Physical Models of Living Matters - The 3rd Symposium of Physical Biology and Biological Physics

30 Aug 2024, 12:00 → 1 Sept 2024, 17:20 Asia/Taipei

205 Meeting Room (The Aspire Resort, Taoyuan)

Keng Hui Lin (Institute of Physics, Academia Sinica)

The Physical Biology and Biological Physics (PBBP) Division of the Taiwanese Physical Society was established in April 2022 and has been working hard to build the biological physics community in Taiwan to bring together people who work at the interface between biology and physics and organize this annual symposium. This year the symposium title is "Physical Models of Living Matters". The topics include the self-organization principles of cells, soft matter approach to biology, liquid-liquid phase separation, and chromatin dynamics.

This is a small to medium-sized international meeting, including invited talks, contributed talks, poster presentations, and networking activities. We bring together speakers from biology, physics, and engineering to talk about their respective work in biological physics and physical biology. Students and postdoctoral fellows are encouraged to present posters or contributed talks. There will be poster awards for students.

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Poster List.pdf

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Friday, 30 August

12:00 Registration

13:20 Opening

Session I

Convener: Keng-hui Lin

1 The resilience and diversification of mechanical stress management during morphogenesis

The separation of yolk from the embryonic cytoplasm characterizes the initial phase of embryonic development in oviparous animals, including fish, frogs and flies. While yolk-cytoplasm separation is known for allocation of energy resources and partitioning of maternally deposited patterning elements critical for cell fate specification, it remains unknown whether such separation changes the material properties of the embryo interior and mechanically influences the development of the blastoderm. In the early Drosophila embryo, lipid droplets (LDs) segregate from yolk and undergo a stereotypical polarized translocation during yolk-cytoplasm separation. In our quest for the mechanical function of yolk-cytoplasm separation, we genetically disrupted distinct aspects of LD segregation and polarized distribution. We observed a common phenotype of reduced packing at the yolk surface, and increased flow of both naturally existing and artificially introduced rheology probes in the yolk region, indicative of perturbed yolk compaction and an apparent increase in cytoplasmic fluidity. We determined that microtubule dynamics, but not myosin contractility, drives the flow in the yolk cytoplasm. We went on to investigate the morphogenetic consequence of the flow and found that the membranes of newly formed blastoderm display dramatic lateral vibrational movement and undamped fluctuations along the apical-basal axis during cellularization. During gastrulation, we observed a loss of stable tissue deformation in all epithelial folds, irrespective of the distinct active mechanisms of cell surface mechanics that initiate these folds, suggesting that epithelial out-of-plane deformation requires a rigid yolk substrate. In sum, these data suggest a non-metabolic, mechanical function for the yolk in addition to its well characterized nutritional role. Yolk-LD segregation is essential for yolk compaction, which rigidifies the embryo interior to dampen flows resulting from microtubule stresses, thereby ensuring stable and productive tissue deformation during gastrulation.

Speaker: Prof. Yu-chiun Wang (RIKEN)

2 Mechanosensitive regulation of integrin beta6 mediated adhesion

The interplay between inside-out and outside-in activation of integrin receptor orchestrates cell motility and tissue regeneration. While such mechanisms of RGD-binding integrin, including integrin beta1 and beta3, are well documented, mechano-sensitive regulations of integrin beta6 remain largely unknown. Using the viscous RGD-membrane as the model system, we find that integrin beta6 and viscous RGD ligands promptly colocalize and assemble dense micrometer-sized clusters in the early phase of adhesion formation (15-min). However, these clusters gradually dissipate, and integrin beta6 and RGD ligands become poorly colocalized (60-min). With the tail-swapping and mutagenesis approach, we find that interactions between the cytoplasmic tail of integrin beta6 and kindlin, rather than talin, act as the critical factor to regulate the adhesion stability. In addition, we will report our latest findings in kindlin-dependent integrin beta6 adhesion assembly and cell migration on compliant surface. Our results suggest that kindlin-mediated inside-out activation can bypass the extracellular force dependent signalling and orchestrate the spatiotemporal assembly of integrin beta6.

Speaker: Cheng-han Yu (The University of Hong Kong)

3 Phase separation promotes receptor clustering and downstream signaling

In many signaling pathways, receptors are spatially organized at the plasma membrane into signaling clusters with a specific composition. Phase separation driven by protein interactions can promote clustering of many types of receptors, including the LAT receptor, Nephrin receptor, and integrin receptor. We use biochemical reconstitutions and cellular experiments to study compositionally complex phase separated signaling clusters. Through recent studies of the cell-cell adhesion receptor nephrin and the cell-matrix adhesion receptor integrin, we’ve gained insight into how phase separation promotes receptor clustering and the ways in which membranes can influence phase separation. Additionally, we’ve found that molecular activity can be regulated by phase separation. Arp2/3-dependent actin polymerization and kinase autophosphorylation are both dramatically increased in phase-separated compartments. Thus, phase separation can contribute to molecular organization and the regulation of signaling pathways at the plasma membrane. However, many questions remain about how classical physical theories can be applied to understand the multicomponent, heterogenous, and often nonequilibrium cellular phase separation.

Speaker: Prof. Lindsay Case (MIT)

4 Wavy Morphology Regulates Cell Structure, Migration, and Phenotype

Elastic tissues such as arteries and tendons have dense extracellular matrices with wavy structures that allow high strain. The resident cells follow the wavy structures that change with load, disease, and aging. Few studies, however, study the impacts of this wavy morphology on cell behavior and mechanotransduction. Using microfabrication techniques, we precisely control single cell shape and characterize cell, nuclear, and cytoskeletal organization. We also examine how these cues modulate cell phenotype and signaling. The wavy structures increase cell contractility, nuclear deformation, lamellipodia formation, smooth muscle actin expression, and YAP nuclear translocation. In addition, the wavy channels suppress motility and directional persistence. These findings are consistent with phenotypic behaviors found in three dimensional wavy scaffolds and in healthy and diseased tissues. We are currently investigating the mechanisms that regulate these behaviors and how these extrinsic factors interact with intrinsic cellular status to control aging and disease.

Speaker: Prof. Grace Pen-hsiu Chao (NTU)

15:10 Coffee Break and check in

Session II

Convener: Grace Pen-hsiu Chao

5 Probing the Nanoscale Membrane Topography in Cells

Cell membranes serve as a central platform to host a variety of proteins essential for cellular activities such as cell signaling, morphogenesis, and membrane trafficking. At the same time, the membranes also undergo drastic morphological changes in a number of essential processes, such as endocytosis, intracellular trafficking, and cytokinesis, etc. An intriguing yet challenging question to answer is whether and how the shapes of the membrane impact the dynamics of membrane proteins or the periphery proteins interacting with the membrane. However, membrane shape changes often happen at sub-micro to the nanoscale, which is approaching the limit of conventional microscopy imaging resolution and difficult to examine quantitatively. In this work, we will introduce our efforts in employing vertically aligned nanostructures to generate defined membrane topography in live cells and in vitro. We will discuss our findings on the membrane curvature-guided accumulation of membrane proteins, including oncogenic Ras proteins and viral proteins. In addition to plasma membrane, we also explore the nanoscale topography guidance on nuclear membrane and its implication in differentiating malignant cancer cells. We envision more new insights would be revealed by bridging advanced nanotechnology to nanoscale dynamics at cell membranes.

Speaker: Prof. Wenting Zhao (Nanyang Technological Unviersity)

6 Dynamics of force-regulated branched actin network density

The assembly of branched actin networks provides the driving force for numerous cell motilities of all eukaryotic cells. While pushing the cytoplasm membrane moving forward, the networks are also polymerizing under a counter force. At the leading edge of the cell motilities, such as Lamellipodium, the pushing force and network formation are dynamically regulated by nucleation, elongation, and capping of individual growing filaments in the branched actin networks. Although it has been shown that the motor activity and mechanical properties of growing networks adapt to the counter forces, the force dependence of many other biochemical events and their molecular mechanisms are still not clear. Here we show how the counter force regulates capping and nucleation at molecular level. We found that the capping of filament polymerizing ends (free barbed ends) is force-regulated in the same way as for filament elongation. We also discovered that counter forces slow the rate of Arp2/3-mediated filament nucleation via a previously unsuspected mechanism, which involves force-dependent balance of free barbed ends, nucleation promoting factor protein, and Arp2/3 complex. This work not only uncovers a previously unknown and functionally significant effects of force in branched actin network assembly, but also reveals the responsible molecular mechanisms. Based on the newly discovered force-dependent capping and nucleation mechanisms, we have successfully explained the previously observed force-insensitive filament length and force-induced increase of number of free barbed ends. This work provides the very fundamental molecular mechanisms for cell motilities and we anticipate our assay to be a start point for more systematic studies on the influence of physical perturbations in actin branched network biochemistry.

Speaker: Prof. Tai-de Li (CUNY)

20240830_Biophysics_Taiwan_short.pptx

7 To repair or regenerate, it is a matter of matrix stiffness

We have worked on the influence of matrix stiffness on cellular physiology in epithelial cells and fibroblasts as well, which plays a very important role in pathophysiology of organ and tissue fibrosis. The current research theme of my research has been to unveil the mechanobiological mechanism of converting wound repair into regeneration. We have discovered that breaking symmetry of cell contractility by lowering the matrix stiffness leads to augmented wound-induced hair follicle neogenesis in mice (Nature Commun 2021) and renal tubule morphogenesis in vitro (PNAS 2024 ). Thus, lowered matrix stiffness promote tissue regeneration and differentiation. In this talk, I will present our data how matrix stiffness controls the fate of stem cell lineage specification.

Speaker: Prof. Ming Jer Tang (National Cheng Kung University College of Medicine)

8 Characterization of Megadalton MALDI Ions with Linear Ion Trap Mass Spectrometer

Detecting megadalton matrix-assisted laser desorption/ionization (MALDI) ions with linear ion trap mass spectrometer (LIT-MS) is a technical challenge. In this talk, we employ MALDI LIT- MS to successfully analyze megadalton protein, polymer, and proteasome ions. A homebuilt linear ion trap mass spectrometer (LIT-MS) equipped with a charge sensing particle detector (CSPD) is used for high mass ion detection. We analyze high mass ions with mass-to charge (m/z) ratios ranging from 100 kTh to 2 MTh, including thyroglobulin, alpha-2-macroglobulin, immunoglobulins (e.g., IgG and IgM), polymer (200k ~ 2MTh), and 20S and 26S proteasomes. Besides, it is also very challenging for ion trap mass spectrometry to detect megadalton ions at low concentrations. By adopting high affinity carboxylated/oxidized detonation nanodiamonds (oxDNDs) to enrich IgM molecules and form antibody-nanodiamond conjugates, ~ 5 nM (5 μg/mL) concentration has successfully reached which is better than that by the other techniques.

Speaker: Prof. Wen Ping Peng (NDHU)

9 Self-organized cellular patterns direct waves of cell death

Large-scale cell death is widely observed during embryonic development and various human pathological conditions. However, a systems-level understanding for how large-scale cell death emerges had been lacking. Harnessing time-lapse imaging, chemical/genetic perturbations and mathematical modeling, we show how metabolic stress quantitatively modulate cellular state for the emergence of redox multistability, allowing reactive oxygen species (ROS) to regenerate and propagate across millions of cells. Intriguingly, these cell death trigger waves (i.e., its initiation, direction and speed) can be oriented by the emergent cellular patterns in a cell population. These cellular patterns dictate cell density and cell-cell alignment that prime cells with heterogeneous sensitivity to metabolic stress. Our findings show how cell death propagation is directed in a cell population via self-organized cellular patterns, featuring how collective cellular behavior in tissues and organs may influence cellular vulnerability to metabolic stress.

Speaker: Prof. Sheng-hong Chen (Academia Sinica)

10 Flash talk by the poster presenter

Flash talk from poster

Speaker: Yu-chiun Wang

Poster List_excel.xlsx

19:00 Dinner

11 Poster Sessions (II)

Flash talk from poster

Saturday, 31 August

Session III

Convener: Prof. Kuo-an Wu

12 Collective chiral behaviors in single cells and a multicellular system

Most animals have systematic left-right asymmetry in their bodies and organs. Their chiral property should be originated from the organization of the chirality of their constituents. However, the mechanisms of how chiral information is brought from the molecular to the cell, tissue and organ scales are largely unresolved. In my talk, I will present our recent study combining experiment and theory on how the cell-scale chirality emerges from molecular-scale chirality in single cells and how a multicellular chiral behavior arises in a colony of epithelial cells.

Speaker: Prof. Tatsuo Shibata (RIKEN)

13 Mechanical waves decode positional information to calibrate wound healing response in zebrafish

Highly regenerative animals, such as salamander and zebrafish, can regrow lost appendages and the rate of regrowth is proportional to the amount of appendage loss. This century-old phenomenon prompted us to investigate whether the mechanism of wound healing, as the first stage of regeneration, is responsible for discerning the amputation position. In vitro studies have revealed great insights into the mechanics of the wound-healing process, including the identification of mechanical waves in collective epithelial cell expansion. It has been suggested that these mechanical waves may also be involved in positional sensing. Here we perform live-cell imaging on adult zebrafish tailfins to monitor the collective migration of basal epithelial cells on tailfin amputation. We observed a cell density wave propagating away from the amputation edge, with the maximum travelling distance proportional to the amputation level and cell proliferation at later stages. We developed a mechanical model to explain this wave behaviour, including the tension-dependent wave speed and amputation-dependent travelling distance. Together, our findings point to an in vivo positional sensing mechanism in regenerative tissues based on a coupling of mechanical signals manifested as a travelling density wave.

Speaker: Prof. Fu-lai Wen (NCU)

14 Detecting and analyzing dynamic interferometric light scattering signals of chromatin in live cell nuclei

Advancements in interferometric scattering microscopy (iSCAT) enable label-free detection of nanoscale structures and dynamics with high sensitivity and fast acquisition rates. This technology overcomes fluorescence imaging limitations, such as photobleaching, facilitating long-term or high-speed measurements. However, analyzing label-free signals to extract specific target information remains challenging. In this work, we employ coherent bright field microscopy (COBRI), an iSCAT microscope in transmission mode, to capture chromatin scattering signals in live cell nuclei at 5000 frames per second. Utilizing back pupil function engineering and a high numerical aperture microscope condenser enhances detection of weak chromatin signals and optical sectioning. Through correlation spectroscopy analysis, we spatially estimate the diffusion coefficient, density, and condensation state of chromatin, specifically. Taken together, we introduce interferometric scattering correlation spectroscopy (iSCORS) to spatially measure nanoscopic chromatin dynamics. Using iSCORS imaging, we successfully observe spontaneous fluctuations in chromatin condensation and chromatin condensation dynamics in response to transcription inhibition. Detailed image processing and temporal analysis will be discussed.

Speaker: Yi-deng Hsiao (Academia Sinica)

15 Endoplasmic reticulum (ER)-mitochondrial junctions (EMJs) reduce intracellular Ca2+ storage by suppressing store-operated Ca2+ entry (SOCE)

Endoplasmic reticulum (ER)-mitochondrial junctions (EMJs) reduce intracellular Ca2+ storage by suppressing store-operated Ca2+ entry (SOCE)

Speaker: Prof. Feng-chiao Tsai (NTU)

FCTsai_Ca_20240831_PBBP.pptx

10:40 Coffee Break

Session IV

Convener: Chi-Shuo Chen

16 Transcription factor dynamics in gene expression: the long and short of it

The organization and dynamics of chromatin is essential for the regulation of gene expression. Transcription factors (TFs) regulate gene expression by binding to specific consensus motifs within enhancers or promoter-proximal regions. The mechanism by which TFs bind to their cognate chromatin targets within a complex nuclear environment to assemble transcriptional machinery at specific genomic loci remains elusive. Single-molecule tracking (SMT) has emerged as a powerful approach to explore chromatin and transcription factor dynamics and interactions in living cells. Using single-molecule tracking and machine learning-based analysis, we show that chromatin displays two distinct low-mobility states. Our experimental observations are consistent with a minimal active copolymer model for interphase chromosomes. Remarkably, we find that a diverse set of transcription factors, transcriptional co-regulators, architectural proteins and remodelers also exhibit two distinct low-mobility states. Ligand activation results in a marked increase in the propensity of steroid receptors to bind in the lowest-mobility state. Mutational analysis reveals that interactions with chromatin in the lowest-mobility state require an intact DNA binding domain and oligomerization domains. We further find that, for the glucocorticoid receptor, an intrinsically disordered region is a key determinant of the second low mobility state. These low mobility states are not spatially separated as believed, but individual H2B and bound-TF molecules can dynamically switch between them on timescales of seconds. We also used single-molecule tracking to directly measure the interaction timescales of a broad spectrum of transcription factors in live cells. We found that TFs follow power-law distributed binding times, with TF molecules of different mobilities exhibiting different dwell time distributions, suggesting that the mobility of TFs is intimately coupled with their binding dynamics. Together, our results elucidate how TF and chromatin mobility regulates transcriptional activation in mammalian cells.

Speaker: Prof. Arpita Upadhyaya (University of Maryland, College Park)

17 An optogenetic toolbox for spatio-temporal control of integrin adhesion complexes.

The activation of integrins and the subsequent formation of focal complexes is a critical function in cellular sensing of ECM substrates and cell migration. Integrin adhesion complexes (IACs) allow for cell adhesion, transduce force, and signal through several pathways. While much work has been done to uncover the components and regulators involved in adhesion formation and dynamics, we have limited understanding of how individual adhesion states dictate cell motility and signaling. Without a way to dynamically control the timing, location, maturation, and disassembly of IACs, it is difficult to discern their roles at different points in their lifetime or in different locations throughout the cell. Thus, we have developed a set of optogenetic tools which allow for both the creation and manipulation of IACs in response to light. These tools allow for the rapid local induction of IACs, control of maturation, as well as the regulation of their stability and disassembly. Optogenetic IACs can be formed within seconds in the light and disassembled within minutes in the dark. These optogenetically induced adhesions signal, bear force, and dictate cell motility. Optogenetic-induced IAC formation is sufficient to polarize cells plated on fibronectin and direct cell migration. Using optical methods, we can switch between modulating adhesion maturation versus nucleation while using the same construct. By recruiting additional regulators, we can enable or disable adhesion disassembly in the light, allowing for many levels of control of adhesion dynamics. These tools enable the study of the role of adhesion formation in a direct and acute way which was not previously possible, allowing us to directly study the role of adhesion formation, its dynamics, and the role of individual proteins in IACs.

Speaker: Prof. Heath Johnson (The University of Hong Kong)

18 Chromatin organization and dynamics resolved by label-free iSCAT microscopy

The study of chromatin nanostructures in living cells is complex due to their constant motion. In this talk, I will introduce a novel correlation spectroscopy approach using interferometric scattering (iSCAT) microscopy, which allows for the spatial mapping of chromatin configurations and dynamics in live, unlabeled cell nuclei. This innovative label-free method detects linear scattering signals from native chromatin, which fluctuate on a millisecond scale driven by thermal energy. These signals help infer the states of chromatin condensation. With iSCAT imaging, we can continuously monitor chromatin dynamics for over 15 hours, observing spontaneous variations and differences in compaction within interphase cells. We also detect changes in iSCAT signals following transcription inhibition, suggesting the capability of iSCAT to explore chromatin structures and dynamics related to transcriptional activities. This scattering-based microscopy is a significant advancement for dynamically visualizing chromatin nano-arrangements in live cells, offering insights into essential processes like stem cell differentiation, mechanotransduction, and DNA repair.

Speaker: Prof. Chia-lung Hsieh (Academia Sinica)

12:30 Lunch

Session V

Convener: Chia-Ching (Josh) Wu

19 Replication-dependent histone (Repli-Histo) labeling specifically visualizes the physical properties of euchromatin/heterochromatin in living human cells

"Replication-dependent histone (Repli-Histo) labeling specifically visualizes physical properties of euchromatin/heterochromatin in living human cells.
Katsuhiko Minami1, 2, Satoru Ide1, 2, Sachiko Tamura1, and Kazuhiro Maeshima1, 2
1 Genome Dynamics Laboratory, National Institute of Genetics
2 Graduate Institute for Advanced Studies, SOKENDAI

Abstract
Recent advanced imaging studies have revealed that euchromatin in higher eukaryotic cells forms condensed liquid-like domains with very limited ""open"" regions [1-3]. While such condensed chromatin organization provides a higher-order regulation of genome functions, it raises intriguing questions: How are euchromatin and heterochromatin physically different in living cells? How relevant is the difference to the regulation of genome functions?
To approach these questions, we have developed two imaging techniques. The first is single-nucleosome imaging and tracking [2, 4], which present the physical nature of chromatin in living cells. Using this, we have demonstrated that nucleosomes in living human cells fluctuate dynamically, mainly driven by thermal fluctuation [5]. The second technique is a novel chromatin labeling method, replication-dependent histone labeling (Repli-Histo labeling), which can specifically label four groups of genome regions from euchromatin (early replicated regions) to heterochromatin (late replicated regions) based on DNA replication-timing. Combining our Repli-Histo labeling with the single-nucleosome imaging, we have found that more euchromatic regions show larger local chromatin motion, whereas more heterochromatic regions have smaller motion. Interestingly, these properties seem to be maintained throughout interphase cell cycle. These findings also reveal that chromatin regions with earlier replication timing have greater chromatin motion. Since local chromatin motion can regulate the chromatin accessibility [6, 7], our study suggest that the genome-wide landscape of local chromatin motion in euchromatin and heterochromatin can regulate DNA replication timing.

[1] Maeshima, K., Iida, S., Shimazoe, M. A., Tamura, S. & Ide, S. Trends in Cell Biology 34, 7-17 (2024)
[2] Nozaki, T. et al. Science Advances 9, eadf1488 (2023)
[3] Miron, E. et al. Science Advances 6, eaba8811 (2020)
[4] Ide, S., Tamura, S. & Maeshima, K. BioEssays 44, 2200043 (2022)
[5] Iida, S. et al. Science advances 8, eabn5626 (2022)
[6] Hihara, S. et al. Cell Reports 2, 1645–1656 (2012)
[7] Maeshima, K. et al. Journal of Physics: Condensed Matter 27, 064116 (2015)
"

Speaker: Prof. Kazuhiro Maeshima (National Institute of Genetics)

20 Tubulin isotypes harness the mechano-sensitive lattice breathing for microtubule luminal accessibility

Microtubules are hollow cylindrical cytoskeletal polymers of laterally associated protofilaments that contain head-to-tail aligned ɑ/β-tubulin heterodimers. While the exposed exterior is within reach for proteins, the mechanism regulating the accessibility of the confined micrometer-long microtubule lumen for the long-observed luminal particles remains unknown. Here, we employed structural analysis, force microscopy, and in vitro reconstitution to reveal that tubulin family proteins (i.e., isotypes) regulate the microtubule accessibility for luminal enzymes via the force-sensitive reversible protofilament separation, referred to as lattice breathing. Computational simulation further demonstrates that the strength of inter-protofilament lateral interactions determines the degree of lattice breathing and luminal accessibility. Microtubule deformation surpassing the lattice stress threshold creates gaps between adjacent protofilaments, which enhance protein entry into the lumen. Together, our findings reveal the mechanical plasticity of non-covalent interactions between tubulin subunits, conferring force sensitivity to the microtubule lattice and rendering the energy barrier for protein to access the lumen.

Speaker: Prof. Jeff Shih-Chieh Ti (The University of Hong Kong)

21 Epigenetic Mechanisms in Cardiomyocyte Maturation

Differentiated cardiomyocytes (CMs) must undergo diverse morphological and functional changes during postnatal development. However, the initiation and coordination of these processes remain unclear. We reveal an integrated, time-ordered transcriptional network that begins with expression of genes for cell-cell connections and leads to a sequence of structural, cell cycle, functional, and metabolic transitions in mouse postnatal hearts. Depletion of histone H2B ubiquitin ligase RNF20 disrupts this gene network and CM polarization. Using ATAC-Seq analysis, we demonstrated that RNF20 contributes to chromatin accessibility. As such, RNF20 is likely to facilitate the binding of transcription factors at the promoters of genes involved in cell-cell connections and actin organization, crucial for CM polarization and functional integration. These results suggest that CM polarization is one of the earliest events during postnatal heart development, and our findings highlight a previously unrecognized role for RNF20 in regulating CM polarity and the transition of postnatal gene program.

Speaker: Prof. Cheng-fu Kao (Academia Sinica)

22 Numerical studies on the influence of mechanical perturbations due to actions of subnuclear molecules on chromatin organization and dynamics

Physical spacing of chromatin is critical in regulating bio-chemical and transcriptional abilities of genes, and proper functionality of the genomic content depends on the nonrandom organization of chromatin. Meanwhile, in a living cell, other subnuclear molecules, such as enzymes like polymerase and topoisomerase, act to facilitate cellular functions. Mechanical perturbation due to actions of such molecules may affect the chromatin organization and dynamics. In this talk, I would like to explain our numerical-simulation studies, based on polymer-physics concepts, where we focused on a type of actions of molecules that we call catch-and-release action and implemented in the way inspired by a class of molecules like topoisomerase-II. I will share with the participants the results of our simulations on how it affects chromatin organization and dynamics. The results clarified (i) that the mechanical perturbation of such actions can modulate the phase separation organizations of chromatin called heterochromatic and euchromatic regions [1], and (ii) that the mechanical perturbation enhances fluctuating dynamics of inclusions in chromatin through the newly-identified dynamic mode of chromatin remodeling [2]. --- References: [1] R Das, T Sakaue, GV Shivashankar, J Prost, T Hiraiwa (2022) "How enzymatic activity is involved in chromatin organization", eLife 11, e79901; [2] R Das, T Sakaue, GV Shivashankar, J Prost, T Hiraiwa (2024) “Chromatin Remodeling Due to Transient-Link-and-Pass Activity Enhances Subnuclear Dynamics", Physical Review Letters 132, 058401.

Speaker: Prof. Tetsuya Hiraiwa (Academia Sinica)

15:50 Coffee Break

Session VI

Convener: Dr Tai-De Li

23 Assembly at Aqueous Phase-separating Systems

In Nature, many dynamic processes take place in purely aqueous environments within relatively narrow range of environmental conditions, such as temperature. How such sophisticated processes across hierarchical lengthscales in the natural biological world remains fascinating to materials scientists. One of the key phenomena that drives the formation of a diverse range of structures is aqueous phase separation, which gives rise to multiple immiscible liquid phases as well as liquid-liquid interfaces. In this talk, I will discuss how we take advantage of both segregative and associative phase separation in all-aqueous systems to assemble membranes, materials structures, and fluid devices. I will discuss the unique dynamics and properties that are uniquely observed in these all-aqueous phase-separating systems. If time allows, I will also share the unique applications that could be inspired using these systems.

Speaker: Prof. Anderson Shum (The University of Hong Kong)

24 BAR protein SNX9 mediates actin assembly at saddle-shaped membranes

Biological membranes undergo dynamic remodeling that is essential for cellular homeostasis. BAR protein SNX9 is known to play a key role in actin-driven membrane remodeling, for example at saddle-shaped or tubular membrane necks connecting vesicular buds to the plasma membrane during endocytosis, and in the more complex membrane remodeling of membrane ruffling during macropinocytosis. SNX9 has a BAR domain that is thought to sense membrane curvature, a PX domain that is known to bind to various phosphoinositide (PI) lipids, and a SH3 domain that can trigger actin assembly by interacting with actin nucleation promoting factors (NPFs) such as N-WASP. However, it remains unclear whether and how SNX9 can sense membrane curvature and modulate actin assembly at curved membranes. In this study, we developed in vitro reconstitution assays to quantitatively characterize the dual functions of SNX9 in curvature sensing and actin assembly. We found that SNX9 can sense both tubular and saddle-shaped membranes. On tubular membranes, SNX9 has a comparable curvature sensing ability on PI(3,4)P2 and PI(4,5)P2 containing membranes. On saddle-shaped membrane necks, SNX9 has a higher enrichment at the necks with a radius of ~200 nm than at necks with ~150 nm and ~300 nm. Furthermore, we showed that SNX9 at membrane necks promotes the assembly of branched actin networks by enriching pVCA, a truncated NPF. Taken together, our results provide a comprehensive framework for SNX9-mediated actin assembly at curved membranes.

Speaker: Feng-ching Tsai (Curie Institute)

25 Through the Computational Lens: Exploring Abeta42 Monomer Diffusion on Diverse Fibril Structures

This study delves into the molecular dynamics that underpin critical biological processes in neurodegeneration. We use molecular dynamics simulations to investigate the interactions of Abeta42 monomers with fibrillar surfaces, a pivotal factor in Alzheimer's disease progression. Employing coarse-grained simulations, we focus on the diffusion behaviors of freely diffusing Abeta42 monomers across various fibril surfaces, considering their structural orientations—parallel and perpendicular. Our results reveal significant correlations between the monomers' diffusion coefficients and their orientations on these surfaces. Notably, differences in diffusion coefficients between N-terminal and C-terminal surfaces highlight the impact of surface roughness on monomer dynamics. The computational study offers crucial insights into molecular interactions that could inform future therapeutic strategies and deepen our understanding of neurodegeneration.

Speaker: Prof. Min-yeh Tsai

26 Membrane curvature induces integrin activation and mechanotransduction

Membrane curvature in the range of tens to hundreds of nanometers is involved in many essential cellular processes. Membrane curvatures in living cells are often below optical resolution and are highly dynamic, making it a technical challenge to explore curvature-initiated signaling events. We use nanofabrication to engineer vertical nanostructures to precisely manipulate the location, degree, and sign (positive or negative) of the interface curvature in live cells. We found that these membrane curvatures drastically affect intracellular signaling on the plasma membrane. Very recently, we found that membrane curvature promotes the formation of a new type of integrin ɑVβ5-mediated cell adhesions – curved adhesions. Curved adhesions are molecularly distinct from focal adhesions and clathrin lattices and are prevalent in soft fiber matrices in 3D. The findings illustrate the molecular basis for the strong molecular connection between membrane topography and intracellular signaling. It also opens up new therapeutic potentials for integrin inhibition.

Speaker: Prof. Bianxiao Cui (Stanford University)

27 Characterization of Megadalton Maldi ions with linear ion trap mass spectrometer

Speaker: Prof. Wen Ping Peng (NDHU)

19:00 Banquet - Capriccio 1F 饗渴望

Sunday, 1 September

Session VII

Convener: Wei-hsiang Lin

28 One-dimensional complex cell motility patterns induced by mechanosensitive adhesion complexes

The complex one-dimensional crawling moving patterns of a cell on a substrate are studied in this theoretical study. A simple model of cell motility, which assumes that the cell-substrate adhesion sites are localized at the cell ends, and the cell crawling dynamics are controlled by the evolution of the myosin density and the number of adhesion complexes at the cell ends, is discussed first. This model predicts that due to the coupling between the first moment of myosin density distribution and the asymmetry of the distribution of mechanosensitive adhesion complexes, a moving cell with weakly mechanosensitive adhesion complexes tends to move at constant velocity. As the mechanosensitivity of the adhesion complexes increases, a cell with sufficiently strong myosin contractile or high actin polymerization rate can exhibit stick-slip motion. Finally, a cell with highly mechanosensitive adhesion complexes exhibits periodic back-and-forth migration. The numerical solutions of an active gel model, which does not assume the localized distribution of adhesion complexes, show qualitative the same cell moving patterns. These results suggest that, in general, complex cell crawling behaviors could result from the interplay between the distribution of contractile force and mechanosensitive adhesion complexes.

Speaker: Prof. Hsuan-yi Chen (NCU)

29 How do active particles diffuse in polymer networks: from simulations to theory

The diffusion of tracer particles within a polymer environment is a promising topic connected with numerous biological and industrial applications, including intracellular macromolecule transport and nanoparticle diffusion. Despite extensive studies, the study of self-propelled particles within a polymer network has received attention recently and poorly understood. Here we study the nonequilibrium diffusion of active tracers navigating through a polymer network. It is shown that active tracers escape the confined geometry with their self-propulsion activity, performing activity-induced hopping diffusion distinguished from that from thermal energy. We investigate how the active hopping diffusion is characterized by physical conditions such as the mesh-to-particle size ratio, bending stiffness of a meshwork, and the Peclet number. We provide a first-passage time theory of active escaping phenomena to explain the observed trapped times of active tracers within a meshwork. Finally, we extend our analysis to randomly cross-linked polymer networks. Through quantitative investigation, we elucidate how heterogeneous non-Gaussian active diffusion emerges in such random polymer networks, shedding light on the complex interplay between polymer structure and active particle dynamics.

Speaker: Prof. Jae-Hyung Jeon (POSTECH)

30 Contributed talk

Speaker: Marie Cutiogco

31 The Interplay of Carotenoids and Reactive Oxygen Species in a Regenerating invertebrate

In this work, we address the participation of primary and secondary “Carotenoids” in the life activity of the regenerating anterior region of A. viride. A. viride is tasked with building entire body segments out of their single starting cell at their amputated region and undergoing epimorphic regeneration, therefore, these annelids are the most suitable for the study of regeneration. In regenerative organisms, regeneration arises with the help of repatterning co-existing tissues after a wound or trauma has occurred. Understanding these mechanisms is crucial as critical metabolic functions are involved during the process of regeneration. A time-dependent study with Resonance Raman spectroscopy at 532 nm wavelength excitation has been acquired from the regenerated site of freshwater A. viride. The Raman spectra at different hours post-amputation (hpa) of A. viride were recorded to elucidate the molecular composition in the regenerating newly formed stem cells. We evaluated the interplay of reactive oxygen species and carotenoids and their vital role in the anterior regeneration of A. viride. In vivo intracellular imaging; of blastema bud was made possible by applying Two-Photon Fluorescence Lifetime Imaging in combination with the phasor analysis. These findings indicate that the Raman signature of carotenoids can be used to detect the process of newly derived stem cells in the study of regeneration.

Speaker: Prof. Chia-liang Cheng (NDHU)

10:20 Coffee break & Take group photo

Session VIII

Convener: Yu-chiun Wang

32 Dynamics of densifying cell monolayers: turbulence enhanced by cancer cell aggregation, void closure, and two-stage percolating transitions

"Dynamics of densifying cell monolayers: turbulence enhanced by cancer cell aggregation, void closure, and two-stage percolating transitions

Yi-Teng Hsiao, Hsiang-Ying Chen, Jun-Yu Liu, Yuan-Xuan Zhang, and Lin I
Department of Physics, National Central University, Jhongli, Taiwan 32001

The cell system is an extended active system exhibiting heterogeneous structure and motion over a wide range of scales, which are important in many biological processes such as embryogenesis, tumorigenesis, and cancer metastasis. Dynamically, the interplay of mutual coupling and self-propelling leads to cooperative motions in the forms of chain-type collective migration, multiscale swirls, and turbulence, etc., which provide feedbacks to alter the subsequent structure and motion. In this talk, I will briefly review our past experimental studies on the spatiotemporal evolutions of structure and motion in densifying cell monolayers through cell proliferation. Examples include the enhanced cancer cell turbulence and endothelial motions through cancer cell aggregation in densifying confluent cancer/endothelia mixtures [1] , the spontaneous formation and closure of multiscale voids without purse-string contraction in densifying monolayers of anisotropic and isotropic cell [2] , and the two-stage structural and slowing down percolation transitions in the densifying cancer cell monolayers [3].

[1] Hsiang-Ying Chen, Yi-Teng Hsiao, Shu-Chen Liu, Tien Hsu, Wei-Yen Woon, and Lin I, , Phys. Rev. Letts, 121, 018101 (2018).
[2] Yun-Xuan Zhang, Chun-Yu Liu, Hsiang Ying Chen, and Lin I,, European Physical Journal E, 45, 89 (2022)
[3] Chun-Yu Liu, Yun-Xuan Zhang, and Lin I, Phys. Rev. Letts. 129, 148102 (2022).

Speaker: Prof. Lin I (NCU)

33 Collective dynamics of spindle-shaped cells on defect topography

Cell collective motion underlies many biological processes such as embryogenesis, morphogenesis, and cancer invasion. Cells can organize into diverse patterns across various spatiotemporal scales through the interplay of self-propulsion and mutual coupling. Topological defects, where the orientational order is undefined, are reported to govern many biological functions. In particular, integer defects are found to coincide with the presence of heads and feet in regenerating Hydra. However, past studies have mainly focused on the impact of half defects on cell dynamics and to a lesser extent on integer defects. In this work, we experimentally address this question by seeding undifferentiated myoblasts on a vortex microstructure. It is found that myoblasts initially migrate along the defect structure due to contact guidance at confluency. With increasing time, cells spontaneously extrude near the defect center, which initiates inward radial flows toward the center across the monolayer, leading to layering behaviors. At the defect core, cells gradually form a 3D cellular mound composed of stacks of ordered cell layers with different orientations.

Speaker: Hsiang-ying Chen (NCU)

34 Cells can adhere at fluid interfaces

"Conventionally, mammalian cells are cultured on stiff plastic or glass dishes. This is because cells have intrinsic contractility and exert mechanical forces to their substrates. It is critical for the cells to receive sufficient mechanical feedback, therefore stiff materials have been chosen for the cell culturing scaffolds, otherwise the cells undergo apoptosis, cellular suicide. On the other hand, our group is developing a new cell culture modality, where the interface of water and hydrophobic liquids, such as perfluorocarbons and ionic liquids, is used as a cell scaffold. By engineering the interfacial and bulk properties of the hydrophobic liquids, we can witness unique dynamic behaviors of cells and proteins at the interfaces.
Ref.) Adv. Mater. 32: 1905942 (2020); ibid, 36: 2310105 (2024); ibid, in press: 2403396."

Speaker: Jun Nakanishi (National Institute for Materials Science)

35 Spherical Microwells for High-throughput 3D Cell Culture and Mechanobiology Investigations

Speaker: Keng-hui Lin

36 Concluding remark. Poster award announcement

13:00 Lunch

Q & A Discuss talk