Efflux transporters are a fundamental component of both prokaryotic and eukaryotic cells, play a crucial role in maintaining cellular homeostasis, and represent a key bridge between single cell and population levels. From a biomedical perspective, they play a crucial role in drug resistance (and especially multi-drug resistance, MDR) in a range of systems spanning bacteria and human cancer cells. Typically, multiple efflux transporters are present in these cells, and the efflux transporters transport a range of substrates (with partially overlapping substrates between transporters). Furthermore, in the context of drug resistance, the levels of transporters may be elevated either due to extra or intracellular factors (feedforward regulation) or due to the drug itself (feedback regulation). As a consequence, there is a real need for a transparent systems-level understanding of the collective functioning of a set of transporters and their response to one or more drugs. We develop a systems framework for this purpose and examine the functioning of sets of transporters, their interplay with one or more drugs and their regulation (both feedforward and feedback). Using computational and analytical work, we obtain transparent insights into the systems level functioning of a set of transporters arising from the interplay between the multiplicity of drugs and transporters, different drug-transporter interaction parameters, sequestration and feedback and feedforward regulation. These insights transparently arising from the most basic consideration of a multiplicity of transporters have broad relevance in natural biology, biomedical engineering and synthetic biology. Insight, Innovation, Integration: Innovation: creating a structured systems framework for evaluating the impact of multiple transporters on drug efflux and drug resistance. Systematic analysis allows us to evaluate the effect of multiple transporters on one/more drugs, and dissect associated resistance mechanisms. Integration allows for elucidation of key cause-and-effect relationships and a transparent systems-level understanding of the collective functioning of transporters and their impact on resistance, revealing the interplay of key underlying factors. Systems-level insights include the essentially different behaviour of transporters as part of a group; unintuitive effects of influx; effects of elevated transporter-levels by feedforward and drug-induced mechanisms. Relevance: a systems understanding of efflux, their role in MDR, providing a framework/platform for use in designing treatment, and in synthetic biology design.

A critical phase of wound healing is the coordinated movement of keratinocytes. To this end, bioglasses show promise in speeding healing in hard tissues and skin wounds. Studies suggest that bioglass materials may promote wound healing by inducing positive cell responses in proliferation, growth factor production, expression of angiogenic factors, and migration. Precise details of how bioglass may stimulate migration are unclear, however, because the common assays for studying migration in wound healing focus on simplified outputs like rate of migration or total change in wound area. These outputs are limited in that they represent the average behavior of the collective, with no connection between the motion of the individual cells and the collective wound healing response. There is a need to apply more refined tools that identify how the motion of the individual cells changes in response to perturbations, such as by bioglass, and in turn affects motion of the cell collective. Here, we apply an integrative biology strategy that combines an in vitro wound healing assay using primary neonatal human keratinocytes with time lapse microscopy and quantitative image analysis. The resulting data set provides the cell velocity field, from which we define key metrics that describe cooperative migration phenotypes. Treatment with growth factors led to faster single-cell speeds compared to control, but the migration was not cooperative, with cells breaking away from their neighbors and migrating as individuals. Treatment with calcium or bioglass led to migration phenotypes that were highly collective, with greater coordination in space compared to control. We discuss the link between bioglass treatment and observed increases in free calcium ions that are hypothesized to promote these distinct coordinated behaviors in primary keratinocytes. These findings have been enabled by the unique descriptors developed through applying image analysis to interpret biological response in migration models. Insight Box/Paragraph Statement: Bioglasses are important materials for tissue engineering and have more recently shown promise in skin and wound healing by mechanisms tied to their unique ionic properties. The precise details, however, of how cell migration may be affected by bioglass are left unclear by traditional cell assay methods. The following describes the integration of migration assays of keratinocytes, cells critical for skin and wound healing, with the tools of time lapse microscopy and image analysis to generate a quantitative description of coordinated, tissue-like migration behavior, stimulated by bioglass, that would not have been accessible without the combination of these analytical tools.

With the expanding ageing population, there is a growing interest in the maintenance of immune health to support healthy ageing. Enthusiasm exists for unravelling the impact of diet on the immune system and its therapeutic potential. However, a key challenge is the lack of studies investigating the effect of dietary patterns and nutrients on immune responses. Thus, we have used an integrative analysis approach to improve our understanding of diet-immune system interactions in older adults. To do so, dietary data were collected in parallel with performing immunophenotyping and functional assays from healthy older (n = 40) participants. Food Frequency Questionnaire (FFQ) was utilised to derive food group intake and multi-colour flow cytometry was performed for immune phenotypic and functional analysis. Spearman correlation revealed the strength of association between all combinations of dietary components, micronutrients, and hallmarks of immunesenescence. In this study, we propose for the first time that higher adherence to the Mediterranean diet is associated with a positive immune-ageing trajectory (Lower IMM-AGE score) in older adults due to the immune protective effects of high dietary fibre and PUFA intake in combating accumulation or pro-inflammatory senescent T cells. Furthermore, a diet rich in Vit A, Vit B6 and Vit B12 is associated with fewer features of immunesenescence [such as accumulation of terminally differentiated memory CD8 T cells] in older adults. Based on our findings we propose a future nutrition-based intervention study evaluating the efficacy of adherence to the MED diet alongside a multi-nutrient supplementation on immune ageing in older adults to set reliable dietary recommendations with policymakers that can be given to geriatricians and older adults. Insight box: There is a growing interest in the maintenance of immune health to boost healthy ageing. However, a key challenge is the lack of studies investigating the effect of dietary patterns and nutrients on immune responses. Thus, to do so we collected dietary data in parallel with performing immunophenotyping and functional assays on healthy older (n = 40) participants, followed by an integrative analysis approach to improve our understanding of diet-immune system interactions in older adults. We strongly believe that these new findings are appropriate for IB and will be of considerable interest to its broad audience.

The standard model of the cell membrane potential Vm describes it as arising from diffusion currents across a membrane with a constant electric field, with zero electric field outside the cell membrane. However, the influence of Vm has been shown to extend into the extracellular space where it alters the cell's ζ-potential, the electrical potential measured a few nm from the cell surface which defines how the cell interacts with charged entities in its environment, including ions, molecules, and other cells. The paradigm arising from surface science is that the ζ-potential arises only from fixed membrane surface charge, and has consequently received little interest. However, if the ζ-potential can mechanistically and dynamically change by alteration of Vm, it allows the cell to dynamically alter cell-cell and cell-molecule interactions and may explain previously unexplained electrophysiological behaviours. Whilst the two potentials Vm and ζ are rarely reported together, they are occasionally described in different studies for the same cell type. By considering published data on these parameters across multiple cell types, as well as incidences of unexplained but seemingly functional Vm changes correlating with changes in cell behaviour, evidence is presented that this may play a functional role in the physiology of red blood cells, macrophages, platelets, sperm, ova, bacteria and cancer. Understanding how these properties will improve understanding of the role of electrical potentials and charges in the regulation of cell function and in the way in which cells interact with their environment. Insight  The zeta (ζ) potential is the electrical potential a few nm beyond the surface of any suspensoid in water. Whilst typically assumed to arise only from fixed charges on the cell surface, recent and historical evidence shows a strong link to the cell's membrane potential Vm, which the cell can alter mechanistically through the use of ion channels. Whilst these two potentials have rarely been studied simultaneously, this review collates data across multiple studies reporting Vm, ζ-potential, electrical properties of changes in cell behaviour. Collectively, this points to Vm-mediated ζ-potential playing a significant role in the physiology and activity of blood cells, immune response, developmental biology and egg fertilization, and cancer among others.

In B cells, the chemokine receptor CXCR3 is expressed only by a subset of B cells. However, CXCR3 is highly expressed in a rare type of B-cell lymphoma known as Mantle Cell Lymphoma (MCL) and CXCR3 inhibitor impairs proliferation and induces apoptosis in the MCL cell line JeKo-1. Despite this, the mechanism responsible for maintaining high levels of CXCR3 in MCL cells remains unclear. In this study, we assessed CXCR3 expression and amplification in MCL samples and confirmed that CXCR3 is overexpressed in MCL tissues. We also observed that CXCR3 amplification is present in a small portion of MCL patients and is associated with MCL classification. We then screened ubiquitin-specific proteases (USPs) that might control the degradation of CXCR3 protein. Our investigation revealed that USP35 acts as a potent stabilizer of CXCR3 protein. Knockdown of USP35 substantially reduced the CXCR3 protein levels in JeKo-1 cells, resulting in reduced cell viability, cell cycle arrest, increased apoptosis, and mitigated migration and invasion in these cells. At the molecular level, USP35 deubiquitinates and stabilizes CXCR3. USP35 deficiency attenuated the activation of the JAK1/STAT1 pathway and reduced the expression of β-catenin and c-Myc in JeKo-1 cells. Furthermore, we observed that overexpression of CXCR3 rescued the impaired tumorigenicity of USP35-deficient JeKo-1 cells, and the mechanism may be related to the fact that USP35 promotes CXCR3 deubiquitination to stabilize its expression. These findings collectively demonstrate the oncogenic role of the USP35-CXCR3 axis in JeKo-1 MCL cells.

Immune responses against cancer are inherently stochastic, with small numbers of individual T cells within a larger ensemble of lymphocytes initiating the molecular cascades that lead to tumor cytotoxicity. A potential source of this intra-tumor variability is the differential ability of immune cells to respond to tumor cells. Classical microwell co-cultures of T cells and tumor cells are inadequate for reliably culturing and analyzing low cell numbers needed to probe this variability, and have failed in recapitulating the heterogeneous small domains observed in tumors. Here we leverage a membrane displacement trap array technology that overcomes limitations of conventional microwell plates for immunodynamic studies. The microfluidic platform supports on-demand formation of dense nanowell cultures under continuous perfusion reflecting the tumor microenvironment, with real-time monitoring of T cell proliferation and activation within each nanowell. The system enables selective ejection of cells for profiling by fluorescence activated cell sorting, allowing observed on-chip variability in immune response to be correlated with off-chip quantification of T cell activation. The technology offers new potential for probing the molecular origins of T cell heterogeneity and identifying specific cell phenotypes responsible for initiating and propagating immune cascades within tumors. Insight Box Variability in T cell activation plays a critical role in the immune response against cancer. New tools are needed to unravel the mechanisms that drive successful anti-tumor immune response, and to support the development of novel immunotherapies utilizing rare T cell phenotypes that promote effective immune surveillance. To this end, we present a microfluidic cell culture platform capable of probing differential T cell activation in an array of nanoliter-scale wells coupled with off-chip cell analysis, enabling a high resolution view of variable immune response within tumor / T cell co-cultures containing cell ensembles orders of magnitude smaller than conventional well plate studies.

Diabetes is a rising global metabolic disorder and leads to long-term consequences. As a multifactorial disease, the gene-associated mechanisms are important to know. This study applied a bioinformatics approach to explore the molecular underpinning of type 2 diabetes mellitus through differential gene expression analysis. We used microarray datasets GSE16415 and GSE29226 to identify differentially expressed genes between type 2 diabetes and normal samples using R software. Following that, using the STRING database, the protein-protein interaction network was constructed and further analyzed by Cytoscape software. The EnrichR database was used for Gene Ontology and pathway enrichment analysis to explore key pathways and functional annotations of hub genes. We also used miRTarBase and TargetScan databases to predict miRNAs targeting hub genes. We identified 21 hub genes in type 2 diabetes, some showing more significant changes in the PPI network. Our results revealed that GLUL, SLC32A1, PC, MAPK10, MAPT, and POSTN genes are more important in the PPI network and can be experimentally investigated as therapeutic targets. Hsa-miR-492 and hsa-miR-16-5p are suggested for diagnosis and prognosis by targeting GLUL, SLC32A1, PC, MAPK10, and MAPT genes involved in the insulin signaling pathway. Insight: Type 2 diabetes, as a rising global and multifactorial disorder, is important to know the gene-associated mechanisms. In an integrative bioinformatics analysis, we integrated different finding datasets to put together and find valuable diagnostic and prognostic hub genes and miRNAs. In contrast, genes, RNAs, and enzymes interact systematically in pathways. Using multiple databases and software, we identified differential expression between hub genes of diabetes and normal samples. We explored different protein-protein interaction networks, gene ontology, key pathway analysis, and predicted miRNAs that target hub genes. This study reported 21 significant hub genes and some miRNAs in the insulin signaling pathway for innovative and potential diagnostic and therapeutic purposes.

Collective dynamics of cells in confined geometry regulate several biological processes including cell migration, proliferation, differentiation, and communication. In this work, combining simulation with experimental data, we studied the oscillatory motion of epithelial sheets in smaller areas of confinement, and we linked the monolayer maturation induced-jamming with the wave formation. We showed that epithelial cell populations with delayed jamming properties use the additional time available from this delay to coordinate their movement, generating wave motion in larger areas of confinement compared to control populations. Furthermore, the effects of combining geometric confinement with contact guiding micro-gratings on this wave formation were investigated. We demonstrated that collective migratory oscillations under large geometrical confinement depend on the jamming state of the cell monolayers. The early dynamical state of the experimental results obtained was simulated by self-propelled Voronoi computations, comparing cells with solid-like and fluid-like behavior. Together our model describes the wave formation under confinement and the nodal oscillatory dynamics of the early dynamic stage of the system. Insight Box: Collective behavior of cells in confined spaces impacts biological processes. Through experimental data combined with simulations, the oscillatory motion of epithelial sheets in small areas of confinement was described. A correlation between the level of cell jamming and the formation of waves was detected. Cell populations with delayed jamming presented wave motion in larger confinement areas. The effects of combining geometric confinement with substrate micro-gratings demonstrated that the collective migratory oscillations in large confinement areas rely on the jamming state of cells. The early dynamical state was simulated using self-propelled Voronoi computations that help to understand wave formation under confinement and the nodal oscillatory dynamics of early-stage systems.

Cosmic radiation, composed of high charge and energy (HZE) particles, causes cellular DNA damage that can result in cell death or mutation that can evolve into cancer. In this work, a cell death model is applied to several cell lines exposed to HZE ions spanning a broad range of linear energy transfer (LET) values. We hypothesize that chromatin movement leads to the clustering of multiple double strand breaks (DSB) within one radiation-induced foci (RIF). The survival probability of a cell population is determined by averaging the survival probabilities of individual cells, which is function of the number of pairwise DSB interactions within RIF. The simulation code RITCARD was used to compute DSB. Two clustering approaches were applied to determine the number of RIF per cell. RITCARD outputs were combined with experimental data from four normal human cell lines to derive the model parameters and expand its predictions in response to ions with LET ranging from ~0.2 keV/μm to ~3000 keV/μm. Spherical and ellipsoidal nuclear shapes and two ion beam orientations were modeled to assess the impact of geometrical properties on cell death. The calculated average number of RIF per cell reproduces the saturation trend for high doses and high-LET values that is usually experimentally observed. The cell survival model generates the recognizable bell shape of LET dependence for the relative biological effectiveness (RBE). At low LET, smaller nuclei have lower survival due to increased DNA density and DSB clustering. At high LET, nuclei with a smaller irradiation area-either because of a smaller size or a change in beam orientation-have a higher survival rate due to a change in the distribution of DSB/RIF per cell. If confirmed experimentally, the geometric characteristics of cells would become a significant factor in predicting radiation-induced biological effects. Insight Box: High-charge and energy (HZE) ions are characterized by dense linear energy transfer (LET) that induce unique spatial distributions of DNA damage in cell nuclei that result in a greater biological effect than sparsely ionizing radiation like X-rays. HZE ions are a prominent component of galactic cosmic ray exposure during human spaceflight and specific ions are being used for radiotherapy. Here, we model DNA damage clustering at sub-micrometer scale to predict cell survival. The model is in good agreement with experimental data for a broad range of LET. Notably, the model indicates that nuclear geometry and ion beam orientation affect DNA damage clustering, which reveals their possible role in mediating cell radiosensitivity.

Recent findings in cancer research have pointed towards the bidirectional interaction between circadian and hypoxia pathways. However, little is known about their crosstalk mechanism. In this work, we aimed to investigate this crosstalk at a network level utilizing the omics information of gallbladder cancer. Differential gene expression and pathway enrichment analysis were used for selecting the crucial genes from both the pathways, followed by the construction of a logical crosstalk model using GINsim. Functional circuit identification and node perturbations were then performed. Significant node combinations were used to investigate the temporal behavior of the network through MaBoSS. Lastly, the model was validated using published in vitro experimentations. Four new positive circuits and a new axis viz. BMAL1/ HIF1αβ/ NANOG, responsible for stemness were identified. Through triple node perturbations viz.a. BMAL:CLOCK (KO or E1) + P53 (E1) + HIF1α (KO); b. P53 (E1) + HIF1α (KO) + MYC (E1); and c. HIF1α (KO) + MYC (E1) + EGFR (KO), the model was able to inhibit cancer growth and maintain a homeostatic condition. This work provides an architecture for drug simulation analysis to entrainment circadian rhythm and in vitro experiments for chronotherapy-related studies. Insight Box. Circadian rhythm and hypoxia are the key dysregulated processes which fuels-up the cancer growth. In the present work we have developed a gallbladder cancer (GBC) specific Boolean model, utilizing the RNASeq data from GBC dataset and tissue specific interactions. This work adequately models the bidirectional nature of interactions previously illustrated in experimental papers showing the effect of hypoxia on dysregulation of circadian rhythm and the influence of this disruption on progression towards metastasis. Through the dynamical study of the model and its response to different perturbations, we report novel triple node combinations that can be targeted to efficiently reduce GBC growth. This network can be used as a generalized framework to investigate different crosstalk pathways linked with cancer progression.

Plant protease inhibitors (PI's) inhibit the activity of gut proteases and thus provide resistance against insect attack. Previously we have published first report on cloning and characterization of a novel Bowman-Birk protease inhibitor gene (RbTI) from ricebean (Vigna umbellata). In this study, the RbTI gene was further characterized and validated as a potential candidate for transferring insect resistance in economically important crops. We have successfully generated transgenic tobacco plants expressing RbTI gene constitutively under CaMV35S promoter using Agrobacterium transformation. Genomic PCR and GUS analysis confirmed the successful integration of RbTI gene into tobacco plant genome. qRT-PCR analysis revealed highest RbTI gene expression in transformed tobacco leaves nearing maturity. Feeding of transformed tobacco leaf tissue showed prominent effect on larval mortality throughout the larval growth stages mainly during first three days of feeding. For functional analysis of RbTI gene, we estimated the inhibitory activity of protein extracts from normal and transformed tobacco plants against gut proteases of Spodoptera litura and H. armigera larval instars. Maximum inhibition of trypsin (82.42% and 73.25%) and chymotrypsin (69.50% and 60.64%) enzymes was recorded at early larval stages of both insects. The results of this study validated the future use of RbTI gene from ricebean legume as a potential candidate for transferring insect resistance in economically important crops. Insight, innovation, integration: Present study was conducted with the aim to utilize the state of art biotechnological techniques for transferring key pest resistant genes from underutilized promising crop ricebean. The tobacco plant has been utilized as modern plant for proof of concept where a protease inhibitor gene from Ricebean has been transferred to tobacco plant which induced larval mortality within first three days of feeding at all larval developmental stages. The biochemical assays on mid-gut total protein extract showed that the transgenic tobacco leaves have inhibiting effect on trypsin and chymotrypsin enzymes of insect which is otherwise required for digestion of food by them. Hence, we provide a novel gene that could be utilized for pest resistance in other crops different developmental stages.

Breast cancer, more prevalent in women, often arises due to abnormalities in the MRN-checkpoint sensor genes (MRN-CSG), responsible for DNA damage detection and repair. Abnormality in this complex is due to the suppression of various effectors such as siRNAs, miRNAs, and transcriptional factors responsible for breast tumor progression. This study analyzed breast tumor samples (n = 60) and identified four common miRNAs (miR-1-3p, miR-210-3p, miR-16-5p, miR-34a-5p) out of 12, exploring their interactions with MRN-CSG. The 3D structures of these miRNA-MRN-CSG complexes displayed strong thermodynamic stability. Screening 7711 natural compounds resulted in two natural compounds (F0870-0001 and F0922-0471) with the lowest ligand binding energies (ΔG = -8.4 to-11.6 kcal/mol), targeting two common miRNAs. Docking results showed that one natural compound (PubChem id-5 281 614) bound to all MRN-CSG components (ΔG = -6.2 to -7.3 kcal/mol), while F6782-0723 bound only to RAD50 and NBN. These compounds exhibited minimal dissociation constants (Kd and Ki) and thermodynamically stable minimum free energy (MMGBSA) values. Molecular dynamics simulations indicated highly stable natural compound-MRN-CSG complexes, with consistent RMSD, RMSF, and strong residual correlation. These top-selected compounds displayed robust intermolecular H-bonding, low carcinogenicity, low toxicity, and drug-like properties. Consequently, these compounds hold promise for regulating miRNA and MRN-CSG DNA repair mechanisms in breast cancer therapy. Insight Box: This study investigated breast tumor samples (n = 60) and identified four miRNAs (miR-1-3p, miR-210-3p, miR-16-5p, miR-34a-5p) that interact with MRN-checkpoint sensor genes (MRN-CSG), crucial for DNA damage repair. Screening 7711 natural compounds highlighted two compounds (F0870-0001 and F0922-0471) with the lowest binding energies (ΔG = -8.4 to -11.6 kcal/mol), targeting two common miRNAs (miR-1-3p and miR-34a-5p). Another natural compound (PubChem id-5 281 614, ΔG = -6.2 to -7.3 kcal/mol) bound all MRN-CSG components, while F6782-0723 targeted RAD50 and NBN. These compounds showed strong binding stability, favorable MMGBSA values, and minimal dissociation constants. Molecular dynamics simulations confirmed the stability and drug-like properties of these compounds, indicating their potential in breast cancer therapy by modulating miRNA and MRN-CSG DNA repair mechanisms.

Mechanical forces are of major importance in regulating vascular homeostasis by influencing endothelial cell behavior and functions. Adherens junctions are critical sites for mechanotransduction in endothelial cells. β-catenin, a component of adherens junctions and the canonical Wnt signaling pathway, plays a role in mechanoactivation. Evidence suggests that β-catenin is involved in flow sensing and responds to tensional forces, impacting junction dynamics. The mechanoregulation of β-catenin signaling is context-dependent, influenced by the type and duration of mechanical loads. In endothelial cells, β-catenin's nuclear translocation and signaling are influenced by shear stress and strain, affecting endothelial permeability. The study investigates how shear stress, strain, and surface topography impact adherens junction dynamics, regulate β-catenin localization, and influence endothelial barrier properties. Insight box Mechanical loads are potent regulators of endothelial functions through not completely elucidated mechanisms. Surface topography, wall shear stress and cyclic wall deformation contribute overlapping mechanical stimuli to which endothelial monolayer respond to adapt and maintain barrier functions. The use of custom developed flow chamber and bioreactor allows quantifying the response of mature human endothelial to well-defined wall shear stress and gradients of strain. Here, the mechanoregulation of β-catenin by substrate topography, wall shear stress, and cyclic stretch is analyzed and linked to the monolayer control of endothelial permeability.

Clustering of cells is an essential component of many biological processes from tissue formation to cancer metastasis. We develop a minimal, Vicsek-based model of cellular interactions that robustly and accurately captures the variable propensity of different cells to form groups when confined. We calibrate and validate the model with experimental data on clustering affinities of four lines of tumor cells. We then show that cell clustering or separation tendencies are retained in environments with higher cell number densities and in cell mixtures. Finally, we calibrate our model with experimental measurements on the separation of cells treated with anti-clustering agents and find that treated cells maintain their distances in denser suspensions. We show that the model reconstructs several cell interaction mechanisms, which makes it suitable for exploring the dynamics of cell cluster formation as well as cell separation. Insight: We developed a model of cellular interactions that captures the clustering and separation of cells in an enclosure. Our model is particularly relevant for microfluidic systems with confined cells and we centered our work around one such emerging assay for the detection and research on clustering breast cancer cells. We calibrated our model using the existing experimental data and used it to explore the functionality of the assay under a broader set of conditions than originally considered. Future usages of our model can include purely theoretical and computational considerations, exploring experimental devices, and supporting research on small to medium-sized cell clusters.

Cells dynamically remodel their internal structures by modulating the arrangement of actin filaments (AFs). In this process, individual AFs exhibit stochastic behavior without knowing the macroscopic higher-order structures they are meant to create or disintegrate, but the mechanism allowing for such stochastic process-driven remodeling of subcellular structures remains incompletely understood. Here we employ percolation theory to explore how AFs interacting only with neighboring ones without recognizing the overall configuration can nonetheless create a substantial structure referred to as stress fibers (SFs) at particular locations. We determined the interaction probabilities of AFs undergoing cellular tensional homeostasis, a fundamental property maintaining intracellular tension. We showed that the duration required for the creation of SFs is shortened by the increased amount of preexisting actin meshwork, while the disintegration occurs independently of the presence of actin meshwork, suggesting that the coexistence of tension-bearing and non-bearing elements allows cells to promptly transition to new states in accordance with transient environmental changes. The origin of this asymmetry between creation and disintegration, consistently observed in actual cells, is elucidated through a minimal model analysis by examining the intrinsic nature of mechano-signal transmission. Specifically, unlike the symmetric case involving biochemical communication, physical communication to sense environmental changes is facilitated via AFs under tension, while other free AFs dissociated from tension-bearing structures exhibit stochastic behavior. Thus, both the numerical and minimal models demonstrate the essence of intracellular percolation, in which macroscopic asymmetry observed at the cellular level emerges not from microscopic asymmetry in the interaction probabilities of individual molecules, but rather only as a consequence of the manner of the mechano-signal transmission. These results provide novel insights into the role of the mutual interplay between distinct subcellular structures with and without tension-bearing capability. Insight: Cells continuously remodel their internal elements or structural proteins in response to environmental changes. Despite the stochastic behavior of individual structural proteins, which lack awareness of the larger subcellular structures they are meant to create or disintegrate, this self-assembly process somehow occurs to enable adaptation to the environment. Here we demonstrated through percolation simulations and minimal model analyses that there is an asymmetry in the response between the creation and disintegration of subcellular structures, which can aid environmental adaptation. This asymmetry inherently arises from the nature of mechano-signal transmission through structural proteins, namely tension-mediated information exchange within cells, despite the stochastic behavior of individual proteins lacking asymmetric characters in themselves.

Oxygen levels vary in the environment. Oxygen availability has a major effect on almost all organisms, and oxygen is far more than a substrate for energy production. However, less is known about related biological processes under hypoxic conditions and about the adaptations to changing oxygen concentrations. The yeast Saccharomyces cerevisiae can adapt its metabolism for growth under different oxygen concentrations and can grow even under anaerobic conditions. Therefore, we developed a microfluidic device that can generate serial, accurately controlled oxygen concentrations for single-cell studies of multiple yeast strains. This device can construct a broad range of oxygen concentrations, [O2] through on-chip gas-mixing channels from two gases fed to the inlets. Gas diffusion through thin polydimethylsiloxane (PDMS) can lead to the equilibration of [O2] in the medium in the cell culture layer under gas cover regions within 2 min. Here, we established six different and stable [O2] varying between ~0.1 and 20.9% in the corresponding layers of the device designed for multiple parallel single-cell culture of four different yeast strains. Using this device, the dynamic responses of different yeast transcription factors and metabolism-related proteins were studied when the [O2] decreased from 20.9% to serial hypoxic concentrations. We showed that different hypoxic conditions induced varying degrees of transcription factor responses and changes in respiratory metabolism levels. This device can also be used in studies of the aging and physiology of yeast under different oxygen conditions and can provide new insights into the relationship between oxygen and organisms. Integration, innovation and insight: Most living cells are sensitive to the oxygen concentration because they depend on oxygen for survival and proper cellular functions. Here, a composite microfluidic device was designed for yeast single-cell studies at a series of accurately controlled oxygen concentrations. Using this device, we studied the dynamic responses of various transcription factors and proteins to changes in the oxygen concentration. This study is the first to examine protein dynamics and temporal behaviors under different hypoxic conditions at the single yeast cell level, which may provide insights into the processes involved in yeast and even mammalian cells. This device also provides a base model that can be extended to oxygen-related biology and can acquire more information about the complex networks of organisms.

Shiga toxin (Stx) causes significant renal microvascular injury and kidney failure in the pediatric population, and an effective targeted therapy has yet to be demonstrated. Here we established a human kidney microvascular endothelial cell line for the study of Stx mediated injuries with respect to their morphologic, phenotypic, and transcriptional changes, and modeled Stx induced thrombotic microangiopathy (TMA) in flow-mediated 3D microvessels. Distinct from other endothelial cell lines, both isolated primary and immortalized human kidney microvascular endothelial cells demonstrate robust cell-surface expression of the Stx receptor Gb3, and concomitant dose-dependent toxicity to Stx, with significant contributions from caspase-dependent cell death. Use of a glucosylceramide synthase inhibitor (GCSi) to target disruption of the synthetic pathway of Gb3 resulted in remarkable protection of kidney microvascular cells from Stx injury, shown in both cellular morphologies, caspase activation and transcriptional analysis from RNA sequencing. Importantly, these findings are recapitulated in 3D engineered kidney microvessels under flow. Moreover, whole blood perfusion through Stx-treated microvessels led to marked platelet binding on the vessel wall, which was significantly reduced with the treatment of GCSi. These results validate the feasibility and utility of a bioengineered ex vivo human microvascular model under flow to recapitulate relevant blood-endothelial interactions in STEC-HUS. The profound protection afforded by GCSi demonstrates a preclinical opportunity for investigation in human tissue approximating physiologic conditions. Moreover, this work provides a broad foundation for novel investigation into TMA injury pathogenesis and treatment. Insight Box: Shiga toxin (Stx) causes endothelial injury that results in significant morbidity and mortality in the pediatric population, with no effective targeted therapy. This paper utilizes human kidney microvascular cells to examine Stx mediated cell death in both 2D culture and flow-mediated 3D microvessels, with injured microvessels also developing marked platelet binding and thrombi formation when perfused with blood, consistent with the clinical picture of HUS. This injury is abrogated with a small molecule inhibitor targeting the synthetic pathway of the Shiga toxin receptor. Our findings shed light onto Stx-induced vascular injuries and pave a way for broad investigation into thrombotic microangiopathies.

Combinations of genes or proteins work in synergy at different times and durations in a signaling pathway. However, which combinations are prevalent at a particular time point or duration is mostly not known. Sensitivity analysis plays a major role in computing the strength of the influence of involved factors in any phenomena under investigation. When applied to expression profiles of various intra/extracellular factors that work in a signaling pathway, the variance- and density-based analysis yields a range of sensitivity indices for individual and various combinations of factors. These combinations denote the higher order interactions among the involved factors, which might be of interest. In this work, after estimating the individual effects of factors for a higher order combination, the individual indices are considered as discriminative features. Exploiting the analogy of prioritizing webpages using ranking algorithms, for a particular order, a full set of combinations of genes can be prioritized based on these features using a powerful support vector ranking algorithm. Recording the changing rankings of the combinations over time points and durations reveals which higher order combinations influence the pathway and when and where an intervention might be necessary to affect the pathway. Integration, innovation, and insight Combinations of genes or proteins work in synergy at different times and durations in a signaling pathway. However, which combinations are prevalent at a particular time point or duration is mostly not known. This work develops a search engine that reveals ground-breaking results in the form of higher order (un)explored/(un)tested combinations (as biological hypotheses), based on sensitivity indices. These indices capture the strength of influence of factors (here genes/proteins) that affect a signaling pathway. Recording the changing rankings of these combinations over time points and durations reveals how higher order combinations behave within the pathway. Significance The manuscript develops a search engine that reveals ground-breaking results in the form of higher order (un)explored/(un)tested combinations of genes/proteins (as biological hypotheses), based on sensitivity indices that capture the strength of influence of factors (here genes/proteins) that affect the Wnt signaling pathway. The pipeline uses kernel-based sensitivity indices to capture the influence of the factors in a pathway and employs powerful support vector ranking algorithm. Because of the above point, biologists/oncologists will be able to narrow down their search to particular combinations that are ranked and, if a synergistic functioning is confirmed, will be able to study the mechanism between the components of a combination, in the Wnt pathway. The search engine design is not only limited to one dataset and a range of combinations of genes/proteins. The framework can be applied/modified to all problems where one is interested in searching for particular combinations of factors involved in a particular phenomena. Recording the changing rankings of the combinations over time points and durations reveals how higher order interactions behave within the pathway and when and where an intervention might be necessary to influence the pathway, for therapeutic purpose. It reveals the various unexplored FZD-WNT combinations that have been untested till now in the Wnt pathway.