Reaction-diffusion systems in intracellular molecular transport and control

The Pathway to Intelligence: Using Stimuli-Responsive Materials as Building Blocks for Constructing Smart and Functional Systems

Systems that are intelligent have the ability to sense their surroundings, analyze, and respond accordingly. In nature, many biological systems are considered intelligent (e.g., humans, animals, and cells). For man-made systems, artificial intelligence is achieved by massively sophisticated electronic machines (e.g., computers and robots operated by advanced algorithms). On the other hand, freestanding materials (i.e., not tethered to a power supply) are usually passive and static. Hence, herein, the question is asked: can materials be fabricated so that they are intelligent? One promising approach is to use stimuli-responsive materials; these "smart" materials use the energy supplied by a stimulus available from the surrounding for performing a corresponding action. After decades of research, many interesting stimuli-responsive materials that can sense and perform smart functions have been developed. Classes of functions discussed include practical functions (e.g., targeting and motion), regulatory functions (e.g., self-regulation and amplification), and analytical processing functions (e.g., memory and computing). The pathway toward creating truly intelligent materials can involve incorporating a combination of these different types of functions into a single integrated system by using stimuli-responsive materials as the basic building blocks.

Small molecule reaction networks that model the ROS dynamics of the rhizosphere

Molecules released by plants and bacteria form complex abiotic reaction diffusion networks that might regulate the ROS dynamics along the roots of the plants.

Stimuli-responsive self-assembly of nanoparticles

Ligand-protected nanoparticles can serve as attractive building blocks for constructing complex chemical systems.

Redox Signaling from and to Peroxisomes: Progress, Challenges, and Prospects

SIGNIFICANCE

Peroxisomes are organelles that are best known for their role in cellular lipid and hydrogen peroxide (H₂O₂) metabolism. Emerging evidence suggests that these organelles serve as guardians and modulators of cellular redox balance, and that alterations in their redox metabolism may contribute to aging and the development of chronic diseases such as neurodegeneration, diabetes, and cancer. Recent Advances: H₂O₂ is an important signaling messenger that controls many cellular processes by modulating protein activity through cysteine oxidation. Somewhat surprisingly, the potential involvement of peroxisomes in H₂O₂-mediated signaling processes has been overlooked for a long time. However, recent advances in the development of live-cell approaches to monitor and modulate spatiotemporal fluxes in redox species at the subcellular level have opened up new avenues for research in redox biology and boosted interest in the concept of peroxisomes as redox signaling platforms.

CRITICAL ISSUES

This review first introduces the reader to what is known about the role of peroxisomes in cellular H₂O₂ production and clearance, with a focus on mammalian cells. Next, it briefly describes the benefits and drawbacks of current strategies used to investigate the complex interplay between peroxisome metabolism and cellular redox state. Furthermore, it integrates and critically evaluates literature dealing with the interrelationship between peroxisomal redox metabolism, cell signaling, and human disease.

FUTURE DIRECTIONS

As the precise molecular mechanisms underlying many of these associations are still poorly understood, a key focus for future research should be the identification of primary targets for peroxisome-derived H₂O₂.

Enzyme-assisted self-assembly within a hydrogel induced by peptide diffusion

Peptide diffusion into an enzymatically active hydrogel induces the formation of a self-assembled network, changing the mechanical and chemical properties.

How Important Is Protein Diffusion in Prokaryotes?

That diffusion is important for the proper functioning of cells is without question. The extent to which the diffusion coefficient is important is explored here for prokaryotic cells. We discuss the principles of diffusion focusing on diffusion-limited reactions, summarize the known values for diffusion coefficients in prokaryotes and in in vitro model systems, and explain a number of cases where diffusion coefficients are either limiting for reaction rates or necessary for the existence of phenomena. We suggest a number of areas that need further study including expanding the range of organism growth temperatures, direct measurements of diffusion limitation, expanding the range of cell sizes, diffusion limitation for membrane proteins, and taking into account cellular context when assessing the possibility of diffusion limitation.

In Vitro Reconstitution of Self-Organizing Protein Patterns on Supported Lipid Bilayers

Many aspects of the fundamental spatiotemporal organization of cells are governed by reaction-diffusion type systems. In vitro reconstitution of such systems allows for detailed studies of their underlying mechanisms which would not be feasible in vivo. Here, we provide a protocol for the in vitro reconstitution of the MinCDE system of Escherichia coli, which positions the cell division septum in the cell middle. The assay is designed to supply only the components necessary for self-organization, namely a membrane, the two proteins MinD and MinE and energy in the form of ATP. We therefore fabricate an open reaction chamber on a coverslip, on which a supported lipid bilayer is formed. The open design of the chamber allows for optimal preparation of the lipid bilayer and controlled manipulation of the bulk content. The two proteins, MinD and MinE, as well as ATP, are then added into the bulk volume above the membrane. Imaging is possible by many optical microscopies, as the design supports confocal, wide-field and TIRF microscopy alike. In a variation of the protocol, the lipid bilayer is formed on a patterned support, on cell-shaped PDMS microstructures, instead of glass. Lowering the bulk solution to the rim of these compartments encloses the reaction in a smaller compartment and provides boundaries that allow mimicking of in vivo oscillatory behavior. Taken together, we describe protocols to reconstitute the MinCDE system both with and without spatial confinement, allowing researchers to precisely control all aspects influencing pattern formation, such as concentration ranges and addition of other factors or proteins, and to systematically increase system complexity in a relatively simple experimental setup.

A chemically encoded timer for dual molecular delivery at tailored ranges and concentrations

Spatiotemporal control of molecular distribution is much in demand in many fields of chemistry. To address this goal, we exploit a low molecular weight branched self-immolative architecture, which acts as a triggerable chemically encoded timer for autonomous sequential release of two chemicals. Using a light-activated model liberating two distinct fluorophores, we generated a tunable spatially contrasted molecular distribution.

Exploring the emergence of complexity using synthetic replicators

A significant number of synthetic systems capable of replicating themselves or entities that are complementary to themselves have appeared in the last 30 years. Building on an understanding of the operation of synthetic replicators in isolation, this field has progressed to examples where catalytic relationships between replicators within the same network and the extant reaction conditions play a role in driving phenomena at the level of the whole system. Systems chemistry has played a pivotal role in the attempts to understand the origin of biological complexity by exploiting the power of synthetic chemistry, in conjunction with the molecular recognition toolkit pioneered by the field of supramolecular chemistry, thereby permitting the bottom-up engineering of increasingly complex reaction networks from simple building blocks. This review describes the advances facilitated by the systems chemistry approach in relating the expression of complex and emergent behaviour in networks of replicators with the connectivity and catalytic relationships inherent within them. These systems, examined within well-stirred batch reactors, represent conceptual and practical frameworks that can then be translated to conditions that permit replicating systems to overcome the fundamental limits imposed on selection processes in networks operating under closed conditions. This shift away from traditional spatially homogeneous reactors towards dynamic and non-equilibrium conditions, such as those provided by reaction-diffusion reaction formats, constitutes a key change that mimics environments within cellular systems, which possess obvious compartmentalisation and inhomogeneity.

From dynamic self-assembly to networked chemical systems

Although dynamic self-assembly, DySA, is a relatively new area of research, the past decade has brought numerous demonstrations of how various types of components - on scales from (macro)molecular to macroscopic - can be arranged into ordered structures thriving in non-equilibrium, steady states. At the same time, none of these dynamic assemblies has so far proven practically relevant, prompting questions about the field's prospects and ultimate objectives. The main thesis of this Review is that formation of dynamic assemblies cannot be an end in itself - instead, we should think more ambitiously of using such assemblies as control elements (reconfigurable catalysts, nanomachines, etc.) of larger, networked systems directing sequences of chemical reactions or assembly tasks. Such networked systems would be inspired by biology but intended to operate in environments and conditions incompatible with living matter (e.g., in organic solvents, elevated temperatures, etc.). To realize this vision, we need to start considering not only the interactions mediating dynamic self-assembly of individual components, but also how components of different types could coexist and communicate within larger, multicomponent ensembles. Along these lines, the review starts with the discussion of the conceptual foundations of self-assembly in equilibrium and non-equilibrium regimes. It discusses key examples of interactions and phenomena that can provide the basis for various DySA modalities (e.g., those driven by light, magnetic fields, flows, etc.). It then focuses on the recent examples where organization of components in steady states is coupled to other processes taking place in the system (catalysis, formation of dynamic supramolecular materials, control of chirality, etc.). With these examples of functional DySA, we then look forward and consider conditions that must be fulfilled to allow components of multiple types to coexist, function, and communicate with one another within the networked DySA systems of the future. As the closing examples show, such systems are already appearing heralding new opportunities - and, to be sure, new challenges - for DySA research.

Pattern dynamics of the reaction-diffusion immune system

In this paper, we will investigate the effect of diffusion, which is ubiquitous in nature, on the immune system using a reaction-diffusion model in order to understand the dynamical behavior of complex patterns and control the dynamics of different patterns. Through control theory and linear stability analysis of local equilibrium, we obtain the optimal condition under which the system loses stability and a Turing pattern occurs. By combining mathematical analysis and numerical simulation, we show the possible patterns and how these patterns evolve. In addition, we establish a bridge between the complex patterns and the biological mechanism using the results from a previous study in Nature Cell Biology. The results in this paper can help us better understand the biological significance of the immune system.

High-Speed Atomic Force Microscopy Reveals the Inner Workings of the MinDE Protein Oscillator

The MinDE protein system from E. coli has recently been identified as a minimal biological oscillator, based on two proteins only: The ATPase MinD and the ATPase activating protein MinE. In E. coli, the system works as the molecular ruler to place the divisome at midcell for cell division. Despite its compositional simplicity, the molecular mechanism leading to protein patterns and oscillations is still insufficiently understood. Here we used high-speed atomic force microscopy to analyze the mechanism of MinDE membrane association/dissociation dynamics on isolated membrane patches, down to the level of individual point oscillators. This nanoscale analysis shows that MinD association to and dissociation from the membrane are both highly cooperative but mechanistically different processes. We propose that they represent the two directions of a single allosteric switch leading to MinD filament formation and depolymerization. Association/dissociation are separated by rather long apparently silent periods. The membrane-associated period is characterized by MinD filament multivalent binding, avidity, while the dissociated period is defined by seeding of individual MinD. Analyzing association/dissociation kinetics with varying MinD and MinE concentrations and dependent on membrane patch size allowed us to disentangle the essential dynamic variables of the MinDE oscillation cycle.

Localized Supramolecular Peptide Self-Assembly Directed by Enzyme-Induced Proton Gradients

Electrodes are ideal substrates for surface localized self-assembly processes. Spatiotemporal control over such processes is generally directed through the release of ions generated by redox reactions occurring specifically at the electrode. The so-used gradients of ions proved their effectiveness over the last decade but are in essence limited to material-based electrodes, considerably reducing the scope of applications. Herein is described a strategy to enzymatically generate proton gradients from non-conductive surfaces. In the presence of oxygen, immobilization of glucose oxidase (GOx) on a multilayer film provides a flow of protons through enzymatic oxidation of glucose by GOx. The confined acidic environment located at the solid-liquid interface allows the self-assembly of Fmoc-AA-OH (Fmoc=fluorenylmethyloxycarbonyl and A=alanine) dipeptides into β-sheet nanofibers exclusively from and near the surface. In the absence of oxygen, a multilayer nanoreactor containing GOx and horseradish peroxidase (HRP) similarly induces Fmoc-AA-OH self-assembly.

Grip on complexity in chemical reaction networks

A new discipline of "systems chemistry" is emerging, which aims to capture the complexity observed in natural systems within a synthetic chemical framework. Living systems rely on complex networks of chemical reactions to control the concentration of molecules in space and time. Despite the enormous complexity in biological networks, it is possible to identify network motifs that lead to functional outputs such as bistability or oscillations. To truly understand how living systems function, we need a complete understanding of how chemical reaction networks (CRNs) create function. We propose the development of a bottom-up approach to design and construct CRNs where we can follow the influence of single chemical entities on the properties of the network as a whole. Ultimately, this approach should allow us to not only understand such complex networks but also to guide and control their behavior.

Serotyping, antibiotic susceptibility, and virulence genes screening of Escherichia coli isolates obtained from diarrheic buffalo calves in Egyptian farms

AIM

In Egypt as in many other countries, river water buffalo (Bubalus bubalis) is considered an important source of high-quality milk and meat supply. The objective of this study was to investigate serotypes, virulence genes, and antibiotic resistance determinants profiles of Escherichia coli isolated from buffalo at some places in Egypt; noticibly, this issue was not discussed in the country yet.

MATERIALS AND METHODS

A number of 58 rectal samples were collected from diarrheic buffalo calves in different regions in Egypt, and bacteriological investigated for E. coli existence. The E. coli isolates were biochemically, serologicaly identified, tested for antibiotic susceptibility, and polymerase chain reaction (PCR) analyzed for the presence of antibiotic resistance determinants and virulence genes.

RESULTS

Overall 14 isolates typed as E. coli (24.1%); 6 were belonged to serogroup O78 (10.3%), followed by O125 (4 isolates, 6.9%), then O158 (3 isolates, 5.2%) and one isolate O8 (1.7%), among them, there were 5 E. coli isolates showed a picture of hemolysis (35.7%). The isolates exhibited a high resistance to β lactams over 60%, followed by sulfa (50%) and aminoglucoside (42.8%) group, in the same time the isolates were sensitive to quinolone, trimethoprim-sulfamethoxazole, tetracycline (100%), and cephalosporine groups (71.4%). A multiplex PCR was applied to the 14 E. coli isolates revealed that all were carrying at least one gene, as 10 carried blaTEM (71.4%), 8 Sul1 (57.1%), and 6 aadB (42.8%), and 9 isolates could be considered multidrug resistant (MDR) by an incidence of 64.3%. A PCR survey was stratified for the most important E. coli virulence genes, and showed the presence of Shiga toxins in 9 isolates carried either one or the two Stx genes (64.3%), 5 isolates carried hylA gene (35.7%), and eae in 2 isolates only (14.3%), all isolates carried at least one virulence gene except two (85.7%).

CONCLUSION

The obtained data displayed that in Egypt, buffalo as well as other ruminants could be a potential source of MDR pathogenic E. coli variants which have a public health importance.

Free-standing supramolecular hydrogel objects by reaction-diffusion

Self-assembly provides access to a variety of molecular materials, yet spatial control over structure formation remains difficult to achieve. Here we show how reaction-diffusion (RD) can be coupled to a molecular self-assembly process to generate macroscopic free-standing objects with control over shape, size, and functionality. In RD, two or more reactants diffuse from different positions to give rise to spatially defined structures on reaction. We demonstrate that RD can be used to locally control formation and self-assembly of hydrazone molecular gelators from their non-assembling precursors, leading to soft, free-standing hydrogel objects with sizes ranging from several hundred micrometres up to centimeters. Different chemical functionalities and gradients can easily be integrated in the hydrogel objects by using different reactants. Our methodology, together with the vast range of organic reactions and self-assembling building blocks, provides a general approach towards the programmed fabrication of soft microscale objects with controlled functionality and shape.

Microscopic agents programmed by DNA circuits

Information stored in synthetic nucleic acids sequences can be used in vitro to create complex reaction networks with precisely programmed chemical dynamics. Here, we scale up this approach to program networks of microscopic particles (agents) dispersed in an enzymatic solution. Agents may possess multiple stable states, thus maintaining a memory and communicate by emitting various orthogonal chemical signals, while also sensing the behaviour of neighbouring agents. Using this approach, we can produce collective behaviours involving thousands of agents, for example retrieving information over long distances or creating spatial patterns. Our systems recapitulate some fundamental mechanisms of distributed decision making and morphogenesis among living organisms and could find applications in cases where many individual clues need to be combined to reach a decision, for example in molecular diagnostics.

Tweezing of Magnetic and Non-Magnetic Objects with Magnetic Fields

Although strong magnetic fields cannot be conveniently "focused" like light, modern microfabrication techniques enable preparation of microstructures with which the field gradients - and resulting magnetic forces - can be localized to very small dimensions. This ability provides the foundation for magnetic tweezers which in their classical variant can address magnetic targets. More recently, the so-called negative magnetophoretic tweezers have also been developed which enable trapping and manipulations of completely nonmagnetic particles provided that they are suspended in a high-magnetic-susceptibility liquid. These two modes of magnetic tweezing are complimentary techniques tailorable for different types of applications. This Progress Report provides the theoretical basis for both modalities and illustrates their specific uses ranging from the manipulation of colloids in 2D and 3D, to trapping of living cells, control of cell function, experiments with single molecules, and more.

Mapping out Min protein patterns in fully confined fluidic chambers

The bacterial Min protein system provides a major model system for studying reaction-diffusion processes in biology. Here we present the first in vitro study of the Min system in fully confined three-dimensional chambers that are lithography-defined, lipid-bilayer coated and isolated through pressure valves. We identify three typical dynamical behaviors that occur dependent on the geometrical chamber parameters: pole-to-pole oscillations, spiral rotations, and traveling waves. We establish the geometrical selection rules and show that, surprisingly, Min-protein spiral rotations govern the larger part of the geometrical phase diagram. Confinement as well as an elevated temperature reduce the characteristic wavelength of the Min patterns, although even for confined chambers with a bacterial-level viscosity, the patterns retain a ~5 times larger wavelength than in vivo. Our results provide an essential experimental base for modeling of intracellular Min gradients in bacterial cell division as well as, more generally, for understanding pattern formation in reaction-diffusion systems.

DOI:http://dx.doi.org/10.7554/eLife.19271.001

Some proteins can spontaneously organize themselves into ordered patterns within living cells. One widely studied pattern is made in a rod-shaped bacterium called Escherichia coli by a group of proteins called the Min proteins. The pattern formed by the Min proteins allows an E. coli cell to produce two equally sized daughter cells when it divides by ensuring that the division machinery correctly assembles at the center of the parent cell. These proteins move back and forth between the two ends of the parent cell so that the levels of Min proteins are highest at the ends and lowest in the middle. Since the Min proteins act to inhibit the assembly of the cell division machinery, this machinery only assembles in locations where the level of Min proteins is at its lowest, that is, at the middle of the cell.

When Min proteins are purified and placed within an artificial compartment that contains a source of chemical energy and is covered by a membrane similar to the membranes that surround cells, they spontaneously form traveling waves on top of the membrane in many directions along to surface. It is not clear how these waves relate to the oscillations seen in E. coli. Caspi and Dekker now analyze the behavior of purified Min proteins inside chambers of various sizes that are fully enclosed by a membrane.

The results show that in narrow chambers, Min proteins move back and forth (i.e. oscillate) from one side to the other. However, in wider containers the wave motion is more common. In containers of medium width the Min proteins rotate in a spiral fashion. Caspi and Dekker propose that the spiral rotations are the underlying pattern formed by Min proteins and that the back and forth motion is caused by spirals being cut short. In other words, if a spiral cannot form because the compartment is too small then the back and forth motion emerges. Similarly, Caspi and Dekker propose that the waves emerge in larger containers when multiple spirals come together.

These findings suggest that the different patterns that Min proteins form in bacterial cells and artificial compartments arise from different underlying mechanisms. The next step will be to investigate other differences in how the patterns of Min proteins form in E. coli and in artificial compartments.

DOI:http://dx.doi.org/10.7554/eLife.19271.002

Fluctuations in reactive networks subject to extrinsic noise studied in the framework of the chemical Langevin equation

Theoretical and experimental studies have shown that the fluctuations of in vivo systems break the fluctuation-dissipation theorem. One can thus ask what information is contained in the correlation functions of protein concentrations and how they relate to the response of the reactive network to a perturbation. Answers to these questions are of prime importance to extract meaningful parameters from the in vivo fluorescence correlation spectroscopy data. In this paper we study the fluctuations of the concentration of a reactive species involved in a cyclic network that is in a nonequilibrium steady state perturbed by a noisy force, taking into account both the breaking of detailed balance and extrinsic noises. Using a generic model for the network and the extrinsic noise, we derive a chemical Langevin equation that describes the dynamics of the system, we determine the expressions of the correlation functions of the concentrations, and we estimate the deviation of the fluctuation-dissipation theorem and the range of parameters in which an effective temperature can be defined.

The nanotechnology of life-inspired systems

For some decades now, nanotechnology has been touted as the 'next big thing' with potential impact comparable to the steam, electricity or Internet revolutions - but has it lived up to these expectations? While advances in top-down nanolithography, now reaching 10-nm resolution, have resulted in devices that are rapidly approaching mass production, attempts to produce nanoscale devices using bottom-up approaches have met with only limited success. We have been inundated with nanoparticles of almost any shape, material and composition, but their societal impact has been far from revolutionary, with growing concerns over their toxicity. Despite nebulous hopes that making hierarchical nanomaterials will lead to new, emergent properties, no breakthrough applications seem imminent. In this Perspective, we argue that the time is ripe to look beyond individual nano-objects and their static assemblies, and instead focus on systems comprising different types of 'nanoparts' interacting and/or communicating with one another to perform desired functions. Such systems are interesting for a variety of reasons: they can act autonomously without external electrical or optical connections, can be dynamic and reconfigurable, and can act as 'nanomachines' by directing the flow of mass, energy or information . In thinking how this systems nanoscience approach could be implemented to design useful - as opposed to toy-model - nanosystems, our choice of applications and our nanoengineering should be inspired by living matter.

On the importance of modelling the internal spatial dynamics of biological cells

Spatial effects such as cell shape have very often been considered negligible in models of cellular pathways, and many existing simulation infrastructures do not take such effects into consideration. Recent experimental results are reversing this judgement by showing that very small spatial variations can make a big difference in the fate of a cell. This is particularly the case when considering eukaryotic cells, which have a complex physical structure and many subtle control mechanisms, but bacteria are also interesting for the huge variation in shape both between species and in different phases of their lifecycle. In this work we perform simulations that measure the effect of three common bacterial shapes on the behaviour of model cellular pathways. To perform these experiments we develop ReDi-Cell, a highly scalable GPGPU cell simulation infrastructure for the modelling of cellular pathways in spatially detailed environments. ReDi-Cell is validated against known-good simulations, prior to its use in new work. We then use ReDi-Cell to conduct novel experiments that demonstrate the effect that three common bacterial shapes (Cocci, Bacilli and Spirilli) have on the behaviour of model cellular pathways. Pathway wavefront shape, pathway concentration gradients, and chemical species distribution are measured in the three different shapes. We also quantify the impact of internal cellular clutter on the same pathways. Through this work we show that variations in the shape or configuration of these common cell shapes alter model cell behaviour.

Bioinspiration: something for everyone

'Bioinspiration'-using phenomena in biology to stimulate research in non-biological science and technology-is a strategy that suggests new areas for research. Beyond its potential to nucleate new ideas, bioinspiration has two other interesting characteristics. It can suggest subjects in research that are relatively simple technically; it can also lead to areas in which results can lead to useful function more directly than some of the more familiar areas now fashionable in chemistry. Bioinspired research thus has the potential to be accessible to laboratories that have limited resources, to offer routes to new and useful function, and to bridge differences in technical and cultural interactions of different geographical regions.

Bifurcation phenomena of two self-propelled camphor disks on an annular field depending on system length

Mode selection and bifurcation of a synchronized motion involving two symmetric self-propelled objects in a periodic one-dimensional domain were investigated numerically and experimentally by using camphor disks placed on an annular water channel. Newton's equation of motion for each camphor disk, whose driving force was the difference in surface tension, and a reaction-diffusion equation for camphor molecules on water were used in the numerical calculations. Among various dynamical behaviors found numerically, four kinds of synchronized motions (reversal oscillation, stop-and-move rotation, equally spaced rotation, and clustered rotation) were also observed in experiments by changing the diameter of the water channel. The mode bifurcation of these motions, including their coexistence, were clarified numerically and analytically in terms of the number density of the disk. These results suggest that the present mathematical model and the analysis of the equations can be worthwhile in understanding the characteristic features of motion, e.g., synchronization, collective motion, and their mode bifurcation.

pH Oscillator Stretched in Space but Frozen in Time

Chemical oscillations are studied using a continuous-flow microfluidic system transforming the time domain of chemical oscillators into a spatial domain. This system allows one (i) to monitor the dynamics of chemical oscillators with the accuracy of vigorously stirred batch reactors but with the ease and speed of CSTRs and (ii) to rapidly screen the phase space of chemical oscillators in just one experiment versus a traditional series of batch measurements.

Coupled Oscillations and Circadian Rhythms in Molecular Replication Networks

Living organisms often display rhythmic and oscillatory behavior. We investigate here a challenge in contemporary Systems Chemistry, that is, to construct "bottom-up" molecular networks that display such complex behavior. We first describe oscillations during self-replication by applying kinetic parameters relevant to peptide replication in an open environment. Small networks of coupled oscillators are then constructed in silico, producing various functions such as logic gates, integrators, counters, triggers, and detectors. These networks are finally utilized to simulate the connectivity and network topology of the Kai proteins circadian clocks from the S. elongatus cyanobacteria, thus producing rhythms whose constant frequency is independent of the input intake rate and robust toward concentration fluctuations. We suggest that this study helps further reveal the underlying principles of biological clocks and may provide clues into their emergence in early molecular evolution.

Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach

Living cells are able to produce a wide variety of biological responses when subjected to biochemical stimuli.

A long-lasting concentration cell based on a magnetic electrolyte

A concentration cell is composed of two equivalent half-cells made of the same material but differing in the concentration of reactants. As these concentrations equilibrate, the increase in entropy is converted into a flow of electricity with the voltage output determined by the Nernst equation and proportional to the logarithm of the concentration ratios. However, as diffusion constantly strives to erase all concentration gradients, concentration cells produce only moderate voltages (typically tens of millivolts at room temperature) over relatively short times and, consequently, such devices have not been regarded as promising for energy storage. Here, we report a concentration cell that produces significantly higher voltages (∼ 0.5 V) for over 100 h. The key to our design is that the citric acid molecules involved in the electrode reactions are tethered onto magnetic nanoparticles, and a sharp gradient (10(7)-10(11) anode/cathode concentration ratio) is maintained at one of the electrodes by a permanent magnet external to the cell. Our cell does not result in corrosion of the electrodes, produces no harmful by-products, and can be regenerated by recoating used nanoparticles with fresh citric acid. We show that a series of such centimetre-sized cells produces enough electricity to power small electronic devices (timers and calculators) for several tens of hours. Our results illustrate how redox-active molecules that are, in themselves, non-magnetic can be effectively concentrated by magnetic fields to produce electrical energy.

Microfabricated Systems and Assays for Studying the Cytoskeletal Organization, Micromechanics, and Motility Patterns of Cancerous Cells

Cell motions are driven by coordinated actions of the intracellular cytoskeleton - actin, microtubules (MTs) and substrate/focal adhesions (FAs). This coordination is altered in metastatic cancer cells resulting in deregulated and increased cellular motility. Microfabrication tools, including photolithography, micromolding, microcontact printing, wet stamping and microfluidic devices have emerged as a powerful set of experimental tools with which to probe and define the differences in cytoskeleton organization/dynamics and cell motility patterns in non-metastatic and metastatic cancer cells. In this review, we discuss four categories of microfabricated systems: (i) micropatterned substrates for studying of cell motility sub-processes (for example, MT targeting of FAs or cell polarization); (ii) systems for studying cell mechanical properties, (iii) systems for probing overall cell motility patterns within challenging geometric confines relevant to metastasis (for example, linear and ratchet geometries), and (iv) microfluidic devices that incorporate co-cultures of multiple cells types and chemical gradients to mimic in vivo intravasation/extravasation steps of metastasis. Together, these systems allow for creating controlled microenvironments that not only mimic complex soft tissues, but are also compatible with live cell high-resolution imaging and quantitative analysis of single cell behavior.

Insights into the Nanobiology of Growth Hormone Secretion

The fact that partially empty vesicles are generated following cell secretion suggested that secretory vesicles do not collapse at the cell plasma membrane but, rather, transiently dock and fuse at the plasma membrane to expel a portion of their contents before retracting or undergoing endocytosis into the cell. Such a process has also been referred to in the literature as a "kiss-and-run" mechanism. This mechanism of cell secretion was conclusively demonstrated following the discovery of permanent cup-shaped lipoprotein structures at the cell plasma membrane, called "porosomes", where secretory vesicles transiently dock and fuse to expel intravesicular contents from the cell. Porosomes are present in all secretory cells, from the digestive enzyme-secreting pancreatic acinar cells, to the hormone-releasing growth hormone cells, mast cells, chromaffin cells, hair cells of the inner ear, to neurons secreting neurotransmitters. Hence, it can be asserted that porosomes are the universal secretory machinery in the plasma membrane of secretory cells. Therefore, the discovery of the porosome has resulted in a paradigm shift in our understanding of cell secretion. Rapid transport of secretory vesicles containing hormones to the plasma membrane is powered by high-energy molecules such as ATP, GTP or NADH. Immunogold labeled transmission electron microscopy (TEM) was used to determine the total number of secretory vesicles in resting and in GH-stimulated porcine pituitary cells. We identified three categories of vesicles: filled, empty, and partly empty. Resting GH cells contained more than twice as many filled vesicles than did the stimulated ones. However, stimulated cells contained nearly twice as many empty vesicles and 2.5 times more partly empty vesicles than did resting cells. Secretory vesicles in GH cells further revealed the localization of GH only in electron dense vesicles in both resting and stimulated cells. No change in the total number of secretory vesicles following secretion was observed. These results are consistent with a mechanism that, after stimulation of secretion, vesicles transiently dock and fuse at the porosome to establish a fusion pore, through which intravesicular contents are released.

DNA-functionalized hydrogels for confined membrane-free in vitro transcription/translation

We microfluidically fabricate bio-orthogonal DNA-functionalized porous hydrogels from hyaluronic acid that are employed in in vitro transcription/translation (IVTT) of a green fluorescent protein. By co-encapsulating individual hydrogel particles and the IVTT machinery in water-in-oil microdroplets, we study protein expression in a defined reaction volume. Our approach enables precise control over protein expression rates by gene dosage. We show that gene transcription and translation are confined to the membrane-free hydrogel matrix, which contributes to the design of membrane-free protocells.

Covalent modification cycles through the spatial prism

Covalent modification cycles are basic units and building blocks of posttranslational modification and cellular signal transduction. We systematically explore different spatial aspects of signal transduction in covalent modification cycles by starting with a basic temporal cycle as a reference and focusing on steady-state signal transduction. We consider, in turn, the effect of diffusion on spatial signal transduction, spatial analogs of ultrasensitive behavior, and the interplay between enzyme localization and substrate diffusion. Our analysis reveals the need to explicitly account for kinetics and diffusional transport (and localization) of enzymes, substrates, and complexes. It demonstrates a complex and subtle interplay between spatial heterogeneity, diffusion, and localization. Overall, examining the spatial dimension of covalent modification reveals that 1), there are important differences between spatial and temporal signal transduction even in this cycle; and 2), spatial aspects may play a substantial role in affecting and distorting information transfer in modules/networks that are usually studied in purely temporal terms. This has important implications for the systematic understanding of signaling in covalent modification cycles, pathways, and networks in multiple cellular contexts.

Threshold sensing through a synthetic enzymatic reaction-diffusion network

A wet stamping method to precisely control concentrations of enzymes and inhibitors in place and time inside layered gels is reported. By combining enzymatic reactions such as autocatalysis and inhibition with spatial delivery of components through soft lithographic techniques, a biochemical reaction network capable of recognizing the spatial distribution of an enzyme was constructed. The experimental method can be used to assess fundamental principles of spatiotemporal order formation in chemical reaction networks.

Energy propagation throughout chemical networks

In order to maintain their metabolism from an energy source, living cells rely on chains of energy transfer involving functionally identified components and organizations. However, propagation of a sustained energy flux through a cascade of reaction cycles has only been recently reproduced at a steady state in simple chemical systems. As observed in living cells, the spontaneous onset of energy-transfer chains notably drives local generation of singular dissipative chemical structures: continuous matter fluxes are dynamically maintained at boundaries between spatially and chemically segregated zones but in the absence of any membrane or predetermined material structure.

Particle invasion, survival, and non-ergodicity in 2D diffusion processes with space-dependent diffusivity

We study the thermal Markovian diffusion of tracer particles in a 2D medium with spatially varying diffusivity D(r), mimicking recently measured, heterogeneous maps of the apparent diffusion coefficient in biological cells. For this heterogeneous diffusion process (HDP) we analyse the mean squared displacement (MSD) of the tracer particles, the time averaged MSD, the spatial probability density function, and the first passage time dynamics from the cell boundary to the nucleus. Moreover we examine the non-ergodic properties of this process which are important for the correct physical interpretation of time averages of observables obtained from single particle tracking experiments. From extensive computer simulations of the 2D stochastic Langevin equation we present an in-depth study of this HDP. In particular, we find that the MSDs along the radial and azimuthal directions in a circular domain obey anomalous and Brownian scaling, respectively. We demonstrate that the time averaged MSD stays linear as a function of the lag time and the system thus reveals a weak ergodicity breaking. Our results will enable one to rationalise the diffusive motion of larger tracer particles such as viruses or submicron beads in biological cells.

Identification of two-step chemical mechanisms and determination of thermokinetic parameters using frequency responses to small temperature oscillations

Increased focus on kinetic signatures in biology, coupled with the lack of simple tools for chemical dynamics characterization, lead us to develop an efficient method for mechanism identification. A small thermal modulation is used to reveal chemical dynamics, which makes the technique compatible with in cellulo imaging. Then, the detection of concentration oscillations in an appropriate frequency range followed by a judicious analytical treatment of the data is sufficient to determine the number of chemical characteristic times, the reaction mechanism, and the full set of associated rate constants and enthalpies of reaction. To illustrate the scope of the method, dimeric protein folding is chosen as a biologically relevant example of nonlinear mechanism with one or two characteristic times.

Fluorescent hydrogels for studying Ca2+-dependent reaction–diffusion processes

Here, we report a convenient experimental platform to study the diffusion of Ca²⁺ in the presence of a Ca²⁺-binding protein (Calbindin D28k). This work opens up new possibilities to elucidate the physical chemistry of complex Ca²⁺-dependent reaction–diffusion networks that are abundant in living cells.