Establishment of cell lines derived from the rat suprachiasmatic nucleus

Conditional cross-map-based technique: From pairwise dynamical causality to causal network reconstruction

Causality detection methods based on mutual cross mapping have been fruitfully developed and applied to data originating from nonlinear dynamical systems, where the causes and effects are non-separable. However, these pairwise methods still have shortcomings in discriminating typical network structures, including common drivers, indirect dependencies, and facing the curse of dimensionality, when they are stepping to causal network reconstruction. A few endeavors have been devoted to conquer these shortcomings. Here, we propose a novel method that could be regarded as one of these endeavors. Our method, named conditional cross-map-based technique, can eliminate third-party information and successfully detect direct dynamical causality, where the detection results can exactly be categorized into four standard normal forms by the designed criterion. To demonstrate the practical usefulness of our model-free, data-driven method, data generated from different representative models covering all kinds of network motifs and measured from real-world systems are investigated. Because correct identification of the direct causal links is essential to successful modeling, predicting, and controlling the underlying complex systems, our method does shed light on uncovering the inner working mechanisms of real-world systems only using the data experimentally obtained in a variety of disciplines.

Nanoscale-tipped wire array injections transfer DNA directly into brain cells ex vivo and in vivo

Genetic modification to restore cell functions in the brain can be performed through the delivery of biomolecules in a minimally invasive manner into live neuronal cells within brain tissues. However, conventional nanoscale needles are too short (lengths of ~10 µm) to target neuronal cells in ~1‐mm‐thick brain tissues because the neuronal cells are located deep within the tissue. Here, we report the use of nanoscale‐tipped wire (NTW) arrays with diameters < 100 nm and wire lengths of ~200 µm to address biomolecule delivery issues. The NTW arrays were manufactured by growth of silicon microwire arrays and nanotip formation. This technique uses pinpoint, multiple‐cell DNA injections in deep areas of brain tissues, enabling target cells to be marked by fluorescent protein (FP) expression vectors. This technique has potential for use for electrophysiological recordings and biological transfection into neuronal cells. Herein, simply pressing an NTW array delivers and expresses plasmid DNA in multiple‐cultured cells and multiple‐neuronal cells within a brain slice with reduced cell damage. Additionally, DNA transfection is demonstrated using brain cells ex vivo and in vivo. Moreover, knockdown of a critical clock gene after injecting a short hairpin RNA (shRNA) and a genome‐editing vector demonstrates the potential to genetically alter the function of living brain cells, for example, pacemaker cells of the mammalian circadian rhythms. Overall, our NTW array injection technique enables genetic and functional modification of living cells in deep brain tissue areas, both ex vivo and in vivo.

Reconstructing directional causal networks with random forest: Causality meeting machine learning

Inspired by the decision tree algorithm in machine learning, a novel causal network reconstruction framework is proposed with the name Importance Causal Analysis (ICA). The ICA framework is designed in a network level and fills the gap between traditional mutual causality detection methods and the reconstruction of causal networks. The potential of the method to identify the true causal relations in complex networks is validated by both benchmark systems and real-world data sets.

A saturated reaction in repressor synthesis creates a daytime dead zone in circadian clocks

Negative feedback loops (NFLs) for circadian clocks include light-responsive reactions that allow the clocks to shift their phase depending on the timing of light signals. Phase response curves (PRCs) for light signals in various organisms include a time interval called a dead zone where light signals cause no phase shift during daytime. Although the importance of the dead zone for robust light entrainment is known, how the dead zone arises from the biochemical reactions in an NFL underlying circadian gene expression rhythms remains unclear. In addition, the observation that the light-responsive reactions in the NFL vary between organisms raises the question as to whether the mechanism for dead zone formation is common or distinct between different organisms. Here we reveal by mathematical modeling that the saturation of a biochemical reaction in repressor synthesis in an NFL is a common mechanism of daytime dead zone generation. If light signals increase the degradation of a repressor protein, as in Drosophila, the saturation of repressor mRNA transcription nullifies the effect of light signals, generating a dead zone. In contrast, if light signals induce the transcription of repressor mRNA, as in mammals, the saturation of repressor translation can generate a dead zone by cancelling the influence of excess amount of mRNA induced by light signals. Each of these saturated reactions is located next to the light-responsive reaction in the NFL, suggesting a design principle for daytime dead zone generation.

Light-entrainable circadian clocks form behavioral and physiological rhythms in organisms. The light-entrainment properties of these clocks have been studied by measuring phase shifts caused by light pulses administered at different times. The phase response curves of various organisms include a time window called the dead zone where the phase of the clock does not respond to light pulses. However, the mechanism underlying the dead zone generation remains unclear. We show that the saturation of biochemical reactions in feedback loops for circadian oscillations generates a dead zone. The proposed mechanism is generic, as it functions in different models of the circadian clocks and biochemical oscillators. Our analysis indicates that light-entrainment properties are determined by biochemical reactions at the single-cell level.

Morphological Analysis of Trafficking and Processing of Anionic and Cationic Liposomes in Cultured Cells

Liposomes, artificial phospholipid vesicles, have been developed as a non-viral drug delivery system to allow contained agents to be efficiently delivered to target sites via systemic circulation. Liposomes have been used as a gene transfer tool with cultured cells; however, their precise trafficking and processing remain uncertain. Furthermore, liposomes with different surface charges are known to exhibit distinct properties. The purpose of the current study was to elucidate the intracellular trafficking and processing of liposomes with anionic and cationic surface charges from a morphological view point. We found that cationic liposomes (CLs) were more effectively taken by the cells than anionic liposomes (ALs). Confocal laser scanning microscopy and transmission electron microscopy demonstrated distinct intracellular localization and processing patterns of ALs and CLs. ALs and their contents were localized in lysosomes but not in cytosol, indicating that ALs are subjected to the endosome-lysosome system. In contrast, contents of CLs were distributed mainly in the cytosol. CLs appear to disturb the cell membrane and then collapse to release their contents into the cytosol. It is feasible that the contents of CLs enter the cytosol directly rather than via the endosome-lysosome system.

Novel Parallelized Electroporation by Electrostatic Manipulation of a Water-in-Oil Droplet as a Microreactor

Electroporation is the most widely used transfection method for delivery of cell-impermeable molecules into cells. We developed a novel gene transfection method, water-in-oil (W/O) droplet electroporation, using dielectric oil and an aqueous droplet containing mammalian cells and transgene DNA. When a liquid droplet suspended between a pair of electrodes in dielectric oil is exposed to a DC electric field, the droplet moves between the pair of electrodes periodically and droplet deformation occurs under the intense DC electric field. During electrostatic manipulation of the droplet, the local intense electric field and instantaneous short circuit via the droplet due to droplet deformation facilitate gene transfection. This method has several advantages over conventional transfection techniques, including co-transfection of multiple transgene DNAs into even as few as 103 cells, transfection into differentiated neural cells, and the capable establishment of stable cell lines. In addition, there have been improvements in W/O droplet electroporation electrodes for disposable 96-well plates making them suitable for concurrent performance without thermal loading by a DC electric field. This technique will lead to the development of cell transfection methods for novel regenerative medicine and gene therapy.

Detecting causality from nonlinear dynamics with short-term time series

Quantifying causality between variables from observed time series data is of great importance in various disciplines but also a challenging task, especially when the observed data are short. Unlike the conventional methods, we find it possible to detect causality only with very short time series data, based on embedding theory of an attractor for nonlinear dynamics. Specifically, we first show that measuring the smoothness of a cross map between two observed variables can be used to detect a causal relation. Then, we provide a very effective algorithm to computationally evaluate the smoothness of the cross map, or "Cross Map Smoothness" (CMS), and thus to infer the causality, which can achieve high accuracy even with very short time series data. Analysis of both mathematical models from various benchmarks and real data from biological systems validates our method.

Small molecule modifiers of circadian clocks

Circadian clocks orchestrate 24-h oscillations of essential physiological and behavioral processes in response to daily environmental changes. These clocks are remarkably precise under constant conditions yet highly responsive to resetting signals. With the molecular composition of the core oscillator largely established, recent research has increasingly focused on clock-modifying mechanisms/molecules. In particular, small molecule modifiers, intrinsic or extrinsic, are emerging as powerful tools for understanding basic clock biology as well as developing putative therapeutic agents for clock-associated diseases. In this review, we will focus on synthetic compounds capable of modifying the period, phase, or amplitude of circadian clocks, with particular emphasis on the mammalian clock. We will discuss the potential of exploiting these small molecule modifiers in both basic and translational research.

In vitro circadian rhythms: imaging and electrophysiology

In vitro assays have localized circadian pacemakers to individual cells, revealed genetic determinants of rhythm generation, identified molecular players in cell-cell synchronization and determined physiological events regulated by circadian clocks. Although they allow strict control of experimental conditions and reduce the number of variables compared with in vivo studies, they also lack many of the conditions in which cellular circadian oscillators normally function. The present review highlights methods to study circadian timing in cultured mammalian cells and how they have shaped the hypothesis that all cells are capable of circadian rhythmicity.

Positive autoregulation delays the expression phase of mammalian clock gene Per2

In mammals, cellular circadian rhythms are generated by a transcriptional-translational autoregulatory network that consists of clock genes that encode transcriptional regulators. Of these clock genes, Period1 (Per1) and Period2 (Per2) are essential for sustainable circadian rhythmicity and photic entrainment. Intriguingly, Per1 and Per2 mRNAs exhibit circadian oscillations with a 4-hour phase difference, but they are similarly transactivated by CLOCK-BMAL1. In this study, we investigated the mechanism underlying the phase difference between Per1 and Per2 through a combination of mathematical simulations and molecular experiments. Mathematical analyses of a model for the mammalian circadian oscillator demonstrated that the slow synthesis and fast degradation of mRNA tend to advance the oscillation phase of mRNA expression. However, the phase difference between Per1 and Per2 was not reproduced by the model, which implemented a 1.1-fold difference in degradation rates and a 3-fold difference in CLOCK-BMAL1 mediated inductions of Per1 and Per2 as estimated in cultured mammalian cells. Thus, we hypothesized the existence of a novel transcriptional activation of Per2 by PER1/2 such that the Per2 oscillation phase was delayed. Indeed, only the Per2 promoter, but not Per1, was strongly induced by both PER1 and PER2 in the presence of CLOCK-BMAL1 in a luciferase reporter assay. Moreover, a 3-hour advance was observed in the transcriptional oscillation of the delta-Per2 reporter gene lacking cis-elements required for the induction by PER1/2. These results indicate that the Per2 positive feedback regulation is a significant factor responsible for generating the phase difference between Per1 and Per2 gene expression.

Identification of functional clock-controlled elements involved in differential timing of Per1 and Per2 transcription

It has been proposed that robust rhythmic gene expression requires clock-controlled elements (CCEs). Transcription of Per1 was reported to be regulated by the E-box and D-box in conventional reporter assays. However, such experiments are inconclusive in terms of how the CCEs and their combinations determine the phase of the Per1 gene. Whereas the phase of Per2 oscillation was found to be the most delayed among the three Period genes, the phase-delaying regions of the Per2 promoter remain to be determined. We therefore investigated the regulatory mechanism of circadian Per1 and Per2 transcription using an in vitro rhythm oscillation-monitoring system. We found that the copy number of the E-box might play an important role in determining the phase of Per1 oscillation. Based on real-time bioluminescence assays with various promoter constructs, we provide evidence that the non-canonical E-box is involved in the phase delay of Per2 oscillation. Transfection experiments confirmed that the non-canonical E-box could be activated by CLOCK/BMAL1. We also show that the D-box in the third conserved segment of the Per2 promoter generated high amplitude. Our experiments demonstrate that the copy number and various combinations of functional CCEs ultimately led to different circadian phases and amplitudes.

A network biology study on circadian rhythm by integrating various omics data

Circadian rhythm is fundamentally important in physiological processes of mammals. To reveal its underlying mechanism, we probed functional interactions among genes, motivated by the basic molecular observation on gene expression data in circadian rhythm that a large number of genes oscillate in a coordinated manner. In this study, a reverse-engineering strategy was applied to infer and analyze the structure and function of a circadian rhythm-related gene regulatory network. Specifically, our method integrated four phase-shift time-course gene expression datasets in rat suprachiasmatic nucleus, protein-protein interactions, phosphorylations of a set of key circadian genes, and prior information of cis-regulatory elements, to construct the gene regulatory network related to circadian rhythm of the rat. By follow-up analysis, we identified four new regulatory hubs that may play crucial roles in the regulation of circadian rhythm. Furthermore, we found that feedback loop motifs were significantly enriched in the predicted network, which may contribute to the genome-wide oscillations of the circadian clock. Compared to the small-scale gene regulatory network conducted by experimental method, our study provides a system-wide overview on the gene regulations, which not only reveals the global network structure but also gives valuable insights into the essential mechanism of circadian rhythm.

Hypothalamic cell lines to investigate neuroendocrine control mechanisms

The hypothalamus is the control center for most physiological processes; yet has been difficult to study due to the inherent heterogeneity of this brain region. For this reason, researchers have turned towards cell models. Primary hypothalamic cultures are difficult to maintain, are heterogeneous neuronal and glial cell populations and often contain a minimal number of viable peptide-secreting neurons. In contrast, immortalized, clonal cell lines represent an unlimited, homogeneous population of neurons that can be manipulated using a number of elegant molecular techniques. Cell line studies and in vivo experimentation are complementary and together provide a powerful tool to drive scientific discovery. This review focuses on three key neuroendocrine systems: energy homeostasis, reproduction, and circadian rhythms; and the use of hypothalamic cell lines to dissect the complex pathways utilized by individual neurons in these systems.

The molecular mechanism regulating the autonomous circadian expression of Topoisomerase I in NIH3T3 cells

To identify whether Topoisomerase I (TopoI) has autonomous circadian rhythms regulated by clock genes, we tested mouse TopoI (mTopoI) promoter oscillation in NIH3T3 cells using a real-time monitoring assay and TopoI mRNA oscillations using real-time RT-PCR. Analysis of the mTopoI promoter region with Matlnspector software revealed two putative E-box (E1 and E2) and one DBP/E4BP4-binding element (D-box). Luciferase assays indicated that mTopoI gene expression was directly regulated by clock genes. The real-time monitoring assay showed that E-box and D-box response elements participate in the regulation of the circadian expression of mTopoI. Furthermore, a gel-shift assay showed that E2 is a direct target of the BMAL1/CLOCK heterodimer and DBP binds to the putative D-site. These results indicate that TopoI is expressed in an autonomous circadian rhythm in NIH3T3 cells.