Three-Dimensional Labeling Program for Elucidation of the Geometric Properties of Biological Particles in Three-Dimensional Space

For all biological particles such as cells or cellular organelles, there are three-dimensional coordinates representing the centroid or center of gravity. These coordinates and other numerical parameters such as volume, fluorescence intensity, surface area, and shape are referred to in this paper as geometric properties, which may provide critical information for the clarification ofin situmechanisms of molecular and cellular functions in living organisms. We have established a method for the elucidation of these properties, designated the three-dimensional labeling program (3DLP). Algorithms of 3DLP are so simple that this method can be carried out through the use of software combinations in image analysis on a personal computer. To evaluate 3DLP, it was applied to a 32-cell-stage sea urchin embryo, double stained with FITC for cellular protein of blastomeres and propidium iodide for nuclear DNA. A stack of optical serial section images was obtained by confocal laser scanning microscopy. The method was found effective for determining geometric properties and should prove applicable to the study of many different kinds of biological particles in three-dimensional space.     

Three-dimensional discrete element method for the prediction of protoplasmic seepage through membrane in a biological cell

This paper presents a three-dimensional and compressible biological cell model based on discrete element method using multiple interacting agent that represent cellular structures within a simulated environment. The cytoplasm and nucleoplasm fluid behavior in the cell is time dependent. When taking this approach, it is important to calibrate protoplasmic flow behaviors through simulation techniques such as compressing the cell and examining the agents representing the cell cytoplasm seeping between the ones representing the confining cell membrane. This type of modelling may motivate future work on simulating simultaneous operations and interactions of multiple cellular agents in an attempt to re-create and predict the appearance of complex phenomena such as protoplasmic seepage that is caused by the force actuations of neighboring cells. Seepage occurs when a cytoplasm agent passes between three membrane particles connected in a triangular network. Based on the force–deformation response of spheres having variable size and stiffness, semi-analytic expressions are developed for the force required to cause seepage and solved numerically to find the maximum resistance offered by the membrane against cytoplasm seepage. The equations are based on force equilibrium and the constitutive relations for particle contact and membrane stiffness. In multi-particle representations of an individual cell undergoing deformation, different modes of cytoplasm seepage through confining cell membranes can occur. This can be avoided if simple criteria are satisfied. These findings can lead to certain fundamental laws for the improvement of novel cell-to-organ simulation techniques based on discrete element method.     

Can a cell be assembled from its constituents?

To date, available are a provisional list of the minimal set of genes required for the functioning and multiplication of a living cell under maximally favorable conditions, methods for the complete chemical synthesis of the minimal genome, and cell-free systems for carrying out all the biochemical reactions comprising the genome replication and expression. The most serious problem that remains on the way to creating an artificial living cell is the need to meet two apparently incompatible requirements: separation of the biochemical reactions from the environment, and exchange between the environment and the cell. A solution to this problem can be provided by molecular colonies (other names: nanocolonies, polonies), which form when RNA or DNA is replicated in a solid medium having pores of a nanometer size. Molecular colonies might also have served as a pre-cellular form of compartmentalization in the RNA World.     

Regulation of apoptotic c-Jun N-terminal kinase signaling by a stabilization-based feed-forward loop

A sequential kinase cascade culminating in activation of c-Jun N-terminal kinases (JNKs) plays a fundamental role in promoting apoptotic death in many cellular contexts. The mechanisms by which this pathway is engaged in response to apoptotic stimuli and suppressed in viable cells are largely unknown. Here, we show that apoptotic stimuli increase endogenous cellular levels of pathway components, including POSH, mixed lineage kinases (MLKs), and JNK interacting protein 1, and that this effect occurs through protein stabilization and requires the presence of POSH as well as activation of MLKs and JNKs. Our findings suggest a self-amplifying, feed-forward loop mechanism by which apoptotic stimuli promote the stabilization of JNK pathway components, thereby contributing to cell death.     

A mechanomolecular model for the movement of chromosomes during mitosis driven by a minimal kinetochore bicyclic cascade

During mitosis chromosomes use a complex network of dynamic microtubules to find the cell equator in preparation for division signals. The roles of cellular chemical signals in mechanisms driving mitotic chromosomal movements are not well understood. In this paper we propose a mathematical model of this process which incorporates a molecular scale model of kinetochore-microtubule interactions into a negative feedback loop between spindle forces and local kinetochore biochemical reactions. This system allows kinetochore biochemical reactions to control and coordinate chromosome movement thus providing a direct connection between mechanical signals and mitosis chemical species. Our feedback control model can recreate chromosome movement from prometaphase to anaphase in good agreement with experimental data.     

Biochemical and statistical network models for systems biology

The normal and abnormal behavior of a living cell is governed by complex networks of interacting biomolecules. Models of these networks allow us to make predictions about cellular behavior under a variety of environmental cues. In this review, we focus on two broad classes of such models: biochemical network models and statistical inference models. In particular, we discuss a number of modeling approaches in the context of the assumptions that they entail, the types of data required for their inference, and the range of their applicability.     

Chemical crosshairs on the central dogma

As cellular machines and processes that regulate the flow of genomic information have come into sharper focus, a new level of chemical control has become possible. The scope of such chemical intervention extends from the mechanistic dissection of biochemical processes in living cells to the targeted control of gene networks and cell fate.     

Effect of temperature on plant elongation and cell wall extensibility

Lockhart equation was derived for explaining plant cell expansion where both cell wall extension and water uptake must occur concomitantly. Its fundamental contribution was to express turgor pressure explicitly in terms of osmosis and wall mechanics. Here we present a new equation in which pressure is determined by temperature. It also accounts for the role of osmosis and consequently the role of water uptake in growing cell. By adopting literature data, we also attempt to report theoretically the close relation between plant elongation and cell wall extensibility. This is accomplished by the modified equation of growth solved for various temperatures in case of two different species. The results enable to interpret empirical data in terms of our model and fully confirm its applicability to the investigation of the problem of plant cell extensibility in function of environmental temperature. Moreover, by separating elastic effects from growth process we specified the characteristic temperature common for both processes which corresponds to the resonance energy of biochemical reactions as well as to the rapid softening of the elastic modes toward the high temperature end where we encountered viscoelastic and/or plastic behavior as dominating. By introducing analytical formulae connected with growth and elastic properties of the cell wall, we conclude with the statement how these both processes contribute quantitatively to the resonance-like shape of the elongation curve. In addition, the tension versus temperature "phase diagram" for a living plant cell is presented.     

抗菌肽对细菌杀伤作用的分子机制

抗菌肽是一类新型的抗菌物质,从最低等的生物病毒、细菌到高等的动植物都有广泛分布. 以往的研究主要集中于抗菌肽对细菌细胞膜的作用机制,已经构建了三种作用模式. 但近几年的研究表明,很多抗菌肽都能有效地穿过细菌的细胞膜,直接与胞内分子相互作用,并不引起膜的破裂. 抗菌肽根据其结构特点有着多种杀菌穿膜的机制,其后分别与胞内的靶分子如核酸,蛋白质,信号转导通路等互相作用,最终实现对细菌的杀伤作用.     

Quantitative cell biology with the Virtual Cell

Cell biological processes are controlled by an interacting set of biochemical and electrophysiological events that are distributed within complex cellular structures. Computational models, comprising quantitative data on the interacting molecular participants in these events, provide a means for applying the scientific method to these complex systems. The Virtual Cell is a computational environment designed for cell biologists, to facilitate the construction of models and the generation of predictive simulations from them. This review summarizes how a Virtual Cell model is assembled and describes the physical principles underlying the calculations that are performed. Applications to problems in nucleocytoplasmic transport and intracellular calcium dynamics will illustrate the power of this paradigm for elucidating cell biology.     

Structure, Affinity, and Availability of Estrogen Receptor Complexes in the Cellular Environment

An ability to measure the biochemical parameters and structures of protein complexes at defined locations within the cellular environment would improve our understanding of cellular function. We describe widely applicable, calibrated Förster resonance energy transfer methods that quantify structural and biochemical parameters for interaction of the human estrogen receptor α-isoform (ERα) with the receptor interacting domains (RIDs) of three cofactors (SRC1, SRC2, SRC3) in living cells. The interactions of ERα with all three SRC-RIDs, measured throughout the cell nucleus, transitioned from structurally similar, high affinity complexes containing two ERαs at low free SRC-RID concentrations (<2 nm) to lower affinity complexes with an ERα monomer at higher SRC-RID concentrations (∼10 nm). The methods also showed that only a subpopulation of ERα was available to form complexes with the SRC-RIDs in the cell. These methods represent a template for extracting unprecedented details of the biochemistry and structure of any complex that is capable of being measured by Förster resonance energy transfer in the cellular environment.     

On the dynamics of controlled metabolic network and cellular behavior

The existence of elaborate control mechanisms for the various biochemical processes inside and within living cells is responsible for the coherent behaviour observed in its spatio-temporal organisation. Stability and sensitivity are both necessary properties of living systems and these are achieved through negetive and positive feedback loops as in other control systems. We have studied a three-step reaction scheme involving a negative and a positive feedback loop in the form of end-product inhibition and allosteric activation. The variety of behaviour exhibited by this system, under different conditions, includes steady state, simple limit cycle oscillations, complex oscillations and period bifurcations leading to random oscillations or chaos. The system also shows the existence of two distinct chaotic regimes under the variation of a single parameter. These results, in comparison with single biochemical control loops, show that new behaviours can be exhibited in a more complex network which are not seen in the single control loops. The results are discussed in the light of a diverse variety of cellular functions in normal and altered cells indicating the role of controlled metabolic network as the underlying basis for cellular behaviour.     

Isologous diversification: A theory of cell differentiation

An isologous diversification theory for cell differentiation is proposed, based on simulations of interacting cells with biochemical networks and the cell division process following consumption of some chemicals. According to the simulations of the interaction-based dynamical systems model, the following scenario of the cell differentiation is proposed. (1) Up to some threshold number, divisions bring about almost identical cells with synchronized biochemical oscillations. (2) As the number is increased, the oscillations lose synchrony, leading to groups of cells with different phases of oscilaations. (3) Amplitudes of oscillation and averaged chemical compositions start to differ by groups of cells. The differentiated behavior of states is transmitted to daughter cells. (4) Recursivity is formed so that the daughter cells keep the identical chemical character. This “memory” is made possible through the transfer of initial conditions. (5) Successive differentiation proceeds. The mechanism of tumor cell formation, origin of stem cells, anomalous differentiation by transplantations, apoptosis and other features of cell differentiation process are also discussed, with some novel predictions.     

Pulsed feedback defers cellular differentiation

Environmental signals induce diverse cellular differentiation programs. In certain systems, cells defer differentiation for extended time periods after the signal appears, proliferating through multiple rounds of cell division before committing to a new fate. How can cells set a deferral time much longer than the cell cycle? Here we study Bacillus subtilis cells that respond to sudden nutrient limitation with multiple rounds of growth and division before differentiating into spores. A well-characterized genetic circuit controls the concentration and phosphorylation of the master regulator Spo0A, which rises to a critical concentration to initiate sporulation. However, it remains unclear how this circuit enables cells to defer sporulation for multiple cell cycles. Using quantitative time-lapse fluorescence microscopy of Spo0A dynamics in individual cells, we observed pulses of Spo0A phosphorylation at a characteristic cell cycle phase. Pulse amplitudes grew systematically and cell-autonomously over multiple cell cycles leading up to sporulation. This pulse growth required a key positive feedback loop involving the sporulation kinases, without which the deferral of sporulation became ultrasensitive to kinase expression. Thus, deferral is controlled by a pulsed positive feedback loop in which kinase expression is activated by pulses of Spo0A phosphorylation. This pulsed positive feedback architecture provides a more robust mechanism for setting deferral times than constitutive kinase expression. Finally, using mathematical modeling, we show how pulsing and time delays together enable “polyphasic” positive feedback, in which different parts of a feedback loop are active at different times. Polyphasic feedback can enable more accurate tuning of long deferral times. Together, these results suggest that Bacillus subtilis uses a pulsed positive feedback loop to implement a “timer” that operates over timescales much longer than a cell cycle.     

3-D clustering: a tool for high throughput docking

This report describes a computer program for clustering docking poses based on their 3-dimensional (3D) coordinates as well as on their chemical structures. This is chiefly intended for reducing a set of hits coming from high throughput docking, since the capacity to prepare and biologically test such molecules is generally far more limited than the capacity to generate such hits. The advantage of clustering molecules based on 3D, rather than 2D, criteria is that small variations on a scaffold may bring about different binding modes for molecules that would not be predicted by 2D similarity alone. The program does a pose-by-pose/atom-by-atom comparison of a set of docking hits (poses), scoring both spatial and chemical similarity. Using these pair-wise similarities, the whole set is clustered based on a user-supplied similarity threshold. An output coordinate file is created that mirrors the input coordinate file, but contains two new properties: a cluster number and similarity to the cluster center. Poses in this output file can easily be sorted by cluster and displayed together for visual inspection with any standard molecular viewing program, and decisions made about which molecule should be selected for biological testing as the best representative of this group of similar molecules with similar binding modes.     

Imaging biochemistry inside cells

Proteins provide the building blocks for multicomponent molecular units, or pathways, from which higher cellular functions emerge. These units consist of either assemblies of physically interacting proteins or dispersed biochemical activities connected by rapidly diffusing second messengers, metabolic intermediates, ions or other proteins. It will probably remain within the realm of genetics to identify the ensemble of proteins that constitute these functional units and to establish the first-order connectivity. The dynamics of interactions within these protein machines can be assessed in living cells by the application of fluorescence spectroscopy on a microscopic level, using fluorescent proteins that are introduced within these functional units. Fluorescence is sensitive, specific and non-invasive, and the spectroscopic properties of a fluorescent probe can be analysed to obtain information on its molecular environment. The development and use of sensors based on the genetically encoded variants of green-fluorescent proteins has facilitated the observation of 'live' biochemistry on a microscopic level, with the advantage of preserving the cellular context of biochemical connectivity, compartmentalization and spatial organization. Protein activities and interactions can be imaged and localized within a single cell, allowing correlation with phenomena such as the cell cycle, migration and morphogenesis.     

Cell communication by periodic cyclic-AMP pulses.

At the surface of aggregating cells of the slime mould, Dictyostelium discoideum, two different sites interacting with extracellular cAMP are detectable: binding sites and cycl-nucleotide phosphodiesterase. Both sites are developmentally regulated. An adequate stimulus for the chemoreceptor system in D. discoideum is the change of cAMP concentration in time, rather than concentration per se: long-term binding of cAMP causes only short-term response. The system is, consequently, adapted to the recognition of pulses rather than to steady-state concentrations of cAMP. The ce,lls are, nevertheless, able to sense stationary spatial gradients and to respond to them by chemotactic orientation. The possibility is discussed that they do so by transforming spatial concentration changes into temporal ones, using extending pseudopods as sensors. The cAMP recognition system is part of a molecular network involved in the generation of spatio-temporal patterns of cellular activities. This system controls the periodic formation of chemotactic signals and their propagation from cell to cell. The phosphodiesterase limits the duration of the cAMP pulses and thus sharply separates the periods of signalling; the binding sites at the cell surface are supposed to be the chemoreceptors. The control of cellular activities via cAMP receptors can be studied with biochemical techniques with cell suspensions in which spatial inhomogeneities are suppressed by intense stirring, whereas the temporal aspect of the spatiotemporal pattern is preserved. Under these conditions it can be shown that the extracellular cAMP concentration changes periodically, and that the phase of the cellular oscillator can be shifted by external pulses of cAMP. It can also be shown that small cAMP pulses induce a high output of cAMP, which demonstrates signal amplification, a function necessary for a cellular relay system.     

Mappings of the plane that simulate prey-predator systems

A prey-predator system that is spatially dependent is built around the familiar logistic equation. The result is a set of coupled integro-differential equations. If at least one of the populations reproduces periodically in a time that is short to other characteristic times, these equations can be transformed to a set of coupled maps, each map representing a spatial point. Various models are developed that include predator ranging as well predator migration via diffusion. In two dimensions the coupling among the spatial points will have the symmetry of the regular polyhedra if the infinite plane is viewed in polar coordinates, or toroidal symmetry if periodic boundary conditions are imposed. Numerical examples are given. Depending on the value of the parameters and on the initial conditions the system can oscillate in a variety of different spatial modes, giving rise to unusual bifurcation portraits, or it can behave chaotically. The solutions show that a patchy distribution of population is more stable against the influences of environmental noise than is a smoothly distributed population. The numerical results in two dimensions are in constrast with the results of a previous study in one dimension.     

A reaction–diffusion model for long bones growth

Bone development is characterized by differentiation and growth of chondrocytes from the proliferation zone to the hypertrophying one. These two cellular processes are controlled by a complex signalling regulatory loop between different biochemical signals, whose production depends on the current cell density, constituting a coupled cell-chemical system. In this work, a mathematical model of the process of early bone growth is presented, extending and generalizing other earlier approaches on the same topic. A reaction–diffusion regulatory loop between two chemical factors: parathyroid hormone-related peptide (PTHrP) and Indian hedgehog (Ihh) is hypothesized, where PTHrP is activated by Ihh and inhibits Ihh production. Chondrocytes proliferation and hypertrophy are described by means of population equations being both regulated by the PTHrP and Ihh concentrations. In the initial stage of bone growth, these two cellular proceses are considered to be directionally dependent, modelling the well known column cell formation, characteristic of endochondral ossification. This coupled set of equations is solved within a finite element framework, getting an estimation of the chondrocytes spatial distribution, growth of the diaphysis and formation of the epiphysis of a long bone. The results obtained are qualitatively similar to the actual physiological ones and quantitatively close to some available experimental data. Finally, this extended approach allows finding important relations between the model parameters to get stability of the physiological process and getting additional insight on the spatial and directional distribution of cells and paracrine factors.     

Bioinformatic and experimental fishing for artemisinin-interacting proteins from human nasopharyngeal cancer cells

Determining interacting cellular partners of drugs by chemical proteomic techniques is complex and tedious. Most approaches rely on activity-based probe profiling and compound-centric chemical proteomics. The anti-malarial artemisinin also exerts profound anti-cancer activity, but the mechanisms of action are incompletely understood. In the present investigation, we present a novel approach to identify artemisinin-interacting target proteins. Our approach overcomes usual problems in traditional fishing procedures, because the drug was attached to a surface without further chemical modification. The proteins identified effect among others, cell cycle arrest, apoptosis, inhibition of angiogenesis, disruption of cell migration, and modulation of nuclear receptor responsiveness. Furthermore, a bioinformatic approach confirmed experimentally identified proteins and suggested a large number of other interacting proteins. Theoretically predicted interaction partners may serve as a starting point to complete the whole set of proteins binding artemisinin.