Cell-level Responses Research Articles

A multiscale finite element model of left ventricular mechanics incorporating baroreflex regulation

Cardiovascular function is regulated by a short-term hemodynamic baroreflex loop, which tries to maintain arterial pressure at a normal level. In this study, we present a new multiscale model of the cardiovascular system named MyoFE. This framework integrates a mechanistic model of contraction at the myosin level into a finite-element-based model of the left ventricle pumping blood through the systemic circulation. The model is coupled with a closed-loop feedback control of arterial pressure inspired by a baroreflex algorithm previously published by our team. The reflex loop mimics the afferent neuron pathway via a normalized signal derived from arterial pressure. The efferent pathway is represented by a kinetic model that simulates the net result of neural processing in the medulla and cell-level responses to autonomic drive. The baroreflex control algorithm modulates parameters such as heart rate and vascular tone of vessels in the lumped-parameter model of systemic circulation. In addition, it spatially modulates intracellular Ca2+ dynamics and molecular-level function of both the thick and the thin myofilaments in the left ventricle. Our study demonstrates that the baroreflex algorithm can maintain arterial pressure in the presence of perturbations such as acute cases of altered aortic resistance, mitral regurgitation, and myocardial infarction. The capabilities of this new multiscale model will be utilized in future research related to computational investigations of growth and remodeling.

A multiscale model of the cardiovascular system that regulates arterial pressure viaclosed loopbaroreflex control of chronotropism, cell-level contractility, and vascular tone.

Multiscale models of the cardiovascular system can provide new insights into physiological and pathological processes. PyMyoVent is a computer model that bridges from molecular- to organ-level function and which simulates a left ventricle pumping blood through the systemic circulation. Initial work with PyMyoVent focused on the end-systolic pressure volume relationship and ranked potential therapeutic strategies by their impact on contractility. This manuscript extends the PyMyoVent framework by adding closed-loop feedback control of arterial pressure. The control algorithm mimics important features of the physiological baroreflex and was developed as part of a long-term program that focuses on growth and biological remodeling. Inspired by the underlying biology, the reflex algorithm uses an afferent signal derived from arterial pressure to drive a kinetic model that mimics the net result of neural processing in the medulla and cell-level responses to autonomic drive. The kinetic model outputs control signals that are constrained between limits that represent maximum parasympathetic and maximum sympathetic drive and which modulate heart rate, intracellular Ca2+ dynamics, the molecular-level function of both the thick and the thin myofilaments, and vascular tone. Simulations show that the algorithm can regulate mean arterial pressure at user-defined setpoints as well as maintaining arterial pressure when challenged by changes in blood volume and/or valve resistance. The reflex also regulates arterial pressure when cell-level contractility is modulated to mimic the idealized impact of myotropes. These capabilities will be important for future work that uses computer modeling to investigate clinical conditions and treatments.

CellDrift: inferring perturbation responses in temporally sampled single-cell data.

Cells and tissues respond to perturbations in multiple ways that can be sensitively reflected in the alterations of gene expression. Current approaches to finding and quantifying the effects of perturbations on cell-level responses over time disregard the temporal consistency of identifiable gene programs. To leverage the occurrence of these patterns for perturbation analyses, we developed CellDrift (https://github.com/KANG-BIOINFO/CellDrift), a generalized linear model-based functional data analysis method that is capable of identifying covarying temporal patterns of various cell types in response to perturbations. As compared to several other approaches, CellDrift demonstrated superior performance in the identification of temporally varied perturbation patterns and the ability to impute missing time points. We applied CellDrift to multiple longitudinal datasets, including COVID-19 disease progression and gastrointestinal tract development, and demonstrated its ability to identify specific gene programs associated with sequential biological processes, trajectories and outcomes.

Fibroblasts as an experimental model system for the study of comparative physiology.

Mechanistic evaluations of processes that underlie organism-level physiology often require reductionist approaches. Dermal fibroblasts offer one such approach. These cells are easily obtained from minimally invasive skin biopsy, making them appropriate for the study of protected and/or logistically challenging species. Cell culture approaches permit extensive and fine-scale sampling regimes as well as gene manipulation techniques that are not feasible in vivo. Fibroblast isolation and culture protocols are outlined here for primary cells, and the benefits and drawbacks of immortalization are discussed. We show examples of physiological metrics that can be used to characterize primary cells (oxygen consumption, translation, proliferation) and readouts that can be informative in understanding cell-level responses to environmental stress (lactate production, heat shock protein induction). Importantly, fibroblasts may display fidelity to whole animal physiological phenotypes, facilitating their study. Fibroblasts from Antarctic Weddell seals show greater resilience to low temperatures and hypoxia exposure than fibroblasts from humans or rats. Fibroblast oxygen consumption rates are not affected by temperature stress in the heat-tolerant camel, whereas similar temperature exposures depress mitochondrial metabolism in fibroblasts from rhinoceros. Finally, dermal fibroblasts from a hibernator, the meadow jumping mouse, better resist experimental cooling than a fibroblast line from the laboratory mouse, with the hibernator demonstrating a greater maintenance of homeostatic processes such as protein translation. These results exemplify the parallels that can be drawn between fibroblast physiology and expectations in vivo, and provide evidence for the power of fibroblasts as a model system to understand comparative physiology and biomedicine.

Systemic and single cell level responses to 1 nm size biomaterials demonstrate distinct biological effects revealed by multi-omics atlas

Although ultra-small nanoclusters (USNCs, < 2 nm) have immense application capabilities in biomedicine, the investigation on body-wide organ responses towards USNCs is scant. Here, applying a novel strategy of single-cell mass cytometry combined with Nano Genome Atlas of multi-tissues, we systematically evaluate the interactions between the host and calcium phosphate (CaP) USNCs at the organism level. Combining single-cell mass cytometry, and magnetic luminex assay results, we identify dynamic immune responses to CaP USNCs at the single cell resolution. The innate immune is initially activated and followed by adaptive immune activation, as evidenced by dynamic immune cells proportions. Furthermore, using Nano Genome Atlas of multi-tissues, we uncover CaP USNCs induce stronger activation of the immune responses in the cartilage and subchondral bone among the five local tissues while promote metabolic activities in the liver and kidney. Moreover, based on the immunological response profiles, histological evaluation of major organs and local tissue, and a body-wide transcriptomics, we demonstrate that CaP USNCs are not more hazardous than the Food and Drug Administration-approved CaP nanoparticles after 14 days of injection. Our findings provide valuable information on the future clinical applications of USNCs and introduce an innovative strategy to decipher the whole body response to implants.

Drought impacts on tree phloem: from cell-level responses to ecological significance.

On-going climate change is increasing the risk of drought stress across large areas worldwide. Such drought events decrease ecosystem productivity and have been increasingly linked to tree mortality. Understanding how trees respond to water shortage is key to predicting the future of ecosystem functions. Phloem is at the core of the tree functions, moving resources such as non-structural carbohydrates, nutrients, and defence and information molecules across the whole plant. Phloem function and ability to transport resources is tightly controlled by the balance of carbon and water fluxes within the tree. As such, drought is expected to impact phloem function by decreasing the amount of available water and new photoassimilates. Yet, the effect of drought on the phloem has received surprisingly little attention in the last decades. Here we review existing knowledge on drought impacts on phloem transport from loading and unloading processes at cellular level to possible effects on long-distance transport and consequences to ecosystems via ecophysiological feedbacks. We also point to new research frontiers that need to be explored to improve our understanding of phloem function under drought. In particular, we show how phloem transport is affected differently by increasing drought intensity, from no response to a slowdown, and explore how severe drought might actually disrupt the phloem transport enough to threaten tree survival. Because transport of resources affects other organisms interacting with the tree, we also review the ecological consequences of phloem response to drought and especially predatory, mutualistic and competitive relations. Finally, as phloem is the main path for carbon from sources to sink, we show how drought can affect biogeochemical cycles through changes in phloem transport. Overall, existing knowledge is consistent with the hypotheses that phloem response to drought matters for understanding tree and ecosystem function. However, future research on a large range of species and ecosystems is urgently needed to gain a comprehensive understanding of the question.

Multiscale computational model of Achilles tendon wound healing: Untangling the effects of repair and loading.

Mechanical stimulation of the healing tendon is thought to regulate scar anisotropy and strength and is relatively easy to modulate through physical therapy. However, in vivo studies of various loading protocols in animal models have produced mixed results. To integrate and better understand the available data, we developed a multiscale model of rat Achilles tendon healing that incorporates the effect of changes in the mechanical environment on fibroblast behavior, collagen deposition, and scar formation. We modified an OpenSim model of the rat right hindlimb to estimate physiologic strains in the lateral/medial gastrocnemius and soleus musculo-tendon units during loading and unloading conditions. We used the tendon strains as inputs to a thermodynamic model of stress fiber dynamics that predicts fibroblast alignment, and to determine local collagen synthesis rates according to a response curve derived from in vitro studies. We then used an agent-based model (ABM) of scar formation to integrate these cell-level responses and predict tissue-level collagen alignment and content. We compared our model predictions to experimental data from ten different studies. We found that a single set of cellular response curves can explain features of observed tendon healing across a wide array of reported experiments in rats–including the paradoxical finding that repairing transected tendon reverses the effect of loading on alignment–without fitting model parameters to any data from those experiments. The key to these successful predictions was simulating the specific loading and surgical protocols to predict tissue-level strains, which then guided cellular behaviors according to response curves based on in vitro experiments. Our model results provide a potential explanation for the highly variable responses to mechanical loading reported in the tendon healing literature and may be useful in guiding the design of future experiments and interventions.

Numerical Analysis of Electrochemical Engineering Models for Lithium Sulfur Batteries

As lithium ion batteries are approaching their performance limits, research on alternative chemistries that can meet the energy demands for electric vehicles and grid applications has increased. Lithium sulfur is one chemistry with a high theoretical specific capacity of 2500 Wh/kg and practical values of 500-600 Wh/kg1. Sulfur is also cheap, making lithium sulfur batteries very attractive. The current issues with these batteries include capacity fade, self-discharge, and high electrical resistance, which mostly stem from the shuttle effect of the polysulfide ions2. During discharge, the solid sulfur at the cathode is dissolved into polysulfide ions; these ions are soluble in the electrolyte and can diffuse to the anode and react with the lithium metal; they form a film on the anode of Li2S, which results in irreversible loss of capacity and active material1. Physics-based battery models can provide control and insight into better battery performance and design by modeling the internal states of a battery. The challenging aspects of modeling lithium sulfur batteries are due to the complicated reaction network, the number of species involved, and the multiple phase changes, from solid sulfur dissolution to Li2S precipitation. Because of this, lithium sulfur battery models result in complex equations and require a stiff solver. Several groups have modeled different aspects of lithium sulfur cells. Mikhaylik and associates3 modeled lithium sulfur system through a zeroth order model. The first one-dimensional model that incorporates the electrochemical and chemical interactions of lithium sulfur batteries was developed by Kumaresan and associates4. Their model includes the kinetics of the electrochemical reactions and the precipitation and dissolution reactions and ionic transport described by the Nernst-Planck equation coupled with electroneutrality. For low currents, the qualitative nature of the lithium sulfur discharge curve is adequately captured. Ghaznavi and Chen performed an extensive sensitivity analysis of the Kumaresan model, including effects of current, reaction kinetics, sulfur loading, and cathode conductivity, which highlighted opportunities for further model development5,6,7. Other groups have built on the original model through focusing on precipitation, charging, or simpler models with fewer fitted parameters8-13. In this work, we propose to do a comparison study of different numerical methods for solving the complicated and stiff equations that arise from the lithium sulfur chemistry (Kumaresan model). The study includes an attempt to reduce the simulation time to enable real-time control and integration into Battery Management Systems (BMS). To this end, the performance of multiple model reformulation techniques and solver algorithms will be evaluated in terms of accuracy, computational performance, and their ability to predict cell-level responses across practical operating conditions. Acknowledgments The authors are thankful for the financial support from the Battery 500 Consortium and the Clean Energy Institute (CEI) at the University of Washington. References X. Zhang, et al., Mater. Sci. Eng. R Reports, 121, 1 (2017).Z. Liu, A. Mistry, and P. P. Mukherjee, J. Electrochem. Energy Convers. Storage, 15, 10802 (2017).Y. V. Mikhaylik and J. R. Akridge, J. Electrochem. Soc., 151, A1969 (2004).K. Kumaresan, Y. Mikhaylik and R. E. White, J. Electrochem. Soc., 155, A576 (2008).M. Ghaznavi and P. Chen, J. Power Sources, 257, 402 (2014).M. Ghaznavi and P. Chen, J. Power Sources, 257, 394 (2014).M. Ghaznavi and P. Chen, Electrochim. Acta, 137, 575 (2014).K. Yoo, M.-K. Song, E. J. Cairns, and P. Dutta, Electrochim. Acta, 213, 174 (2016).Y. X. Ren, T. S. Zhao, M. Liu, P. Tan, and Y. K. Zeng, J. Power Sources, 336, 115 (2016).T. Zhang, M. Marinescu, L. O’Neill, M. Wild, and G. Offer, Phys. Chem. Chem. Phys., 17, 22581 (2015).M. Marinescu, T. Zhang, and G. J. Offer, Phys. Chem. Chem. Phys., 18, 584 (2016).D. N. Fronczek, and W. G. Bessler, J. Power Sources, 244, 183 (2013).A. F. Hofmann, D. N. Fronczek, and W. G. Bessler, J. Power Sources, 259, 300 (2014).

Measuring cell cycle-dependent DNA damage responses and p53 regulation on a cell-by-cell basis from image analysis

ABSTRACTDNA damage in cells occurs from both endogenous and exogenous sources, and failure to repair such damage is associated with the emergence of different cancers, neurological disorders and aging. DNA damage responses (DDR) in cells are closely associated with the cell cycle. While most of our knowledge of DDR comes from bulk biochemistry, such methods require cells to be arrested at specific stages for cell cycle studies, potentially altering measured responses; nor is cell to cell variability in DDR or direct cell-level correlation of two response metrics measured in such methods. To overcome these limitations we developed a microscopy-based assay for determining cell cycle stages over large cell numbers. This method can be used to study cell-cycle-dependent DDR in cultured cells without the need for cell synchronization. Upon DNA damage γH2A.X induction was correlated to nuclear enrichment of p53 on a cell-by-cell basis and in a cell cycle dependent manner. Imaging-based cell cycle staging was combined with single molecule P53 mRNA detection and immunofluorescence for p53 protein in the very same cells to reveal an intriguing repression of P53 transcript numbers due to reduced transcription across different stages of the cell cycle during DNA damage. Our study hints at an unexplored mechanism for p53 regulation and underscores the importance of measuring single cell level responses to DNA damage.

Optogenetic control of RhoA reveals zyxin-mediated elasticity of stress fibres

Cytoskeletal mechanics regulates cell morphodynamics and many physiological processes. While contractility is known to be largely RhoA-dependent, the process by which localized biochemical signals are translated into cell-level responses is poorly understood. Here we combine optogenetic control of RhoA, live-cell imaging and traction force microscopy to investigate the dynamics of actomyosin-based force generation. Local activation of RhoA not only stimulates local recruitment of actin and myosin but also increased traction forces that rapidly propagate across the cell via stress fibres and drive increased actin flow. Surprisingly, this flow reverses direction when local RhoA activation stops. We identify zyxin as a regulator of stress fibre mechanics, as stress fibres are fluid-like without flow reversal in its absence. Using a physical model, we demonstrate that stress fibres behave elastic-like, even at timescales exceeding turnover of constituent proteins. Such molecular control of actin mechanics likely plays critical roles in regulating morphodynamic events.

Screening for drought tolerance of maize hybrids by multi-scale analysis of root and shoot traits at the seedling stage.

We studied the drought response of eight commercial hybrid maize lines with contrasting drought sensitivity together with the reference inbred line B73 using a non-invasive platform for root and shoot phenotyping and a kinematics approach to quantify cell level responses in the leaf. Drought treatments strongly reduced leaf growth parameters including projected leaf area, elongation rate, final length and width of the fourth and fifth leaf. Physiological measurements including water use efficiency, chlorophyll fluorescence and photosynthesis were also significantly affected. By performing a kinematic analysis, we show that leaf growth reduction in response to drought is mainly due to a decrease in cell division rate, whereas a marked reduction in cell expansion rate is compensated by increased duration of cell expansion. Detailed analysis of root growth in rhizotrons under drought conditions revealed a strong reduction in total root length as well as rooting depth and width. This was reflected by corresponding decreases in fresh and dry weight of the root system. We show that phenotypic differences between lines differing in geographic origin (African vs. European) and in drought tolerance under field conditions can already be identified at the seedling stage by measurements of total root length and shoot dry weight of the plants. Moreover, we propose a list of candidate traits that could potentially serve as traits for future screening strategies.

Moderate strength (0.23–0.28 T) static magnetic fields (SMF) modulate signaling and differentiation in human embryonic cells

BackgroundCompelling evidence exists that magnetic fields modulate living systems. To date, however, rigorous studies have focused on identifying the molecular-level biosensor (e.g., radical ion pairs or membranes) or on the behavior of whole animals leaving a gap in understanding how molecular effects are translated into tissue-wide and organism-level responses. This study begins to bridge this gulf by investigating static magnetic fields (SMF) through global mRNA profiling in human embryonic cells coupled with software analysis to identify the affected signaling pathways.ResultsSoftware analysis of gene expression in cells exposed to 0.23–0.28 T SMF showed that nine signaling networks responded to SMF; of these, detailed biochemical validation was performed for the network linked to the inflammatory cytokine IL-6. We found the short-term (<24 h) activation of IL-6 involved the coordinate up-regulation of toll-like receptor-4 (TLR4) with complementary changes to NEU3 and ST3GAL5 that reduced ganglioside GM3 in a manner that augmented the activation of TLR4 and IL-6. Loss of GM3 also provided a plausible mechanism for the attenuation of cellular responses to SMF that occurred over longer exposure periods. Finally, SMF-mediated responses were manifest at the cellular level as morphological changes and biochemical markers indicative of pre-oligodendrocyte differentiation.ConclusionThis study provides a framework describing how magnetic exposure is transduced from a plausible molecular biosensor (lipid membranes) to cell-level responses that include differentiation toward neural lineages. In addition, SMF provided a stimulus that uncovered new relationships – that exist even in the absence of magnetic fields – between gangliosides, the time-dependent regulation of IL-6 signaling by these glycosphingolipids, and the fate of embryonic cells.

Spaceflight bioreactor studies of cells and tissues

Studies of the fundamental role of gravity in the development and function of biological organisms are a central component of the human exploration of space. Microgravity affects numerous physical phenomena relevant to biological research, including the hydrostatic pressure in fluid filled vesicles, sedimentation of organelles, and buoyancy-driven convection of flow and heat. These physical phenomena can in turn directly and indirectly affect cellular morphology, metabolism, locomotion, secretion of extracellular matrix and soluble signals, and assembly into functional tissues. Studies aimed at distinguishing specific effects of gravity on biological systems require the ability to: (i) control and systematically vary gravity, e.g. by utilizing the microgravity environment of space in conjunction with an in-flight centrifuge; and (ii) maintain constant all other factors in the immediate environment, including in particular concentrations and exchange rates of biochemical species and hydrodynamic shear. The latter criteria imply the need for gravity-independent mechanisms to provide for mass transport between the cells and their environment. Available flight hardware has largely determined the experimental design and scientific objectives of spaceflight cell and tissue culture studies carried out to date. Simple culture vessels have yielded important quantitative data, and helped establish in vitro models of cell locomotion, growth and differentiation in various mammalian cell types including embryonic lung cells [6], lymphocytes [2,8], and renal cells [7,31]. Studies done using bacterial cells established the first correlations between gravity-dependent factors such as cell settling velocity and diffusional distance and the respective cell responses [12]. The development of advanced bioreactors for microgravity cell and tissue culture and for tissue engineering has benefited both research areas and provided relevant in vitro model systems for studies of astronaut well-being (loss of muscle and skeletal tissues [15-17]) and gene- and cell-level responses to the mechanical environment [13,14,18]. All five of the spaceflight bioreactor studies described above utilized three-dimensional cell culture systems in which the cells were associated with biodegradable polymer scaffolds [17], collagen gel [16], or microcarrier beads [13-15,18] in order to promote the expression of differentiated cell function. In four of the five spaceflight bioreactor studies [15-18], cells were cultured in perfused vessels (cartridges or rotating bioreactors) within recirculating loops designed to maintain medium composition within target ranges by a combination of gas exchange and fresh medium supply. Future spaceflight studies of cells and tissues are likely to involve a three-dimensional culture system, to promote cellular differentiation, and perfusion with or without rotation, to provide a gravity-independent mechanism for fluid mixing and mass transport. Previous spaceflight studies have guided the ongoing development of NASA flight hardware for the ISS (e.g. the EDU-2 and the CCU). This next generation of hardware will have extended operational capabilities including on-line microscopy, in-line sensors for the monitoring and control of metabolic parameters, modular design for replicate cultures, and, perhaps most importantly of all, compatibility with the ISS centrifuge. The latter will permit in-flight, 1 g control cultures, and thereby allow the experimental variable to be gravity itself rather than the more general "spaceflight environment". Technical limitations of spaceflight studies (e.g. allowable size, mass, and power) continue to motivate a creative approach to system design and to result in "spin-off" technologies (e.g. the STLV) for ground-based cell and tissue culture research. The increasing scientific and medical relevance of this work is evidenced by the growing number of publications in which advanced bioreactors are used for in vitro studies in physiologically relevant cell and tissue models.