Chaos in synthetic microbial communities.

Predictability is a fundamental requirement in biological engineering. As we move to building coordinated multicellular systems, the potential for such systems to display chaotic behaviour becomes a concern. Therefore understanding which systems show chaos is an important design consideration. We developed a methodology to explore the potential for chaotic dynamics in small microbial communities governed by resource competition, intercellular communication and competitive bacteriocin interactions. Our model selection pipeline uses Approximate Bayesian Computation to first identify oscillatory behaviours as a route to finding chaotic behaviour. We have shown that we can expect to find chaotic states in relatively small synthetic microbial systems, understand the governing dynamics and provide insights into how to control such systems. This work is the first to query the existence of chaotic behaviour in synthetic microbial communities and has important ramifications for the fields of biotechnology, bioprocessing and synthetic biology.

Mechanical positioning of multiple nuclei in muscle cells.

Many types of large cells have multiple nuclei. In skeletal muscle fibers, the nuclei are distributed along the cell to maximize their internuclear distances. This myonuclear positioning is crucial for cell function. Although microtubules, microtubule associated proteins, and motors have been implicated, mechanisms responsible for myonuclear positioning remain unclear. We used a combination of rough interacting particle and detailed agent-based modeling to examine computationally the hypothesis that a force balance generated by microtubules positions the muscle nuclei. Rather than assuming the nature and identity of the forces, we simulated various types of forces between the pairs of nuclei and between the nuclei and cell boundary to position the myonuclei according to the laws of mechanics. We started with a large number of potential interacting particle models and computationally screened these models for their ability to fit biological data on nuclear positions in hundreds of Drosophila larval muscle cells. This reverse engineering approach resulted in a small number of feasible models, the one with the best fit suggests that the nuclei repel each other and the cell boundary with forces that decrease with distance. The model makes nontrivial predictions about the increased nuclear density near the cell poles, the zigzag patterns of the nuclear positions in wider cells, and about correlations between the cell width and elongated nuclear shapes, all of which we confirm by image analysis of the biological data. We support the predictions of the interacting particle model with simulations of an agent-based mechanical model. Taken together, our data suggest that microtubules growing from nuclear envelopes push on the neighboring nuclei and the cell boundaries, which is sufficient to establish the nearly-uniform nuclear spreading observed in muscle fibers.

Counter-propagating wave patterns in a swarm model with memory.

Hyperbolic transport-reaction equations are abundant in the description of movement of motile organisms. Here, we focus on a system of four coupled transport-reaction equations that arises from an age-structuring of a species of turning individuals. By modeling how the behavior depends on the time since the last reversal, we introduce a memory effect. The highlight consists of the explicit construction and characterization of counter-propagating traveling waves, patterns which have been observed in bacterial colonies. Stability analysis reveals conditions for the wave formation as well as pulsating-in-time spatially constant solutions.

Analyzing collective motion with machine learning and topology.

We use topological data analysis and machine learning to study a seminal model of collective motion in biology [M. R. D'Orsogna et al., Phys. Rev. Lett. 96, 104302 (2006)]. This model describes agents interacting nonlinearly via attractive-repulsive social forces and gives rise to collective behaviors such as flocking and milling. To classify the emergent collective motion in a large library of numerical simulations and to recover model parameters from the simulation data, we apply machine learning techniques to two different types of input. First, we input time series of order parameters traditionally used in studies of collective motion. Second, we input measures based on topology that summarize the time-varying persistent homology of simulation data over multiple scales. This topological approach does not require prior knowledge of the expected patterns. For both unsupervised and supervised machine learning methods, the topological approach outperforms the one that is based on traditional order parameters.

A Retrospective Assessment of Four Antigen Assays for the Detection of Invasive Candidiasis Among High-Risk Hospitalized Patients.

Because of their high mortality rates and non-specific symptoms, invasive Candida infections pose a huge diagnostic and therapeutic challenge. In this study, we evaluated the three mannan antigen assays Platelia, Platelia Plus and Serion, and the (1-3)-ß-D-glucan assay Fungitell in a group of high-risk (hematological and surgical) patients. Test results of 305 patients hospitalized at the Vienna General Hospital and the University Hospital of Innsbruck were retrospectively analyzed. We assessed the test accuracy by means of descriptive statistics. Nine (2.95%) patients were affected by invasive candidiasis (IC), and 25 (8.2%) patients had a probable/possible infection. The majority of patients (271; 88.9%) showed no signs of infection. The Platelia and Serion mannan assays had a low sensitivity (65% and 52%, respectively), but high specificity (98% for both tests). The newer version of the Platelia assay, the Platelia Plus, had a higher sensitivity (85%) but a lower specificity (89%). The sensitivity of the Fungitell assay was high (100%), while its specificity was low (58%). The positive predictive values were 0.48 for the Platelia and 0.41 for the Serion assay, 0.26 for the Platelia Plus and 0.09 for the Fungitell assay. Our limited, retrospective study suggests the efficacy of mannan assays as screening (Platelia Plus) and confirmatory (Serion) tests, while the Fungitell assay can be used to exclude invasive Candida infections.

Existence of and decay to equilibrium of the filament end density along the leading edge of the lamellipodium.

A model for the dynamics of actin filament ends along the leading edge of the lamellipodium is analyzed. It contains accounts of nucleation by branching, of deactivation by capping, and of lateral flow along the leading edge by polymerization. A nonlinearity arises from a Michaelis-Menten type modeling of the branching process. For branching rates large enough compared to capping rates, the existence and stability of nontrivial steady states is investigated. The main result is exponential convergence to nontrivial steady states, proven by investigating the decay of an appropriate Lyapunov functional.

Sequence-Controlled Polymers via Simultaneous Living Anionic Copolymerization of Competing Monomers.

Natural macromolecules, i.e., sequence-controlled polymers, build the basis for life. In synthetic macromolecular chemistry, reliable tools for the formation of sequence-controlled macromolecules are rare. A robust and efficient chain-growth approach based on the simultaneous living anionic polymerization of sulfonamide-activated aziridines for sequence control of up to five competing monomers resulting in gradient copolymers is presented. The simultaneous azaanionic copolymerization is monitored by real-time (1) H NMR spectroscopy for each monomer at any time during the reaction. The monomer sequence can be adjusted by the monomer reactivity, depending on the electron-withdrawing effect by the sulfonamide (nosyl-, brosyl-, tosyl-, mesyl-, busyl) groups. This method offers unique opportunities for sequence control by competing copolymerization: a step forward to well-engineered synthetic polymers with defined microstructures.

An extended Filament Based Lamellipodium Model produces various moving cell shapes in the presence of chemotactic signals.

The Filament Based Lamellipodium Model (FBLM) is a two-phase two-dimensional continuum model, describing the dynamics of two interacting families of locally parallel actin filaments (Oelz and Schmeiser, 2010b). It contains accounts of the filaments' bending stiffness, of adhesion to the substrate, and of cross-links connecting the two families. An extension of the model is presented with contributions from nucleation of filaments by branching, from capping, from contraction by actin-myosin interaction, and from a pressure-like repulsion between parallel filaments due to Coulomb interaction. The effect of a chemoattractant is described by a simple signal transduction model influencing the polymerization speed. Simulations with the extended model show its potential for describing various moving cell shapes, depending on the signal transduction procedure, and for predicting transients between non-moving and moving states as well as changes of direction.

Large-scale mitochondrial DNA analysis in Southeast Asia reveals evolutionary effects of cultural isolation in the multi-ethnic population of Myanmar.

BACKGROUND: Myanmar is the largest country in mainland Southeast Asia with a population of 55 million people subdivided into more than 100 ethnic groups. Ruled by changing kingdoms and dynasties and lying on the trade route between India and China, Myanmar was influenced by numerous cultures. Since its independence from British occupation, tensions between the ruling Bamar and ethnic minorities increased. RESULTS: Our aim was to search for genetic footprints of Myanmar's geographic, historic and sociocultural characteristics and to contribute to the picture of human colonization by describing and dating of new mitochondrial DNA (mtDNA) haplogroups. Therefore, we sequenced the mtDNA control region of 327 unrelated donors and the complete mitochondrial genome of 44 selected individuals according to highest quality standards. CONCLUSION: Phylogenetic analyses of the entire mtDNA genomes uncovered eight new haplogroups and three unclassified basal M-lineages. The multi-ethnic population and the complex history of Myanmar were reflected in its mtDNA heterogeneity. Population genetic analyses of Burmese control region sequences combined with population data from neighboring countries revealed that the Myanmar haplogroup distribution showed a typical Southeast Asian pattern, but also Northeast Asian and Indian influences. The population structure of the extraordinarily diverse Bamar differed from that of the Karen people who displayed signs of genetic isolation. Migration analyses indicated a considerable genetic exchange with an overall positive migration balance from Myanmar to neighboring countries. Age estimates of the newly described haplogroups point to the existence of evolutionary windows where climatic and cultural changes gave rise to mitochondrial haplogroup diversification in Asia.

Controlling periodic long-range signalling to drive a morphogenetic transition.

Cells use signal relay to transmit information across tissue scales. However, the production of information carried by signal relay remains poorly characterised. To determine how the coding features of signal relay are generated, we used the classic system for long-range signalling: the periodic cAMP waves that drive Dictyostelium collective migration. Combining imaging and optogenetic perturbation of cell signalling states, we find that migration is triggered by an increase in wave frequency generated at the signalling centre. Wave frequency is regulated by cAMP wave circulation, which organises the long-range signal. To determine the mechanisms modulating wave circulation, we combined mathematical modelling, the general theory of excitable media, and mechanical perturbations to test competing models. Models in which cell density and spatial patterning modulate the wave frequency cannot explain the temporal evolution of signalling waves. Instead, our evidence leads to a model where wave circulation increases the ability for cells to relay the signal, causing further increase in the circulation rate. This positive feedback between cell state and signalling pattern regulates the long-range signal coding that drives morphogenesis.

Autocrine IL-6 drives cell and extracellular matrix anisotropy in scar fibroblasts.

Fibrosis is associated with dramatic changes in extracellular matrix (ECM) architecture of unknown etiology. Here we exploit keloid scars as a paradigm to understand fibrotic ECM organization. We reveal that keloid patient fibroblasts uniquely produce a globally aligned ECM network in 2-D culture as observed in scar tissue. ECM anisotropy develops after rapid initiation of a fibroblast supracellular actin network, suggesting that cell alignment initiates ECM patterning. Keloid fibroblasts produce elevated levels of IL-6, and autocrine IL-6 production is both necessary and sufficient to induce cell and ECM alignment, as evidenced by ligand stimulation of normal dermal fibroblasts and treatment of keloid fibroblasts with the function blocking IL-6 receptor monoclonal antibody, tocilizumab. Downstream of IL-6, supracellular organization of keloid fibroblasts is controlled by activation of cell-cell adhesion. Adhesion formation inhibits contact-induced cellular overlap leading to nematic organization of cells and an alignment of focal adhesions. Keloid fibroblasts placed on isotropic ECM align the pre-existing matrix, suggesting that focal adhesion alignment leads to active anisotropic remodeling. These results show that IL-6-induced fibroblast cooperativity can control the development of a nematic ECM, highlighting both IL-6 signaling and cell-cell adhesions as potential therapeutic targets to inhibit this common feature of fibrosis.

How environment affects active particle swarms: a case study.

We investigate the collective motion of self-propelled agents in an environment filled with obstacles that are tethered to fixed positions via springs. The active particles are able to modify the environment by moving the obstacles through repulsion forces. This creates feedback interactions between the particles and the obstacles from which a breadth of patterns emerges (trails, band, clusters, honey-comb structures, etc.). We will focus on a discrete model first introduced in Aceves-Sanchez P et al. (2020, Bull. Math. Biol. 82, 125 (doi:10.1007/s11538-020-00805-z)), and derived into a continuum PDE model. As a first major novelty, we perform an in-depth investigation of pattern formation of the discrete and continuum models in two dimensions: we provide phase-diagrams and determine the key mechanisms for bifurcations to happen using linear stability analysis. As a result, we discover that the agent-agent repulsion, the agent-obstacle repulsion and the obstacle's spring stiffness are the key forces in the appearance of patterns, while alignment forces between the particles play a secondary role. The second major novelty lies in the development of an innovative methodology to compare discrete and continuum models that we apply here to perform an in-depth analysis of the agreement between the discrete and continuum models.

Reverse-engineering forces responsible for dynamic clustering and spreading of multiple nuclei in developing muscle cells.

How cells position their organelles is a fundamental biological question. During Drosophila embryonic muscle development, multiple nuclei transition from being clustered together to splitting into two smaller clusters to spreading along the myotube's length. Perturbations of microtubules and motor proteins disrupt this sequence of events. These perturbations do not allow intuiting which molecular forces govern the nuclear positioning; we therefore used computational screening to reverse-engineer and identify these forces. The screen reveals three models. Two suggest that the initial clustering is due to nuclear repulsion from the cell poles, while the third, most robust, model poses that this clustering is due to a short-ranged internuclear attraction. All three models suggest that the nuclear spreading is due to long-ranged internuclear repulsion. We test the robust model quantitatively by comparing it with data from perturbed muscle cells. We also test the model using agent-based simulations with elastic dynamic microtubules and molecular motors. The model predicts that, in longer mammalian myotubes with a large number of nuclei, the spreading stage would be preceded by segregation of the nuclei into a large number of clusters, proportional to the myotube length, with a small average number of nuclei per cluster.

Cubosomes stabilized by a polyphosphoester-analog of Pluronic F127 with reduced cytotoxicity.

Lyotropic liquid crystalline nanoparticles with bicontinuous cubic internal nanostructure, known as cubosomes, have been proposed as nanocarriers in various medical applications. However, as these nanoparticles show a certain degree of cytotoxicity, particularly against erythrocytes, their application in systemic administrations is limited to date. Intending to produce a more biocompatible formulation, we prepared cubosomes for the first time stabilized with a biodegradable polyphosphoester-analog of the commonly used Pluronic F127. The ABA-triblock copolymer poly(methyl ethylene phosphate)-block-poly(propylene oxide)-block-poly(methyl ethylene phosphate) (PMEP-b-PPO-b-PMEP) was prepared by organocatalyzed ring-opening polymerization of MEP. The cytotoxic features of the resulting formulation were investigated against two different cell lines (HEK-293 and HUVEC) and human red blood cells. The response of the complement system was also evaluated. Results proved the poly(phosphoester)-based formulation was significantly less toxic than that prepared using Pluronic F127 with respect to all the tested cell lines and, more importantly, hemolysis assay and complement system activation tests demonstrated its very high hemocompatibility. The potentially biodegradable poly(phosphoester)-based cubosomes represent a new and versatile platform for preparation of functional and smart nanocarriers.

Centering and symmetry breaking in confined contracting actomyosin networks.

Centering and decentering of cellular components is essential for internal organization of cells and their ability to perform basic cellular functions such as division and motility. How cells achieve proper localization of their organelles is still not well-understood, especially in large cells such as oocytes. Here, we study actin-based positioning mechanisms in artificial cells with persistently contracting actomyosin networks, generated by encapsulating cytoplasmic Xenopus egg extracts into cell-sized 'water-in-oil' droplets. We observe size-dependent localization of the contraction center, with a symmetric configuration in larger cells and a polar one in smaller cells. Centering is achieved via a hydrodynamic mechanism based on Darcy friction between the contracting network and the surrounding cytoplasm. During symmetry breaking, transient attachments to the cell boundary drive the contraction center to a polar location. The centering mechanism is cell-cycle dependent and weakens considerably during interphase. Our findings demonstrate a robust, yet tunable, mechanism for subcellular localization.

In order to survive, cells need to react to their environment and change their shape or the localization of their internal components. For example, the nucleus ­ the compartment that contains the genetic information ­ is often localized at the center of the cell, but it can also be positioned at the side, for instance when cells move or divide asymmetrically. Cells use multiple positioning mechanisms to move their internal components, including a process that relies on networks of filaments made of a protein known as actin. These networks are constantly remodeled as actin proteins are added and removed from the network. Embedded molecular motors can cause the network of actin filaments to contract and push or pull on the compartments. Yet, the exact way these networks localize components in the cell remains unclear, especially in eggs and other large cells. To investigate this question, Ierushalmi et al. studied the actin networks in artificial cells that they created by enclosing the contents of frog eggs in small droplets surrounded by oil. This showed that the networks contracted either to the center of the cell or to its side. Friction between the contracting actin network and the fluid in the cell generated a force that tends to push the contraction center towards the middle of the cell. In larger cells, this led to the centering of the actin network. In smaller cells however, the network transiently attached to the boundary of the cell, leading the contraction center to be pulled to one side. By developing simpler artificial cells that mimic the positioning processes seen in real-life cells, Ierushalmi et al. discovered new mechanisms for how cells may center or de-center their components. This knowledge may be useful to understand diseases that can emerge when the nucleus or other compartments fail to move to the right location, and which are associated with certain organs developing incorrectly.

Nuclear Scaling Is Coordinated among Individual Nuclei in Multinucleated Muscle Fibers.

Optimal cell performance depends on cell size and the appropriate relative size, i.e., scaling, of the nucleus. How nuclear scaling is regulated and contributes to cell function is poorly understood, especially in skeletal muscle fibers, which are among the largest cells, containing hundreds of nuclei. Here, we present a Drosophila in vivo system to analyze nuclear scaling in whole multinucleated muscle fibers, genetically manipulate individual components, and assess muscle function. Despite precise global coordination, we find that individual nuclei within a myofiber establish different local scaling relationships by adjusting their size and synthetic activity in correlation with positional or spatial cues. While myonuclei exhibit compensatory potential, even minor changes in global nuclear size scaling correlate with reduced muscle function. Our study provides the first comprehensive approach to unraveling the intrinsic regulation of size in multinucleated muscle fibers. These insights to muscle cell biology will accelerate the development of interventions for muscle diseases.

Quantitative regulation of the dynamic steady state of actin networks.

Principles of regulation of actin network dimensions are fundamentally important for cell functions, yet remain unclear. Using both in vitro and in silico approaches, we studied the effect of key parameters, such as actin density, ADF/Cofilin concentration and network width on the network length. In the presence of ADF/Cofilin, networks reached equilibrium and became treadmilling. At the trailing edge, the network disintegrated into large fragments. A mathematical model predicts the network length as a function of width, actin and ADF/Cofilin concentrations. Local depletion of ADF/Cofilin by binding to actin is significant, leading to wider networks growing longer. A single rate of breaking network nodes, proportional to ADF/Cofilin density and inversely proportional to the square of the actin density, can account for the disassembly dynamics. Selective disassembly of heterogeneous networks by ADF/Cofilin controls steering during motility. Our results establish general principles on how the dynamic steady state of actin network emerges from biochemical and structural feedbacks.

Microwave-Assisted Desulfonylation of Polysulfonamides toward Polypropylenimine.

Linear polyethylenimine (L-PEI) has been the gold standard for gene delivery and is typically prepared by hydrolysis from poly(2-oxazoline)s. Recently, also the anionic polymerization of activated aziridines was reported as a potential pathway toward linear and well-defined polyamines. However, only sulfonamide-activated aziridines so far undergo the living anionic polymerization and their desulfonylation was only reported scarcely. This is mainly due to the relatively high stability of the sulfonamides and the drastic change in solubility during the desulfonylation. Herein, we investigated the desulfonylation of such poly(aziridine)s prepared from tosylated or mesylated propyleneimine to afford linear polypropylenimine (L-PPI) as an alternative to L-PEI. Different desulfonylation strategies for tosylated (Ts) and mesylated (Ms) PPI were studied. The reductive cleavage of the sulfonamide with sodium bis(2-methoxy ethoxy) aluminum hydride yielded 80% of deprotected amine groups. Quantitative conversion to L-PPI was obtained, when the tosylated PPI was hydrolyzed under acidic conditions with pTsOH under microwave (MW) irradiation. The same treatment removed 90% of the mesyl groups from the mesylated PPI analog. The MW-assisted acidic hydrolysis represents a fast, inexpensive and easy approach in comparison to other methods, where complex reaction conditions and tedious purifications are major drawbacks, however some chain scission may occur. The high purity of the obtained products, in combination with the versatility of the activated aziridine chemistry, demonstrate many advantages of our strategy, especially for future biomedical implementations.

Agent-based modeling: case study in cleavage furrow models.

The number of studies in cell biology in which quantitative models accompany experiments has been growing steadily. Roughly, mathematical and computational techniques of these models can be classified as "differential equation based" (DE) or "agent based" (AB). Recently AB models have started to outnumber DE models, but understanding of AB philosophy and methodology is much less widespread than familiarity with DE techniques. Here we use the history of modeling a fundamental biological problem-positioning of the cleavage furrow in dividing cells-to explain how and why DE and AB models are used. We discuss differences, advantages, and shortcomings of these two approaches.

Multihydroxy Polyamines by Living Anionic Polymerization of Aziridines.

Acetal-protected and sulfonamide-activated aziridines (Az) have been prepared and polymerized by living anionic polymerization with molecular weight dispersities in most cases below D < 1.2 and controlled molecular weights. Three new monomers have been prepared varying in the length of the pendant chain. The resulting double protected polymers can be selectively deprotected in order to release the polyamine or the polyol structures. Detailed structural characterization was performed for all polymers, and chain extension proves their living polymerization behavior and the formation of block copolymers. Thermal analysis can be used in order to follow the deprotection steps. These new protected monomers broaden the scope of the azaanionic polymerization of aziridines and may find useful applications as well-defined functional poly(ethylene imine) derivatives.