Bulletin of the American Physical Society
APS March Meeting 2023
Volume 68, Number 3
Las Vegas, Nevada (March 5-10)
Virtual (March 20-22); Time Zone: Pacific Time
Session Q11: Intracellular Transport and OrganizationFocus
|
Hide Abstracts |
Sponsoring Units: DBIO Chair: Ajay Gopinathan, University of California Merced Room: Room 203 |
Wednesday, March 8, 2023 3:00PM - 3:36PM |
Q11.00001: Super-resolution imaging of intracellular transport Invited Speaker: Melike Lakadamyali Intracellular transport takes place in the crowded, complex environment of a cell. To capture this complexity and understand how the microtubule cytoskeleton and motor proteins collectively regulate the transport of organelles like lysosomes, we have been employing a combination of live cell imaging and super-resolution microscopy. I will present our results on how microtubule post-translational modifications, in particular detyrosination, regulate the transport and fusion of lysosomes with autophagosomes. In addition, I will present our work that combines multi-color super-resolution microscopy, single molecule tracking and modelling to study how cells build up and maintain a small subpopulation of microtubules that are highly enriched in detyrosination and how detyrosination propagates along the microtubule lattice. |
Wednesday, March 8, 2023 3:36PM - 3:48PM |
Q11.00002: Effects of Network Morphology in Cargo Transport Nimisha Krishnan, Jennifer L Ross We are interested to know how the organization of the cytoskeleton filaments can affect the transport of cargo by motor proteins. Here, we investigate the effects of microtubule network complexity on kinesin mediated cargo transport. We quantify both the network characteristics and the trajectories of single kinesin and kinesin-loaded quantum dot cargos. The network complexity comes from different densities of microtubule intersections and random networks of filaments. These studies will help us understand how motors can intrinsically navigate complex networks of filaments in live cells. |
Wednesday, March 8, 2023 3:48PM - 4:00PM |
Q11.00003: Impact of the number of motors on cargo on the switching probability and pause duration at microtubule intersections. Maria Gamez, Niranjan Sarpangala, Nimisha Krishnan, Jennifer L Ross, Ajay Gopinathan Cells achieve proper distribution of cargo like vesicles and organelles using molecular motor-based transport on cytoskeletal networks. Rapid redistribution of cargoes, like during color change in melanophores, is believed to be achieved by varying parameters like the switching probability at cytoskeletal intersections. The switching probability depends on various parameters like the cargo size, whether the cargo is moving on an overpass or underpass, etc. It is unclear how other relevant parameters like the number of motors on cargo, and network properties like the intersection angle impact switching and pausing. To explore these features, we collected fluorescence microscope videos of Qdot on in-vitro networks of MTs for different numbers of motors on cargo. We then tracked cargo trajectories and analyzed pause duration, switching probability, velocity distribution, etc. To get a better estimate of switching probability, we extracted MT network data from the experimental images, ran coarse-grained simulations on the network, and compared experimental and simulated trajectories. Our work provides new insights into the importance of motor concentration, and network properties on intracellular transport. We also share a unique method of measuring switching probability from experimental trajectories. |
Wednesday, March 8, 2023 4:00PM - 4:12PM |
Q11.00004: Kinesin-1, -2 and -3 motors use family-specific mechanochemical strategies to effectively compete with dynein during bidirectional transport William O Hancock Bidirectional cargo transport in neurons requires competing activity of motors from the kinesin-1, -2 and -3 superfamilies against cytoplasmic dynein-1. Previous studies demonstrated that when kinesin-1 attached to dynein-dynactin-BicD2 (DDB) complex, the tethered motors move slowly with a slight plus-end bias, suggesting kinesin-1 overpowers DDB but DDB generates a substantial hindering load. Compared to kinesin-1, motors from the kinesin-2 and -3 families display a higher sensitivity to load in single-molecule assays and are thus predicted to be overpowered by dynein complexes in cargo transport. To test this prediction, we used a DNA scaffold to pair DDB with members of the kinesin-1, -2 and -3 families to recreate bidirectional transport in vitro, and tracked the motor pairs using two-channel TIRF microscopy. Unexpectedly, we find that when both kinesin and dynein are engaged and stepping on the microtubule, kinesin-1, -2, and -3 motors are able to effectively withstand hindering loads generated by DDB. Stochastic stepping simulations reveal that kinesin-2 and -3 motors compensate for their faster detachment rates under load with faster reattachment kinetics. The similar performance between the three kinesin transport families highlights how motor kinetics play critical roles in balancing forces between kinesin and dynein, and emphasizes the importance of motor regulation by cargo adaptors, regulatory proteins, and the microtubule track for tuning the speed and directionality of cargo transport in cells. |
Wednesday, March 8, 2023 4:12PM - 4:24PM |
Q11.00005: Optimising search times for motor driven cargo within cytoskeletal traps by tuning attachment and detachment kinetics Niranjan Sarpangala, Oleg B Kogan, Ajay Gopinathan Cytoskeletal networks in cells often have junctions where filament ends of the same polarity come together. This results in a basin of attraction or trap for cargoes carried by molecular motors along filaments. These are biologically significant. For example, in neurons, the accumulation of vesicles in such a trap promotes the formation of growth cones. In pancreatic beta cells, microtubule traps help regulate insulin secretion. Here we study the effectiveness of such traps using minimal one and two-dimensional models of cargo transport with a basin of attraction created by oppositely oriented microtubules. In our model, a cargo switches between advection on microtubules and one-dimensional diffusion in the cytoplasm with specific on and off rates. We then measure the time it takes for the cargo to reach absorbing boundaries or specific target locations in the cytoplasm. We find that when the trap or target is asymmetrically placed, the time to escape or find the target is minimized for certain optimum values of on and off rates. Interestingly this effect has analogies in the stochastic resetting processes. Our results give insights into how cells might exploit cytoskeletal traps to regulate intracellular transport processes. |
Wednesday, March 8, 2023 4:24PM - 4:36PM |
Q11.00006: The Differential Roles of Neurofilament Gene Expression and the Slowing of their Transport in the Radial Growth of Myelinated Axons Rawan M Nowier, Anika Friedman, Anthony Brown, Peter Jung The axon's conduction velocity, and thus neuronal function, is dependent on the axonal cross-sectional area. The growth of axonal caliber is therefore a crucial developmental process. In mammals, most of the radial growth occurs after birth and is driven by an accumulation of neurofilaments (NFs), which are cytoskeletal protein polymers that serve a space-filling role in the cytoskeleton. NFs are synthesized in the cell body and transported into axons along microtubule (MT) tracks by molecular motor proteins. The NF accumulation is driven by an increase in the influx of NFs from the cell body and a decrease in their transport velocity within the axon. However, the relative contributions of these two mechanisms are unknown. To address this, we developed a computational model that is constrained by published data on cytoskeletal morphometry and NF transport kinetics to simulate the radial growth of axons in the ventral root and sciatic nerve of rats. Results show that early in postnatal development the radial growth of axons is driven primarily by an increase in the influx of NFs, but the slowing of NF transport becomes dominant later, indicating a possible metabolic advantage. We show that the slowing of NF transport can be explained by changes in the accessibility of the NFs for their MT tracks, which may be an important regulator of NF transport. |
Wednesday, March 8, 2023 4:36PM - 4:48PM |
Q11.00007: Reaction diffusion model for understanding the drug-target interaction in single cell Subrata Dev Drug target interaction determines the drug efficacy. While drug-target binding/unbinding kinetics can inform the interaction, the kinetics have not been well characterized inside the cell. To better understand this, we study the binding/unbinding kinetics of benzimidazole-derivative DNA binding drugs (Hoechst 33342 dye) in E. coli cells. Simple reaction kinetic models cannot explain the slow binding/unbinding kinetics observed in our experiments as compared to the in vitro measurement. Hence, we develop a reaction diffusion model which incorporates the passive diffusion of Hoechst molecules through the membrane, active efflux, and intracellular diffusion of the Hoechst molecules. We test the model prediction by experimentally measuring Hoechst binding/unbinding to/from DNA. Our model can be a basis for understanding the effects of the intracellular diffusion and permeability of cell membrane of the cell on the in vivo drug target interaction. |
Wednesday, March 8, 2023 4:48PM - 5:00PM |
Q11.00008: Alien Proteomics Reveals Physical Rules for Diffusion through the Nuclear Pore Margarita Gordiychuk, Nishant Pappireddi, Thao Nguyen, Olenka Jain, Andreas Mayer, Marianne Bauer, Alex Johnson, Michael Stadlmeier, Ned S Wingreen, Martin Wühr, Yaojun Zhang The separation of proteins between the nucleus and cytoplasm is key to many eukaryotic processes. This partitioning results from regulated diffusion through nuclear pores, but it is still unclear how protein size and surface properties govern these diffusion rates. In our experiments, we injected "alien" bacterial lysate into the cytoplasm of frog oocytes. We quantified the nucleocytoplasmic partitioning for ~1000 bacterial proteins at various times after injection using mass spectrometry. The proteome-wide data suggests a polymer physics-based diffusion model for passage through the nuclear pore complex. In this model, the free-energy cost of a protein entering the pore depends on the excluded volume and the interactions between the protein's surface and nucleoporins. We further improved this model by taking into account the diffusion throughout the cytoplasm and nucleus. This study demonstrates the integration of biochemical measurements with physical insight to predict cellular biology on a systems level. |
Wednesday, March 8, 2023 5:00PM - 5:12PM |
Q11.00009: Translocation of a cone-shaped HIV-1 capsid through the nuclear pore complex Bhavya Mishra, Roya Zandi, Ajay Gopinathan In recent experiments, it has been observed that an intact cone-shaped HIV-1 capsid translocates through the nuclear pore complex (NPC) before capsid disassembly within the host cell nucleus. Capsid translocation through the NPC raises numerous interesting questions. How does the capsid, with size comparable to the NPC diameter, overcome the nuclear protein (nup) created barrier within the pore? Since the HIV-1 capsid has a cone shape with a narrow tip and a broad back, does translocation efficiency and time depend on the end that enters the NPC first? To answer these questions, we develop an analytical model for the transport of a cone-shaped HIV-1 capsid through the NPC, focusing on the energy barrier created by nups within the pore and the capsid-nup interactions that can reduce the barrier. We derive the free energy profile for the capsid as it translocates along the pore and use it to compute the capsid's translocation probability for reaching the trans end of the pore. Our results show that the capsid's translocation through NPC is favored for entry with the narrow end first. We also predict a minimal strength for the capsid-nup interaction below which translocation is arrested and above which the capsid's probability of reaching the nucleus increases, and the translocation process speeds up. Our results are consistent with experimental observations of the orientation of the capsid in the pore and mutation studies that inhibit translocation. |
Wednesday, March 8, 2023 5:12PM - 5:24PM |
Q11.00010: The endoplasmic reticulum as a transport and delivery network for calcium ions. Elena F Koslover, Cecile Crapart, Zubenelgenubi C Scott, Laura M Westrate, Edward Avezov The endoplasmic reticulum serves as an interconnected network of tunnels for the distribution and sorting of proteins, lipids, and ions throughout a cell. The structure of the network can be perturbed by a variety of morphogen mutations and drug treatments, and defects in the proteins responsible for ER shaping are associated with some human neurodegenerative diseases. Using a combination of mathematical modeling, numerical simulations, and experimental measurements we explore how the architecture of the ER modulates transport within it. In particular, we focus on the role of intra-luminal transport of buffer proteins and calcium ions in determining the rate and magnitude of local calcium release events from the ER. We show that mobile buffers of moderate binding strength and a well-connected network are predicted to enhance local calcium release. Using genetic perturbation of ER morphogens that lead to fragmentation or increased tubule length in the ER we demonstrate that these morphological changes indeed lead to reduced magnitude in observed localized calcium puffs. Our work highlights the importance of ER morphology in controlling its structure as an intracellular transport hub. |
Wednesday, March 8, 2023 5:24PM - 5:36PM |
Q11.00011: Nonequilibrium assembly, maintenance and control of a system of Golgi cisternae in the trafficking pathway Amit Kumar, Sudipto Muhuri, Madan Rao How do cellular organelles, such as the Golgi, self-assemble to a specific steady state size and maintain it in the face of a steady trafficking of vesicles? We address this nonequilibrium assembly using a Master equation approach that involves the mechanochemical cycle of active fission-fusion. This gives rise to nonlinear dynamical equations with feedback control for the cisternal masses. These dynamical equations exhibit a variety of phases, such as stable cisternae and limit cycles, that we identify with vesicular transport, cisternal progression and cisternal dissolution. We show that the homeostatic balance can be disrupted by sudden spurts of material influx; in this case, we propose control strategies that may be operative to restore the assembly to the vicinity of the homeostatic set point. |
Wednesday, March 8, 2023 5:36PM - 5:48PM |
Q11.00012: System-scale quantitative measurement recognizes scaling exponents between multiple organelle volumes Shixing Wang, Shankar Mukherji A fundamental question in cellular biophysics is how the multiple components of the cell are coordinately built to optimize physiological function. A powerful tool to infer the constraints that a given compartment places on other compartments is to examine how their physical volumes scale with each other: bulk process constraints tend to lead to isometric scaling between volumes, while transport limited relations yield sublinear scaling. However, these simple interpretations of scaling exponents are complicated by the constraint that the components as a whole must simultaneously share the volume of the cell, a constraint whose consequences have been virtually unexplored due to technological limitations to simultaneously imaging multiple compartments at a time. To map out the landscape of inferred constraints in the eukaryotic cell at systems-scale, we extracted volume scaling exponents between every pair of the 6 major metabolic organelles measured simultaneously in the budding yeast Saccharomyces cerevisiae as well as the volume of the cell and an estimate of the volume of the nucleocytoplasm. The exponents revealed a variety of relationships, ranging from 0 (independence) to 3/2 (area-volume relationship). Finally, by examining how these scaling relations change with both the size of the cell as well as their growth rates, we will present our initial work on using these scaling rules to constrain models of cellular resource allocation during cellular growth. |
Wednesday, March 8, 2023 5:48PM - 6:00PM |
Q11.00013: Interdependence in Organelle Biogenesis Kiandokht Panjtan Amiri, Shankar Mukherji Eukaryotic cells contain hundreds of subcellular structures that serve different functions to maintain cellular homeostasis. The main characteristic of Eukaryotic cells is their compartmentalization into membrane-bound organelles. While the function of individual organelles and their role in cellular homeostasis is well studied, less is known about the cell's coordinated control over their synthesis. In our recent discoveries we have shed light on the mechanisms by which cells regulate the size and abundance of individual membranous organelles. However, we know little about the autonomy or dependence of biogenesis amongst different types of organelles. Here we have characterized the systems-level patterns of interdependence in organelle biogenesis using Saccharomyces cerevisiae as a model system. We have engineered budding yeast cells to fluorescently label six of their membranous organelles simultaneously and imaged them using confocal hyperspectral microscopy. By perturbing genetic factors involved in the biogenesis of each individual organelle, we measured the response in the growth of other organelles. Our statistical analyses reveal correlations between the growth of different organelles that we will incorporate into our mathematical model of organelle biogenesis control as a step toward capturing the principles by which the cell allocates its finite resources during growth and homeostasis. |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700