Cell polarity regulates the orientation of the cytoskeleton members that directs intracellular transport for cargo-like organelles, using chemical gradients sustained by ATP or GTP hydrolysis. However, how cargo transports are directly mediated by chemical gradients remains unknown. We previously proposed a physical mechanism that enables directed movement of cargos, referred to as chemophoresis. According to the mechanism, a cargo with reaction sites is subjected to a chemophoresis force in the direction of the increased concentration. Based on this, we introduce an extended model, the chemophoresis engine , as a general mechanism of cargo motion, which transforms chemical free energy into directed motion through the catalytic ATP hydrolysis. We applied the engine to plasmid motion in a ParABS system to demonstrate the self-organization system for directed plasmid movement and pattern dynamics of ParA-ATP concentration, thereby explaining plasmid equi-positioning and pole-to-pole oscillation observed in bacterial cells and in vitro experiments. We mathematically show the existence and stability of the plasmid-surfing pattern, which allows the cargo-directed motion through the symmetry-breaking transition of the ParA-ATP spatiotemporal pattern. We also quantitatively demonstrate that the chemophoresis engine can work even under in vivo conditions. Finally, we discuss the chemophoresis engine as one of the general mechanisms of hydrolysis-driven intracellular transport.

ABSTRACT Cell polarity regulates the orientation of the cytoskeleton members that directs intracellular transport for cargo-like organelles, using chemical gradients sustained by ATP or GTP hydrolysis. However, how cargo transports are directly mediated by chemical gradients remains unknown. We previously proposed a physical mechanism that enables directed movement of cargos, referred to as chemophoresis. According to the mechanism, a cargo with reaction sites is subjected to a chemophoresis force in the direction of the increased concentration. Based on this, we introduce an extended model, the chemophoresis engine , as a general mechanism of cargo motion, which transforms chemical free energy into directed motion through the catalytic ATP hydrolysis. We applied the engine to plasmid motion in a parABS system to demonstrate the the self-organization system for directed plasmid movement and pattern dynamics of ParA-ATP concentration, thereby explaining plasmid equi-positioning and pole-to-pole oscillation observed in bacterial cells and in vitro experiments. We mathematically show the existence and stability of the plasmid-surfing pattern, which allows the cargo-directed motion through the symmetry-breaking transition of the ParA-ATP spatiotemporal pattern. Finally, based on its generality, we discuss the chemophoresis engine as a universal principle of hydrolysis-driven intracellular transport. SIGNIFICANCE The formation of organelle/macromolecule patterns depending on chemical concentration under non-equilibrium conditions, first observed during macroscopic morphogenesis (1), has recently been observed at the intracellular level as well, and its relevance as intracellular morphogen has been demonstrated in the case of bacterial cell division. These studies have discussed how cargos maintain positional information provided by chemical concentration gradients/localization. However, how cargo transports are directly mediated by chemical gradients remains unknown. Based on the previously proposed mechanism of chemotaxis-like behavior of cargos (referred to as chemophoresis, (2, 3)), we introduce a chemophoresis engine as a physicochemical mechanism of cargo motion, which transforms chemical free energy to directed motion. The engine is based on the chemophoresis force to make cargoes move in the direction of the increasing ATPase(-ATP) concentration and an enhanced catalytic ATPase hydrolysis at the positions of the cargoes. Applying the engine to ATPase-driven movement of plasmid-DNAs in bacterial cells, we constructed a mathematical model to demonstrate the self-organization for directed plasmid motion and pattern dynamics of ATPase concentration, as is consistent with in vitro and in vivo experiments. We propose that this chemophoresis engine works as a universal principle of hydrolysis-driven intracellular transport.

a Fuji­Nikoniko­Clinic, 1287 Funatu, Fujikawaguchiko­cho, Minamituru­gun, Yamanashi 401­0301, Japan b Nakada Clinic Chinese Institute of Medicine Director, 608 Wakamiko, Sutamachou, Hokuto­shi, Yamanashi 408­0112, Japan c Kenyudo­Clinic, Miyabara Town, 211­1 Kofu City, Yamanashi 400­0058, Japan d Kofu Kyoritsu Hospital, 1­9­1 Takara, Kofu City, Yamanashi 400­0034, Japan e Minobusan Hospital, 2483­167 Umedaira, Minobu­cho, Minamikoma­gun, Yamanashi 409­2531, Japan f Department of Anesthesiology, University of Yamanashi, 1110 Shimokato Chuo City, Yamanashi 409­3898, Japan g Koshu Rehabilitation Hospital, 415 Ninomiya, Misak­cho, Fuefukishi, Yamanashi 406­0807, Japan h Tamaho Fureai Clinic, 2439­1 Narushima, Chuo­shi, Yamanashi 409­3815, Japan

Computational modelling methods for Hi-C data have revealed averaged and static features of the 3D genome in cell nuclei. Here, we describe a 4D simulation method, PHi-C (Polymer dynamics deciphered from Hi-C data), that depicts dynamic 3D genome features through polymer modelling. This method allows for demonstrations of dynamic characteristics of genomic loci and chromosomes, as observed in live-cell imaging experiments, and provides physical insights into Hi-C data.

The one-dimensional information of genomic DNA is hierarchically packed inside the eukaryotic cell nucleus and organized in a three-dimensional (3D) space. Genome-wide chromosome conformation capture (Hi-C) methods have uncovered the 3D genome organization and revealed multiscale chromatin domains of compartments and topologically associating domains (TADs). Moreover, single-nucleosome live-cell imaging experiments have revealed the dynamic organization of chromatin domains caused by stochastic thermal fluctuations. However, the mechanism underlying the dynamic regulation of such hierarchical and structural chromatin units within the microscale thermal medium remains unclear. Microrheology is a way to measure dynamic viscoelastic properties coupling between thermal microenvironment and mechanical response. Here, we propose a new, to our knowledge, microrheology for Hi-C data to analyze the dynamic compliance property as a measure of rigidness and flexibility of genomic regions along with the time evolution. Our method allows the conversion of an Hi-C matrix into the spectrum of the dynamic rheological property along the genomic coordinate of a single chromosome. To demonstrate the power of the technique, we analyzed Hi-C data during the neural differentiation of mouse embryonic stem cells. We found that TAD boundaries behave as more rigid nodes than the intra-TAD regions. The spectrum clearly shows the dynamic viscoelasticity of chromatin domain formation at different timescales. Furthermore, we characterized the appearance of synchronous and liquid-like intercompartment interactions in differentiated cells. Together, our microrheology data derived from Hi-C data provide physical insights into the dynamics of the 3D genome organization.

The complexity of chromatin dynamics is orchestrated by several active processes. In fission yeast, the centromeres are clustered around the spindle pole body (SPB) and oscillate in a microtubule- and adenosine triphosphate (ATP)-dependent manner. However, whether and how SPB oscillation are affected by different environmental conditions remain poorly understood. In this study, we quantitated movements of the SPB component, which colocalizes with the centromere in fission yeast. We found that SPB movement was significantly reduced at low glucose concentrations. Movement of the SPB was also affected by the presence of ammonium chloride. Power spectral analysis revealed that periodic movement of the SPB is disrupted by low glucose concentrations. Measurement of ATP levels in living cells by quantitative single-cell imaging suggests that ATP levels are not the only determinant of SPB movement. Our results provide novel insight into how SPB movement is regulated by cellular energy status and additional factors such as the medium nutritional composition.

Remarkable progress has been made in understanding chromosome structures inside the cell nucleus. Recent advances in Hi-C technologies enable the detection of genome-wide chromatin interactions, providing insight into three-dimensional (3D) genome organization. Advancements in the spatial and temporal resolutions of imaging as well as in molecular biological techniques allow the tracking of specific chromosomal loci, improving our understanding of chromosome movements. From these data, we are beginning to understand how the intra-nuclear locations of chromatin loci and the 3D genome structure change during development and differentiation. This emerging field of genome structure and dynamics research requires an interdisciplinary approach including efficient collaborations between experimental biologists and physicists, informaticians, or engineers. Quantitative and mathematical analyses based on polymer physics are becoming increasingly important for processing and interpreting experimental data on 3D chromosome structures and dynamics. In this review, we aim to provide an overview of recent research on the physical aspects of chromosome structure and dynamics oriented for biologists. These studies have mainly focused on chromosomes at the cellular level, using unicellular organisms and cultured cells. However, physical parameters that change during development, such as nuclear size, may impact genome structure and dynamics. Here, we discuss how chromatin dynamics and genome structures in early embryos change during development, which we expect will be a hot topic in the field of chromatin dynamics in the near future. We hope this review helps developmental biologists to quantitatively investigate the physical natures of chromosomes in developmental biology research.

In differentiated cells, chromosomes are packed inside the cell nucleus in an organised fashion. In contrast, little is known about how chromosomes are packed in undifferentiated cells and how nuclear organization changes during development. To assess changes in nuclear organization during the earliest stages of development, we quantified the mobility of a pair of homologous chromosomal loci in the interphase nuclei of Caenorhabditis elegans embryos. The distribution of distances between homologous loci was consistent with a random distribution up to the 8-cell stage but not at later stages. The mobility of the loci was significantly reduced from the 2-cell to the 48-cell stage. Nuclear foci corresponding to epigenetic marks as well as heterochromatin and the nucleolus also appeared around the 8-cell stage. We propose that the earliest global transformation in nuclear organization occurs at the 8-cell stage during C. elegans embryogenesis.

Luminescent thin films composed of thermostable lanthanide coordination polymers on glass electrodes were prepared using a novel combination of micelle reactions and electrochemical deposition techniques. The micelle-encapsulated luminescent polymers were obtained by the polymerization of [Eu(hfa)3 ] (hfa=hexafluoroacetylacetonate) with bridging phosphine oxide ligands in micelles using a redox-active ferrocenyl-containing surfactant in water. Films were electrochemically deposited on indium tin oxide coated glass electrodes by potentiostatic polarization of micelle-encapsulated EuIII coordination polymers. The luminescence properties of the electrochemically deposited films were characterized by measuring their emission spectra, emission lifetimes and emission quantum yields.

In mammals and other higher organisms, interphase chromosomes remain separated from each other and compartmentalized into chromosome territories. In yeast, chromosomes adopt a Rabl configuration, with arms extending from centromeres tethered at the spindle pole body(SPB), functionally equivalent to the centrosome, to telomeres at the opposite nuclear envelope. These organizations generally constrain chromatin motion, and contribute to gene positioning inside the nucleus. On the other hand, active genes escape from such physical constraints and are located at active regions such as transcription factories and nuclear pore complexes(NPCs). In spite of extensive studies for these phenomena, how gene loci sustain and change their positioning during the cell cycle still remains unclear. In order to elucidate chromatin dynamics during interphase, we visualized several gene loci and the centromeres (and the SPB) on the fission yeast S. pombe chromosomes that show a Rabl configuration, and then tracked the positions of the loci on a longer time scale than conventional one. The statistical analysis of the physical distance from the SPB to each locus suggested that the gene loci show not only restricted diffusion due to the physical constraint of the Rabl configuration, but also a novel dynamic property, that is quite different from simple diffusive behaviors reported so far. In this presentation, we will discuss functional roles that such chromatin dynamics possibly play within the interphase nucleus.

The cover picture shows luminescent thin films composed of lanthanide coordination polymers on a glass electrode. The luminescent thin films are prepared using micelle techniques in water media. Thermostable thin films of EuIII coordination polymers on electrodes are expected to open up a new field spanning inorganic chemistry, electrochemistry, and materials and colloid science. More details can be found in the Full Paper by Yasuchika Hasegawa et al. on page 187 in Issue 2, 2016 (DOI: 10.1002/cplu.201500382).

The relationship between genome organization and gene expression has recently been established. However, the relationships between spatial organization, dynamics, and transcriptional regulation of the genome remain unknown. In this study, we developed a live-imaging method for simultaneous measurements of the transcriptional activity and nuclear position of endogenous genes, which we termed the 'Real-time Observation of Localization and EXpression (ROLEX)' system. We demonstrated that ROLEX is highly specific and does not affect the expression level of the target gene. ROLEX enabled detection of sub-genome-wide mobility changes that depended on the state of Nanog transactivation in embryonic stem cells. We believe that the ROLEX system will become a powerful tool for exploring the relationship between transcription and nuclear dynamics in living cells.

Mouse embryonic stem cells (mESCs) are self-renewing and capable of differentiating into any of the three germ layers. An interesting feature of mESCs is the presence of cell-to-cell heterogeneity in gene expression that may be responsible for cell fate decisions. Nanog, a key transcription factor for pluripotency, displays heterogeneous expression in mESCs, via mechanisms that are not fully understood. To understand this variability, we quantitatively analyzed Nanog transcription and found that Nanog was both infrequently transcribed and transcribed in a pulsatile and stochastic manner. It is possible that such stochastic transcriptional activation could contribute to the heterogeneity observed in Nanog expression as "intrinsic noise." To discriminate the effects of both intrinsic noise from other (extrinsic) noise on the expression variability of Nanog mRNA, we performed allele-specific single-molecule RNA fluorescent in situ hybridization in a reporter cell line and found that intrinsic noise contributed to approximately 45% of the total variability in Nanog expression. Furthermore, we found that Nanog mRNA and protein levels were well correlated in individual cells. These results suggest that stochastic promoter activation significantly affects the Nanog expression variability in mESCs.

Biomolecular motor such as kinesin converts chemical energy into mechanical work with a high efficiency and moves along the microtubule (MT).MTs, introducing biotin-streptavidin interaction, were integrated into assembled structures on a kinesin-coated surface and MT assemblies provide specific motion.However, reversible control of the MT association / dissociation was not achieved.Hence, we prepared DNAmodified MT and control the self-organization of MTs by using DNA interaction.DNA-modified MTs can reversibly associate and dissociate depending on the DNA sequence used.It will offer means to control the assembly of MT and thereby may widen the application of biomolecular motor based nanodevice.