Synchronizing a multicellular system by external input: an artificial control strategy

MOTIVATION: Although there are significant advances on elucidating the collective behaviors on biological organisms in recent years, the essential mechanisms by which the collective rhythms arise remain to be fully understood, and further how to synchronize multicellular networks by artificial control strategy has not yet been well explored. RESULTS: A control strategy is developed to synchronize gene regulatory networks in a multicellular system when spontaneous synchronization cannot be achieved. We first construct an impulsive control system to model the process of periodically injecting coupling substances with constant or random impulsive control amounts into the common extracellular medium, and further study its effects on the dynamics of individual cells. We derive the threshold of synchronization induced by the periodic substance input. Therefore, we can synchronize the multicellular network to a specific collective behavior by changing the frequency and amplitude of the periodic stimuli. Moreover, a two-stage scheme is proposed to facilitate the synchronization in this paper. We show that the presence of the external input may also initiate different dynamics. The multicellular network of coupled repressilators is used to show the effectiveness of the proposed method. The results not only provide a perspective to understand the interactions between external stimuli and intrinsic physiological rhythms, but also may lead to development of realistic artificial control strategy and medical therapy. AVAILABILITY: CONTACT: aihara@sat.t.u-tokyo.ac.jp.     

Encapsulated fusion protein confers “sense and respond” activity to chitosan–alginate capsules to manipulate bacterial quorum sensing

We demonstrate that “nanofactory”‐loaded biopolymer capsules placed in the midst of a bacterial population can direct bacterial communication. Quorum sensing (QS) is a process by which bacteria communicate through small‐molecules, such as autoinducer‐2 (AI‐2), leading to collective behaviors such as virulence and biofilm formation. In our approach, a “nanofactory” construct is created, which comprises an antibody complexed with a fusion protein that produces AI‐2. These nanofactories are entrapped within capsules formed by electrostatic complexation of cationic (chitosan) and anionic (sodium alginate) biopolymers. The chitosan capsule shell is crosslinked by tripolyphosphate (TPP) to confer structural integrity. The capsule shell is impermeable to the encapsulated nanofactories, but freely permeable to small molecules. In turn, the capsules are able to take in substrates from the external medium via diffusion, and convert these via the nanofactories into AI‐2, which then diffuses out. The exported AI‐2 is shown to stimulate QS responses in vicinal Escherichia coli. Directing bacterial population behavior has potential applications in next‐generation antimicrobial therapy and pathogen detection. We also envision such capsules to be akin to artificial “cells” that can participate in native biological signaling and communicate in real‐time with the human microbiome. Through such interaction capabilities, these “cells” may sense the health of the microbiome, and direct its function in a desired, host‐friendly manner. Biotechnol. Bioeng. 2013; 110: 552–562. © 2012 Wiley Periodicals, Inc.     

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.     

Stomatal development: from neighborly to global communication

Stomata are epidermal structures that are responsible for modulating the exchange of gases between the plant and the environment. Stomata are formed and patterned by asymmetric cell divisions. The number and orientation of these asymmetric divisions is informed by plant intrinsic signals acting locally (among epidermal cells) or at a distance (from mature to young leaves) and by plant extrinsic factors such as the quantity of light, water and CO(2) in the atmosphere. Recent studies have implicated a set of conserved cell surface receptors and intracellular signaling molecules in the perception and response to developmental cues. Complementary studies have probed the nature of environmental signals and how these signals are transduced from the site of perception to the cells in the stomatal lineage.     

Stem cells in adult tissues

In recent years the concept of a stem cell has evolved to encompass the hypotheses that stem cells exist within many adult tissues, and that a common 'interchangeable' progenitor cell may exist within the bone marrow capable of regenerating and repairing tissues throughout the body. As more knowledge is gained about stem cells, their potential roles in disease processes, including the development and progression of cancer, have moved to the forefront. The underlying hypothesis of this review is that cell fate is determined by a combination of intrinsic and extrinsic factors; growth and differentiation are regulated through intracellular integration of a multitude of signals initiated by internal and external stimuli. The development of successful stem cell based therapies may depend on experimental approaches that consider both the intrinsic and extrinsic factors that control cell fate.     

Paradoxical phase response of gamma rhythms facilitates their entrainment in heterogeneous networks

The synchronization of different γ-rhythms arising in different brain areas has been implicated in various cognitive functions. Here, we focus on the effect of the ubiquitous neuronal heterogeneity on the synchronization of ING (interneuronal network gamma) and PING (pyramidal-interneuronal network gamma) rhythms. The synchronization properties of rhythms depends on the response of their collective phase to external input. We therefore determine the macroscopic phase-response curve for finite-amplitude perturbations (fmPRC) of ING- and PING-rhythms in all-to-all coupled networks comprised of linear (IF) or quadratic (QIF) integrate-and-fire neurons. For the QIF networks we complement the direct simulations with the adjoint method to determine the infinitesimal macroscopic PRC (imPRC) within the exact mean-field theory. We show that the intrinsic neuronal heterogeneity can qualitatively modify the fmPRC and the imPRC. Both PRCs can be biphasic and change sign (type II), even though the phase-response curve for the individual neurons is strictly non-negative (type I). Thus, for ING rhythms, say, external inhibition to the inhibitory cells can, in fact, advance the collective oscillation of the network, even though the same inhibition would lead to a delay when applied to uncoupled neurons. This paradoxical advance arises when the external inhibition modifies the internal dynamics of the network by reducing the number of spikes of inhibitory neurons; the advance resulting from this disinhibition outweighs the immediate delay caused by the external inhibition. These results explain how intrinsic heterogeneity allows ING- and PING-rhythms to become synchronized with a periodic forcing or another rhythm for a wider range in the mismatch of their frequencies. Our results identify a potential function of neuronal heterogeneity in the synchronization of coupled γ-rhythms, which may play a role in neural information transfer via communication through coherence.     

The cytoplasmic tyrosine kinase Arg regulates gastrulation via control of actin organization

Coordinated cell movements are crucial for vertebrate gastrulation and are controlled by multiple signals. Although many factors are shown to mediate non-canonical Wnt pathways to regulate cell polarity and intercalation during gastrulation, signaling molecules acting in other pathways are less investigated and the connections between various signals and cytoskeleton are not well understood. In this study, we show that the cytoplasmic tyrosine kinase Arg modulates gastrulation movements through control of actin remodeling. Arg is expressed in the dorsal mesoderm at the onset of gastrulation, and both gain- and loss-of-function of Arg disrupted axial development in Xenopus embryos. Arg controlled migration of anterior mesendoderm, influenced cell decision on individual versus collective migration, and modulated spreading and protrusive activities of anterior mesendodermal cells. Arg also regulated convergent extension of the trunk mesoderm by influencing cell intercalation behaviors. Arg modulated actin organization to control dynamic F-actin distribution at the cell-cell contact or in membrane protrusions. The functions of Arg required an intact tyrosine kinase domain but not the actin-binding motifs in its carboxyl terminus. Arg acted downstream of receptor tyrosine kinases to regulate phosphorylation of endogenous CrkII and paxillin, adaptor proteins involved in activation of Rho family GTPases and actin reorganization. Our data demonstrate that Arg is a crucial cytoplasmic signaling molecule that controls dynamic actin remodeling and mesodermal cell behaviors during Xenopus gastrulation.     

Tumor necrosis factor-alpha mediated signaling in neuronal homeostasis and dysfunction

Tumor necrosis factor-alpha (TNF-α) is a potent pro-inflammatory molecule, which upon engagement with its cognate receptors on target cells, triggers downstream signaling cascades that control a number of cellular processes related to cell viability, gene expression, ion homeostasis, and synaptic integrity. In the central nervous system (CNS), TNF-α is produced by brain-resident astrocytes, microglia, and neurons in response to numerous intrinsic and extrinsic stimuli. This review will summarize the key events that lead to TNF-α elaboration in the CNS, and the effects that these inflammatory signals impart on neuronal signaling in the context of homeostasis and neuropathology.     

Skeletal loading in animals

A number of in vivo skeletal loading models have been developed to test specific hypotheses addressing the key mechanical and biochemical signals involved in bone's adaptive response to loading. Exercise protocols, osteotomy procedures, loading of surgically implanted pins, and force application through the soft tissues are common approaches to alter the mechanical environment of a bone. Although each animal overload model has a number of assets and limitations, models employing extrinsic forces allow greater control of the mechanical environment. Sham controls, for both surgical intervention (when performed) and loading, are required to unequivocally demonstrate that responses to loading are mechanically adaptive. Collectively, extrinsic loading models have fostered a greater understanding of the mechanical signals important for stimulating bone cells, and highlighted the roles of key signaling molecules in the adaptive response.     

BMP and FGF regulate the development of EGF-responsive neural progenitor cells

Temporal changes in progenitor cell responses to extrinsic signals play an important role in development, but little is known about the mechanisms that determine how these changes occur. In the rodent CNS, expression of epidermal growth factor receptors (EGFRs) increases during embryonic development, conferring mitotic responsiveness to EGF among multipotent stem cells. Here we show that cell-cell signaling controls this change. Whereas EGF-responsive stem cells develop on schedule in explant and aggregate cultures of embryonic cortex, co-culture with younger cortical cells delays their development. Exogenous BMP4 mimics the effect of younger cells, reversibly inhibiting changes in EGFR expression and responsiveness. Moreover, blocking endogenous BMP receptors in progenitors with a virus transducing dnBMPR1B accelerates changes in EGFR signaling. This involves a non-cell-autonomous mechanism, suggesting that BMP negatively regulates signal(s) that promote the development of EGF-responsive stem cells. FGF2 is a good candidate for such a signal, as we find that it antagonizes the inhibitory effects of younger cortical cells and exogenous BMP4. These findings suggest that a balance between antagonistic extrinsic signals regulates temporal changes in an intrinsic property of neural progenitor cells.     

The cerebrospinal fluid provides a proliferative niche for neural progenitor cells

Cortical development depends on the active integration of cell-autonomous and extrinsic cues, but the coordination of these processes is poorly understood. Here, we show that the apical complex protein Pals1 and Pten have opposing roles in localizing the Igf1R to the apical, ventricular domain of cerebral cortical progenitor cells. We found that the cerebrospinal fluid (CSF), which contacts this apical domain, has an age-dependent effect on proliferation, much of which is attributable to Igf2, but that CSF contains other signaling activities as well. CSF samples from patients with glioblastoma multiforme show elevated Igf2 and stimulate stem cell proliferation in an Igf2-dependent manner. Together, our findings demonstrate that the apical complex couples intrinsic and extrinsic signaling, enabling progenitors to sense and respond appropriately to diffusible CSF-borne signals distributed widely throughout the brain. The temporal control of CSF composition may have critical relevance to normal development and neuropathological conditions.     

PDFR and CRY signaling converge in a subset of clock neurons to modulate the amplitude and phase of circadian behavior in Drosophila

Background

To synchronize their molecular rhythms, circadian pacemaker neurons must input both external and internal timing cues and, therefore, signal integration between sensory information and internal clock status is fundamental to normal circadian physiology.

Methodology/Principal Findings

We demonstrate the specific convergence of clock-derived neuropeptide signaling with that of a deep brain photoreceptor. We report that the neuropeptide PDF receptor and the circadian photoreceptor CRYPTOCROME (CRY) are precisely co-expressed in a subset of pacemakers, and that these pathways together provide a requisite drive for circadian control of daily locomotor rhythms. These convergent signaling pathways influence the phase of rhythm generation, but also its amplitude. In the absence of both pathways, PER rhythms were greatly reduced in only those specific pacemakers that receive convergent inputs and PER levels remained high in the nucleus throughout the day. This suggested a large-scale dis-regulation of the pacemaking machinery. Behavioral rhythms were likewise disrupted: in light∶dark conditions they were aberrant, and under constant dark conditions, they were lost.

Conclusions/Significance

We speculate that the convergence of environmental and clock-derived signals may produce a coincident detection of light, synergistic responses to it, and thus more accurate and more efficient re-setting properties.     

CTLA-4, T helper lymphocytes and dendritic cells: an internal perspective of T-cell homeostasis

In mice and humans, the size of the peripheral lymphocyte pool remains relatively constant throughout adult life, in the absence of disease. Among the factors that influence the survival and homeostasis of T cells, external stimuli such as infections have long been considered to be of primary importance. However, emerging data indicate that internal stimuli, including self-peptide (presented in association with major-histocompatibility-complex molecules) and cytokines, might also control the size and composition of T-cell pools. Recent evidence suggests that cytotoxic-T-lymphocyte-associated antigen 4, an immune attenuator, contributes significantly to the homeostatic control of T-helper-cell proliferation through mechanisms that are both intrinsic and extrinsic to the T cell.     

血管生成素在细胞凋亡调节中的作用机制

血管生成素（angiogenin,ANG）是一种核糖核酸酶;最近研究证明,作为一种抗凋亡因子,ANG参与各种抗细胞凋亡过程. ANG对内源性及外源性相关信号途径中的重要分子,如Bcl-2抗凋亡蛋白具有调节作用.此外,ANG对内、外部信号途径中的重要环节--p53依赖的凋亡也具有调节作用.