Bulletin of the American Physical Society
APS March Meeting 2021
Volume 66, Number 1
Monday–Friday, March 15–19, 2021; Virtual; Time Zone: Central Daylight Time, USA
Session R13: Irreversible Dynamics, Aging and Death: From Cells to OrganismsFocus Live
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Sponsoring Units: DBIO DSOFT Chair: Srividya Iyer-Biswas, Purdue University; Christopher Kempes |
Thursday, March 18, 2021 8:00AM - 8:36AM Live |
R13.00001: How stochastic thermodynamics changes in systems with multiple interacting components Invited Speaker: David Wolpert Stochastic thermodynamics has resulted in profound new insights into the thermodynamic irreversibility of non-equilibrium processes at the scale of biological cells. These range from information-theoretic extensions of the second law, to fluctuation theorems governing the relative probabilities of amounts of entropy production (EP) in any particular sample of a non-equilibrium process, to thermodynamic uncertainty relations relating the expected EP of a process to the precisions of currents with it, to speed limits relating expected EP of the process to how fast the state space probability distribution changes. Almost all of this research has focused on systems with no internal structure, in the sense that they are not explicitly decomposed into a set of distinct, interacting subsystems. However, such internal structures are a crucial feature of very many systems of interest - especially in biology. Typically in systems with such structure the rate matrix of each subsystem i only depends on a proper subset of the remaining subsystems. Such dependency can be represented with a directed graph, connecting the subsystems. In this talk I summarize the many ways that the form of that directed graph modifies the standard results of stochastic thermodynamics. In particular, I show how the form of that graph: 1) specifies a strengthened form of the second law; 2) specifies "vector-valued" extensions of the fluctuation theorems, concerning the joint probability of the entropy productions of the subsystems; 3) specifies extensions of the thermodynamic uncertainty relations to relate entropy productions and current precisions among the subsystems; 4) specifies extensions of the thermodynamic speed limits, to involve the speeds of changes of the probability distributions of all of the subsystems as well as expected EP. |
Thursday, March 18, 2021 8:36AM - 8:48AM Live |
R13.00002: A minimal one-dimensional model of pattern formation in bacterial community phototaxis Ritwika Vallomparambath PanikkasserySu, Rosanna Man Wah Chau, Tristan Ursell, Devaki Bhaya, Kerwyn C Huang, Ajay Gopinathan Synechocystis sp. PCC6803 is a phototactic cyanobacterium that moves directionally in response to a light source. During phototaxis, these bacterial communities show emergent spatial organisation, resulting in the formation of finger-like projections at the propagating front. We propose a one-dimensional analytical model to predict the critical value of the phototactic bias force for instabilities to manifest as finger-like projections. We also predict the wavelengths of the fastest growing mode and the critical mode (above which the instabilities disappear). In addition, our model predicts the observed loss of instabilities in taxD1 mutants, which lack an important photoreceptor. We compare predictions from this minimal, analytically solvable one-dimensional model to results from a 2-dimensional computational model in terms of how the growth rate and the wavelength of the fastest growing mode vary as a function of phototactic bias, the secretion rate of mobility-enhancing slime by bacteria, and the initial bacterial concentration. We also validate our predictions using experimental data obtained from phototaxis assays of Synechocystis communities |
Thursday, March 18, 2021 8:48AM - 9:00AM Live |
R13.00003: Scale invariance of bacterial cell size fluctuations during starvation Takuro Shimaya, Reiko Okura, Yuichi Wakamoto, Kazumasa A. Takeuchi In stable environments, cell size fluctuations have been reported to show simple statistical properties. For instance, the cell size distribution of various species of eukaryotes is expressed by a common function, which is scaled by the mean body size of the species [1]. However, the typical body size is easily affected by environmental changes, e.g., the bacterial cell size drastically decreases in response to nutrient starvation. |
Thursday, March 18, 2021 9:00AM - 9:12AM Live |
R13.00004: Spatio-Temporal Supercontinuum Growth Spectroscopy of Rhodobacter Sphaeroides Mehmet Kilinc, Jacky Wan, Thomas E Kuhlman, Nathaniel Monroe Gabor, Richard Cogdell The primary steps of photosynthesis involve energy transport operating near the theoretical quantum limits in efficiency. These steps are the focus of intense research utilizing powerful laser spectroscopic tools. However, new measurements are needed to bridge the microscopic energy transport processes and the macroscopic cellular function with precise excitation control. Here, we present a novel method, called Spatio-Temporal Supercontinuum Growth Spectroscopy (STSGS), that combines broadband supercontinuum excitation and real-time laser probes of microbial growth in highly controlled environments. We demonstrate our data-intensive approach by measuring the growth of highly characterized and metabolically diverse bacteria, Rhodobacter sphaeroides, at each supercontinuum laser wavelength from 400 nm to 2300 nm. This method results in a high-resolution, spatial, temporal, and spectral characterization of microbial growth. Our highly parallel approach provides a novel, high throughput method to analyze cellular population growth under diverse illumination conditions from the visible to mid-infrared. Such a data-intensive technique allows us to unravel the complexities of photosynthesis with a comprehensive observation of the organisms’ macroscopic behavior. |
Thursday, March 18, 2021 9:12AM - 9:24AM Live |
R13.00005: Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms Gabi Steinbach, Cristian Crisan, Siu Lung Ng, Brian K. Hammer, Peter Yunker Bacteria often live in biofilms, crowded, surface-attached microbial consortia that typically feature a variety of species and strains. Social interactions between the different organisms govern the spatial organization of biofilms. These interactions can turn deadly, ultimately affecting biofilm composition. Bacteria have evolved deathly weapons that require killer cells to directly contact target cells, such as via the Type VI Secretion System (T6SS). The T6SS is hypothesized to be a highly potent weapon, capable of facilitating the invasion and defense of bacterial populations. However, we find that contact killing is self-limiting as dead cells accumulate. Time-lapse confocal microscopy of Vibrio cholerae strains that kill via the T6S shows that dead cell debris accumulates between competing strains, preventing physical contact and thus preventing killing. This renders contact killing V. cholerae incapable of invading or eliminating competitors on a community level. Instead, we find that contact killing can facilitate coexistence between nominally antagonistic strains. While a variety of defensive strategies against microbial warfare exist, the material consequences of cell death provide target cells with their first line of defense. |
Thursday, March 18, 2021 9:24AM - 9:36AM Live |
R13.00006: Age-related loss of gene-to-gene transcriptional coordination among single cells. Orr Levy, Guy Amit, Dana Vaknin, Tom Snir, Sol Efroni, Peter Castaldi, Yang-Yu Liu, Haim Cohen, Amir Bashan A long-standing model holds that stochastic aberrations of transcriptional regulation play a key role in the process of ageing. While transcriptional dysregulation is observed in many cell types in the form of increased cell-to-cell variability, its generality to all cell types remains doubted. Here, we propose a new approach for analysing transcriptional regulation in single-cell RNA sequencing data by focusing on the global coordination between the genes rather than the variability of individual genes or correlations between pairs of genes. Consistently, across very different organisms and cell types, we find a decrease in the gene-to-gene transcriptional coordination in ageing cells. In addition, we find that loss of gene-to-gene transcriptional coordination is associated with high mutational load of a specific, age-related signature and with radiation-induced DNA damage. These observations suggest a general, potentially universal, stochastic attribute of transcriptional dysregulation in ageing. |
Thursday, March 18, 2021 9:36AM - 9:48AM Live |
R13.00007: Who Is to Thank for the Rhythms of My Tail? – A Mathematical Study of Circadian Rhythmicity in Poly(A) Tail Length Xiangyu Yao, Shihoko Kojima, Jing Chen The circadian rhythm in our body ultimately derives from rhythmic gene expression in individual cells. As the core clock circuit includes several transcription factors with broad targets in the genome, studies of circadian gene expression have long focused on rhythmic transcriptional control. However, recent studies suggest the importance of rhythmic post-transcriptional controls. A notable one of such rhythmic controls occurs to the poly(A) tail of mRNAs, a nearly universal feature of mRNAs which controls mRNA stability and translation. In many mRNAs the length of poly(A) tail oscillate over the day. Here we constructed a parsimonious model to investigate rhythmic control of poly(A) tail length as a coupled process to rhythmic mRNA expression. A global parameter sensitivity analysis on the model reveals that the rhythmicity of poly(A) tail length and mRNA translatability most strongly depend on the rhythmicity of deadenylation, the process that shortens the poly(A) tail. This impact is so strong that deadenylation can potentially synchronize the rhythms of target gene expression. Our findings highlight the critical role of rhythmic deadenylation in regulating poly(A) rhythms and circadian gene expression. |
Thursday, March 18, 2021 9:48AM - 10:24AM On Demand |
R13.00008: Development of phenotypic heterogeneity in different environmental niches in Mycobacterium tuberculosis Invited Speaker: Bree Aldridge Mycobacterium tuberculosis (Mtb) infects billions of people worldwide and kills more than 1.5 million per year. TB remains a major cause of death worldwide. TB is difficult to treat because the bacteria occupy lesions that create pockets of persisters. The variable course of disease and treatment response suggests that functionally heterogeneous populations of mycobacteria respond differently to stress. We describe how mycobacteria deterministically generate diversity in their growth characteristics through asymmetric growth and division. Coupled with a unique mechanism of cell size regulation utilizing parallel adders from initiation, this asymmetry creates subpopulations of cells with distinct cell sizes that are differentially susceptible to antibiotics. This innate heterogeneity gives rise to subpopulations of cells that are differentially susceptible to clinically relevant classes of antibiotics. We find that Mtb alter their cell size distributions under different environmental stressors that are encountered in the host in a strain-specific manner. We combine quantitative live-cell imaging, fixed-cell imaging, and mathematical modeling to understand how Mtb cell growth and replication processes are mediated in various environmental conditions encountered in host tissues and how these characteristics determine antibiotic susceptibility. |
Thursday, March 18, 2021 10:24AM - 10:36AM On Demand |
R13.00009: Biophysical principles of the Chlamydomonas reinhardtii CO2-concentrating mechanism Chenyi Fei, Alexandra Wilson, Niall Mangan, Martin C Jonikas, Ned S Wingreen Photosynthesis allows human life on Earth: it harvests light energy to fix atmospheric CO2 which produces food and fuels. Its efficiency is limited by the catalytic properties of the CO2-fixing enzyme Rubisco – which works at only 10% of its maximum rate under air-level CO2. The alga Chlamydomonas reinhardtii operates a CO2-concentrating mechanism (CCM) that locally elevates the CO2 level around Rubisco in a phase-separated organelle called the pyrenoid, thus enhancing photosynthetic performance. To better understand how this CCM works, we developed a multi-compartment reaction-diffusion model. We find that diffusion barriers preventing CO2 efflux from the pyrenoid are key to a functional and energetically efficient CCM. Our model reveals two distinct CCM strategies: (1) passive uptake of CO2 which is then trapped in the chloroplast as HCO3-; (2) active pumping in of HCO3-. Interestingly, our model predicts that feasible CCM strategies vary with environmental CO2 levels, which sheds light on a long confounding growth phenotype. Finally, our model provides insights into the localization of key CCM components, and can guide engineering a CCM into higher plants. |
Thursday, March 18, 2021 10:36AM - 10:48AM Live |
R13.00010: E. coli Bacteria near "Black Hole" Trung Phan, Robert Austin, Buming Gou, Paul M Chaikin, Stefano Martiniani In microfluidic environment, we create hydrodynamic horizon from which no E. coli bacteria can escape ("black hole") to study the collective behaviors of those organisms under the influence of such background, probing for their strategy to avoid potentially harmful region where part of the population disappears. |
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