Anna Gavrilova, Nickolay Korabel, Victoria J. Allan
et al.
Transport of dense core vesicles (DCVs) in neurons is crucial for distributing molecules like neuropeptides and growth factors. We studied the experimental trajectories of dynein-driven directed movement of DCVs in the ALA neuron C. elegans over a duration of up to 6 seconds. We analysed the DCV movement in three strains of C. elegans: 1) with normal kinesin-1 function, 2) with reduced function in kinesin light chain 2 (KLC-2), and 3) a null mutation in kinesin light chain 1 (KLC-1). We find that DCVs move superdiffusively with displacement variance $var(x) \sim t^2$ in all three strains with low reversal rates and frequent immobilization of DCVs. The distribution of DCV displacements fits a beta-binomial distribution with the mean and the variance following linear and quadratic growth patterns, respectively. We propose a simple heterogeneous random walk model to explain the observed superdiffusive retrograde transport behaviour of DCV movement. This model involves a random probability with the beta density for a DCV to resume its movement or remain in the same position.
Protoplasts represent a unique experimental system for the circulation and formation of genetically modified plants. Here, protoplasts were isolated from genetically modified hairy root tissues of Brassica oleracea L. induced by the Agrobacterium rhizogenes strain (ATCC13332). The concentration of enzyme solutions utilized for protoplast isolation was 1.5 % Cellulase YC and 0.1 % Pectolyase Y23 in 13% mannitol solution, which resulted in high efficiency of isolation within 8 hours, in which the protoplast yield was 2 x 104 cells ml-1 and the percentage of viability was 72%. Each protoplast has one nucleus with a nucleation of 48%. A polymerase chain reaction (PCR) assay verified the presence of rol B and rol C genes in hairy root tissues by detaching a single bundle of DNA replication from these roots using a specific pair of primers. The current study demonstrated that A. rhizogenes strain (ATCC13332) is a vector for the incorporation of T-DNA genes into cauliflower plants, as well as the success of the hairy roots retention of rol B and rol C genes transferred to it.
Nickolay Korabel, Daniel Han, Alessandro Taloni
et al.
A major open problem in biophysics is to understand the highly heterogeneous transport of many structures inside living cells, such as endosomes. We find that mathematically it is described by spatio-temporal heterogeneous fractional Brownian motion (hFBM) which is defined as FBM with a randomly switching anomalous exponent and random generalized diffusion coefficient. Using a comprehensive local analysis of a large ensemble of experimental endosome trajectories (> 10^5), we show that their motion is characterized by power-law probability distributions of displacements and displacement increments, exponential probability distributions of local anomalous exponents and power-law probability distributions of local generalized diffusion coefficients of endosomes which are crucial ingredients of spatio-temporal hFBM. The increased sensitivity of deep learning neural networks for FBM characterisation corroborates the development of this multi-fractal analysis. Our findings are an important step in understanding endosome transport. We also provide a powerful tool for studying other heterogeneous cellular processes.
Liquid-liquid phase separated (LLPS) states are key to compartmentalise components in the absence of membranes, however it is unclear whether LLPS condensates are actively and specifically organized in the sub-cellular space and by which mechanisms. Here, we address this question by focusing on the ParABS DNA segregation system, composed of a centromeric-like sequence (parS), a DNA-binding protein (ParB) and a motor (ParA). We show that parS-ParB associate to form nanometer-sized, round condensates. ParB molecules diffuse rapidly within the nucleoid volume, but display confined motions when trapped inside ParB condensates. Single ParB molecules are able to rapidly diffuse between different condensates, and nucleation is strongly favoured by parS. Notably, the ParA motor is required to prevent the fusion of ParB condensates. These results describe a novel active mechanism that splits, segregates and localises non-canonical LLPS condensates in the sub-cellular space.
Many proteins that undergo sequential enzymatic modification in the Golgi cisternae are displayed at the plasma membrane as cell identity markers. The modified proteins, called glycans, represent a molecular code. The fidelity of this glycan code is measured by how accurately the glycan synthesis machinery realises the desired target glycan distribution for a particular cell type and niche. In this paper, we quantitatively analyse the tradeoffs between the number of cisternae and the number and specificity of enzymes, in order to synthesize a prescribed target glycan distribution of a certain complexity. We find that to synthesize complex distributions, such as those observed in real cells, one needs to have multiple cisternae and precise enzyme partitioning in the Golgi. Additionally, for fixed number of enzymes and cisternae, there is an optimal level of specificity of enzymes that achieves the target distribution with high fidelity. Our results show how the complexity of the target glycan distribution places functional constraints on the Golgi cisternal number and enzyme specificity.
Helge S. Stein, Edwin Soedarmadji, Paul F. Newhouse
et al.
AbstractOptical absorption spectroscopy is an important materials characterization for applications such as solar energy generation. This data descriptor describes the to date (Dec 2018) largest publicly available curated materials science dataset for near infrared to near UV (UV-Vis) light absorbance, composition and processing properties of metal oxides. By supplying the complete synthesis and processing history of each of the 179072 samples from 99965 unique compositions we believe the dataset will enable the community to develop predictive models for materials, such as prediction of optical properties based on composition and processing, and ultimately serve as a benchmark dataset for continued integration of machine learning in materials science. The dataset is also a resource for identifying materials composition and synthesis to attain specific optical properties.
Daniele Cappelletti, Ankit Gupta, Mustafa Khammash
Biochemical systems that express certain chemical species of interest at the same level at any positive equilibrium are called "absolute concentration robust" (ACR). These species behave in a stable, predictable way, in the sense that their expression is robust with respect to sudden changes in the species concentration, regardless the new positive equilibrium reached by the system. Such a property has been proven to be fundamentally important in certain gene regulatory networks and signaling systems. In the present paper, we mathematically prove that a well-known class of ACR systems studied by Shinar and Feinberg in 2010 hides an internal integral structure. This structure confers these systems with a higher degree of robustness that what was previously unknown. In particular, disturbances much more general than sudden changes in the species concentrations can be rejected, and robust perfect adaptation is achieved. Significantly, we show that these properties are maintained when the system is interconnected with other chemical reaction networks. This key feature enables design of insulator devices that are able to buffer the loading effect from downstream systems - a crucial requirement for modular circuit design in synthetic biology.
Keshav B. Patel, Shengtan Mao, M. Gregory Forest
et al.
Single kinesin molecular motors can processively move along a microtubule (MT) a few micrometers on average before dissociating. However, cellular length scales over which transport occurs are several hundred microns and more. Why seemingly unreliable motors are used to transport cellular cargo remains poorly understood. We propose a new theory for how low processivity, the average length of a single bout of directed motion, can enhance cellular transport when motors and cargoes must first diffusively self assemble into complexes. We employ stochastic modeling to determine the effect of processivity on overall cargo transport flux. We show that, under a wide range of physiologically relevant conditions, possessing "infinite" processivity does not maximize flux along MTs. Rather, we find that low processivity i.e., weak binding of motors to MTs, is optimal. These results shed light on the relationship between processivity and transport efficiency and offer a new theory for the physiological benefits of low motor processivity.
Nonlinear systems driven by recurrent signals are known to exhibit complex dynamical responses which, in the physiological context, can have important functional consequences. One of the simplest biological systems that is exposed to such repeated stimuli is the intra-cellular signaling network. In this paper we investigate the periodic activation of an evolutionarily conserved motif of this network, viz., the mitogen-activated protein kinase (MAPK) signaling cascade, with a train of pulses. The resulting response of the cascade, which shows integrative capability over several successive pulses, is characterized by complex adaptive behavior. These include aspects of non-associative learning, in particular, habituation and sensitization, which are observed in response to high- and low-frequency stimulation, respectively. In addition, the existence of a response threshold of the cascade, an apparent refractory behavior following stimulation with short inter-pulse interval, and an alternans-like response under certain conditions suggest an analogy with excitable media.
Franziska Foertsch, Mykhailo Ilchenko, Thomas Heitkamp
et al.
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. Previous FLIM measurements (K. Busch and coworkers) of complex II and III unravelled differences in the local environment of the membrane enzymes in the cristae. Here, we tagged complex IV and V with mNeonGreen and investigated their mitochondrial nano-environment by FLIM and superresolution microscopy in living human cells. Different lifetimes and anisotropy values were found and will be discussed.
Carlos S. Floyd, Christopher Jarzynski, Garegin A. Papoian
Actin filaments are critical components of the eukaryotic cytoskeleton, playing important roles in a number of cellular functions, such as cell migration, organelle transport, and mechanosensation. They are helical polymers with a well-defined polarity, composed of globular monomers that bind nucleotides in one of three hydrolysis states (ATP, ADP-Pi, or ADP). Mean-field models of the dynamics of actin polymerization have succeeded in, among other things, determining the nucleotide profile of an average filament and resolving the mechanisms of accessory proteins, however these models require numerical solution of a high-dimensional system of nonlinear ODE's. By truncating a set of recursion equations, the Brooks-Carlsson model reduces dimensionality to 11, but it remains nonlinear and does not admit an analytical solution, hence, significantly hindering understanding of its resulting dynamics. In this work, by taking advantage of the fast timescales of the hydrolysis states of the filament tips, we propose two model reduction schemes that achieve low dimensionality and linearity. We provide an exact solution of the resulting linear equations and use it to shed light on the dynamical behaviors of the full BC model, highlighting the relative ordering of the timescales of various collective processes, and explaining some unusual dependence of the steady-state behavior on initial conditions.
The first proposed hypothesis about the mechanism of chloroquine (CQ) action on malaria parasites is DNA intercalation hypothesis which indicates that the site of CQ action is within the nucleus. Later on the interest of research was shifted from nucleus to lysosome due to the report of CQ accumulation within lysosome. The current opinions about CQ action and resistance are mainly based on the results of more than 30-year studies on lysosome, which can be used to explain some facts but still remains incomplete and controversial. Based on recently published papers and our related data it is possible that the key CQ target protein may exist in the nucleus. Development of CQ resistance is probably mainly due to the alteration in the CQ target protein or certain mechanism which prevents CQ from reaching its target protein in the nucleus. In conclusion, the key site of CQ action may be in the nucleus though it has not been well explored while CQ action in lysosome which has been well studied may be secondarily important in CQ action and resistance.
Manuel Razo-Mejia, Stephanie L. Barnes, Nathan M. Belliveau
et al.
Allosteric regulation is found across all domains of life, yet we still lack simple, predictive theories that directly link the experimentally tunable parameters of a system to its input-output response. To that end, we present a general theory of allosteric transcriptional regulation using the Monod-Wyman-Changeux model. We rigorously test this model using the ubiquitous simple repression motif in bacteria by first predicting the behavior of strains that span a large range of repressor copy numbers and DNA binding strengths and then constructing and measuring their response. Our model not only accurately captures the induction profiles of these strains but also enables us to derive analytic expressions for key properties such as the dynamic range and $[EC_{50}]$. Finally, we derive an expression for the free energy of allosteric repressors which enables us to collapse our experimental data onto a single master curve that captures the diverse phenomenology of the induction profiles.
Thorsten Erdmann, Kathrin Bartelheimer, Ulrich S. Schwarz
Based on a detailed crossbridge model for individual myosin II motors, we systematically study the influence of mechanical load and adenosine triphosphate (ATP) concentration on small myosin II ensembles made from different isoforms. For skeletal and smooth muscle myosin II, which are often used in actomyosin gels that reconstitute cell contractility, fast forward movement is restricted to a small region of phase space with low mechanical load and high ATP concentration, which is also characterized by frequent ensemble detachment. At high load, these ensembles are stalled or move backwards, but forward motion can be restored by decreasing ATP concentration. In contrast, small ensembles of nonmuscle myosin II isoforms, which are found in the cytoskeleton of nonmuscle cells, are hardly affected by ATP concentration due to the slow kinetics of the bound states. For all isoforms, the thermodynamic efficiency of ensemble movement increases with decreasing ATP concentration, but this effect is weaker for the nonmuscle myosin II isoforms.
Davide Michieletto, Davide Marenduzzo, Ajazul H. Wani
Three-dimensional interphase organization of metazoan genomes has been linked to cellular identity. However, the principles governing 3D interphase genome architecture and its faithful transmission through disruptive events of cell-cycle, like mitosis, are not fully understood. By using Brownian dynamics simulations of Drosophila chromosome 3R up to time-scales of minutes, we show that chromatin binding profile of Polycomb-repressive-complex-1 robustly predicts a sub-set of topologically associated domains (TADs), and inclusion of other factors recapitulates the profile of all TADs, as observed experimentally. Our simulations show that chromosome 3R attains interphase organization from mitotic state by a two-step process in which formation of local TADs is followed by long-range interactions. Our model also explains statistical features and tracks the assembly kinetics of polycomb subnuclear clusters. In conclusion, our approach can be used to predict structural and kinetic features of 3D chromosome folding and its associated proteins in biological relevant genomic and time scales.
Serge Dmitrieff, Adolfo Alsina, Aastha Mathur
et al.
The fast blood stream of animals is associated with large shear stresses. Consequently, blood cells have evolved a special morphology and a specific internal architecture allowing them to maintain their integrity over several weeks. For instance, non-mammalian red blood cells, mammalian erythroblasts and platelets have a peripheral ring of microtubules, called the marginal band, that flattens the overall cell morphology by pushing on the cell cortex. In this article, we model how the shape of these cells stems from the balance between marginal band elasticity and cortical tension. We predict that the diameter of the cell scales with the total microtubule polymer, and verify the predicted law across a wide range of species. Our analysis also shows that the combination of the marginal band rigidity and cortical tension increases the ability of the cell to withstand forces without deformation. Finally, we model the marginal band coiling that occurs during the disc-to-sphere transition observed for instance at the onset of blood platelet activation. We show that when cortical tension increases faster than crosslinkers can unbind, the marginal band will coil, whereas if the tension increases slower, the marginal band may shorten as microtubules slide relative to each other.
Ion transport is the major determining factor of salinity tolerance in plants. A simple scheme of a plant cell with ion fluxes provides basic understanding of ion transport and the corresponding changes of ion concentrations under salinity. The review describes in detail basic principles of ion transport for a plant cell, introduces set of transporters essential for sodium and potassium uptake and efflux, analyses driving forces of ion transport and compares ion fluxes measured by several techniques. Study of differences in ion transport between salt tolerant halophytes and salt-sensitive plants with an emphasis on transport of potassium and sodium via plasma membranes offers knowledge for increasing salinity tolerance. Effects of salt stress on ion transport properties of membranes show huge opportunities for manipulating ion transport. Several attempts to overexpress or knockout ion transporters for changing salinity tolerance are described. Future perspectives are questioned with more attention given to potential candidate ion channels and transporters for altered expression. The potential direction of increasing salinity tolerance by modifying ion channels and transporters is discussed and questioned. An alternative approach from synthetic biology is to modify the existing membrane transport proteins or create new ones with desired properties for transforming agricultural crops. The approach had not been widely used earlier and leads also to theoretical and pure scientific aspects of protein chemistry, structure-function relations of membrane proteins, systems biology and physiology of stress and ion homeostasis.
Molecular motors are specialized proteins which perform active, directed transport of cellular cargoes on cytoskeletal filaments. In many cases, cargo motion powered by motor proteins is found to be bidirectional, and may be viewed as a biased random walk with fast unidirectional runs interspersed with slow `tug-of-war' states. The statistical properties of this walk are not known in detail, and here, we study memory and bias, as well as directional correlations between successive runs in bidirectional transport. We show, based on a study of the direction reversal probabilities of the cargo using a purely stochastic (tug-of-war) model, that bidirectional motion of cellular cargoes is, in general, a correlated random walk. In particular, while the motion of a cargo driven by two oppositely pulling motors is a Markovian random walk, memory of direction appears when multiple motors haul the cargo in one or both directions. In the latter case, the Markovian nature of the underlying single motor processes is hidden by internal transitions between degenerate run and pause states of the cargo. Interestingly, memory is found to be a non-monotonic function of the number of motors. Stochastic numerical simulations of the tug-of-war model support our mathematical results and extend them to biologically relevant situations.
In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated. Two of the three methods that will be discussed in detail have been previously reported in the literature; the two-regime method (TRM) and the compartment-placement method (CPM). The third method that is introduced and analysed in this paper is the ghost cell method (GCM). Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step $Δt$ (for updating the molecular-based part of the model) approaches zero. It is found that the error behaviour depends on another fundamental computational parameter $h$, the compartment size in the mesoscopic part of the model. Two important limiting cases, which appear in applications, are considered: (i) Δt approaches 0 and h is fixed; and (ii) Δt approaches 0 and h approaches 0 such that Δt/h^2 is fixed. The error for previously developed approaches (the TRM and CPM) converges to zero only in the limiting case (ii), but not in case (i). It is shown that the error of the GCM converges in the limiting case (i). Thus the GCM is superior to previous coupling techniques if the mesoscopic description is much coarser than the microscopic part of the model.
Under dilute in vitro conditions transcription factors rapidly locate their target sequence on DNA by using the facilitated diffusion mechanism. However, whether this strategy of alternating between three-dimensional bulk diffusion and one-dimensional sliding along the DNA contour is still beneficial in the crowded interior of cells is highly disputed. Here we use a simple model for the bacterial genome inside the cell and present a semi-analytical model for the in vivo target search of transcription factors within the facilitated diffusion framework. Without having to resort to extensive simulations we determine the mean search time of a lac repressor in a living E. coli cell by including parameters deduced from experimental measurements. The results agree very well with experimental findings, and thus the facilitated diffusion picture emerges as a quantitative approach to gene regulation in living bacteria cells. Furthermore we see that the search time is not very sensitive to the parameters characterizing the DNA configuration and that the cell seems to operate very close to optimal conditions for target localization. Local searches as implied by the colocalization mechanism are only found to mildly accelerate the mean search time within our model.