Quantitative Biology - Subcellular Processes Publications (50)

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Quantitative Biology - Subcellular Processes Publications

Current understanding of how contractility emerges in disordered actomyosin networks of non-muscle cells is still largely based on the intuition derived from earlier works on muscle contractility. This view, however, largely overlooks the free energy gain following passive cross-linker binding, which, even in the absence of active fluctuations, provides a thermodynamic drive towards highly overlapping filamentous states. In this work, we shed light on this phenomenon, showing that passive cross-linkers, when considered in the context of two anti-parallel filaments, generate noticeable contractile forces. Read More


Telomeres, the nucleoprotein complexes at the termini of linear chromosomes, are essential roles for end-replication, end protection, and chromatin segregation. Each process represents an obstacle for genome stability. How these problems were overcome in evolution is unknown. Read More


Natural phenomena frequently involve a very large number of interacting molecules moving in confined regions of space. Cellular transport by motor proteins is an example of such collective behavior. We derive a deterministic compartmental model for the unidirectional flow of particles along a one-dimensional lattice of sites with nearest-neighbor interactions between the particles. Read More


Neurotransmitter receptor molecules, concentrated in synaptic membrane domains along with scaffolds and other kinds of proteins, are crucial for signal transmission across chemical synapses. In common with other membrane protein domains, synaptic domains are characterized by low protein copy numbers and protein crowding, with rapid stochastic turnover of individual molecules. We study here in detail a stochastic lattice model of the receptor-scaffold reaction-diffusion dynamics at synaptic domains that was found previously to capture, at the mean-field level, the self-assembly, stability, and characteristic size of synaptic domains observed in experiments. Read More


Crowded environments modify the diffusion of macromolecules, generally slowing their movement and inducing transient anomalous subdiffusion. The presence of obstacles also modifies the kinetics and equilibrium behavior of tracers. While previous theoretical studies of particle diffusion have typically assumed either impenetrable obstacles or binding interactions that immobilize the particle, in many cellular contexts bound particles remain mobile. Read More


We report here new electrical laws, derived from nonlinear electro-diffusion theory, about the effect of the local geometrical structure, such as curvature, on the electrical properties of a cell. We adopt the Poisson-Nernst-Planck (PNP) equations for charge concentration and electric potential as a model of electro-diffusion. In the case at hand, the entire boundary is impermeable to ions and the electric field satisfies the compatibility condition of Poisson's equation. Read More


Local Ca Releases (LCRs) are crucial events involved in cardiac pacemaker cell function. However, specific algorithms for automatic LCR detection and analysis have not been developed in live, spontaneously beating pacemaker cells. Here we measured LCRs using a high-speed 2D-camera in spontaneously contracting sinoatrial (SA) node cells isolated from rabbit and guinea pig and developed a new algorithm capable of detecting and analyzing the LCRs spatially in two-dimensions, and in time. Read More


We present a conditional generative model to learn variation in cell and nuclear morphology and the location of subcellular structures from microscopy images. Our model generalizes to a wide range of subcellular localization and allows for a probabilistic interpretation of cell and nuclear morphology and structure localization from fluorescence images. We demonstrate the effectiveness of our approach by producing photo-realistic cell images using our generative model. Read More


One of the causes of high fidelity of copying in biological systems is kinetic discrimination. In this mechanism larger dissipation and copying velocity result in improved copying accuracy. We consider a model of a polymerase which simultaneously copies a single stranded RNA and opens a single- to double-stranded junction serving as an obstacle. Read More


Ammonium assimilation in E. coli is regulated by two paralogous proteins (GlnB and GlnK), which orchestrate interactions with regulators of gene expression, transport proteins and metabolic pathways. Yet how they conjointly modulate the activity of glutamine synthetase (GS), the key enzyme for nitrogen assimilation, is poorly understood. Read More


The intrinsic stochasticity of gene expression can give rise to large fluctuations and rare events that drive phenotypic variation in a population of genetically identical cells. Characterizing the fluctuations that give rise to such rare events motivates the analysis of large deviations in stochastic models of gene expression. Recent developments in non-equilibrium statistical mechanics have led to a framework for analyzing Markovian processes conditioned on rare events and for representing such processes by conditioning-free driven Markovian processes. Read More


Hyperamylinemia, a condition characterized by above-normal blood levels of the pancreas-derived peptide amylin, accompanies obesity and precedes type II diabetes. Human amylin oligomerizes easily and can deposit in the pancreas, brain, and heart, where they have been associated with calcium dysregulation. In the heart, accumulating evidence suggests that human amylin oligomers form modestly cation-selective, voltage-dependent ion channels that embed in the cell sarcolemma (SL). Read More


The chromosome is a key player of cell physiology, and its dynamics provides valuable information about its physical organization. In both prokaryotes and eukaryotes, the short-time motion of chromosomal loci has been described as a Rouse model in a simple or viscoelastic medium. However, little emphasis has been put on the role played by the folded organization of chromosomes on the local dynamics. Read More


Transcription of the genetic message encoded chemically in the sequence of the DNA template is carried out by a molecular machine called RNA polymerase (RNAP). Backward or forward slippage of the nascent RNA with respect to the DNA template strand give rise to a transcript that is, respectively, longer or shorter than the corresponding template. We model a RNAP as a "Tape-copying Turing machine" (TCTM) where the DNA template is the input tape while the nascent RNA strand is the output tape. Read More


In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses to enzyme perturbations only from network topology, and then proved a theorem, called the law of localization, explaining response patterns in terms of network topology. In this paper, we generalize these results to reaction networks with conserved concentrations, which allows us to study any reaction systems. Read More


During asymmetric cell divisions, cortical dyneins generate forces essential to position the spindle after polarity cues, prescribing daughter cells fate. In nematode zygote, cortical dynein pulls on microtubules transiently, raising the question of its targeting and dynamics. Tracking and fluorescence correlation spectroscopy revealed that in the cytoplasm, dynein spots displayed directed motions toward the cortex, localized at microtubule plus-ends through EBP-2/EB but are not actively transported. Read More


The plant hormones brassinosteroid (BR) and gibberellin (GA) have important roles in a wide range of processes involved in plant growth and development. The BR signalling pathway acts by altering the phosphorylation state of its transcription factors BZR1/2, whereas the GA signalling pathway acts by reducing the stability of its transcription factor DELLA. Both signalling pathways include a negative feedback, with high levels of BR causing increased repression of key BR-biosynthetic genes mediated by BZR1/2, and high levels of GA causing decreased stability of DELLA, where DELLA is responsible for activating key genes involved in GA biosynthesis. Read More


We develope a two-species exclusion process with a distinct pair of entry and exit sites for each species of rigid rods. The relatively slower forward stepping of the rods in an extended bottleneck region, located in between the two entry sites, controls the extent of interference of the co-directional flow of the two species of rods. The relative positions of the sites of entry of the two species of rods with respect to the location of the bottleneck are motivated by a biological phenomenon. Read More


Via a concomitant communication (the first part of my work), I have conclusively debunked the prevailing explanations for mitochondrial oxidative phosphorylation and established the need for a novel rationale to account for the reaction paradigm. Towards the same, murburn concept is hereby floated as a viable explanation (in the second part of my work). It is proposed that the inner mitochondrial membrane (harboring the various metal and flavin enzyme complexes) serves as means to confine and stabilize radical reactions, which effectively couple and bring about ATP synthesis in the proton-deficient microcosm. Read More


Robustness of spatial pattern against perturbations is an indispensable property of developmental processes for organisms, which need to adapt to changing environments. Although specific mechanisms for this robustness have been extensively investigated, little is known about a general mechanism for achieving robustness in reaction-diffusion systems. Here, we propose a buffered reaction-diffusion system, in which active states of chemicals mediated by buffer molecules contribute to reactions, and demonstrate that robustness of the pattern wavelength is achieved by the dynamics of the buffer molecule. Read More


Here we report on a set of programs developed at the ZMBH Bio-Imaging Facility for tracking real-life images of cellular processes. These programs perform 1) automated tracking; 2) quantitative and comparative track analyses of different images in different groups; 3) different interactive visualization schemes; and 4) interactive realistic simulation of different cellular processes for validation and optimal problem-specific adjustment of image acquisition parameters (tradeoff between speed, resolution, and quality with feedback from the very final results). The collection of programs is primarily developed for the common bio-image analysis software ImageJ (as a single Java Plugin). Read More


We study a generic one-dimensional model for an intracellular cargo driven by N motor proteins against an external applied force. The model includes motor-cargo and motor-motor interactions. The cargo motion is described by an over-damped Langevin equation, while motor dynamics is specified by hopping rates which follow a local detailed balance condition with respect to change in energy per hopping event. Read More


Allosteric molecules serve as regulators of cellular activity across all domains of life. We present a general theory of allosteric transcriptional regulation that permits quantitative predictions for how physiological responses are tuned to environmental stimuli. To test the model's predictive power, we apply it to the specific case of the ubiquitous simple repression motif in bacteria. Read More


Efficient bacterial chromosome segregation typically requires the coordinated action of a three-components, ATP-fueled machinery called the partition complex. We present a phenomenological model accounting for the dynamic activity of this system. The model is obtained by coupling simple linear reaction-diffusion equations with a proteophoresis, or "volumetric" chemophoresis, force field. Read More


As a cheap and safe antimalarial agent, chloroquine (CQ) has been used in the battle against malaria for more than half century. However, the mechanism of CQ action and resistance in Plasmodium falciparum remains elusive. Based on further analysis of our published experimental results, we propose that the mechanism of CQ action and resistance might be closely linked with cell-cycle-associated amplified genomic-DNA fragments (CAGFs, singular form = CAGF) as CQ induces CAGF production in P. Read More


Background: During asymmetric division of the Caenorhabditis elegans nematode zygote, the polarity cues distribution and daughter cell fates depend on the correct positioning of the mitotic spindle which results from both centering and cortical pulling forces. Revealed by spindle rocking, these pulling forces are regulated by the force generator dynamics, which are related to mitosis progression. This may be combined with a second regulation, this one by the posterior spindle pole position, which can be seen when comparing related species. Read More


Protein synthesis rates are determined, at the translational level, by properties of the transcript's sequence. The efficiency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of the ribosomes, or the codon usage establishing the speed of protein elongation. In this work we promote transcript length as a further key determinant of translation efficiency. Read More


Cytochrome C oxidase and FoF1-ATP synthase constitute complex IV and V, respectively, of the five membrane-bound enzymes in mitochondria comprising the respiratory chain. These enzymes are located in the inner mitochondrial membrane (IMM), which exhibits large invaginations called cristae. According to recent cryo-tomography, FoF1-ATP synthases are located predominantly at the rim of the cristae, while cytochrome C oxidases are likely distributed in planar membrane areas of the cristae. Read More


We study the coarsening of strongly microphase separated membrane domains in the presence of recycling of material. We study the dynamics of the domain size distribution under both scale-free and size-dependent recycling. Closed form solutions to the steady state distributions and its associated central moments are obtained in both cases. Read More


We present a framework for computing the gating properties of ligand-gated ion channel mutants using the Monod-Wyman-Changeux (MWC) model of allostery. We derive simple analytic formulas for key functional properties such as the leakiness, dynamic range, half-maximal effective concentration, and effective Hill coefficient, and explore the full spectrum of phenotypes that are accessible through mutations. Specifically, we consider mutations in the channel pore of nicotinic acetylcholine receptor (nAChR) and the ligand binding domain of a cyclic nucleotide-gated (CNG) ion channel, demonstrating how each mutation can be characterized as only affecting a subset of the biophysical parameters. Read More


Gene transcription is a critical step in gene expression. The currently accepted physical model of transcription predicts the existence of a physical limit on the maximal rate of transcription, which does not depend on the transcribed gene. This limit appears as a result of polymerase "traffic jams" forming in the bulk of the 1D DNA chain at high polymerase concentrations. Read More


Cells contain elaborate and interconnected networks of protein polymers which make up the cytoskeleton. The cytoskeleton governs the internal positioning and movement of vesicles and organelles, and controls dynamic changes in cell polarity, shape and movement. Many of these processes require tight control of the size and shape of cytoskeletal structures, which is achieved despite rapid turnover of their molecular components. Read More


Current treatment strategy for chronic myeloid leukemia (CML) mainly includes inhibition of tyrosine kinase activity, which has dramatically improved the prognosis of the disease but without cure. In addition some patients may become drug resistant. Thus there is still the need for other therapies to avoid resistance and if possible to cure the disease. Read More


We present a generalized Landau-Brazovskii free energy for the solidification of chiral molecules on a spherical surface in the context of the assembly of viral shells. We encounter two types of icosahedral solidification transitions. The first type is a conventional first-order phase transition from the uniform to the icosahedral state. Read More


The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic processes, yet a simple and unified treatment of the effects of allostery in enzymes has been lacking. In this work, we take the first step towards this goal by modeling allosteric enzymes and their interaction with two key molecular players - allosteric regulators and competitive inhibitors. Read More


A tri-block nanoparticle (TBN) comprising of an enzymatically cleavable porous gelatin nanocore encapsulated with gefitinib (tyrosine kinase inhibitor (TKI)) and surface functionalized with cetuximab-siRNA conjugate has been synthesized. Targeted delivery of siRNA to undruggable KRAS mutated non-small cell lung cancer cells would sensitize the cells to TKI drugs and offers an efficient therapy for treating cancer; however, efficient delivery of siRNA and releasing it in cytoplasm remains a major challenge. We have shown TBN can efficiently deliver siRNA to cytoplasm of KRAS mutant H23 Non-Small Cell Lung Cancer (NSCLC) cells for oncogene knockdown; subsequently, sensitizing it to TKI. Read More


Understanding the operation of biological molecular motors, nanoscale machines that transduce electrochemical energy into mechanical work, is enhanced by bottom-up strategies to synthesize novel motors. Read More


Viruses are incapable of autonomous energy production. Although many experimental studies make it clear that viruses are parasitic entities that hijack the host's molecular resources, a detailed estimate for the energetic cost of viral synthesis is largely lacking. To quantify the energetic cost of viruses to their hosts, we enumerated the costs associated with two very distinct but representative DNA and RNA viruses, namely T4 and influenza. Read More


HIV-1 virions assemble as immature particles containing Gag polyproteins that are processed by the viral protease into individual components, resulting in the formation of mature infectious particles. There are two competing models for the process of forming the mature HIV-1 core: the disassembly and de novo reassembly model and the non-diffusional displacive model. To study the maturation pathway, we simulate HIV-1 maturation in vitro by digesting immature particles and assembled virus-like particles with recombinant HIV-1 protease and monitor the process with biochemical assays and cryoEM structural analysis in parallel. Read More


Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. In 2000, Elowitz and Leibler showed that by rational design of the reaction network, and using existing biological components, they could create a network that exhibits periodic gene expression, dubbed the repressilator (Elowitz and Leibler, Nature, 2000). More recently, Stricker et al. Read More


In this paper, we develop and analyze a minimal model for a 2D network of cross-linked actin filaments and myosin motors, representing the cortical cytoskeleton of eukaryotic cells. We implement coarse-grained representations of force production by myosin motors and stress dissipation through an effective cross-link friction and filament turnover. We use this model to characterize how the sustained production of active stress, and the steady dissipation of elastic stress, depend individually on motor activity, effective cross-link friction and filament turnover. Read More


Membrane-protein systems constitute an important avenue for a variety of targeted therapies. The ability to alter these systems remotely via physical fields is highly desirable for the advance of noninvasive therapies. Biophysical action of acoustic fields in particular holds immense potential for applications in drug delivery and neuro-modulation. Read More


Theoretical analysis, which maps single molecule time trajectories of a molecular motor onto unicyclic Markov processes, allows us to evaluate the heat dissipated from the motor and to elucidate its dependence on the mean velocity and diffusivity. Unlike passive Brownian particles in equilibrium, the velocity and diffusion constant of molecular motors are closely inter-related to each other. In particular, our study makes it clear that the increase of diffusivity with the heat production is a natural outcome of active particles, which is reminiscent of the recent experimental premise that the diffusion of an exothermic enzyme is enhanced by the heat released from its own catalytic turnover. Read More


Using a microfluidic trap, we study the behavior of individual phospholipid vesicles in contact with fatty acids. We show that spontaneous fatty acids insertion inside the bilayer is controlled by the vesicle size, osmotic pressure difference across the membrane and fatty acids concentration in the external bath. Depending on these parameters, vesicles can grow spherically or become unstable and fragment into several daughter vesicles. Read More


This article presents an algorithm for the evaluation of organelles' movements inside of an unmodified live cell. We used a time-lapse image series obtained using wide-field bright-field photon transmission microscopy as an algorithm input. The benefit of the algorithm is the application of the R\'enyi information entropy, namely a variable called a point information gain, which enables to highlight the borders of the intracellular organelles and to localize the organelles' centers of mass with the precision of one pixel. Read More


In a previous paper, we examined a class of possible conformations for helically patterned filaments in contact with a bonding surface. In particular, we investigated geometries where contact between the pattern and the surface was improved through a periodic twisting and lifting of the filament. A consequence of this lifting is that the total length of the filament projected onto the surface decreases after bonding. Read More


We report an experimental study of the influences of the fixed charge and bulk ionic concentrations on the conduction of biological ion channels, and we consider the results within the framework of the ionic Coulomb blockade model of permeation and selectivity. Voltage clamp recordings were used to investigate the Na$^+$/Ca$^{2+}$ anomalous mole fraction effect (AMFE) exhibited by the bacterial sodium channel NaChBac and its mutants. Site-directed mutagenesis was used to study the effect of either increasing or decreasing the fixed charge in their selectivity filters for comparison with the predictions of the Coulomb blockade model. Read More


The principal pacemaker of the circadian clock of the cyanobacterium S. elongatus is a protein phosphorylation cycle consisting of three proteins, KaiA, KaiB and KaiC. KaiC forms a homohexamer, with each monomer consisting of two domains, CI and CII. Read More


Recently the physical characterization of a number of biological processes has proven indispensable for a full understanding of natural phenomena. One such example is the mechanical properties of transcription, which have been shown to have significant effects in gene expression. In this letter we introduce a simple description of the basic physical elements of transcription where RNA elongation, RNA polymerase rotation and DNA supercoiling are coupled. Read More


Gene expression is a noisy process that leads to regime shift between alternative steady states among individual living cells, inducing phenotypic variability. The effects of white noise on the regime shift in bistable systems have been well characterized, however little is known about such effects of colored noise (noise with non-zero correlation time). Here, we show that noise correlation time, by considering a genetic circuit of autoactivation, can have significant effect on the regime shift in gene expression. Read More