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74
Date Added: Jul 12, 2021
Date Added: Jul 12, 2021
Fireflies flashing in unison is a mesmerizing manifestation of animal collective behavior and an archetype of biological synchrony. To elucidate synchronization mechanisms and inform theoretical models, we recorded the collective display of thousands of Photinus carolinus fireflies in natural swarms, and provide the first spatiotemporal description of the onset of synchronization. At low firefly density, flashes appear uncorrelated. At high density, the swarm produces synchronous flashes within periodic bursts. Using three-dimensional reconstruction, we demonstrate that flash bursts nucleate and propagate across the swarm in a relay-like process. Our results suggest that fireflies interact locally through a dynamic network of visual connections defined by visual occlusion from terrain and vegetation. This model illuminates the importance of the environment in shaping self-organization and collective behavior. Flash bursts relay around vegetation across the swarm, illuminating the role of the environment in shaping self-organization. Flash bursts relay around vegetation across the swarm, illuminating the role of the environment in shaping self-organization.
8
Date Added: Jun 2, 2021
Date Added: Jun 2, 2021
TGFβ mediated epithelial to mesenchymal transition (EMT) proceeds through hybrid "E/M" states. A deeper understanding of these states and events which regulate entry to and exit from the E/M states is needed for therapeutic exploitation. We quantified >60,000 molecules across ten time points and twelve omic layers in mammary epithelial cells. Proteomes of whole cells, phosphoproteins, nucleus, extracellular vesicles, secretome and membrane resolved major shifts, E→E/M and E/M→M during EMT, and defined state-specific signatures. Metabolomics identified early activation of arachidonic acid pathway and an enzyme-mediated switch from Cytochrome P450 to Cyclooxygenase / Lipoxygenase branches during E→E/M. Single-cell transcriptomics identified GLIS2 as an early modulator of EMT. Integrative modeling-predicted combinatorial inhibition of AURKB, PP2A and SRC exposed vulnerabilities at E→E/M juncture. Covariance analysis revealed remarkable discordance between proteins and transcripts, and between proteomic layers, implying insufficiency of current approaches. Overall, this dataset provides an unprecedented resource on TGFβ signaling, EMT and cancer.
1
Date Added: Jan 22, 2021
Date Added: Jan 22, 2021
Motivation: Ligand-receptor (LR) analysis allows the characterization of cellular crosstalk from single cell RNA-seq data. However, current LR methods provide limited approaches for prioritization of cell types, ligands or receptors or characterizing changes in crosstalk between two biological conditions. Results: CrossTalkeR is a framework for network analysis and visualisation of LR networks. CrossTalkeR identifies relevant ligands, receptors and cell types contributing to changes in cell communication when contrasting two biological states: disease vs. homeostasis. A case study on scRNA-seq of human myeloproliferative neoplasms reinforces the strengths of CrossTalkeR for characterisation of changes in cellular crosstalk in disease state. Availability and Implementation: CrosstalkeR is as a package in R and available as a package in https://github.com/CostaLab/CrossTalkeR.
2
Date Added: Jan 22, 2021
Date Added: Jan 22, 2021
Cancer stem cells (CSCs) often switch on their self-renewal programming aggressively to cause a relapse of cancer. Intriguingly, glucose differentially triggers the proliferation propensities in CSCs in an origin-dependent manner by controlling the expression of the key transcription factor like Nanog. However, the factors that critically govern this glucose-stimulated proliferation dynamics of CSCs remains elusive. Herein, by proposing a mathematical model of glucose-mediated Nanog regulation in CSCs, we showed that the differential proliferation behavior of CSCs can be explained by considering the experimentally observed varied expression levels of key positive (STAT3) and negative (p53) regulators of Nanog. Our model reconciles various experimental observations and predicts ways to fine-tune the proliferation dynamics of specific CSCs in a context-dependent manner. In future, these modeling insights will be useful in developing improved therapeutic strategies to get rid of harmful CSCs.
1
Date Added: Jan 22, 2021
Date Added: Jan 22, 2021
Asymmetric inheritance of organelle and cellular compounds between daughter cells impacts on the phenotypic variability and was found to be a hallmark for differentiation and rejuvenation in stem-like cells as much as a mechanism for enhancing resistance in bacteria populations. Whether the same processes take place in the context of cancer cell lines is still poorly investigated. Here, we follow the proliferation of a population of human Jurkat T-cells with the use of multicolor flow cytometry, simultaneously measuring the partitioning of three kinds of cellular elements, i.e. cytoplasm, membrane, and mitochondria. The use of multiple live cell markers permits us both to follow the partitioning process for multiple generations and to investigate the correlations between the partitioning of different cellular constituents. Assuming a minimal model of asymmetric partitioning where cell sub-components are divided according to a biased binomial statistics, we derived exact analytical relationships for the average fluorescence intensity and its fluctuations as a function of the generation, obtaining an excellent agreement with the experimental measurements. We found that although cell cytoplasm is divided symmetrically, mitochondria and membrane lipids are asymmetrically distributed between the two daughter cells and present a stable positive correlation with cytoplasm apportioning, which is incompatible with an independent division mechanism. Therefore, our findings show that asymmetric segregation mechanisms can also arise in cancer cell populations, helping us to understand the high phenotypic variability reported in these cancer cell lines. Variability is especially significant for traits like the cell cycle and the growth rate which are deeply interlinked with the mitochondria function. Moreover, the developed experimental and theoretical apparatus can be easily generalized to different cell lines and different kinds of compounds providing a powerful tool for understanding partitioning-driven heterogeneity. In perspective, this could be particularly relevant in the case of tumor micro-environment diversity, where comprehension of the non-genetic cell heterogeneity could pave the way to novel and more targeted therapies.
1
Date Added: Jan 22, 2021
Date Added: Jan 22, 2021
Candida albicans, an opportunistic fungal pathogen, is a significant cause of human infections, particularly in immunocompromised individuals. Phenotypic plasticity between two morphological phenotypes, yeast and hyphae, is a key mechanism by which C. albicans can thrive in many microenvironments and cause disease in the host. Understanding the decision points and key driver genes controlling this important transition, and how these genes respond to different environmental signals, is critical to understanding how C. albicans causes infections in the host. Here we build and analyze a Boolean dynamical model of the C. albicans yeast to hyphal transition, integrating multiple environmental factors and regulatory mechanisms. We validate the model by a systematic comparison to prior experiments, which led to agreement in 18 out of 22 cases. The discrepancies motivate alternative hypotheses that are testable by follow-up experiments. Analysis of this model revealed two time-constrained windows of opportunity that must be met for the complete transition from the yeast to hyphal phenotype, as well as control strategies that can robustly prevent this transition. We experimentally validate two of these control predictions in C. albicans strains lacking the transcription factor UME6 and the histone deacetylase HDA1, respectively. This model will serve as a strong base from which to develop a systems biology understanding of C. albicans morphogenesis.
3
Date Added: Jan 18, 2021
Date Added: Jan 18, 2021
Background: Accurately determining changes in tumor size during therapy is essential to evaluating response or progression. However, individual imaging methodologies often poorly reflect pathologic response and long-term treatment efficacy in patients with estrogen receptor positive (ER+) early-stage breast cancer. Mathematical models that measure tumor progression over time by integrating diverse imaging and tumor measurement modalities are not currently used but could increase accuracy in measuring response and provide biological insights into cancer evolution. Methods: For ER+ breast cancer patients enrolled on a neoadjuvant clinical trial, we reconstructed their tumor size trajectories during therapy by combining all available information on tumor size, including different imaging modalities, physical examinations and pathological assessment data. Tumor trajectories during six months of treatment were generated, using a Gaussian process and the most probable trajectories were evaluated, based on clinical data, using measurement models that account for biases and differences in precision between tumor measurement methods, such as MRI, ultrasound and mammograms. Results: Reconstruction of tumor trajectories during treatment identified five distinct patterns of tumor size changes, including rebound growth not evident from any single modality. These results increase specificity to distinguish innate or acquired resistance compared to using any single measurement alone. The speed of therapeutic response and extent of subsequent rebound tumor growth quantify sensitivity or resistance in this patient population. Conclusions: Tumor trajectory reconstruction integrating multiple modalities of tumor measurement accurately describes tumor progression on therapy and reveals various patterns of patient responses. Mathematical models can integrate diverse response assessments and account for biases in tumor measurement, thereby providing insights into the timing and rate at which resistance emerges.
1
Date Added: Jan 22, 2021
Date Added: Jan 22, 2021
Quantitative traits such as human height are measurable phenotypes that show continuous variation over a wide phenotypic range. Enormous effort has recently been put into determining the genetic influences on a variety of quantitative traits, including human genetic diseases, with mixed success. We identified a quantitative trait in a tractable model system, the GAL pathway in yeast, which controls the uptake and metabolism of the sugar galactose. GAL pathway activation depends both on galactose concentration and on the concentrations of competing, preferred sugars such as glucose. Natural yeast isolates show substantial variation in the behavior of the pathway. All studied yeast strains exhibit bimodal responses relative to external galactose concentration, i.e. a set of galactose concentrations existed at which both GAL-induced and GAL-repressed subpopulations were observed. However, these concentrations differed in different strains. We built a mechanistic model of the GAL pathway and identified parameters that are plausible candidates for capturing the phenotypic features of a set of strains including standard lab strains, natural variants, and mutants. In silico perturbation of these parameters identified variation in the intracellular galactose sensor, Gal3p, the negative feedback node within the GAL regulatory network, Gal80p, and the hexose transporters, HXT, as the main sources of the bimodal range variation. We were able to switch the phenotype of individual yeast strains in silico by tuning parameters related to these three elements. Determining the basis for these behavioral differences may give insight into how the GAL pathway processes information, and into the evolution of nutrient metabolism preferences in different strains. More generally, our method of identifying the key parameters that explain phenotypic variation in this system should be generally applicable to other quantitative traits.
1
Date Added: Jan 18, 2021
Date Added: Jan 18, 2021
The Hereditary Spastic Paraplegias are a group of neurodegenerative diseases characterized by spasticity and weakness in the lower body. Despite the identification of causative mutations in over 70 genes, the molecular aetiology remains unclear. Due to the combination of genetic diversity and variable clinical presentation, the Hereditary Spastic Paraplegias are a strong candidate for protein-protein interaction network analysis as a tool to understand disease mechanism(s) and to aid functional stratification of phenotypes. In this study, experimentally validated human protein-protein interactions were used to create a protein-protein interaction network based on the causative Hereditary Spastic Paraplegia genes. Network evaluation as a combination of both topological analysis and functional annotation led to the identification of core proteins in putative shared biological processes such as intracellular transport and vesicle trafficking. The application of machine learning techniques suggested a functional dichotomy linked with distinct sets of clinical presentations, suggesting there is scope to further classify conditions currently described under the same umbrella term of Hereditary Spastic Paraplegias based on specific molecular mechanisms of disease.
1
Date Added: Jan 22, 2021
Date Added: Jan 22, 2021
Single-cell RNA-sequencing data can revolutionize our understanding of the patterns of cell-cell and ligand-receptor connectivity that influence the function of tissues and organs. However, the quantification and visualization of these patterns are major computational and epistemological challenges. Here, we present , a software package for R which facilitates rapid calculation, and interactive exploration, of cell-cell signaling network topologies contained in single-cell RNA-sequencing data. can be used with any reference set of known ligand-receptor mechanisms. It has built-in functionality to facilitate differential and comparative connectomics, in which complete mechanistic networks are quantitatively compared between systems. includes computational and graphical tools designed to analyze and explore cell-cell connectivity patterns across disparate single-cell datasets. We present approaches to quantify these topologies and discuss some of the biologic theory leading to their design.