The connections between particle flow and mechanical, electrical and chemical work

An analysis is made of the generation of different types of field within biological systems. The fields are interactive being electrical, entropic (concentration gradients), chemical potential or mechanical in character. It is the primary disposition of proteins both in membranes and other organized systems which create the initial pattern of fields, but subsequently the distribution of proteins and the fields are mutually dependent. The value of the patterns is discussed.     

A receptor-electromigration-based model for cellular electrotactic sensing and migration

Directed cell migration in tissues mediates various physiological processes and is guided by complex cellular factors such as chemoattractant gradients and electric fields. Direct current (DC) electric fields can be generated in physiological settings and the electric field guided migration of various cell types (i.e., electrotaxis) has been demonstrated both in vitro and in vivo. Although several mechanisms have been proposed for electrotaxis, there are so far very few quantitative models. Furthermore, because chemoattractant gradients and electric fields co-exist in tissues, it is important to understand how chemotaxis and electrotaxis interact for mediating cell migration and trafficking. In this study, we developed a mathematical model to investigate the role of electromigration of cell surface chemoattractant receptors in mediating electrochemical sensing and migration of cells. Our results show that electromigration of chemoattractant receptors enables cell electrotactic sensing and migration in the presence of a uniform chemoattractant field. Furthermore, in the physiologically-relevant range of receptor electromigration rates, application of electric fields overcomes chemical guiding signals for directional sensing and migration of cells in co-existing competing electric fields and chemoattractant gradients.     

Stochastic signal processing and transduction in chemotactic response of eukaryotic cells

Single-molecule imaging analysis of chemotactic response in eukaryotic cells has revealed a stochastic nature in the input signals and the signal transduction processes. This leads to a fundamental question about the signaling processes: how does the signaling system operate under stochastic fluctuations or noise? Here, we report a stochastic model of chemotactic signaling in which noise and signal propagation along the transmembrane signaling pathway by chemoattractant receptors can be analyzed quantitatively. The results obtained from this analysis reveal that the second-messenger-production reactions by the receptors generate noisy signals that contain intrinsic noise inherently generated at this reaction and extrinsic noise propagated from the ligand-receptor binding. Such intrinsic and extrinsic noise limits the directional sensing ability of chemotactic cells, which may explain the dependence of chemotactic accuracy on chemical gradients that has been observed experimentally. Our analysis also reveals regulatory mechanisms for signal improvement in the stochastically operating signaling system by analyzing how the SNR of chemotactic signals can be improved on or deteriorated by the stochastic properties of receptors and second-messenger molecules. Theoretical consideration of noisy signal transduction by chemotactic signaling systems can further be applied to signaling systems in general.     

Microfluidic devices for studying chemotaxis and electrotaxis

Directed cell migration plays important roles in physiological processes such as host defense, wound healing, cancer metastasis and embryogenesis. Many organisms are capable of directional migration, which can be guided by diverse cellular factors including chemical and electrical cues. Recently, microfluidic devices that consist of small channels with micrometer dimensions are being developed for cell migration studies. These devices can precisely configure and flexibly manipulate chemical concentration gradients and electric fields, and thus can be used to study the complex guiding mechanisms for cell migration. In this paper we highlight recent applications of microfluidic devices for cell migration research, with a focus on electric field-directed cell migration, to provide important and timely updates of this rapidly developing research field.     

Chemical signaling processes in the marine environment

Understanding the mechanisms by which environmental chemical signals, chemical defenses, and other chemical agents mediate various life-history processes can lead to important insights about the forces driving the ecology and evolution of marine systems. For chemical signals released into the environment, establishing the principles that mediate chemical production and transport is critical for interpreting biological responses to these stimuli within appropriate natural, historical contexts. Recent technological advancements provide outstanding opportunities for new discoveries, thus allowing quantification of interactions between hydrodynamic, chemical, and biological factors at numerous spatial and temporal scales. Past work on chemically mediated processes involving organisms and their environment have emphasized habitat colonization by larvae and trophic relationships. Future research priorities should include these topics as well as courtship and mating, fertilization, competition, symbiosis, and microbial chemical ecology. There are now vast new opportunities for determining how organisms respond to chemical signals and employ chemical defenses under environmentally realistic conditions. Integrating these findings within a larger ecological and evolutionary framework should lead to improved understanding of natural physicochemical phenomena that constrain biological responses at the individual, population, and community levels of organization.     

Biphasic responses, quantal signals and cellular behaviour

It is commonplace to think of thresholds in biological systems. Biphasic responses, with both thresholds and upper limits, or lintels, are also surprisingly common. In this paper we show that they are found in many systems in which an aspect of cellular behaviour is controlled by chemical signals. In some cases the biphasic response can lead to the partitioning of a tissue into regions expressing different behaviours and, therefore, in principle able to take different developmental and evolutionary paths within the same organism. Several other features are common; these include brief, all-or-nothing responses and the expression of different behaviours evoked by a signal of a single chemical species in one or more cell types, but over different concentration ranges. Such behaviour is illustrated very clearly by the differentiation of cells in the mammalian immune system as well as by developing slime mould cells, so the underlying principle is widespread. We suggest that the interaction of unitary behaviours with chemical signals showing such non-linear concentration dependences will account for the complexity of development.     

Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria

Molecular entities present in a cell (mRNA, proteins, metabolites,…) do not act in isolation, but rather in cooperation with each other to define an organisms form and function. Their concerted action can be viewed as networks of interacting entities that are active under certain conditions within the cell or upon certain environmental signals. A main challenge in systems biology is to model these networks, or in other words studying which entities interact to form cellular systems or accomplish similar functions. On the contrary, viewing a single entity or an experimental dataset in the light of an interaction network can reveal previous unknown insights in biological processes. In this review we give an overview of how integrated networks can be reconstructed from multiple omics data and how they can subsequently be used for network-based modeling of cellular function in bacteria.     

Signaling pathways mediating chemotaxis in the social amoeba, Dictyostelium discoideum

Chemotaxis, or cell migration guided by chemical cues, is critical for a multitude of biological processes in a diverse array of organisms. Dictyostelium discoideum amoebae rely on chemotaxis to find food and to survive starvation conditions, and we have taken advantage of this system to study the molecular regulation of this vital cell behavior. Previous work has identified phosphoinositide signaling as one mechanism which may contribute to directional sensing and actin polymerization during chemotaxis; a mechanism which is conserved in mammalian neutrophils. In this review, we will discuss recent data on genes and pathways governing directional sensing and actin polymerization, with a particular emphasis on contributions from our laboratory.     

Modeling robustness tradeoffs in yeast cell polarization induced by spatial gradients

Cells localize (polarize) internal components to specific locations in response to external signals such as spatial gradients. For example, yeast cells form a mating projection toward the source of mating pheromone. There are specific challenges associated with cell polarization including amplification of shallow external gradients of ligand to produce steep internal gradients of protein components (e.g. localized distribution), response over a broad range of ligand concentrations, and tracking of moving signal sources. In this work, we investigated the tradeoffs among these performance objectives using a generic model that captures the basic spatial dynamics of polarization in yeast cells, which are small. We varied the positive feedback, cooperativity, and diffusion coefficients in the model to explore the nature of this tradeoff. Increasing the positive feedback gain resulted in better amplification, but also produced multiple steady-states and hysteresis that prevented the tracking of directional changes of the gradient. Feedforward/feedback coincidence detection in the positive feedback loop and multi-stage amplification both improved tracking with only a modest loss of amplification. Surprisingly, we found that introducing lateral surface diffusion increased the robustness of polarization and collapsed the multiple steady-states to a single steady-state at the cost of a reduction in polarization. Finally, in a more mechanistic model of yeast cell polarization, a surface diffusion coefficient between 0.01 and 0.001 μm(2)/s produced the best polarization performance, and this range is close to the measured value. The model also showed good gradient-sensitivity and dynamic range. This research is significant because it provides an in-depth analysis of the performance tradeoffs that confront biological systems that sense and respond to chemical spatial gradients, proposes strategies for balancing this tradeoff, highlights the critical role of lateral diffusion of proteins in the membrane on the robustness of polarization, and furnishes a framework for future spatial models of yeast cell polarization.     

Molecules into Cells: Specifying Spatial Architecture

A living cell is not an aggregate of molecules but an organized pattern, structured in space and in time. This article addresses some conceptual issues in the genesis of spatial architecture, including how molecules find their proper location in cell space, the origins of supramolecular order, the role of the genes, cell morphology, the continuity of cells, and the inheritance of order. The discussion is framed around a hierarchy of physiological processes that bridge the gap between nanometer-sized molecules and cells three to six orders of magnitude larger. Stepping stones include molecular self-organization, directional physiology, spatial markers, gradients, fields, and physical forces. The knowledge at hand leads to an unconventional interpretation of biological order. I have come to think of cells as self-organized systems composed of genetically specified elements plus heritable structures. The smallest self that can be fairly said to organize itself is the whole cell. If structure, form, and function are ever to be computed from data at a lower level, the starting point will be not the genome, but a spatially organized system of molecules. This conclusion invites us to reconsider our understanding of what genes do, what organisms are, and how living systems could have arisen on the early Earth.     

Molecules into cells: specifying spatial architecture.

A living cell is not an aggregate of molecules but an organized pattern, structured in space and in time. This article addresses some conceptual issues in the genesis of spatial architecture, including how molecules find their proper location in cell space, the origins of supramolecular order, the role of the genes, cell morphology, the continuity of cells, and the inheritance of order. The discussion is framed around a hierarchy of physiological processes that bridge the gap between nanometer-sized molecules and cells three to six orders of magnitude larger. Stepping stones include molecular self-organization, directional physiology, spatial markers, gradients, fields, and physical forces. The knowledge at hand leads to an unconventional interpretation of biological order. I have come to think of cells as self-organized systems composed of genetically specified elements plus heritable structures. The smallest self that can be fairly said to organize itself is the whole cell. If structure, form, and function are ever to be computed from data at a lower level, the starting point will be not the genome, but a spatially organized system of molecules. This conclusion invites us to reconsider our understanding of what genes do, what organisms are, and how living systems could have arisen on the early Earth.     

Interaction between pancreatic β cell and electromagnetic fields: A systematic study toward finding the natural frequency spectrum of β cell system

Interaction between biological systems and environmental electric or magnetic fields has gained attention during the past few decades. Although there are a lot of studies that have been conducted for investigating such interaction, the reported results are considerably inconsistent. Besides the complexity of biological systems, the important reason for such inconsistent results may arise due to different excitation protocols that have been applied in different experiments. In order to investigate carefully the way that external electric or magnetic fields interact with a biological system, the parameters of excitation, such as intensity or frequency, should be selected purposefully due to the influence of these parameters on the system response. In this study, pancreatic β cell, the main player of blood glucose regulating system, is considered and the study is focused on finding the natural frequency spectrum of the system using modeling approach. Natural frequencies of a system are important characteristics of the system when external excitation is applied. The result of this study can help researchers to select proper frequency parameter for electrical excitation of β cell system. The results show that there are two distinct frequency ranges for natural frequency of β cell system, which consist of extremely low (or near zero) and 100–750 kHz frequency ranges. There are experimental works on β cell exposure to electromagnetic fields that support such finding.     

Directional movement of entomopathogenic nematodes in response to electrical field: effects of species, magnitude of voltage, and infective juvenile age

Entomopathogenic nematodes respond to a variety of stimuli when foraging. Previously, we reported a directional response to electrical fields for two entomopathogenic nematode species; specifically, when electrical fields were generated on agar plates Steinernema glaseri (a nematode that utilizes a cruiser-type foraging strategy) moved to a higher electric potential, whereas Steinernema carpocapsae, an ambush-type forager, moved to a lower potential. Thus, we hypothesized that entomopathogenic nematode directional response to electrical fields varies among species, and may be related to foraging strategy. In this study, we tested the hypothesis by comparing directional response among seven additional nematode species: Heterorhabditis bacteriophora, Heterorhabditis georgiana, Heterorhabditis indica, Heterorhabditis megidis, Steinernema feltiae, Steinernema riobrave, and Steinernema siamkayai. S. carpocapsae and S. glaseri were also included as positive controls. Heterorhabditids tend toward cruiser foraging approaches whereas S. siamkayai is an ambusher and S. feltiae and S. riobrave are intermediate. Additionally, we determined the lowest voltage that would elicit a directional response (tested in S. feltiae and S. carpocapsae), and we investigated the impact of nematode age on response to electrical field in S. carpocapsae. In the experiment measuring diversity of response among species, we did not detect any response to electrical fields among the heterorhabditids except for H. georgiana, which moved to a higher electrical potential; S. glaseri and S. riobrave also moved to a higher potential, whereas S. carpocapsae, S. feltiae, and S. siamkayai moved to a lower potential. Overall our hypothesis that foraging strategy can predict directional response was supported (in the nematodes that exhibited a response). The lowest electric potential that elicited a response was 0.1 V, which is comparable to electrical potential associated with some insects and plant roots. The level of response to electrical potential diminished with nematode age. These results expand our knowledge of electrical fields as cues that may be used by entomopathogenic nematodes for host-finding or other aspects of navigation in the soil.     

Modularity, noise, and natural selection

Most biological systems are formed by component parts that are to some degree interrelated. Groups of parts that are more associated among themselves and are relatively autonomous from others are called modules. One of the consequences of modularity is that biological systems usually present an unequal distribution of the genetic variation among traits. Estimating the covariance matrix that describes these systems is a difficult problem due to a number of factors such as poor sample sizes and measurement errors. We show that this problem will be exacerbated whenever matrix inversion is required, as in directional selection reconstruction analysis. We explore the consequences of varying degrees of modularity and signal-to-noise ratio on selection reconstruction. We then present and test the efficiency of available methods for controlling noise in matrix estimates. In our simulations, controlling matrices for noise vastly improves the reconstruction of selection gradients. We also perform an analysis of selection gradients reconstruction over a New World Monkeys skull database to illustrate the impact of noise on such analyses. Noise-controlled estimates render far more plausible interpretations that are in full agreement with previous results.     

A Novel Method to Produce Immobilised Biomolecular Concentration Gradients to Study Cell Activities: Design and Modelling

It is well known that many cell functions are activated by chemical signals with a time and space-dependent profile. To mimic these profiles in vitro, it is necessary to develop a system that is able to generate concentration gradients with a resolution similar to that perceived by cells, which is around nanomolar with a spatial resolution of a few tens of microns. Many devices capable of generating steady-state concentration gradients have been developed using continuous flow micro-fluidic techniques. However, these systems cannot reproduce the immobilised concentration gradients that are present in the extracellular matrix. For this reason, we have developed a new gradient generator to enable precise and reproducible studies on the effects of immobilised concentration gradients on cell behaviour. A well-known gradient of a desired molecule was generated on the bottom surface of a hydrogel, which was then used as a stamp to immobilise the molecule on a functionalised substrate. A concentration gradient was thus obtained using a simple silane-based chemical reaction. To validate the method, image analysis was performed on glass slides printed with fluorescein isothiocyanate (FITC)- collagen and FITC-poly-lysine concentration gradients. Preliminary cell adhesion tests were also carried out by seeding NIH-3T3 and mesencephalic cells on lab-glass slides printed with concentration profiles of collagen and poly-lysine, respectively.     

Species abundance, sexual encounter and bioluminescent signalling in the deep sea

The problems faced by deep-sea animals in achieving sexual and other encounters require sensory and effector systems the synergy of which can span the often very substantial distances that separate individuals. Bioluminescent systems provide one of the links between individuals, and the sexual dimorphism of some photophores suggests that they are employed to attract a mate. However, nearest-neighbour values for many deep-sea animals put them beyond the effective range of bioluminescent signals and it is therefore likely that these signals are employed at intermediate ranges, once an initial contact (perhaps olfactory) has been made.     

Ah,sweet mystery of death! Galectins and control of cell fate

Control of cell death is critical in eukaryotic development, immune system homeostasis, and control of tumorigenesis. The galectin family of lectins is implicated in all of these processes. Other families of molecules function as death receptors or death effectors, but galectins are uniquely capable of acting both extracellularly and intracellularly to control cell death. Extracellularly, galectins cross-link glycan ligands to transduce signals that lead directly to death or that influence other signals regulating cell fate. Intracellular expression of galectins can modulate other signals controlling cell viability. Individual galectins can act on multiple cell types, and multiple galectins can act on the same cell. Understanding how galectins regulate cell viability and function will broaden our knowledge of the roles of galectins in basic biological processes and facilitate development of therapeutic applications for galectins in autoimmunity, transplant-related disease, and cancer.     

Lymphocyte electrotaxis in vitro and in vivo

Electric fields are generated in vivo in a variety of physiologic and pathologic settings, including penetrating injury to epithelial barriers. An applied electric field with strength within the physiologic range can induce directional cell migration (i.e., electrotaxis) of epithelial cells, endothelial cells, fibroblasts, and neutrophils suggesting a potential role in cell positioning during wound healing. In the present study, we investigated the ability of lymphocytes to respond to applied direct current (DC) electric fields. Using a modified Transwell assay and a simple microfluidic device, we show that human PBLs migrate toward the cathode in physiologically relevant DC electric fields. Additionally, electrical stimulation activates intracellular kinase signaling pathways shared with chemotactic stimuli. Finally, video microscopic tracing of GFP-tagged immunocytes in the skin of mouse ears reveals that motile cutaneous T cells actively migrate toward the cathode of an applied DC electric field. Lymphocyte positioning within tissues can thus be manipulated by externally applied electric fields, and may be influenced by endogenous electrical potential gradients as well.     

The role of cell geometry and cell-cell communication in gradient sensing

Cells can measure shallow gradients of external signals to initiate and accomplish a migration or a morphogenetic process. Recently, starting from mathematical models like the local-excitation global-inhibition (LEGI) model and with the support of empirical evidence, it has been proposed that cellular communication improves the measurement of an external gradient. However, the mathematical models that have been used have over-simplified geometries (e.g., they are uni-dimensional) or assumptions about cellular communication, which limit the possibility to analyze the gradient sensing ability of more complex cellular systems. Here, we generalize the existing models to study the effects on gradient sensing of cell number, geometry and of long- versus short-range cellular communication in 2D systems representing epithelial tissues. We find that increasing the cell number can be detrimental for gradient sensing when the communication is weak and limited to nearest neighbour cells, while it is beneficial when there is long-range communication. We also find that, with long-range communication, the gradient sensing ability improves for tissues with more disordered geometries; on the other hand, an ordered structure with mostly hexagonal cells is advantageous with nearest neighbour communication. Our results considerably extend the current models of gradient sensing by epithelial tissues, making a step further toward predicting the mechanism of communication and its putative mediator in many biological processes.     

Microfluidic‐Assisted Blade Coating of Compositional Libraries for Combinatorial Applications: The Case of Organic Photovoltaics

Microfluidic technologies are highly adept at generating controllable compositional gradients in fluids, a feature that has accelerated the understanding of the importance of chemical gradients in biological processes. That said, the development of versatile methods to generate controllable compositional gradients in the solid‐state has been far more elusive. The ability to produce such gradients would provide access to extensive compositional libraries, thus enabling the high‐throughput exploration of the parametric landscape of functional solids and devices in a resource‐, time‐, and cost‐efficient manner. Herein, the synergic integration of microfluidic technologies is reported with blade coating to enable the controlled formation of compositional lateral gradients in solution. Subsequently, the transformation of liquid‐based compositional gradients into solid‐state thin films using this method is demonstrated. To demonstrate efficacy of the approach, microfluidic‐assisted blade coating is used to optimize blending ratios in organic solar cells. Importantly, this novel technology can be easily extended to other solution processable systems that require the formation of solid‐state compositional lateral gradients.