of weak chimera states in modular networks of electrochemical oscillations during the electrodissulution of nickel in sulfuric acid. In experiment and simulation, we consider two globally coupled populations of highly non-linear oscillators which are weakly coupled through a collective resistance. Without cross coupling, the system exhibits bistability between a one- and a two-cluster state, whose frequencies are distinct. For weak cross coupling and initial conditions for the one- and two-cluster states for populations 1 and 2, respectively, weak chimera dynamics are generated. The weak chimera state exhibits localized frequency synchrony: The oscillators in each population are frequency-synchronized while the two populations are not. The chimera state is very robust: The behavior is maintained for hundreds of cycles for the rather heterogeneous natural frequencies of the oscillators. The experimental results are confirmed with numerical simulations of a kinetic model for the chemical process. The features of the chimera states are compared to other previously observed chimeras with oscillators close to Hopf bifurcation, coupled with parallel resistances and capacitances or with a non-linear delayed feedback. The experimentally observed synchronization patterns could provide a mechanism for generation of chimeras in biological systems, where robust response is essential

APC/C and SCF cyclin F Constitute a Reciprocal Feedback Circuit Controlling S-Phase Entry

The anaphase promoting complex/cyclosome (APC/C) is an ubiquitin ligase and core component of the cell-cycle oscillator. During G1 phase, APC/C binds to its substrate receptor Cdh1 and APC/C(Cdh1) plays an important role in restricting S-phase entry and maintaining genome integrity. We describe a reciprocal feedback circuit between APC/C and a second ubiquitin ligase, the SCF (Skp1-Cul1-F box). We show that cyclin F, a cell-cycle-regulated substrate receptor (F-box protein) for the SCF, is targeted for degradation by APC/C. Furthermore, we establish that Cdh1 is itself a substrate of SCF(cyclin F). Cyclin F loss impairs Cdh1 degradation and delays S-phase entry, and this delay is reversed by simultaneous removal of Cdh1. These data indicate that the coordinated, temporal ordering of cyclin F and Cdh1 degradation, organized in a double-negative feedback loop, represents a fundamental aspect of cell-cycle control. This mutual antagonism could be a feature of other oscillating systems