Biological competition: Decision rules, pattern formation, and oscillations

PubMed Central

Grossberg, Stephen

1980-01-01

Competition solves a universal problem about pattern processing by cellular systems. Competition allows cells to automatically retune their sensitivity to avoid noise and saturation effects. All competitive systems induce decision schemes that permit them to be classified. Systems are identified that achieve global pattern formation, or decision-making, no matter how their parameters are chosen. Oscillations can occur due to contradictions in a system's decision scheme. The pattern formation and oscillation results are extreme examples of a complementarity principle that seems to hold for competitive systems. Nonlinear competitive systems can sometimes appear, to a macroscopic observer, to have linear and cooperative properties, although the two types of systems are not equivalent. This observation is relevant to theories about the evolutionary transition from competitive to cooperative behavior. PMID:16592807

Self-organized pattern dynamics of somitogenesis model in embryos

NASA Astrophysics Data System (ADS)

Guan, Linan; Shen, Jianwei

2018-09-01

Somitogenesis, the sequential formation of a periodic pattern along the anteroposterior axis of vertebrate embryos, is one of the most obvious examples of the segmental patterning processes that take place during embryogenesis and also one of the major unresolved events in developmental biology. In this paper, we investigate the effect of diffusion on pattern formation use a modified two dimensional model which can be used to explain somitogenesis during embryonic development. This model is suitable for exploring a design space of somitogenesis and can explain many aspects of somitogenesis that previous models cannot. In the present paper, by analyzing the local linear stability of the equation, we acquired the conditions of Hopf bifurcation and Turing bifurcation. In addition, the amplitude equation near the Turing bifurcation point is obtained by using the methods of multi-scale expansion and symmetry analysis. By analyzing the stability of the amplitude equation, we know that there are various complex phenomena, including Spot pattern, mixture of spot-stripe patterns and labyrinthine. Finally, numerical simulation are given to verify the correctness of our theoretical results. Somitogenesis occupies an important position in the process of biological development, and as a pattern process can be used to investigate many aspects of embryogenesis. Therefore, our study helps greatly to cell differentiation, gene expression and embryonic development. What is more, it is of great significance for the diagnosis and treatment of human diseases to study the related knowledge of model biology.

Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity

PubMed Central

Bennett, James E. M.; Bair, Wyeth

2015-01-01

Traveling waves in the developing brain are a prominent source of highly correlated spiking activity that may instruct the refinement of neural circuits. A candidate mechanism for mediating such refinement is spike-timing dependent plasticity (STDP), which translates correlated activity patterns into changes in synaptic strength. To assess the potential of these phenomena to build useful structure in developing neural circuits, we examined the interaction of wave activity with STDP rules in simple, biologically plausible models of spiking neurons. We derive an expression for the synaptic strength dynamics showing that, by mapping the time dependence of STDP into spatial interactions, traveling waves can build periodic synaptic connectivity patterns into feedforward circuits with a broad class of experimentally observed STDP rules. The spatial scale of the connectivity patterns increases with wave speed and STDP time constants. We verify these results with simulations and demonstrate their robustness to likely sources of noise. We show how this pattern formation ability, which is analogous to solutions of reaction-diffusion systems that have been widely applied to biological pattern formation, can be harnessed to instruct the refinement of postsynaptic receptive fields. Our results hold for rich, complex wave patterns in two dimensions and over several orders of magnitude in wave speeds and STDP time constants, and they provide predictions that can be tested under existing experimental paradigms. Our model generalizes across brain areas and STDP rules, allowing broad application to the ubiquitous occurrence of traveling waves and to wave-like activity patterns induced by moving stimuli. PMID:26308406

Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity.

PubMed

Bennett, James E M; Bair, Wyeth

2015-08-01

Traveling waves in the developing brain are a prominent source of highly correlated spiking activity that may instruct the refinement of neural circuits. A candidate mechanism for mediating such refinement is spike-timing dependent plasticity (STDP), which translates correlated activity patterns into changes in synaptic strength. To assess the potential of these phenomena to build useful structure in developing neural circuits, we examined the interaction of wave activity with STDP rules in simple, biologically plausible models of spiking neurons. We derive an expression for the synaptic strength dynamics showing that, by mapping the time dependence of STDP into spatial interactions, traveling waves can build periodic synaptic connectivity patterns into feedforward circuits with a broad class of experimentally observed STDP rules. The spatial scale of the connectivity patterns increases with wave speed and STDP time constants. We verify these results with simulations and demonstrate their robustness to likely sources of noise. We show how this pattern formation ability, which is analogous to solutions of reaction-diffusion systems that have been widely applied to biological pattern formation, can be harnessed to instruct the refinement of postsynaptic receptive fields. Our results hold for rich, complex wave patterns in two dimensions and over several orders of magnitude in wave speeds and STDP time constants, and they provide predictions that can be tested under existing experimental paradigms. Our model generalizes across brain areas and STDP rules, allowing broad application to the ubiquitous occurrence of traveling waves and to wave-like activity patterns induced by moving stimuli.

Boundary-induced pattern formation from uniform temporal oscillation

NASA Astrophysics Data System (ADS)

Kohsokabe, Takahiro; Kaneko, Kunihiko

2018-04-01

Pattern dynamics triggered by fixing a boundary is investigated. By considering a reaction-diffusion equation that has a unique spatially uniform and limit cycle attractor under a periodic or Neumann boundary condition, and then by choosing a fixed boundary condition, we found three novel phases depending on the ratio of diffusion constants of activator to inhibitor: transformation of temporally periodic oscillation into a spatially periodic fixed pattern, travelling wave emitted from the boundary, and aperiodic spatiotemporal dynamics. The transformation into a fixed, periodic pattern is analyzed by crossing of local nullclines at each spatial point, shifted by diffusion terms, as is analyzed by using recursive equations, to obtain the spatial pattern as an attractor. The generality of the boundary-induced pattern formation as well as its relevance to biological morphogenesis is discussed.

A Kinesthetic Model Demonstrating Molecular Interactions Involved in Anterior-Posterior Pattern Formation in "Drosophila"

ERIC Educational Resources Information Center

Douglas, Kristin R.

2008-01-01

Prerequisites for the Developmental Biology course at Augustana College are introductory courses in zoology and cell biology. After introductory courses students appreciate the fact that proteins have three-dimensional structures; however, they often fail to recognize how protein interactions with other cellular components can lead to specific…

Predicting spiral wave patterns from cell properties in a model of biological self-organization.

PubMed

Geberth, Daniel; Hütt, Marc-Thorsten

2008-09-01

In many biological systems, biological variability (i.e., systematic differences between the system components) can be expected to outrank statistical fluctuations in the shaping of self-organized patterns. In principle, the distribution of single-element properties should thus allow predicting features of such patterns. For a mathematical model of a paradigmatic and well-studied pattern formation process, spiral waves of cAMP signaling in colonies of the slime mold Dictyostelium discoideum, we explore this possibility and observe a pronounced anticorrelation between spiral waves and cell properties (namely, the firing rate) and particularly a clustering of spiral wave tips in regions devoid of spontaneously firing (pacemaker) cells. Furthermore, we observe local inhomogeneities in the distribution of spiral chiralities, again induced by the pacemaker distribution. We show that these findings can be explained by a simple geometrical model of spiral wave generation.

Predicting spiral wave patterns from cell properties in a model of biological self-organization

NASA Astrophysics Data System (ADS)

Geberth, Daniel; Hütt, Marc-Thorsten

2008-09-01

In many biological systems, biological variability (i.e., systematic differences between the system components) can be expected to outrank statistical fluctuations in the shaping of self-organized patterns. In principle, the distribution of single-element properties should thus allow predicting features of such patterns. For a mathematical model of a paradigmatic and well-studied pattern formation process, spiral waves of cAMP signaling in colonies of the slime mold Dictyostelium discoideum, we explore this possibility and observe a pronounced anticorrelation between spiral waves and cell properties (namely, the firing rate) and particularly a clustering of spiral wave tips in regions devoid of spontaneously firing (pacemaker) cells. Furthermore, we observe local inhomogeneities in the distribution of spiral chiralities, again induced by the pacemaker distribution. We show that these findings can be explained by a simple geometrical model of spiral wave generation.

Stochastic many-body problems in ecology, evolution, neuroscience, and systems biology

NASA Astrophysics Data System (ADS)

Butler, Thomas C.

Using the tools of many-body theory, I analyze problems in four different areas of biology dominated by strong fluctuations: The evolutionary history of the genetic code, spatiotemporal pattern formation in ecology, spatiotemporal pattern formation in neuroscience and the robustness of a model circadian rhythm circuit in systems biology. In the first two research chapters, I demonstrate that the genetic code is extremely optimal (in the sense that it manages the effects of point mutations or mistranslations efficiently), more than an order of magnitude beyond what was previously thought. I further show that the structure of the genetic code implies that early proteins were probably only loosely defined. Both the nature of early proteins and the extreme optimality of the genetic code are interpreted in light of recent theory [1] as evidence that the evolution of the genetic code was driven by evolutionary dynamics that were dominated by horizontal gene transfer. I then explore the optimality of a proposed precursor to the genetic code. The results show that the precursor code has only limited optimality, which is interpreted as evidence that the precursor emerged prior to translation, or else never existed. In the next part of the dissertation, I introduce a many-body formalism for reaction-diffusion systems described at the mesoscopic scale with master equations. I first apply this formalism to spatially-extended predator-prey ecosystems, resulting in the prediction that many-body correlations and fluctuations drive population cycles in time, called quasicycles. Most of these results were previously known, but were derived using the system size expansion [2, 3]. I next apply the analytical techniques developed in the study of quasi-cycles to a simple model of Turing patterns in a predator-prey ecosystem. This analysis shows that fluctuations drive the formation of a new kind of spatiotemporal pattern formation that I name "quasi-patterns." These quasi-patterns exist over a much larger range of physically accessible parameters than the patterns predicted in mean field theory and therefore account for the apparent observations in ecology of patterns in regimes where Turing patterns do not occur. I further show that quasi-patterns have statistical properties that allow them to be distinguished empirically from mean field Turing patterns. I next analyze a model of visual cortex in the brain that has striking similarities to the activator-inhibitor model of ecosystem quasi-pattern formation. Through analysis of the resulting phase diagram, I show that the architecture of the neural network in the visual cortex is configured to make the visual cortex robust to unwanted internally generated spatial structure that interferes with normal visual function. I also predict that some geometric visual hallucinations are quasi-patterns and that the visual cortex supports a new phase of spatially scale invariant behavior present far from criticality. In the final chapter, I explore the effects of fluctuations on cycles in systems biology, specifically the pervasive phenomenon of circadian rhythms. By exploring the behavior of a generic stochastic model of circadian rhythms, I show that the circadian rhythm circuit exploits leaky mRNA production to safeguard the cycle from failure. I also show that this safeguard mechanism is highly robust to changes in the rate of leaky mRNA production. Finally, I explore the failure of the deterministic model in two different contexts, one where the deterministic model predicts cycles where they do not exist, and another context in which cycles are not predicted by the deterministic model.

Wrinkling pattern evolution of cylindrical biological tissues with differential growth.

PubMed

Jia, Fei; Li, Bo; Cao, Yan-Ping; Xie, Wei-Hua; Feng, Xi-Qiao

2015-01-01

Three-dimensional surface wrinkling of soft cylindrical tissues induced by differential growth is explored. Differential volumetric growth can cause their morphological stability, leading to the formation of hexagonal and labyrinth wrinkles. During postbuckling, multiple bifurcations and morphological transitions may occur as a consequence of continuous growth in the surface layer. The physical mechanisms underpinning the morphological evolution are examined from the viewpoint of energy. Surface curvature is found to play a regulatory role in the pattern evolution. This study may not only help understand the morphogenesis of soft biological tissues, but also inspire novel routes for creating desired surface patterns of soft materials.

Emergent pattern formation in an interstitial biofilm

NASA Astrophysics Data System (ADS)

Zachreson, Cameron; Wolff, Christian; Whitchurch, Cynthia B.; Toth, Milos

2017-01-01

Collective behavior of bacterial colonies plays critical roles in adaptability, survivability, biofilm expansion and infection. We employ an individual-based model of an interstitial biofilm to study emergent pattern formation based on the assumptions that rod-shaped bacteria furrow through a viscous environment and excrete extracellular polymeric substances which bias their rate of motion. Because the bacteria furrow through their environment, the substratum stiffness is a key control parameter behind the formation of distinct morphological patterns. By systematically varying this property (which we quantify with a stiffness coefficient γ ), we show that subtle changes in the substratum stiffness can give rise to a stable state characterized by a high degree of local order and long-range pattern formation. The ordered state exhibits characteristics typically associated with bacterial fitness advantages, even though it is induced by changes in environmental conditions rather than changes in biological parameters. Our findings are applicable to a broad range of biofilms and provide insights into the relationship between bacterial movement and their environment, and basic mechanisms behind self-organization of biophysical systems.

Pattern formation in a model for mountain pine beetle dispersal: linking model predictions to data.

PubMed

Strohm, S; Tyson, R C; Powell, J A

2013-10-01

Pattern formation occurs in a wide range of biological systems. This pattern formation can occur in mathematical models because of diffusion-driven instability or due to the interaction between reaction, diffusion, and chemotaxis. In this paper, we investigate the spatial pattern formation of attack clusters in a system for Mountain Pine Beetle. The pattern formation (aggregation) of the Mountain Pine Beetle in order to attack susceptible trees is crucial for their survival and reproduction. We use a reaction-diffusion equation with chemotaxis to model the interaction between Mountain Pine Beetle, Mountain Pine Beetle pheromones, and susceptible trees. Mathematical analysis is utilized to discover the spacing in-between beetle attacks on the susceptible landscape. The model predictions are verified by analysing aerial detection survey data of Mountain Pine Beetle Attack from the Sawtooth National Recreation Area. We find that the distance between Mountain Pine Beetle attack clusters predicted by our model closely corresponds to the observed attack data in the Sawtooth National Recreation Area. These results clarify the spatial mechanisms controlling the transition from incipient to epidemic populations and may lead to control measures which protect forests from Mountain Pine Beetle outbreak.

Formation of superhydrophobic/superhydrophilic patterns by combination of nanostructure-imprinted perfluoropolymer and nanostructured silicon oxide for biological droplet generation

NASA Astrophysics Data System (ADS)

Kobayashi, Taizo; Shimizu, Kazunori; Kaizuma, Yoshihiro; Konishi, Satoshi

2011-03-01

In this letter, we report a technology for fabricating superhydrophobic/superhydrophilic patterns using a combination of a nanostructure-imprinted perfluoropolymer and nanostructured silicon oxide. In our previous study, we used a combination of hydrophobic and superhydrophilic materials. However, it was difficult to split low-surface-tension liquids such as biological liquids into droplets solely using hydrophobic/hydrophilic patterns. In this study, the contact angle of the hydrophobic region was enhanced from 109.3° to 155.6° by performing nanostructure imprinting on a damage-reduced perfluoropolymer. The developed superhydrophobic/superhydrophilic patterns allowed the splitting of even those media that contained fetal bovine serum into droplets of a desired shape.

A perturbation analysis of a mechanical model for stable spatial patterning in embryology

NASA Astrophysics Data System (ADS)

Bentil, D. E.; Murray, J. D.

1992-12-01

We investigate a mechanical cell-traction mechanism that generates stationary spatial patterns. A linear analysis highlights the model's potential for these heterogeneous solutions. We use multiple-scale perturbation techniques to study the evolution of these solutions and compare our solutions with numerical simulations of the model system. We discuss some potential biological applications among which are the formation of ridge patterns, dermatoglyphs, and wound healing.

Numerical approaches to model perturbation fire in turing pattern formations

NASA Astrophysics Data System (ADS)

Campagna, R.; Brancaccio, M.; Cuomo, S.; Mazzoleni, S.; Russo, L.; Siettos, K.; Giannino, F.

2017-11-01

Turing patterns were observed in chemical, physical and biological systems described by coupled reaction-diffusion equations. Several models have been formulated proposing the water as the causal mechanism of vegetation pattern formation, but this isn't an exhaustive hypothesis in some natural environments. An alternative explanation has been related to the plant-soil negative feedback. In Marasco et al. [1] the authors explored the hypothesis that both mechanisms contribute in the formation of regular and irregular vegetation patterns. The mathematical model consists in three partial differential equations (PDEs) that take into account for a dynamic balance between biomass, water and toxic compounds. A numerical approach is mandatory also to investigate on the predictions of this kind of models. In this paper we start from the mathematical model described in [1], set the model parameters such that the biomass reaches a stable spatial pattern (spots) and present preliminary studies about the occurrence of perturbing events, such as wildfire, that can affect the regularity of the biomass configuration.

Turing mechanism underlying a branching model for lung morphogenesis.

PubMed

Xu, Hui; Sun, Mingzhu; Zhao, Xin

2017-01-01

The mammalian lung develops through branching morphogenesis. Two primary forms of branching, which occur in order, in the lung have been identified: tip bifurcation and side branching. However, the mechanisms of lung branching morphogenesis remain to be explored. In our previous study, a biological mechanism was presented for lung branching pattern formation through a branching model. Here, we provide a mathematical mechanism underlying the branching patterns. By decoupling the branching model, we demonstrated the existence of Turing instability. We performed Turing instability analysis to reveal the mathematical mechanism of the branching patterns. Our simulation results show that the Turing patterns underlying the branching patterns are spot patterns that exhibit high local morphogen concentration. The high local morphogen concentration induces the growth of branching. Furthermore, we found that the sparse spot patterns underlie the tip bifurcation patterns, while the dense spot patterns underlies the side branching patterns. The dispersion relation analysis shows that the Turing wavelength affects the branching structure. As the wavelength decreases, the spot patterns change from sparse to dense, the rate of tip bifurcation decreases and side branching eventually occurs instead. In the process of transformation, there may exists hybrid branching that mixes tip bifurcation and side branching. Since experimental studies have reported that branching mode switching from side branching to tip bifurcation in the lung is under genetic control, our simulation results suggest that genes control the switch of the branching mode by regulating the Turing wavelength. Our results provide a novel insight into and understanding of the formation of branching patterns in the lung and other biological systems.

Self-organization: the fundament of cell biology.

PubMed

Wedlich-Söldner, Roland; Betz, Timo

2018-05-26

Self-organization refers to the emergence of an overall order in time and space of a given system that results from the collective interactions of its individual components. This concept has been widely recognized as a core principle in pattern formation for multi-component systems of the physical, chemical and biological world. It can be distinguished from self-assembly by the constant input of energy required to maintain order-and self-organization therefore typically occurs in non-equilibrium or dissipative systems. Cells, with their constant energy consumption and myriads of local interactions between distinct proteins, lipids, carbohydrates and nucleic acids, represent the perfect playground for self-organization. It therefore comes as no surprise that many properties and features of self-organized systems, such as spontaneous formation of patterns, nonlinear coupling of reactions, bi-stable switches, waves and oscillations, are found in all aspects of modern cell biology. Ultimately, self-organization lies at the heart of the robustness and adaptability found in cellular and organismal organization, and hence constitutes a fundamental basis for natural selection and evolution.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).

Interference-mediated synaptonemal complex formation with embedded crossover designation

PubMed Central

Zhang, Liangran; Espagne, Eric; de Muyt, Arnaud; Zickler, Denise; Kleckner, Nancy E.

2014-01-01

Biological systems exhibit complex patterns at length scales ranging from the molecular to the organismic. Along chromosomes, events often occur stochastically at different positions in different nuclei but nonetheless tend to be relatively evenly spaced. Examples include replication origin firings, formation of chromatin loops along chromosome axes and, during meiosis, localization of crossover recombination sites (“crossover interference”). We present evidence in the fungus Sordaria macrospora that crossover interference is part of a broader pattern that includes synaptonemal complex (SC) nucleation. This pattern comprises relatively evenly spaced SC nucleation sites, among which a subset are crossover sites that show a classical interference distribution. This pattern ensures that SC forms regularly along the entire length of the chromosome as required for the maintenance of homolog pairing while concomitantly having crossover interactions locally embedded within the SC structure as required for both DNA recombination and structural events of chiasma formation. This pattern can be explained by a threshold-based designation and spreading interference process. This model can be generalized to give diverse types of related and/or partially overlapping patterns, in two or more dimensions, for any type of object. PMID:25380597

Light-driven dynamic Archimedes spirals and periodic oscillatory patterns of topological solitons in anisotropic soft matter

DOE PAGES

Martinez, Angel; Smalyukh, Ivan I.

2015-02-12

Oscillatory and excitable systems very commonly exhibit formation of dynamic non-equilibrium patterns. For example, rotating spiral patterns are observed in biological, chemical, and physical systems ranging from organization of slime mold cells to Belousov-Zhabotinsky reactions, and to crystal growth from nuclei with screw dislocations. Here we describe spontaneous formation of spiral waves and a large variety of other dynamic patterns in anisotropic soft matter driven by low-intensity light. The unstructured ambient or microscope light illumination of thin liquid crystal films in contact with a self-assembled azobenzene monolayer causes spontaneous formation, rich spatial organization, and dynamics of twisted domains and topologicalmore » solitons accompanied by the dynamic patterning of azobenzene group orientations within the monolayer. Linearly polarized incident light interacts with the twisted liquid crystalline domains, mimicking their dynamics and yielding patterns in the polarization state of transmitted light, which can be transformed to similar dynamic patterns in its intensity and interference color. This shows that the delicate light-soft-matter interaction can yield complex self-patterning of both. Finally, we uncover underpinning physical mechanisms and discuss potential uses.« less

Mechanisms for the target patterns formation in a stochastic bistable excitable medium

NASA Astrophysics Data System (ADS)

Verisokin, Andrey Yu.; Verveyko, Darya V.; Postnov, Dmitry E.

2018-04-01

We study the features of formation and evolution of spatiotemporal chaotic regime generated by autonomous pacemakers in excitable deterministic and stochastic bistable active media using the example of the FitzHugh - Nagumo biological neuron model under discrete medium conditions. The following possible mechanisms for the formation of autonomous pacemakers have been studied: 1) a temporal external force applied to a small region of the medium, 2) geometry of the solution region (the medium contains regions with Dirichlet or Neumann boundaries). In our work we explore the conditions for the emergence of pacemakers inducing target patterns in a stochastic bistable excitable system and propose the algorithm for their analysis.

Self-organization: the fundament of cell biology

PubMed Central

Betz, Timo

2018-01-01

Self-organization refers to the emergence of an overall order in time and space of a given system that results from the collective interactions of its individual components. This concept has been widely recognized as a core principle in pattern formation for multi-component systems of the physical, chemical and biological world. It can be distinguished from self-assembly by the constant input of energy required to maintain order—and self-organization therefore typically occurs in non-equilibrium or dissipative systems. Cells, with their constant energy consumption and myriads of local interactions between distinct proteins, lipids, carbohydrates and nucleic acids, represent the perfect playground for self-organization. It therefore comes as no surprise that many properties and features of self-organized systems, such as spontaneous formation of patterns, nonlinear coupling of reactions, bi-stable switches, waves and oscillations, are found in all aspects of modern cell biology. Ultimately, self-organization lies at the heart of the robustness and adaptability found in cellular and organismal organization, and hence constitutes a fundamental basis for natural selection and evolution. This article is part of the theme issue ‘Self-organization in cell biology’. PMID:29632257

Flow-driven instabilities during pattern formation of Dictyostelium discoideum

NASA Astrophysics Data System (ADS)

Gholami, A.; Steinbock, O.; Zykov, V.; Bodenschatz, E.

2015-06-01

The slime mold Dictyostelium discoideum is a well known model system for the study of biological pattern formation. In the natural environment, aggregating populations of starving Dictyostelium discoideum cells may experience fluid flows that can profoundly change the underlying wave generation process. Here we study the effect of advection on the pattern formation in a colony of homogeneously distributed Dictyostelium discoideum cells described by the standard Martiel-Goldbeter model. The external flow advects the signaling molecule cyclic adenosine monophosphate (cAMP) downstream, while the chemotactic cells attached to the solid substrate are not transported with the flow. The evolution of small perturbations in cAMP concentrations is studied analytically in the linear regime and by corresponding numerical simulations. We show that flow can significantly influence the dynamics of the system and lead to a flow-driven instability that initiate downstream traveling cAMP waves. We also show that boundary conditions have a significant effect on the observed patterns and can lead to a new kind of instability.

Pattern formation and self-organization in plasmas interacting with surfaces

NASA Astrophysics Data System (ADS)

Trelles, Juan Pablo

2016-10-01

Pattern formation and self-organization are fascinating phenomena commonly observed in diverse types of biological, chemical and physical systems, including plasmas. These phenomena are often responsible for the occurrence of coherent structures found in nature, such as recirculation cells and spot arrangements; and their understanding and control can have important implications in technology, e.g. from determining the uniformity of plasma surface treatments to electrode erosion rates. This review comprises theoretical, computational and experimental investigations of the formation of spatiotemporal patterns that result from self-organization events due to the interaction of low-temperature plasmas in contact with confining or intervening surfaces, particularly electrodes. The basic definitions associated to pattern formation and self-organization are provided, as well as some of the characteristics of these phenomena within natural and technological contexts, especially those specific to plasmas. Phenomenological aspects of pattern formation include the competition between production/forcing and dissipation/transport processes, as well as nonequilibrium, stability, bifurcation and nonlinear interactions. The mathematical modeling of pattern formation in plasmas has encompassed from theoretical approaches and canonical models, such as reaction-diffusion systems, to drift-diffusion and nonequilibrium fluid flow models. The computational simulation of pattern formation phenomena imposes distinct challenges to numerical methods, such as high sensitivity to numerical approximations and the occurrence of multiple solutions. Representative experimental and numerical investigations of pattern formation and self-organization in diverse types of low-temperature electrical discharges (low and high pressure glow, dielectric barrier and arc discharges, etc) in contact with solid and liquid electrodes are reviewed. Notably, plasmas in contact with liquids, found in diverse emerging applications ranging from nanomaterial synthesis to medicine, show marked sensitivity to pattern formation and a broadened range of controlling parameters. The results related to the characteristics of the patterns, such as their geometric configuration and static or dynamic nature; as well as their controlling factors, including gas composition, driving voltage and current, electrode cooling, and imposed gas flow, are summarized and discussed. The article finalizes with an outlook of the research area, including theoretical, computational, and experimental needs to advance the field.

Biophysical evaluation of radiofrequency electromagnetic field effects on male reproductive pattern.

PubMed

Kesari, Kavindra Kumar; Kumar, Sanjay; Nirala, Jayprakash; Siddiqui, Mohd Haris; Behari, Jitendra

2013-03-01

There are possible hazardous health effects of exposure to radiofrequency electromagnetic radiations emitted from mobile phone on the human reproductive pattern. It is more effective while keeping mobile phones in pocket or near testicular organs. Present review examines the possible concern on radio frequency radiation interaction and biological effects such as enzyme induction, and toxicological effects, including genotoxicity and carcinogenicity, testicular cancer, and reproductive outcomes. Testicular infertility or testicular cancer due to mobile phone or microwave radiations suggests an increased level of reactive oxygen species (ROS). Though generation of ROS in testis has been responsible for possible toxic effects on physiology of reproduction, the reviews of last few decades have well established that these radiations are very harmful and cause mutagenic changes in reproductive pattern and leads to infertility. The debate will be focused on bio-interaction mechanism between mobile phone and testicular cancer due to ROS formation. This causes the biological damage and leads to several changes like decreased sperm count, enzymatic and hormonal changes, DNA damage, and apoptosis formation. In the present review, physics of mobile phone including future research on various aspects has been discussed.

Dermatoglyphics--a possible biomarker in the neurodevelopmental model for the origin of mental disorders.

PubMed

Ahmed-Popova, Ferihan M; Mantarkov, Mladen J; Sivkov, Stefan T; Akabaliev, Valentin H

2014-01-01

Dermatoglyphic pattern formation and differentiation are complex processes which have been in the focus of research interest ever since dermatoglyphics became a science. The patterns' early differentiation and genetic uniqueness as well as the relatively simple methods used to obtain and store fingerprints make it possible to study the relationship between certain dermatoglyphic characteristics and the underlying pathological processes in a number of diseases, including mental disorders. The present review reports published data from fundamental and clinical studies on dermatoglyphics primarily in schizophrenia and bipolar disorder to lend additional support for the neurodevelopmental hypothesis in the etiology of these disorders. Following an analysis of the theories of dermatoglyphics formation and the complex association between ridge patterns and central nervous system in early embryogenesis, an attempt is made to present dermatoglyphics as possible biological markers of impaired neurodevelopment. The contradictory data in the literature on dermatoglyphics in mental disorders suggest the need for further studies on these biological markers in order to identify their place in the neurodevelopmental etiological model of these diseases.

Pattern Formation in Keller-Segel Chemotaxis Models with Logistic Growth

NASA Astrophysics Data System (ADS)

Jin, Ling; Wang, Qi; Zhang, Zengyan

In this paper, we investigate pattern formation in Keller-Segel chemotaxis models over a multidimensional bounded domain subject to homogeneous Neumann boundary conditions. It is shown that the positive homogeneous steady state loses its stability as chemoattraction rate χ increases. Then using Crandall-Rabinowitz local theory with χ being the bifurcation parameter, we obtain the existence of nonhomogeneous steady states of the system which bifurcate from this homogeneous steady state. Stability of the bifurcating solutions is also established through rigorous and detailed calculations. Our results provide a selection mechanism of stable wavemode which states that the only stable bifurcation branch must have a wavemode number that minimizes the bifurcation value. Finally, we perform extensive numerical simulations on the formation of stable steady states with striking structures such as boundary spikes, interior spikes, stripes, etc. These nontrivial patterns can model cellular aggregation that develop through chemotactic movements in biological systems.

Data Mining in Cyber Operations

DTIC Science & Technology

2014-07-01

information processing units intended to mimic the network of neurons in the human brain for performing pattern recognition  Self- organizing maps (SOM...patterns are mined from in order to influence the learning model . An exploratory attack does not alter the training process , but rather uses other...New Jersey: Prentice Hall. 21) Kohonen, T. (1982). Self- organized formation of topologically correct feature maps. Biological Cybernetics , 43, 59–69

Pattern formation by curvature-inducing proteins on spherical membranes

NASA Astrophysics Data System (ADS)

Agudo-Canalejo, Jaime; Golestanian, Ramin

2017-12-01

Spatial organisation is a hallmark of all living cells, and recreating it in model systems is a necessary step in the creation of synthetic cells. It is therefore of both fundamental and practical interest to better understand the basic mechanisms underlying spatial organisation in cells. In this work, we use a continuum model of membrane and protein dynamics to study the behaviour of curvature-inducing proteins on membranes of spherical shape, such as living cells or lipid vesicles. We show that the interplay between curvature energy, entropic forces, and the geometric constraints on the membrane can result in the formation of patterns of highly-curved/protein-rich and weakly-curved/protein-poor domains on the membrane. The spontaneous formation of such patterns can be triggered either by an increase in the average density of curvature-inducing proteins, or by a relaxation of the geometric constraints on the membrane imposed by the membrane tension or by the tethering of the membrane to a rigid cell wall or cortex. These parameters can also be tuned to select the size and number of the protein-rich domains that arise upon pattern formation. The very general mechanism presented here could be related to protein self-organisation in many biological processes, ranging from (proto)cell division to the formation of membrane rafts.

Evo-devo: Hydra raises its Noggin.

PubMed

Chandramore, Kalpana; Ghaskadbi, Surendra

2011-08-01

Noggin, along with other secreted bone morphogenetic protein (BMP) inhibitors, plays a crucial role in neural induction and neural tube patterning as well as in somitogenesis, cardiac morphogenesis and formation of the skeleton in vertebrates. The BMP signalling pathway is one of the seven fundamental pathways that drive embryonic development and pattern formation in animals. Understanding its evolutionary origin and role in pattern formation is, therefore, important to evolutionary developmental biology (evo-devo). We have studied the evolutionary origin of BMP-Noggin antagonism in hydra, which is a powerful diploblastic model to study evolution of pattern-forming mechanisms because of the unusual cellular dynamics during its pattern formation and its remarkable ability to regenerate. We cloned and characterized the noggin gene from hydra and found it to exhibit considerable similarity with its orthologues at the amino acid level. Microinjection of hydra Noggin mRNA led to duplication of the dorsoventral axis in Xenopus embryos, demonstrating its functional conservation across the taxa. Our data, along with those of others, indicate that the evolutionarily conserved antagonism between BMP and its inhibitors predates bilateral divergence. This article reviews the various roles of Noggin in different organisms and some of our recent work on hydra Noggin in the context of evolution of developmental signalling pathways.

Reverse and forward engineering of protein pattern formation.

PubMed

Kretschmer, Simon; Harrington, Leon; Schwille, Petra

2018-05-26

Living systems employ protein pattern formation to regulate important life processes in space and time. Although pattern-forming protein networks have been identified in various prokaryotes and eukaryotes, their systematic experimental characterization is challenging owing to the complex environment of living cells. In turn, cell-free systems are ideally suited for this goal, as they offer defined molecular environments that can be precisely controlled and manipulated. Towards revealing the molecular basis of protein pattern formation, we outline two complementary approaches: the biochemical reverse engineering of reconstituted networks and the de novo design, or forward engineering, of artificial self-organizing systems. We first illustrate the reverse engineering approach by the example of the Escherichia coli Min system, a model system for protein self-organization based on the reversible and energy-dependent interaction of the ATPase MinD and its activating protein MinE with a lipid membrane. By reconstituting MinE mutants impaired in ATPase stimulation, we demonstrate how large-scale Min protein patterns are modulated by MinE activity and concentration. We then provide a perspective on the de novo design of self-organizing protein networks. Tightly integrated reverse and forward engineering approaches will be key to understanding and engineering the intriguing phenomenon of protein pattern formation.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).

Application of reaction-diffusion models to cell patterning in Xenopus retina. Initiation of patterns and their biological stability.

PubMed

Shoaf, S A; Conway, K; Hunt, R K

1984-08-07

We have examined the behavior of two reaction-diffusion models, originally proposed by Gierer & Meinhardt (1972) and by Kauffman, Shymko & Trabert (1978), for biological pattern formation. Calculations are presented for pattern formation on a disc (approximating the geometry of a number of embryonic anlagen including the frog eye rudiment), emphasizing the sensitivity of patterns to changes in initial conditions and to perturbations in the geometry of the morphogen-producing space. Analysis of the linearized equations from the models enabled us to select appropriate parameters and disc size for pattern growth. A computer-implemented finite element method was used to solve the non-linear model equations reiteratively. For the Gierer-Meinhardt model, initial activation (varying in size over two orders of magnitude) of one point on the disc's edge was sufficient to generate the primary gradient. Various parts of the disc were removed (remaining only as diffusible space) from the morphogen-producing cycle to investigate the effects of cells dropping out of the cycle due to cell death or malfunction (single point removed) or differentiation (center removed), as occur in the Xenopus eye rudiment. The resulting patterns had the same general shape and amplitude as normal gradients. Nor did a two-fold increase in disc size affect the pattern-generating ability of the model. Disc fragments bearing their primary gradient patterns were fused (with gradients in opposite directions, but each parallel to the fusion line). The resulting patterns generated by the model showed many similarities to results of "compound eye" experiments in Xenopus. Similar patterns were obtained with the model of Kauffman's group (1978), but we found less stability of the pattern subject to simulations of central differentiation. However, removal of a single point from the morphogen cycle (cell death) did not result in any change. The sensitivity of the Kauffman et al. model to shape perturbations is not surprising since the model was originally designed to use shape and increasing size during growth to generate a sequence of transient patterns. However, the Gierer-Meinhardt model is remarkably stable even when subjected to a wide range of perturbations in the diffusible space, thus allowing it to cope with normal biological variability, and offering an exciting range of possibilities for reaction-diffusion models as mechanisms underlying the spatial patterns of tissue structures.

Weekly Formative Exams and Creative Grading Enhance Student Learning in an Introductory Biology Course.

PubMed

Bailey, E G; Jensen, J; Nelson, J; Wiberg, H K; Bell, J D

2017-01-01

First-year students often become discouraged during introductory biology courses when repeated attempts to understand concepts nevertheless result in poor test scores. This challenge is exacerbated by traditional course structures that impose premature judgments on students' achievements. Repeated testing has been shown to benefit student ability to recognize and recall information, but an effective means to similarly facilitate skill with higher-order problems in introductory courses is needed. Here, we show that an innovative format that uses a creative grading scheme together with weekly formative midterm exams produced significant gains in student success with difficult items requiring analysis and interpretation. This format is designed to promote tenacity and avoid discouragement by providing multiple opportunities to attempt demanding problems on exams, detailed immediate feedback, and strong incentives to retain hope and improve. Analysis of individual performance trajectories with heat maps reveals the diversity of learning patterns and provides rational means for advising students. © 2017 E. G. Bailey et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Using micro-patterned surfaces to inhibit settlement and biofilm formation by Bacillus subtilis.

PubMed

Chang, Siyuan; Chen, Xiaodong; Jiang, Shuo; Chen, Jinchun; Shi, Lin

2017-07-01

Biofilm is a biological complex caused by bacteria attachment to the substrates and their subsequent reproduction and secretion. This phenomenon reduces heat transfer efficiency and causes significant losses in treated sewage heat-recovering systems. This paper describes a physical approach to inhibit bacteria settlement and biofilm formation by Bacillus subtilis, which is the dominant species in treated sewage. Here, micro-patterned surfaces with different characteristics (stripe and cube) and dimensions (1-100 μm) were fabricated as surfaces of interest. Model sewage was prepared and a rotating coupon device was used to form the biofilms. Precision balance, scanning electron microscopy, and confocal laser scanning microscopy (CLSM) were employed to investigate the inhibitory effects and the mechanisms of the biofilm-surface interactions. The results have shown that surfaces with small pattern sizes (1 and 2 μm) all reduced biofilm formation significantly. Interestingly, the CLSM images showed that the surfaces do not play a role in "killing" the bacteria. These findings are useful for future development of new process surfaces on which bacteria settlement and biofilm formation can be inhibited or minimized.

Controlling Interacting Systems in Noisy Environments

DTIC Science & Technology

2010-01-11

pattern formation and swarming as observed in biological populations including bacterial colonies [1, 3, 4], slime molds [22, 27], locusts [13] and fish...2968–2973, IEEE, Piscataway, NJ, 2001. [22] Herbert Levine and William Reynolds. Streaming instability of aggregating slime mold amoebae. Phys. Rev. Lett

Desiccation of a Sessile Drop of Blood: Cracks Formation and Delamination

NASA Astrophysics Data System (ADS)

Sobac, Benjamin; Brutin, David

2011-11-01

The evaporation of drops of biological fluids has been studied since few years du to several applications in medical fields such as medical tests, drug screening, biostabilization... The evaporation of a drop of whole blood leads to the formation of final typical pattern of cracks. Flow motion, adhesion, gelation and fracturation all occur during the evaporation of this complex matter. During the drying, a sol-gel transition develops. The drying kinetics is explained by a simple model of evaporation taking account of the evolution of the gelation front. The system solidifies and when stresses are too important, cracks nucleate. The cracks formation and the structure of the crack pattern are investigated. The initial crack spacing is found in good agreement with the implementation in open geometry of the model of cracks formation induced by evaporation proposed by Allain and Limat. Finally, the drop is still drying after the end of the formation of cracks which leads, like in the situation of colloid suspensions, to the observation of a delamination phenomenon.

Collective motion patterns of swarms with delay coupling: Theory and experiment.

PubMed

Szwaykowska, Klementyna; Schwartz, Ira B; Mier-Y-Teran Romero, Luis; Heckman, Christoffer R; Mox, Dan; Hsieh, M Ani

2016-03-01

The formation of coherent patterns in swarms of interacting self-propelled autonomous agents is a subject of great interest in a wide range of application areas, ranging from engineering and physics to biology. In this paper, we model and experimentally realize a mixed-reality large-scale swarm of delay-coupled agents. The coupling term is modeled as a delayed communication relay of position. Our analyses, assuming agents communicating over an Erdös-Renyi network, demonstrate the existence of stable coherent patterns that can be achieved only with delay coupling and that are robust to decreasing network connectivity and heterogeneity in agent dynamics. We also show how the bifurcation structure for emergence of different patterns changes with heterogeneity in agent acceleration capabilities and limited connectivity in the network as a function of coupling strength and delay. Our results are verified through simulation as well as preliminary experimental results of delay-induced pattern formation in a mixed-reality swarm.

PatternLab for proteomics 4.0: A one-stop shop for analyzing shotgun proteomic data

PubMed Central

Carvalho, Paulo C; Lima, Diogo B; Leprevost, Felipe V; Santos, Marlon D M; Fischer, Juliana S G; Aquino, Priscila F; Moresco, James J; Yates, John R; Barbosa, Valmir C

2017-01-01

PatternLab for proteomics is an integrated computational environment that unifies several previously published modules for analyzing shotgun proteomic data. PatternLab contains modules for formatting sequence databases, performing peptide spectrum matching, statistically filtering and organizing shotgun proteomic data, extracting quantitative information from label-free and chemically labeled data, performing statistics for differential proteomics, displaying results in a variety of graphical formats, performing similarity-driven studies with de novo sequencing data, analyzing time-course experiments, and helping with the understanding of the biological significance of data in the light of the Gene Ontology. Here we describe PatternLab for proteomics 4.0, which closely knits together all of these modules in a self-contained environment, covering the principal aspects of proteomic data analysis as a freely available and easily installable software package. All updates to PatternLab, as well as all new features added to it, have been tested over the years on millions of mass spectra. PMID:26658470

Collective motion patterns of swarms with delay coupling: Theory and experiment

NASA Astrophysics Data System (ADS)

Szwaykowska, Klementyna; Schwartz, Ira B.; Mier-y-Teran Romero, Luis; Heckman, Christoffer R.; Mox, Dan; Hsieh, M. Ani

2016-03-01

The formation of coherent patterns in swarms of interacting self-propelled autonomous agents is a subject of great interest in a wide range of application areas, ranging from engineering and physics to biology. In this paper, we model and experimentally realize a mixed-reality large-scale swarm of delay-coupled agents. The coupling term is modeled as a delayed communication relay of position. Our analyses, assuming agents communicating over an Erdös-Renyi network, demonstrate the existence of stable coherent patterns that can be achieved only with delay coupling and that are robust to decreasing network connectivity and heterogeneity in agent dynamics. We also show how the bifurcation structure for emergence of different patterns changes with heterogeneity in agent acceleration capabilities and limited connectivity in the network as a function of coupling strength and delay. Our results are verified through simulation as well as preliminary experimental results of delay-induced pattern formation in a mixed-reality swarm.

Turing patterns and a stochastic individual-based model for predator-prey systems

NASA Astrophysics Data System (ADS)

Nagano, Seido

2012-02-01

Reaction-diffusion theory has played a very important role in the study of pattern formations in biology. However, a group of individuals is described by a single state variable representing population density in reaction-diffusion models and interaction between individuals can be included only phenomenologically. Recently, we have seamlessly combined individual-based models with elements of reaction-diffusion theory. To include animal migration in the scheme, we have adopted a relationship between the diffusion and the random numbers generated according to a two-dimensional bivariate normal distribution. Thus, we have observed the transition of population patterns from an extinction mode, a stable mode, or an oscillatory mode to the chaotic mode as the population growth rate increases. We show our phase diagram of predator-prey systems and discuss the microscopic mechanism for the stable lattice formation in detail.

Tissue culture on a chip: Developmental biology applications of self-organized capillary networks in microfluidic devices.

PubMed

Miura, Takashi; Yokokawa, Ryuji

2016-08-01

Organ culture systems are used to elucidate the mechanisms of pattern formation in developmental biology. Various organ culture techniques have been used, but the lack of microcirculation in such cultures impedes the long-term maintenance of larger tissues. Recent advances in microfluidic devices now enable us to utilize self-organized perfusable capillary networks in organ cultures. In this review, we will overview past approaches to organ culture and current technical advances in microfluidic devices, and discuss possible applications of microfluidics towards the study of developmental biology. © 2016 Japanese Society of Developmental Biologists.

Weekly Formative Exams and Creative Grading Enhance Student Learning in an Introductory Biology Course

PubMed Central

Bailey, E. G.; Jensen, J.; Nelson, J.; Wiberg, H. K.; Bell, J. D.

2017-01-01

First-year students often become discouraged during introductory biology courses when repeated attempts to understand concepts nevertheless result in poor test scores. This challenge is exacerbated by traditional course structures that impose premature judgments on students’ achievements. Repeated testing has been shown to benefit student ability to recognize and recall information, but an effective means to similarly facilitate skill with higher-order problems in introductory courses is needed. Here, we show that an innovative format that uses a creative grading scheme together with weekly formative midterm exams produced significant gains in student success with difficult items requiring analysis and interpretation. This format is designed to promote tenacity and avoid discouragement by providing multiple opportunities to attempt demanding problems on exams, detailed immediate feedback, and strong incentives to retain hope and improve. Analysis of individual performance trajectories with heat maps reveals the diversity of learning patterns and provides rational means for advising students. PMID:28130269

Time rescaling and pattern formation in biological evolution.

PubMed

Igamberdiev, Abir U

2014-09-01

Biological evolution is analyzed as a process of continuous measurement in which biosystems interpret themselves in the environment resulting in changes of both. This leads to rescaling of internal time (heterochrony) followed by spatial reconstructions of morphology (heterotopy). The logical precondition of evolution is the incompleteness of biosystem's internal description, while the physical precondition is the uncertainty of quantum measurement. The process of evolution is based on perpetual changes in interpretation of information in the changing world. In this interpretation the external biospheric gradients are used for establishment of new features of organization. It is concluded that biological evolution involves the anticipatory epigenetic changes in the interpretation of genetic symbolism which cannot generally be forecasted but can provide canalization of structural transformations defined by the existing organization and leading to predictable patterns of form generation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Microenvironments engineered by inkjet bioprinting spatially direct adult stem cells toward muscle- and bone-like subpopulations.

PubMed

Phillippi, Julie A; Miller, Eric; Weiss, Lee; Huard, Johnny; Waggoner, Alan; Campbell, Phil

2008-01-01

In vivo, growth factors exist both as soluble and as solid-phase molecules, immobilized to cell surfaces and within the extracellular matrix. We used this rationale to develop more biologically relevant approaches to study stem cell behaviors. We engineered stem cell microenvironments using inkjet bioprinting technology to create spatially defined patterns of immobilized growth factors. Using this approach, we engineered cell fate toward the osteogenic lineage in register to printed patterns of bone morphogenetic protein (BMP) 2 contained within a population of primary muscle-derived stem cells (MDSCs) isolated from adult mice. This patterning approach was conducive to patterning the MDSCs into subpopulations of osteogenic or myogenic cells simultaneously on the same chip. When cells were cultured under myogenic conditions on BMP-2 patterns, cells on pattern differentiated toward the osteogenic lineage, whereas cells off pattern differentiated toward the myogenic lineage. Time-lapse microscopy was used to visualize the formation of multinucleated myotubes, and immunocytochemistry was used to demonstrate expression of myosin heavy chain (fast) in cells off BMP-2 pattern. This work provides proof-of-concept for engineering spatially controlled multilineage differentiation of stem cells using patterns of immobilized growth factors. This approach may be useful for understanding cell behaviors to immobilized biological patterns and could have potential applications for regenerative medicine.

A qualitative characterization of an introductory college nonmajors biology laboratory

NASA Astrophysics Data System (ADS)

Lee, Cherin Ann

The nature of an undergraduate, nonmajors biology laboratory was investigated in this study. Student participants were enrolled in a general education biology laboratory course at the University of Northern Iowa. The researcher's purpose was to gain a characterization of the instructional format and laboratory activities experienced by students. Interpretation of student and instructor responses enabled an insider's view of the biology laboratory. The laboratory period was consistently described by both students and instructors as having three parts, Beginning, Middle, and End, with the End being of special importance for conceptual development. The instructional format of the three instructors differed within the three portions of the laboratory period, ranging from an inquiry-oriented, partial learning cycle to a fairly expository model labeled inform/verify/practice. There was striking similarity in intrasectional student and teacher descriptions of instructional format. Additionally, students experiencing the alternate instructor provided the same characterizations of instructional format as those provided by the instructor's usual students. There were no discernible patterns of instructional format based on sex or reasoning level. In addition to the central role of instructional format, three areas of importance emerged: the social aspects of learning, the collaborative and cooperative nature of laboratory work and learning, and the role of self-efficacy. Theory developed from and grounded in the data showed six factors important in the introductory college biology laboratory: collaborative and cooperative learning, student-student and teacher-student interactions, attitude and self-efficacy, learning process and learning style, effective instructional format, and science content. These factors were found to be similar to factors identified in the literature as important in K-12 science education. These factors were set in the context of schooling and learning paradigms, paralleling J. J. Schwab's four conditions of a curriculum (subject matter, learners, teachers, and milieus), Benjamin Bloom's model of important factors in student achievement and schooling (cognitive entry behaviors, affective entry behaviors, and quality of instruction), and fitting a constructivist epistemological framework.

An automated graphics tool for comparative genomics: the Coulson plot generator

PubMed Central

2013-01-01

Background Comparative analysis is an essential component to biology. When applied to genomics for example, analysis may require comparisons between the predicted presence and absence of genes in a group of genomes under consideration. Frequently, genes can be grouped into small categories based on functional criteria, for example membership of a multimeric complex, participation in a metabolic or signaling pathway or shared sequence features and/or paralogy. These patterns of retention and loss are highly informative for the prediction of function, and hence possible biological context, and can provide great insights into the evolutionary history of cellular functions. However, representation of such information in a standard spreadsheet is a poor visual means from which to extract patterns within a dataset. Results We devised the Coulson Plot, a new graphical representation that exploits a matrix of pie charts to display comparative genomics data. Each pie is used to describe a complex or process from a separate taxon, and is divided into sectors corresponding to the number of proteins (subunits) in a complex/process. The predicted presence or absence of proteins in each complex are delineated by occupancy of a given sector; this format is visually highly accessible and makes pattern recognition rapid and reliable. A key to the identity of each subunit, plus hierarchical naming of taxa and coloring are included. A java-based application, the Coulson plot generator (CPG) automates graphic production, with a tab or comma-delineated text file as input and generating an editable portable document format or svg file. Conclusions CPG software may be used to rapidly convert spreadsheet data to a graphical matrix pie chart format. The representation essentially retains all of the information from the spreadsheet but presents a graphically rich format making comparisons and identification of patterns significantly clearer. While the Coulson plot format is highly useful in comparative genomics, its original purpose, the software can be used to visualize any dataset where entity occupancy is compared between different classes. Availability CPG software is available at sourceforge http://sourceforge.net/projects/coulson and http://dl.dropbox.com/u/6701906/Web/Sites/Labsite/CPG.html PMID:23621955

Multistability, local pattern formation, and global collective firing in a small-world network of nonleaky integrate-and-fire neurons.

PubMed

Rothkegel, Alexander; Lehnertz, Klaus

2009-03-01

We investigate numerically the collective dynamical behavior of pulse-coupled nonleaky integrate-and-fire neurons that are arranged on a two-dimensional small-world network. To ensure ongoing activity, we impose a probability for spontaneous firing for each neuron. We study network dynamics evolving from different sets of initial conditions in dependence on coupling strength and rewiring probability. Besides a homogeneous equilibrium state for low coupling strength, we observe different local patterns including cyclic waves, spiral waves, and turbulentlike patterns, which-depending on network parameters-interfere with the global collective firing of the neurons. We attribute the various network dynamics to distinct regimes in the parameter space. For the same network parameters different network dynamics can be observed depending on the set of initial conditions only. Such a multistable behavior and the interplay between local pattern formation and global collective firing may be attributable to the spatiotemporal dynamics of biological networks.

Patterned Cell Alignment in Response to Macroscale Curvature

NASA Astrophysics Data System (ADS)

Bade, Nathan; Kamien, Randall; Assoian, Richard; Stebe, Kathleen

The formation of spatial behavior patterns in tissues is a long-standing problem in biology. Decades of research have focused on understanding how biochemical signaling and morphogen gradients establish cell patterns during development and tissue morphogenesis. Here, we show that geometry and physical cues can drive organization and pattern formation. We find that mouse embryonic fibroblasts and human vascular smooth muscle cells sense curvature differently when in monolayers than when isolated on surfaces with various amounts of Gaussian curvature. While the long, apical stress fibers within these cells align in the direction of minimum curvature on cylindrical substrates, a subpopulation of stress fibers beneath the nucleus aligns in the circumferential direction and is bent maximally. We find dramatic reorganization of the actin cytoskeleton upon activation of RhoA, which is associated with increased contractility of the fibers. Thus, stress fiber alignment is likely a result of a complex balance between energy penalties associated with stress fiber bending, contractility, and the dynamics of F-actin assembly.

Mechanical control of tissue and organ development

PubMed Central

Mammoto, Tadanori; Ingber, Donald E.

2010-01-01

Many genes and molecules that drive tissue patterning during organogenesis and tissue regeneration have been discovered. Yet, we still lack a full understanding of how these chemical cues induce the formation of living tissues with their unique shapes and material properties. Here, we review work based on the convergence of physics, engineering and biology that suggests that mechanical forces generated by living cells are as crucial as genes and chemical signals for the control of embryological development, morphogenesis and tissue patterning. PMID:20388652

Dynamic patterns in a supported lipid bilayer driven by standing surface acoustic waves.

PubMed

Hennig, Martin; Neumann, Jürgen; Wixforth, Achim; Rädler, Joachim O; Schneider, Matthias F

2009-11-07

In the past decades supported lipid bilayers (SLBs) have been an important tool in order to study the physical properties of biological membranes and cells. So far, controlled manipulation of SLBs is very limited. Here we present a new technology to create lateral patterns in lipid membranes controllable in both space and time. Surface acoustic waves (SAWs) are used to generate lateral standing waves on a piezoelectric substrate which create local "traps" in the lipid bilayer and lead to a lateral modulation in lipid concentration. We demonstrate that pattern formation is reversible and does not affect the integrity of the lipid bilayer as shown by extracting the diffusion constant of fluid membranes. The described method could possibly be used to design switchable interfaces for the lateral transport and organization of membrane bound macromolecules to create dynamic bioarrays and control biofilm formation.

Intergenerational Patterns of Union Formation and Relationship Quality

ERIC Educational Resources Information Center

Sassler, Sharon; Cunningham, Anna; Lichter, Daniel T.

2009-01-01

The authors examine whether young adults who experienced their parents' divorce and new relationships have different relationship trajectories than those who spent their childhoods living with biological parents in married-couple families. The analysis is based on longitudinal reports from more than 1,500 children from Wave 1 of the 1987-1988…

Suggested Mechanisms of Tracheal Occlusion Mediated Accelerated Fetal Lung Growth: A Case for Heterogeneous Topological Zones

PubMed Central

Marwan, Ahmed I.; Shabeka, Uladzimir; Dobrinskikh, Evgenia

2018-01-01

In this article, we report an up-to-date summary on tracheal occlusion (TO) as an approach to drive accelerated lung growth and strive to review the different maternal- and fetal-derived local and systemic signals and mechanisms that may play a significant biological role in lung growth and formation of heterogeneous topological zones following TO. Pulmonary hypoplasia is a condition whereby branching morphogenesis and embryonic pulmonary vascular development are globally affected and is classically seen in congenital diaphragmatic hernia. TO is an innovative approach aimed at driving accelerated lung growth in the most severe forms of diaphragmatic hernia and has been shown to result in improved neonatal outcomes. Currently, most research on mechanisms of TO-induced lung growth is focused on mechanical forces and is viewed from the perspective of homogeneous changes within the lung. We suggest that the key principle in understanding changes in fetal lungs after TO is taking into account formation of unique variable topological zones. Following TO, fetal lungs might temporarily look like a dynamically changing topologic mosaic with varying proliferation rates, dissimilar scale of vasculogenesis, diverse patterns of lung tissue damage, variable metabolic landscape, and different structures. The reasons for this dynamic topological mosaic pattern may include distinct degree of increased hydrostatic pressure in different parts of the lung, dissimilar degree of tissue stress/damage and responses to this damage, and incomparable patterns of altered lung zones with variable response to systemic maternal and fetal factors, among others. The local interaction between these factors and their accompanying processes in addition to the potential role of other systemic factors might lead to formation of a common vector of biological response unique to each zone. The study of the interaction between various networks formed after TO (action of mechanical forces, activation of mucosal mast cells, production and secretion of damage-associated molecular pattern substances, low-grade local pulmonary inflammation, and cardiac contraction-induced periodic agitation of lung tissue, among others) will bring us closer to an appreciation of the biological phenomenon of topological heterogeneity within the fetal lungs. PMID:29376042

Endothelial cell motility, coordination and pattern formation during vasculogenesis.

PubMed

Czirok, Andras

2013-01-01

How vascular networks assemble is a fundamental problem of developmental biology that also has medical importance. To explain the organizational principles behind vascular patterning, we must understand how can tissue level structures be controlled through cell behavior patterns like motility and adhesion that, in turn, are determined by biochemical signal transduction processes? We discuss the various ideas that have been proposed as mechanisms for vascular network assembly: cell motility guided by extracellular matrix alignment (contact guidance), chemotaxis guided by paracrine and autocrine morphogens, and multicellular sprouting guided by cell-cell contacts. All of these processes yield emergent patterns, thus endothelial cells can form an interconnected structure autonomously, without guidance from an external pre-pattern. © 2013 Wiley Periodicals, Inc.

Diatom-sedimentation feedback generates a self-organized geomorphic landscape on intertidal mudflats (Invited)

NASA Astrophysics Data System (ADS)

van de Koppel, J.; Weerman, E.; Herman, P.

2010-12-01

During spring, intertidal flats can exhibit strikingly regular spatial patterns of diatom-covered hummocks alternating with almost bare, water-filled hollows. We hypothesize that 1) the formation of this geomorphic landscape is caused by a strong interaction between benthic diatoms and sediment dynamics, inducing spatial self-organization, and 2) that self-organization affects ecosystem functioning by increasing the net average sedimentation on the tidal flat. We present a combined empirical and mathematical study to test the first hypothesis. We determined how the sediment erosion threshold varied with diatom cover and elevation. Our results were incorporated into a mathematical model to investigate whether the proposed mechanism could explain the formation of the observed patterns. Our mathematical model confirmed that the interaction between sedimentation, diatom growth and water redistribution could induce the formation of regular patterns on the intertidal mudflat. The model predicts that areas exhibiting spatially-self-organized patterns have increased sediment accretion and diatom biomass compared with areas lacking spatial patterns. We tested this prediction by following the sediment elevation during the season on both patterned and unpatterned parts of the mudflat. The results of our study confirmed our model prediction, as more sediment was found to accumulate in patterned parts of the mudflat, revealing how self-organization affected the functioning of mudflat ecosystems. Our study on intertidal mudflats provides a simple but clear-cut example of how the interaction between biological and geomorphological processes, through the process of self-organization, induces a self-organized geomorphic landscape.

Pattern Formation on Networks: from Localised Activity to Turing Patterns

PubMed Central

McCullen, Nick; Wagenknecht, Thomas

2016-01-01

Networks of interactions between competing species are used to model many complex systems, such as in genetics, evolutionary biology or sociology and knowledge of the patterns of activity they can exhibit is important for understanding their behaviour. The emergence of patterns on complex networks with reaction-diffusion dynamics is studied here, where node dynamics interact via diffusion via the network edges. Through the application of a generalisation of dynamical systems analysis this work reveals a fundamental connection between small-scale modes of activity on networks and localised pattern formation seen throughout science, such as solitons, breathers and localised buckling. The connection between solutions with a single and small numbers of activated nodes and the fully developed system-scale patterns are investigated computationally using numerical continuation methods. These techniques are also used to help reveal a much larger portion of of the full number of solutions that exist in the system at different parameter values. The importance of network structure is also highlighted, with a key role being played by nodes with a certain so-called optimal degree, on which the interaction between the reaction kinetics and the network structure organise the behaviour of the system. PMID:27273339

Molecular engineering of polymersome surface topology

PubMed Central

Ruiz-Pérez, Lorena; Messager, Lea; Gaitzsch, Jens; Joseph, Adrian; Sutto, Ludovico; Gervasio, Francesco Luigi; Battaglia, Giuseppe

2016-01-01

Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from the molecular to mesoscopic level. We report an example of using fully synthetic systems that mimic two levels of self-assembly. We show the formation of vesicles using amphiphilic copolymers whose chemical nature is chosen to control both membrane formation and membrane-confined interactions. We report polymersomes with patterns that emerge by engineering interfacial tension within the polymersome surface. This allows the formation of domains whose topology is tailored by chemical synthesis, paving the avenue to complex supramolecular designs functionally similar to those found in viruses and trafficking vesicles. PMID:27152331

A Comparative Study of Visual Representations in Conventional, Digitized and Interactive High School Science Textbooks

ERIC Educational Resources Information Center

Chen, Xiaoning

2017-01-01

With emerging new technologies being applied in teaching and learning, this study compares visual representations in three different high school biology textbook formats and analyses the senses engaged in viewing and understanding the science content represented through these visuals. The findings show that while a similar pattern is observed in…

Eric Davidson and deep time.

PubMed

Erwin, Douglas H

2017-10-13

Eric Davidson had a deep and abiding interest in the role developmental mechanisms played in generating evolutionary patterns documented in deep time, from the origin of the euechinoids to the processes responsible for the morphological architectures of major animal clades. Although not an evolutionary biologist, Davidson's interests long preceded the current excitement over comparative evolutionary developmental biology. Here I discuss three aspects at the intersection between his research and evolutionary patterns in deep time: First, understanding the mechanisms of body plan formation, particularly those associated with the early diversification of major metazoan clades. Second, a critique of early claims about ancestral metazoans based on the discoveries of highly conserved genes across bilaterian animals. Third, Davidson's own involvement in paleontology through a collaborative study of the fossil embryos from the Ediacaran Doushantuo Formation in south China.

Patterns of calcium oxalate monohydrate crystallization in complex biological systems

NASA Astrophysics Data System (ADS)

Golovanova, O. A.; Korol'kov, V. V.; Kuimova, M. V.

2017-01-01

The paper presents the features of calcium oxalate crystallization in the presence of additives revealed through experimental modeling. The patterns of phase formation are shown for the Ca2+ - C2O4 2- - H2O and Ca2+ - C2O4 2- - PO4 3- - H2O systems with the components and pH of the saline varying over a wide concentrations range. The effect of additives on crystallization of calcium oxalate monohydrate was investigated. It was found that the ionic strength and magnesium ions are inhibitors, and calcium oxalate and hydroxyapatite crystals are catalysts of calcium oxalate monohydrate crystallization. The basic calcium phosphate (apatite) was found to be most thermodynamically stable, which indicates its special role in kidney stone formation since it is found in virtually all stones.

A biologically inspired neural net for trajectory formation and obstacle avoidance.

PubMed

Glasius, R; Komoda, A; Gielen, S C

1996-06-01

In this paper we present a biologically inspired two-layered neural network for trajectory formation and obstacle avoidance. The two topographically ordered neural maps consist of analog neurons having continuous dynamics. The first layer, the sensory map, receives sensory information and builds up an activity pattern which contains the optimal solution (i.e. shortest path without collisions) for any given set of current position, target positions and obstacle positions. Targets and obstacles are allowed to move, in which case the activity pattern in the sensory map will change accordingly. The time evolution of the neural activity in the second layer, the motor map, results in a moving cluster of activity, which can be interpreted as a population vector. Through the feedforward connections between the two layers, input of the sensory map directs the movement of the cluster along the optimal path from the current position of the cluster to the target position. The smooth trajectory is the result of the intrinsic dynamics of the network only. No supervisor is required. The output of the motor map can be used for direct control of an autonomous system in a cluttered environment or for control of the actuators of a biological limb or robot manipulator. The system is able to reach a target even in the presence of an external perturbation. Computer simulations of a point robot and a multi-joint manipulator illustrate the theory.

Microbial trace-fossil formation, biogenous, and abiotic weathering in the Antarctic cold desert

NASA Technical Reports Server (NTRS)

Friedmann, E. Imre; Weed, Rebecca

1987-01-01

In the Antarctic cold desert (Ross Desert), the survival of the cryptoendolithic microorganisms that colonize the near-surface layer of porous sandstone rocks depends on a precarious equilibrium of biological and geological factors. An unfavorable shift of this equilibrium results in death, and this may be followed by formation of trace fossils that preserve the characteristic iron-leaching pattern caused by microbial activity. Similar microbial trace fossils may exist in the geological record. If life ever arose on early Mars, similar processes may have occurred there and left recognizable traces.

Synergetic topography and chemistry cues guiding osteogenic differentiation in bone marrow stromal cells through ERK1/2 and p38 MAPK signaling pathway.

PubMed

Zhang, Xinran; Li, Haotian; Lin, Chucheng; Ning, Congqin; Lin, Kaili

2018-01-30

Both the topographic surface and chemical composition modification can enhance rapid osteogenic differentiation and bone formation. Till now, the synergetic effects of topography and chemistry cues guiding biological responses have been rarely reported. Herein, the ordered micro-patterned topography and classically essential trace element of strontium (Sr) ion doping were selected to imitate topography and chemistry cues, respectively. The ordered micro-patterned topography on Sr ion-doped bioceramics was successfully duplicated using the nylon sieve as the template. Biological response results revealed that the micro-patterned topography design or Sr doping could promote cell attachment, ALP activity, and osteogenic differentiation of bone marrow-derived mesenchymal stem cells (BMSCs). Most importantly, the samples both with micro-patterned topography and Sr doping showed the highest promotion effects, and could synergistically activate the ERK1/2 and p38 MAPK signaling pathways. The results suggested that the grafts with both specific topography and chemistry cues have synergetic effects on osteogenic activity of BMSCs and provide an effective approach to design functional bone grafts and cell culture substrates.

Study on micro fabricated stainless steel surface to anti-biofouling using electrochemical fabrication

NASA Astrophysics Data System (ADS)

Hwang, Byeong Jun; Lee, Sung Ho

2017-12-01

Biofilm formed on the surface of the object by the microorganism resulting in fouling organisms. This has led to many problems in daily life, medicine, health and industrial community. In this study, we tried to prevent biofilm formation on the stainless steel (SS304) sheet surface with micro fabricated structure. After then forming the microscale colloid patterns on the surface of stainless steel by using an electrochemical etching forming a pattern by using a FeCl3 etching was further increase the surface roughness. Culturing the Pseudomonas aeruginosa on the stainless steel fabricated with a micro structure on the surface was observed a relationship between the surface roughness and the biological fouling of the micro structure. As a result, the stainless steel surface with a micro structure was confirmed to be the biological fouling occurs less. We expect to be able to solve the problems caused by biological fouling in various fields such as medicine, engineering, using this research.

Modeling the formation of cell-matrix adhesions on a single 3D matrix fiber.

PubMed

Escribano, J; Sánchez, M T; García-Aznar, J M

2015-11-07

Cell-matrix adhesions are crucial in different biological processes like tissue morphogenesis, cell motility, and extracellular matrix remodeling. These interactions that link cell cytoskeleton and matrix fibers are built through protein clutches, generally known as adhesion complexes. The adhesion formation process has been deeply studied in two-dimensional (2D) cases; however, the knowledge is limited for three-dimensional (3D) cases. In this work, we simulate different local extracellular matrix properties in order to unravel the fundamental mechanisms that regulate the formation of cell-matrix adhesions in 3D. We aim to study the mechanical interaction of these biological structures through a three dimensional discrete approach, reproducing the transmission pattern force between the cytoskeleton and a single extracellular matrix fiber. This numerical model provides a discrete analysis of the proteins involved including spatial distribution, interaction between them, and study of the different phenomena, such as protein clutches unbinding or protein unfolding. Copyright © 2015 Elsevier Ltd. All rights reserved.

Self-Organization of Stem Cell Colonies and of Early Mammalian Embryos: Recent Experiments Shed New Light on the Role of Autonomy vs. External Instructions in Basic Body Plan Development

PubMed Central

Denker, Hans-Werner

2016-01-01

“Organoids”, i.e., complex structures that can develop when pluripotent or multipotent stem cells are maintained in three-dimensional cultures, have become a new area of interest in stem cell research. Hopes have grown that when focussing experimentally on the mechanisms behind this type of in vitro morphogenesis, research aiming at tissue and organ replacements can be boosted. Processes leading to the formation of organoids in vitro are now often addressed as self-organization, a term referring to the formation of complex tissue architecture in groups of cells without depending on specific instruction provided by other cells or tissues. The present article focuses on recent reports using the term self-organization in the context of studies on embryogenesis, specifically addressing pattern formation processes in human blastocysts attaching in vitro, or in colonies of pluripotent stem cells (“gastruloids”). These morphogenetic processes are of particular interest because, during development in vivo, they lead to basic body plan formation and individuation. Since improved methodologies like those employed by the cited authors became available, early embryonic pattern formation/self-organization appears to evolve now as a research topic of its own. This review discusses concepts concerning the involved mechanisms, focussing on autonomy of basic body plan development vs. dependence on external signals, as possibly provided by implantation in the uterus, and it addresses biological differences between an early mammalian embryo, e.g., a morula, and a cluster of pluripotent stem cells. It is concluded that, apart from being of considerable biological interest, the described type of research needs to be contemplated carefully with regard to ethical implications when performed with human cells. PMID:27792143

Self-Organization of Stem Cell Colonies and of Early Mammalian Embryos: Recent Experiments Shed New Light on the Role of Autonomy vs. External Instructions in Basic Body Plan Development.

PubMed

Denker, Hans-Werner

2016-10-25

" Organoids ", i.e., complex structures that can develop when pluripotent or multipotent stem cells are maintained in three-dimensional cultures, have become a new area of interest in stem cell research. Hopes have grown that when focussing experimentally on the mechanisms behind this type of in vitro morphogenesis, research aiming at tissue and organ replacements can be boosted. Processes leading to the formation of organoids in vitro are now often addressed as self-organization , a term referring to the formation of complex tissue architecture in groups of cells without depending on specific instruction provided by other cells or tissues. The present article focuses on recent reports using the term self-organization in the context of studies on embryogenesis , specifically addressing pattern formation processes in human blastocysts attaching in vitro, or in colonies of pluripotent stem cells (" gastruloids "). These morphogenetic processes are of particular interest because, during development in vivo, they lead to basic body plan formation and individuation. Since improved methodologies like those employed by the cited authors became available, early embryonic pattern formation/self-organization appears to evolve now as a research topic of its own. This review discusses concepts concerning the involved mechanisms, focussing on autonomy of basic body plan development vs. dependence on external signals, as possibly provided by implantation in the uterus, and it addresses biological differences between an early mammalian embryo, e.g., a morula, and a cluster of pluripotent stem cells. It is concluded that, apart from being of considerable biological interest, the described type of research needs to be contemplated carefully with regard to ethical implications when performed with human cells.

Environment-dependent morphology in plasmodium of true slime mold Physarum polycephalum and a network growth model.

PubMed

Takamatsu, Atsuko; Takaba, Eri; Takizawa, Ginjiro

2009-01-07

Branching network growth patterns, depending on environmental conditions, in plasmodium of true slime mold Physarum polycephalum were investigated. Surprisingly, the patterns resemble those in bacterial colonies even though the biological mechanisms differ greatly. Bacterial colonies are collectives of microorganisms in which individual organisms have motility and interact through nutritious and chemical fields. In contrast, the plasmodium is a giant amoeba-like multinucleated unicellular organism that forms a network of tubular structures through which protoplasm streams. The cell motility of the plasmodium is generated by oscillation phenomena observed in the partial bodies, which interact through the tubular structures. First, we analyze characteristics of the morphology quantitatively, then we abstract local rules governing the growing process to construct a simple network growth model. This model is independent of specific systems, in which only two rules are applied. Finally, we discuss the mechanism of commonly observed biological pattern formations through comparison with the system of bacterial colonies.

Nanoscale patterning controls inorganic-membrane interface structure

NASA Astrophysics Data System (ADS)

Almquist, Benjamin D.; Verma, Piyush; Cai, Wei; Melosh, Nicholas A.

2011-02-01

The ability to non-destructively integrate inorganic structures into or through biological membranes is essential to realizing full bio-inorganic integration, including arrayed on-chip patch-clamps, drug delivery, and biosensors. Here we explore the role of nanoscale patterning on the strength of biomembrane-inorganic interfaces. AFM measurements show that inorganic probes functionalized with hydrophobic bands with thicknesses complimentary to the hydrophobic lipid bilayer core exhibit strong attachment in the bilayer. As hydrophobic band thickness increases to 2-3 times the bilayer core the interfacial strength decreases, comparable to homogeneously hydrophobic probes. Analytical calculations and molecular dynamics simulations predict a transition between a `fused' interface and a `T-junction' that matches the experimental results, showing lipid disorder and defect formation for thicker bands. These results show that matching biological length scales leads to more intimate bio-inorganic junctions, enabling rational design of non-destructive membrane interfaces.The ability to non-destructively integrate inorganic structures into or through biological membranes is essential to realizing full bio-inorganic integration, including arrayed on-chip patch-clamps, drug delivery, and biosensors. Here we explore the role of nanoscale patterning on the strength of biomembrane-inorganic interfaces. AFM measurements show that inorganic probes functionalized with hydrophobic bands with thicknesses complimentary to the hydrophobic lipid bilayer core exhibit strong attachment in the bilayer. As hydrophobic band thickness increases to 2-3 times the bilayer core the interfacial strength decreases, comparable to homogeneously hydrophobic probes. Analytical calculations and molecular dynamics simulations predict a transition between a `fused' interface and a `T-junction' that matches the experimental results, showing lipid disorder and defect formation for thicker bands. These results show that matching biological length scales leads to more intimate bio-inorganic junctions, enabling rational design of non-destructive membrane interfaces. Electronic supplementary information (ESI) available: Breakthrough rate as a function of force plots for 5 nm, 10 nm and ∞-probes.. See DOI: 10.1039/c0nr00486c

Pattern formation with proportionate growth

NASA Astrophysics Data System (ADS)

Dhar, Deepak

It is a common observation that as baby animals grow, different body parts grow approximately at same rate. This property, called proportionate growth is remarkable in that it is not encountered easily outside biology. The models of growth that have been studied in Physics so far, e.g diffusion -limited aggregation, surface deposition, growth of crystals from melt etc. involve only growth at the surface, with the inner structure remaining frozen. Interestingly, patterns formed in growing sandpiles provide a very wide variety of patterns that show proportionate growth. One finds patterns with different features, with sharply defined boundaries. In particular, even with very simple rules, one can produce patterns that show striking resemblance to those seen in nature. We can characterize the asymptotic pattern exactly in some special cases. I will discuss in particular the patterns grown on noisy backgrounds. Supported by J. C. Bose fellowship from DST (India).

Robust stochastic Turing patterns in the development of a one-dimensional cyanobacterial organism.

PubMed

Di Patti, Francesca; Lavacchi, Laura; Arbel-Goren, Rinat; Schein-Lubomirsky, Leora; Fanelli, Duccio; Stavans, Joel

2018-05-01

Under nitrogen deprivation, the one-dimensional cyanobacterial organism Anabaena sp. PCC 7120 develops patterns of single, nitrogen-fixing cells separated by nearly regular intervals of photosynthetic vegetative cells. We study a minimal, stochastic model of developmental patterns in Anabaena that includes a nondiffusing activator, two diffusing inhibitor morphogens, demographic fluctuations in the number of morphogen molecules, and filament growth. By tracking developing filaments, we provide experimental evidence for different spatiotemporal roles of the two inhibitors during pattern maintenance and for small molecular copy numbers, justifying a stochastic approach. In the deterministic limit, the model yields Turing patterns within a region of parameter space that shrinks markedly as the inhibitor diffusivities become equal. Transient, noise-driven, stochastic Turing patterns are produced outside this region, which can then be fixed by downstream genetic commitment pathways, dramatically enhancing the robustness of pattern formation, also in the biologically relevant situation in which the inhibitors' diffusivities may be comparable.

Isotopic, petrologic and biogeochemical investigations of banded iron-formations

NASA Technical Reports Server (NTRS)

Hayes, J. M.; Kaufman, A. J.; Klein, C.; Studley, S. A.; Baur, M. E.; Walter, M. R.

1986-01-01

It is recognized that the first occurrence of banded iron-formations (BIFs) clearly predates biological oxygenation of the atmosphere-hydrosphere system and that their last occurrences extend beyond plausible dates of pervasive biological oxygenation. For this reason, and because enormous quantities of oxidizing power have been sequestered in them, it is widely thought that these massive, but enigmatic, sediments must encode information about the mechanism and timing of the rise of atmospheric O2. By coupling isotopic analyses of iron-formation carbonates with biogeochemical and petrologic investigations, we are studying (1) the mechanism of initial sedimentation of iron; (2) the role of iron in microbially mediated diagenetic processes in fresh iron-formation sediments; and (3) the logical integration of mechanisms of deposition with observed levels of banding. Thus far, it has been shown that (1) carbonates in BIFs of the Hamersley Group of Western Australia are isotopically inhomogenous; (2) the nature and pattern of isotopic ordering is not consistent with a metamorphic origin for the overall depletion of C-13 observed in the carbonates; (3) if biological, the origin of the C-13 depleted carbonate could be either respiratory or fermentative; (4) iron may have been precipitate d as Fe(3+), then reduced to Fe(2+) within the sediment; and (5) sedimentary biogeochemical systems may have been at least partially closed to mass transport of carbonate species.

Forging patterns and making waves from biology to geology: a commentary on Turing (1952) 'The chemical basis of morphogenesis'.

PubMed

Ball, Philip

2015-04-19

Alan Turing was neither a biologist nor a chemist, and yet the paper he published in 1952, 'The chemical basis of morphogenesis', on the spontaneous formation of patterns in systems undergoing reaction and diffusion of their ingredients has had a substantial impact on both fields, as well as in other areas as disparate as geomorphology and criminology. Motivated by the question of how a spherical embryo becomes a decidedly non-spherical organism such as a human being, Turing devised a mathematical model that explained how random fluctuations can drive the emergence of pattern and structure from initial uniformity. The spontaneous appearance of pattern and form in a system far away from its equilibrium state occurs in many types of natural process, and in some artificial ones too. It is often driven by very general mechanisms, of which Turing's model supplies one of the most versatile. For that reason, these patterns show striking similarities in systems that seem superficially to share nothing in common, such as the stripes of sand ripples and of pigmentation on a zebra skin. New examples of 'Turing patterns' in biology and beyond are still being discovered today. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.

Active Brownian Particles. From Individual to Collective Stochastic Dynamics

NASA Astrophysics Data System (ADS)

Romanczuk, P.; Bär, M.; Ebeling, W.; Lindner, B.; Schimansky-Geier, L.

2012-03-01

We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework of statistical mechanics. Examples of such active units in complex physico-chemical and biological systems are chemically powered nano-rods, localized patterns in reaction-diffusion system, motile cells or macroscopic animals. Based on the description of individual motion of point-like active particles by stochastic differential equations, we discuss different velocity-dependent friction functions, the impact of various types of fluctuations and calculate characteristic observables such as stationary velocity distributions or diffusion coefficients. Finally, we consider not only the free and confined individual active dynamics but also different types of interaction between active particles. The resulting collective dynamical behavior of large assemblies and aggregates of active units is discussed and an overview over some recent results on spatiotemporal pattern formation in such systems is given.

New gene evolution in the bonus-TIF1-γ/TRIM33 family impacted the architecture of the vertebrate dorsal-ventral patterning network.

PubMed

Wisotzkey, Robert G; Quijano, Janine C; Stinchfield, Michael J; Newfeld, Stuart J

2014-09-01

Uncovering how a new gene acquires its function and understanding how the function of a new gene influences existing genetic networks are important topics in evolutionary biology. Here, we demonstrate nonconservation for the embryonic functions of Drosophila Bonus and its newest vertebrate relative TIF1-γ/TRIM33. We showed previously that TIF1-γ/TRIM33 functions as an ubiquitin ligase for the Smad4 signal transducer and antagonizes the Bone Morphogenetic Protein (BMP) signaling network underlying vertebrate dorsal-ventral axis formation. Here, we show that Bonus functions as an agonist of the Decapentaplegic (Dpp) signaling network underlying dorsal-ventral axis formation in flies. The absence of conservation for the roles of Bonus and TIF1-γ/TRIM33 reveals a shift in the dorsal-ventral patterning networks of flies and mice, systems that were previously considered wholly conserved. The shift occurred when the new gene TIF1-γ/TRIM33 replaced the function of the ubiquitin ligase Nedd4L in the lineage leading to vertebrates. Evidence of this replacement is our demonstration that Nedd4 performs the function of TIF1-γ/TRIM33 in flies during dorsal-ventral axis formation. The replacement allowed vertebrate Nedd4L to acquire novel functions as a ubiquitin ligase of vertebrate-specific Smad proteins. Overall our data reveal that the architecture of the Dpp/BMP dorsal-ventral patterning network continued to evolve in the vertebrate lineage, after separation from flies, via the incorporation of new genes. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A feedback mechanism controlling SCRAMBLED receptor accumulation and cell-type pattern in Arabidopsis.

PubMed

Kwak, Su-Hwan; Schiefelbein, John

2008-12-23

Cellular pattern formation in the root epidermis of Arabidopsis occurs in a position-dependent manner, generating root-hair (H) cells contacting two underlying cortical cells and nonhair (N) cells contacting one cortical cell. SCRAMBLED (SCM), a leucine-rich repeat receptor-like kinase (LRR-RLK), mediates this process through its effect on a downstream transcription factor regulatory network. After perception of a positional cue, the SCM signaling pathway is proposed to preferentially repress WEREWOLF (WER) transcription factor expression in H cells and thereby bias the outcome of mutual lateral inhibition acting between H and N cells. However, the molecular mechanism responsible for this preferential SCM signaling is unknown. Here, we analyze the distribution of the SCM receptor and the biological effect of altering its accumulation pattern. We find that SCM expression and accumulation in the epidermal cell layer is necessary and sufficient to direct the cell-type pattern. Further, SCM preferentially accumulates in H cells, and this accumulation pattern is dependent on the downstream transcription factors. Thus, SCM participates in an autoregulatory feedback loop, enabling cells engaged in SCM signaling to maintain high levels of SCM receptor, which provides a simple mechanism for reinforcing a bias in receptor-mediated signaling to ensure robust pattern formation.

Spatial pattern and ecological process in the coffee agroforestry system.

PubMed

Perfecto, Ivette; Vandermeer, John

2008-04-01

The coffee agroforestry system provides an ideal platform for the study of spatial ecology. The uniform pattern of the coffee plants and shade trees allows for the study of pattern generation through intrinsic biological forces rather than extrinsic habitat patchiness. Detailed studies, focusing on a key mutualism between an ant (Azteca instabilis) and a scale insect (Coccus viridis), conducted in a 45-ha plot in a coffee agroforestry system have provided insights into (1) the quantitative evaluation of spatial pattern of the scale insect Coccus viridis on coffee bushes, (2) the mechanisms for the generation of patterns through the combination of local satellite ant nest formation and regional control from natural enemies, and (3) the consequences of the spatial pattern for the stability of predator-prey (host-parasitoid) systems, for a key coccinelid beetle preying on the scale insects and a phorid fly parasitoid parasitizing the ant.

A Simulation Study of Mutations in the Genetic Regulatory Hierarchy for Butterfly Eyespot Focus Determination

PubMed Central

Marcus, Jeffrey M.; Evans, Travis M.

2008-01-01

The color patterns on the wings of butterflies have been an important model system in evolutionary developmental biology. A recent computational model tested genetic regulatory hierarchies hypothesized to underlie the formation of butterfly eyespot foci (Evans and Marcus, 2006). The computational model demonstrated that one proposed hierarchy was incapable of reproducing the known patterns of gene expression associated with eyespot focus determination in wild-type butterflies, but that two slightly modified alternative hierarchies were capable of reproducing all of the known gene expressions patterns. Here we extend the computational models previously implemented in Delphi 2.0 to two mutants derived from the squinting bush brown butterfly (Bicyclus anynana). These two mutants, comet and Cyclops, have aberrantly shaped eyespot foci that are produced by different mechanisms. The comet mutation appears to produce a modified interaction between the wing margin and the eyespot focus that results in a series of comet-shaped eyespot foci. The Cyclops mutation causes the failure of wing vein formation between two adjacent wing-cells and the fusion of two adjacent eyespot foci to form a single large elongated focus in their place. The computational approach to modeling pattern formation in these mutants allows us to make predictions about patterns of gene expression, which are largely unstudied in butterfly mutants. It also suggests a critical experiment that will allow us to distinguish between two hypothesized genetic regulatory hierarchies that may underlie all butterfly eyespot foci. PMID:18586070

Analysis of Biophysical Mechanisms of Gilgai Microrelief Formation in Dryland Swelling Soils Using Ultra-High Resolution Aerial Imagery

NASA Astrophysics Data System (ADS)

Krell, N.; DeCarlo, K. F.; Caylor, K. K.

2015-12-01

Microrelief formations ("gilgai"), which form due to successive wetting-drying cycles typical of swelling soils, provide ecological hotspots for local fauna and flora, including higher and more robust vegetative growth. The distribution of these gilgai suggests a remarkable degree of regularity. However, it is unclear to what extent the mechanisms that drive gilgai formation are physical, such as desiccation-induced fracturing, or biological in nature, namely antecedent vegetative clustering. We investigated gilgai genesis and pattern formation in a 100 x 100 meter study area with swelling soils in a semiarid grassland at the Mpala Research Center in central Kenya. Our ongoing experiment is composed of three 9m2 treatments: we removed gilgai and limited vegetative growth by herbicide application in one plot, allowed for unrestricted seed dispersal in another, and left gilgai unobstructed in a control plot. To estimate the spatial frequencies of the repeating patterns of gilgai, we obtained ultra-high resolution (0.01-0.03m/pixel) images with an unmanned aerial vehicle (UAV) from which digital elevation models were also generated. Geostatistical analyses using wavelet and fourier methods in 1- and 2-dimensions were employed to characterize gilgai size and distribution. Preliminary results support regular spatial patterning across the gilgaied landscape and heterogeneities may be related to local soil properties and biophysical influences. Local data on gilgai and fracture characteristics suggest that gilgai form at characteristic heights and spacing based on fracture morphology: deep, wide cracks result in large, highly vegetated mounds whereas shallow cracks, induced by animal trails, are less correlated with gilgai size and shape. Our experiments will help elucidate the links between shrink-swell processes and gilgai-vegetation patterning in high activity clay soils and advance our understanding of the mechanisms of gilgai formation in drylands.

Molecular insights into the novel aspects of diatom biology.

PubMed

Scala, S; Bowler, C

2001-10-01

Diatoms are unicellular photosynthetic eukaryotes that are thought to contribute as much as 25% of global primary productivity. In spite of their ecological importance in the worlds oceans, very little information is available at the molecular level about the novel aspects of their biology. Recent advances, such as the development of gene transfer protocols, are now allowing the genetic dissection of diatom biology. Notable examples are advances in understanding the genetic basis for the silica-based bioinorganic pattern formation of their cell walls and for elucidating key aspects of diatom ecophysiology. The potentiation of current research will allow an evaluation of the use of diatoms to construct submicrometre-scale silicon structures for the nanotechnology industry and will reveal the molecular secrets underlying their ecological success.

Developing JSequitur to Study the Hierarchical Structure of Biological Sequences in a Grammatical Inference Framework of String Compression Algorithms.

PubMed

Galbadrakh, Bulgan; Lee, Kyung-Eun; Park, Hyun-Seok

2012-12-01

Grammatical inference methods are expected to find grammatical structures hidden in biological sequences. One hopes that studies of grammar serve as an appropriate tool for theory formation. Thus, we have developed JSequitur for automatically generating the grammatical structure of biological sequences in an inference framework of string compression algorithms. Our original motivation was to find any grammatical traits of several cancer genes that can be detected by string compression algorithms. Through this research, we could not find any meaningful unique traits of the cancer genes yet, but we could observe some interesting traits in regards to the relationship among gene length, similarity of sequences, the patterns of the generated grammar, and compression rate.

Decoding the Principles of Emergence and Resiliency in Biological Collective Systems - A Multi-Scale Approach: Final Report

DTIC Science & Technology

2018-02-15

models and approaches are also valid using other invasive and non - invasive technologies. Finally, we illustrate and experimentally evaluate this...2017 Project Outline q  Pattern formation diversity in wild microbial societies q  Experimental and mathematical analysis methodology q  Skeleton...chemotaxis, nutrient degradation, and the exchange of amino acids between cells. Using both quantitative experimental methods and several theoretical

Effects of live crown on vertical patterns of wood density and growth in Douglas-fir.

Treesearch

Barbara L. Gartner; Eric M. North; G.R. Johnson; Ryan Singleton

2002-01-01

It would be valuable economically to know what are the biological triggers for formation of mature wood (currently of high value) and (or) what maintains production of juvenile wood (currently of low value), to develop silvicultural regimes that control the relative production of the two types of wood. Foresters commonly assume the bole of softwoods produces juvenile...

Size-Dependent Protein-Nanoparticle Interactions in Citrate-Stabilized Gold Nanoparticles: The Emergence of the Protein Corona.

PubMed

Piella, Jordi; Bastús, Neus G; Puntes, Víctor

2017-01-18

Surface modifications of highly monodisperse citrate-stabilized gold nanoparticles (AuNPs) with sizes ranging from 3.5 to 150 nm after their exposure to cell culture media supplemented with fetal bovine serum were studied and characterized by the combined use of UV-vis spectroscopy, dynamic light scattering, and zeta potential measurements. In all the tested AuNPs, a dynamic process of protein adsorption was observed, evolving toward the formation of an irreversible hard protein coating known as Protein Corona. Interestingly, the thickness and density of this protein coating were strongly dependent on the particle size, making it possible to identify different transition regimes as the size of the particles increased: (i) NP-protein complexes (or incomplete corona), (ii) the formation of a near-single dense protein corona layer, and (iii) the formation of a multilayer corona. In addition, the different temporal patterns in the evolution of the protein coating came about more quickly for small particles than for the larger ones, further revealing the significant role that size plays in the kinetics of this process. Since the biological identity of the NPs is ultimately determined by the protein corona and different NP-biological interactions take place at different time scales, these results are relevant to biological and toxicological studies.

The Hydra model - a model for what?

PubMed

Gierer, Alfred

2012-01-01

The introductory personal remarks refer to my motivations for choosing research projects, and for moving from physics to molecular biology and then to development, with Hydra as a model system. Historically, Trembley's discovery of Hydra regeneration in 1744 was the beginning of developmental biology as we understand it, with passionate debates about preformation versus de novo generation, mechanisms versus organisms. In fact, seemingly conflicting bottom-up and top-down concepts are both required in combination to understand development. In modern terms, this means analysing the molecules involved, as well as searching for physical principles underlying development within systems of molecules, cells and tissues. During the last decade, molecular biology has provided surprising and impressive evidence that the same types of molecules and molecular systems are involved in pattern formation in a wide range of organisms, including coelenterates like Hydra, and thus appear to have been "invented" early in evolution. Likewise, the features of certain systems, especially those of developmental regulation, are found in many different organisms. This includes the generation of spatial structures by the interplay of self-enhancing activation and "lateral" inhibitory effects of wider range, which is a main topic of my essay. Hydra regeneration is a particularly clear model for the formation of defined patterns within initially near-uniform tissues. In conclusion, this essay emphasizes the analysis of development in terms of physical laws, including the application of mathematics, and insists that Hydra was, and will continue to be, a rewarding model for understanding general features of embryogenesis and regeneration.

Dynamic optimization of distributed biological systems using robust and efficient numerical techniques.

PubMed

Vilas, Carlos; Balsa-Canto, Eva; García, Maria-Sonia G; Banga, Julio R; Alonso, Antonio A

2012-07-02

Systems biology allows the analysis of biological systems behavior under different conditions through in silico experimentation. The possibility of perturbing biological systems in different manners calls for the design of perturbations to achieve particular goals. Examples would include, the design of a chemical stimulation to maximize the amplitude of a given cellular signal or to achieve a desired pattern in pattern formation systems, etc. Such design problems can be mathematically formulated as dynamic optimization problems which are particularly challenging when the system is described by partial differential equations.This work addresses the numerical solution of such dynamic optimization problems for spatially distributed biological systems. The usual nonlinear and large scale nature of the mathematical models related to this class of systems and the presence of constraints on the optimization problems, impose a number of difficulties, such as the presence of suboptimal solutions, which call for robust and efficient numerical techniques. Here, the use of a control vector parameterization approach combined with efficient and robust hybrid global optimization methods and a reduced order model methodology is proposed. The capabilities of this strategy are illustrated considering the solution of a two challenging problems: bacterial chemotaxis and the FitzHugh-Nagumo model. In the process of chemotaxis the objective was to efficiently compute the time-varying optimal concentration of chemotractant in one of the spatial boundaries in order to achieve predefined cell distribution profiles. Results are in agreement with those previously published in the literature. The FitzHugh-Nagumo problem is also efficiently solved and it illustrates very well how dynamic optimization may be used to force a system to evolve from an undesired to a desired pattern with a reduced number of actuators. The presented methodology can be used for the efficient dynamic optimization of generic distributed biological systems.

Smectite clays in Mars soil - Evidence for their presence and role in Viking biology experimental results

NASA Technical Reports Server (NTRS)

Banin, A.; Rishpon, J.

1979-01-01

Evidence for the presence of smectite clays in Martian soils is reviewed and results of experiments with certain active clays simulating the Viking biology experiments are reported. Analyses of Martian soil composition by means of X-ray fluorescence spectrometry and dust storm spectroscopy and Martian geological history strongly suggest the presence of a mixture of weathered ferro-silicate minerals, mainly nontronite and montmorillonite, accompanied by soluble sulphate salts, as major constituents. Samples of montmorillonite and nontronite incubated with (C-14)-formate or the radioactive nutrient medium solution used in the Viking Labeled Release experiment, were found to produce patterns of release of radioactive gas very similar to those observed in the Viking experiments, indicating the iron-catalyzed decomposition of formate as the reaction responsible for the Viking results. The experimental results of Hubbard (1979) simulating the results of the Viking Pyrolytic Release experiment using iron montmorillonites are pointed out, and it is concluded that many of the results of the Viking biology experiments can be explained in terms of the surface activity of smectite clays in catalysis and adsorption.

Trace elements during primordial plexiform network formation in human cerebral organoids

PubMed Central

Sartore, Rafaela C.; Cardoso, Simone C.; Lages, Yury V.M.; Paraguassu, Julia M.; Stelling, Mariana P.; Madeiro da Costa, Rodrigo F.; Guimaraes, Marilia Z.; Pérez, Carlos A.

2017-01-01

Systematic studies of micronutrients during brain formation are hindered by restrictions to animal models and adult post-mortem tissues. Recently, advances in stem cell biology have enabled recapitulation of the early stages of human telencephalon development in vitro. In the present work, we analyzed cerebral organoids derived from human pluripotent stem cells by synchrotron radiation X-ray fluorescence in order to measure biologically valuable micronutrients incorporated and distributed into the exogenously developing brain. Our findings indicate that elemental inclusion in organoids is consistent with human brain tissue and involves P, S, K, Ca, Fe and Zn. Occurrence of different concentration gradients also suggests active regulation of elemental transmembrane transport. Finally, the analysis of pairs of elements shows interesting elemental interaction patterns that change from 30 to 45 days of development, suggesting short- or long-term associations, such as storage in similar compartments or relevance for time-dependent biological processes. These findings shed light on which trace elements are important during human brain development and will support studies aimed to unravel the consequences of disrupted metal homeostasis for neurodevelopmental diseases, including those manifested in adulthood. PMID:28194309

[A NATURAL PLAGUE FOCUS. IN GORNYI ALTAI: FORMATION, DEVELOPMENT, AND FUNCTIONING].

PubMed

Korzun, V M; Balakhoiov, S V; Chpanin, E V; Denisov, A V; Mikhailov, E P; Mischenko, A J; Yarygina, M B; Rozhdestvensky, E N; Fomina, L A

2016-01-01

The paper gives the results of analyzing the data of long-term studies of the natural focal pattern of plague in the Gornyi Altai natural focus. It describes a wide range of biological processes occurring in the focus and shows the most important patterns of its functioning as a complex multilevel ecological system. The key features of the formation of the focus have been revealed. The plague focus in South-Western Altai has formed relatively, recently, about half a century ago, then it has intensively developed and its enzootic area and the activity of epizootic manifestations have considerably increased. This process is due to the space-time transformations of the basic ecological and population characteristics of Pallas' pika (Ochotoma pallasi), the principal vector of the pathogen of plague and fleas parasitizing the mammal, which is in turn related to the aridization of mountain steppes in South-Western Altai.

Forging patterns and making waves from biology to geology: a commentary on Turing (1952) ‘The chemical basis of morphogenesis’

PubMed Central

Ball, Philip

2015-01-01

Alan Turing was neither a biologist nor a chemist, and yet the paper he published in 1952, ‘The chemical basis of morphogenesis’, on the spontaneous formation of patterns in systems undergoing reaction and diffusion of their ingredients has had a substantial impact on both fields, as well as in other areas as disparate as geomorphology and criminology. Motivated by the question of how a spherical embryo becomes a decidedly non-spherical organism such as a human being, Turing devised a mathematical model that explained how random fluctuations can drive the emergence of pattern and structure from initial uniformity. The spontaneous appearance of pattern and form in a system far away from its equilibrium state occurs in many types of natural process, and in some artificial ones too. It is often driven by very general mechanisms, of which Turing's model supplies one of the most versatile. For that reason, these patterns show striking similarities in systems that seem superficially to share nothing in common, such as the stripes of sand ripples and of pigmentation on a zebra skin. New examples of ‘Turing patterns' in biology and beyond are still being discovered today. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society. PMID:25750229

4D Biofabrication of Branching Multicellular Structures: A Morphogenesis Simulation Based on Turing’s Reaction-Diffusion Dynamics

NASA Astrophysics Data System (ADS)

Zhu, Xiaolu; Yang, Hao

2017-12-01

The recently emerged four-dimensional (4D) biofabrication technique aims to create dynamic three-dimensional (3D) biological structures that can transform their shapes or functionalities with time when an external stimulus is imposed or when cell postprinting self-assembly occurs. The evolution of 3D pattern of branching geometry via self-assembly of cells is critical for 4D biofabrication of artificial organs or tissues with branched geometry. However, it is still unclear that how the formation and evolution of these branching pattern are biologically encoded. We study the 4D fabrication of lung branching structures utilizing a simulation model on the reaction-diffusion mechanism, which is established using partial differential equations of four variables, describing the reaction and diffusion process of morphogens with time during the development process of lung branching. The simulation results present the forming process of 3D branching pattern, and also interpret the behaviors of side branching and tip splitting as the stalk growing, through 3D visualization of numerical simulation.

Directed formation of micro- and nanoscale patterns of functional light-harvesting LH2 complexes.

PubMed

Reynolds, Nicholas P; Janusz, Stefan; Escalante-Marun, Maryana; Timney, John; Ducker, Robert E; Olsen, John D; Otto, Cees; Subramaniam, Vinod; Leggett, Graham J; Hunter, C Neil

2007-11-28

The precision placement of the desired protein components on a suitable substrate is an essential prelude to any hybrid "biochip" device, but a second and equally important condition must also be met: the retention of full biological activity. Here we demonstrate the selective binding of an optically active membrane protein, the light-harvesting LH2 complex from Rhodobacter sphaeroides, to patterned self-assembled monolayers at the micron scale and the fabrication of nanometer-scale patterns of these molecules using near-field photolithographic methods. In contrast to plasma proteins, which are reversibly adsorbed on many surfaces, the LH2 complex is readily patterned simply by spatial control of surface polarity. Near-field photolithography has yielded rows of light-harvesting complexes only 98 nm wide. Retention of the native optical properties of patterned LH2 molecules was demonstrated using in situ fluorescence emission spectroscopy.

Modeling digits. Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients.

PubMed

Raspopovic, J; Marcon, L; Russo, L; Sharpe, J

2014-08-01

During limb development, digits emerge from the undifferentiated mesenchymal tissue that constitutes the limb bud. It has been proposed that this process is controlled by a self-organizing Turing mechanism, whereby diffusible molecules interact to produce a periodic pattern of digital and interdigital fates. However, the identities of the molecules remain unknown. By combining experiments and modeling, we reveal evidence that a Turing network implemented by Bmp, Sox9, and Wnt drives digit specification. We develop a realistic two-dimensional simulation of digit patterning and show that this network, when modulated by morphogen gradients, recapitulates the expression patterns of Sox9 in the wild type and in perturbation experiments. Our systems biology approach reveals how a combination of growth, morphogen gradients, and a self-organizing Turing network can achieve robust and reproducible pattern formation. Copyright © 2014, American Association for the Advancement of Science.

Post-Self-Assembly Cross-Linking to Integrate Molecular Nanofibers with Copolymers in Oscillatory Hydrogels

DTIC Science & Technology

2013-05-09

The BZ reaction provides a model system to mimic a variety of complex processes, such as biological morphogenesis, in monodisperse microemulsions .15...surfaces, ion-exchange resins, membranes, and microemulsions . For example, in addition to minimizing the hydrodynamic effects and formation of bubbles...Reaction-Diffusion Microemulsions Reveals Three-Dimensional Tu- ring Patterns. Science (Washington, DC, U.S.) 2011, 331, 1309−1312. (16) Agladze, K. I

Main regulatory pathways, key genes and microRNAs involved in flower formation and development of moso bamboo (Phyllostachys edulis).

PubMed

Ge, Wei; Zhang, Ying; Cheng, Zhanchao; Hou, Dan; Li, Xueping; Gao, Jian

2017-01-01

Moso bamboo is characterized by infrequent sexual reproduction and erratic flowering habit; however, the molecular biology of flower formation and development is not well studied in this species. We studied the molecular regulation mechanisms of moso bamboo development and flowering by selecting three key regulatory pathways: plant-pathogen interaction, plant hormone signal transduction and protein processing in endoplasmic reticulum at different stages of flowering in moso bamboo. We selected PheDof1, PheMADS14 and six microRNAs involved in the three pathways through KEGG pathway and cluster analysis. Subcellular localization, transcriptional activation, Western blotting, in situ hybridization and qRT-PCR were used to further investigate the expression patterns and regulatory roles of pivotal genes at different flower development stages. Differential expression patterns showed that PheDof1, PheMADS14 and six miRNAs may play vital regulatory roles in flower development and floral transition in moso bamboo. Our research paves way for further studies on metabolic regulatory networks and provides insight into the molecular regulation mechanisms of moso bamboo flowering and senescence. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

[Biological role of fetuin A and its potential importance for prediction of cardiovascular risk in patients with type 2 diabetes mellitus].

PubMed

Horshuns'ka, M Iu; Karachentsev, Iu I; Kravchun, N O; Ĭensen, É; Leshchenko, Zh A; Hladkykh, O I; Krasova, N S; Tyzhnenko, T V; Opaleĭko, Iu A; Poltorak, V V

2013-01-01

The authors' data and those from literature concerning biological role of fetuin A glycoprotein have been generalized in the article. A direct correlation has been established between fetuin A and some adipokines involved in the formation of insulin resistance and atherogenesis (progranulin, omentin-1), and osteoprotegerin (the novel cardiovascular risk factor) as well as an increase of circulating levels of fetuin A in patients with type 2 diabetes mellitus with high cardiovascular risk metabolic pattern but without manifestations of macrovascular complications. This substantiates the involvement of fetuin A in the complex of biomarkers of subclinical atherosclerosis.

Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis1[OPEN

PubMed Central

Bustillo-Avendaño, Estefano; Ibáñez, Sergio; Sanz, Oscar; Sousa Barros, Jessica Aline; Gude, Inmaculada; Perianez-Rodriguez, Juan; Micol, José Luis; Del Pozo, Juan Carlos

2018-01-01

Body regeneration through formation of new organs is a major question in developmental biology. We investigated de novo root formation using whole leaves of Arabidopsis (Arabidopsis thaliana). Our results show that local cytokinin biosynthesis and auxin biosynthesis in the leaf blade followed by auxin long-distance transport to the petiole leads to proliferation of J0121-marked xylem-associated tissues and others through signaling of INDOLE-3-ACETIC ACID INDUCIBLE28 (IAA28), CRANE (IAA18), WOODEN LEG, and ARABIDOPSIS RESPONSE REGULATORS1 (ARR1), ARR10, and ARR12. Vasculature proliferation also involves the cell cycle regulator KIP-RELATED PROTEIN2 and ABERRANT LATERAL ROOT FORMATION4, resulting in a mass of cells with rooting competence that resembles callus formation. Endogenous callus formation precedes specification of postembryonic root founder cells, from which roots are initiated through the activity of SHORT-ROOT, PLETHORA1 (PLT1), and PLT2. Primordia initiation is blocked in shr plt1 plt2 mutant. Stem cell regulators SCHIZORIZA, JACKDAW, BLUEJAY, and SCARECROW also participate in root initiation and are required to pattern the new organ, as mutants show disorganized and reduced number of layers and tissue initials resulting in reduced rooting. Our work provides an organ regeneration model through de novo root formation, stating key stages and the primary pathways involved. PMID:29233938

Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis.

PubMed

Bustillo-Avendaño, Estefano; Ibáñez, Sergio; Sanz, Oscar; Sousa Barros, Jessica Aline; Gude, Inmaculada; Perianez-Rodriguez, Juan; Micol, José Luis; Del Pozo, Juan Carlos; Moreno-Risueno, Miguel Angel; Pérez-Pérez, José Manuel

2018-02-01

Body regeneration through formation of new organs is a major question in developmental biology. We investigated de novo root formation using whole leaves of Arabidopsis ( Arabidopsis thaliana ). Our results show that local cytokinin biosynthesis and auxin biosynthesis in the leaf blade followed by auxin long-distance transport to the petiole leads to proliferation of J0121-marked xylem-associated tissues and others through signaling of INDOLE-3-ACETIC ACID INDUCIBLE28 (IAA28), CRANE (IAA18), WOODEN LEG, and ARABIDOPSIS RESPONSE REGULATORS1 (ARR1), ARR10, and ARR12. Vasculature proliferation also involves the cell cycle regulator KIP-RELATED PROTEIN2 and ABERRANT LATERAL ROOT FORMATION4, resulting in a mass of cells with rooting competence that resembles callus formation. Endogenous callus formation precedes specification of postembryonic root founder cells, from which roots are initiated through the activity of SHORT-ROOT, PLETHORA1 (PLT1), and PLT2. Primordia initiation is blocked in shr plt1 plt2 mutant. Stem cell regulators SCHIZORIZA, JACKDAW, BLUEJAY, and SCARECROW also participate in root initiation and are required to pattern the new organ, as mutants show disorganized and reduced number of layers and tissue initials resulting in reduced rooting. Our work provides an organ regeneration model through de novo root formation, stating key stages and the primary pathways involved. © 2018 American Society of Plant Biologists. All Rights Reserved.

Programming Cells for Dynamic Assembly of Inorganic Nano-Objects with Spatiotemporal Control.

PubMed

Wang, Xinyu; Pu, Jiahua; An, Bolin; Li, Yingfeng; Shang, Yuequn; Ning, Zhijun; Liu, Yi; Ba, Fang; Zhang, Jiaming; Zhong, Chao

2018-04-01

Programming living cells to organize inorganic nano-objects (NOs) in a spatiotemporally precise fashion would advance new techniques for creating ordered ensembles of NOs and new bio-abiotic hybrid materials with emerging functionalities. Bacterial cells often grow in cellular communities called biofilms. Here, a strategy is reported for programming dynamic biofilm formation for the synchronized assembly of discrete NOs or hetero-nanostructures on diverse interfaces in a dynamic, scalable, and hierarchical fashion. By engineering Escherichia coli to sense blue light and respond by producing biofilm curli fibers, biofilm formation is spatially controlled and the patterned NOs' assembly is simultaneously achieved. Diverse and complex fluorescent quantum dot patterns with a minimum patterning resolution of 100 µm are demonstrated. By temporally controlling the sequential addition of NOs into the culture, multilayered heterostructured thin films are fabricated through autonomous layer-by-layer assembly. It is demonstrated that biologically dynamic self-assembly can be used to advance a new repertoire of nanotechnologies and materials with increasing complexity that would be otherwise challenging to produce. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Establishment of spatial pattern.

PubMed

Slack, Jonathan

2014-01-01

An overview and perspective are presented of mechanisms for the development of spatial pattern in animal embryos. It is intended both for new entrants to developmental biology and for specialists in other fields, with only a basic knowledge of animal life cycles being required. The first event of pattern formation is normally the localization of a cytoplasmic determinant in the egg, either during oogenesis or post-fertilization. Following cleavage to a multicellular stage, some cells contain the determinant and others do not. The determinant confers a specific developmental pathway on the cells that contain it, often making them the source of the first extracellular signal, or inducing factor. Inducing factors often form concentration gradients to which cells respond by up or downregulating genes at various concentration thresholds. This enables an initial situation consisting of two cell states (with or without the determinant) to generate a multistate pattern. Multiple rounds of gradient signaling, interspersed with phases of morphogenetic movements, can generate a complex pattern using a small number of signals and responding genes. Development proceeds in a hierarchical manner, with broad body subdivisions being specified initially, and becoming successively subdivided to give individual organs and tissues composed of multiple cell types in a characteristic arrangement. Double gradient models can account for embryonic regulation, whereby a similarly proportioned body pattern is formed following removal of material. Processes that are involved at the later stages include the formation of repeating structures by the combination of an oscillator with a gradient, and the formation of tissues with one cell type scattered in a background of another through a process called lateral inhibition. This set of processes make up a 'developmental toolkit' which can be deployed in various sequences and combinations to generate a very wide variety of structures and cell types. © 2014 Wiley Periodicals, Inc.

A simulation study of mutations in the genetic regulatory hierarchy for butterfly eyespot focus determination.

PubMed

Marcus, Jeffrey M; Evans, Travis M

2008-09-01

The color patterns on the wings of butterflies have been an important model system in evolutionary developmental biology. A recent computational model tested genetic regulatory hierarchies hypothesized to underlie the formation of butterfly eyespot foci [Evans, T.M., Marcus, J.M., 2006. A simulation study of the genetic regulatory hierarchy for butterfly eyespot focus determination. Evol. Dev. 8, 273-283]. The computational model demonstrated that one proposed hierarchy was incapable of reproducing the known patterns of gene expression associated with eyespot focus determination in wild-type butterflies, but that two slightly modified alternative hierarchies were capable of reproducing all of the known gene expressions patterns. Here we extend the computational models previously implemented in Delphi 2.0 to two mutants derived from the squinting bush brown butterfly (Bicyclus anynana). These two mutants, comet and Cyclops, have aberrantly shaped eyespot foci that are produced by different mechanisms. The comet mutation appears to produce a modified interaction between the wing margin and the eyespot focus that results in a series of comet-shaped eyespot foci. The Cyclops mutation causes the failure of wing vein formation between two adjacent wing-cells and the fusion of two adjacent eyespot foci to form a single large elongated focus in their place. The computational approach to modeling pattern formation in these mutants allows us to make predictions about patterns of gene expression, which are largely unstudied in butterfly mutants. It also suggests a critical experiment that will allow us to distinguish between two hypothesized genetic regulatory hierarchies that may underlie all butterfly eyespot foci.

Power Law Patch Scaling and Lack of Characteristic Wavelength Suggest "Scale-Free" Processes Drive Pattern Formation in the Florida Everglades

NASA Astrophysics Data System (ADS)

Kaplan, D. A.; Casey, S. T.; Cohen, M. J.; Acharya, S.; Jawitz, J. W.

2016-12-01

A century of hydrologic modification has altered the physical and biological drivers of landscape processes in the Everglades (Florida, USA). Restoring the ridge-slough patterned landscape, a dominant feature of the historical system, is a priority, but requires an understanding of pattern genesis and degradation mechanisms. Physical experiments to evaluate alternative pattern formation mechanisms are limited by the long time scales of peat accumulation and loss, necessitating model-based comparisons, where support for a particular mechanism is based on model replication of extant patterning and trajectories of degradation. However, multiple mechanisms yield patch elongation in the direction of historical flow (a central feature of ridge-slough patterning), limiting the utility of that characteristic for discriminating among alternatives. Using data from vegetation maps, we investigated the statistical features of ridge-slough spatial patterning (ridge density, patch perimeter, elongation, patch-size distributions, and spatial periodicity) to establish more rigorous criteria for evaluating model performance and to inform controls on pattern variation across the contemporary system. Two independent analyses (2-D periodograms and patch size distributions) provide strong evidence against regular patterning, with the landscape exhibiting neither a characteristic wavelength nor a characteristic patch size, both of which are expected under conditions that produce regular patterns. Rather, landscape properties suggest robust scale-free patterning, indicating genesis from the coupled effects of local facilitation and a global negative feedback operating uniformly at the landscape-scale. This finding challenges widespread invocation of scale-dependent negative feedbacks for explaining ridge-slough pattern origins. These results help discern among genesis mechanisms and provide an improved statistical description of the landscape that can be used to compare among model outputs, as well as to assess the success of future restoration projects.

Nestedness across biological scales

PubMed Central

Marquitti, Flavia M. D.; Raimundo, Rafael L. G.; Sebastián-González, Esther; Coltri, Patricia P.; Perez, S. Ivan; Brandt, Débora Y. C.; Nunes, Kelly; Daura-Jorge, Fábio G.; Floeter, Sergio R.; Guimarães, Paulo R.

2017-01-01

Biological networks pervade nature. They describe systems throughout all levels of biological organization, from molecules regulating metabolism to species interactions that shape ecosystem dynamics. The network thinking revealed recurrent organizational patterns in complex biological systems, such as the formation of semi-independent groups of connected elements (modularity) and non-random distributions of interactions among elements. Other structural patterns, such as nestedness, have been primarily assessed in ecological networks formed by two non-overlapping sets of elements; information on its occurrence on other levels of organization is lacking. Nestedness occurs when interactions of less connected elements form proper subsets of the interactions of more connected elements. Only recently these properties began to be appreciated in one-mode networks (where all elements can interact) which describe a much wider variety of biological phenomena. Here, we compute nestedness in a diverse collection of one-mode networked systems from six different levels of biological organization depicting gene and protein interactions, complex phenotypes, animal societies, metapopulations, food webs and vertebrate metacommunities. Our findings suggest that nestedness emerge independently of interaction type or biological scale and reveal that disparate systems can share nested organization features characterized by inclusive subsets of interacting elements with decreasing connectedness. We primarily explore the implications of a nested structure for each of these studied systems, then theorize on how nested networks are assembled. We hypothesize that nestedness emerges across scales due to processes that, although system-dependent, may share a general compromise between two features: specificity (the number of interactions the elements of the system can have) and affinity (how these elements can be connected to each other). Our findings suggesting occurrence of nestedness throughout biological scales can stimulate the debate on how pervasive nestedness may be in nature, while the theoretical emergent principles can aid further research on commonalities of biological networks. PMID:28166284

Memory instability as a gateway to generalization

PubMed Central

2018-01-01

Our present frequently resembles our past. Patterns of actions and events repeat throughout our lives like a motif. Identifying and exploiting these patterns are fundamental to many behaviours, from creating grammar to the application of skill across diverse situations. Such generalization may be dependent upon memory instability. Following their formation, memories are unstable and able to interact with one another, allowing, at least in principle, common features to be extracted. Exploiting these common features creates generalized knowledge that can be applied across varied circumstances. Memory instability explains many of the biological and behavioural conditions necessary for generalization and offers predictions for how generalization is produced. PMID:29554094

Top-down models in biology: explanation and control of complex living systems above the molecular level.

PubMed

Pezzulo, Giovanni; Levin, Michael

2016-11-01

It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. © 2016 The Author(s).

Top-down models in biology: explanation and control of complex living systems above the molecular level

PubMed Central

2016-01-01

It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. PMID:27807271

In search of the Golden Fleece: Unraveling principles of morphogenesis by studying the integrative biology of skin appendages

PubMed Central

Hughes, Michael W.; Wu, Ping; Jiang, Ting-Xin; Lin, Sung-Jan; Dong, Chen-Yuan; Li, Ang; Hsieh, Fon-Jou; Widelitz, Randall B.; Choung, Cheng Ming

2013-01-01

Summary The mythological story of the Golden Fleece symbolizes the magical regenerative power of skin appendages. Similar to the adventurous pursuit of the Golden Fleece by the multi-talented Argonauts, today we also need an integrated multi-disciplined approach to understand the cellular and molecular processes during development, regeneration and evolution of skin appendages. To this end, we have explored several aspects of skin appendage biology that contribute to the Turing activator / inhibitor model in feather pattern formation, the topo-biological arrangement of stem cells in organ shape determination, the macro-environmental regulation of stem cells in regenerative hair waves, and potential novel molecular pathways in the morphological evolution of feathers. Here we show our current integrative biology efforts to unravel the complex cellular behavior in patterning stem cells and the control of regional specificity in skin appendages. We use feather / scale tissue recombination to demonstrate the timing control of competence and inducibility. Feathers from different body regions are used to study skin regional specificity. Bioinformatic analyses of transcriptome microarrays show the potential involvement of candidate molecular pathways. We further show Hox genes exhibit some region specific expression patterns. To visualize real time events, we applied time-lapse movies, confocal microscopy and multiphoton microscopy to analyze the morphogenesis of cultured embryonic chicken skin explants. These modern imaging technologies reveal unexpectedly complex cellular flow and organization of extracellular matrix molecules in three dimensions. While these approaches are in preliminary stages, this perspective highlights the challenges we face and new integrative tools we will use. Future work will follow these leads to develop a systems biology view and understanding in the morphogenetic principles that govern the development and regeneration of ectodermal organs. PMID:21437328

Biological pattern formation: from basic mechanisms to complex structures

NASA Astrophysics Data System (ADS)

Koch, A. J.; Meinhardt, H.

1994-10-01

The reliable development of highly complex organisms is an intriguing and fascinating problem. The genetic material is, as a rule, the same in each cell of an organism. How then do cells, under the influence of their common genes, produce spatial patterns? Simple models are discussed that describe the generation of patterns out of an initially nearly homogeneous state. They are based on nonlinear interactions of at least two chemicals and on their diffusion. The concepts of local autocatalysis and of long-range inhibition play a fundamental role. Numerical simulations show that the models account for many basic biological observations such as the regeneration of a pattern after excision of tissue or the production of regular (or nearly regular) arrays of organs during (or after) completion of growth. Very complex patterns can be generated in a reproducible way by hierarchical coupling of several such elementary reactions. Applications to animal coats and to the generation of polygonally shaped patterns are provided. It is further shown how to generate a strictly periodic pattern of units that themselves exhibit a complex and polar fine structure. This is illustrated by two examples: the assembly of photoreceptor cells in the eye of Drosophila and the positioning of leaves and axillary buds in a growing shoot. In both cases, the substructures have to achieve an internal polarity under the influence of some primary pattern-forming system existing in the fly's eye or in the plant. The fact that similar models can describe essential steps in organisms as distantly related as animals and plants suggests that they reveal some universal mechanisms.

Asymmetric Brownian motor driven by bubble formation in a hydrophobic channel.

PubMed

Arai, Noriyoshi; Yasuoka, Kenji; Koishi, Takahiro; Ebisuzaki, Toshikazu

2010-10-26

The "asymmetric brownian ratchet model" is a variation of Feynman's ratchet and pawl system proposed. In this model, a system consisting of a motor and a rail has two binding states. One is the random brownian state, and the other is the asymmetric potential state. When the system is alternatively switched between these states, the motor can be driven in one direction. This model is believed to explain nanomotor behavior in biological systems. The feasibility of the model has been demonstrated using electrical and magnetic forces; however, switching of these forces is unlikely to be found in biological systems. In this paper, we propose an original mechanism of transition between states by bubble formation in a nanosized channel surrounded by hydrophobic atoms. This amounts to a nanoscale motor system using bubble propulsion. The motor system consists of a hydrophobic motor and a rail on which hydrophobic patterns are printed. Potential asymmetry can be produced by using a left-right asymmetric pattern shape. Hydrophobic interactions are believed to play an important role in the binding of biomolecules and molecular recognition. The bubble formation is controlled by changing the width of the channel by an atomic distance (∼0.1 nm). Therefore, the motor is potentially more efficient than systems controlled by other forces, in which a much larger change in the motor position is necessary. We have simulated the bubble-powered motor using dissipative particle dynamics and found behavior in good agreement with that of motor proteins. Energy efficiency is as high as 60%.

Morphological, biochemical, physiological and molecular aspects of the response of Fusobacterium nucleatum exposed to subinhibitory concentrations of antimicrobials.

PubMed

de Souza Filho, Job Alves; Diniz, Cláudio Galuppo; Barbosa, Natália Bento; de Freitas, Michele Cristine Ribeiro; Lopes Neves, Mariana Silva; da Gama Mazzei, Rafaella Nogueira; Gameiro, Jacy; Coelho, Cíntia Marques; da Silva, Vânia Lúcia

2012-12-01

Subinhibitory concentrations (SICs) of antimicrobials may result in alterations in bacterial biology with implications for its potential aggression. This has considerable importance for the resident microbiota. Our aim was to analyze the effects of SICs of antimicrobials on the morphological, biochemical, physiological and molecular characteristics of the resident anaerobic Fusobacterium nucleatum. Fourteen strains were obtained from F. nucleatum ATCC 25586, selected by culturing on SICs of ampicillin, ampicillin/sulbactam, clindamycin, chloramphenicol, levofloxacin, metronidazole and piperacillin/tazobactam and subsequent culturing in the absence of drugs. Antimicrobial susceptibility, bacterial morphology, biochemical profiles and biofilm formation were evaluated. Genotyping and analysis of protein profiles were also performed. The antimicrobial susceptibility patterns showed that most of the derived strains were less sensitive to the antimicrobials, even after culturing them without drugs. Morphological and cell complexity alterations were observed, mainly in strains grown in SICs of β-lactam; these strains also expressed a reduced ability for biofilm formation. The other strains showed an increase in biofilm formation but no apparent morphological changes. Alterations were observed in the carbohydrate metabolism patterns and in the activity of microbial enzymes. Several proteins were positively or negatively regulated and there was polymorphism in the DNA from all derived strains. Therefore, SICs of antimicrobials induce alterations in F. nucleatum, which directly impact its biology. These results emphasize the risk of inadequate antibioticotherapy, which may have serious implications for clinical microbiology and infectious diseases and also may interfere with the host-bacteria relationship. Copyright © 2012 Elsevier Ltd. All rights reserved.

Mathematics and biology: a Kantian view on the history of pattern formation theory.

PubMed

Roth, Siegfried

2011-12-01

Driesch's statement, made around 1900, that the physics and chemistry of his day were unable to explain self-regulation during embryogenesis was correct and could be extended until the year 1972. The emergence of theories of self-organisation required progress in several areas including chemistry, physics, computing and cybernetics. Two parallel lines of development can be distinguished which both culminated in the early 1970s. Firstly, physicochemical theories of self-organisation arose from theoretical (Lotka 1910-1920) and experimental work (Bray 1920; Belousov 1951) on chemical oscillations. However, this research area gained broader acceptance only after thermodynamics was extended to systems far from equilibrium (1922-1967) and the mechanism of the prime example for a chemical oscillator, the Belousov-Zhabotinski reaction, was deciphered in the early 1970s. Secondly, biological theories of self-organisation were rooted in the intellectual environment of artificial intelligence and cybernetics. Turing wrote his The chemical basis of morphogenesis (1952) after working on the construction of one of the first electronic computers. Likewise, Gierer and Meinhardt's theory of local activation and lateral inhibition (1972) was influenced by ideas from cybernetics. The Gierer-Meinhardt theory provided an explanation for the first time of both spontaneous formation of spatial order and of self-regulation that proved to be extremely successful in elucidating a wide range of patterning processes. With the advent of developmental genetics in the 1980s, detailed molecular and functional data became available for complex developmental processes, allowing a new generation of data-driven theoretical approaches. Three examples of such approaches will be discussed. The successes and limitations of mathematical pattern formation theory throughout its history suggest a picture of the organism, which has structural similarity to views of the organic world held by the philosopher Immanuel Kant at the end of the eighteenth century. © The Author(s) 2011. This article is published with open access at Springerlink.com

Development, Regeneration, and Evolution of Feathers

PubMed Central

Chen, Chih-Feng; Foley, John; Tang, Pin-Chi; Li, Ang; Jiang, Ting Xin; Wu, Ping; Widelitz, Randall B.; Chuong, Cheng Ming

2017-01-01

The feather is a complex ectodermal organ with hierarchical branching patterns. It provides functions in endothermy, communication, and flight. Studies of feather growth, cycling, and health are of fundamental importance to avian biology and poultry science. In addition, feathers are an excellent model for morphogenesis studies because of their accessibility, and their distinct patterns can be used to assay the roles of specific molecular pathways. Here we review the progress in aspects of development, regeneration, and evolution during the past three decades. We cover the development of feather buds in chicken embryos, regenerative cycling of feather follicle stem cells, formation of barb branching patterns, emergence of intrafeather pigmentation patterns, interplay of hormones and feather growth, and the genetic identification of several feather variants. The discovery of feathered dinosaurs redefines the relationship between feathers and birds. Inspiration from biomaterials and flight research further fuels biomimetic potential of feathers as a multidisciplinary research focal point. PMID:25387232

Spatial pattern formation of microbes at the soil microscale affect soil C and N turnover in an individual-based microbial community model

NASA Astrophysics Data System (ADS)

Kaiser, Christina; Evans, Sarah; Dieckmann, Ulf; Widder, Stefanie

2016-04-01

At the μm-scale, soil is a highly structured and complex environment, both in physical as well as in biological terms, characterized by non-linear interactions between microbes, substrates and minerals. As known from mathematics and theoretical ecology, spatial structure significantly affects the system's behaviour by enabling synergistic dynamics, facilitating diversity, and leading to emergent phenomena such as self-organisation and self-regulation. Such phenomena, however, are rarely considered when investigating mechanisms of microbial soil organic matter turnover. Soil organic matter is the largest terrestrial reservoir for organic carbon (C) and nitrogen (N) and plays a pivotal role in global biogeochemical cycles. Still, the underlying mechanisms of microbial soil organic matter buildup and turnover remain elusive. We explored mechanisms of microbial soil organic matter turnover using an individual-based, stoichiometrically and spatially explicit computer model, which simulates the microbial de-composer system at the soil microscale (i.e. on a grid of 100 x 100 soil microsites). Soil organic matter dynamics in our model emerge as the result of interactions among individual microbes with certain functional traits (f.e. enzyme production rates, growth rates, cell stoichiometry) at the microscale. By degrading complex substrates, and releasing labile substances microbes in our model continusly shape their environment, which in turn feeds back to spatiotemporal dynamics of the microbial community. In order to test the effect of microbial functional traits and organic matter input rate on soil organic matter turnover and C and N storage, we ran the model into steady state using continuous inputs of fresh organic material. Surprisingly, certain parameter settings that induce resource limitation of microbes lead to regular spatial pattern formation (f.e. moving spiral waves) of microbes and substrate at the μm-scale at steady-state. The occurrence of these pattern can be explained by the Turing mechanism. These pattern formation had strong consequences for process rates, as well as for C and N storage in the soil at the steady state: Scenarios that exhibited pattern formation were generally associated with higher C storage at steady state compared to those without pattern formation (i.e. at non-limiting conditions for microbes). Moreover, pattern formation lead to a spatial decoupling of C and N turnover processes, and to a spatial decoupling of microbial N mineralization and N immobilization. Taken together, our theoretical analysis shows that self-organisation may be a feature of the soil decomposer system, with consequences for process rates of microbial C and N turnover. Pattern formation through spatial self-organization, which has been observed on larger spatial scales in other resource-limited communities (e.g., vegetation patterns in arid or wetland eco-systems), may also occur at the soil microscale, leaving its mark on the soil's storage capacity for C and N.

Endocytosis and Signaling during Development

PubMed Central

Bökel, Christian

2014-01-01

The development of multicellular organisms relies on an intricate choreography of intercellular communication events that pattern the embryo and coordinate the formation of tissues and organs. It is therefore not surprising that developmental biology, especially using genetic model organisms, has contributed significantly to the discovery and functional dissection of the associated signal-transduction cascades. At the same time, biophysical, biochemical, and cell biological approaches have provided us with insights into the underlying cell biological machinery. Here we focus on how endocytic trafficking of signaling components (e.g., ligands or receptors) controls the generation, propagation, modulation, reception, and interpretation of developmental signals. A comprehensive enumeration of the links between endocytosis and signal transduction would exceed the limits of this review. We will instead use examples from different developmental pathways to conceptually illustrate the various functions provided by endocytic processes during key steps of intercellular signaling. PMID:24591521

Science supervisors' conceptions of biology and the field of science: A qualitative study

NASA Astrophysics Data System (ADS)

Young, Jean Radcliff

1999-12-01

This study examined the nature, source and formation of science supervisors' cognitive frameworks for biology and for the field of science and the impact of these frameworks on their work in school divisions. The design for this qualitative study was an emergent case study using ethnographic methods. The purposeful sample consisted of five science supervisors selected from different school divisions in three geographic regions of a middle-Atlantic state. Each participant had a background in biology, classroom teaching and full-time supervisory experience. To collect data for this study, an open-ended questionnaire was used to gain an understanding of the nature of the supervisors' conceptions of biology and for the field of science. Two semi-structured interviews, each lasting 1--2 hours in length, were designed to explore the source and formation of the supervisors' conceptual frameworks, and the impact of these frameworks on their work in school divisions. Data were inductively analyzed using a constant comparative approach. The major findings of this study were: (1) All of the supervisors in this study were remarkably cognizant of possessing a framework for biology and for the field of science. (2) The supervisors' frameworks were well-formed, relatively highly complex and showed a variety of organizational patterns. (3) All of the supervisors' diagrams showed evidence of coherent, integrated themes with emphasis on the importance of connections and interrelationships. (4) The supervisors were able to readily articulate sound rationales for construction of their diagrams. (5) Instead of seeing biology as an isolated discipline, the supervisors view biology in the context of science. Overall, the supervisors no longer see their frameworks as biology-content related, but as science-related. (6) Major influences on the source and formation of the supervisors' conceptual frameworks were a result of selected work-related experiences. (7) The supervisors' conceptual frameworks, in the context of implementation of state Standards of Learning, have had a major impact on their work in their school divisions with teachers and indirectly with students, parents and the public. Results are discussed in comparison with prior studies of non-supervisors using a similar methodology. Implications for educational practice and further research are included.

Growth ring formation in the starch granules of potato tubers.

PubMed

Pilling, Emma; Smith, Alison M

2003-05-01

Starch granules from higher plants contain alternating zones of semicrystalline and amorphous material known as growth rings. The regulation of growth ring formation is not understood. We provide several independent lines of evidence that growth ring formation in the starch granules of potato (Solanum tuberosum) tubers is not under diurnal control. Ring formation is not abolished by growth in constant conditions, and ring periodicity and appearance are relatively unaffected by a change from a 24-h to a 40-h photoperiod, and by alterations in substrate supply to the tuber that are known to affect the diurnal pattern of tuber starch synthesis. Some, but not all, of the features of ring formation are consistent with the involvement of a circadian rhythm. Such a rhythm might operate by changing the relative activities of starch-synthesizing enzymes: Growth ring formation is disrupted in tubers with reduced activity of a major isoform of starch synthase. We suggest that physical as well as biological mechanisms may contribute to the control of ring formation, and that a complex interplay of several factors may by involved.

Growth Ring Formation in the Starch Granules of Potato Tubers1

PubMed Central

Pilling, Emma; Smith, Alison M.

2003-01-01

Starch granules from higher plants contain alternating zones of semicrystalline and amorphous material known as growth rings. The regulation of growth ring formation is not understood. We provide several independent lines of evidence that growth ring formation in the starch granules of potato (Solanum tuberosum) tubers is not under diurnal control. Ring formation is not abolished by growth in constant conditions, and ring periodicity and appearance are relatively unaffected by a change from a 24-h to a 40-h photoperiod, and by alterations in substrate supply to the tuber that are known to affect the diurnal pattern of tuber starch synthesis. Some, but not all, of the features of ring formation are consistent with the involvement of a circadian rhythm. Such a rhythm might operate by changing the relative activities of starch-synthesizing enzymes: Growth ring formation is disrupted in tubers with reduced activity of a major isoform of starch synthase. We suggest that physical as well as biological mechanisms may contribute to the control of ring formation, and that a complex interplay of several factors may by involved. PMID:12746541

In Situ Tissue Engineering Using Magnetically Guided Three-Dimensional Cell Patterning

PubMed Central

Grogan, Shawn P.; Pauli, Chantal; Chen, Peter; Du, Jiang; Chung, Christine B.; Kong, Seong Deok; Colwell, Clifford W.; Lotz, Martin K.; Jin, Sungho

2012-01-01

Manipulation of cell patterns in three dimensions in a manner that mimics natural tissue organization and function is critical for cell biological studies and likely essential for successfully regenerating tissues—especially cells with high physiological demands, such as those of the heart, liver, lungs, and articular cartilage.1,2 In the present study, we report on the feasibility of arranging iron oxide-labeled cells in three-dimensional hydrogels using magnetic fields. By manipulating the strength, shape, and orientation of the magnetic field and using crosslinking gradients in hydrogels, multi-directional cell arrangements can be produced in vitro and even directly in situ. We show that these ferromagnetic particles are nontoxic between 0.1 and 10 mg/mL; certain species of particles can permit or even enhance tissue formation, and these particles can be tracked using magnetic resonance imaging. Taken together, this approach can be adapted for studying basic biological processes in vitro, for general tissue engineering approaches, and for producing organized repair tissues directly in situ. PMID:22224660

Morphomechanics and Developmental Constraints in the Evolution of Ammonites Shell Form.

PubMed

Erlich, Alexander; Moulton, Derek E; Goriely, Alain; Chirat, Regis

2016-11-01

The idea that physical processes involved in biological development underlie morphogenetic rules and channel morphological evolution has been central to the rise of evolutionary developmental biology. Here, we explore this idea in the context of seashell morphogenesis. We show that a morphomechanical model predicts the effects of variations in shell shape on the ornamental pattern in ammonites, a now extinct group of cephalopods with external chambered shell. Our model shows that several seemingly unrelated characteristics of synchronous, ontogenetic, intraspecific, and evolutionary variations in ornamental patterns among various ammonite species may all be understood from the fact that the mechanical forces underlying the oscillatory behavior of the shell secreting system scale with the cross-sectional curvature of the shell aperture. This simple morphogenetic rule, emerging from biophysical interactions during shell formation, introduced a non-random component in the production of phenotypic variation and channeled the morphological evolution of ammonites over millions of years. As such, it provides a paradigm for the concept of "developmental constraints." © 2016 Wiley Periodicals, Inc.

Mothers’ Repartnering after a Nonmarital Birth

PubMed Central

Bzostek, Sharon H.; McLanahan, Sara S.; Carlson, Marcia J.

2012-01-01

This paper examines the prevalence, predictors and outcomes of unmarried mothers’ repartnering patterns following a nonmarital birth. Results indicate that, within five years after a birth, approximately two-thirds of unmarried mothers ended their relationship with the focal child’s biological father, and over half of these mothers entered new partnerships. Among those who repartnered, 60 percent of mothers formed unions with men with higher economic capabilities than their former partners, 20 percent formed unions with men with similar capabilities, and 20 percent formed unions with men with lower capabilities. This pattern holds for both nonresidential and coresidential unions. Our findings are consistent with marriage market, learning, and evolutionary biology theories about union formation, and they provide support for qualitative evidence that unmarried mothers have high standards for new partners. While many mothers are able to successfully find new partners with better economic capabilities, many other mothers remain unpartnered, likely due (at least in part) to the limited pool of potential partners with relatively high levels of economic capabilities. PMID:23015762

Pavement cells: a model system for non-transcriptional auxin signalling and crosstalks.

PubMed

Chen, Jisheng; Wang, Fei; Zheng, Shiqin; Xu, Tongda; Yang, Zhenbiao

2015-08-01

Auxin (indole acetic acid) is a multifunctional phytohormone controlling various developmental patterns, morphogenetic processes, and growth behaviours in plants. The transcription-based pathway activated by the nuclear TRANSPORT INHIBITOR RESISTANT 1/auxin-related F-box auxin receptors is well established, but the long-sought molecular mechanisms of non-transcriptional auxin signalling remained enigmatic until very recently. Along with the establishment of the Arabidopsis leaf epidermal pavement cell (PC) as an exciting and amenable model system in the past decade, we began to gain insight into non-transcriptional auxin signalling. The puzzle-piece shape of PCs forms from intercalated or interdigitated cell growth, requiring local intra- and inter-cellular coordination of lobe and indent formation. Precise coordination of this interdigitated pattern requires auxin and an extracellular auxin sensing system that activates plasma membrane-associated Rho GTPases from plants and subsequent downstream events regulating cytoskeletal reorganization and PIN polarization. Apart from auxin, mechanical stress and cytokinin have been shown to affect PC interdigitation, possibly by interacting with auxin signals. This review focuses upon signalling mechanisms for cell polarity formation in PCs, with an emphasis on non-transcriptional auxin signalling in polarized cell expansion and pattern formation and how different auxin pathways interplay with each other and with other signals. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Stress-driven buckling patterns in spheroidal core/shell structures.

PubMed

Yin, Jie; Cao, Zexian; Li, Chaorong; Sheinman, Izhak; Chen, Xi

2008-12-09

Many natural fruits and vegetables adopt an approximately spheroidal shape and are characterized by their distinct undulating topologies. We demonstrate that various global pattern features can be reproduced by anisotropic stress-driven buckles on spheroidal core/shell systems, which implies that the relevant mechanical forces might provide a template underpinning the topological conformation in some fruits and plants. Three dimensionless parameters, the ratio of effective size/thickness, the ratio of equatorial/polar radii, and the ratio of core/shell moduli, primarily govern the initiation and formation of the patterns. A distinct morphological feature occurs only when these parameters fall within certain ranges: In a prolate spheroid, reticular buckles take over longitudinal ridged patterns when one or more parameters become large. Our results demonstrate that some universal features of fruit/vegetable patterns (e.g., those observed in Korean melons, silk gourds, ribbed pumpkins, striped cavern tomatoes, and cantaloupes, etc.) may be related to the spontaneous buckling from mechanical perspectives, although the more complex biological or biochemical processes are involved at deep levels.

Spontaneous formation of spiral-like patterns with distinct periodic physical properties by confined electrodeposition of Co-In disks

NASA Astrophysics Data System (ADS)

Golvano-Escobal, Irati; Gonzalez-Rosillo, Juan Carlos; Domingo, Neus; Illa, Xavi; López-Barberá, José Francisco; Fornell, Jordina; Solsona, Pau; Aballe, Lucia; Foerster, Michael; Suriñach, Santiago; Baró, Maria Dolors; Puig, Teresa; Pané, Salvador; Nogués, Josep; Pellicer, Eva; Sort, Jordi

2016-07-01

Spatio-temporal patterns are ubiquitous in different areas of materials science and biological systems. However, typically the motifs in these types of systems present a random distribution with many possible different structures. Herein, we demonstrate that controlled spatio-temporal patterns, with reproducible spiral-like shapes, can be obtained by electrodeposition of Co-In alloys inside a confined circular geometry (i.e., in disks that are commensurate with the typical size of the spatio-temporal features). These patterns are mainly of compositional nature, i.e., with virtually no topographic features. Interestingly, the local changes in composition lead to a periodic modulation of the physical (electric, magnetic and mechanical) properties. Namely, the Co-rich areas show higher saturation magnetization and electrical conductivity and are mechanically harder than the In-rich ones. Thus, this work reveals that confined electrodeposition of this binary system constitutes an effective procedure to attain template-free magnetic, electric and mechanical surface patterning with specific and reproducible shapes.

Painting with light-powered bacteria.

PubMed

Arlt, Jochen; Martinez, Vincent A; Dawson, Angela; Pilizota, Teuta; Poon, Wilson C K

2018-02-22

Self-assembly is a promising route for micro- and nano-fabrication with potential to revolutionise many areas of technology, including personalised medicine. Here we demonstrate that external control of the swimming speed of microswimmers can be used to self assemble reconfigurable designer structures in situ. We implement such 'smart templated active self assembly' in a fluid environment by using spatially patterned light fields to control photon-powered strains of motile Escherichia coli bacteria. The physics and biology governing the sharpness and formation speed of patterns is investigated using a bespoke strain designed to respond quickly to changes in light intensity. Our protocol provides a distinct paradigm for self-assembly of structures on the 10 μm to mm scale.

Spatiotemporal evolution in a (2+1)-dimensional chemotaxis model

NASA Astrophysics Data System (ADS)

Banerjee, Santo; Misra, Amar P.; Rondoni, L.

2012-01-01

Simulations are performed to investigate the nonlinear dynamics of a (2+1)-dimensional chemotaxis model of Keller-Segel (KS) type, with a logistic growth term. Because of its ability to display auto-aggregation, the KS model has been widely used to simulate self-organization in many biological systems. We show that the corresponding dynamics may lead to steady-states, to divergencies in a finite time as well as to the formation of spatiotemporal irregular patterns. The latter, in particular, appears to be chaotic in part of the range of bounded solutions, as demonstrated by the analysis of wavelet power spectra. Steady-states are achieved with sufficiently large values of the chemotactic coefficient (χ) and/or with growth rates r below a critical value rc. For r>rc, the solutions of the differential equations of the model diverge in a finite time. We also report on the pattern formation regime, for different values of χ, r and of the diffusion coefficient D.

Femtosecond laser microstructured Alumina toughened Zirconia: A new strategy to improve osteogenic differentiation of hMSCs

NASA Astrophysics Data System (ADS)

Carvalho, Angela; Cangueiro, Liliana; Oliveira, Vítor; Vilar, Rui; Fernandes, Maria H.; Monteiro, Fernando J.

2018-03-01

The use of topographic patterns has been a continuously growing area of research for tissue engineering and it is widely accepted that the surface topography of biomaterials can influence and modulate the initial biological response. Ultrafast lasers are extremely powerful tools to machine and pattern the surface of a wide range of biomaterials, however, only few work has been performed on ceramics with the intent of biomedical applications, and the biological characterization of these structured materials is scarce. In this work, relevance is given to the biological performance of such materials. A femtosecond laser ablation technique was used to modify Alumina toughened Zirconia (ATZ) surface topography, developing surfaces structured at the micro and nanoscale levels (μATZ), in a controlled and reproducible manner. Materials characterization was performed before and after laser treatment, and both materials were compared in terms of osteogenic response of human bone marrow derived mesenchymal stem cells cultured under basal conditions, expecting that the micro/nanofeatures will improve the biological response of cells. Cells metabolic activity and proliferation increased with the culture time and surface microtopography modulated cells alignment and guided proliferation. The modified surface, displayed significantly higher expression of osteogenic transcription factors and genes and, additionally, the formation of a mineralized extracellular matrix, when compared to the control surface, i.e. unmodified ATZ.

Central cell-derived peptides regulate early embryo patterning in flowering plants.

PubMed

Costa, Liliana M; Marshall, Eleanor; Tesfaye, Mesfin; Silverstein, Kevin A T; Mori, Masashi; Umetsu, Yoshitaka; Otterbach, Sophie L; Papareddy, Ranjith; Dickinson, Hugh G; Boutiller, Kim; VandenBosch, Kathryn A; Ohki, Shinya; Gutierrez-Marcos, José F

2014-04-11

Plant embryogenesis initiates with the establishment of an apical-basal axis; however, the molecular mechanisms accompanying this early event remain unclear. Here, we show that a small cysteine-rich peptide family is required for formation of the zygotic basal cell lineage and proembryo patterning in Arabidopsis. EMBRYO SURROUNDING FACTOR 1 (ESF1) peptides accumulate before fertilization in central cell gametes and thereafter in embryo-surrounding endosperm cells. Biochemical and structural analyses revealed cleavage of ESF1 propeptides to form biologically active mature peptides. Further, these peptides act in a non-cell-autonomous manner and synergistically with the receptor-like kinase SHORT SUSPENSOR to promote suspensor elongation through the YODA mitogen-activated protein kinase pathway. Our findings demonstrate that the second female gamete and its sexually derived endosperm regulate early embryonic patterning in flowering plants.

Emergent mechanics of biological structures

PubMed Central

Dumont, Sophie; Prakash, Manu

2014-01-01

Mechanical force organizes life at all scales, from molecules to cells and tissues. Although we have made remarkable progress unraveling the mechanics of life's individual building blocks, our understanding of how they give rise to the mechanics of larger-scale biological structures is still poor. Unlike the engineered macroscopic structures that we commonly build, biological structures are dynamic and self-organize: they sculpt themselves and change their own architecture, and they have structural building blocks that generate force and constantly come on and off. A description of such structures defies current traditional mechanical frameworks. It requires approaches that account for active force-generating parts and for the formation of spatial and temporal patterns utilizing a diverse array of building blocks. In this Perspective, we term this framework “emergent mechanics.” Through examples at molecular, cellular, and tissue scales, we highlight challenges and opportunities in quantitatively understanding the emergent mechanics of biological structures and the need for new conceptual frameworks and experimental tools on the way ahead. PMID:25368421

Impact of graphic format on perception of change in biological data: implications for health monitoring in conditions such as asthma.

PubMed

Jansen, Jesse; McCaffery, Kirsten J; Hayen, Andrew; Ma, David; Reddel, Helen K

2012-03-01

Variation in graphic format can substantially influence interpretation of data. Despite a large body of literature on the optimal design of graphs, little attention has been paid to the format of charts for health monitoring. This study assessed the effect of aspect ratio (x:y ratio) and interconnecting lines on visual identification of change in biological data, such as during asthma exacerbations. Eighty volunteers viewed 72 sets of six consecutive blocks of unidentified biological data, recording if each block of data was increasing, decreasing, or the same as the previous block. Three chart aspect ratios were examined (A, 5.2:1; B, 3.0:1; C, 1.1:1), with or without lines between data points. Datasets from lung function monitoring by asthma patients included a mild/moderate/severe fall ('exacerbation') or no exacerbation. False negative (missing true exacerbations) and false positive (identifying non-existent exacerbations) responses were calculated. 84% of exacerbation blocks were correctly identified. There was a significant interaction between exacerbation severity and aspect ratio (p=0.0048). The most compressed chart (C) had the fewest false negative responses. Moderate falls were missed in 24%, 12%, and 5% of trials on charts A, B, and C, respectively (C vs A: adjusted relative risk 0.19 (95% CI 0.12 to 0.30)). False positive responses were infrequent (A, 2.5%; B, 3.8%; C, 8.3%), increasing slightly if data points were joined with lines (4.3% vs 5.1%, p=0.004) . Compressed charts can improve the visual detection of change in biological data by up to 80%. The aspect ratio of charts should be standardised to facilitate clinical pattern recognition.

The de novo formation of a vascular network, in warm-blooded embryos, occurs via a self-assembly process that spans multiple length and time scales

NASA Astrophysics Data System (ADS)

Little, Charles D.

2007-03-01

Taking advantage of wide-field, time-lapse microscopy we examined the assembly of vascular polygonal networks in whole bird embryos and in explanted embryonic mouse tissue (allantois). Primary vasculogenesis assembly steps range from cellular (1-10 μm) to tissue (100μm-1mm) level events: Individual vascular endothelial cells extend protrusions and move with respect to the extracellular matrix/surrounding tissue. Consequently, long-range, tissue-level, deformations directly influence the vascular pattern. Experimental perturbation of endothelial-specific cell-cell adhesions (VE-cadherin), during mouse vasculogenesis, permitted dissection of the cellular motion required for sprout formation. In particular, cells are shown to move actively onto vascular cords that are subject to strain via tissue deformations. Based on the empirical data we propose a simple model of preferential migration along stretched cells. Numerical simulations reveal that the model evolves into a quasi-stationary pattern containing linear segments, which interconnect above a critical volume fraction. In the quasi-stationary state the generation of new branches offsets the coarsening driven by surface tension. In agreement with empirical data, the characteristic size of the resulting polygonal pattern is density-independent within a wide range of volume fractions. These data underscore the potential of combining physical studies with experimental embryology as a means of studying complex morphogenetic systems. In collaboration with Brenda J. Rongish^1, Andr'as Czir'ok^1,2, Erica D. Perryn^1, Cheng Cui^1, and Evan A. Zamir^1 ^1Department of Anatomy and Cell Biology, the University of Kansas Medical Center, Kansas City, KS ^2Department of Biological Physics, E"otv"os Lor'and University, Budapest, Hungary.

COPS: Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets

PubMed Central

Lohmann, Ingrid

2012-01-01

In multi-cellular organisms, spatiotemporal activity of cis-regulatory DNA elements depends on their occupancy by different transcription factors (TFs). In recent years, genome-wide ChIP-on-Chip, ChIP-Seq and DamID assays have been extensively used to unravel the combinatorial interaction of TFs with cis-regulatory modules (CRMs) in the genome. Even though genome-wide binding profiles are increasingly becoming available for different TFs, single TF binding profiles are in most cases not sufficient for dissecting complex regulatory networks. Thus, potent computational tools detecting statistically significant and biologically relevant TF-motif co-occurrences in genome-wide datasets are essential for analyzing context-dependent transcriptional regulation. We have developed COPS (Co-Occurrence Pattern Search), a new bioinformatics tool based on a combination of association rules and Markov chain models, which detects co-occurring TF binding sites (BSs) on genomic regions of interest. COPS scans DNA sequences for frequent motif patterns using a Frequent-Pattern tree based data mining approach, which allows efficient performance of the software with respect to both data structure and implementation speed, in particular when mining large datasets. Since transcriptional gene regulation very often relies on the formation of regulatory protein complexes mediated by closely adjoining TF binding sites on CRMs, COPS additionally detects preferred short distance between co-occurring TF motifs. The performance of our software with respect to biological significance was evaluated using three published datasets containing genomic regions that are independently bound by several TFs involved in a defined biological process. In sum, COPS is a fast, efficient and user-friendly tool mining statistically and biologically significant TFBS co-occurrences and therefore allows the identification of TFs that combinatorially regulate gene expression. PMID:23272209

From soil mechanics to chick development.

PubMed

Wolpert, Lewis

2018-01-01

Here, I provide some recollections of my life, starting as a civil engineer in South Africa and how I gradually became interested in biology, particularly pattern formation. In retrospect, I think that my decision to work on chick embryos to study limb development back in 1966 turned out to be the right one. The principles discovered in these 50 years, both by my collaborators and by other colleagues, have established the principles of how the limb develops in higher vertebrates, including humans.

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals.

PubMed

Marcon, Luciano; Diego, Xavier; Sharpe, James; Müller, Patrick

2016-04-08

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems.

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals

PubMed Central

Marcon, Luciano; Diego, Xavier; Sharpe, James; Müller, Patrick

2016-01-01

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems. DOI: http://dx.doi.org/10.7554/eLife.14022.001 PMID:27058171

Some Physical Principles Governing Spatial and Temporal Organization in Living Systems

NASA Astrophysics Data System (ADS)

Ali, Md Zulfikar

Spatial and temporal organization in living organisms are crucial for a variety of biological functions and arise from the interplay of large number of interacting molecules. One of the central questions in systems biology is to understand how such an intricate organization emerges from the molecular biochemistry of the cell. In this dissertation we explore two projects. The first project relates to pattern formation in a cell membrane as an example of spatial organization, and the second project relates to the evolution of oscillatory networks as a simple example of temporal organization. For the first project, we introduce a model for pattern formation in a two-component lipid bilayer and study the interplay between membrane composition and membrane geometry, demonstrating the existence of a rich phase diagram. Pattern formation is governed by the interplay between phase separation driven by lipid-lipid interactions and tendency of lipid domains with high intrinsic curvature to deform the membrane away from its preferred position. Depending on membrane parameters, we find the formation of compact lipid micro-clusters or of striped domains. We calculate the stripe width analytically and find good agreement with stripe widths obtained from the simulations. For the second project, we introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm and apply it to study the following problems. Using the model, we study robustness and designabilty of a 2-component network that generate oscillations. We completely enumerate the sequence space and the phenotypic space, and discuss the relationship between designabilty, robustness and evolvability. We further apply the model to studies of neutral drift in networks that yield oscillatory dynamics, e.g. starting with a relatively simple network and allowing it to evolve by adding nodes and connections while requiring that oscillatory dynamics be preserved. Our studies demonstrate both the importance of employing a sequence-based evolutionary scheme and the relative rapidity (in evolutionary time) for the redistribution of function over new nodes via neutral drift. In addition we discovered another much slower timescale for network evolution, reflecting hidden order in sequence space that we interpret in terms of sparsely connected domains. Finally, we use the model to study the evolution of an oscillator from a non-oscillatory network under the influence of external periodic forcing as a model for evolution of circadian rhythm in living systems. We use a greedy algorithm based on optimizing biologically motivated fitness functions and find that the algorithm successfully produces oscillators. However, the distribution of free-period of evolved oscillators depends on the choice of fitness functions and the nature of forcing.

Improving clustering with metabolic pathway data.

PubMed

Milone, Diego H; Stegmayer, Georgina; López, Mariana; Kamenetzky, Laura; Carrari, Fernando

2014-04-10

It is a common practice in bioinformatics to validate each group returned by a clustering algorithm through manual analysis, according to a-priori biological knowledge. This procedure helps finding functionally related patterns to propose hypotheses for their behavior and the biological processes involved. Therefore, this knowledge is used only as a second step, after data are just clustered according to their expression patterns. Thus, it could be very useful to be able to improve the clustering of biological data by incorporating prior knowledge into the cluster formation itself, in order to enhance the biological value of the clusters. A novel training algorithm for clustering is presented, which evaluates the biological internal connections of the data points while the clusters are being formed. Within this training algorithm, the calculation of distances among data points and neurons centroids includes a new term based on information from well-known metabolic pathways. The standard self-organizing map (SOM) training versus the biologically-inspired SOM (bSOM) training were tested with two real data sets of transcripts and metabolites from Solanum lycopersicum and Arabidopsis thaliana species. Classical data mining validation measures were used to evaluate the clustering solutions obtained by both algorithms. Moreover, a new measure that takes into account the biological connectivity of the clusters was applied. The results of bSOM show important improvements in the convergence and performance for the proposed clustering method in comparison to standard SOM training, in particular, from the application point of view. Analyses of the clusters obtained with bSOM indicate that including biological information during training can certainly increase the biological value of the clusters found with the proposed method. It is worth to highlight that this fact has effectively improved the results, which can simplify their further analysis.The algorithm is available as a web-demo at http://fich.unl.edu.ar/sinc/web-demo/bsom-lite/. The source code and the data sets supporting the results of this article are available at http://sourceforge.net/projects/sourcesinc/files/bsom.

Hydrogen peroxide photocycling in the Gulf of Aqaba, Red Sea.

PubMed

Shaked, Yeala; Harris, Raviv; Klein-Kedem, Nir

2010-05-01

The dynamics of hydrogen peroxide (H(2)O(2)) was investigated from December 2007 to October 2008 in the Gulf of Aqaba, which in the absence of H(2)O(2) contribution from biological production, rain and runoff, turned out to be a unique natural photochemical laboratory. A distinct seasonal pattern emerged, with highest midday surface H(2)O(2) concentrations in spring-summer (30-90 nM) as compared to winter (10-30 nM). Similarly, irradiation normalized net H(2)O(2) formation rates obtained in concurrent ship-board experiments were faster in spring-summer than in winter. These seasonal patterns were attributed to changes in water characteristics, namely elevated spring-summer chromophoric dissolved organic matter (CDOM). The role of trace elements in H(2)O(2) photoformation was studied by simultaneously measuring superoxide (O(2)(-)), Fe(II), and H(2)O(2) formation and loss in ambient seawater and in the presence of superoxide dismutase, iron and copper. O(2)(-) was found to decay fast in the Gulf water, with a half-life of 15-28 s, primarily due to catalytic reactions with trace metals (predominantly copper). Hence, H(2)O(2) formation in the Gulf involves metal-catalyzed O(2)(-) disproptionation. Added iron moderately lowered net H(2)O(2) photoformation, probably due to its participation in Fe(II) oxidation, a process that may also modify H(2)O(2) formation in situ.

New gene functions in megakaryopoiesis and platelet formation

PubMed Central

Gieger, Christian; Radhakrishnan, Aparna; Cvejic, Ana; Tang, Weihong; Porcu, Eleonora; Pistis, Giorgio; Serbanovic-Canic, Jovana; Elling, Ulrich; Goodall, Alison H.; Labrune, Yann; Lopez, Lorna M.; Mägi, Reedik; Meacham, Stuart; Okada, Yukinori; Pirastu, Nicola; Sorice, Rossella; Teumer, Alexander; Voss, Katrin; Zhang, Weihua; Ramirez-Solis, Ramiro; Bis, Joshua C.; Ellinghaus, David; Gögele, Martin; Hottenga, Jouke-Jan; Langenberg, Claudia; Kovacs, Peter; O’Reilly, Paul F.; Shin, So-Youn; Esko, Tõnu; Hartiala, Jaana; Kanoni, Stavroula; Murgia, Federico; Parsa, Afshin; Stephens, Jonathan; van der Harst, Pim; van der Schoot, C. Ellen; Allayee, Hooman; Attwood, Antony; Balkau, Beverley; Bastardot, François; Basu, Saonli; Baumeister, Sebastian E.; Biino, Ginevra; Bomba, Lorenzo; Bonnefond, Amélie; Cambien, François; Chambers, John C.; Cucca, Francesco; D’Adamo, Pio; Davies, Gail; de Boer, Rudolf A.; de Geus, Eco J. C.; Döring, Angela; Elliott, Paul; Erdmann, Jeanette; Evans, David M.; Falchi, Mario; Feng, Wei; Folsom, Aaron R.; Frazer, Ian H.; Gibson, Quince D.; Glazer, Nicole L.; Hammond, Chris; Hartikainen, Anna-Liisa; Heckbert, Susan R.; Hengstenberg, Christian; Hersch, Micha; Illig, Thomas; Loos, Ruth J. F.; Jolley, Jennifer; Khaw, Kay Tee; Kühnel, Brigitte; Kyrtsonis, Marie-Christine; Lagou, Vasiliki; Lloyd-Jones, Heather; Lumley, Thomas; Mangino, Massimo; Maschio, Andrea; Leach, Irene Mateo; McKnight, Barbara; Memari, Yasin; Mitchell, Braxton D.; Montgomery, Grant W.; Nakamura, Yusuke; Nauck, Matthias; Navis, Gerjan; Nöthlings, Ute; Nolte, Ilja M.; Porteous, David J.; Pouta, Anneli; Pramstaller, Peter P.; Pullat, Janne; Ring, Susan M.; Rotter, Jerome I.; Ruggiero, Daniela; Ruokonen, Aimo; Sala, Cinzia; Samani, Nilesh J.; Sambrook, Jennifer; Schlessinger, David; Schreiber, Stefan; Schunkert, Heribert; Scott, James; Smith, Nicholas L.; Snieder, Harold; Starr, John M.; Stumvoll, Michael; Takahashi, Atsushi; Tang, W. H. Wilson; Taylor, Kent; Tenesa, Albert; Thein, Swee Lay; Tönjes, Anke; Uda, Manuela; Ulivi, Sheila; van Veldhuisen, Dirk J.; Visscher, Peter M.; Völker, Uwe; Wichmann, H.-Erich; Wiggins, Kerri L.; Willemsen, Gonneke; Yang, Tsun-Po; Zhao, Jing Hua; Zitting, Paavo; Bradley, John R.; Dedoussis, George V.; Gasparini, Paolo; Hazen, Stanley L.; Metspalu, Andres; Pirastu, Mario; Shuldiner, Alan R.; van Pelt, L. Joost; Zwaginga, Jaap-Jan; Boomsma, Dorret I.; Deary, Ian J.; Franke, Andre; Froguel, Philippe; Ganesh, Santhi K.; Jarvelin, Marjo-Riitta; Martin, Nicholas G.; Meisinger, Christa; Psaty, Bruce M.; Spector, Timothy D.; Wareham, Nicholas J.; Akkerman, Jan-Willem N.; Ciullo, Marina; Deloukas, Panos; Greinacher, Andreas; Jupe, Steve; Kamatani, Naoyuki; Khadake, Jyoti; Kooner, Jaspal S.; Penninger, Josef; Prokopenko, Inga; Stemple, Derek; Toniolo, Daniela; Wernisch, Lorenz; Sanna, Serena; Hicks, Andrew A.; Rendon, Augusto; Ferreira, Manuel A.; Ouwehand, Willem H.; Soranzo, Nicole

2012-01-01

Platelets are the second most abundant cell type in blood and are essential for maintaining haemostasis. Their count and volume are tightly controlled within narrow physiological ranges, but there is only limited understanding of the molecular processes controlling both traits. Here we carried out a high-powered meta-analysis of genome-wide association studies (GWAS) in up to 66,867 individuals of European ancestry, followed by extensive biological and functional assessment. We identified 68 genomic loci reliably associated with platelet count and volume mapping to established and putative novel regulators of megakaryopoiesis and platelet formation. These genes show megakaryocyte-specific gene expression patterns and extensive network connectivity. Using gene silencing in Danio rerio and Drosophila melanogaster, we identified 11 of the genes as novel regulators of blood cell formation. Taken together, our findings advance understanding of novel gene functions controlling fate-determining events during megakaryopoiesis and platelet formation, providing a new example of successful translation of GWAS to function. PMID:22139419

Systems biology derived source-sink mechanism of BMP gradient formation

PubMed Central

Zinski, Joseph; Bu, Ye; Wang, Xu; Dou, Wei

2017-01-01

A morphogen gradient of Bone Morphogenetic Protein (BMP) signaling patterns the dorsoventral embryonic axis of vertebrates and invertebrates. The prevailing view in vertebrates for BMP gradient formation is through a counter-gradient of BMP antagonists, often along with ligand shuttling to generate peak signaling levels. To delineate the mechanism in zebrafish, we precisely quantified the BMP activity gradient in wild-type and mutant embryos and combined these data with a mathematical model-based computational screen to test hypotheses for gradient formation. Our analysis ruled out a BMP shuttling mechanism and a bmp transcriptionally-informed gradient mechanism. Surprisingly, rather than supporting a counter-gradient mechanism, our analyses support a fourth model, a source-sink mechanism, which relies on a restricted BMP antagonist distribution acting as a sink that drives BMP flux dorsally and gradient formation. We measured Bmp2 diffusion and found that it supports the source-sink model, suggesting a new mechanism to shape BMP gradients during development. PMID:28826472

Systems biology derived source-sink mechanism of BMP gradient formation.

PubMed

Zinski, Joseph; Bu, Ye; Wang, Xu; Dou, Wei; Umulis, David; Mullins, Mary C

2017-08-09

A morphogen gradient of Bone Morphogenetic Protein (BMP) signaling patterns the dorsoventral embryonic axis of vertebrates and invertebrates. The prevailing view in vertebrates for BMP gradient formation is through a counter-gradient of BMP antagonists, often along with ligand shuttling to generate peak signaling levels. To delineate the mechanism in zebrafish, we precisely quantified the BMP activity gradient in wild-type and mutant embryos and combined these data with a mathematical model-based computational screen to test hypotheses for gradient formation. Our analysis ruled out a BMP shuttling mechanism and a bmp transcriptionally-informed gradient mechanism. Surprisingly, rather than supporting a counter-gradient mechanism, our analyses support a fourth model, a source-sink mechanism, which relies on a restricted BMP antagonist distribution acting as a sink that drives BMP flux dorsally and gradient formation. We measured Bmp2 diffusion and found that it supports the source-sink model, suggesting a new mechanism to shape BMP gradients during development.

The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature.

PubMed

Özgür, Arzucan; Hur, Junguk; He, Yongqun

2016-01-01

The Interaction Network Ontology (INO) logically represents biological interactions, pathways, and networks. INO has been demonstrated to be valuable in providing a set of structured ontological terms and associated keywords to support literature mining of gene-gene interactions from biomedical literature. However, previous work using INO focused on single keyword matching, while many interactions are represented with two or more interaction keywords used in combination. This paper reports our extension of INO to include combinatory patterns of two or more literature mining keywords co-existing in one sentence to represent specific INO interaction classes. Such keyword combinations and related INO interaction type information could be automatically obtained via SPARQL queries, formatted in Excel format, and used in an INO-supported SciMiner, an in-house literature mining program. We studied the gene interaction sentences from the commonly used benchmark Learning Logic in Language (LLL) dataset and one internally generated vaccine-related dataset to identify and analyze interaction types containing multiple keywords. Patterns obtained from the dependency parse trees of the sentences were used to identify the interaction keywords that are related to each other and collectively represent an interaction type. The INO ontology currently has 575 terms including 202 terms under the interaction branch. The relations between the INO interaction types and associated keywords are represented using the INO annotation relations: 'has literature mining keywords' and 'has keyword dependency pattern'. The keyword dependency patterns were generated via running the Stanford Parser to obtain dependency relation types. Out of the 107 interactions in the LLL dataset represented with two-keyword interaction types, 86 were identified by using the direct dependency relations. The LLL dataset contained 34 gene regulation interaction types, each of which associated with multiple keywords. A hierarchical display of these 34 interaction types and their ancestor terms in INO resulted in the identification of specific gene-gene interaction patterns from the LLL dataset. The phenomenon of having multi-keyword interaction types was also frequently observed in the vaccine dataset. By modeling and representing multiple textual keywords for interaction types, the extended INO enabled the identification of complex biological gene-gene interactions represented with multiple keywords.

Efficient Mining of Interesting Patterns in Large Biological Sequences

PubMed Central

Rashid, Md. Mamunur; Karim, Md. Rezaul; Jeong, Byeong-Soo

2012-01-01

Pattern discovery in biological sequences (e.g., DNA sequences) is one of the most challenging tasks in computational biology and bioinformatics. So far, in most approaches, the number of occurrences is a major measure of determining whether a pattern is interesting or not. In computational biology, however, a pattern that is not frequent may still be considered very informative if its actual support frequency exceeds the prior expectation by a large margin. In this paper, we propose a new interesting measure that can provide meaningful biological information. We also propose an efficient index-based method for mining such interesting patterns. Experimental results show that our approach can find interesting patterns within an acceptable computation time. PMID:23105928

Efficient mining of interesting patterns in large biological sequences.

PubMed

Rashid, Md Mamunur; Karim, Md Rezaul; Jeong, Byeong-Soo; Choi, Ho-Jin

2012-03-01

Pattern discovery in biological sequences (e.g., DNA sequences) is one of the most challenging tasks in computational biology and bioinformatics. So far, in most approaches, the number of occurrences is a major measure of determining whether a pattern is interesting or not. In computational biology, however, a pattern that is not frequent may still be considered very informative if its actual support frequency exceeds the prior expectation by a large margin. In this paper, we propose a new interesting measure that can provide meaningful biological information. We also propose an efficient index-based method for mining such interesting patterns. Experimental results show that our approach can find interesting patterns within an acceptable computation time.

Using Grid Cells for Navigation

PubMed Central

Bush, Daniel; Barry, Caswell; Manson, Daniel; Burgess, Neil

2015-01-01

Summary Mammals are able to navigate to hidden goal locations by direct routes that may traverse previously unvisited terrain. Empirical evidence suggests that this “vector navigation” relies on an internal representation of space provided by the hippocampal formation. The periodic spatial firing patterns of grid cells in the hippocampal formation offer a compact combinatorial code for location within large-scale space. Here, we consider the computational problem of how to determine the vector between start and goal locations encoded by the firing of grid cells when this vector may be much longer than the largest grid scale. First, we present an algorithmic solution to the problem, inspired by the Fourier shift theorem. Second, we describe several potential neural network implementations of this solution that combine efficiency of search and biological plausibility. Finally, we discuss the empirical predictions of these implementations and their relationship to the anatomy and electrophysiology of the hippocampal formation. PMID:26247860

Effect of aging temperature on formation of sol-gel derived fluor-hydroxyapatite nanoparticles.

PubMed

Joughehdoust, S; Behnamghader, A; Jahandideh, R; Manafi, S

2010-04-01

Synthetic hydroxyapatite (HA) has been recognized as one of the most important bone substitute materials in orthopaedics and dentistry over past few decades because of its chemical and biological similarity to the mineral phase of human bone. One solution for reduction the solubility of HA in biological environments is replacing F- by OH in HA structure and forming fluor-hydroxyapatite (FHA) solid solution. In this paper, FHA nanoparticles were successfully synthesized by a sol-gel method. Also, the influence of aging temperature on formation of FHA powder was studied. Equimolar solutions of calcium nitrate tetrahydrate, triethyl phosphite and ammonium fluoride in ethanol were used as Ca, P and F precursors. After aging at different temperatures, the synthesized powders were heat treated at 550 degrees C. The powders were investigated with X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), transmission electron microscopy (TEM), selected area electron diffraction pattern (SAED), energy dispersive analysis of X-ray (EDAX) and zetasizer measurement. The results of XRD proved the presence of fluorapatite (FA) and HA in all samples. In addition, the formation of FHA was confirmed by FT-IR results. XRD studies also showed that the crystallites were in nanometric scale. At the same time, this result was in good agreement with the result of zetasizer analysis.

Pattern Driven Stress Localization

NASA Astrophysics Data System (ADS)

Croll, Andrew; Crosby, Alfred

2010-03-01

The self-assembly of patterns from isotropic initial states is a major driver of modern soft-matter research. This avenue of study is directed by the desire to understand the complex physics of the varied structures found in Nature, and by technological interest in functional materials that may be derived through biomimicry. In this work we show how a simple striped phase can respond with significant complexity to an appropriately chosen perturbation. In particular, we show how a buckled elastic plate transitions into a state of stress localization using a simple, self-assembled variation in surface topography. The collection of topographic boundaries act in concert to change the state from isotropic sinusoidal wrinkles, to sharp folds or creases separated by relatively flat regions. By varying the size of the imposed topographic pattern or the wavelength of the wrinkles, we construct a state diagram of the system. The localized state has implications for both biological systems, and for the control of non-linear pattern formation.

Micropatterned arrays of porous silicon: toward sensory biointerfaces.

PubMed

Flavel, Benjamin S; Sweetman, Martin J; Shearer, Cameron J; Shapter, Joseph G; Voelcker, Nicolas H

2011-07-01

We describe the fabrication of arrays of porous silicon spots by means of photolithography where a positive photoresist serves as a mask during the anodization process. In particular, photoluminescent arrays and porous silicon spots suitable for further chemical modification and the attachment of human cells were created. The produced arrays of porous silicon were chemically modified by means of a thermal hydrosilylation reaction that facilitated immobilization of the fluorescent dye lissamine, and alternatively, the cell adhesion peptide arginine-glycine-aspartic acid-serine. The latter modification enabled the selective attachment of human lens epithelial cells on the peptide functionalized regions of the patterns. This type of surface patterning, using etched porous silicon arrays functionalized with biological recognition elements, presents a new format of interfacing porous silicon with mammalian cells. Porous silicon arrays with photoluminescent properties produced by this patterning strategy also have potential applications as platforms for in situ monitoring of cell behavior.

Laser-based three-dimensional multiscale micropatterning of biocompatible hydrogels for customized tissue engineering scaffolds

PubMed Central

Applegate, Matthew B.; Coburn, Jeannine; Partlow, Benjamin P.; Moreau, Jodie E.; Mondia, Jessica P.; Marelli, Benedetto; Kaplan, David L.; Omenetto, Fiorenzo G.

2015-01-01

Light-induced material phase transitions enable the formation of shapes and patterns from the nano- to the macroscale. From lithographic techniques that enable high-density silicon circuit integration, to laser cutting and welding, light–matter interactions are pervasive in everyday materials fabrication and transformation. These noncontact patterning techniques are ideally suited to reshape soft materials of biological relevance. We present here the use of relatively low-energy (< 2 nJ) ultrafast laser pulses to generate 2D and 3D multiscale patterns in soft silk protein hydrogels without exogenous or chemical cross-linkers. We find that high-resolution features can be generated within bulk hydrogels through nearly 1 cm of material, which is 1.5 orders of magnitude deeper than other biocompatible materials. Examples illustrating the materials, results, and the performance of the machined geometries in vitro and in vivo are presented to demonstrate the versatility of the approach. PMID:26374842

A biosensor for cadmium based on bioconvective patterns

NASA Technical Reports Server (NTRS)

Noever, David A.; Matsos, Helen C.

1990-01-01

An 'in vitro' method for monitoring cadmium, one of the most lethal bivalent heavy metals, can detect biologically active levels. The effects of cadmium tend to concentrate in protozoa far above natural levels and therein begin transferring through freshwater food chains to animals and humans. In a small sample volume (approximately 5 ml) the method uses the toxic response to the protozoa, Tetrahymena pyriformis, to cadmium. The assay relies on macroscopic bioconvective patterns to measure the toxic response, giving a sensitivity better than 1 micro-g/1 and a toxicity threshold to 7 micro-g/1 for Cd(2+). Cadmium hinders pattern formation in a dose-dependent manner. Arrested organism growth arises from slowed division and mutation to non-dividing classes. Unlike previous efforts, this method can be performed in a shallow flow device and does not require electronic or chemical analyses to monitor toxicity.

Nearest pattern interaction and global pattern formation

NASA Astrophysics Data System (ADS)

Jeong, Seong-Ok; Moon, Hie-Tae; Ko, Tae-Wook

2000-12-01

We studied the effect of nearest pattern interaction on a global pattern formation in a two-dimensional space, where patterns are to grow initially from a noise in the presence of a periodic supply of energy. Although our approach is general, we found that this study is relevant in particular to the pattern formation on a periodically vibrated granular layer, as it gives a unified perspective of the experimentally observed pattern dynamics such as oscillon and stripe formations, skew-varicose and crossroll instabilities, and also a kink formation and decoration.

Non-Linear Pattern Formation in Bone Growth and Architecture

PubMed Central

Salmon, Phil

2014-01-01

The three-dimensional morphology of bone arises through adaptation to its required engineering performance. Genetically and adaptively bone travels along a complex spatiotemporal trajectory to acquire optimal architecture. On a cellular, micro-anatomical scale, what mechanisms coordinate the activity of osteoblasts and osteoclasts to produce complex and efficient bone architectures? One mechanism is examined here – chaotic non-linear pattern formation (NPF) – which underlies in a unifying way natural structures as disparate as trabecular bone, swarms of birds flying, island formation, fluid turbulence, and others. At the heart of NPF is the fact that simple rules operating between interacting elements, and Turing-like interaction between global and local signals, lead to complex and structured patterns. The study of “group intelligence” exhibited by swarming birds or shoaling fish has led to an embodiment of NPF called “particle swarm optimization” (PSO). This theoretical model could be applicable to the behavior of osteoblasts, osteoclasts, and osteocytes, seeing them operating “socially” in response simultaneously to both global and local signals (endocrine, cytokine, mechanical), resulting in their clustered activity at formation and resorption sites. This represents problem-solving by social intelligence, and could potentially add further realism to in silico computer simulation of bone modeling. What insights has NPF provided to bone biology? One example concerns the genetic disorder juvenile Pagets disease or idiopathic hyperphosphatasia, where the anomalous parallel trabecular architecture characteristic of this pathology is consistent with an NPF paradigm by analogy with known experimental NPF systems. Here, coupling or “feedback” between osteoblasts and osteoclasts is the critical element. This NPF paradigm implies a profound link between bone regulation and its architecture: in bone the architecture is the regulation. The former is the emergent consequence of the latter. PMID:25653638

Non-linear pattern formation in bone growth and architecture.

PubMed

Salmon, Phil

2014-01-01

The three-dimensional morphology of bone arises through adaptation to its required engineering performance. Genetically and adaptively bone travels along a complex spatiotemporal trajectory to acquire optimal architecture. On a cellular, micro-anatomical scale, what mechanisms coordinate the activity of osteoblasts and osteoclasts to produce complex and efficient bone architectures? One mechanism is examined here - chaotic non-linear pattern formation (NPF) - which underlies in a unifying way natural structures as disparate as trabecular bone, swarms of birds flying, island formation, fluid turbulence, and others. At the heart of NPF is the fact that simple rules operating between interacting elements, and Turing-like interaction between global and local signals, lead to complex and structured patterns. The study of "group intelligence" exhibited by swarming birds or shoaling fish has led to an embodiment of NPF called "particle swarm optimization" (PSO). This theoretical model could be applicable to the behavior of osteoblasts, osteoclasts, and osteocytes, seeing them operating "socially" in response simultaneously to both global and local signals (endocrine, cytokine, mechanical), resulting in their clustered activity at formation and resorption sites. This represents problem-solving by social intelligence, and could potentially add further realism to in silico computer simulation of bone modeling. What insights has NPF provided to bone biology? One example concerns the genetic disorder juvenile Pagets disease or idiopathic hyperphosphatasia, where the anomalous parallel trabecular architecture characteristic of this pathology is consistent with an NPF paradigm by analogy with known experimental NPF systems. Here, coupling or "feedback" between osteoblasts and osteoclasts is the critical element. This NPF paradigm implies a profound link between bone regulation and its architecture: in bone the architecture is the regulation. The former is the emergent consequence of the latter.

Rapid Long-Range Disynaptic Inhibition Explains the Formation of Cortical Orientation Maps

PubMed Central

Antolík, Ján

2017-01-01

Competitive interactions are believed to underlie many types of cortical processing, ranging from memory formation, attention and development of cortical functional organization (e.g., development of orientation maps in primary visual cortex). In the latter case, the competitive interactions happen along the cortical surface, with local populations of neurons reinforcing each other, while competing with those displaced more distally. This specific configuration of lateral interactions is however in stark contrast with the known properties of the anatomical substrate, i.e., excitatory connections (mediating reinforcement) having longer reach than inhibitory ones (mediating competition). No satisfactory biologically plausible resolution of this conflict between anatomical measures, and assumed cortical function has been proposed. Recently a specific pattern of delays between different types of neurons in cat cortex has been discovered, where direct mono-synaptic excitation has approximately the same delay, as the combined delays of the disynaptic inhibitory interactions between excitatory neurons (i.e., the sum of delays from excitatory to inhibitory and from inhibitory to excitatory neurons). Here we show that this specific pattern of delays represents a biologically plausible explanation for how short-range inhibition can support competitive interactions that underlie the development of orientation maps in primary visual cortex. We demonstrate this statement analytically under simplifying conditions, and subsequently show using network simulations that development of orientation maps is preserved when long-range excitation, direct inhibitory to inhibitory interactions, and moderate inequality in the delays between excitatory and inhibitory pathways is added. PMID:28408869

How and why does the immunological synapse form? Physical chemistry meets cell biology.

PubMed

Chakraborty, Arup K

2002-03-05

During T lymphocyte (T cell) recognition of an antigen, a highly organized and specific pattern of membrane proteins forms in the junction between the T cell and the antigen-presenting cell (APC). This specialized cell-cell junction is called the immunological synapse. It is several micrometers large and forms over many minutes. A plethora of experiments are being performed to study the mechanisms that underlie synapse formation and the way in which information transfer occurs across the synapse. The wealth of experimental data that is beginning to emerge must be understood within a mechanistic framework if it is to prove useful in developing modalities to control the immune response. Quantitative models can complement experiments in the quest for such a mechanistic understanding by suggesting experimentally testable hypotheses. Here, a quantitative synapse assembly model is described. The model uses concepts developed in physical chemistry and cell biology and is able to predict the spatiotemporal evolution of cell shape and receptor protein patterns observed during synapse formation. Attention is directed to how the juxtaposition of model predictions and experimental data has led to intriguing hypotheses regarding the role of null and self peptides during synapse assembly, as well as correlations between T cell effector functions and the robustness of synapse assembly. We remark on some ways in which synergistic experiments and modeling studies can improve current models, and we take steps toward a better understanding of information transfer across the T cell-APC junction.

Non-Covalent Photo-Patterning of Gelatin Matrices Using Caged Collagen Mimetic Peptides

PubMed Central

Li, Yang; Hoa San, Boi; L. Kessler, Julian; Hwan Kim, Jin; Xu, Qingguo; Hanes, Justin; Yu, Seungju Michael

2015-01-01

Advancements in photolithography have enabled us to spatially encode biochemical cues in biocompatible platforms such as synthetic hydrogels. Conventional patterning works through photo-activated chemical reactions on inert polymer networks. However, these techniques cannot be directly applied to protein hydrogels without chemically altering the protein scaffolds. To this end, we developed a non-covalent photo-patterning strategy for gelatin (denatured collagen) hydrogels utilizing a caged collagen mimetic peptide (caged CMP) which binds to gelatin strands through UV activated, triple helix hybridization. Here we present 2D and 3D photo-patterning of gelatin hydrogels enabled by the caged CMPs as well as creation of concentration gradients of CMPs. We show that photo-patterning of PEG-conjugated caged CMPs can be used to spatially control cell adhesion on gelatin films. CMP’s specificity for binding to gelatin allows patterning of almost any synthetic or natural gelatin-containing matrix, such as zymograms, gelatin-methacrylate hydrogels, and even a corneal tissue. Since the CMP is a chemically and biologically inert peptide which is proven to be an ideal carrier for bioactive molecules, our patterning method provides a radically new tool for immobilizing drugs to natural tissues and for functionalizing scaffolds for complex tissue formation. PMID:25476588

A Modified Consumer Inkjet for Spatiotemporal Control of Gene Expression

PubMed Central

Cohen, Daniel J.; Morfino, Roberto C.; Maharbiz, Michel M.

2009-01-01

This paper presents a low-cost inkjet dosing system capable of continuous, two-dimensional spatiotemporal regulation of gene expression via delivery of diffusible regulators to a custom-mounted gel culture of E. coli. A consumer-grade, inkjet printer was adapted for chemical printing; E. coli cultures were grown on 750 µm thick agar embedded in micro-wells machined into commercial compact discs. Spatio-temporal regulation of the lac operon was demonstrated via the printing of patterns of lactose and glucose directly into the cultures; X-Gal blue patterns were used for visual feedback. We demonstrate how the bistable nature of the lac operon's feedback, when perturbed by patterning lactose (inducer) and glucose (inhibitor), can lead to coordination of cell expression patterns across a field in ways that mimic motifs seen in developmental biology. Examples of this include sharp boundaries and the generation of traveling waves of mRNA expression. To our knowledge, this is the first demonstration of reaction-diffusion effects in the well-studied lac operon. A finite element reaction-diffusion model of the lac operon is also presented which predicts pattern formation with good fidelity. PMID:19763256

Aggregation Pattern Transitions by Slightly Varying the Attractive/Repulsive Function

PubMed Central

Cheng, Zhao; Zhang, Hai-Tao; Chen, Michael Z. Q.; Zhou, Tao; Valeyev, Najl V.

2011-01-01

Among collective behaviors of biological swarms and flocks, the attractive/repulsive (A/R) functional links between particles play an important role. By slightly changing the cutoff distance of the A/R function, a drastic transition between two distinct aggregation patterns is observed. More precisely, a large cutoff distance yields a liquid-like aggregation pattern where the particle density decreases monotonously from the inside to the outwards within each aggregated cluster. Conversely, a small cutoff distance produces a crystal-like aggregation pattern where the distance between each pair of neighboring particles remains constant. Significantly, there is an obvious spinodal in the variance curve of the inter-particle distances along the increasing cutoff distances, implying a legible transition pattern between the liquid-like and crystal-like aggregations. This work bridges the aggregation phenomena of physical particles and swarming of organisms in nature upon revealing some common mechanism behind them by slightly varying their inter-individual attractive/repulsive functions, and may find its potential engineering applications, for example, in the formation design of multi-robot systems and unmanned aerial vehicles (UAVs). PMID:21799776

Cytokinin signalling inhibitory fields provide robustness to phyllotaxis

NASA Astrophysics Data System (ADS)

Besnard, Fabrice; Refahi, Yassin; Morin, Valérie; Marteaux, Benjamin; Brunoud, Géraldine; Chambrier, Pierre; Rozier, Frédérique; Mirabet, Vincent; Legrand, Jonathan; Lainé, Stéphanie; Thévenon, Emmanuel; Farcot, Etienne; Cellier, Coralie; Das, Pradeep; Bishopp, Anthony; Dumas, Renaud; Parcy, François; Helariutta, Ykä; Boudaoud, Arezki; Godin, Christophe; Traas, Jan; Guédon, Yann; Vernoux, Teva

2014-01-01

How biological systems generate reproducible patterns with high precision is a central question in science. The shoot apical meristem (SAM), a specialized tissue producing plant aerial organs, is a developmental system of choice to address this question. Organs are periodically initiated at the SAM at specific spatial positions and this spatiotemporal pattern defines phyllotaxis. Accumulation of the plant hormone auxin triggers organ initiation, whereas auxin depletion around organs generates inhibitory fields that are thought to be sufficient to maintain these patterns and their dynamics. Here we show that another type of hormone-based inhibitory fields, generated directly downstream of auxin by intercellular movement of the cytokinin signalling inhibitor ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6), is involved in regulating phyllotactic patterns. We demonstrate that AHP6-based fields establish patterns of cytokinin signalling in the meristem that contribute to the robustness of phyllotaxis by imposing a temporal sequence on organ initiation. Our findings indicate that not one but two distinct hormone-based fields may be required for achieving temporal precision during formation of reiterative structures at the SAM, thus indicating an original mechanism for providing robustness to a dynamic developmental system.

The role of hydroxo-bridged dinuclear species and the influence of "innocent" buffers in the reactivity of cis-[Co(III)(cyclen)(H₂O)₂]³⁺ and [Co(III)(tren)(H₂O)₂]³⁺ complexes with biologically relevant ligands at physiological pH.

PubMed

Basallote, Manuel G; Martínez, Manuel; Vázquez, Marta

2014-07-28

In view of the relevance of the reactivity of inert tetraamine Co(III) complexes having two substitutionally active cis positions capable of interact with biologically relevant ligands, the study of the reaction of cis-[Co(cyclen)(H2O)2](3+) and [Co(tren)(H2O)2](3+) with chlorides, inorganic phosphate and 5'-CMP (5'-cytidinemonophosphate) has been pursued at physiological pH. The results indicate that, in addition to the actuation of the expected labilising conjugate-base mechanism, the formation of mono and inert bis hydroxo-bridged species is relevant for understanding their speciation and reactivity. The reactivity pattern observed also indicates the key role played by the "innocent" buffers frequently used in most in vitro studies, which can make the results unreliable in many cases. The differences between the reactivity of inorganic and biologically relevant phosphates has also been found to be remarkable, with outer-sphere hydrogen bonding interactions being a dominant factor for the process. While for the inorganic phosphate substitution process the formation of μ-η(2)-OPO2O represents the termination of the reactivity monitored, for 5'-CMP only the formation of η(1)-OPO3 species is observed, which evolve with time to the final dead-end bis hydroxo-bridged complexes. The promoted hydrolysis of the 5'-CMP phosphate has not been observed in any of the processes studied.

Minimal mechanisms for school formation in self-propelled particles

NASA Astrophysics Data System (ADS)

Li, Yue-Xian; Lukeman, Ryan; Edelstein-Keshet, Leah

2008-05-01

In the context of social organisms, a school refers to a cohesive group of organisms that share a common speed and direction of motion, as well as a common axis of body alignment or polarization. Schools are also noted for the relatively fixed nearest-neighbour distances between individuals. The rules of interaction that lead to the formation and maintenance of a school structure have been explored experimentally, analytically, and by simulation. Interest in biological examples, and non-biological “self-propelled particles” such as robots, vehicles, or autonomous agents leads to the question of what are the simplest possible sets of rules that can assure the formation and the stability of the “perfect school”: an aggregate in which the nearest-neighbour distances and speeds are identical. Here we explore mechanisms that lead to a perfect school structure in one and two dimensions. We consider distance-detection as well as velocity-detection between the interacting pairs of self-propelled particles. We construct interaction forces and formulate schooling equations. In the simplest cases, these equations have analytic solutions. In many cases, the stability of the perfect school can be explored. We then investigate how these structures form and evolve over time from various initial configurations using simulations. We study the relationship between the assumed interaction forces and the school patterns that emerge. While true biological schools are far from perfect, the insights gained from this investigation can help to understand some properties of real schools, and to suggest the appropriate properties of artificial schools where coordinated motion is desired.

Phenotypically heterogeneous deletion of the ABH antigen from the transformed bladder urothelium. A scanning electron microscope study.

PubMed

De Harven, E; He, S; Hanna, W; Bootsma, G; Connolly, J G

1987-10-01

The deletion of ABH blood group antigens from the luminal surface of the bladder mucosa in cases of well differentiated transitional cell carcinomata, and the formation of pleomorphic microvilli have both been associated with aggressive biological behaviour and invasiveness of the tumors. We have studied cold cup biopsies from 8 normal mucosae and 17 papillary transitional cell carcinomata of the urinary bladder. The aim of our study was to correlate the formation of uniform or pleomorphic microvilli with the extent of deletion of the ABH blood group antigens on the surface of normal and transformed bladder urothelium. Immunogold scanning electron microscopy (SEM) in the backscattered electron (BE) imaging mode was used for this purpose. In the normal urothelium, uniform labeling of the luminal cells was demonstrated. In well differentiated tumors, the superficial cells exhibited uniform microvilli and a heterogeneous expression of the ABH antigens, giving characteristic 'mosaic' patterns of the antigenic labeling across the mucosal surface. These patterns were sharply delimitated at cell junctions when viewed by SEM; these observations were confirmed by transmission electron microscopy. In higher grade tumors, decreased ABH antigen expression, pleomorphic microvilli and/or featureless luminal cells were observed. In the transformed urothelium, the formation of uniform microvilli appeared to precede the loss of ABH antigen in most cases.

[Seed geography: its concept and basic scientific issues].

PubMed

Yu, Shun-Li; Wang, Zong-Shuai; Zeren, Wangmu

2010-01-01

In this paper, a new concept 'seed geography' was provided, and its definition, research contents, and scientific issues were put forward. Seed geography is a newly developed interdisciplinary science from plant geography, seed ecology, and phytosociology, which studies the geographic variation patterns of seed biological traits as well as their relationships with environmental factors from macroscopic to microscopic, and the seed formation, development, and change trends. The main research contents would include geography of seed mass, geography of seed chemical components, geography of seed morphology, geography of seed cell biological characteristics, geography of seed physiological characteristics, geography of seed genetic characteristics, and geography of flower and fruit. To explore the scientific issues in seed geography would help us to better understand the long-term adaptation and evolution of seed characteristics to natural environments.

Collective ordering of microscale matters in natural analogy

PubMed Central

Ahn, Sungsook; Joon Lee, Sang

2015-01-01

Collective interaction occurs in many natural and artificial matters in broad scales. In a biological system, collective spatial organization of live individuals in a colony is important for their viability determination. Interactive motions between a single individual and an agglomerate are critical for whole procedure of the collective behaviors, but few has been clarified for these intermediate range behaviors. Here, collective interactions of microscale matters are investigated with human cells, plant seeds and artificial microspheres in terms of commonly occurring spatial arrangements. Human cancer cells are inherently attractive to form an agglomerate by cohesive motion, while plant chia seeds are repulsive by excreting mucilage. Microsphere model is employed to investigate the dynamic assembly equilibrated by an attraction and repulsion. There is a fundamental analogy in terms of an onset of regular pattern formation even without physical contact of individuals. The collective interactions are suggested to start before the individual components become physically agglomerated. This study contributes to fundamental understanding on the microscale particulate matters and natural pattern formation which are further useful for various applications both in academic and industrial areas. PMID:26027819

Measurement of Strain Distributions in Mouse Femora with 3D-Digital Speckle Pattern Interferometry

PubMed Central

Yang, Lianxiang; Zhang, Ping; Liu, Sheng; Samala, Praveen R; Su, Min; Yokota, Hiroki

2007-01-01

Bone is a mechanosensitive tissue that adapts its mass, architecture and mechanical properties to external loading. Appropriate mechanical loads offer an effective means to stimulate bone remodeling and prevent bone loss. A role of in situ strain in bone is considered essential in enhancement of bone formation, and establishing a quantitative relationship between 3D strain distributions and a rate of local bone formation is important. Digital speckle pattern interferometry (DSPI) can achieve whole-field, non-contacting measurements of microscopic deformation for high-resolution determination of 3D strain distributions. However, the current system does not allow us to derive accurate strain distributions because of complex surface contours inherent to biological samples. Through development of a custom-made piezoelectric loading device as well as a new DSPI-based force calibration system, we built an advanced DSPI system and integrated local contour information to deformation data. Using a mouse femur in response to a knee loading modality as a model system, we determined 3D strain distributions and discussed effectiveness and limitations of the described system. PMID:18670581

Pattern formation, social forces, and diffusion instability in games with success-driven motion

NASA Astrophysics Data System (ADS)

Helbing, Dirk

2009-02-01

A local agglomeration of cooperators can support the survival or spreading of cooperation, even when cooperation is predicted to die out according to the replicator equation, which is often used in evolutionary game theory to study the spreading and disappearance of strategies. In this paper, it is shown that success-driven motion can trigger such local agglomeration and may, therefore, be used to supplement other mechanisms supporting cooperation, like reputation or punishment. Success-driven motion is formulated here as a function of the game-theoretical payoffs. It can change the outcome and dynamics of spatial games dramatically, in particular as it causes attractive or repulsive interaction forces. These forces act when the spatial distributions of strategies are inhomogeneous. However, even when starting with homogeneous initial conditions, small perturbations can trigger large inhomogeneities by a pattern-formation instability, when certain conditions are fulfilled. Here, these instability conditions are studied for the prisoner’s dilemma and the snowdrift game. Furthermore, it is demonstrated that asymmetrical diffusion can drive social, economic, and biological systems into the unstable regime, if these would be stable without diffusion.

Glassy dynamics in three-dimensional embryonic tissues

PubMed Central

Schötz, Eva-Maria; Lanio, Marcos; Talbot, Jared A.; Manning, M. Lisa

2013-01-01

Many biological tissues are viscoelastic, behaving as elastic solids on short timescales and fluids on long timescales. This collective mechanical behaviour enables and helps to guide pattern formation and tissue layering. Here, we investigate the mechanical properties of three-dimensional tissue explants from zebrafish embryos by analysing individual cell tracks and macroscopic mechanical response. We find that the cell dynamics inside the tissue exhibit features of supercooled fluids, including subdiffusive trajectories and signatures of caging behaviour. We develop a minimal, three-parameter mechanical model for these dynamics, which we calibrate using only information about cell tracks. This model generates predictions about the macroscopic bulk response of the tissue (with no fit parameters) that are verified experimentally, providing a strong validation of the model. The best-fit model parameters indicate that although the tissue is fluid-like, it is close to a glass transition, suggesting that small changes to single-cell parameters could generate a significant change in the viscoelastic properties of the tissue. These results provide a robust framework for quantifying and modelling mechanically driven pattern formation in tissues. PMID:24068179

Toward 4D Nanoprinting with Tip-Induced Organic Surface Reactions.

PubMed

Carbonell, Carlos; Braunschweig, Adam B

2017-02-21

Future nanomanufacturing tools will prepare organic materials with complex four-dimensional (4D) structure, where the position (x, y, z) and chemical composition within a volume is controlled with sub-1 μm spatial resolution. Such tools could produce substrates that mimic biological interfaces, like the cell surface or the extracellular matrix, whose topology and chemical complexity combine to direct some of the most sophisticated biological events. The control of organic materials at the nanoscale-level of spatial resolution could revolutionize the assembly of next generation optical and electronic devices or substrates for tissue engineering or enable fundamental biological or material science investigations. Organic chemistry provides the requisite control over the orientation and position of matter within a nanoscale reference frame through the formation of new covalent bonds. Several challenges however preclude the integration of organic chemistry with conventional nanomanufacturing approaches, namely most nanolithography platforms would denature or destroy delicate organic and biologically active matter, confirming covalent bond formation at interfaces remains difficult, and finally, only a small handful of the reactions used to transform molecules in solution have been validated on surfaces. Thus, entirely new approaches, where organic transformations and spatial control are considered equally important contributors, are needed to create 4D organic nanoprinting platforms. This Account describes efforts from our group to reconcile nanolithography, and specifically massively parallel scanning probe lithography (SPL), with organic chemistry to further the goal of 4D organic nanoprinting. Massively parallel SPL involves arrays of elastomeric pyramids mounted onto piezoelectric actuators, and creates patterns with feature diameters below 50 nm by using the pyramidal tips for either the direct deposition of ink or the localized delivery of energy to a surface. While other groups have focused on tip and array architetctures, our efforts have been on exploring their use for localizing organic chemistry on surfaces with nanoscale spatial resolution in 3D. Herein we describe the use of massively parallel SPL to create covalently immobilized patterns of organic materials using thermal, catalytic, photochemical, and force-accelerated reactions. In doing so, we have developed a high-throughput protocol for confirming interfacial bond formation. These efforts have resulted in new opportunities for the preparation of glycan arrays, novel approaches for covalently patterning graphene, and a 3D nanoprinter by combining photochemical brush polymerizations with SPL. Achieving true 4D nanoprinting involves advances in surface chemistry and instrumentation development, and to this end 4D micropatterns were produced in a microfluidic photoreactor that can position polymers composed of different monomers within micrometer proximity. A substantial gap remains, however, between these current technologies and the future's 4D nanomanufacturing tools, but the marriage of SPL with organic chemistry is an important step toward this goal. As this field continues to mature we can expect bottom-up 4D nanomanufacturing to begin supplanting conventional top-down strategies for preparing electronics, bioarrays, and functional substrates. In addition, these new printing technologies may enable the preparation of synthetic targets, such as artificial biological interfaces, with a level of organic sophistication that is entirely unachievable using existing technologies.

Stretch force guides finger-like pattern of bone formation in suture

PubMed Central

Kou, Xiao-Xing; Zhang, Ci; Zhang, Yi-Mei; Cui, Zhen; Wang, Xue-Dong; Liu, Yan; Liu, Da-Wei; Zhou, Yan-Heng

2017-01-01

Mechanical tension is widely applied on the suture to modulate the growth of craniofacial bones. Deeply understanding the features of bone formation in expanding sutures could help us to improve the outcomes of clinical treatment and avoid some side effects. Although there are reports that have uncovered some biological characteristics, the regular pattern of sutural bone formation in response to expansion forces is still unknown. Our study was to investigate the shape, arrangement and orientation of new bone formation in expanding sutures and explore related clinical implications. The premaxillary sutures of rat, which histologically resembles the sutures of human beings, became wider progressively under stretch force. Micro-CT detected new bones at day 3. Morphologically, these bones were forming in a finger-like pattern, projecting from the maxillae into the expanded sutures. There were about 4 finger-like bones appearing on the selected micro-CT sections at day 3 and this number increased to about 18 at day 7. The average length of these projections increased from 0.14 mm at day 3 to 0.81 mm at day 7. The volume of these bony protuberances increased to the highest level of 0.12 mm3 at day 7. HE staining demonstrated that these finger-like bones had thick bases connecting with the maxillae and thin fronts stretching into the expanded suture. Nasal sections had a higher frequency of finger-like bones occuring than the oral sections at day 3 and day 5. Masson-stained sections showed stretched fibers embedding into maxillary margins. Osteocalcin-positive osteoblasts changed their shapes from cuboidal to spindle and covered the surfaces of finger-like bones continuously. Alizarin red S and calcein deposited in the inner and outer layers of finger-like bones respectively, which showed that longer and larger bones formed on the nasal side of expanded sutures compared with the oral side. Interestingly, these finger-like bones were almost paralleling with the direction of stretch force. Inclined force led to inclined finger-like bones formation and deflection of bilateral maxillae. Additionally, heavily compressive force caused fracture of finger-like bones in the sutures. These data together proposed the special finger-like pattern of bone formation in sutures guided by stretch force, providing important implications for maxillary expansion. PMID:28472133

Pattern-formation mechanisms in motility mutants of Myxococcus xanthus

PubMed Central

Starruß, Jörn; Peruani, Fernando; Jakovljevic, Vladimir; Søgaard-Andersen, Lotte; Deutsch, Andreas; Bär, Markus

2012-01-01

Formation of spatial patterns of cells is a recurring theme in biology and often depends on regulated cell motility. Motility of the rod-shaped cells of the bacterium Myxococcus xanthus depends on two motility machineries, type IV pili (giving rise to S-motility) and the gliding motility apparatus (giving rise to A-motility). Cell motility is regulated by occasional reversals. Moving M. xanthus cells can organize into spreading colonies or spore-filled fruiting bodies, depending on their nutritional status. To ultimately understand these two pattern-formation processes and the contributions by the two motility machineries, as well as the cell reversal machinery, we analyse spatial self-organization in three M. xanthus strains: (i) a mutant that moves unidirectionally without reversing by the A-motility system only, (ii) a unidirectional mutant that is also equipped with the S-motility system, and (iii) the wild-type that, in addition to the two motility systems, occasionally reverses its direction of movement. The mutant moving by means of the A-engine illustrates that collective motion in the form of large moving clusters can arise in gliding bacteria owing to steric interactions of the rod-shaped cells, without the need of invoking any biochemical signal regulation. The two-engine strain mutant reveals that the same phenomenon emerges when both motility systems are present, and as long as cells exhibit unidirectional motion only. From the study of these two strains, we conclude that unidirectional cell motion induces the formation of large moving clusters at low and intermediate densities, while it results in vortex formation at very high densities. These findings are consistent with what is known from self-propelled rod models, which strongly suggests that the combined effect of self-propulsion and volume exclusion interactions is the pattern-formation mechanism leading to the observed phenomena. On the other hand, we learn that when cells occasionally reverse their moving direction, as observed in the wild-type, cells form small but strongly elongated clusters and self-organize into a mesh-like structure at high enough densities. These results have been obtained from a careful analysis of the cluster statistics of ensembles of cells, and analysed in the light of a coagulation Smoluchowski equation with fragmentation. PMID:24312730

AN OVERVIEW OF COMPUTATIONAL LIFE SCIENCE DATABASES & EXCHANGE FORMATS OF RELEVANCE TO CHEMICAL BIOLOGY RESEARCH

PubMed Central

Hall, Aaron Smalter; Shan, Yunfeng; Lushington, Gerald; Visvanathan, Mahesh

2016-01-01

Databases and exchange formats describing biological entities such as chemicals and proteins, along with their relationships, are a critical component of research in life sciences disciplines, including chemical biology wherein small information about small molecule properties converges with cellular and molecular biology. Databases for storing biological entities are growing not only in size, but also in type, with many similarities between them and often subtle differences. The data formats available to describe and exchange these entities are numerous as well. In general, each format is optimized for a particular purpose or database, and hence some understanding of these formats is required when choosing one for research purposes. This paper reviews a selection of different databases and data formats with the goal of summarizing their purposes, features, and limitations. Databases are reviewed under the categories of 1) protein interactions, 2) metabolic pathways, 3) chemical interactions, and 4) drug discovery. Representation formats will be discussed according to those describing chemical structures, and those describing genomic/proteomic entities. PMID:22934944

An overview of computational life science databases & exchange formats of relevance to chemical biology research.

PubMed

Smalter Hall, Aaron; Shan, Yunfeng; Lushington, Gerald; Visvanathan, Mahesh

2013-03-01

Databases and exchange formats describing biological entities such as chemicals and proteins, along with their relationships, are a critical component of research in life sciences disciplines, including chemical biology wherein small information about small molecule properties converges with cellular and molecular biology. Databases for storing biological entities are growing not only in size, but also in type, with many similarities between them and often subtle differences. The data formats available to describe and exchange these entities are numerous as well. In general, each format is optimized for a particular purpose or database, and hence some understanding of these formats is required when choosing one for research purposes. This paper reviews a selection of different databases and data formats with the goal of summarizing their purposes, features, and limitations. Databases are reviewed under the categories of 1) protein interactions, 2) metabolic pathways, 3) chemical interactions, and 4) drug discovery. Representation formats will be discussed according to those describing chemical structures, and those describing genomic/proteomic entities.

Predictability of spatio-temporal patterns in a lattice of coupled FitzHugh–Nagumo oscillators

PubMed Central

Grace, Miriam; Hütt, Marc-Thorsten

2013-01-01

In many biological systems, variability of the components can be expected to outrank statistical fluctuations in the shaping of self-organized patterns. In pioneering work in the late 1990s, it was hypothesized that a drift of cellular parameters (along a ‘developmental path’), together with differences in cell properties (‘desynchronization’ of cells on the developmental path) can establish self-organized spatio-temporal patterns (in their example, spiral waves of cAMP in a colony of Dictyostelium discoideum cells) starting from a homogeneous state. Here, we embed a generic model of an excitable medium, a lattice of diffusively coupled FitzHugh–Nagumo oscillators, into a developmental-path framework. In this minimal model of spiral wave generation, we can now study the predictability of spatio-temporal patterns from cell properties as a function of desynchronization (or ‘spread’) of cells along the developmental path and the drift speed of cell properties on the path. As a function of drift speed and desynchronization, we observe systematically different routes towards fully established patterns, as well as strikingly different correlations between cell properties and pattern features. We show that the predictability of spatio-temporal patterns from cell properties contains important information on the pattern formation process as well as on the underlying dynamical system. PMID:23349439

Sequential and selective localized optical heating in water via on-chip dielectric nanopatterning.

PubMed

Morsy, Ahmed M; Biswas, Roshni; Povinelli, Michelle L

2017-07-24

We study the use of nanopatterned silicon membranes to obtain optically-induced heating in water. We show that by varying the detuning between an absorptive optical resonance of the patterned membrane and an illumination laser, both the magnitude and response time of the temperature rise can be controlled. This allows for either sequential or selective heating of different patterned areas on chip. We obtain a steady-state temperature of approximately 100 °C for a 805.5nm CW laser power density of 66 µW/μm 2 and observe microbubble formation. The ability to spatially and temporally control temperature on the microscale should enable the study of heat-induced effects in a variety of chemical and biological lab-on-chip applications.

Replumbing of the Biological Pump caused by Millennial Climate Variability

NASA Astrophysics Data System (ADS)

Galbraith, E.; Sarmiento, J.

2008-12-01

It has been hypothesized that millennial-timescale variability in the biological pump was a critical instigator of glacial-interglacial cycles. However, even in the absence of changes in ecosystem function (e.g. due to iron fertilization), determining the mechanisms by which physical climate variability alters the biological pump is not simple. Changes in upper ocean circulation and deep water formation have previously been shown to alter both the downward flux of organic matter and the mass of respired carbon in the ocean interior, often in non- intuitive ways. For example, a reduced upward flux of nutrients at the global scale will decrease the global rate of export production, but it could either increase or decrease the respired carbon content of the ocean interior, depending on where the reduced upward flux of nutrients occurs. Furthermore, viable candidates for physical climate forcing are numerous, including changes in the westerly winds, changes in the depth of the thermocline, and changes in the formation rate of North Atlantic Deep Water, among others. We use a simple, prognostic, light-and temperature-dependent model of biogeochemical cycling within a state-of-the- art global coupled ocean-atmosphere model to examine the response of the biological pump to changes in the coupled Earth system over multiple centuries. The biogeochemical model explicitly distinguishes respired carbon from preformed and saturation carbon, allowing the activity of the biological pump to be clearly quantified. Changes are forced in the model by altering the background climate state, and by manipulating the flux of freshwater to the North Atlantic region. We show how these changes in the physical state of the coupled ocean-atmosphere system impact the distribution and mass of respired carbon in the ocean interior, and the relationship these changes bear to global patterns of export production via the redistribution of nutrients.

Optical Pattern Formation in Cold Atoms: Explaining the Red-Blue Asymmetry

NASA Astrophysics Data System (ADS)

Schmittberger, Bonnie; Gauthier, Daniel

2013-05-01

The study of pattern formation in atomic systems has provided new insight into fundamental many-body physics and low-light-level nonlinear optics. Pattern formation in cold atoms in particular is of great interest in condensed matter physics and quantum information science because atoms undergo self-organization at ultralow input powers. We recently reported the first observation of pattern formation in cold atoms but found that our results were not accurately described by any existing theoretical model of pattern formation. Previous models describing pattern formation in cold atoms predict that pattern formation should occur using both red and blue-detuned pump beams, favoring a lower threshold for blue detunings. This disagrees with our recent work, in which we only observed pattern formation with red-detuned pump beams. Previous models also assume a two-level atom, which cannot account for the cooling processes that arise when beams counterpropagate through a cold atomic vapor. We describe a new model for pattern formation that accounts for Sisyphus cooling in multi-level atoms, which gives rise to a new nonlinearity via spatial organization of the atoms. This spatial organization causes a sharp red-blue detuning asymmetry, which agrees well with our experimental observations. We gratefully acknowledge the financial support of the NSF through Grant #PHY-1206040.

Nonconstant Positive Steady States and Pattern Formation of 1D Prey-Taxis Systems

NASA Astrophysics Data System (ADS)

Wang, Qi; Song, Yang; Shao, Lingjie

2017-02-01

Prey-taxis is the process that predators move preferentially toward patches with highest density of prey. It is well known to have an important role in biological control and the maintenance of biodiversity. To model the coexistence and spatial distributions of predator and prey species, this paper concerns nonconstant positive steady states of a wide class of prey-taxis systems with general functional responses over 1D domain. Linearized stability of the positive equilibrium is analyzed to show that prey-taxis destabilizes prey-predator homogeneity when prey repulsion (e.g., due to volume-filling effect in predator species or group defense in prey species) is present, and prey-taxis stabilizes the homogeneity otherwise. Then, we investigate the existence and stability of nonconstant positive steady states to the system through rigorous bifurcation analysis. Moreover, we provide detailed and thorough calculations to determine properties such as pitchfork and turning direction of the local branches. Our stability results also provide a stable wave mode selection mechanism for thee reaction-advection-diffusion systems including prey-taxis models considered in this paper. Finally, we provide numerical studies of prey-taxis systems with Holling-Tanner kinetics to illustrate and support our theoretical findings. Our numerical simulations demonstrate that the 2× 2 prey-taxis system is able to model the formation and evolution of various striking patterns, such as spikes, periodic oscillations, and coarsening even when the domain is one-dimensional. These dynamics can model the coexistence and spatial distributions of interacting prey and predator species. We also give some insights on how system parameters influence pattern formation in these models.

Local behavioral rules sustain the cell allocation pattern in the combs of honey bee colonies (Apis mellifera).

PubMed

Montovan, Kathryn J; Karst, Nathaniel; Jones, Laura E; Seeley, Thomas D

2013-11-07

In the beeswax combs of honey bees, the cells of brood, pollen, and honey have a consistent spatial pattern that is sustained throughout the life of a colony. This spatial pattern is believed to emerge from simple behavioral rules that specify how the queen moves, where foragers deposit honey/pollen and how honey/pollen is consumed from cells. Prior work has shown that a set of such rules can explain the formation of the allocation pattern starting from an empty comb. We show that these rules cannot maintain the pattern once the brood start to vacate their cells, and we propose new, biologically realistic rules that better sustain the observed allocation pattern. We analyze the three resulting models by performing hundreds of simulation runs over many gestational periods and a wide range of parameter values. We develop new metrics for pattern assessment and employ them in analyzing pattern retention over each simulation run. Applied to our simulation results, these metrics show alteration of an accepted model for honey/pollen consumption based on local information can stabilize the cell allocation pattern over time. We also show that adding global information, by biasing the queen's movements towards the center of the comb, expands the parameter regime over which pattern retention occurs. © 2013 Published by Elsevier Ltd. All rights reserved.

Testing the effect of the rock record on diversity: a multidisciplinary approach to elucidating the generic richness of sauropodomorph dinosaurs through time.

PubMed

Mannion, Philip D; Upchurch, Paul; Carrano, Matthew T; Barrett, Paul M

2011-02-01

The accurate reconstruction of palaeobiodiversity patterns is central to a detailed understanding of the macroevolutionary history of a group of organisms. However, there is increasing evidence that diversity patterns observed directly from the fossil record are strongly influenced by fluctuations in the quality of our sampling of the rock record; thus, any patterns we see may reflect sampling biases, rather than genuine biological signals. Previous dinosaur diversity studies have suggested that fluctuations in sauropodomorph palaeobiodiversity reflect genuine biological signals, in comparison to theropods and ornithischians whose diversity seems to be largely controlled by the rock record. Most previous diversity analyses that have attempted to take into account the effects of sampling biases have used only a single method or proxy: here we use a number of techniques in order to elucidate diversity. A global database of all known sauropodomorph body fossil occurrences (2024) was constructed. A taxic diversity curve for all valid sauropodomorph genera was extracted from this database and compared statistically with several sampling proxies (rock outcrop area and dinosaur-bearing formations and collections), each of which captures a different aspect of fossil record sampling. Phylogenetic diversity estimates, residuals and sample-based rarefaction (including the first attempt to capture 'cryptic' diversity in dinosaurs) were implemented to investigate further the effects of sampling. After 'removal' of biases, sauropodomorph diversity appears to be genuinely high in the Norian, Pliensbachian-Toarcian, Bathonian-Callovian and Kimmeridgian-Tithonian (with a small peak in the Aptian), whereas low diversity levels are recorded for the Oxfordian and Berriasian-Barremian, with the Jurassic/Cretaceous boundary seemingly representing a real diversity trough. Observed diversity in the remaining Triassic-Jurassic stages appears to be largely driven by sampling effort. Late Cretaceous diversity is difficult to elucidate and it is possible that this interval remains relatively under-sampled. Despite its distortion by sampling biases, much of sauropodomorph palaeobiodiversity can be interpreted as a reflection of genuine biological signals, and fluctuations in sea level may account for some of these diversity patterns. © 2010 The Authors. Biological Reviews © 2010 Cambridge Philosophical Society.

Paleo-environmental conditions of the Early Cambrian Niutitang Formation in the Fenggang area, the southwestern margin of the Yangtze Platform, southern China: Evidence from major elements, trace elements and other proxies

NASA Astrophysics Data System (ADS)

Li, Jin; Tang, Shuheng; Zhang, Songhang; Xi, Zhaodong; Yang, Ning; Yang, Guoqiao; Li, Lei; Li, Yanpeng

2018-06-01

The Precambrian/Cambrian transition was a key time in Earth history, especially for marine biological evolution and oceanic chemistry. The redox-stratification with oxic shallow water and anoxic (even euxinic) deeper water in the Early Cambrian Yangtze Sea, which gradually became completely oxygenated, has been suggested as a possible trigger for the "Cambrian explosion" of biological diversity. However, for some areas in northern Guizhou where the exploration and research are lacking, identifying this pattern of redox-stratification by paleo-environmental analysis from borehole data is still in need. Here, we report a remarkable variation range in trace elements (Mo, V, U, Ni, Th, Co, Sc, Zn and Cu), molar Corg:P ratios and pyrite morphology from 27 core samples from one new drill hole (XY1, located in the Fenggang area, northern Guizhou) on the Yangtze Platform, South China. High levels of Ba (from 3242 ppm to 33,800 ppm) and total organic carbon (TOC; from 4% to 9.36%) in 15 core samples in the Lower Member (LM) of the Niutitang Formation indicated elevated primary productivity in the study area. Redox change was recorded based on enrichment factors (EFs) for RSTEs (Mo, U, and V), redox proxies (V/(V + Ni), Ni/Co, V/Sc and Th/U), Corg:P ratios and particle size of framboidal pyrite. These signatures demonstrate that the LM was deposited under anoxic conditions with sulfidic episodes, whereas the Upper Member (UM) of the Niutitang Formation was deposited under suboxic/oxic conditions with intermittently anoxic episodes. Mo/TOC ratios (from 3.72 to 39.86, mean 18.76) suggest weak-moderate water mass restriction. Mo-U covariation patterns (strong but variable enrichment of Mo and U; MoEF ranging from 31.45 to 257.97; UEF ranging from 4.68 to 39.07) in the LM show alternation of particulate shuttling and redox conditions occurred in the Early Cambrian Yangtze Sea, whereas Mo-U covariation patterns (moderate Mo enrichment but depletion or non-enrichment of U; mean MoEF: 7.29; mean UEF: 0.95) in the UM may indicate the combined influence of particulate shuttling and diagenetic diffusion of U via bioactivities, which result in low U values and an anoxic signature from frambiodal pyrite particle size (mean: 4.556 μm; median: 4.41 μm). Additionally, excess Ba (Baxs) concentration (33,800 ppm and 32,500 ppm) and association patterns of trace-metal enrichment in the LM indicate the existence of submarine hydrothermal events. In addition, during deposition of the UM, bioactivities indicated by Mo-U systematics and oxic conditions indicated by redox sensitive trace elements (RSTEs) and multiple-proxies, may be a cause of biological diversification recorded in the Early Cambrian. Finally, data in this record a progressive transition from anoxic bottom waters with euxinic episodes to overwhelming oxic conditions during Early Cambrian.

Modeling biological gradient formation: combining partial differential equations and Petri nets.

PubMed

Bertens, Laura M F; Kleijn, Jetty; Hille, Sander C; Heiner, Monika; Koutny, Maciej; Verbeek, Fons J

2016-01-01

Both Petri nets and differential equations are important modeling tools for biological processes. In this paper we demonstrate how these two modeling techniques can be combined to describe biological gradient formation. Parameters derived from partial differential equation describing the process of gradient formation are incorporated in an abstract Petri net model. The quantitative aspects of the resulting model are validated through a case study of gradient formation in the fruit fly.

Foster Mother-Infant Bonding: Associations Between Foster Mothers’ Oxytocin Production, Electrophysiological Brain Activity, Feelings of Commitment, and Caregiving Quality

PubMed Central

Bick, Johanna; Dozier, Mary; Bernard, Kristin; Simons, Robert; Grasso, Damion

2012-01-01

This study examined the biological processes associated with foster mother-infant bonding. In an examination of foster mother-infant dyads (N = 41, mean infant age = 8.5 months), foster mothers’ oxytocin production was associated with their expressions of behavioral delight toward their foster infant and their average P3 response to images of all infant faces in the first two months of the relationship. Three months later, foster mothers’ oxytocin production was still associated with delight toward their foster infant and was also specifically associated with their P3 response to an image of their foster infant. Similar to biologically-related mothers and infants, oxytocin appears to be associated with foster mothers’ brain activity and caregiving behavior, with patterns suggestive of bond formation. PMID:23163703

Biologically inspired artificial compound eyes.

PubMed

Jeong, Ki-Hun; Kim, Jaeyoun; Lee, Luke P

2006-04-28

This work presents the fabrication of biologically inspired artificial compound eyes. The artificial ommatidium, like that of an insect's compound eyes, consists of a refractive polymer microlens, a light-guiding polymer cone, and a self-aligned waveguide to collect light with a small angular acceptance. The ommatidia are omnidirectionally arranged along a hemispherical polymer dome such that they provide a wide field of view similar to that of a natural compound eye. The spherical configuration of the microlenses is accomplished by reconfigurable microtemplating, that is, polymer replication using the deformed elastomer membrane with microlens patterns. The formation of polymer waveguides self-aligned with microlenses is also realized by a self-writing process in a photosensitive polymer resin. The angular acceptance is directly measured by three-dimensional optical sectioning with a confocal microscope, and the detailed optical characteristics are studied in comparison with a natural compound eye.

Templating Biomineralization: Surface Directed Protein Self-assembly and External Magnetic Field Stimulation of Osteoblasts

NASA Astrophysics Data System (ADS)

Ba, Xiaolan

Biomineralization is a wide-spread phenomenon in the biological systems, which is the process of mineral formation by organisms through interaction between its organic contents and the inorganic minerals. The process is essential in a broad spectrum of biological phenomena ranging from bone and tooth formation to pathological mineralization under hypoxic conditions or cancerous formations. In this thesis I studied biomineralization at the earliest stages in order to obtain a better understanding of the fundamental principals involved. This knowledge is essential if we want to engineer devices which will increase bone regeneration or prevent unwanted mineral deposits. Extracellular matrix (ECM) proteins play an essential role during biomineralization in bone and engineered tissues. In this dissertation, I present an approach to mimic the ECM in vitro to probe the interactions of these proteins with calcium phosphate mineral and with each other. Early stage of mineralization is investigated by mechanical properties of the protein fibers using Scanning Probe Microscopy (SPM) and Shear Modulation Force Microscopy (SMFM). The development of mineral crystals on the protein matrices is also characterized by Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM) and Grazing Incidence X-ray Diffraction (GIXRD). The results demonstrate complementary actions of the two ECM proteins to collect cations and template calcium phosphate mineral, respectively. Magnets have been clinically used as an "induction source" in various bone or orthodontic treatments. However, the mechanism and effects of magnetic fields remain unclear. In this dissertation, I also undertake the present investigation to study the effects of 150 mT static magnetic fields (SMF) on ECM development and cell biomineralization using MC3T3-E1 osteobalst-like cells. Early stage of biomineralization is characterized by SPM, SMFM and confocal laser scanning microscopy (CSLM). Late stage of biomineralization is investigated by SEM, GIXRD and energy dispersive X-ray spectroscopy (EDXS). Gene expression during the exposure of SMF is also studies by RT-PCR. The results indicated that exposure to SMF induces osteoblasts to produce larger quantities of HA, with higher degree of crystalline order. The controlling and understanding of protein on the surface is of great interest in biomedical application such as implant medicine, biosensor design, food processing, and chromatographic separations. The adsorbed protein onto the surface significantly determines the performance of biomaterials in a biological environment. Recent studies have suggested that the preservation of the native secondary structure of protein adsorbed is essential for biological application. In order to manipulate protein adsorption and design biocompatible materials, the mechanisms underlying protein-surface interactions, especially how surface properties of materials induce conformational changes of adsorbed proteins, needs to be well understood. Here we demonstrated that even though SPS is a necessary condition, it is not sufficient. We show that low substrate conductivity as well as proper salt concentration are also critical in sustained protein adsorption continuously. These factors allow one to pattern regions of different conducting properties and for the first time patterns physiologically relevant protein structures. Here we show that we can achieve patterned biomineralized regimes, both with plasma proteins in a simple and robust manner without additional functionalization or application of electrochemical gradients. Since the data indicate that the patterns just need to differ in electrical conductivity, rather than surface chemistry, we propose that the creation of transient image charges, due to incomplete charge screening, may be responsible for sustain the driving force for continual protein absorption.

Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach.

PubMed

van Roekel, Hendrik W H; Rosier, Bas J H M; Meijer, Lenny H H; Hilbers, Peter A J; Markvoort, Albert J; Huck, Wilhelm T S; de Greef, Tom F A

2015-11-07

Living cells are able to produce a wide variety of biological responses when subjected to biochemical stimuli. It has become apparent that these biological responses are regulated by complex chemical reaction networks (CRNs). Unravelling the function of these circuits is a key topic of both systems biology and synthetic biology. Recent progress at the interface of chemistry and biology together with the realisation that current experimental tools are insufficient to quantitatively understand the molecular logic of pathways inside living cells has triggered renewed interest in the bottom-up development of CRNs. This builds upon earlier work of physical chemists who extensively studied inorganic CRNs and showed how a system of chemical reactions can give rise to complex spatiotemporal responses such as oscillations and pattern formation. Using purified biochemical components, in vitro synthetic biologists have started to engineer simplified model systems with the goal of mimicking biological responses of intracellular circuits. Emulation and reconstruction of system-level properties of intracellular networks using simplified circuits are able to reveal key design principles and molecular programs that underlie the biological function of interest. In this Tutorial Review, we present an accessible overview of this emerging field starting with key studies on inorganic CRNs followed by a discussion of recent work involving purified biochemical components. Finally, we review recent work showing the versatility of programmable biochemical reaction networks (BRNs) in analytical and diagnostic applications.

Numerical simulation of electrically stimulated osteogenesis in dental implants.

PubMed

Vanegas-Acosta, J C; Garzón-Alvarado, D A; Lancellotti, V

2014-04-01

Cell behavior and tissue formation are influenced by a static electric field (EF). Several protocols for EF exposure are aimed at increasing the rate of tissue recovery and reducing the healing times in wounds. However, the underlying mechanisms of the EF action on cells and tissues are still a matter of research. In this work we introduce a mathematical model for electrically stimulated osteogenesis at the bone-dental implant interface. The model describes the influence of the EF in the most critical biological processes leading to bone formation at the bone-dental implant interface. The numerical solution is able to reproduce the distribution of spatial-temporal patterns describing the influence of EF during blood clotting, osteogenic cell migration, granulation tissue formation, displacements of the fibrillar matrix, and formation of new bone. In addition, the model describes the EF-mediated cell behavior and tissue formation which lead to an increased osteogenesis in both smooth and rough implant surfaces. Since numerical results compare favorably with experimental evidence, the model can be used to predict the outcome of using electrostimulation in other types of wounds and tissues. Copyright © 2013 Elsevier B.V. All rights reserved.

Cooperativity to increase Turing pattern space for synthetic biology.

PubMed

Diambra, Luis; Senthivel, Vivek Raj; Menendez, Diego Barcena; Isalan, Mark

2015-02-20

It is hard to bridge the gap between mathematical formulations and biological implementations of Turing patterns, yet this is necessary for both understanding and engineering these networks with synthetic biology approaches. Here, we model a reaction-diffusion system with two morphogens in a monostable regime, inspired by components that we recently described in a synthetic biology study in mammalian cells.1 The model employs a single promoter to express both the activator and inhibitor genes and produces Turing patterns over large regions of parameter space, using biologically interpretable Hill function reactions. We applied a stability analysis and identified rules for choosing biologically tunable parameter relationships to increase the likelihood of successful patterning. We show how to control Turing pattern sizes and time evolution by manipulating the values for production and degradation relationships. More importantly, our analysis predicts that steep dose-response functions arising from cooperativity are mandatory for Turing patterns. Greater steepness increases parameter space and even reduces the requirement for differential diffusion between activator and inhibitor. These results demonstrate some of the limitations of linear scenarios for reaction-diffusion systems and will help to guide projects to engineer synthetic Turing patterns.

Using Grid Cells for Navigation.

PubMed

Bush, Daniel; Barry, Caswell; Manson, Daniel; Burgess, Neil

2015-08-05

Mammals are able to navigate to hidden goal locations by direct routes that may traverse previously unvisited terrain. Empirical evidence suggests that this "vector navigation" relies on an internal representation of space provided by the hippocampal formation. The periodic spatial firing patterns of grid cells in the hippocampal formation offer a compact combinatorial code for location within large-scale space. Here, we consider the computational problem of how to determine the vector between start and goal locations encoded by the firing of grid cells when this vector may be much longer than the largest grid scale. First, we present an algorithmic solution to the problem, inspired by the Fourier shift theorem. Second, we describe several potential neural network implementations of this solution that combine efficiency of search and biological plausibility. Finally, we discuss the empirical predictions of these implementations and their relationship to the anatomy and electrophysiology of the hippocampal formation. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Bone Genes in the Kidney of Stone Formers

NASA Astrophysics Data System (ADS)

Evan, Andrew P.; Bledsoe, Sharon B.

2008-09-01

Intraoperative papillary biopsies from kidneys of idiopathic-calcium oxalate stone formers (ICSF) have revealed a distinct pattern of mineral deposition in the interstitium of the renal papilla. The earliest sites of these deposits, termed Randall's plaque, are found in the basement membrane of thin loops of Henle and appear to spread into the surrounding interstitium down to the papillary epithelium. Recent studies show kidney stones of ICSF patients grow attached to the renal papilla and at sites of Randall's plaque. Together these observations suggest that plaque formation may be the critical step in stone formation. In order to control plaque formation and thereby reduce future kidney stone development, the mechanism of plaque deposition must be understood. Because the renal papilla has unique anatomical features similar to bone and the fact that the interstitial deposits of ICSF patients are formed of biological apatite, this paper tests the hypothesis that sites of interstitial plaque form as a result of cell-mediated osteoblast-like activity.

Non-random mate choice in humans: insights from a genome scan.

PubMed

Laurent, R; Toupance, B; Chaix, R

2012-02-01

Little is known about the genetic factors influencing mate choice in humans. Still, there is evidence for non-random mate choice with respect to physical traits. In addition, some studies suggest that the Major Histocompatibility Complex may affect pair formation. Nowadays, the availability of high density genomic data sets gives the opportunity to scan the genome for signatures of non-random mate choice without prior assumptions on which genes may be involved, while taking into account socio-demographic factors. Here, we performed a genome scan to detect extreme patterns of similarity or dissimilarity among spouses throughout the genome in three populations of African, European American, and Mexican origins from the HapMap 3 database. Our analyses identified genes and biological functions that may affect pair formation in humans, including genes involved in skin appearance, morphogenesis, immunity and behaviour. We found little overlap between the three populations, suggesting that the biological functions potentially influencing mate choice are population specific, in other words are culturally driven. Moreover, whenever the same functional category of genes showed a significant signal in two populations, different genes were actually involved, which suggests the possibility of evolutionary convergences. © 2011 Blackwell Publishing Ltd.

Role of Lipid Metabolism in Plant Pollen Exine Development.

PubMed

Zhang, Dabing; Shi, Jianxin; Yang, Xijia

2016-01-01

Pollen plays important roles in the life cycle of angiosperms plants. It acts as not only a biological protector of male sperms but also a communicator between the male and the female reproductive organs, facilitating pollination and fertilization. Pollen is produced within the anther, and covered by the specialized outer envelope, pollen wall. Although the morphology of pollen varies among different plant species, the pollen wall is mainly comprised of three layers: the pollen coat, the outer exine layer, and the inner intine layer. Except the intine layer, the other two layers are basically of lipidic nature. Particularly, the outer pollen wall layer, the exine, is a highly resistant biopolymer of phenylpropanoid and lipidic monomers covalently coupled by ether and ester linkages. The precise molecular mechanisms underlying pollen coat formation and exine patterning remain largely elusive. Herein, we summarize the current genetic, phenotypic and biochemical studies regarding to the pollen exine development and underlying molecular regulatory mechanisms mainly obtained from monocot rice (Oryza sativa) and dicot Arabidopsis thaliana, aiming to extend our understandings of plant male reproductive biology. Genes, enzymes/proteins and regulatory factors that appear to play conserved and diversified roles in lipid biosynthesis, transportation and modification during pollen exine formation, were highlighted.

A comparative study of biological and metabolic biomarkers between healthy individuals and patients with acne vulgaris

PubMed Central

Kim, Kyuseok; Ha, Injin; Kim, Eunok; Kim, Kyunglee

2017-01-01

Abstract Acne is a multifactorial dermatosis, which is influenced not only by hormones but also by the biochemical relationship between them and the pilosebaceous unit. Inflammatory cytokines, chemokines, active oxygen, and zinc are known to be associated with the development of acne. Further, steroid metabolism is known as one of the important factors related to sebum secretion and comedone formation in acne. However, there is a lack of studies comparing these human biomarkers between healthy individuals and patients with acne. In particular, no study has investigated the relationship between human biomarkers and patterns of acne yet. The purpose of this study is to investigate diagnostic human biomarkers in acne by comparing the biological and metabolic biomarkers between healthy individuals and patients with acne and identify the relationship between human biomarkers and patterns of acne. This study is a protocol for a cross-sectional study. Forty healthy participants and 60 patients with acne will be recruited at 1 center. We will collect their blood samples and analyze the molecular biological and metabolic biomarkers (cytokines, chemokines, reactive oxygen species, corticotropin-releasing hormone, zinc, amino acid, 1-carbon metabolite, lipid metabolite, etc.). Further, we will administer questionnaires regarding their diet, sleep, stress, and other factors relating to acne and measure their skin elasticity. The study protocol was approved by the Institutional Review Board of Oriental Medical Hospital at Kyung Hee Medical Center (KOMCIRB-161118-HR-062). Written informed consent will be obtained from all the participants. The trial was registered in the Clinical Research Information Service, Republic of Korea: KCT0002212. This trial will provide evidence regarding diagnostic human biomarkers in acne and the relationship between the human biomarkers and patterns of acne. PMID:29137071

A comparative study of biological and metabolic biomarkers between healthy individuals and patients with acne vulgaris: A cross-sectional study protocol.

PubMed

Kim, Kyuseok; Ha, Injin; Kim, Eunok; Kim, Kyunglee

2017-11-01

Acne is a multifactorial dermatosis, which is influenced not only by hormones but also by the biochemical relationship between them and the pilosebaceous unit. Inflammatory cytokines, chemokines, active oxygen, and zinc are known to be associated with the development of acne. Further, steroid metabolism is known as one of the important factors related to sebum secretion and comedone formation in acne. However, there is a lack of studies comparing these human biomarkers between healthy individuals and patients with acne. In particular, no study has investigated the relationship between human biomarkers and patterns of acne yet.The purpose of this study is to investigate diagnostic human biomarkers in acne by comparing the biological and metabolic biomarkers between healthy individuals and patients with acne and identify the relationship between human biomarkers and patterns of acne.This study is a protocol for a cross-sectional study. Forty healthy participants and 60 patients with acne will be recruited at 1 center. We will collect their blood samples and analyze the molecular biological and metabolic biomarkers (cytokines, chemokines, reactive oxygen species, corticotropin-releasing hormone, zinc, amino acid, 1-carbon metabolite, lipid metabolite, etc.). Further, we will administer questionnaires regarding their diet, sleep, stress, and other factors relating to acne and measure their skin elasticity.The study protocol was approved by the Institutional Review Board of Oriental Medical Hospital at Kyung Hee Medical Center (KOMCIRB-161118-HR-062). Written informed consent will be obtained from all the participants. The trial was registered in the Clinical Research Information Service, Republic of Korea: KCT0002212.This trial will provide evidence regarding diagnostic human biomarkers in acne and the relationship between the human biomarkers and patterns of acne.

The Dynamics of Visual Experience, an EEG Study of Subjective Pattern Formation

PubMed Central

Elliott, Mark A.; Twomey, Deirdre; Glennon, Mark

2012-01-01

Background Since the origin of psychological science a number of studies have reported visual pattern formation in the absence of either physiological stimulation or direct visual-spatial references. Subjective patterns range from simple phosphenes to complex patterns but are highly specific and reported reliably across studies. Methodology/Principal Findings Using independent-component analysis (ICA) we report a reduction in amplitude variance consistent with subjective-pattern formation in ventral posterior areas of the electroencephalogram (EEG). The EEG exhibits significantly increased power at delta/theta and gamma-frequencies (point and circle patterns) or a series of high-frequency harmonics of a delta oscillation (spiral patterns). Conclusions/Significance Subjective-pattern formation may be described in a way entirely consistent with identical pattern formation in fluids or granular flows. In this manner, we propose subjective-pattern structure to be represented within a spatio-temporal lattice of harmonic oscillations which bind topographically organized visual-neuronal assemblies by virtue of low frequency modulation. PMID:22292053

Integrating patterning signals: Wnt/GSK3 regulates the duration of the BMP/Smad1 signal.

PubMed

Fuentealba, Luis C; Eivers, Edward; Ikeda, Atsushi; Hurtado, Cecilia; Kuroda, Hiroki; Pera, Edgar M; De Robertis, Edward M

2007-11-30

BMP receptors determine the intensity of BMP signals via Smad1 C-terminal phosphorylations. Here we show that a finely controlled cell biological pathway terminates this activity. The duration of the activated pSmad1(Cter) signal was regulated by sequential Smad1 linker region phosphorylations at conserved MAPK and GSK3 sites required for its polyubiquitinylation and transport to the centrosome. Proteasomal degradation of activated Smad1 and total polyubiquitinated proteins took place in the centrosome. Inhibitors of the Erk, p38, and JNK MAPKs, as well as GSK3 inhibitors, prolonged the duration of a pulse of BMP7. Wnt signaling decreased pSmad1(GSK3) antigen levels and redistributed it from the centrosome to cytoplasmic LRP6 signalosomes. In Xenopus embryos, it was found that Wnts induce epidermis and that this required an active BMP-Smad pathway. Epistatic experiments suggested that the dorsoventral (BMP) and anteroposterior (Wnt/GSK3) patterning gradients are integrated at the level of Smad1 phosphorylations during embryonic pattern formation.

Defects formation and spiral waves in a network of neurons in presence of electromagnetic induction.

PubMed

Rostami, Zahra; Jafari, Sajad

2018-04-01

Complex anatomical and physiological structure of an excitable tissue (e.g., cardiac tissue) in the body can represent different electrical activities through normal or abnormal behavior. Abnormalities of the excitable tissue coming from different biological reasons can lead to formation of some defects. Such defects can cause some successive waves that may end up to some additional reorganizing beating behaviors like spiral waves or target waves. In this study, formation of defects and the resulting emitted waves in an excitable tissue are investigated. We have considered a square array network of neurons with nearest-neighbor connections to describe the excitable tissue. Fundamentally, electrophysiological properties of ion currents in the body are responsible for exhibition of electrical spatiotemporal patterns. More precisely, fluctuation of accumulated ions inside and outside of cell causes variable electrical and magnetic field. Considering undeniable mutual effects of electrical field and magnetic field, we have proposed the new Hindmarsh-Rose (HR) neuronal model for the local dynamics of each individual neuron in the network. In this new neuronal model, the influence of magnetic flow on membrane potential is defined. This improved model holds more bifurcation parameters. Moreover, the dynamical behavior of the tissue is investigated in different states of quiescent, spiking, bursting and even chaotic state. The resulting spatiotemporal patterns are represented and the time series of some sampled neurons are displayed, as well.

Theory of periodic swarming of bacteria: Application to Proteus mirabilis

NASA Astrophysics Data System (ADS)

Czirók, A.; Matsushita, M.; Vicsek, T.

2001-03-01

The periodic swarming of bacteria is one of the simplest examples for pattern formation produced by the self-organized collective behavior of a large number of organisms. In the spectacular colonies of Proteus mirabilis (the most common species exhibiting this type of growth), a series of concentric rings are developed as the bacteria multiply and swarm following a scenario that periodically repeats itself. We have developed a theoretical description for this process in order to obtain a deeper insight into some of the typical processes governing the phenomena in systems of many interacting living units. Our approach is based on simple assumptions directly related to the latest experimental observations on colony formation under various conditions. The corresponding one-dimensional model consists of two coupled differential equations investigated here both by numerical integrations and by analyzing the various expressions obtained from these equations using a few natural assumptions about the parameters of the model. We determine the phase diagram corresponding to systems exhibiting periodic swarming, and discuss in detail how the various stages of the colony development can be interpreted in our framework. We point out that all of our theoretical results are in excellent agreement with the complete set of available observations. Thus the present study represents one of the few examples where self-organized biological pattern formation is understood within a relatively simple theoretical approach, leading to results and predictions fully compatible with experiments.

Hydrophobic mismatch sorts SNARE proteins into distinct membrane domains

PubMed Central

Milovanovic, Dragomir; Honigmann, Alf; Koike, Seiichi; Göttfert, Fabian; Pähler, Gesa; Junius, Meike; Müllar, Stefan; Diederichsen, Ulf; Janshoff, Andreas; Grubmüller, Helmut; Risselada, Herre J.; Eggeling, Christian; Hell, Stefan W.; van den Bogaart, Geert; Jahn, Reinhard

2015-01-01

The clustering of proteins and lipids in distinct microdomains is emerging as an important principle for the spatial patterning of biological membranes. Such domain formation can be the result of hydrophobic and ionic interactions with membrane lipids as well as of specific protein–protein interactions. Here using plasma membrane-resident SNARE proteins as model, we show that hydrophobic mismatch between the length of transmembrane domains (TMDs) and the thickness of the lipid membrane suffices to induce clustering of proteins. Even when the TMDs differ in length by only a single residue, hydrophobic mismatch can segregate structurally closely homologous membrane proteins in distinct membrane domains. Domain formation is further fine-tuned by interactions with polyanionic phosphoinositides and homo and heterotypic protein interactions. Our findings demonstrate that hydrophobic mismatch contributes to the structural organization of membranes. PMID:25635869

Intercentrosomal angular separation during mitosis plays a crucial role for maintaining spindle stability

NASA Astrophysics Data System (ADS)

Sutradhar, S.; Basu, S.; Paul, R.

2015-10-01

Cell division through proper spindle formation is one of the key puzzles in cell biology. In most mammalian cells, chromosomes spontaneously arrange to achieve a stable bipolar spindle during metaphase which eventually ensures proper segregation of the DNA into the daughter cells. In this paper, we present a robust three-dimensional mechanistic model to investigate the formation and maintenance of a bipolar mitotic spindle in mammalian cells under different physiological constraints. Using realistic parameters, we test spindle viability by measuring the spindle length and studying the chromosomal configuration. The model strikingly predicts a feature of the spindle instability arising from the insufficient intercentrosomal angular separation and impaired sliding of the interpolar microtubules. In addition, our model successfully reproduces chromosomal patterns observed in mammalian cells, when activity of different motor proteins is perturbed.

Development and function of human cerebral cortex neural networks from pluripotent stem cells in vitro

PubMed Central

Kirwan, Peter; Turner-Bridger, Benita; Peter, Manuel; Momoh, Ayiba; Arambepola, Devika; Robinson, Hugh P. C.; Livesey, Frederick J.

2015-01-01

A key aspect of nervous system development, including that of the cerebral cortex, is the formation of higher-order neural networks. Developing neural networks undergo several phases with distinct activity patterns in vivo, which are thought to prune and fine-tune network connectivity. We report here that human pluripotent stem cell (hPSC)-derived cerebral cortex neurons form large-scale networks that reflect those found in the developing cerebral cortex in vivo. Synchronised oscillatory networks develop in a highly stereotyped pattern over several weeks in culture. An initial phase of increasing frequency of oscillations is followed by a phase of decreasing frequency, before giving rise to non-synchronous, ordered activity patterns. hPSC-derived cortical neural networks are excitatory, driven by activation of AMPA- and NMDA-type glutamate receptors, and can undergo NMDA-receptor-mediated plasticity. Investigating single neuron connectivity within PSC-derived cultures, using rabies-based trans-synaptic tracing, we found two broad classes of neuronal connectivity: most neurons have small numbers (<10) of presynaptic inputs, whereas a small set of hub-like neurons have large numbers of synaptic connections (>40). These data demonstrate that the formation of hPSC-derived cortical networks mimics in vivo cortical network development and function, demonstrating the utility of in vitro systems for mechanistic studies of human forebrain neural network biology. PMID:26395144

Simulating Microbial Community Patterning Using Biocellion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, Seung-Hwa; Kahan, Simon H.; Momeni, Babak

2014-04-17

Mathematical modeling and computer simulation are important tools for understanding complex interactions between cells and their biotic and abiotic environment: similarities and differences between modeled and observed behavior provide the basis for hypothesis forma- tion. Momeni et al. [5] investigated pattern formation in communities of yeast strains engaging in different types of ecological interactions, comparing the predictions of mathematical modeling and simulation to actual patterns observed in wet-lab experiments. However, simu- lations of millions of cells in a three-dimensional community are ex- tremely time-consuming. One simulation run in MATLAB may take a week or longer, inhibiting exploration of the vastmore » space of parameter combinations and assumptions. Improving the speed, scale, and accu- racy of such simulations facilitates hypothesis formation and expedites discovery. Biocellion is a high performance software framework for ac- celerating discrete agent-based simulation of biological systems with millions to trillions of cells. Simulations of comparable scale and accu- racy to those taking a week of computer time using MATLAB require just hours using Biocellion on a multicore workstation. Biocellion fur- ther accelerates large scale, high resolution simulations using cluster computers by partitioning the work to run on multiple compute nodes. Biocellion targets computational biologists who have mathematical modeling backgrounds and basic C++ programming skills. This chap- ter describes the necessary steps to adapt the original Momeni et al.'s model to the Biocellion framework as a case study.« less

Endogenous voltage gradients as mediators of cell-cell communication: strategies for investigating bioelectrical signals during pattern formation

PubMed Central

Adams, Dany S.; Levin, Michael

2013-01-01

Alongside the well-known chemical modes of cell-cell communication, we find an important and powerful system of bioelectrical signaling: changes in the resting voltage potential (Vmem) of the plasma membrane driven by ion channels, pumps and gap junctions. Slow Vmem changes in all cells serve as a highly conserved, information-bearing pathway that regulates cell proliferation, migration and differentiation. In embryonic and regenerative pattern formation and in the disorganization of neoplasia, bioelectrical cues serve as mediators of large-scale anatomical polarity, organ identity and positional information. Recent developments have resulted in tools that enable a high-resolution analysis of these biophysical signals and their linkage with upstream and downstream canonical genetic pathways. Here, we provide an overview for the study of bioelectric signaling, focusing on state-of-the-art approaches that use molecular physiology and developmental genetics to probe the roles of bioelectric events functionally. We highlight the logic, strategies and well-developed technologies that any group of researchers can employ to identify and dissect ionic signaling components in their own work and thus to help crack the bioelectric code. The dissection of bioelectric events as instructive signals enabling the orchestration of cell behaviors into large-scale coherent patterning programs will enrich on-going work in diverse areas of biology, as biophysical factors become incorporated into our systems-level understanding of cell interactions. PMID:22350846

Development and function of human cerebral cortex neural networks from pluripotent stem cells in vitro.

PubMed

Kirwan, Peter; Turner-Bridger, Benita; Peter, Manuel; Momoh, Ayiba; Arambepola, Devika; Robinson, Hugh P C; Livesey, Frederick J

2015-09-15

A key aspect of nervous system development, including that of the cerebral cortex, is the formation of higher-order neural networks. Developing neural networks undergo several phases with distinct activity patterns in vivo, which are thought to prune and fine-tune network connectivity. We report here that human pluripotent stem cell (hPSC)-derived cerebral cortex neurons form large-scale networks that reflect those found in the developing cerebral cortex in vivo. Synchronised oscillatory networks develop in a highly stereotyped pattern over several weeks in culture. An initial phase of increasing frequency of oscillations is followed by a phase of decreasing frequency, before giving rise to non-synchronous, ordered activity patterns. hPSC-derived cortical neural networks are excitatory, driven by activation of AMPA- and NMDA-type glutamate receptors, and can undergo NMDA-receptor-mediated plasticity. Investigating single neuron connectivity within PSC-derived cultures, using rabies-based trans-synaptic tracing, we found two broad classes of neuronal connectivity: most neurons have small numbers (<10) of presynaptic inputs, whereas a small set of hub-like neurons have large numbers of synaptic connections (>40). These data demonstrate that the formation of hPSC-derived cortical networks mimics in vivo cortical network development and function, demonstrating the utility of in vitro systems for mechanistic studies of human forebrain neural network biology. © 2015. Published by The Company of Biologists Ltd.

Crowning: a novel Escherichia coli colonizing behaviour generating a self-organized corona

PubMed Central

2014-01-01

Background Encased in a matrix of extracellular polymeric substances (EPS) composed of flagella, adhesins, amyloid fibers (curli), and exopolysaccharides (cellulose, β-1,6-N-acetyl-D-glucosamine polymer-PGA-, colanic acid), the bacteria Escherichia coli is able to attach to and colonize different types of biotic and abiotic surfaces forming biofilms and colonies of intricate morphological architectures. Many of the biological aspects that underlie the generation and development of these E. coli’s formations are largely poorly understood. Results Here, we report the characterization of a novel E. coli sessile behaviour termed "crowning" due to the bacterial generation of a new 3-D architectural pattern: a corona. This bacterial pattern is formed by joining bush-like multilayered "coronal flares or spikes" arranged in a ring, which self-organize through the growth, self-clumping and massive self-aggregation of cells tightly interacting inside semisolid agar on plastic surfaces. Remarkably, the corona’s formation is developed independently of the adhesiveness of the major components of E. coli’s EPS matrix, the function of chemotaxis sensory system, type 1 pili and the biofilm master regulator CsgD, but its formation is suppressed by flagella-driven motility and glucose. Intriguingly, this glucose effect on the corona development is not mediated by the classical catabolic repression system, the cyclic AMP (cAMP)-cAMP receptor protein (CRP) complex. Thus, corona formation departs from the canonical regulatory transcriptional core that controls biofilm formation in E. coli. Conclusions With this novel "crowning" activity, E. coli expands its repertoire of colonizing collective behaviours to explore, invade and exploit environments whose critical viscosities impede flagella driven-motility. PMID:24568619

21 CFR 601.14 - Regulatory submissions in electronic format.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 7 2012-04-01 2012-04-01 false Regulatory submissions in electronic format. 601... SERVICES (CONTINUED) BIOLOGICS LICENSING Biologics Licensing § 601.14 Regulatory submissions in electronic format. (a) General. Electronic format submissions must be in a form that FDA can process, review, and...

21 CFR 601.14 - Regulatory submissions in electronic format.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Regulatory submissions in electronic format. 601... SERVICES (CONTINUED) BIOLOGICS LICENSING Biologics Licensing § 601.14 Regulatory submissions in electronic format. (a) General. Electronic format submissions must be in a form that FDA can process, review, and...

21 CFR 601.14 - Regulatory submissions in electronic format.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 7 2014-04-01 2014-04-01 false Regulatory submissions in electronic format. 601... SERVICES (CONTINUED) BIOLOGICS LICENSING Biologics Licensing § 601.14 Regulatory submissions in electronic format. (a) General. Electronic format submissions must be in a form that FDA can process, review, and...

Spatio-temporal dynamics induced by competing instabilities in two asymmetrically coupled nonlinear evolution equations.

PubMed

Schüler, D; Alonso, S; Torcini, A; Bär, M

2014-12-01

Pattern formation often occurs in spatially extended physical, biological, and chemical systems due to an instability of the homogeneous steady state. The type of the instability usually prescribes the resulting spatio-temporal patterns and their characteristic length scales. However, patterns resulting from the simultaneous occurrence of instabilities cannot be expected to be simple superposition of the patterns associated with the considered instabilities. To address this issue, we design two simple models composed by two asymmetrically coupled equations of non-conserved (Swift-Hohenberg equations) or conserved (Cahn-Hilliard equations) order parameters with different characteristic wave lengths. The patterns arising in these systems range from coexisting static patterns of different wavelengths to traveling waves. A linear stability analysis allows to derive a two parameter phase diagram for the studied models, in particular, revealing for the Swift-Hohenberg equations, a co-dimension two bifurcation point of Turing and wave instability and a region of coexistence of stationary and traveling patterns. The nonlinear dynamics of the coupled evolution equations is investigated by performing accurate numerical simulations. These reveal more complex patterns, ranging from traveling waves with embedded Turing patterns domains to spatio-temporal chaos, and a wide hysteretic region, where waves or Turing patterns coexist. For the coupled Cahn-Hilliard equations the presence of a weak coupling is sufficient to arrest the coarsening process and to lead to the emergence of purely periodic patterns. The final states are characterized by domains with a characteristic length, which diverges logarithmically with the coupling amplitude.

Global stability and pattern formation in a nonlocal diffusive Lotka-Volterra competition model

NASA Astrophysics Data System (ADS)

Ni, Wenjie; Shi, Junping; Wang, Mingxin

2018-06-01

A diffusive Lotka-Volterra competition model with nonlocal intraspecific and interspecific competition between species is formulated and analyzed. The nonlocal competition strength is assumed to be determined by a diffusion kernel function to model the movement pattern of the biological species. It is shown that when there is no nonlocal intraspecific competition, the dynamics properties of nonlocal diffusive competition problem are similar to those of classical diffusive Lotka-Volterra competition model regardless of the strength of nonlocal interspecific competition. Global stability of nonnegative constant equilibria are proved using Lyapunov or upper-lower solution methods. On the other hand, strong nonlocal intraspecific competition increases the system spatiotemporal dynamic complexity. For the weak competition case, the nonlocal diffusive competition model may possess nonconstant positive equilibria for some suitably large nonlocal intraspecific competition coefficients.

On the role of sparseness in the evolution of modularity in gene regulatory networks

PubMed Central

2018-01-01

Modularity is a widespread property in biological systems. It implies that interactions occur mainly within groups of system elements. A modular arrangement facilitates adjustment of one module without perturbing the rest of the system. Therefore, modularity of developmental mechanisms is a major factor for evolvability, the potential to produce beneficial variation from random genetic change. Understanding how modularity evolves in gene regulatory networks, that create the distinct gene activity patterns that characterize different parts of an organism, is key to developmental and evolutionary biology. One hypothesis for the evolution of modules suggests that interactions between some sets of genes become maladaptive when selection favours additional gene activity patterns. The removal of such interactions by selection would result in the formation of modules. A second hypothesis suggests that modularity evolves in response to sparseness, the scarcity of interactions within a system. Here I simulate the evolution of gene regulatory networks and analyse diverse experimentally sustained networks to study the relationship between sparseness and modularity. My results suggest that sparseness alone is neither sufficient nor necessary to explain modularity in gene regulatory networks. However, sparseness amplifies the effects of forms of selection that, like selection for additional gene activity patterns, already produce an increase in modularity. That evolution of new gene activity patterns is frequent across evolution also supports that it is a major factor in the evolution of modularity. That sparseness is widespread across gene regulatory networks indicates that it may have facilitated the evolution of modules in a wide variety of cases. PMID:29775459

On the role of sparseness in the evolution of modularity in gene regulatory networks.

PubMed

Espinosa-Soto, Carlos

2018-05-01

Modularity is a widespread property in biological systems. It implies that interactions occur mainly within groups of system elements. A modular arrangement facilitates adjustment of one module without perturbing the rest of the system. Therefore, modularity of developmental mechanisms is a major factor for evolvability, the potential to produce beneficial variation from random genetic change. Understanding how modularity evolves in gene regulatory networks, that create the distinct gene activity patterns that characterize different parts of an organism, is key to developmental and evolutionary biology. One hypothesis for the evolution of modules suggests that interactions between some sets of genes become maladaptive when selection favours additional gene activity patterns. The removal of such interactions by selection would result in the formation of modules. A second hypothesis suggests that modularity evolves in response to sparseness, the scarcity of interactions within a system. Here I simulate the evolution of gene regulatory networks and analyse diverse experimentally sustained networks to study the relationship between sparseness and modularity. My results suggest that sparseness alone is neither sufficient nor necessary to explain modularity in gene regulatory networks. However, sparseness amplifies the effects of forms of selection that, like selection for additional gene activity patterns, already produce an increase in modularity. That evolution of new gene activity patterns is frequent across evolution also supports that it is a major factor in the evolution of modularity. That sparseness is widespread across gene regulatory networks indicates that it may have facilitated the evolution of modules in a wide variety of cases.

Coconut as a Medium for the Experimental Production of Aflatoxin

PubMed Central

Arseculeratne, S. N.; De Silva, L. M.; Wijesundera, S.; Bandunatha, C. H. S. R.

1969-01-01

Fresh, grated coconut has been found to be an excellent medium for aflatoxin production by Aspergillus flavus. Under optimal conditions, yields of 8 mg of total aflatoxin per g of substrate were obtained. Continuous agitation of the growth medium under moist conditions at 24 C produced highest yields. Aflatoxin was assayed both biologically and chromatographically. The aflatoxin content of cultures varied biphasically with the duration of incubation. It is suggested that this pattern could result from the sequential operation of factors promoting aflatoxin formation on the one hand and a detoxifying mechanism on the other. Images PMID:5803632

Intratumoral heterogeneity of the epigenome

PubMed Central

Song, Jun S.; Costello, Joseph F.

2016-01-01

Investigation into intratumoral heterogeneity (ITH) of the epigenome is in a formative stage. The patterns of tumor evolution inferred from epigenetic ITH and genetic ITH are remarkably similar, suggesting widespread co-dependency of these disparate mechanisms. The biological and clinical relevance of epigenetic ITH are becoming more apparent. Rare tumor cells with unique and reversible epigenetic states may drive drug resistance, and the degree of epigenetic ITH at diagnosis may predict patient outcome. This perspective presents these current concepts and clinical implications of epigenetic ITH, and the experimental and computational techniques at the forefront of ITH exploration. PMID:27070699

A Method to Categorize 2-Dimensional Patterns Using Statistics of Spatial Organization.

PubMed

López-Sauceda, Juan; Rueda-Contreras, Mara D

2017-01-01

We developed a measurement framework of spatial organization to categorize 2-dimensional patterns from 2 multiscalar biological architectures. We propose that underlying shapes of biological entities can be approached using the statistical concept of degrees of freedom, defining it through expansion of area variability in a pattern. To help scope this suggestion, we developed a mathematical argument recognizing the deep foundations of area variability in a polygonal pattern (spatial heterogeneity). This measure uses a parameter called eutacticity . Our measuring platform of spatial heterogeneity can assign particular ranges of distribution of spatial areas for 2 biological architectures: ecological patterns of Namibia fairy circles and epithelial sheets. The spatial organizations of our 2 analyzed biological architectures are demarcated by being in a particular position among spatial order and disorder. We suggest that this theoretical platform can give us some insights about the nature of shapes in biological systems to understand organizational constraints.

Clustering change patterns using Fourier transformation with time-course gene expression data.

PubMed

Kim, Jaehee

2011-01-01

To understand the behavior of genes, it is important to explore how the patterns of gene expression change over a period of time because biologically related gene groups can share the same change patterns. In this study, the problem of finding similar change patterns is induced to clustering with the derivative Fourier coefficients. This work is aimed at discovering gene groups with similar change patterns which share similar biological properties. We developed a statistical model using derivative Fourier coefficients to identify similar change patterns of gene expression. We used a model-based method to cluster the Fourier series estimation of derivatives. We applied our model to cluster change patterns of yeast cell cycle microarray expression data with alpha-factor synchronization. It showed that, as the method clusters with the probability-neighboring data, the model-based clustering with our proposed model yielded biologically interpretable results. We expect that our proposed Fourier analysis with suitably chosen smoothing parameters could serve as a useful tool in classifying genes and interpreting possible biological change patterns.

Desiccation of a pool of blood: from fluid mechanics to forensic investigations

NASA Astrophysics Data System (ADS)

Nicloux, Celine; Brutin, David

2012-11-01

The evaporation of biological fluids (with droplet configuration) has been studied since a few years due to several applications in medical fields such as medical tests, drug screening, biostabilization... The evaporation of a drop of whole blood leads to the formation of final typical pattern of cracks. Flow motion, adhesion, gelation and fracturation all occur during the evaporation of this complex matter. During the drying, a sol-gel transition develops. The evaporation of a pool of blood is studied in order to link the pattern formation and the evaporation dynamics. We intend to transfer the knowledge acquired for drops on pool to improve the forensic investigations. In this study, we focus on both pool of blood and pure water to determine the transition region from drop to pool and then to characterize the evaporation rate in the pool configuration. The spreading of blood which can be seen as a complex fluid is strongly influenced the substrate nature. The initial contact angle of blood on different substrate nature will influence the maximum thickness of the layer and then will influence the evaporation mass flux. The authors gratefully acknowledge the help and the fruitful discussions raised with A. Boccoz.

A Topological Paradigm for Hippocampal Spatial Map Formation Using Persistent Homology

PubMed Central

Dabaghian, Y.; Mémoli, F.; Frank, L.; Carlsson, G.

2012-01-01

An animal's ability to navigate through space rests on its ability to create a mental map of its environment. The hippocampus is the brain region centrally responsible for such maps, and it has been assumed to encode geometric information (distances, angles). Given, however, that hippocampal output consists of patterns of spiking across many neurons, and downstream regions must be able to translate those patterns into accurate information about an animal's spatial environment, we hypothesized that 1) the temporal pattern of neuronal firing, particularly co-firing, is key to decoding spatial information, and 2) since co-firing implies spatial overlap of place fields, a map encoded by co-firing will be based on connectivity and adjacency, i.e., it will be a topological map. Here we test this topological hypothesis with a simple model of hippocampal activity, varying three parameters (firing rate, place field size, and number of neurons) in computer simulations of rat trajectories in three topologically and geometrically distinct test environments. Using a computational algorithm based on recently developed tools from Persistent Homology theory in the field of algebraic topology, we find that the patterns of neuronal co-firing can, in fact, convey topological information about the environment in a biologically realistic length of time. Furthermore, our simulations reveal a “learning region” that highlights the interplay between the parameters in combining to produce hippocampal states that are more or less adept at map formation. For example, within the learning region a lower number of neurons firing can be compensated by adjustments in firing rate or place field size, but beyond a certain point map formation begins to fail. We propose that this learning region provides a coherent theoretical lens through which to view conditions that impair spatial learning by altering place cell firing rates or spatial specificity. PMID:22912564

Calcium-dependent depletion zones in the cortical microtubule array coincide with sites of, but do not regulate, wall ingrowth papillae deposition in epidermal transfer cells.

PubMed

Zhang, Hui-ming; Talbot, Mark J; McCurdy, David W; Patrick, John W; Offler, Christina E

2015-09-01

Trans-differentiation to a transfer-cell morphology is characterized by the localized deposition of wall ingrowth papillae that protrude into the cytosol. Whether the cortical microtubule array directs wall ingrowth papillae formation was investigated using a Vicia faba cotyledon culture system in which their adaxial epidermal cells were spontaneously induced to trans-differentiate to transfer cells. During deposition of wall ingrowth papillae, the aligned cortical microtubule arrays in precursor epidermal cells were reorganized into a randomized array characterized by circular depletion zones. Concurrence of the temporal appearance, spatial pattern, and size of depletion zones and wall ingrowth papillae was consistent with each papilla occupying a depletion zone. Surprisingly, microtubules appeared not to regulate construction of wall ingrowth papillae, as neither depolymerization nor stabilization of cortical microtubules changed their deposition pattern or morphology. Moreover, the size and spatial pattern of depletion zones was unaltered when the formation of wall ingrowth papillae was blocked by inhibiting cellulose biosynthesis. In contrast, the depletion zones were absent when the cytosolic calcium plumes, responsible for directing wall ingrowth papillae formation, were blocked or dissipated. Thus, we conclude that the depletion zones within the cortical microtubule array result from localized depolymerization of microtubules initiated by elevated cytosolic Ca(2+) levels at loci where wall ingrowth papillae are deposited. The physiological significance of the depletion zones as a mechanism to accommodate the construction of wall ingrowth papillae without compromising maintenance of the plasma membrane-microtubule inter-relationship is discussed. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Recent advances in symmetric and network dynamics

NASA Astrophysics Data System (ADS)

Golubitsky, Martin; Stewart, Ian

2015-09-01

We summarize some of the main results discovered over the past three decades concerning symmetric dynamical systems and networks of dynamical systems, with a focus on pattern formation. In both of these contexts, extra constraints on the dynamical system are imposed, and the generic phenomena can change. The main areas discussed are time-periodic states, mode interactions, and non-compact symmetry groups such as the Euclidean group. We consider both dynamics and bifurcations. We summarize applications of these ideas to pattern formation in a variety of physical and biological systems, and explain how the methods were motivated by transferring to new contexts René Thom's general viewpoint, one version of which became known as "catastrophe theory." We emphasize the role of symmetry-breaking in the creation of patterns. Topics include equivariant Hopf bifurcation, which gives conditions for a periodic state to bifurcate from an equilibrium, and the H/K theorem, which classifies the pairs of setwise and pointwise symmetries of periodic states in equivariant dynamics. We discuss mode interactions, which organize multiple bifurcations into a single degenerate bifurcation, and systems with non-compact symmetry groups, where new technical issues arise. We transfer many of the ideas to the context of networks of coupled dynamical systems, and interpret synchrony and phase relations in network dynamics as a type of pattern, in which space is discretized into finitely many nodes, while time remains continuous. We also describe a variety of applications including animal locomotion, Couette-Taylor flow, flames, the Belousov-Zhabotinskii reaction, binocular rivalry, and a nonlinear filter based on anomalous growth rates for the amplitude of periodic oscillations in a feed-forward network.

DETERMINATION OF APPARENT QUANTUM YIELD SPECTRA FOR THE FORMATION OF BIOLOGICALLY LABILE PHOTOPRODUCTS

EPA Science Inventory

Quantum yield spectra for the photochemical formation of biologically labile photoproducts from dissolved organic matter (DOM) have not been available previously, although they would greatly facilitate attempts to model photoproduct formation rates across latitudinal, seasonal, a...

Finger-like pattern formation in dilute surfactant pentaethylene glycol monododecyl ether solutions.

PubMed

Kubo, Yoshihide; Yokoyama, Yasuhiro; Tanaka, Shinpei

2013-04-07

We report here peculiar finger-like patterns observed during the phase separation process of dilute micellar pentaethylene glycol monododecyl ether solutions. The patterns were composed of parallel and periodic threads of micelle-rich domains. Prior to this pattern formation, the phase separation always started with the appearance of water-rich domains rimmed by the micelle-rich domains. It was found that these rims played a significant role in the pattern formation. We explain this pattern formation using a simple simulation model with disconnectable springs. The simulation results suggested that the spatially inhomogeneous elasticity or connectivity of a transient gel of worm-like micelles was responsible for the rim formation. The rims thus formed lead rim-induced nucleation, growth, and elongation of the domains owing to their small mobility and the elastic frustration around them. These rim-induced processes eventually produce the observed finger-like patterns.

Hydrology or biology? Modeling simplistic physical constraints on lake carbon biogeochemistry to identify when and where biology is likely to matter

NASA Astrophysics Data System (ADS)

Jones, S.; Zwart, J. A.; Solomon, C.; Kelly, P. T.

2017-12-01

Current efforts to scale lake carbon biogeochemistry rely heavily on empirical observations and rarely consider physical or biological inter-lake heterogeneity that is likely to regulate terrestrial dissolved organic carbon (tDOC) decomposition in lakes. This may in part result from a traditional focus of lake ecologists on in-lake biological processes OR physical-chemical pattern across lake regions, rather than on process AND pattern across scales. To explore the relative importance of local biological processes and physical processes driven by lake hydrologic setting, we created a simple, analytical model of tDOC decomposition in lakes that focuses on the regulating roles of lake size and catchment hydrologic export. Our simplistic model can generally recreate patterns consistent with both local- and regional-scale patterns in tDOC concentration and decomposition. We also see that variation in lake hydrologic setting, including the importance of evaporation as a hydrologic export, generates significant, emergent variation in tDOC decomposition at a given hydrologic residence time, and creates patterns that have been historically attributed to variation in tDOC quality. Comparing predictions of this `biologically null model' to field observations and more biologically complex models could indicate when and where biology is likely to matter most.

Bioconvective patterns, synchrony, and survival. [in light-limited growth model of motile algae culture

NASA Technical Reports Server (NTRS)

Noever, David A.

1990-01-01

With and without bioconvective pattern formation, a theoretical model predicts growth in light-limited cultures of motile algae. At the critical density for pattern formation, the resulting doubly exponential population curves show an inflection. Such growth corresponds quantitatively to experiments in mechanically unstirred cultures. This attaches survival value to synchronized pattern formation.

Pattern dynamics of the reaction-diffusion immune system.

PubMed

Zheng, Qianqian; Shen, Jianwei; Wang, Zhijie

2018-01-01

In this paper, we will investigate the effect of diffusion, which is ubiquitous in nature, on the immune system using a reaction-diffusion model in order to understand the dynamical behavior of complex patterns and control the dynamics of different patterns. Through control theory and linear stability analysis of local equilibrium, we obtain the optimal condition under which the system loses stability and a Turing pattern occurs. By combining mathematical analysis and numerical simulation, we show the possible patterns and how these patterns evolve. In addition, we establish a bridge between the complex patterns and the biological mechanism using the results from a previous study in Nature Cell Biology. The results in this paper can help us better understand the biological significance of the immune system.

Recent Advances in the Chemical Biology of Nitroxyl (HNO) Detection and Generation

PubMed Central

Miao, Zhengrui; King, S. Bruce

2016-01-01

Nitroxyl or azanone (HNO) represents the redox-related (one electron reduced and protonated) relative of the well-known biological signaling molecule nitric oxide (NO). Despite the close structural similarity to NO, defined biological roles and endogenous formation of HNO remain unclear due to the high reactivity of HNO with itself, soft nucleophiles and transition metals. While significant work has been accomplished in terms of the physiology, biology and chemistry of HNO, important and clarifying work regarding HNO detection and formation has occurred within the last 10 years. This review summarizes advances in the areas of HNO detection and donation and their application to normal and pathological biology. Such chemical biological tools allow a deeper understanding of biological HNO formation and the role that HNO plays in a variety of physiological systems. PMID:27108951

Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells.

PubMed

Biase, Fernando H; Kimble, Katelyn M

2018-05-10

The maturation and successful acquisition of developmental competence by an oocyte, the female gamete, during folliculogenesis is highly dependent on molecular interactions with somatic cells. Most of the cellular interactions identified, thus far, are modulated by growth factors, ions or metabolites. We hypothesized that this interaction is also modulated at the transcriptional level, which leads to the formation of gene regulatory networks between the oocyte and cumulus cells. We tested this hypothesis by analyzing transcriptome data from single oocytes and the surrounding cumulus cells collected from antral follicles employing an analytical framework to determine interdependencies at the transcript level. We overlapped our transcriptome data with putative protein-protein interactions and identified hundreds of ligand-receptor pairs that can transduce paracrine signaling between an oocyte and cumulus cells. We determined that 499 ligand-encoding genes expressed in oocytes and cumulus cells are functionally associated with transcription regulation (FDR < 0.05). Ligand-encoding genes with specific expression in oocytes or cumulus cells were enriched for biological functions that are likely associated with the coordinated formation of transzonal projections from cumulus cells that reach the oocyte's membrane. Thousands of gene pairs exhibit significant linear co-expression (absolute correlation > 0.85, FDR < 1.8 × 10 - 5 ) patterns between oocytes and cumulus cells. Hundreds of co-expressing genes showed clustering patterns associated with biological functions (FDR < 0.5) necessary for a coordinated function between the oocyte and cumulus cells during folliculogenesis (i.e. regulation of transcription, translation, apoptosis, cell differentiation and transport). Our analyses revealed a complex and functional gene regulatory circuit between the oocyte and surrounding cumulus cells. The regulatory profile of each cumulus-oocyte complex is likely associated with the oocytes' developmental potential to derive an embryo.

Pattern formation in rotating Bénard convection

NASA Astrophysics Data System (ADS)

Fantz, M.; Friedrich, R.; Bestehorn, M.; Haken, H.

1992-12-01

Using an extension of the Swift-Hohenberg equation we study pattern formation in the Bénard experiment close to the onset of convection in the case of rotating cylindrical fluid containers. For small Taylor numbers we emphasize the existence of slowly rotating patterns and describe behaviour exhibiting defect motion. Finally, we study pattern formation close to the Küppers-Lortz instability. The instability is nucleated at defects and proceeds through front propagation into the bulk patterns.

Vegetation pattern formation in semiarid systems induced by long-range competition in the absence of facilitation mechanisms.

NASA Astrophysics Data System (ADS)

Martinez-Garcia, Ricardo; Calabrese, Justin M.; Hernandez-Garcia, Emilio; Lopez, Cristobal

2014-05-01

Regular patterns and spatial organization of vegetation have been observed in many arid and semiarid ecosystems worldwide, covering a diverse range of plant taxa and soil types. A key common ingredient in these systems is that plant growth is severely limited by water availability, and thus plants likely compete strongly for water. The study of such patterns is especially interesting because their features may reveal much about the underlying physical and biological processes that generated them in addition to giving information on the characteristics of the ecosystem. It is possible, for instance, to infer their resilience against anthropogenic disturbances or climatic changes that could cause abrupt shifts in the system and lead it to a desert state. Therefore much research has focused on identifying the underlying mechanisms that can produce spatial patterning in water-limited systems (Klausmeier, 1999). They are believed to arise from the interplay between long-range competition and facilitation processes acting at smaller distances (Borgogno et al., 2009). This combination of mechanisms is justified by arguing that water percolates more readily through the soil in vegetated areas (short range), and that plants compete for water resources over greater distances via long lateral roots (long range). However, recent studies have shown that even in the limit of local facilitation patterns may still appear (Martinez-Garcia et al., 2013). In this work (Martinez-Garcia et al., 2013b), we show that, under rather general conditions, long-range competition alone is the minimal ingredient to shape gapped and stripped vegetation patterns typical of models that also account for facilitation in addition to competition. To this end we propose a simple, general model for the dynamics of vegetation, which includes only long-range competition between plants. Competition is introduced through a nonlocal term, where the kernel function quantifies the intensity of the interaction and its range. When the finite range of the competitive interaction is considered used kernel functions with a finite range, whose Fourier transform may have negative values, patterns emerge in the system. This is a rather general condition if we consider the finite length of the roots responsible of long-range competition for water in plant ecosystems.Therefore, our findings support the notion that, under fairly broad conditions, only competition is required for patterns to occur and suggest that the role of short-range facilitation mechanisms may not be as fundamental to pattern formation as has previously been thought. REFERENCES: C.A. Klausmeier, Science, 284, 1826-1828 (1999). F. Borgogno, P. D'Odorico, F. Laio and L. Ridolfi, Reviews of Geophysics, 4, RG1005 (2009). R. Martinez-Garcia, J.M. Calabrese, and C. Lopez, Journal of Theoretical Biology, 333, 156-165 (2013). R. Martinez-Garcia, J. M. Calabrese, E. Hernandez-Garcia, and C. Lopez, Geophysical Research Letters, 40, 6143-6147,(2013).

Dynamic pathway modeling of signal transduction networks: a domain-oriented approach.

PubMed

Conzelmann, Holger; Gilles, Ernst-Dieter

2008-01-01

Mathematical models of biological processes become more and more important in biology. The aim is a holistic understanding of how processes such as cellular communication, cell division, regulation, homeostasis, or adaptation work, how they are regulated, and how they react to perturbations. The great complexity of most of these processes necessitates the generation of mathematical models in order to address these questions. In this chapter we provide an introduction to basic principles of dynamic modeling and highlight both problems and chances of dynamic modeling in biology. The main focus will be on modeling of s transduction pathways, which requires the application of a special modeling approach. A common pattern, especially in eukaryotic signaling systems, is the formation of multi protein signaling complexes. Even for a small number of interacting proteins the number of distinguishable molecular species can be extremely high. This combinatorial complexity is due to the great number of distinct binding domains of many receptors and scaffold proteins involved in signal transduction. However, these problems can be overcome using a new domain-oriented modeling approach, which makes it possible to handle complex and branched signaling pathways.

PREFACE: Scales of understanding in biological development Scales of understanding in biological development

NASA Astrophysics Data System (ADS)

Newman, Timothy

2011-08-01

The development of an adult organism from a fertilized egg remains one of the deep mysteries of biology. Great strides have been made in the past three decades, primarily through ever more sophisticated genetic analyses and the advent of live-cell imaging, yet the underlying principles governing development are elusive. Recently, a new generation of biological physicists has entered the field, attracted by the hallmarks of development— coordinated dynamics and pattern formation arising from cell-cell interactions—which reflect tantalizing analogs with many-body systems in condensed matter physics and related fields. There have been corresponding influxes of researchers from other quantitative disciplines. With new workers come new questions and foci at different scales in space, time and complexity. The reductionist philosophy of developmental genetics has become increasingly complemented by a search for effective mechanisms at higher scales, a strategy which has a proven track record of success in the study of complex systems in physics. Are there new and universal mechanisms of development, supra-genetic in nature, waiting to be discovered by focusing on higher scales, or is development fundamentally the intricately scripted unfolding of complex genetic instructions? In this special focus issue of Physical Biology, we present cutting-edge research into embryo development from a broad spectrum of groups representing cell and developmental biology, biological physics, bioengineering and biomathematics. We are provided with a sense of how this multidisciplinary community views the fundamental issue of scale in development and are given some excellent examples of how we can bridge these scales through interdisciplinary collaboration, in order to create new levels of understanding. We start with two reviews which will provide newcomers with a guide to some of the outstanding questions in the field. Winklbauer and Müller use the phenomenon of mesoderm spreading as a platform to discuss the fascinating challenge of connecting cell-level behaviours to tissue-scale dynamics, thereby putting meat on the bones of traditional physical metaphors of 'the embryonic tissue as a material'. A fresh look at natural variation in embryonic phenotypes through the lens of physics, especially mechanics, is provided by von Dassow and Davidson. They stress the importance of environmental scales in providing both physical challenges and an evolutionary backdrop for robust development. The next two papers are concerned with the crucial role of signalling in morphogenesis. Zartman et al study in detail a stage of oogenesis in Drosophila, and show how quantitative experimental determination of pattern formation can be used as a stringent test of proposed underlying molecular mechanisms; in turn, they show how such selected mechanisms can thereafter be tested by newly designed experiments. Streichan et al consider collective cell motion in the zebrafish embryo. They propose an elegant theoretical mechanism to explain how directed collective cell motion can be generated in a uniform signalling landscape through a non-linear chemotactic feedback loop, and propose experimental tests of this idea. The next two papers describe state-of-the-art spatio-temporal quantification of whole embryo dynamics with cell-level resolution. Fernandez-Gonzalez and Zallen study the fascinating phenomenon of cell surface oscillations during axis elongation in Drosophila. They use a newly designed computer algorithm to measure spatio-temporal statistics of the oscillations and connect this information to intracellular actomyosin dynamics. Szabó et al study extracellular matrix (ECM) dynamics during primitive streak extension in the avian embryo. Using computer tracking and analysis they are able to measure spatial and temporal correlations of the ECM during development and use this data to inform the crucial, yet poorly understood, role of cell-ECM interactions. The last two papers are companion articles by Sandersius et al. The first paper describes the integration of active subcellular dynamics into an existing multicellular simulation algorithm. The resulting algorithm, which is parameterized at length and time scales of microns and seconds, is capable of reproducing various experimentally observed phenotypes at significantly higher scales, namely large-strain cell stretching, effective viscosity of embryonic epithelia and streaming patterns of collective cell motion within tissues. The second paper uses this new algorithm to quantitatively test the hypothesis that a dipolar arrangement of chemotactic sources is capable of driving primitive streak formation in amniotes. The hypothesis is found to be consistent with experimental data on cell movement patterns and quantitative estimates are given for the robustness of the chemotaxis mechanism. Is the simplest model of an embryo an embryo? Alternatively, are there higher scales of understanding that will provide predictive and powerful new insights into development? We hope this special focus issue of Physical Biology will provide a snapshot of how quantitative and interdisciplinary approaches are helping to answer these fundamental questions.

Anomalously enhanced hydration of aqueous electrolyte solution in hydrophobic carbon nanotubes to maintain stability.

PubMed

Ohba, Tomonori

2014-02-24

An understanding of the structure and behavior of electrolyte solutions in nanoenvironements is crucial not only for a wide variety of applications, but also for the development of physical, chemical, and biological processes. We demonstrate the structure and stability of electrolyte in carbon nanotubes using hybrid reverse Monte Carlo simulations of X-ray diffraction patterns. Hydrogen bonds between water are adequately formed in carbon nanotubes, although some hydrogen bonds are restricted by the interfaces of carbon nanotubes. The hydrogen bonding network of water in electrolyte in the carbon nanotubes is further weakened. On the other hand, formation of the ion hydration shell is significantly enhanced in the electrolyte in the carbon nanotubes in comparison to ion hydration in bulk electrolyte. The significant hydrogen bond and hydration shell formation are a result of gaining stability in the hydrophobic nanoenvironment. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Regioselective Galactofuranosylation for the Synthesis of Disaccharide Patterns Found in Pathogenic Microorganisms.

PubMed

Legentil, Laurent; Cabezas, Yari; Tasseau, Olivier; Tellier, Charles; Daligault, Franck; Ferrières, Vincent

2017-07-21

Koenigs-Knorr glycosylation of acceptors with more than one free hydroxyl group by 2,3,5,6-tetrabenzoyl galactofuranosyl bromide was performed using diphenylborinic acid 2-aminoethyl ester (DPBA) as inducer of regioselectivity. High regioselectivity for the glycosylation on the equatorial hydroxyl group of the acceptor was obtained thanks to the transient formation of a borinate adduct of the corresponding 1,2-cis diol. Nevertheless formation of orthoester byproducts hampered the efficiency of the method. Interestingly electron-withdrawing groups on O-6 or on C-1 of the acceptor displaced the reaction in favor of the desired galactofuranosyl containing disaccharide. The best yield was obtained for the furanosylation of p-nitrophenyl 6-O-acetyl mannopyranoside. Precursors of other disaccharides, found in the glycocalix of some pathogens, were synthesized according to the same protocol with yields ranging from 45 to 86%. This is a good alternative for the synthesis of biologically relevant glycoconjugates.

Interdependency of formation and localisation of the Min complex controls symmetric plastid division.

PubMed

Maple, Jodi; Møller, Simon G

2007-10-01

Plastid division represents a fundamental biological process essential for plant development; however, the molecular basis of symmetric plastid division is unclear. AtMinE1 plays a pivotal role in selection of the plastid division site in concert with AtMinD1. AtMinE1 localises to discrete foci in chloroplasts and interacts with AtMinD1, which shows a similar localisation pattern. Here, we investigate the importance of Min protein complex formation during the chloroplast division process. Dissection of the assembly of the Min protein complex and determination of the interdependency of complex assembly and localisation in planta allow us to present a model of the molecular basis of selection of the division site in plastids. Moreover, functional analysis of AtMinE1 in bacteria demonstrates the level of functional conservation and divergence of the plastidic MinE proteins.

Meeting report: advancing practical applications of biodiversity ontologies

PubMed Central

2014-01-01

We describe the outcomes of three recent workshops aimed at advancing development of the Biological Collections Ontology (BCO), the Population and Community Ontology (PCO), and tools to annotate data using those and other ontologies. The first workshop gathered use cases to help grow the PCO, agreed upon a format for modeling challenging concepts such as ecological niche, and developed ontology design patterns for defining collections of organisms and population-level phenotypes. The second focused on mapping datasets to ontology terms and converting them to Resource Description Framework (RDF), using the BCO. To follow-up, a BCO hackathon was held concurrently with the 16th Genomics Standards Consortium Meeting, during which we converted additional datasets to RDF, developed a Material Sample Core for the Global Biodiversity Information Framework, created a Web Ontology Language (OWL) file for importing Darwin Core classes and properties into BCO, and developed a workflow for converting biodiversity data among formats.

Grouping of multicopper oxidases in Lentinula edodes by sequence similarities and expression patterns.

PubMed

Sakamoto, Yuichi; Nakade, Keiko; Yoshida, Kentaro; Natsume, Satoshi; Miyazaki, Kazuhiro; Sato, Shiho; van Peer, Arend F; Konno, Naotake

2015-12-01

The edible white rot fungus Lentinula edodes possesses a variety of lignin degrading enzymes such as manganese peroxidases and laccases. Laccases belong to the multicopper oxidases, which have a wide range of catalytic activities including polyphenol degradation and synthesis, lignin degradation, and melanin formation. The exact number of laccases in L. edodes is unknown, as are their complete properties and biological functions. We analyzed the draft genome sequence of L. edodes D703PP-9 and identified 13 multicopper oxidase-encoding genes; 11 laccases in sensu stricto, of which three are new, and two ferroxidases. lcc8, a laccase previously reported in L. edodes, was not identified in D703PP-9 genome. Phylogenetic analysis showed that the 13 multicopper oxidases can be classified into laccase sensu stricto subfamily 1, laccase sensu stricto subfamily 2 and ferroxidases. From sequence similarities and expression patterns, laccase sensu stricto subfamily 1 can be divided into two subgroups. Laccase sensu stricto subfamily 1 group A members are mainly secreted from mycelia, while laccase sensu stricto subfamily 1 group B members are expressed mainly in fruiting bodies during growth or after harvesting but are lowly expressed in mycelia. Laccase sensu stricto subfamily 2 members are mainly expressed in mycelia, and two ferroxidases are mainly expressed in the fruiting body during growth or after harvesting, and are expressed at very low levels in mycelium. Our data suggests that L. edodes laccases in same group share expression patterns and would have common biological functions.

Evolutionary transition from biological to social systems via generation of reflexive models of externality.

PubMed

Igamberdiev, Abir U

2017-12-01

Evolutionary transition from biological to social systems corresponds to the emergence of the structure of subject that incorporates the internal image of the external world. This structure, established on the basis of referral of the subject (self) to its symbolic image, acquires a potential to rationally describe the external world through the semiotic structure of human language. It has been modelled in reflexive psychology using the algebra of simple relations (Lefebvre, V.A., J. Soc. Biol. Struct. 10, 129-175, 1987). The model introduces a substantial opposition of the two basic complementary types of reflexion defined as Western (W) and Eastern (E). These types generate opposite models of behavior and opposite organizations of societies. Development of human societies involves the interactions of W and E types not only between the societies but also within one society underlying its homeostasis and dynamics. Invention of new ideas and implementation of new technologies shift the probability pattern of reflexive choices, appearing as internal assessments of the individual agents within a society, and direct changes in the preference of reflexive types. The dynamics of societies and of interactions between societies is based on the interference of opposite reflexive structures and on the establishment of different patterns during such interference. At different times in the history of human civilization these changing patterns resulted in the formation and splitting of large empires, the development and spreading of new technologies, the consecutive periods of wellness and decline. Copyright © 2017 Elsevier Ltd. All rights reserved.

Patterns of pair formation and mating in an ectoparasitic caligid copepod Lepeophtheirus salmonis (Krøyer 1837): implications for its sensory and mating biology

PubMed Central

Hull, M. Q.

1998-01-01

Non-invasive observations of single cohort and manipulated populations of the sealouse on laboratory-maintained salmon established the sequence of reproductive events and mating. Protandry occurs with adult male emergence synchronized with pre-adult II female emergence, the stage at which most pair formation and pre-copular guarding takes place. Male competence for pair formation and mating was achieved within 24 h of the final moult and pairing occurred according to the preference hierarchy, virgin adult females greater than pre-adult II females much greater than pre-adult I females. This hierarchy broke down when the adult male to unmated female ratio increased rapidly. Males mated successfully not only with newly moulted adult females, but also with older virgin females in which enlargement of the genital complex and premature extrusion of egg strings had occurred. Multiple mating by adult males was demonstrated and may be widespread. Significant inter-host transfer was also demonstrated. Adult males were more mobile than adult females and showed significantly more inter-host transfer. Ablation of the distal tip of the antennules significantly reduced the success of host-finding, pair formation and males' mating.

Desktop Nanofabrication with Massively Multiplexed Beam Pen Lithography

PubMed Central

Liao, Xing; Brown, Keith A.; Schmucker, Abrin L.; Liu, Guoliang; He, Shu; Shim, Wooyoung; Mirkin, Chad A.

2013-01-01

The development of a lithographic method that can rapidly define nanoscale features across centimeter-scale surfaces has been a long standing goal of the nanotechnology community. If such a ‘desktop nanofab’ could be implemented in a low-cost format, it would bring the possibility of point-of-use nanofabrication for rapidly prototyping diverse functional structures. Here we report the development of a new tool that is capable of writing arbitrary patterns composed of diffraction-unlimited features over square centimeter areas that are in registry with existing patterns and nanostructures. Importantly, this instrument is based on components that are inexpensive compared to the combination of state-of-the-art nanofabrication tools that approach its capabilities. This tool can be used to prototype functional electronic devices in a mask-free fashion in addition to providing a unique platform for performing high throughput nano- to macroscale photochemistry with relevance to biology and medicine. PMID:23868336

The biogeodynamics of microbial landscapes

NASA Astrophysics Data System (ADS)

Battin, T. J.; Hödl, I.; Bertuzzo, E.; Mari, L.; Suweis, S. S.; Rinaldo, A.

2011-12-01

Spatial configuration is fundamental in defining the structural and functional properties of biological systems. Biofilms, surface-attached and matrix-enclosed microorganisms, are a striking example of spatial organisation. Coupled biotic and abiotic processes shape the spatial organisation across scales of the landscapes formed by these benthic biofilms in streams and rivers. Experimenting with such biofilms in streams, we found that, depending on the streambed topography and the related hydrodynamic microenvironment, biofilm landscapes form increasingly diverging spatial patterns as they grow. Strikingly, however, cluster size distributions tend to converge even in contrasting hydrodynamic microenvironments. To reproduce the observed cluster size distributions we used a continuous, size-structured population model. The model accounts for the formation, growth, erosion and merging of biofilm clusters. Our results suggest not only that hydrodynamic forcing induce the diverging patterning of the microbial landscape, but also that microorganisms have developed strategies to equally exploit spatial resources independently of the physical structure of the microenvironment where they live.

The mode branching route to localization of the finite-length floating elastica

NASA Astrophysics Data System (ADS)

Rivetti, Marco; Neukirch, Sébastien

2014-09-01

The beam on elastic foundation is a general model used in physical, biological, and technological problems to study delamination, wrinkling, or pattern formation. Recent focus has been given to the buckling of beams deposited on liquid baths, and in the regime where the beam is soft compared to hydrostatic forces the wrinkling pattern observed at buckling has been shown to lead to localization of the deformation when the confinement is increased. Here we perform a global study of the general case where the intensity of the liquid foundation and the confinement are both varied. We compute equilibrium and stability of the solutions and unravel secondary bifurcations that play a major role in the route to localization. Moreover we classify the post-buckling solutions and shed light on the mechanism leading to localization. Finally, using an asymptotic technique imported from fluid mechanics, we derive an approximated analytical solution to the problem.

Desktop nanofabrication with massively multiplexed beam pen lithography.

PubMed

Liao, Xing; Brown, Keith A; Schmucker, Abrin L; Liu, Guoliang; He, Shu; Shim, Wooyoung; Mirkin, Chad A

2013-01-01

The development of a lithographic method that can rapidly define nanoscale features across centimetre-scale surfaces has been a long-standing goal for the nanotechnology community. If such a 'desktop nanofab' could be implemented in a low-cost format, it would bring the possibility of point-of-use nanofabrication for rapidly prototyping diverse functional structures. Here we report the development of a new tool that is capable of writing arbitrary patterns composed of diffraction-unlimited features over square centimetre areas that are in registry with existing patterns and nanostructures. Importantly, this instrument is based on components that are inexpensive compared with the combination of state-of-the-art nanofabrication tools that approach its capabilities. This tool can be used to prototype functional electronic devices in a mask-free fashion in addition to providing a unique platform for performing high-throughput nano- to macroscale photochemistry with relevance to biology and medicine.

Patterning of a compound eye on an extinct dipteran wing.

PubMed

Dinwiddie, April; Rachootin, Stan

2011-04-23

We have discovered unexpected similarities between a novel and characteristic wing organ in an extinct biting midge from Baltic amber, Eohelea petrunkevitchi, and the surface of a dipteran's compound eye. Scanning electron microscope images now reveal vestigial mechanoreceptors between the facets of the organ. We interpret Eohelea's wing organ as the blending of these two developmental systems: the formation and patterning of the cuticle in the eye and of the wing. Typically, only females in the genus carry this distinctive, highly organized structure. Two species were studied (E. petrunkevitchi and E. sinuosa), and the structure differs in form between them. We examine Eohelea's wing structures for modes of fabrication, material properties and biological functions, and the effective ecological environment in which these midges lived. We argue that the current view of the wing organ's function in stridulation has been misconstrued since it was described half a century ago.

Identifying gene coexpression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions.

PubMed

Zinkgraf, Matthew; Liu, Lijun; Groover, Andrew; Filkov, Vladimir

2017-06-01

Trees modify wood formation through integration of environmental and developmental signals in complex but poorly defined transcriptional networks, allowing trees to produce woody tissues appropriate to diverse environmental conditions. In order to identify relationships among genes expressed during wood formation, we integrated data from new and publically available datasets in Populus. These datasets were generated from woody tissue and include transcriptome profiling, transcription factor binding, DNA accessibility and genome-wide association mapping experiments. Coexpression modules were calculated, each of which contains genes showing similar expression patterns across experimental conditions, genotypes and treatments. Conserved gene coexpression modules (four modules totaling 8398 genes) were identified that were highly preserved across diverse environmental conditions and genetic backgrounds. Functional annotations as well as correlations with specific experimental treatments associated individual conserved modules with distinct biological processes underlying wood formation, such as cell-wall biosynthesis, meristem development and epigenetic pathways. Module genes were also enriched for DNase I hypersensitivity footprints and binding from four transcription factors associated with wood formation. The conserved modules are excellent candidates for modeling core developmental pathways common to wood formation in diverse environments and genotypes, and serve as testbeds for hypothesis generation and testing for future studies. No claim to original US government works. New Phytologist © 2017 New Phytologist Trust.

Space Biology: Patterns of Life

ERIC Educational Resources Information Center

Salisbury, Frank B.

1971-01-01

Present knowledge about Mars is compared with past beliefs about the planet. Biological experiments that indicate life may exist on Mars are interpreted. Life patterns or biological features that might be postulated for extraterrestrial life are presented at the molecular, cellular, organism, and ecosystem levels. (DS)

Spatio-temporal dynamics induced by competing instabilities in two asymmetrically coupled nonlinear evolution equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schüler, D.; Alonso, S.; Bär, M.

2014-12-15

Pattern formation often occurs in spatially extended physical, biological, and chemical systems due to an instability of the homogeneous steady state. The type of the instability usually prescribes the resulting spatio-temporal patterns and their characteristic length scales. However, patterns resulting from the simultaneous occurrence of instabilities cannot be expected to be simple superposition of the patterns associated with the considered instabilities. To address this issue, we design two simple models composed by two asymmetrically coupled equations of non-conserved (Swift-Hohenberg equations) or conserved (Cahn-Hilliard equations) order parameters with different characteristic wave lengths. The patterns arising in these systems range from coexistingmore » static patterns of different wavelengths to traveling waves. A linear stability analysis allows to derive a two parameter phase diagram for the studied models, in particular, revealing for the Swift-Hohenberg equations, a co-dimension two bifurcation point of Turing and wave instability and a region of coexistence of stationary and traveling patterns. The nonlinear dynamics of the coupled evolution equations is investigated by performing accurate numerical simulations. These reveal more complex patterns, ranging from traveling waves with embedded Turing patterns domains to spatio-temporal chaos, and a wide hysteretic region, where waves or Turing patterns coexist. For the coupled Cahn-Hilliard equations the presence of a weak coupling is sufficient to arrest the coarsening process and to lead to the emergence of purely periodic patterns. The final states are characterized by domains with a characteristic length, which diverges logarithmically with the coupling amplitude.« less

Electrical Field Guided Electrospray Deposition for Production of Gradient Particle Patterns.

PubMed

Yan, Wei-Cheng; Xie, Jingwei; Wang, Chi-Hwa

2018-06-06

Our previous work demonstrated the uniform particle pattern formation on the substrates using electrical field guided electrospray deposition. In this work, we reported for the first time the fabrication of gradient particle patterns on glass slides using an additional point, line, or bar electrode based on our previous electrospray deposition configuration. We also demonstrated that the polydimethylsiloxane (PDMS) coating could result in the formation of uniform particle patterns instead of gradient particle patterns on glass slides using the same experimental setup. Meanwhile, we investigated the effect of experimental configurations on the gradient particle pattern formation by computational simulation. The simulation results are in line with experimental observations. The formation of gradient particle patterns was ascribed to the gradient of electric field and the corresponding focusing effect. Cell patterns can be formed on the particle patterns deposited on PDMS-coated glass slides. The formed particle patterns hold great promise for high-throughput screening of biomaterial-cell interactions and sensing.

Adaptation of video game UVW mapping to 3D visualization of gene expression patterns

NASA Astrophysics Data System (ADS)

Vize, Peter D.; Gerth, Victor E.

2007-01-01

Analysis of gene expression patterns within an organism plays a critical role in associating genes with biological processes in both health and disease. During embryonic development the analysis and comparison of different gene expression patterns allows biologists to identify candidate genes that may regulate the formation of normal tissues and organs and to search for genes associated with congenital diseases. No two individual embryos, or organs, are exactly the same shape or size so comparing spatial gene expression in one embryo to that in another is difficult. We will present our efforts in comparing gene expression data collected using both volumetric and projection approaches. Volumetric data is highly accurate but difficult to process and compare. Projection methods use UV mapping to align texture maps to standardized spatial frameworks. This approach is less accurate but is very rapid and requires very little processing. We have built a database of over 180 3D models depicting gene expression patterns mapped onto the surface of spline based embryo models. Gene expression data in different models can easily be compared to determine common regions of activity. Visualization software, both Java and OpenGL optimized for viewing 3D gene expression data will also be demonstrated.

Characteristics of proportionate growth observed in instability patterns of miscible fluids

NASA Astrophysics Data System (ADS)

Bischofberger, Irmgard; Ramachandran, Radha; Nagel, Sidney R.; Nagel lab Team

2014-11-01

As a baby mammal grows, different parts of its body develop at the nearly the same rate and thus to a good approximation in direct proportion to one another. This type of growth is called proportionate growth. As familiar as it appears to us, it is very rarely found in physical systems outside of the biological world. We here show an example of proportionate growth that occurs in the instability formed when a less viscous liquid, of viscosity ηin displaces a more viscous miscible one, of viscosity ηout. We investigate the growth of these patterns in a quasi-two-dimensional geometry. Within a range of viscosity ratios 0.1 <ηin /ηout <0.3, we observe the formation of small blunt structures that form at the edges of an inner circular region devoid of fingers. As the pattern grows, the size of these structures increases in proportion to the size of the inner circle, such that even small details in the shape of the pattern remain essentially unchanged during growth. These characteristics of proportionate growth are reflected in the shape of the interface in the third dimension as well.

Endogenous electromagnetic fields in plant leaves: a new hypothesis for vascular pattern formation.

PubMed

Pietak, Alexis Mari

2011-06-01

Electromagnetic (EM) phenomena have long been implicated in biological development, but few detailed, practical mechanisms have been put forth to connect electromagnetism with morphogenetic processes. This work describes a new hypothesis for plant leaf veination, whereby an endogenous electric field forming as a result of a coherent Frohlich process, and corresponding to an EM resonant mode of the developing leaf structure, is capable of instigating leaf vascularisation. In order to test the feasibility of this hypothesis, a three-dimensional, EM finite-element model (FEM) of a leaf primordium was constructed to determine if suitable resonant modes were physically possible for geometric and physical parameters similar to those of developing leaf tissue. Using the FEM model, resonant EM modes with patterns of relevance to developing leaf vein modalities were detected. On account of the existence of shared geometric signatures in a leaf's vascular pattern and the electric field component of EM resonant modes supported by a developing leaf structure, further theoretical and experimental investigations are warranted. Significantly, this hypothesis is not limited to leaf vascular patterning, but may be applicable to a variety of morphogenetic phenomena in a number of living systems.

Chemical synthesis of La1 isolated from the venom of the scorpion Liocheles australasiae and determination of its disulfide bonding pattern.

PubMed

Nagao, Junya; Miyashita, Masahiro; Nakagawa, Yoshiaki; Miyagawa, Hisashi

2015-08-01

La1 is a 73-residue cysteine-rich peptide isolated from the scorpion Liocheles australasiae venom. Although La1 is the most abundant peptide in the venom, its biological function remains unknown. Here, we describe a method for efficient chemical synthesis of La1 using the native chemical ligation (NCL) strategy, in which three peptide components of less than 40 residues were sequentially ligated. The peptide thioester necessary for NCL was synthesized using an aromatic N-acylurea approach with Fmoc-SPPS. After completion of sequential NCL, disulfide bond formation was carried out using a dialysis method, in which the linear peptide dissolved in an acidic solution was dialyzed against a slightly alkaline buffer to obtain correctly folded La1. Next, we determined the disulfide bonding pattern of La1. Enzymatic and chemical digests of La1 without reduction of disulfide bonds were analyzed by liquid chromatography/mass spectrometry (LC/MS), which revealed two of four disulfide bond linkages. The remaining two linkages were assigned based on MS/MS analysis of a peptide fragment containing two disulfide bonds. Consequently, the disulfide bonding pattern of La1 was found to be similar to that of a von Willebrand factor type C (VWC) domain. To our knowledge, this is the first report of the experimental determination of the disulfide bonding pattern of peptides having a single VWC domain as well as their chemical synthesis. La1 synthesized in this study will be useful for investigation of its biological role in the venom. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

Contrasting Pathology of the Stress Granule Proteins TIA-1 and G3BP in Tauopathies

PubMed Central

Vanderweyde, Tara; Yu, Haung; Varnum, Megan; Liu-Yesucevitz, Liqun; Citro, Allison; Ikezu, Tsuneya; Duff, Karen; Wolozin, Benjamin

2012-01-01

Stress induces aggregation of RNA-binding proteins to form inclusions, termed stress granules (SGs). Recent evidence suggests that SG proteins also colocalize with neuropathological structures, but whether this occurs in Alzheimer’s disease is unknown. We examined the relationship between SG proteins and neuropathology in brain tissue from P301L Tau transgenic mice, as well as in cases of Alzheimer’s disease and FTDP-17. The pattern of SG pathology differs dramatically based on the RNA-binding protein examined. SGs positive for T-cell intracellular antigen-1 (TIA-1) or tristetraprolin (TTP) initially do not colocalize with tau pathology, but then merge with tau inclusions as disease severity increases. In contrast, G3BP (ras GAP-binding protein) identifies a novel type of molecular pathology that shows increasing accumulation in neurons with increasing disease severity, but often is not associated with classic markers of tau pathology. TIA-1 and TTP both bind phospho-tau, and TIA-1 overexpression induces formation of inclusions containing phospho-tau. These data suggest that SG formation might stimulate tau pathophysiology. Thus, study of RNA-binding proteins and SG biology highlights novel pathways interacting with the pathophysiology of AD, providing potentially new avenues for identifying diseased neurons and potentially novel mechanisms regulating tau biology. PMID:22699908

Neuromuscular Junction Formation between Human Stem cell-derived Motoneurons and Human Skeletal Muscle in a Defined System

PubMed Central

Guo, Xiufang; Gonzalez, Mercedes; Stancescu, Maria; Vandenburgh, Herman; Hickman, James

2011-01-01

Functional in vitro models composed of human cells will constitute an important platform in the next generation of system biology and drug discovery. This study reports a novel human-based in vitro Neuromuscular Junction (NMJ) system developed in a defined serum-free medium and on a patternable non-biological surface. The motoneurons and skeletal muscles were derived from fetal spinal stem cells and skeletal muscle stem cells. The motoneurons and skeletal myotubes were completely differentiated in the co-culture based on morphological analysis and electrophysiology. NMJ formation was demonstrated by phase contrast microscopy, immunocytochemistry and the observation of motoneuron-induced muscle contractions utilizing time lapse recordings and their subsequent quenching by D-Tubocurarine. Generally, functional human based systems would eliminate the issue of species variability during the drug development process and its derivation from stem cells bypasses the restrictions inherent with utilization of primary human tissue. This defined human-based NMJ system is one of the first steps in creating functional in vitro systems and will play an important role in understanding NMJ development, in developing high information content drug screens and as test beds in preclinical studies for spinal or muscular diseases/injuries such as muscular dystrophy, Amyotrophic lateral sclerosis and spinal cord repair. PMID:21944471

Neuromuscular junction formation between human stem cell-derived motoneurons and human skeletal muscle in a defined system.

PubMed

Guo, Xiufang; Gonzalez, Mercedes; Stancescu, Maria; Vandenburgh, Herman H; Hickman, James J

2011-12-01

Functional in vitro models composed of human cells will constitute an important platform in the next generation of system biology and drug discovery. This study reports a novel human-based in vitro Neuromuscular Junction (NMJ) system developed in a defined serum-free medium and on a patternable non-biological surface. The motoneurons and skeletal muscles were derived from fetal spinal stem cells and skeletal muscle stem cells. The motoneurons and skeletal myotubes were completely differentiated in the co-culture based on morphological analysis and electrophysiology. NMJ formation was demonstrated by phase contrast microscopy, immunocytochemistry and the observation of motoneuron-induced muscle contractions utilizing time-lapse recordings and their subsequent quenching by d-Tubocurarine. Generally, functional human based systems would eliminate the issue of species variability during the drug development process and its derivation from stem cells bypasses the restrictions inherent with utilization of primary human tissue. This defined human-based NMJ system is one of the first steps in creating functional in vitro systems and will play an important role in understanding NMJ development, in developing high information content drug screens and as test beds in preclinical studies for spinal or muscular diseases/injuries such as muscular dystrophy, Amyotrophic lateral sclerosis and spinal cord repair. Copyright © 2011 Elsevier Ltd. All rights reserved.

Developmental role of phenylalanine-ammonia-lyase (PAL) and cinnamate 4-hydroxylase (C4H) genes during adventitious rooting of Juglans regia L. microshoots.

PubMed

Cheniany, Monireh; Ganjeali, Ali

2016-12-01

Phenylalanine-ammonia-lyase and cinnamate-4-hydroxylase play important role in the phenylpropanoid pathway, which produces many biologically important secondary metabolites participating in normal plant development. Flavonol quercetin is the main representant of these compounds that has been identified in numerous Juglans spp. In this survey, the developmental expression patterns of PAL and C4H genes during in vitro rooting of two walnut cultivars 'Sunland' and 'Howard' was examined by RT-PCR. To understand the potential role in rooting, the changing pattern of endogenous content of quercetin was also analyzed by HPLC. The 'Sunland' with better capacity to root had more quercetin content during the "inductive phase" of rooting than 'Howard'. In each cultivar, the level of PAL transcripts showed the same behavior with the changing patterns of quercetin during root formation of microshoots. The positive correlation between the changes of quercetin and PAL-mRNA indicated that PAL gene may have an immediate effect on flavonoid pathway metabolites including quercetin. Although the behavioral change of C4H expression was similar in both cultivars during root formation (with significantly more level for 'Howard'), it was not coincide with the changes of quercerin concentrations. Our results showed that C4H function is important for the normal development, but its transcriptional regulation does not correlate with quercetin as an efficient phenolic compound for walnut rhizogenesis.

A computational image analysis glossary for biologists.

PubMed

Roeder, Adrienne H K; Cunha, Alexandre; Burl, Michael C; Meyerowitz, Elliot M

2012-09-01

Recent advances in biological imaging have resulted in an explosion in the quality and quantity of images obtained in a digital format. Developmental biologists are increasingly acquiring beautiful and complex images, thus creating vast image datasets. In the past, patterns in image data have been detected by the human eye. Larger datasets, however, necessitate high-throughput objective analysis tools to computationally extract quantitative information from the images. These tools have been developed in collaborations between biologists, computer scientists, mathematicians and physicists. In this Primer we present a glossary of image analysis terms to aid biologists and briefly discuss the importance of robust image analysis in developmental studies.

Correlation analysis of symmetry breaking in the surface nanostructure ordering: case study of the ventral scale of the snake Morelia viridis

NASA Astrophysics Data System (ADS)

Kovalev, A.; Filippov, A.; Gorb, S. N.

2016-03-01

In contrast to the majority of inorganic or artificial materials, there is no ideal long-range ordering of structures on the surface in biological systems. Local symmetry of the ordering on biological surfaces is also often broken. In the present paper, the particular symmetry violation was analyzed for dimple-like nano-pattern on the belly scales of the skin of the pythonid snake Morelia viridis using correlation analysis and statistics of the distances between individual nanostructures. The results of the analysis performed on M. viridis were compared with a well-studied nano-nipple pattern on the eye of the sphingid moth Manduca sexta, used as a reference. The analysis revealed non-random, but very specific symmetry violation. In the case of the moth eye, the nano-nipple arrangement forms a set of domains, while in the case of the snake skin, the nano-dimples arrangement resembles an ordering of particles (molecules) in amorphous (glass) state. The function of the nano-dimples arrangement may be to provide both friction and strength isotropy of the skin. A simple model is suggested, which provides the results almost perfectly coinciding with the experimental ones. Possible mechanisms of the appearance of the above nano-formations are discussed.

Morphology-Induced Collective Behaviors: Dynamic Pattern Formation in Water-Floating Elements

PubMed Central

Nakajima, Kohei; Ngouabeu, Aubery Marchel Tientcheu; Miyashita, Shuhei; Göldi, Maurice; Füchslin, Rudolf Marcel; Pfeifer, Rolf

2012-01-01

Complex systems involving many interacting elements often organize into patterns. Two types of pattern formation can be distinguished, static and dynamic. Static pattern formation means that the resulting structure constitutes a thermodynamic equilibrium whose pattern formation can be understood in terms of the minimization of free energy, while dynamic pattern formation indicates that the system is permanently dissipating energy and not in equilibrium. In this paper, we report experimental results showing that the morphology of elements plays a significant role in dynamic pattern formation. We prepared three different shapes of elements (circles, squares, and triangles) floating in a water-filled container, in which each of the shapes has two types: active elements that were capable of self-agitation with vibration motors, and passive elements that were mere floating tiles. The system was purely decentralized: that is, elements interacted locally, and subsequently elicited global patterns in a process called self-organized segregation. We showed that, according to the morphology of the selected elements, a different type of segregation occurs. Also, we quantitatively characterized both the local interaction regime and the resulting global behavior for each type of segregation by means of information theoretic quantities, and showed the difference for each case in detail, while offering speculation on the mechanism causing this phenomenon. PMID:22715370

Evolutionary history of the recruitment of conserved developmental genes in association to the formation and diversification of a novel trait.

PubMed

Shirai, Leila T; Saenko, Suzanne V; Keller, Roberto A; Jerónimo, Maria A; Brakefield, Paul M; Descimon, Henri; Wahlberg, Niklas; Beldade, Patrícia

2012-02-15

The origin and modification of novel traits are important aspects of biological diversification. Studies combining concepts and approaches of developmental genetics and evolutionary biology have uncovered many examples of the recruitment, or co-option, of genes conserved across lineages for the formation of novel, lineage-restricted traits. However, little is known about the evolutionary history of the recruitment of those genes, and of the relationship between them -for example, whether the co-option involves whole or parts of existing networks, or whether it occurs by redeployment of individual genes with de novo rewiring. We use a model novel trait, color pattern elements on butterfly wings called eyespots, to explore these questions. Eyespots have greatly diversified under natural and sexual selection, and their formation involves genetic circuitries shared across insects. We investigated the evolutionary history of the recruitment and co-recruitment of four conserved transcription regulators to the larval wing disc region where circular pattern elements develop. The co-localization of Antennapedia, Notch, Distal-less, and Spalt with presumptive (eye)spot organizers was examined in 13 butterfly species, providing the largest comparative dataset available for the system. We found variation between families, between subfamilies, and between tribes. Phylogenetic reconstructions by parsimony and maximum likelihood methods revealed an unambiguous evolutionary history only for Antennapedia, with a resolved single origin of eyespot-associated expression, and many homoplastic events for Notch, Distal-less, and Spalt. The flexibility in the (co-)recruitment of the targeted genes includes cases where different gene combinations are associated with morphologically similar eyespots, as well as cases where identical protein combinations are associated with very different phenotypes. The evolutionary history of gene (co-)recruitment is consistent with both divergence from a recruited putative ancestral network, and with independent co-option of individual genes. The diversity in the combinations of genes expressed in association with eyespot formation does not parallel diversity in characteristics of the adult phenotype. We discuss these results in the context of inferring homology. Our study underscores the importance of widening the representation of phylogenetic, morphological, and genetic diversity in order to establish general principles about the mechanisms behind the evolution of novel traits.

Mathematical study on robust tissue pattern formation in growing epididymal tubule.

PubMed

Hirashima, Tsuyoshi

2016-10-21

Tissue pattern formation during development is a reproducible morphogenetic process organized by a series of kinetic cellular activities, leading to the building of functional and stable organs. Recent studies focusing on mechanical aspects have revealed physical mechanisms on how the cellular activities contribute to the formation of reproducible tissue patterns; however, the understanding for what factors achieve the reproducibility of such patterning and how it occurs is far from complete. Here, I focus on a tube pattern formation during murine epididymal development, and show that two factors influencing physical design for the patterning, the proliferative zone within the tubule and the viscosity of tissues surrounding to the tubule, control the reproducibility of epididymal tubule pattern, using a mathematical model based on experimental data. Extensive numerical simulation of the simple mathematical model revealed that a spatially localized proliferative zone within the tubule, observed in experiments, results in more reproducible tubule pattern. Moreover, I found that the viscosity of tissues surrounding to the tubule imposes a trade-off regarding pattern reproducibility and spatial accuracy relating to the region where the tubule pattern is formed. This indicates an existence of optimality in material properties of tissues for the robust patterning of epididymal tubule. The results obtained by numerical analysis based on experimental observations provide a general insight on how physical design realizes robust tissue pattern formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Physical-chemical mechanisms of pattern formation during gastrulation

NASA Astrophysics Data System (ADS)

Bozorgui, Behnaz; Kolomeisky, Anatoly B.; Teimouri, Hamid

2018-03-01

Gastrulation is a fundamental phase during the biological development of most animals when a single layer of identical embryo cells is transformed into a three-layer structure, from which the organs start to develop. Despite a remarkable progress in quantifying the gastrulation processes, molecular mechanisms of these processes remain not well understood. Here we theoretically investigate early spatial patterning in a geometrically confined colony of embryonic stem cells. Using a reaction-diffusion model, a role of Bone-Morphogenetic Protein 4 (BMP4) signaling pathway in gastrulation is specifically analyzed. Our results show that for slow diffusion rates of BMP4 molecules, a new length scale appears, which is independent of the size of the system. This length scale separates the central region of the colony with uniform low concentrations of BMP molecules from the region near the colony edge where the concentration of signaling molecules is elevated. The roles of different components of the signaling pathway are also explained. Theoretical results are consistent with recent in vitro experiments, providing microscopic explanations for some features of early embryonic spatial patterning. Physical-chemical mechanisms of these processes are discussed.

Sub-micron magnetic patterns and local variations of adhesion force induced in non-ferromagnetic amorphous steel by femtosecond pulsed laser irradiation

NASA Astrophysics Data System (ADS)

Zhang, Huiyan; Feng, Yuping; Nieto, Daniel; García-Lecina, Eva; Mcdaniel, Clare; Díaz-Marcos, Jordi; Flores-Arias, María Teresa; Gerard M., O.'connor; Baró, Maria Dolors; Pellicer, Eva; Sort, Jordi

2016-05-01

Periodic ripple and nanoripple patterns are formed at the surface of amorphous steel after femtosecond pulsed laser irradiation (FSPLI). Formation of such ripples is accompanied with the emergence of a surface ferromagnetic behavior which is not initially present in the non-irradiated amorphous steel. The occurrence of ferromagnetic properties is associated with the laser-induced devitrification of the glassy structure to form ferromagnetic (α-Fe and Fe3C) and ferrimagnetic [(Fe,Mn)3O4 and Fe2CrO4] phases located in the ripples. The generation of magnetic structures by FSPLI turns out to be one of the fastest ways to induce magnetic patterning without the need of any shadow mask. Furthermore, local variations of the adhesion force, wettability and nanomechanical properties are also observed and compared to those of the as-cast amorphous alloy. These effects are of interest for applications (e.g., biological, magnetic recording, etc.) where both ferromagnetism and tribological/adhesion properties act synergistically to optimize material performance.

Magnetophoretic Conductors and Diodes in a 3D Magnetic Field.

PubMed

Abedini-Nassab, Roozbeh; Joh, Daniel Y; Van Heest, Melissa; Baker, Cody; Chilkoti, Ashutosh; Murdoch, David M; Yellen, Benjamin B

2016-06-14

We demonstrate magnetophoretic conductor tracks that can transport single magnetized beads and magnetically labeled single cells in a 3-dimensional time-varying magnetic field. The vertical field bias, in addition to the in-plane rotating field, has the advantage of reducing the attraction between particles, which inhibits the formation of particle clusters. However, the inclusion of a vertical field requires the re-design of magnetic track geometries which can transport magnetized objects across the substrate. Following insights from magnetic bubble technology, we found that successful magnetic conductor geometries defined in soft magnetic materials must be composed of alternating sections of positive and negative curvature. In addition to the previously studied magnetic tracks taken from the magnetic bubble literature, a drop-shape pattern was found to be even more adept at transporting small magnetic beads and single cells. Symmetric patterns are shown to achieve bi-directional conduction, whereas asymmetric patterns achieve unidirectional conduction. These designs represent the electrical circuit corollaries of the conductor and diode, respectively. Finally, we demonstrate biological applications in transporting single cells and in the size based separation of magnetic particles.

Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers

PubMed Central

Bennett, W. F. Drew; Sapay, Nicolas; Tieleman, D. Peter

2014-01-01

Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DMPC, and DPPC bilayers, with pore formation free energies of 17, 45, and 78 kJ/mol, respectively. By using atomistic computer simulations, we are able to determine not only the free energy for pore formation, but also the enthalpy and entropy, which yields what is believed to be significant new insights in the molecular driving forces behind membrane defects. The free energy cost for pore formation is due to a large unfavorable entropic contribution and a favorable change in enthalpy. Changes in hydrogen bonding patterns occur, with increased lipid-water interactions, and fewer water-water hydrogen bonds, but the total number of overall hydrogen bonds is constant. Equilibrium pore formation is directly observed in the thin DLPC lipid bilayer. Multiple long timescale simulations of pore closure are used to predict pore lifetimes. Our results are important for biological applications, including the activity of antimicrobial peptides and a better understanding of membrane protein folding, and improve our understanding of the fundamental physicochemical nature of membranes. PMID:24411253

Large-Scale Constraint-Based Pattern Mining

ERIC Educational Resources Information Center

Zhu, Feida

2009-01-01

We studied the problem of constraint-based pattern mining for three different data formats, item-set, sequence and graph, and focused on mining patterns of large sizes. Colossal patterns in each data formats are studied to discover pruning properties that are useful for direct mining of these patterns. For item-set data, we observed robustness of…

A model for the biological precipitation of Precambrian iron-formation

NASA Technical Reports Server (NTRS)

Laberge, G. L.

1986-01-01

A biological model for the precipitation of Precambrian iron formations is presented. Assuming an oxygen deficient atmosphere and water column to allow sufficient Fe solubility, it is proposed that local oxidizing environments, produced biologically, led to precipitation of iron formations. It is further suggested that spheroidal structures about 30 mm in diameter, which are widespread in low grade cherty rion formations, are relict forms of the organic walled microfossil Eosphaera tylerii. The presence of these structures suggests that the organism may have had a siliceous test, which allowed sufficient rigidity for accumulation and preservation. The model involves precipitation of ferric hydrates by oxidation of iron in the photic zone by a variety of photosynthetic organisms. Silica may have formed in the frustules of silica secreting organisms, including Eosphaera tylerii. Iron formates formed, therefore, by a sediment rain of biologically produced ferric hydrates and silica and other organic material. Siderite and hematite formed diagenetically on basin floors, and subsequent metamorphism produced magnetite and iron silicates.

Evaluation of the Concepts and Subjects in Biology Perceived to Be Difficult to Learn and Teach by the Pre-Service Teachers Registered in the Pedagogical Formation Program

ERIC Educational Resources Information Center

Gungor, Sema Nur; Ozkan, Muhlis

2017-01-01

This study examines the subjects and concepts in biology perceived to be difficult to learn and teach by 759 pre-service biology teachers registered in the pedagogical formation program at Uludag University Faculty of Education in the academic year of 2005-2016, as well as the associations that word "biology" first calls to their mind.…

Nuclear 3D organization and radiosensitivity

NASA Astrophysics Data System (ADS)

Eidelman, Y. A.; Slanina, S. V.; Aleshchenko, A. V.; Sen'ko, O. V.; Kononkova, A. D.; Andreev, S. G.

2017-01-01

Current mechanisms of radiation-induced chromosomal aberration (CA) formation suggest misrepair of chromosomal lesions being in spatial proximity. In this case CAs have to depend on pattern of chromosomal contacts and on chromosome spatial organization in a cell nucleus. We were interested in whether variation of nucleus 3D organization results in difference of radiation induced CA formation frequency. Experimental data available do not provide information sufficient for definite conclusions. To have more deep insight in this issue we developed the biophysical modeling technique taking into account different levels of chromosome/nuclear organization and radiation damage of DNA and chromosomes. Computer experiments on gamma irradiation were carried out for two types of cells with different 3D organization of nuclei, preferentially peripheral and internal. CA frequencies were found to depend on spatial positioning of chromosomes within a nucleus which determines a pattern of interchromosomal contacts. For individual chromosomes this effect can be more pronounced than for genome averaged. Since significant part of aberrations, for example dicentrics, results in cell death, the proposed technique is capable of evaluating radiosensitivity of cells, both normal and cancer, with the incorporation of 3D genome information. This predictive technology allows to reduce uncertainties of prognosis of biological effects of radiation compared to phenomenological methods and may have variety of biomedical applications, in particular, in cancer radiation therapy.

The functional role of xylem parenchyma cells and aquaporins during recovery from severe water stress.

PubMed

Secchi, Francesca; Pagliarani, Chiara; Zwieniecki, Maciej A

2017-06-01

Xylem parenchyma cells [vessel associated cells (VACs)] constitute a significant fraction of the xylem in woody plants. These cells are often closely connected with xylem vessels or tracheids via simple pores (remnants of plasmodesmata fields). The close contact and biological activity of VACs during times of severe water stress and recovery from stress suggest that they are involved in the maintenance of xylem transport capacity and responsible for the restoration of vessel/tracheid functionality following embolism events. As recovery from embolism requires the transport of water across xylem parenchyma cell membranes, an understanding of stem-specific aquaporin expression patterns, localization and activity is a crucial part of any biological model dealing with embolism recovery processes in woody plants. In this review, we provide a short overview of xylem parenchyma cell biology with a special focus on aquaporins. In particular we address their distributions and activity during the development of drought stress, during the formation of embolism and the subsequent recovery from stress that may result in refilling. Complemented by the current biological model of parenchyma cell function during recovery from stress, this overview highlights recent breakthroughs on the unique ability of long-lived perennial plants to undergo cycles of embolism-recovery related to drought/rewetting or freeze/thaw events. © 2016 John Wiley & Sons Ltd.

EnsMart: A Generic System for Fast and Flexible Access to Biological Data

PubMed Central

Kasprzyk, Arek; Keefe, Damian; Smedley, Damian; London, Darin; Spooner, William; Melsopp, Craig; Hammond, Martin; Rocca-Serra, Philippe; Cox, Tony; Birney, Ewan

2004-01-01

The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools. The system consists of a query-optimized database and interactive, user-friendly interfaces. EnsMart has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval of customized data sets. A wide variety of complex queries, on various types of annotations, for numerous species are supported. These can be applied to many research problems, ranging from SNP selection for candidate gene screening, through cross-species evolutionary comparisons, to microarray annotation. Users can group and refine biological data according to many criteria, including cross-species analyses, disease links, sequence variations, and expression patterns. Both tabulated list data and biological sequence output can be generated dynamically, in HTML, text, Microsoft Excel, and compressed formats. A wide range of sequence types, such as cDNA, peptides, coding regions, UTRs, and exons, with additional upstream and downstream regions, can be retrieved. The EnsMart database can be accessed via a public Web site, or through a Java application suite. Both implementations and the database are freely available for local installation, and can be extended or adapted to `non-Ensembl' data sets. PMID:14707178

KinView: A visual comparative sequence analysis tool for integrated kinome research

PubMed Central

McSkimming, Daniel Ian; Dastgheib, Shima; Baffi, Timothy R.; Byrne, Dominic P.; Ferries, Samantha; Scott, Steven Thomas; Newton, Alexandra C.; Eyers, Claire E.; Kochut, Krzysztof J.; Eyers, Patrick A.

2017-01-01

Multiple sequence alignments (MSAs) are a fundamental analysis tool used throughout biology to investigate relationships between protein sequence, structure, function, evolutionary history, and patterns of disease-associated variants. However, their widespread application in systems biology research is currently hindered by the lack of user-friendly tools to simultaneously visualize, manipulate and query the information conceptualized in large sequence alignments, and the challenges in integrating MSAs with multiple orthogonal data such as cancer variants and post-translational modifications, which are often stored in heterogeneous data sources and formats. Here, we present the Multiple Sequence Alignment Ontology (MSAOnt), which represents a profile or consensus alignment in an ontological format. Subsets of the alignment are easily selected through the SPARQL Protocol and RDF Query Language for downstream statistical analysis or visualization. We have also created the Kinome Viewer (KinView), an interactive integrative visualization that places eukaryotic protein kinase cancer variants in the context of natural sequence variation and experimentally determined post-translational modifications, which play central roles in the regulation of cellular signaling pathways. Using KinView, we identified differential phosphorylation patterns between tyrosine and serine/threonine kinases in the activation segment, a major kinase regulatory region that is often mutated in proliferative diseases. We discuss cancer variants that disrupt phosphorylation sites in the activation segment, and show how KinView can be used as a comparative tool to identify differences and similarities in natural variation, cancer variants and post-translational modifications between kinase groups, families and subfamilies. Based on KinView comparisons, we identify and experimentally characterize a regulatory tyrosine (Y177PLK4) in the PLK4 C-terminal activation segment region termed the P+1 loop. To further demonstrate the application of KinView in hypothesis generation and testing, we formulate and validate a hypothesis explaining a novel predicted loss-of-function variant (D523NPKCβ) in the regulatory spine of PKCβ, a recently identified tumor suppressor kinase. KinView provides a novel, extensible interface for performing comparative analyses between subsets of kinases and for integrating multiple types of residue specific annotations in user friendly formats. PMID:27731453

Biological plywood film formation from para-nematic liquid crystalline organization.

PubMed

Aguilar Gutierrez, Oscar F; Rey, Alejandro D

2017-11-15

In vitro non-equilibrium chiral phase ordering processes of biomacromolecular solutions offer a systematic and reproducible way of generating material architectures found in Nature, such as biological plywoods. Accelerated progress in biomimetic engineering of mesoscopic plywoods and other fibrous structures requires a fundamental understanding of processing and transport principles. In this work we focus on collagen I based materials and structures to find processing conditions that lead to defect-free collagen films displaying the helicoidal plywood architecture. Here we report experimentally-guided theory and simulations of the chiral phase ordering of collagen molecules through water solvent evaporation of pre-aligned dilute collagen solutions. We develop, implement and a posteriori validate an integrated liquid crystal chiral phase ordering-water transport model that captures the essential features of spatio-temporal chiral structure formation in shrinking film domains due to directed water loss. Three microstructural (texture) modes are identified depending on the particular value of the time-scale ratio defined by collagen rotational diffusion to water translational diffusion. The magnitude of the time scale ratio provides the conditions for the synchronization of the helical axis morphogenesis with the increase in the mesogen concentration due to water loss. Slower than critical water removal rates leads to internal multiaxial cellular patterns, reminiscent of the classical columnar-equiaxed metallurgical casting structures. Excessive water removal rates lead to destabilization of the chiral axis and multidomain defected films. The predictions of the integrated model are in qualitative agreement with experimental results and can potentially guide solution processing of other bio-related mesogenic solutions that seek to mimic the architecture of biological fibrous composites.

Next generation multi-scale biophysical characterization of high precision cancer particle radiotherapy using clinical proton, helium-, carbon- and oxygen ion beams

PubMed Central

Niklas, Martin; Zimmermann, Ferdinand; Chaudhri, Naved; Krunic, Damir; Tessonnier, Thomas; Ferrari, Alfredo; Parodi, Katia; Jäkel, Oliver; Debus, Jürgen; Haberer, Thomas; Abdollahi, Amir

2016-01-01

The growing number of particle therapy facilities worldwide landmarks a novel era of precision oncology. Implementation of robust biophysical readouts is urgently needed to assess the efficacy of different radiation qualities. This is the first report on biophysical evaluation of Monte Carlo simulated predictive models of prescribed dose for four particle qualities i.e., proton, helium-, carbon- or oxygen ions using raster-scanning technology and clinical therapy settings at HIT. A high level of agreement was found between the in silico simulations, the physical dosimetry and the clonogenic tumor cell survival. The cell fluorescence ion track hybrid detector (Cell-Fit-HD) technology was employed to detect particle traverse per cell nucleus. Across a panel of radiobiological surrogates studied such as late ROS accumulation and apoptosis (caspase 3/7 activation), the relative biological effectiveness (RBE) chiefly correlated with the radiation species-specific spatio-temporal pattern of DNA double strand break (DSB) formation and repair kinetic. The size and the number of residual nuclear γ-H2AX foci increased as a function of linear energy transfer (LET) and RBE, reminiscent of enhanced DNA-damage complexity and accumulation of non-repairable DSB. These data confirm the high relevance of complex DSB formation as a central determinant of cell fate and reliable biological surrogates for cell survival/RBE. The multi-scale simulation, physical and radiobiological characterization of novel clinical quality beams presented here constitutes a first step towards development of high precision biologically individualized radiotherapy. PMID:27494855

Mammalian Cardiovascular Patterning as Determined by Hemodynamic Forces and Blood Vessel Genetics

NASA Astrophysics Data System (ADS)

Anderson, Gregory Arthur

Cardiovascular development is a process that involves the timing of multiple molecular events, and numerous subtle three-dimensional conformational changes. Traditional developmental biology techniques have provided large quantities of information as to how these complex organ systems develop. However, the major drawback of the majority of current developmental biological imaging is that they are two-dimensional in nature. It is now well recognized that circulation of blood is required for normal patterning and remodeling of blood vessels. Normal blood vessel formation is dependent upon a complex network of signaling pathways, and genetic mutations in these pathways leads to impaired vascular development, heart failure, and lethality. As such, it is not surprising that mutant mice with aberrant cardiovascular patterning are so common, since normal development requires proper coordination between three systems: the heart, the blood, and the vasculature. This thesis describes the implementation of a three-dimensional imaging technique, optical projection tomography (OPT), in conjunction with a computer-based registration algorithm to statistically analyze developmental differences in groups of wild-type mouse embryos. Embryos that differ by only a few hours' gestational time are shown to have developmental differences in blood vessel formation and heart development progression that can be discerned. This thesis describes how we analyzed mouse models of cardiovascular perturbation by OPT to detect morphological differences in embryonic development in both qualitative and quantitative ways. Both a blood vessel specific mutation and a cardiac specific mutation were analyzed, providing evidence that developmental defects of these types can be quantified. Finally, we describe the implementation of OPT imaging to identify statistically significant phenotypes from three different mouse models of cardiovascular perturbation across a range of developmental time points. Image registration methods, combined with intensity- and deformation-based analyses are described and utilized to fully characterize myosin light chain 2a (Mlc2a), delta-like ligand 4 (Dll4), and Endoglin (Eng) mutant mouse embryos. We show that Eng mutant embryos are statistically similar to the Mlc2a phenotype, confirming that these mouse mutants suffer from a primary cardiac developmental defect. Thus, a loss of hemodynamic force caused by defective pumping of the heart is the primary developmental defect affecting these mice.

Dynamical Signatures of Living Systems

NASA Technical Reports Server (NTRS)

Zak, M.

1999-01-01

One of the main challenges in modeling living systems is to distinguish a random walk of physical origin (for instance, Brownian motions) from those of biological origin and that will constitute the starting point of the proposed approach. As conjectured, the biological random walk must be nonlinear. Indeed, any stochastic Markov process can be described by linear Fokker-Planck equation (or its discretized version), only that type of process has been observed in the inanimate world. However, all such processes always converge to a stable (ergodic or periodic) state, i.e., to the states of a lower complexity and high entropy. At the same time, the evolution of living systems directed toward a higher level of complexity if complexity is associated with a number of structural variations. The simplest way to mimic such a tendency is to incorporate a nonlinearity into the random walk; then the probability evolution will attain the features of diffusion equation: the formation and dissipation of shock waves initiated by small shallow wave disturbances. As a result, the evolution never "dies:" it produces new different configurations which are accompanied by an increase or decrease of entropy (the decrease takes place during formation of shock waves, the increase-during their dissipation). In other words, the evolution can be directed "against the second law of thermodynamics" by forming patterns outside of equilibrium in the probability space. Due to that, a specie is not locked up in a certain pattern of behavior: it still can perform a variety of motions, and only the statistics of these motions is constrained by this pattern. It should be emphasized that such a "twist" is based upon the concept of reflection, i.e., the existence of the self-image (adopted from psychology). The model consists of a generator of stochastic processes which represents the motor dynamics in the form of nonlinear random walks, and a simulator of the nonlinear version of the diffusion equation which represents the mental dynamics. It has been demonstrated that coupled mental-motor dynamics can simulate emerging self-organization, prey-predator games, collaboration and competition, "collective brain," etc.

Rethinking the nature of fibrolamellar bone: an integrative biological revision of sauropod plexiform bone formation.

PubMed

Stein, Koen; Prondvai, Edina

2014-02-01

We present novel findings on sauropod bone histology that cast doubt on general palaeohistological concepts concerning the true nature of woven bone in primary cortical bone and its role in the rapid growth and giant body sizes of sauropod dinosaurs. By preparing and investigating longitudinal thin sections of sauropod long bones, of which transverse thin sections were published previously, we found that the amount of woven bone in the primary complex has been largely overestimated. Using comparative cellular and light-extinction characteristics in the two section planes, we revealed that the majority of the bony lamina consists of longitudinally organized primary bone, whereas woven bone is usually represented only by a layer a few cells thin in the laminae. Previous arguments on sauropod biology, which have been based on the overestimated amount, misinterpreted formation process and misjudged role of woven bone in the plexiform bone formation of sauropod dinosaurs, are thereby rejected. To explain the observed pattern in fossil bones, we review the most recent advances in bone biology concerning bone formation processes at the cellular and tissue levels. Differentiation between static and dynamic osteogenesis (SO and DO) and the revealed characteristics of SO- versus DO-derived bone tissues shed light on several questions raised by our palaeohistological results and permit identification of these bone tissues in fossils with high confidence. By presenting the methods generally used for investigating fossil bones, we show that the major cause of overestimation of the amount of woven bone in previous palaeohistological studies is the almost exclusive usage of transverse sections. In these sections, cells and crystallites of the longitudinally organized primary bone are cut transversely, thus cells appear rounded and crystallites remain dark under crossed plane polarizers, thereby giving the false impression of woven bone. In order to avoid further confusion in palaeohistological studies, we introduce new osteohistological terms as well as revise widely used but incorrect terminology. To infer the role of woven bone in the bone formation of fast-growing tetrapods, we review some aspects of the interrelationships between the vascularity of bone tissues, basal metabolic rate, body size and growth rate. By putting our findings into the context of osteogenesis, we provide a new model for the diametrical limb bone growth of sauropods and present new implications for the evolution of fast growth in vertebrates. Since biomechanical studies of bone tissues suggest that predominant collagen fibre orientation (CFO) is controlled by endogenous, functional and perhaps phylogenetic factors, the relationship between CFO and bone growth rate as defined by Amprino's rule, which has been the basis for the biological interpretation of several osteohistological features, must be revised. Our findings draw attention to the urgent need for revising widely accepted basic concepts of palaeohistological studies, and for a more integrative approach to bone formation, biomechanics and bone microstructural features of extant and extinct vertebrates to infer life history traits of long extinct, iconic animals like dinosaurs. © 2013 The Authors. Biological Reviews © 2013 Cambridge Philosophical Society.

Pattern formation in the iodate-sulfite-thiosulfate reaction-diffusion system.

PubMed

Liu, Haimiao; Pojman, John A; Zhao, Yuemin; Pan, Changwei; Zheng, Juhua; Yuan, Ling; Horváth, Attila K; Gao, Qingyu

2012-01-07

Sodium polyacrylate-induced pH pattern formation and starch-induced iodine pattern formation were investigated in the iodate-sulfite-thiosulfate (IST) reaction in a one-side fed disc gel reactor (OSFR). As binding agents of the autocatalyst of hydrogen ions or iodide ions, different content of sodium polyacrylate or starch has induced various types of pattern formation. We observed pH pulses, striped patterns, mixed spots and stripes, and hexagonal spots upon increasing the content of sodium polyacrylate and observed iodine pulses, branched patterns, and labyrinthine patterns upon increasing the starch content in the system. Coexistence of a pH front and an iodine front was also studied in a batch IST reaction-diffusion system. Both pH and iodine front instabilities were observed in the presence of sodium polyacrylate, i.e., cellular fronts and transient Turing structures resulting from the decrease in diffusion coefficients of activators. The mechanism of multiple feedback may explain the different patterns in the IST reaction-diffusion system.

Ring-shaped stain patterns driven by solute reactive mesogens in liquid crystal solution

NASA Astrophysics Data System (ADS)

Cha, Tae Woon; Bulliard, Xavier; Choi, Sang Gun; Lee, Hyoung Sub; Kong, Hyang-Shik; Han, Sang Youn

2014-07-01

We report on the formation of ring-shaped stain patterns in a polymer-stabilized patterned vertical alignment mode liquid crystal display (LCD) during the cell filling process. Through the interpretation of the formation mechanism, an effective way to control its development is provided. Systematic trace of the reactive mesogens reveals that the formation of patterns is strongly related to the segregation of solute mesogens in the stain area. These undesirable patterns can be avoided or controlled by reducing the drop volume at each droplet using an inkjet printing technique, meaning that the printing technique could be a useful solution in display technology. For the formation of ring-shaped patterns, the dragging of reactive mesogens during the spreading of the liquid crystal solution plays a key role in the closed LCD cell.

Modelling and formation of spatiotemporal patterns of fractional predation system in subdiffusion and superdiffusion scenarios

NASA Astrophysics Data System (ADS)

Owolabi, Kolade M.; Atangana, Abdon

2018-02-01

This paper primarily focused on the question of how population diffusion can affect the formation of the spatial patterns in the spatial fraction predator-prey system by Turing mechanisms. Our numerical findings assert that modeling by fractional reaction-diffusion equations should be considered as an appropriate tool for studying the fundamental mechanisms of complex spatiotemporal dynamics. We observe that pure Hopf instability gives rise to the formation of spiral patterns in 2D and pure Turing instability destroys the spiral pattern and results to the formation of chaotic or spatiotemporal spatial patterns. Existence and permanence of the species is also guaranteed with the 3D simulations at some instances of time for subdiffusive and superdiffusive scenarios.

Soliton interactions and the formation of solitonic patterns

NASA Astrophysics Data System (ADS)

Sears, Suzanne M.

From the stripes of a zebra, to the spirals of cream in a hot cup of coffee, we are surrounded by patterns in the natural world. But why are there patterns? Why drives their formation? In this thesis we study some of the diverse ways patterns can arise due to the interactions between solitary waves in nonlinear systems, sometimes starting from nothing more than random noise. What follows is a set of three studies. In the first, we show how a nonlinear system that supports solitons can be driven to generate exact (regular) Cantor set fractals. As an example, we use numerical simulations to demonstrate the formation of Cantor set fractals by temporal optical solitons. This fractal formation occurs in a cascade of nonlinear optical fibers through the dynamical evolution of a single input soliton. In the second study, we investigate pattern formation initiated by modulation instability in nonlinear partially coherent wave fronts and show that anisotropic noise and/or anisotropic correlation statistics can lead to ordered patterns such as grids and stripes. For the final study, we demonstrate the spontaneous clustering of solitons in partially coherent wavefronts during the final stages of pattern formation initiated by modulation instability and noise. Experimental observations are in agreement with theoretical predictions and are confirmed using numerical simulations.

Shaping tissues by balancing active forces and geometric constraints

NASA Astrophysics Data System (ADS)

Foolen, Jasper; Yamashita, Tadahiro; Kollmannsberger, Philip

2016-02-01

The self-organization of cells into complex tissues during growth and regeneration is a combination of physical-mechanical events and biochemical signal processing. Cells actively generate forces at all stages in this process, and according to the laws of mechanics, these forces result in stress fields defined by the geometric boundary conditions of the cell and tissue. The unique ability of cells to translate such force patterns into biochemical information and vice versa sets biological tissues apart from any other material. In this topical review, we summarize the current knowledge and open questions of how forces and geometry act together on scales from the single cell to tissues and organisms, and how their interaction determines biological shape and structure. Starting with a planar surface as the simplest type of geometric constraint, we review literature on how forces during cell spreading and adhesion together with geometric constraints impact cell shape, stress patterns, and the resulting biological response. We then move on to include cell-cell interactions and the role of forces in monolayers and in collective cell migration, and introduce curvature at the transition from flat cell sheets to three-dimensional (3D) tissues. Fibrous 3D environments, as cells experience them in the body, introduce new mechanical boundary conditions and change cell behaviour compared to flat surfaces. Starting from early work on force transmission and collagen remodelling, we discuss recent discoveries on the interaction with geometric constraints and the resulting structure formation and network organization in 3D. Recent literature on two physiological scenarios—embryonic development and bone—is reviewed to demonstrate the role of the force-geometry balance in living organisms. Furthermore, the role of mechanics in pathological scenarios such as cancer is discussed. We conclude by highlighting common physical principles guiding cell mechanics, tissue patterning and matrix organization under geometric constraints across multiple length and time scales.

Microalga Scenedesmus sp.: A potential low-cost green machine for silver nanoparticle synthesis.

PubMed

Jena, Jayashree; Pradhan, Nilotpala; Nayak, Rati Ranjan; Dash, Bishnu P; Sukla, Lala Behari; Panda, Prasanna K; Mishra, Barada K

2014-04-01

Bionanotechnology has revolutionized nanomaterial synthesis by providing a green synthetic platform using biological systems. Among such biological systems, microalgae have tremendous potential to take up metal ions and produce nanoparticles by a detoxification process. The present study explores the intracellular and extracellular biogenic syntheses of silver nanoparticles (SNPs) using the unicellular green microalga Scenedesmus sp. Biosynthesized SNPs were characterized by AAS, UV-Vis spectroscopy, TEM, XRD, FTIR, DLS, and TGA studies and finally checked for antibacterial activity. Intracellular nanoparticle biosynthesis was initiated by a high rate of Ag(+) ion accumulation in the microalgal biomass and subsequent formation of spherical crystalline SNPs (average size, 15-20 nm) due to the biochemical reduction of Ag(+) ions. The synthesized nanoparticles were intracellular, as confirmed by the UV-Vis spectra of the outside medium. Furthermore, extracellular synthesis using boiled extract showed the formation of well scattered, highly stable, spherical SNPs with an average size of 5-10 nm. The size and morphology of the nanoparticles were confirmed by TEM. The crystalline nature of the SNPs was evident from the diffraction peaks of XRD and bright circular ring pattern of SAED. FTIR and UV-Vis spectra showed that biomolecules, proteins and peptides, are mainly responsible for the formation and stabilization of SNPs. Furthermore, the synthesized nanoparticles exhibited high antimicrobial activity against pathogenic gram-negative and gram-positive bacteria. Use of such a microalgal system provides a simple, cost-effective alternative template for the biosynthesis of nanomaterials in a large-scale system that could be of great use in biomedical applications.

Degradation of pesticide mixture on modified matrix of a biopurification system with alternatives lignocellulosic wastes.

PubMed

Urrutia, C; Rubilar, O; Tortella, G R; Diez, M C

2013-08-01

The biobed systems were designed to retain and to degrade pesticides through the properties of a biomixture composed of straw (ST), topsoil and peat (PT) 2:1:1 v/v. The ST is the main substrate in the biomixture, as it allows the proliferation of fungi that promotes pesticide degradation. The use of readily available components in the biomixture is an important aspect to build a biobed. Therefore, potential use of readily available wastes as barley husk (BH), sawdust (SW) and oat husk (OH), as total or partial substitutes of ST were tested in pesticide degradation studies. Metabolite formation and the biological activities were also evaluated. Biomixture composed of OH was highly efficient in pesticide degradation, with t½ values of 28.6, 58.9 and 26.8 d for atrazine (ATZ), chlorpyrifos (CHL) and isoproturon (ISP). On the other hand, comparable for degrading capacities with the ST based biomixture were obtained with SW and BH, but only as partial replacement. Contrarily, high t½ values (more than 100 d) were obtained in biomixtures with total substitution of ST by SW or BH. Metabolite formation was observed in all biomixtures tested, but without clear formation patterns. Moreover, high and stable biological activity was observed in the biomixtures composed of OH. Therefore, our results demonstrated that ST can be partial or totally replaced by OH in the biomixture allowing an efficient degradation of pesticide mixture. However, it is recommended that ST can be only partially replaced by BH and SW in the biomixture to allow efficient pesticide degradation. Copyright © 2013. Published by Elsevier Ltd.

Argon ion beam induced surface pattern formation on Si

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hofsäss, H.; Bobes, O.; Zhang, K.

The development of self-organized surface patterns on Si due to noble gas ion irradiation has been studied extensively in the past. In particular, Ar ions are commonly used and the pattern formation was analyzed as function of ion incidence angle, ion fluence, and ion energies between 250 eV and 140 keV. Very few results exist for the energy regime between 1.5 keV and 10 keV and it appears that pattern formation is completely absent for these ion energies. In this work, we present experimental data on pattern formation for Ar ion irradiation between 1 keV and 10 keV and ion incidence angles between 50° and 75°.more » We confirm the absence of patterns at least for ion fluences up to 10{sup 18} ions/cm{sup 2}. Using the crater function formalism and Monte Carlo simulations, we calculate curvature coefficients of linear continuum models of pattern formation, taking into account contribution due to ion erosion and recoil redistribution. The calculations consider the recently introduced curvature dependence of the erosion crater function as well as the dynamic behavior of the thickness of the ion irradiated layer. Only when taking into account these additional contributions to the linear theory, our simulations clearly show that that pattern formation is strongly suppressed between about 1.5 keV and 10 keV, most pronounced at 3 keV. Furthermore, our simulations are now able to predict whether or not parallel oriented ripple patterns are formed, and in case of ripple formation the corresponding critical angles for the whole experimentally studied energies range between 250 eV and 140 keV.« less

78 FR 12760 - Guidance for Industry on Labeling for Human Prescription Drug and Biological Products...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-25

...The Food and Drug Administration (FDA) is announcing the availability of a guidance for industry entitled ``Labeling for Human Prescription Drug and Biological Products--Implementing the PLR Content and Format Requirements.'' This guidance is intended to assist applicants in complying with the content and format requirements of labeling for human prescription drug and biological products. The recommendations in this guidance will help ensure that the labeling is clear; useful; informative; and to the extent possible, consistent in content and format. It will assist applicants in developing labeling for new products, revising existing labeling, and implementing the requirements on content and format of labeling for human prescription drug and biological products (71 FR 3922), which appeared in the Federal Register of January 24, 2006. The rule is commonly referred to as the ``Physician Labeling Rule'' (PLR) because it addresses prescription drug labeling that is used by prescribers and other health care practitioners.

Control of Oscillation Patterns in a Symmetric Coupled Biological Oscillator System

NASA Astrophysics Data System (ADS)

Takamatsu, Atsuko; Tanaka, Reiko; Yamamoto, Takatoki; Fujii, Teruo

2003-08-01

A chain of three-oscillator system was constructed with living biological oscillators of phasmodial slime mold, Physarum polycehalum and the oscillation patterns were analyzed by the symmetric Hopf bifurcation theory using group theory. Multi-stability of oscillation patterns was observed, even when the coupling strength was fixed. This suggests that the coupling strength is not an effective parameter to obtain a desired oscillation pattern among the multiple patterns. Here we propose a method to control oscillation patterns using resonance to external stimulus and demonstrate pattern switching induced by frequency resonance given to only one of oscillators in the system.

Biofilm Formation and Dispersal under the Influence of the Global Regulator CsrA of Escherichia coli

PubMed Central

Jackson, Debra W.; Suzuki, Kazushi; Oakford, Lawrence; Simecka, Jerry W.; Hart, Mark E.; Romeo, Tony

2002-01-01

The predominant mode of growth of bacteria in the environment is within sessile, matrix-enclosed communities known as biofilms. Biofilms often complicate chronic and difficult-to-treat infections by protecting bacteria from the immune system, decreasing antibiotic efficacy, and dispersing planktonic cells to distant body sites. While the biology of bacterial biofilms has become a major focus of microbial research, the regulatory mechanisms of biofilm development remain poorly defined and those of dispersal are unknown. Here we establish that the RNA binding global regulatory protein CsrA (carbon storage regulator) of Escherichia coli K-12 serves as both a repressor of biofilm formation and an activator of biofilm dispersal under a variety of culture conditions. Ectopic expression of the E. coli K-12 csrA gene repressed biofilm formation by related bacterial pathogens. A csrA knockout mutation enhanced biofilm formation in E. coli strains that were defective for extracellular, surface, or regulatory factors previously implicated in biofilm formation. In contrast, this csrA mutation did not affect biofilm formation by a glgA (glycogen synthase) knockout mutant. Complementation studies with glg genes provided further genetic evidence that the effects of CsrA on biofilm formation are mediated largely through the regulation of intracellular glycogen biosynthesis and catabolism. Finally, the expression of a chromosomally encoded csrA′-′lacZ translational fusion was dynamically regulated during biofilm formation in a pattern consistent with its role as a repressor. We propose that global regulation of central carbon flux by CsrA is an extremely important feature of E. coli biofilm development. PMID:11741870

Spongiosa Primary Development: A Biochemical Hypothesis by Turing Patterns Formations

PubMed Central

López-Vaca, Oscar Rodrigo; Garzón-Alvarado, Diego Alexander

2012-01-01

We propose a biochemical model describing the formation of primary spongiosa architecture through a bioregulatory model by metalloproteinase 13 (MMP13) and vascular endothelial growth factor (VEGF). It is assumed that MMP13 regulates cartilage degradation and the VEGF allows vascularization and advances in the ossification front through the presence of osteoblasts. The coupling of this set of molecules is represented by reaction-diffusion equations with parameters in the Turing space, creating a stable spatiotemporal pattern that leads to the formation of the trabeculae present in the spongy tissue. Experimental evidence has shown that the MMP13 regulates VEGF formation, and it is assumed that VEGF negatively regulates MMP13 formation. Thus, the patterns obtained by ossification may represent the primary spongiosa formation during endochondral ossification. Moreover, for the numerical solution, we used the finite element method with the Newton-Raphson method to approximate partial differential nonlinear equations. Ossification patterns obtained may represent the primary spongiosa formation during endochondral ossification. PMID:23193429

Guided by curvature: shaping cells by coupling curved membrane proteins and cytoskeletal forces.

PubMed

Gov, N S

2018-05-26

Eukaryote cells have flexible membranes that allow them to have a variety of dynamical shapes. The shapes of the cells serve important biological functions, both for cells within an intact tissue, and during embryogenesis and cellular motility. How cells control their shapes and the structures that they form on their surface has been a subject of intensive biological research, exposing the building blocks that cells use to deform their membranes. These processes have also drawn the interest of theoretical physicists, aiming to develop models based on physics, chemistry and nonlinear dynamics. Such models explore quantitatively different possible mechanisms that the cells can employ to initiate the spontaneous formation of shapes and patterns on their membranes. We review here theoretical work where one such class of mechanisms was investigated: the coupling between curved membrane proteins, and the cytoskeletal forces that they recruit. Theory indicates that this coupling gives rise to a rich variety of membrane shapes and dynamics, while experiments indicate that this mechanism appears to drive many cellular shape changes.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).

Remote sensing of ocean color in the Arctic

NASA Technical Reports Server (NTRS)

Maynard, N. G.

1988-01-01

The main objectives of the research are: to increase the understanding of biological production (and carbon fluxes) along the ice edge, in frontal regions, and in open water areas of the Arctic and the physical factors controlling that production through the use of satellite and aircraft remote sensing techniques; and to develop relationships between measured radiances from the Multichannel Aircraft Radiometer System (MARS) and the bio-optical properties of the water in the Arctic and adjacent seas. Several recent Coastal Zone Color Scanner (CZCS) studies in the Arctic have shown that, despite constraints imposed by cloud cover, satellite ocean color is a useful means of studying mesoscale physical and biological oceanographic phenomena at high latitudes. The imagery has provided detailed information on ice edge and frontal processes such as spring breakup and retreat of the ice edge, influence of ice on ice effects of stratification on phytoplankton production, river sediment transport, effects of spring runoff, water mass boundaries, circulation patterns, and eddy formation in Icelandic waters and in the Greenland, Barents, Norwegian, and Bering Seas.

Clustering and Network Analysis of Reverse Phase Protein Array Data.

PubMed

Byron, Adam

2017-01-01

Molecular profiling of proteins and phosphoproteins using a reverse phase protein array (RPPA) platform, with a panel of target-specific antibodies, enables the parallel, quantitative proteomic analysis of many biological samples in a microarray format. Hence, RPPA analysis can generate a high volume of multidimensional data that must be effectively interrogated and interpreted. A range of computational techniques for data mining can be applied to detect and explore data structure and to form functional predictions from large datasets. Here, two approaches for the computational analysis of RPPA data are detailed: the identification of similar patterns of protein expression by hierarchical cluster analysis and the modeling of protein interactions and signaling relationships by network analysis. The protocols use freely available, cross-platform software, are easy to implement, and do not require any programming expertise. Serving as data-driven starting points for further in-depth analysis, validation, and biological experimentation, these and related bioinformatic approaches can accelerate the functional interpretation of RPPA data.

The heparanome--the enigma of encoding and decoding heparan sulfate sulfation.

PubMed

Lamanna, William C; Kalus, Ina; Padva, Michael; Baldwin, Rebecca J; Merry, Catherine L R; Dierks, Thomas

2007-04-30

Heparan sulfate (HS) is a cell surface carbohydrate polymer modified with sulfate moieties whose highly ordered composition is central to directing specific cell signaling events. The ability of the cell to generate these information rich glycans with such specificity has opened up a new field of "heparanomics" which seeks to understand the systems involved in generating these cell type and developmental stage specific HS sulfation patterns. Unlike other instances where biological information is encrypted as linear sequences in molecules such as DNA, HS sulfation patterns are generated through a non-template driven process. Thus, deciphering the sulfation code and the dynamic nature of its generation has posed a new challenge to system biologists. The recent discovery of two sulfatases, Sulf1 and Sulf2, with the unique ability to edit sulfation patterns at the cell surface, has opened up a new dimension as to how we understand the regulation of HS sulfation patterning and pattern-dependent cell signaling events. This review will focus on the functional relationship between HS sulfation patterning and biological processes. Special attention will be given to Sulf1 and Sulf2 and how these key editing enzymes might act in concert with the HS biosynthetic enzymes to generate and regulate specific HS sulfation patterns in vivo. We will further explore the use of knock out mice as biological models for understanding the dynamic systems involved in generating HS sulfation patterns and their biological relevance. A brief overview of new technologies and innovations summarizes advances in the systems biology field for understanding non-template molecular networks and their influence on the "heparanome".

Biomimetic engineering of a generic cell-on-membrane architecture by microfluidic engraving for on-chip bioassays.

PubMed

Lee, Sang-Wook; Noh, Ji-Yoon; Park, Seung Chul; Chung, Jin-Ho; Lee, Byoungho; Lee, Sin-Doo

2012-05-22

We develop a biomimetic cell-on-membrane architecture in close-volume format which allows the interfacial biocompatibility and the reagent delivery capability for on-chip bioassays. The key concept lies in the microfluidic engraving of lipid membranes together with biological cells on a supported substrate with topographic patterns. The simultaneous engraving process of a different class of fluids is promoted by the front propagation of an air-water interface inside a flow-cell. This highly parallel, microfluidic cell-on-membrane approach opens a door to the natural biocompatibility in mimicking cellular stimuli-response behavior essential for diverse on-chip bioassays that can be precisely controlled in the spatial and temporal manner.

Biology of Bone: The Vasculature of the Skeletal System.

PubMed

Watson, Emma C; Adams, Ralf H

2017-09-11

Blood vessels are essential for the distribution of oxygen, nutrients, and immune cells, as well as the removal of waste products. In addition to this conventional role as a versatile conduit system, the endothelial cells forming the innermost layer of the vessel wall also possess important signaling capabilities and can control growth, patterning, homeostasis, and regeneration of the surrounding organ. In the skeletal system, blood vessels regulate developmental and regenerative bone formation as well as hematopoiesis by providing vascular niches for hematopoietic stem cells. Here we provide an overview of blood vessel architecture, growth and properties in the healthy, aging, and diseased skeletal system. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Site Formation Processes and Hunter-Gatherers Use of Space in a Tropical Environment: A Geo-Ethnoarchaeological Approach from South India

PubMed Central

Friesem, David E.; Lavi, Noa; Madella, Marco; Ajithprasad, P.; French, Charles

2016-01-01

Hunter-gatherer societies have distinct social perceptions and practices which are expressed in unique use of space and material deposition patterns. However, the identification of archaeological evidence associated with hunter-gatherer activity is often challenging, especially in tropical environments such as rainforests. We present an integrated study combining ethnoarchaeology and geoarchaeology in order to study archaeological site formation processes related to hunter-gatherers’ ways of living in tropical forests. Ethnographic data was collected from an habitation site of contemporary hunter-gatherers in the forests of South India, aimed at studying how everyday activities and way of living dictate patterns of material deposition. Ethnoarchaeological excavations of abandoned open-air sites and a rock-shelter of the same group located deep in the forests, involved field observations and sampling of sediments from the abandoned sites and the contemporary site. Laboratory analyses included geochemical analysis (i.e., FTIR, ICP-AES), phytolith concentration analysis and soil micromorphology. The results present a dynamic spatial deposition pattern of macroscopic, microscopic and chemical materials, which stem from the distinctive ways of living and use of space by hunter-gatherers. This study shows that post-depositional processes in tropical forests result in poor preservation of archaeological materials due to acidic conditions and intensive biological activity within the sediments. Yet, the multiple laboratory-based analyses were able to trace evidence for activity surfaces and their maintenance practices as well as localized concentrations of activity remains such as the use of plants, metals, hearths and construction materials. PMID:27783683

Spatial Control of Bacteria Using Screen Printing

PubMed Central

Moon, Soonhee; Fritz, Ian L.; Singer, Zakary S.

2016-01-01

Abstract Synthetic biology has led to advances in both our understanding and engineering of genetic circuits that affect spatial and temporal behaviors in living cells. A growing array of native and synthetic circuits such as oscillators, pattern generators, and cell–cell communication systems has been studied, which exhibit spatiotemporal properties. To better understand the design principles of these genetic circuits, there is a need for versatile and precise methods for patterning cell populations in various configurations. In this study, we develop a screen printing methodology to pattern bacteria on agar, glass, and paper surfaces. Initially, we tested three biocompatible resuspension media with appropriate rheological properties for screen printing. Using microscopy, we characterized the resolution and bleed of bacteria screen prints on agar and glass surfaces, obtaining resolutions as low as 188 μm. Next, we engineered bacterial strains producing visible chromoproteins analogous to the cyan, magenta, and yellow subtractive color system for the creation of multicolored bacteria images. Using this system, we printed distinct populations in overlapping or interlocking designs on both paper and agar substrates. These proof-of-principle experiments demonstrated how the screen printing method could be used to study microbial community interactions and pattern formation of biofilms at submillimeter length scales. Overall, our approach allows for rapid and precise prototyping of patterned bacteria species that will be useful in the understanding and engineering of spatiotemporal behaviors in microbial communities. PMID:29577061

Effects of convection patterns on freckle formation of directionally solidified Nickel-based superalloy casting with abruptly varying cross-sections

NASA Astrophysics Data System (ADS)

Qin, Ling; Shen, Jun; Li, Qiudong; Shang, Zhao

2017-05-01

The effects of convection patterns on freckle formation of directionally solidified Nickel-based superalloy sample with abruptly varying cross-sections were investigated experimentally and numerically. The experimental results demonstrate that freckles were only observed at the bottom of larger cross-section. Numerical results indicate that this phenomenon should be attributed to the different convection patterns at front of solidification interface. As the withdrawal rate increased, the primary dendrites spacing has an obvious influence on freckle formation. A more in-depth investigation of the convection patterns can provide a better understanding of freckle formation and perhaps offer methods to minimize freckles in turbine blades.

Using self-assembled monolayers to pattern ECM proteins and cells on substrates.

PubMed

Ostuni, Emanuele; Whitesides, George M; Ingber, Donald E; Chen, Christopher S

2009-01-01

We present a method that uses microcontact printing of alkanethiols on gold to generate patterned substrates presenting "islands" of extracellular matrix (ECM) surrounded by nonadhesive regions such that single cells attach and spread only on the adhesive regions. We have used this micropatterning technology to demonstrate that mammalian cells can be switched between growth and apoptosis programs in the presence of saturating concentrations of growth factors by either promoting or preventing cell spreading (Science 276:1425-1428, 1997). From the perspective of fundamental cell biology, these results suggested that the local differentials in growth and viability that are critical for the formation of complex tissue patterns may be generated by local changes in cell-ECM interactions. In the context of cell culture technologies, such as bioreactors and cellular engineering applications, the regulation of cell function by cell shape indicates that the adhesive microenvironment around cells can be carefully optimized by patterning a substrate in addition to using soluble factors (Biotech. Prog. 14:356-363, 1998). Micropatterning technology is playing a central role both in our understanding how ECM and cell shape regulate cell physiology and in facilitating the development of cellular biosensor and tissue engineering applications (Science 264:696-698, 1994; J. Neurosci. Res. 13:213-20, 1985; Biotech. Bioeng. 43:792-800, 1994).

Sugar-Based Polyamides: Self-Organization in Strong Polar Organic Solvents.

PubMed

Rosu, Cornelia; Russo, Paul S; Daly, William H; Cueto, Rafael; Pople, John A; Laine, Roger A; Negulescu, Ioan I

2015-09-14

Periodic patterns resembling spirals were observed to form spontaneously upon unassisted cooling of d-glucaric acid- and d-galactaric acid-based polyamide solutions in N-methyl-N-morpholine oxide (NMMO) monohydrate. Similar observations were made in d-galactaric acid-based polyamide/ionic liquid (IL) solutions. The morphologies were investigated by optical, polarized light and confocal microscopy assays to reveal pattern details. Differential scanning calorimetry was used to monitor solution thermal behavior. Small- and wide-angle X-ray scattering data reflected the complex and heterogeneous nature of the self-organized patterns. Factors such as concentration and temperature were found to influence spiral dimensions and geometry. The distance between rings followed a first-order exponential decay as a function of polymer concentration. Fourier-Transform Infrared Microspectroscopy analysis of spirals pointed to H-bonding between the solvent and the pendant hydroxyl groups of the glucose units from the polymer backbone. Tests on self-organization into spirals of ketal-protected d-galactaric acid polyamides in NMMO monohydrate confirmed the importance of the monosaccharide's pendant free hydroxyl groups on the formation of these patterns. Rheology performed on d-galactaric-based polyamides at high concentration in NMMO monohydrate solution revealed the optimum conditions necessary to process these materials as fibers by spinning. The self-organization of these sugar-based polyamides mimics certain biological materials.

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.

PubMed

McDonald, Daniel; Clemente, Jose C; Kuczynski, Justin; Rideout, Jai Ram; Stombaugh, Jesse; Wendel, Doug; Wilke, Andreas; Huse, Susan; Hufnagle, John; Meyer, Folker; Knight, Rob; Caporaso, J Gregory

2012-07-12

We present the Biological Observation Matrix (BIOM, pronounced "biome") format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observation metadata. As the number of categories of comparative omics data types (collectively, the "ome-ome") grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses. The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages. The BIOM file format and the biom-format project are steps toward reducing the "bioinformatics bottleneck" that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium.

Velocity-curvature patterns limit human-robot physical interaction

PubMed Central

Maurice, Pauline; Huber, Meghan E.; Hogan, Neville; Sternad, Dagmar

2018-01-01

Physical human-robot collaboration is becoming more common, both in industrial and service robotics. Cooperative execution of a task requires intuitive and efficient interaction between both actors. For humans, this means being able to predict and adapt to robot movements. Given that natural human movement exhibits several robust features, we examined whether human-robot physical interaction is facilitated when these features are considered in robot control. The present study investigated how humans adapt to biological and non-biological velocity patterns in robot movements. Participants held the end-effector of a robot that traced an elliptic path with either biological (two-thirds power law) or non-biological velocity profiles. Participants were instructed to minimize the force applied on the robot end-effector. Results showed that the applied force was significantly lower when the robot moved with a biological velocity pattern. With extensive practice and enhanced feedback, participants were able to decrease their force when following a non-biological velocity pattern, but never reached forces below those obtained with the 2/3 power law profile. These results suggest that some robust features observed in natural human movements are also a strong preference in guided movements. Therefore, such features should be considered in human-robot physical collaboration. PMID:29744380

Velocity-curvature patterns limit human-robot physical interaction.

PubMed

Maurice, Pauline; Huber, Meghan E; Hogan, Neville; Sternad, Dagmar

2018-01-01

Physical human-robot collaboration is becoming more common, both in industrial and service robotics. Cooperative execution of a task requires intuitive and efficient interaction between both actors. For humans, this means being able to predict and adapt to robot movements. Given that natural human movement exhibits several robust features, we examined whether human-robot physical interaction is facilitated when these features are considered in robot control. The present study investigated how humans adapt to biological and non-biological velocity patterns in robot movements. Participants held the end-effector of a robot that traced an elliptic path with either biological (two-thirds power law) or non-biological velocity profiles. Participants were instructed to minimize the force applied on the robot end-effector. Results showed that the applied force was significantly lower when the robot moved with a biological velocity pattern. With extensive practice and enhanced feedback, participants were able to decrease their force when following a non-biological velocity pattern, but never reached forces below those obtained with the 2/3 power law profile. These results suggest that some robust features observed in natural human movements are also a strong preference in guided movements. Therefore, such features should be considered in human-robot physical collaboration.

Studies with infections fragments of phage DNA. Final report, January 1, 1970--June 30, 1976

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schachtele, C. F.

The minute, virulent and structurally intricate Bacillus subtilis bacteriophage phi 29 was utilized to study in vivo viral development. Purified strands of phi 29 DNA were used to analyze transcription of the viral genome. Early mRNA hybridizes to the light DNA strand which controls DNA replication and other early functions. Late mRNA hybridizes to the heavy DNA strand which codes for phage structural proteins. The temporal sequence of specific viral protein synthesis was analyzed by gel electrophoresis and was shown to directly correlate with the RNA transcription pattern. The genes carried by phi 29 have been marked with ts andmore » sus mutations and mapped by appropriate crosses yielding a linear map of 17 cistrons. Fragments of the phi 29 DNA were shown to retain their biological activity and marker rescue studies indicated that gene transfer could be performed with pieces having a molecular weight of less than 1 million daltons. Mutant infection under nonpermissive conditions and the analysis of precursor structures has allowed the formation of a tentative morphogenetic pathway leading to the formation of infectious particles. Work with phi 29 has established this virus as an advantageous model system for studying a variety of problems in molecular biology and approximately a dozen laboratories in the country and abroad are working with this phage.« less

Stem cell- and scaffold-based tissue engineering approaches to osteochondral regenerative medicine

PubMed Central

Sundelacruz, Sarah; Kaplan, David L.

2009-01-01

In osteochondral tissue engineering, cell recruitment, proliferation, differentiation, and patterning are critical for forming biologically and structurally viable constructs for repair of damaged or diseased tissue. However, since constructs prepared ex vivo lack the multitude of cues present in the in vivo microenvironment, cells often need to be supplied with external biological and physical stimuli to coax them towards targeted tissue functions. To determine which stimuli to present to cells, bioengineering strategies can benefit significantly from endogenous examples of skeletogenesis. As an example of developmental skeletogenesis, the developing limb bud serves as an excellent model system in which to study how an osteochondral structures form from undifferentiated precursor cells. Alongside skeletal formation during embryogenesis, bone also possesses innate regenerative capacity, displaying remarkable ability to heal after damage. Bone fracture healing shares many features with bone development, driving the hypothesis that the regenerative process generally recapitulates development. Similarities and differences between the two modes of bone formation may offer insight into the special requirements for healing damaged or diseased bone. Thus, endogenous fracture healing, as an example of regenerative skeletogenesis, may also inform bioengineering strategies. In this review, we summarize the key cellular events involving stem and progenitor cells in developmental and regenerative skeletogenesis, and discuss in parallel the corresponding cell- and scaffold-based strategies that tissue engineers employ to recapitulate these events in vitro. PMID:19508851

Formation mechanism of complex pattern on fishes' skin

NASA Astrophysics Data System (ADS)

Li, Xia; Liu, Shuhua

2009-10-01

In this paper, the formation mechanism of the complex patterns observed on the skin of fishes has been investigated by a two-coupled reaction diffusion model. The effects of coupling strength between two layers play an important role in the pattern-forming process. It is found that only the epidermis layer can produce complicated patterns that have structures on more than one length scale. These complicated patterns including super-stripe pattern, mixture of spots and stripe, and white-eye pattern are similar to the pigmentation patterns on fishes' skin.

Analytic model for ring pattern formation by bacterial swarmers

NASA Astrophysics Data System (ADS)

Arouh, Scott

2001-03-01

We analyze a model proposed by Medvedev, Kaper, and Kopell (the MKK model) for ring formation in two-dimensional bacterial colonies of Proteus mirabilis. We correct the model to formally include a feature crucial of the ring generation mechanism: a bacterial density threshold to the nonlinear diffusivity of the MKK model. We numerically integrate the model equations, and observe the logarithmic profiles of the bacterial densities near the front. These lead us to define a consolidation front distinct from the colony radius. We find that this consolidation front propagates outward toward the colony radius with a nearly constant velocity. We then implement the corrected MKK equations in two dimensions and compare our results with biological experiment. Our numerical results indicate that the two-dimensional corrected MKK model yields smooth (rather than branched) rings, and that colliding colonies merge if grown in phase but not if grown out of phase. We also introduce a model, based on coupling the MKK model to a nutrient field, for simulating experimentally observed branched rings.

Wound Healing Problems in the Mouth

PubMed Central

Politis, Constantinus; Schoenaers, Joseph; Jacobs, Reinhilde; Agbaje, Jimoh O.

2016-01-01

Wound healing is a primary survival mechanism that is largely taken for granted. The literature includes relatively little information about disturbed wound healing, and there is no acceptable classification describing wound healing process in the oral region. Wound healing comprises a sequence of complex biological processes. All tissues follow an essentially identical pattern to complete the healing process with minimal scar formation. The oral cavity is a remarkable environment in which wound healing occurs in warm oral fluid containing millions of microorganisms. The present review provides a basic overview of the wound healing process and with a discussion of the local and general factors that play roles in achieving efficient would healing. Results of oral cavity wound healing can vary from a clinically healed wound without scar formation and with histologically normal connective tissue under epithelial cells to extreme forms of trismus caused by fibrosis. Many local and general factors affect oral wound healing, and an improved understanding of these factors will help to address issues that lead to poor oral wound healing. PMID:27853435

PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables.

PubMed

Pounds, Stan; Cheng, Cheng; Cao, Xueyuan; Crews, Kristine R; Plunkett, William; Gandhi, Varsha; Rubnitz, Jeffrey; Ribeiro, Raul C; Downing, James R; Lamba, Jatinder

2009-08-15

In some applications, prior biological knowledge can be used to define a specific pattern of association of multiple endpoint variables with a genomic variable that is biologically most interesting. However, to our knowledge, there is no statistical procedure designed to detect specific patterns of association with multiple endpoint variables. Projection onto the most interesting statistical evidence (PROMISE) is proposed as a general procedure to identify genomic variables that exhibit a specific biologically interesting pattern of association with multiple endpoint variables. Biological knowledge of the endpoint variables is used to define a vector that represents the biologically most interesting values for statistics that characterize the associations of the endpoint variables with a genomic variable. A test statistic is defined as the dot-product of the vector of the observed association statistics and the vector of the most interesting values of the association statistics. By definition, this test statistic is proportional to the length of the projection of the observed vector of correlations onto the vector of most interesting associations. Statistical significance is determined via permutation. In simulation studies and an example application, PROMISE shows greater statistical power to identify genes with the interesting pattern of associations than classical multivariate procedures, individual endpoint analyses or listing genes that have the pattern of interest and are significant in more than one individual endpoint analysis. Documented R routines are freely available from www.stjuderesearch.org/depts/biostats and will soon be available as a Bioconductor package from www.bioconductor.org.

The thioredoxin TRX-1 modulates the function of the insulin-like neuropeptide DAF-28 during dauer formation in Caenorhabditis elegans.

PubMed

Fierro-González, Juan Carlos; Cornils, Astrid; Alcedo, Joy; Miranda-Vizuete, Antonio; Swoboda, Peter

2011-01-27

Thioredoxins comprise a conserved family of redox regulators involved in many biological processes, including stress resistance and aging. We report that the C. elegans thioredoxin TRX-1 acts in ASJ head sensory neurons as a novel modulator of the insulin-like neuropeptide DAF-28 during dauer formation. We show that increased formation of stress-resistant, long-lived dauer larvae in mutants for the gene encoding the insulin-like neuropeptide DAF-28 requires TRX-1 acting in ASJ neurons, upstream of the insulin-like receptor DAF-2. Genetic rescue experiments demonstrate that redox-independent functions of TRX-1 specifically in ASJ neurons are needed for the dauer formation constitutive (Daf-c) phenotype of daf-28 mutants. GFP reporters of trx-1 and daf-28 show opposing expression patterns in dauers (i.e. trx-1 is up-regulated and daf-28 is down-regulated), an effect that is not observed in growing L2/L3 larvae. In addition, functional TRX-1 is required for the down-regulation of a GFP reporter of daf-28 during dauer formation, a process that is likely subject to DAF-28-mediated feedback regulation. Our findings demonstrate that TRX-1 modulates DAF-28 signaling by contributing to the down-regulation of daf-28 expression during dauer formation. We propose that TRX-1 acts as a fluctuating neuronal signaling modulator within ASJ neurons to monitor the adjustment of neuropeptide expression, including insulin-like proteins, during dauer formation in response to adverse environmental conditions.

The Thioredoxin TRX-1 Modulates the Function of the Insulin-Like Neuropeptide DAF-28 during Dauer Formation in Caenorhabditis elegans

PubMed Central

Fierro-González, Juan Carlos; Cornils, Astrid; Alcedo, Joy

2011-01-01

Thioredoxins comprise a conserved family of redox regulators involved in many biological processes, including stress resistance and aging. We report that the C. elegans thioredoxin TRX-1 acts in ASJ head sensory neurons as a novel modulator of the insulin-like neuropeptide DAF-28 during dauer formation. We show that increased formation of stress-resistant, long-lived dauer larvae in mutants for the gene encoding the insulin-like neuropeptide DAF-28 requires TRX-1 acting in ASJ neurons, upstream of the insulin-like receptor DAF-2. Genetic rescue experiments demonstrate that redox-independent functions of TRX-1 specifically in ASJ neurons are needed for the dauer formation constitutive (Daf-c) phenotype of daf-28 mutants. GFP reporters of trx-1 and daf-28 show opposing expression patterns in dauers (i.e. trx-1 is up-regulated and daf-28 is down-regulated), an effect that is not observed in growing L2/L3 larvae. In addition, functional TRX-1 is required for the down-regulation of a GFP reporter of daf-28 during dauer formation, a process that is likely subject to DAF-28-mediated feedback regulation. Our findings demonstrate that TRX-1 modulates DAF-28 signaling by contributing to the down-regulation of daf-28 expression during dauer formation. We propose that TRX-1 acts as a fluctuating neuronal signaling modulator within ASJ neurons to monitor the adjustment of neuropeptide expression, including insulin-like proteins, during dauer formation in response to adverse environmental conditions. PMID:21304598

Assessment of the Effectiveness of the Studio Format in Introductory Undergraduate Biology

PubMed Central

Rintoul, David A.; Williams, Larry G.

2008-01-01

Kansas State University converted its introductory biology course, previously taught as an audio-tutorial (A-T), to a studio format in 1997. We share with others information about the process involved and present assessment data for the studio format course that address 1) student exam performance in A-T and studio; 2) student course grades in A-T and studio; 3) student and instructor perceptions and attitudes for A-T and studio; 4) student performance in subsequent biology courses for A-T and studio; and 5) gains in student learning for the studio course and other traditional lecture/lab courses. Collectively, these measures demonstrate that the studio format is as effective as or more effective (for some measures) than the A-T approach and traditional approaches in providing an effective learning environment. We discuss the issues involved in comparing course formats. PMID:18519615

Erianthus arundinaceus HSP70 (EaHSP70) Acts as a Key Regulator in the Formation of Anisotropic Interdigitation in Sugarcane (Saccharum spp. hybrid) in Response to Drought Stress.

PubMed

Augustine, Sruthy Maria; Cherian, Anoop V; Syamaladevi, Divya P; Subramonian, N

2015-12-01

Plant growth during abiotic stress is a long sought-after trait especially in crop plants in the context of global warming and climate change. Previous studies on leaf epidermal cells have revealed that during normal growth and development, adjacent cells interdigitate anisotropically to form cell morphological patterns known as interlocking marginal lobes (IMLs), involving the cell wall-cell membrane-cortical actin continuum. IMLs are growth-associated cell morphological changes in which auxin-binding protein (ABP), Rho GTPases and actin are known to play important roles. In the present study, we investigated the formation of IMLs under drought stress and found that Erianthus arundinaceus, a drought-tolerant wild relative of sugarcane, develops such growth-related cell morphological patterns under drought stress. Using confocal microscopy, we showed an increasing trend in cortical F-actin intensity in drought-tolerant plants with increasing soil moisture stress. In order to check the role of drought tolerance-related genes in IML formation under soil moisture stress, we adopted a structural data mining strategy and identified indirect connections between the ABPs and heat shock proteins (HSPs). Initial experimental evidence for this connection comes from the high transcript levels of HSP70 observed in drought-stressed Erianthus, which developed anisotropic interdigitation, i.e. IMLs. Subsequently, by overexpressing the E. arundinaceus HSP70 gene (EaHSP70) in sugarcane (Saccharum spp. hybrid), we confirm the role of HSP70 in the formation of anisotropic interdigitation under drought stress. Taken together, our results suggest that EaHSP70 acts as a key regulator in the formation of anisotropic interdigitation in drought-tolerant plants (Erianthus and HSP70 transgenic sugarcane) under moisture stress in an actin-mediated pathway. The possible biological significance of the formation of drought-associated interlocking marginal lobes (DaIMLs) in sugarcane plants upon drought stress is discussed. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Biological invasion hotspots: a trait-based perspective reveals new sub-continental patterns

Treesearch

Basil V. Iannone III; Kevin M. Potter; Qinfeng Guo; Andrew M. Liebhold; Bryan C. Pijanowski; Christopher M. Oswalt; Songlin Fei

2015-01-01

Invader traits (including plant growth form) may play an important, and perhaps overlooked, role in determining macroscale patterns of biological invasions and therefore warrant greater consideration in future investigations aimed at understanding these patterns. To assess this need, we used empirical data from a national-level survey of forest in the contiguous 48...

Effects of Scoring by Section and Independent Scorers' Patterns on Scorer Reliability in Biology Essay Tests

ERIC Educational Resources Information Center

Ebuoh, Casmir N.; Ezeudu, S. A.

2015-01-01

The study investigated the effects of scoring by section, use of independent scorers and conventional patterns on scorer reliability in Biology essay tests. It was revealed from literature review that conventional pattern of scoring all items at a time in essay tests had been criticized for not being reliable. The study was true experimental study…

LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification.

PubMed

Gonçalves, Joana P; Madeira, Sara C

2014-01-01

Identifying patterns in temporal data is key to uncover meaningful relationships in diverse domains, from stock trading to social interactions. Also of great interest are clinical and biological applications, namely monitoring patient response to treatment or characterizing activity at the molecular level. In biology, researchers seek to gain insight into gene functions and dynamics of biological processes, as well as potential perturbations of these leading to disease, through the study of patterns emerging from gene expression time series. Clustering can group genes exhibiting similar expression profiles, but focuses on global patterns denoting rather broad, unspecific responses. Biclustering reveals local patterns, which more naturally capture the intricate collaboration between biological players, particularly under a temporal setting. Despite the general biclustering formulation being NP-hard, considering specific properties of time series has led to efficient solutions for the discovery of temporally aligned patterns. Notably, the identification of biclusters with time-lagged patterns, suggestive of transcriptional cascades, remains a challenge due to the combinatorial explosion of delayed occurrences. Herein, we propose LateBiclustering, a sensible heuristic algorithm enabling a polynomial rather than exponential time solution for the problem. We show that it identifies meaningful time-lagged biclusters relevant to the response of Saccharomyces cerevisiae to heat stress.

Specific Eph receptor-cytoplasmic effector signaling mediated by SAM-SAM domain interactions.

PubMed

Wang, Yue; Shang, Yuan; Li, Jianchao; Chen, Weidi; Li, Gang; Wan, Jun; Liu, Wei; Zhang, Mingjie

2018-05-11

The Eph receptor tyrosine kinase (RTK) family is the largest subfamily of RTKs playing critical roles in many developmental processes such as tissue patterning, neurogenesis and neuronal circuit formation, angiogenesis, etc. How the 14 Eph proteins, via their highly similar cytoplasmic domains, can transmit diverse and sometimes opposite cellular signals upon engaging ephrins is a major unresolved question. Here we systematically investigated the bindings of each SAM domain of Eph receptors to the SAM domains from SHIP2 and Odin, and uncover a highly specific SAM-SAM interaction-mediated cytoplasmic Eph-effector binding pattern. Comparative X-ray crystallographic studies of several SAM-SAM heterodimer complexes, together with biochemical and cell biology experiments, not only revealed the exquisite specificity code governing Eph/effector interactions but also allowed us to identify SAMD5 as a new Eph binding partner. Finally, these Eph/effector SAM heterodimer structures can explain many Eph SAM mutations identified in patients suffering from cancers and other diseases. © 2018, Wang et al.

Integrative Mechanisms of Oriented Neuronal Migration in the Developing Brain

PubMed Central

Evsyukova, Irina; Plestant, Charlotte; Anton, E.S.

2014-01-01

The emergence of functional neuronal connectivity in the developing cerebral cortex depends on neuronal migration. This process enables appropriate positioning of neurons and the emergence of neuronal identity so that the correct patterns of functional synaptic connectivity between the right types and numbers of neurons can emerge. Delineating the complexities of neuronal migration is critical to our understanding of normal cerebral cortical formation and neurodevelopmental disorders resulting from neuronal migration defects. For the most part, the integrated cell biological basis of the complex behavior of oriented neuronal migration within the developing mammalian cerebral cortex remains an enigma. This review aims to analyze the integrative mechanisms that enable neurons to sense environmental guidance cues and translate them into oriented patterns of migration toward defined areas of the cerebral cortex. We discuss how signals emanating from different domains of neurons get integrated to control distinct aspects of migratory behavior and how different types of cortical neurons coordinate their migratory activities within the developing cerebral cortex to produce functionally critical laminar organization. PMID:23937349

Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants.

PubMed

Li, Shu-Fen; Su, Ting; Cheng, Guang-Qian; Wang, Bing-Xiao; Li, Xu; Deng, Chuan-Liang; Gao, Wu-Jun

2017-10-24

Chromosome evolution is a fundamental aspect of evolutionary biology. The evolution of chromosome size, structure and shape, number, and the change in DNA composition suggest the high plasticity of nuclear genomes at the chromosomal level. Repetitive DNA sequences, which represent a conspicuous fraction of every eukaryotic genome, particularly in plants, are found to be tightly linked with plant chromosome evolution. Different classes of repetitive sequences have distinct distribution patterns on the chromosomes. Mounting evidence shows that repetitive sequences may play multiple generative roles in shaping the chromosome karyotypes in plants. Furthermore, recent development in our understanding of the repetitive sequences and plant chromosome evolution has elucidated the involvement of a spectrum of epigenetic modification. In this review, we focused on the recent evidence relating to the distribution pattern of repetitive sequences in plant chromosomes and highlighted their potential relevance to chromosome evolution in plants. We also discussed the possible connections between evolution and epigenetic alterations in chromosome structure and repatterning, such as heterochromatin formation, centromere function, and epigenetic-associated transposable element inactivation.

Regulatory mechanisms for specification and patterning of plant vascular tissues.

PubMed

Caño-Delgado, Ana; Lee, Ji-Young; Demura, Taku

2010-01-01

Plant vascular tissues, the conduits of water, nutrients, and small molecules, play important roles in plant growth and development. Vascular tissues have allowed plants to successfully adapt to various environmental conditions since they evolved 450 Mya. The majority of plant biomass, an important source of renewable energy, comes from the xylem of the vascular tissues. Efforts have been made to identify the underlying mechanisms of cell specification and patterning of plant vascular tissues and their proliferation. The formation of the plant vascular system is a complex process that integrates signaling and gene regulation at transcriptional and posttranscriptional levels. Recently, a wealth of molecular genetic studies and the advent of cell biology and genomic tools have enabled important progress toward understanding its underlying mechanisms. Here, we provide a comprehensive review of the cell and developmental processes of plant vascular tissue and resources recently available for studying them that will enable the discovery of new ways to develop sustainable energy using plant biomass.

Making structures for cell engineering.

PubMed

Wilkinson, C D W

2004-10-22

This is a mainly historical account of the events, methods and artifacts arising from my collaboration with Adam Curtis over the past twenty years to make exercise grounds for biological cells. Initially the structures were made in fused silica by photo-lithography and dry etching. The need to make micron-sized features in biodegradable polymers, led to the development of embossing techniques. Some cells response to grooves only a few tens of nanometers deep--this led to a desire to find the response of cells to features of nanometric size overall. Regular arrays of such features were made using electron beam lithography for definition of the pattern. Improvements were made in the lithographic techniques to allow arrays to be defined over areas bigger than 1 cm2. Structures with microelectrodes arranged inside guiding grooves to allow the formation of sparse predetermined networks of neurons were made. It is concluded that the creation of pattern, as in vivo, in assemblies of regrown cells in scaffolds may well be necessary in advanced cell engineering applications.

The role of phase separation for self-organized surface pattern formation by ion beam erosion and metal atom co-deposition

NASA Astrophysics Data System (ADS)

Hofsäss, H.; Zhang, K.; Pape, A.; Bobes, O.; Brötzmann, M.

2013-05-01

We investigate the ripple pattern formation on Si surfaces at room temperature during normal incidence ion beam erosion under simultaneous deposition of different metallic co-deposited surfactant atoms. The co-deposition of small amounts of metallic atoms, in particular Fe and Mo, is known to have a tremendous impact on the evolution of nanoscale surface patterns on Si. In previous work on ion erosion of Si during co-deposition of Fe atoms, we proposed that chemical interactions between Fe and Si atoms of the steady-state mixed Fe x Si surface layer formed during ion beam erosion is a dominant driving force for self-organized pattern formation. In particular, we provided experimental evidence for the formation of amorphous iron disilicide. To confirm and generalize such chemical effects on the pattern formation, in particular the tendency for phase separation, we have now irradiated Si surfaces with normal incidence 5 keV Xe ions under simultaneous gracing incidence co-deposition of Fe, Ni, Cu, Mo, W, Pt, and Au surfactant atoms. The selected metals in the two groups (Fe, Ni, Cu) and (W, Pt, Au) are very similar regarding their collision cascade behavior, but strongly differ regarding their tendency to silicide formation. We find pronounced ripple pattern formation only for those co deposited metals (Fe, Mo, Ni, W, and Pt), which are prone to the formation of mono and disilicides. In contrast, for Cu and Au co-deposition the surface remains very flat, even after irradiation at high ion fluence. Because of the very different behavior of Cu compared to Fe, Ni and Au compared to W, Pt, phase separation toward amorphous metal silicide phases is seen as the relevant process for the pattern formation on Si in the case of Fe, Mo, Ni, W, and Pt co-deposition.

Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations

PubMed Central

Gurunathan, Rajalakshmi; Van Emden, Bernard; Panchanathan, Sethuraman; Kumar, Sudhir

2004-01-01

Background Modern developmental biology relies heavily on the analysis of embryonic gene expression patterns. Investigators manually inspect hundreds or thousands of expression patterns to identify those that are spatially similar and to ultimately infer potential gene interactions. However, the rapid accumulation of gene expression pattern data over the last two decades, facilitated by high-throughput techniques, has produced a need for the development of efficient approaches for direct comparison of images, rather than their textual descriptions, to identify spatially similar expression patterns. Results The effectiveness of the Binary Feature Vector (BFV) and Invariant Moment Vector (IMV) based digital representations of the gene expression patterns in finding biologically meaningful patterns was compared for a small (226 images) and a large (1819 images) dataset. For each dataset, an ordered list of images, with respect to a query image, was generated to identify overlapping and similar gene expression patterns, in a manner comparable to what a developmental biologist might do. The results showed that the BFV representation consistently outperforms the IMV representation in finding biologically meaningful matches when spatial overlap of the gene expression pattern and the genes involved are considered. Furthermore, we explored the value of conducting image-content based searches in a dataset where individual expression components (or domains) of multi-domain expression patterns were also included separately. We found that this technique improves performance of both IMV and BFV based searches. Conclusions We conclude that the BFV representation consistently produces a more extensive and better list of biologically useful patterns than the IMV representation. The high quality of results obtained scales well as the search database becomes larger, which encourages efforts to build automated image query and retrieval systems for spatial gene expression patterns. PMID:15603586

Evolution-development congruence in pattern formation dynamics: Bifurcations in gene expression and regulation of networks structures.

PubMed

Kohsokabe, Takahiro; Kaneko, Kunihiko

2016-01-01

Search for possible relationships between phylogeny and ontogeny is important in evolutionary-developmental biology. Here we uncover such relationships by numerical evolution and unveil their origin in terms of dynamical systems theory. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell-to-cell interaction under external morphogen gradient, gene regulation networks are evolved under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Both in the evolution and development pattern changes consist of several epochs where stripes are formed in a short time, while for other temporal regimes, pattern hardly changes. In evolution, these quasi-stationary regimes are generations needed to hit relevant mutations, while in development, they are due to some gene expression that varies slowly and controls the pattern change. The morphogenesis is regulated by combinations of feedback or feedforward regulations, where the upstream feedforward network reads the external morphogen gradient, and generates a pattern used as a boundary condition for the later patterns. The ordering from up to downstream is common in evolution and development, while the successive epochal changes in development and evolution are represented as common bifurcations in dynamical-systems theory, which lead to the evolution-development congruence. Mechanism of exceptional violation of the congruence is also unveiled. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution Published by Wiley Periodicals, Inc.

Evolution‐development congruence in pattern formation dynamics: Bifurcations in gene expression and regulation of networks structures

PubMed Central

Kohsokabe, Takahiro

2016-01-01

ABSTRACT Search for possible relationships between phylogeny and ontogeny is important in evolutionary‐developmental biology. Here we uncover such relationships by numerical evolution and unveil their origin in terms of dynamical systems theory. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell‐to‐cell interaction under external morphogen gradient, gene regulation networks are evolved under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Both in the evolution and development pattern changes consist of several epochs where stripes are formed in a short time, while for other temporal regimes, pattern hardly changes. In evolution, these quasi‐stationary regimes are generations needed to hit relevant mutations, while in development, they are due to some gene expression that varies slowly and controls the pattern change. The morphogenesis is regulated by combinations of feedback or feedforward regulations, where the upstream feedforward network reads the external morphogen gradient, and generates a pattern used as a boundary condition for the later patterns. The ordering from up to downstream is common in evolution and development, while the successive epochal changes in development and evolution are represented as common bifurcations in dynamical‐systems theory, which lead to the evolution‐development congruence. Mechanism of exceptional violation of the congruence is also unveiled. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis. J. Exp. Zool. (Mol. Dev. Evol.) 326B:61–84, 2016. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution Published by Wiley Periodicals, Inc. PMID:26678220

Blood drop patterns: Formation and applications.

PubMed

Chen, Ruoyang; Zhang, Liyuan; Zang, Duyang; Shen, Wei

2016-05-01

The drying of a drop of blood or plasma on a solid substrate leads to the formation of interesting and complex patterns. Inter- and intra-cellular and macromolecular interactions in the drying plasma or blood drop are responsible for the final morphologies of the dried patterns. Changes in these cellular and macromolecular components in blood caused by diseases have been suspected to cause changes in the dried drop patterns of plasma and whole blood, which could be used as simple diagnostic tools to identify the health of humans and livestock. However, complex physicochemical driving forces involved in the pattern formation are not fully understood. This review focuses on the scientific development in microscopic observations and pattern interpretation of dried plasma and whole blood samples, as well as the diagnostic applications of pattern analysis. Dried drop patterns of plasma consist of intricate visible cracks in the outer region and fine structures in the central region, which are mainly influenced by the presence and concentration of inorganic salts and proteins during drying. The shrinkage of macromolecular gel and its adhesion to the substrate surface have been thought to be responsible for the formation of the cracks. Dried drop patterns of whole blood have three characteristic zones; their formation as functions of drying time has been reported in the literature. Some research works have applied engineering treatment to the evaporation process of whole blood samples. The sensitivities of the resultant patterns to the relative humidity of the environment, the wettability of the substrates, and the size of the drop have been reported. These research works shed light on the mechanisms of spreading, evaporation, gelation, and crack formation of the blood drops on solid substrates, as well as on the potential applications of dried drop patterns of plasma and whole blood in diagnosis. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

Structure Formation of Ultrathin PEO Films at Solid Interfaces—Complex Pattern Formation by Dewetting and Crystallization

PubMed Central

Braun, Hans-Georg; Meyer, Evelyn

2013-01-01

The direct contact of ultrathin polymer films with a solid substrate may result in thin film rupture caused by dewetting. With crystallisable polymers such as polyethyleneoxide (PEO), molecular self-assembly into partial ordered lamella structures is studied as an additional source of pattern formation. Morphological features in ultrathin PEO films (thickness < 10 nm) result from an interplay between dewetting patterns and diffusion limited growth pattern of ordered lamella growing within the dewetting areas. Besides structure formation of hydrophilic PEO molecules, n-alkylterminated (hydrophobic) PEO oligomers are investigated with respect to self-organization in ultrathin films. Morphological features characteristic for pure PEO are not changed by the presence of the n-alkylgroups. PMID:23385233

Pattern formation and geometry of the manifold

NASA Astrophysics Data System (ADS)

Haji, Amir Hossein; Mahzoon, Mojtaba; Javadpour, Sirus

2011-03-01

The objective of the present work is to investigate how pattern formation in the Cahn-Hilliard system can be influenced by geometry of the manifold. This is in contrast to control methods in which the physical field is modified and the pattern formation of the original system changes in response to control inputs. The idea begins with the cylindrical manifold symmetry leading to circumferential rolls while the torus manifold can be used to produce and control helical rolls. The next step is to search for a weaker restriction on the geometry of the manifold in order to reduce its dimension. In particular a short amplitude sinusoidal modulation on a flat surface is studied. At the final step a sequential pattern formation is presented.

Neon ion beam induced pattern formation on amorphous carbon surfaces

NASA Astrophysics Data System (ADS)

Bobes, Omar; Hofsäss, Hans; Zhang, Kun

2018-02-01

We investigate the ripple pattern formation on amorphous carbon surfaces at room temperature during low energy Ne ion irradiation as a function of the ion incidence angle. Monte Carlo simulations of the curvature coefficients applied to the Bradley-Harper and Cater-Vishnyakov models, including the recent extensions by Harrison-Bradley and Hofsäss predict that pattern formation on amorphous carbon thin films should be possible for low energy Ne ions from 250 eV up to 1500 eV. Moreover, simulations are able to explain the absence of pattern formation in certain cases. Our experimental results are compared with prediction using current linear theoretical models and applying the crater function formalism, as well as Monte Carlo simulations to calculate curvature coefficients using the SDTrimSP program. Calculations indicate that no patterns should be generated up to 45° incidence angle if the dynamic behavior of the thickness of the ion irradiated layer introduced by Hofsäss is taken into account, while pattern formation most pronounced from 50° for ion energy between 250 eV and 1500 eV, which are in good agreement with our experimental data.

Estimation, modeling, and simulation of patterned growth in extreme environments.

PubMed

Strader, B; Schubert, K E; Quintana, M; Gomez, E; Curnutt, J; Boston, P

2011-01-01

In the search for life on Mars and other extraterrestrial bodies or in our attempts to identify biological traces in the most ancient rock record of Earth, one of the biggest problems facing us is how to recognize life or the remains of ancient life in a context very different from our planet's modern biological examples. Specific chemistries or biological properties may well be inapplicable to extraterrestrial conditions or ancient Earth environments. Thus, we need to develop an arsenal of techniques that are of broader applicability. The notion of patterning created in some fashion by biological processes and properties may provide such a generalized property of biological systems no matter what the incidentals of chemistry or environmental conditions. One approach to recognizing these kinds of patterns is to look at apparently organized arrangements created and left by life in extreme environments here on Earth, especially at various spatial scales, different geologies, and biogeochemical circumstances.

Random Evolution of Idiotypic Networks: Dynamics and Architecture

NASA Astrophysics Data System (ADS)

Brede, Markus; Behn, Ulrich

The paper deals with modelling a subsystem of the immune system, the so-called idiotypic network (INW). INWs, conceived by N.K. Jerne in 1974, are functional networks of interacting antibodies and B cells. In principle, Jernes' framework provides solutions to many issues in immunology, such as immunological memory, mechanisms for antigen recognition and self/non-self discrimination. Explaining the interconnection between the elementary components, local dynamics, network formation and architecture, and possible modes of global system function appears to be an ideal playground of statistical mechanics. We present a simple cellular automaton model, based on a graph representation of the system. From a simplified description of idiotypic interactions, rules for the random evolution of networks of occupied and empty sites on these graphs are derived. In certain biologically relevant parameter ranges the resultant dynamics leads to stationary states. A stationary state is found to correspond to a specific pattern of network organization. It turns out that even these very simple rules give rise to a multitude of different kinds of patterns. We characterize these networks by classifying `static' and `dynamic' network-patterns. A type of `dynamic' network is found to display many features of real INWs.

Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador.

PubMed

Arteaga, Alejandro; Pyron, R Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H; Guayasamin, Juan M

2016-01-01

Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history.

Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador

PubMed Central

Pyron, R. Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H.; Guayasamin, Juan M.

2016-01-01

Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history. PMID:27120100

Open sepulchers and closed boundaries? Biodistance analysis of cemetery structure and postmarital residence in the late prehispanic Andes.

PubMed

Velasco, Matthew C

2018-05-16

In the Late Intermediate Period Andes (AD 1100-1450), the proliferation of above-ground sepulchers reconfigured social boundaries within and between communities engaged in protracted conflict. However, the biosocial dimensions of these mortuary practices, and their implications for conflict and alliance formation, remain unexplored. This study examines patterns of phenotypic variation to: (1) evaluate if open sepulchers were organized on the basis of biological relatedness, and (2) explore if sex-specific phenotypic variability conforms to models of postmarital residence. Cranial nonmetric traits were recorded in five skeletal samples from two cemeteries in the Colca Valley, Peru. Biological distances between burial groups were calculated using the Mean Measure of Divergence (MMD) statistic. Postmarital residence was explored by calculating and bootstrapping the ratio of male-to-female mean pairwise differences (MPD) at the within-group level. The MMD analysis yields greater than expected between-group distances for burial groups with a minimum sample size of 20 individuals. In contrast, a prevailing pattern of sex-specific, within-group phenotypic variability is not apparent from the analysis of MPD. The use of 12 or 24 dichotomous traits produces similar results. Greater than expected biological distances suggest that above-ground mortuary practices reinforced biosocial boundaries between corporate household groups. Intracemetery heterogeneity persisted even as cranial vault modification, a correlate of social identity, became more homogenous, revealing how corporate group organization was negotiated at multiple scales. Sex-specific variation does not conform to traditional migration models. If migration occurred, it did not have a homogenizing effect on phenotypic variation. These results should be viewed with caution in light of the smaller sample sizes of sex-specific groupings. © 2018 Wiley Periodicals, Inc.

Polariton Pattern Formation and Photon Statistics of the Associated Emission

NASA Astrophysics Data System (ADS)

Whittaker, C. E.; Dzurnak, B.; Egorov, O. A.; Buonaiuto, G.; Walker, P. M.; Cancellieri, E.; Whittaker, D. M.; Clarke, E.; Gavrilov, S. S.; Skolnick, M. S.; Krizhanovskii, D. N.

2017-07-01

We report on the formation of a diverse family of transverse spatial polygon patterns in a microcavity polariton fluid under coherent driving by a blue-detuned pump. Patterns emerge spontaneously as a result of energy-degenerate polariton-polariton scattering from the pump state to interfering high-order vortex and antivortex modes, breaking azimuthal symmetry. The interplay between a multimode parametric instability and intrinsic optical bistability leads to a sharp spike in the value of second-order coherence g(2 )(0 ) of the emitted light, which we attribute to the strongly superlinear kinetics of the underlying scattering processes driving the formation of patterns. We show numerically by means of a linear stability analysis how the growth of parametric instabilities in our system can lead to spontaneous symmetry breaking, predicting the formation and competition of different pattern states in good agreement with experimental observations.

Form and motion make independent contributions to the response to biological motion in occipitotemporal cortex.

PubMed

Thompson, James C; Baccus, Wendy

2012-01-02

Psychophysical and computational studies have provided evidence that both form and motion cues are used in the perception of biological motion. However, neuroimaging and neurophysiological studies have suggested that the neural processing of actions in temporal cortex might rely on form cues alone. Here we examined the contribution of form and motion to the spatial pattern of response to biological motion in ventral and lateral occipitotemporal cortex, using functional magnetic resonance imaging (fMRI) and multivoxel pattern analysis (MVPA). We found that selectivity to intact versus scrambled biological motion in lateral occipitotemporal cortex was correlated with selectivity for bodies and not for motion. However, this appeared to be due to the fact that subtracting scrambled from intact biological motion removes any contribution of local motion cues. Instead, we found that form and motion made independent contributions to the spatial pattern of responses to biological motion in lateral occipitotemporal regions MT, MST, and the extrastriate body area. The motion contribution was position-dependent, and consistent with the representation of contra- and ipsilateral visual fields in MT and MST. In contrast, only form contributed to the response to biological motion in the fusiform body area, with a bias towards central versus peripheral presentation. These results indicate that the pattern of response to biological motion in ventral and lateral occipitotemporal cortex reflects the linear combination of responses to form and motion. Copyright © 2011 Elsevier Inc. All rights reserved.

Stochastic nonlinear dynamics pattern formation and growth models

PubMed Central

Yaroslavsky, Leonid P

2007-01-01

Stochastic evolutionary growth and pattern formation models are treated in a unified way in terms of algorithmic models of nonlinear dynamic systems with feedback built of a standard set of signal processing units. A number of concrete models is described and illustrated by numerous examples of artificially generated patterns that closely imitate wide variety of patterns found in the nature. PMID:17908341

Dynamic Pattern Formation in Electron-Beam-Induced Etching [Emergent formation of dynamic topographic patterns in electron beam induced etching

DOE PAGES

Martin, Aiden A.; Bahm, Alan; Bishop, James; ...

2015-12-15

Here, we report highly ordered topographic patterns that form on the surface of diamond, span multiple length scales, and have a symmetry controlled by the precursor gas species used in electron-beam-induced etching (EBIE). The pattern formation dynamics reveals an etch rate anisotropy and an electron energy transfer pathway that is overlooked by existing EBIE models. Therefore, we, modify established theory such that it explains our results and remains universally applicable to EBIE. Furthermore, the patterns can be exploited in controlled wetting, optical structuring, and other emerging applications that require nano- and microscale surface texturing of a wide band-gap material.

The axolotl limb blastema: cellular and molecular mechanisms driving blastema formation and limb regeneration in tetrapods

PubMed Central

McCusker, Catherine; Bryant, Susan V.

2015-01-01

Abstract The axolotl is one of the few tetrapods that are capable of regenerating complicated biological structures, such as complete limbs, throughout adulthood. Upon injury the axolotl generates a population of regeneration‐competent limb progenitor cells known as the blastema, which will grow, establish pattern, and differentiate into the missing limb structures. In this review we focus on the crucial early events that occur during wound healing, the neural−epithelial interactions that drive the formation of the early blastema, and how these mechanisms differ from those of other species that have restricted regenerative potential, such as humans. We also discuss how the presence of cells from the different axes of the limb is required for the continued growth and establishment of pattern in the blastema as described in the polar coordinate model, and how this positional information is reprogrammed in blastema cells during regeneration. Multiple cell types from the mature limb stump contribute to the blastema at different stages of regeneration, and we discuss the contribution of these types to the regenerate with reference to whether they are “pattern‐forming” or “pattern‐following” cells. Lastly, we explain how an engineering approach will help resolve unanswered questions in limb regeneration, with the goal of translating these concepts to developing better human regenerative therapies. PMID:27499868

A Graph Approach to Mining Biological Patterns in the Binding Interfaces.

PubMed

Cheng, Wen; Yan, Changhui

2017-01-01

Protein-RNA interactions play important roles in the biological systems. Searching for regular patterns in the Protein-RNA binding interfaces is important for understanding how protein and RNA recognize each other and bind to form a complex. Herein, we present a graph-mining method for discovering biological patterns in the protein-RNA interfaces. We represented known protein-RNA interfaces using graphs and then discovered graph patterns enriched in the interfaces. Comparison of the discovered graph patterns with UniProt annotations showed that the graph patterns had a significant overlap with residue sites that had been proven crucial for the RNA binding by experimental methods. Using 200 patterns as input features, a support vector machine method was able to classify protein surface patches into RNA-binding sites and non-RNA-binding sites with 84.0% accuracy and 88.9% precision. We built a simple scoring function that calculated the total number of the graph patterns that occurred in a protein-RNA interface. That scoring function was able to discriminate near-native protein-RNA complexes from docking decoys with a performance comparable with that of a state-of-the-art complex scoring function. Our work also revealed possible patterns that might be important for binding affinity.

Modeling mammary organogenesis from biological first principles: Cells and their physical constraints.

PubMed

Montévil, Maël; Speroni, Lucia; Sonnenschein, Carlos; Soto, Ana M

2016-10-01

In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing non-identical cells, which organize in tri-dimensional patterns. These association patterns and cells types change as tissues and organs are formed. This contextuality and circularity makes it difficult to establish detailed cause and effect relationships. Here we propose an approach to overcome these intrinsic difficulties by combining the use of two models; 1) an experimental one that employs 3D culture technology to obtain the structures of the mammary gland, namely, ducts and acini, and 2) a mathematical model based on biological principles. The typical approach for mathematical modeling in biology is to apply mathematical tools and concepts developed originally in physics or computer sciences. Instead, we propose to construct a mathematical model based on proper biological principles. Specifically, we use principles identified as fundamental for the elaboration of a theory of organisms, namely i) the default state of cell proliferation with variation and motility and ii) the principle of organization by closure of constraints. This model has a biological component, the cells, and a physical component, a matrix which contains collagen fibers. Cells display agency and move and proliferate unless constrained; they exert mechanical forces that i) act on collagen fibers and ii) on other cells. As fibers organize, they constrain the cells on their ability to move and to proliferate. The model exhibits a circularity that can be interpreted in terms of closure of constraints. Implementing the mathematical model shows that constraints to the default state are sufficient to explain ductal and acinar formation, and points to a target of future research, namely, to inhibitors of cell proliferation and motility generated by the epithelial cells. The success of this model suggests a step-wise approach whereby additional constraints imposed by the tissue and the organism could be examined in silico and rigorously tested by in vitro and in vivo experiments, in accordance with the organicist perspective we embrace. Copyright © 2016. Published by Elsevier Ltd.

Modeling mammary organogenesis from biological first principles: Cells and their physical constraints

PubMed Central

Montévil, Maël; Speroni, Lucia; Sonnenschein, Carlos; Soto, Ana M.

2017-01-01

In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing non-identical cells, which organize in tri-dimensional patterns. These association patterns and cells types change as tissues and organs are formed. This contextuality and circularity makes it difficult to establish detailed cause and effect relationships. Here we propose an approach to overcome these intrinsic difficulties by combining the use of two models; 1) an experimental one that employs 3D culture technology to obtain the structures of the mammary gland, namely, ducts and acini, and 2) a mathematical model based on biological principles. The typical approach for mathematical modeling in biology is to apply mathematical tools and concepts developed originally in physics or computer sciences. Instead, we propose to construct a mathematical model based on proper biological principles. Specifically, we use principles identified as fundamental for the elaboration of a theory of organisms, namely i) the default state of cell proliferation with variation and motility and ii) the principle of organization by closure of constraints. This model has a biological component, the cells, and a physical component, a matrix which contains collagen fibers. Cells display agency and move and proliferate unless constrained; they exert mechanical forces that i) act on collagen fibers and ii) on other cells. As fibers organize, they constrain the cells on their ability to move and to proliferate. The model exhibits a circularity that can be interpreted in terms of closure of constraints. Implementing the mathematical model shows that constraints to the default state are sufficient to explain ductal and acinar formation, and points to a target of future research, namely, to inhibitors of cell proliferation and motility generated by the epithelial cells. The success of this model suggests a step-wise approach whereby additional constraints imposed by the tissue and the organism could be examined in silico and rigorously tested by in vitro and in vivo experiments, in accordance with the organicist perspective we embrace. PMID:27544910

How Escherichia coli lands and forms cell clusters on a surface: a new role of surface topography

PubMed Central

Gu, Huan; Chen, Aaron; Song, Xinran; Brasch, Megan E.; Henderson, James H.; Ren, Dacheng

2016-01-01

Bacterial response to surface topography during biofilm formation was studied using 5 μm tall line patterns of poly (dimethylsiloxane) (PDMS). Escherichia coli cells attached on top of protruding line patterns were found to align more perpendicularly to the orientation of line patterns when the pattern narrowed. Consistently, cell cluster formation per unit area on 5 μm wide line patterns was reduced by 14-fold compared to flat PDMS. Contrasting the reduced colony formation, cells attached on narrow patterns were longer and had higher transcriptional activities, suggesting that such unfavorable topography may present a stress to attached cells. Results of mutant studies indicate that flagellar motility is involved in the observed preference in cell orientation on narrow patterns, which was corroborated by the changes in cell rotation pattern before settling on different surface topographies. These findings led to a set of new design principles for creating antifouling topographies, which was validated using 10 μm tall hexagonal patterns. PMID:27412365

Hydrologic controls on aperiodic spatial organization of the ridge-slough patterned landscape

NASA Astrophysics Data System (ADS)

Casey, Stephen T.; Cohen, Matthew J.; Acharya, Subodh; Kaplan, David A.; Jawitz, James W.

2016-11-01

A century of hydrologic modification has altered the physical and biological drivers of landscape processes in the Everglades (Florida, USA). Restoring the ridge-slough patterned landscape, a dominant feature of the historical system, is a priority but requires an understanding of pattern genesis and degradation mechanisms. Physical experiments to evaluate alternative pattern formation mechanisms are limited by the long timescales of peat accumulation and loss, necessitating model-based comparisons, where support for a particular mechanism is based on model replication of extant patterning and trajectories of degradation. However, multiple mechanisms yield a central feature of ridge-slough patterning (patch elongation in the direction of historical flow), limiting the utility of that characteristic for discriminating among alternatives. Using data from vegetation maps, we investigated the statistical features of ridge-slough spatial patterning (ridge density, patch perimeter, elongation, patch size distributions, and spatial periodicity) to establish more rigorous criteria for evaluating model performance and to inform controls on pattern variation across the contemporary system. Mean water depth explained significant variation in ridge density, total perimeter, and length : width ratios, illustrating an important pattern response to existing hydrologic gradients. Two independent analyses (2-D periodograms and patch size distributions) provide strong evidence against regular patterning, with the landscape exhibiting neither a characteristic wavelength nor a characteristic patch size, both of which are expected under conditions that produce regular patterns. Rather, landscape properties suggest robust scale-free patterning, indicating genesis from the coupled effects of local facilitation and a global negative feedback operating uniformly at the landscape scale. Critically, this challenges widespread invocation of scale-dependent negative feedbacks for explaining ridge-slough pattern origins. These results help discern among genesis mechanisms and provide an improved statistical description of the landscape that can be used to compare among model outputs, as well as to assess the success of future restoration projects.

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

PubMed Central

2012-01-01

Background We present the Biological Observation Matrix (BIOM, pronounced “biome”) format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observation metadata. As the number of categories of comparative omics data types (collectively, the “ome-ome”) grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses. Findings The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages. Conclusions The BIOM file format and the biom-format project are steps toward reducing the “bioinformatics bottleneck” that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium. PMID:23587224

PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables

PubMed Central

Pounds, Stan; Cheng, Cheng; Cao, Xueyuan; Crews, Kristine R.; Plunkett, William; Gandhi, Varsha; Rubnitz, Jeffrey; Ribeiro, Raul C.; Downing, James R.; Lamba, Jatinder

2009-01-01

Motivation: In some applications, prior biological knowledge can be used to define a specific pattern of association of multiple endpoint variables with a genomic variable that is biologically most interesting. However, to our knowledge, there is no statistical procedure designed to detect specific patterns of association with multiple endpoint variables. Results: Projection onto the most interesting statistical evidence (PROMISE) is proposed as a general procedure to identify genomic variables that exhibit a specific biologically interesting pattern of association with multiple endpoint variables. Biological knowledge of the endpoint variables is used to define a vector that represents the biologically most interesting values for statistics that characterize the associations of the endpoint variables with a genomic variable. A test statistic is defined as the dot-product of the vector of the observed association statistics and the vector of the most interesting values of the association statistics. By definition, this test statistic is proportional to the length of the projection of the observed vector of correlations onto the vector of most interesting associations. Statistical significance is determined via permutation. In simulation studies and an example application, PROMISE shows greater statistical power to identify genes with the interesting pattern of associations than classical multivariate procedures, individual endpoint analyses or listing genes that have the pattern of interest and are significant in more than one individual endpoint analysis. Availability: Documented R routines are freely available from www.stjuderesearch.org/depts/biostats and will soon be available as a Bioconductor package from www.bioconductor.org. Contact: stanley.pounds@stjude.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19528086

Femtosecond laser patterning of biological materials

NASA Astrophysics Data System (ADS)

Grigoropoulos, Costas P.; Jeon, Hojeong; Hidai, Hirofumi; Hwang, David J.

2011-03-01

This paper aims at presenting a review of work at the Laser Thermal Laboratory on the microscopic laser modification of biological materials using ultrafast laser pulses. We have devised a new method for fabricating high aspect ratio patterns of varying height by using two-photon polymerization process in order to study contact guidance and directed growth of biological cells. Studies using NIH-3T3 and MDCK cells indicate that cell morphology on fiber scaffolds is influenced by the pattern of actin microfilament bundles. Cells experienced different strength of contact guidance depending on the ridge height. Cell morphology and motility was investigated on micronscale anisotropic cross patterns and parallel line patterns having different aspect ratios. A significant effect on cell alignment and directionality of migration was observed. Cell morphology and motility were influenced by the aspect ratio of the cross pattern, the grid size, and the ridge height. Cell contractility was examined microscopically in order to measure contractile forces generated by individual cells on self-standing fiber scaffolds.

An improved Pearson's correlation proximity-based hierarchical clustering for mining biological association between genes.

PubMed

Booma, P M; Prabhakaran, S; Dhanalakshmi, R

2014-01-01

Microarray gene expression datasets has concerned great awareness among molecular biologist, statisticians, and computer scientists. Data mining that extracts the hidden and usual information from datasets fails to identify the most significant biological associations between genes. A search made with heuristic for standard biological process measures only the gene expression level, threshold, and response time. Heuristic search identifies and mines the best biological solution, but the association process was not efficiently addressed. To monitor higher rate of expression levels between genes, a hierarchical clustering model was proposed, where the biological association between genes is measured simultaneously using proximity measure of improved Pearson's correlation (PCPHC). Additionally, the Seed Augment algorithm adopts average linkage methods on rows and columns in order to expand a seed PCPHC model into a maximal global PCPHC (GL-PCPHC) model and to identify association between the clusters. Moreover, a GL-PCPHC applies pattern growing method to mine the PCPHC patterns. Compared to existing gene expression analysis, the PCPHC model achieves better performance. Experimental evaluations are conducted for GL-PCPHC model with standard benchmark gene expression datasets extracted from UCI repository and GenBank database in terms of execution time, size of pattern, significance level, biological association efficiency, and pattern quality.

An Improved Pearson's Correlation Proximity-Based Hierarchical Clustering for Mining Biological Association between Genes

PubMed Central

Booma, P. M.; Prabhakaran, S.; Dhanalakshmi, R.

2014-01-01

Microarray gene expression datasets has concerned great awareness among molecular biologist, statisticians, and computer scientists. Data mining that extracts the hidden and usual information from datasets fails to identify the most significant biological associations between genes. A search made with heuristic for standard biological process measures only the gene expression level, threshold, and response time. Heuristic search identifies and mines the best biological solution, but the association process was not efficiently addressed. To monitor higher rate of expression levels between genes, a hierarchical clustering model was proposed, where the biological association between genes is measured simultaneously using proximity measure of improved Pearson's correlation (PCPHC). Additionally, the Seed Augment algorithm adopts average linkage methods on rows and columns in order to expand a seed PCPHC model into a maximal global PCPHC (GL-PCPHC) model and to identify association between the clusters. Moreover, a GL-PCPHC applies pattern growing method to mine the PCPHC patterns. Compared to existing gene expression analysis, the PCPHC model achieves better performance. Experimental evaluations are conducted for GL-PCPHC model with standard benchmark gene expression datasets extracted from UCI repository and GenBank database in terms of execution time, size of pattern, significance level, biological association efficiency, and pattern quality. PMID:25136661

[GNU Pattern: open source pattern hunter for biological sequences based on SPLASH algorithm].

PubMed

Xu, Ying; Li, Yi-xue; Kong, Xiang-yin

2005-06-01

To construct a high performance open source software engine based on IBM SPLASH algorithm for later research on pattern discovery. Gpat, which is based on SPLASH algorithm, was developed by using open source software. GNU Pattern (Gpat) software was developped, which efficiently implemented the core part of SPLASH algorithm. Full source code of Gpat was also available for other researchers to modify the program under the GNU license. Gpat is a successful implementation of SPLASH algorithm and can be used as a basic framework for later research on pattern recognition in biological sequences.

A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model

PubMed Central

Beldade, Patrícia; Rudd, Stephen; Gruber, Jonathan D; Long, Anthony D

2006-01-01

Background Butterfly wing color patterns are a key model for integrating evolutionary developmental biology and the study of adaptive morphological evolution. Yet, despite the biological, economical and educational value of butterflies they are still relatively under-represented in terms of available genomic resources. Here, we describe an Expression Sequence Tag (EST) project for Bicyclus anynana that has identified the largest available collection to date of expressed genes for any butterfly. Results By targeting cDNAs from developing wings at the stages when pattern is specified, we biased gene discovery towards genes potentially involved in pattern formation. Assembly of 9,903 ESTs from a subtracted library allowed us to identify 4,251 genes of which 2,461 were annotated based on BLAST analyses against relevant gene collections. Gene prediction software identified 2,202 peptides, of which 215 longer than 100 amino acids had no homology to any known proteins and, thus, potentially represent novel or highly diverged butterfly genes. We combined gene and Single Nucleotide Polymorphism (SNP) identification by constructing cDNA libraries from pools of outbred individuals, and by sequencing clones from the 3' end to maximize alignment depth. Alignments of multi-member contigs allowed us to identify over 14,000 putative SNPs, with 316 genes having at least one high confidence double-hit SNP. We furthermore identified 320 microsatellites in transcribed genes that can potentially be used as genetic markers. Conclusion Our project was designed to combine gene and sequence polymorphism discovery and has generated the largest gene collection available for any butterfly and many potential markers in expressed genes. These resources will be invaluable for exploring the potential of B. anynana in particular, and butterflies in general, as models in ecological, evolutionary, and developmental genetics. PMID:16737530

An adaptable neuromorphic model of orientation selectivity based on floating gate dynamics

PubMed Central

Gupta, Priti; Markan, C. M.

2014-01-01

The biggest challenge that the neuromorphic community faces today is to build systems that can be considered truly cognitive. Adaptation and self-organization are the two basic principles that underlie any cognitive function that the brain performs. If we can replicate this behavior in hardware, we move a step closer to our goal of having cognitive neuromorphic systems. Adaptive feature selectivity is a mechanism by which nature optimizes resources so as to have greater acuity for more abundant features. Developing neuromorphic feature maps can help design generic machines that can emulate this adaptive behavior. Most neuromorphic models that have attempted to build self-organizing systems, follow the approach of modeling abstract theoretical frameworks in hardware. While this is good from a modeling and analysis perspective, it may not lead to the most efficient hardware. On the other hand, exploiting hardware dynamics to build adaptive systems rather than forcing the hardware to behave like mathematical equations, seems to be a more robust methodology when it comes to developing actual hardware for real world applications. In this paper we use a novel time-staggered Winner Take All circuit, that exploits the adaptation dynamics of floating gate transistors, to model an adaptive cortical cell that demonstrates Orientation Selectivity, a well-known biological phenomenon observed in the visual cortex. The cell performs competitive learning, refining its weights in response to input patterns resembling different oriented bars, becoming selective to a particular oriented pattern. Different analysis performed on the cell such as orientation tuning, application of abnormal inputs, response to spatial frequency and periodic patterns reveal close similarity between our cell and its biological counterpart. Embedded in a RC grid, these cells interact diffusively exhibiting cluster formation, making way for adaptively building orientation selective maps in silicon. PMID:24765062

Object-oriented parsing of biological databases with Python.

PubMed

Ramu, C; Gemünd, C; Gibson, T J

2000-07-01

While database activities in the biological area are increasing rapidly, rather little is done in the area of parsing them in a simple and object-oriented way. We present here an elegant, simple yet powerful way of parsing biological flat-file databases. We have taken EMBL, SWISSPROT and GENBANK as examples. EMBL and SWISS-PROT do not differ much in the format structure. GENBANK has a very different format structure than EMBL and SWISS-PROT. Extracting the desired fields in an entry (for example a sub-sequence with an associated feature) for later analysis is a constant need in the biological sequence-analysis community: this is illustrated with tools to make new splice-site databases. The interface to the parser is abstract in the sense that the access to all the databases is independent from their different formats, since parsing instructions are hidden.

Instabilities and spatiotemporal patterns behind predator invasions with nonlocal prey competition.

PubMed

Merchant, Sandra M; Nagata, Wayne

2011-12-01

We study the influence of nonlocal intraspecies prey competition on the spatiotemporal patterns arising behind predator invasions in two oscillatory reaction-diffusion integro-differential models. We use three common types of integral kernels as well as develop a caricature system, to describe the influence of the standard deviation and kurtosis of the kernel function on the patterns observed. We find that nonlocal competition can destabilize the spatially homogeneous state behind the invasion and lead to the formation of complex spatiotemporal patterns, including stationary spatially periodic patterns, wave trains and irregular spatiotemporal oscillations. In addition, the caricature system illustrates how large standard deviation and low kurtosis facilitate the formation of these spatiotemporal patterns. This suggests that nonlocal competition may be an important mechanism underlying spatial pattern formation, particularly in systems where the competition between individuals varies over space in a platykurtic manner. Copyright © 2011 Elsevier Inc. All rights reserved.

The laser radiation action on the crystal formation processes in the biological fluids

NASA Astrophysics Data System (ADS)

Malov, Alexander N.; Vaichas, Andrey A.; Novikova, Evgeniya A.

2016-11-01

The results of an experimental study of the laser radiation effect on the crystal`s formation in the volume of biological fluids that are complex multi-component solutions have been discussing. Are investigated white and natural bile in vitro. The qualitative changes were observed. Thus, at the bottom of the cell in which bile is not exposed to the laser radiation, the crystals are formed. In the irradiated bile gallstone has a thin layer of a homogeneous viscous colloidal liquid with very small, visible in polarized light crystalline formations was got. Irradiated laser bile's gallstone was covered evenly white deposit without surface defect unlike gallstone in bile without radiation exposure. A possible mechanism to explain the laser radiation action on the mineral formation in biological fluids and also practical application of this effect have been suggesting too.

Pattern recognition neural-net by spatial mapping of biology visual field

NASA Astrophysics Data System (ADS)

Lin, Xin; Mori, Masahiko

2000-05-01

The method of spatial mapping in biology vision field is applied to artificial neural networks for pattern recognition. By the coordinate transform that is called the complex-logarithm mapping and Fourier transform, the input images are transformed into scale- rotation- and shift- invariant patterns, and then fed into a multilayer neural network for learning and recognition. The results of computer simulation and an optical experimental system are described.

Co-ordinated spatial propagation of blood plasma clotting and fibrinolytic fronts

PubMed Central

Zhalyalov, Ansar S.; Panteleev, Mikhail A.; Gracheva, Marina A.; Ataullakhanov, Fazoil I.

2017-01-01

Fibrinolysis is a cascade of proteolytic reactions occurring in blood and soft tissues, which functions to disintegrate fibrin clots when they are no more needed. In order to elucidate its regulation in space and time, fibrinolysis was investigated using an in vitro reaction-diffusion experimental model of blood clot formation and dissolution. Clotting was activated by a surface with immobilized tissue factor in a thin layer of recalcified blood plasma supplemented with tissue plasminogen activator (TPA), urokinase plasminogen activator or streptokinase. Formation and dissolution of fibrin clot was monitored by videomicroscopy. Computer systems biology model of clot formation and lysis was developed for data analysis and experimental planning. Fibrin clot front propagated in space from tissue factor, followed by a front of clot dissolution propagating from the same source. Velocity of lysis front propagation linearly depended on the velocity clotting front propagation (correlation r2 = 0.91). Computer model revealed that fibrin formation was indeed the rate-limiting step in the fibrinolysis front propagation. The phenomenon of two fronts which switched the state of blood plasma from liquid to solid and then back to liquid did not depend on the fibrinolysis activator. Interestingly, TPA at high concentrations began to increase lysis onset time and to decrease lysis propagation velocity, presumably due to plasminogen depletion. Spatially non-uniform lysis occurred simultaneously with clot formation and detached the clot from the procoagulant surface. These patterns of spatial fibrinolysis provide insights into its regulation and might explain clinical phenomena associated with thrombolytic therapy. PMID:28686711

Genome-scale biological models for industrial microbial systems.

PubMed

Xu, Nan; Ye, Chao; Liu, Liming

2018-04-01

The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

Biomimetic Phases of Microtubule-Motor Mixtures

NASA Astrophysics Data System (ADS)

Ross, Jennifer

2014-03-01

We try to determine the universal principles of organization from the molecular scale that gives rise to architecture on the cellular scale. We are specifically interested in the organization of the microtubule cytoskeleton, a rigid, yet versatile network in most cell types. Microtubules in the cell are organized by motor proteins and crosslinkers. This work applies the ideas of statistical mechanics and condensed matter physics to the non-equilibrium pattern formation behind intracellular organization using the microtubule cytoskeleton as the building blocks. We examine these processes in a bottom-up manner by adding increasingly complex protein actors into the system. Our systematic experiments expose nature's laws for organization and has large impacts on biology as well as illuminating new frontiers of non-equilibrium physics.

Improved Fibroblast Functionalities by Microporous Pattern Fabricated by Microelectromechanical Systems

PubMed Central

Wei, Hongbo; Zhao, Lingzhou; Chen, Bangdao; Bai, Shizhu; Zhao, Yimin

2014-01-01

Fibroblasts, which play an important role in biological seal formation and maintenance, determine the long-term success of percutaneous implants. In this study, well-defined microporous structures with micropore diameters of 10–60 µm were fabricated by microelectromechanical systems and their influence on the fibroblast functionalities was observed. The results show that the microporous structures with micropore diameters of 10–60 µm did not influence the initial adherent fibroblast number; however, those with diameters of 40 and 50 µm improved the spread, actin stress fiber organization, proliferation and fibronectin secretion of the fibroblasts. The microporous structures with micropore diameters of 40–50 µm may be promising for application in the percutaneous part of an implant. PMID:25054322

Coordination of Cell Polarity, Mechanics and Fate in Tissue Self-organization.

PubMed

Kim, Esther Jeong Yoon; Korotkevich, Ekaterina; Hiiragi, Takashi

2018-07-01

Self-organization guides robust, spatiotemporally ordered formation of complex tissues and ultimately whole organisms. While products of gene expression serve as building blocks of living matter, how these interact to give rise to tissues of distinct patterns and function remains a central question in biology. Tissue self-organization relies on dynamic interactions between constituents spanning a range of spatiotemporal scales with tuneable chemical and mechanical parameters. This review highlights recent studies dissecting mechanisms of these interactions. We propose that feedback interactions between cell polarity, mechanics, and fate are a key principle underlying tissue self-organization. We also provide a glimpse into how such processes can be studied in future endeavors. Copyright © 2018 Elsevier Ltd. All rights reserved.

We need wrinkle on the skin

NASA Astrophysics Data System (ADS)

Ahn, Sungsook; Lee, Sang Joon

2015-11-01

Wrinkle formation on the skin is an unwelcome guest to everybody. But if we truly understand how wrinkles can contribute to important biological functions, then we readily admit the wrinkles positively. In this study, we show how the wrinkles are advantageous and useful in many systems. In a plant system for example, by forming line patterned wrinkles the hydrogels covering on the seed surface contribute to delay the dehydration against varying water supply environments. Inspired by this plant hydrogel, it is experimentally and theoretically investigated how lined wrinkles are useful to conserve water inside while protect the individual from drying-out. This study would contribute to a variety of humidity-sensitive system development including artificial skin, humidity-actuated sensors and the like.

Magnetically modified bioсells in constant magnetic field

NASA Astrophysics Data System (ADS)

Abramov, E. G.; Panina, L. K.; Kolikov, V. A.; Bogomolova, E. V.; Snetov, V. N.; Cherepkova, I. A.; Kiselev, A. A.

2017-02-01

Paper addresses the inverse problem in determining the area, where the external constant magnetic field captures the biological cells modified by the magnetic nanoparticles. Zero velocity isolines, in area where the modified cells are captured by the magnetic field were determined by numerical method for two locations of the magnet. The problem was solved taking into account the gravitational field, magnetic induction, density of medium, concentration and size of cells, and size and magnetization of nanoparticles attached to the cell. Increase in the number of the nanoparticles attached to the cell and decrease in the cell' size, enlarges the area, where the modified cells are captured and concentrated by the magnet. Solution is confirmed by the visible pattern formation of the modified cells Saccharomyces cerevisiae.

In situ protocol for butterfly pupal wings using riboprobes.

PubMed

Ramos, Diane; Monteiro, Antonia

2007-01-01

Here we present, in video format, a protocol for in situ hybridizations in pupal wings of the butterfly Bicyclus anynana using riboprobes. In situ hybridizations, a mainstay of developmental biology, are useful to study the spatial and temporal patterns of gene expression in developing tissues at the level of transcription. If antibodies that target the protein products of gene transcription have not yet been developed, and/or there are multiple gene copies of a particular protein in the genome that cannot be differentiated using available antibodies, in situs can be used instead. While an in situ technique for larval wing discs has been available to the butterfly community for several years, the current protocol has been optimized for the larger and more fragile pupal wings.

BicPAMS: software for biological data analysis with pattern-based biclustering.

PubMed

Henriques, Rui; Ferreira, Francisco L; Madeira, Sara C

2017-02-02

Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entities). However, given its computational complexity, only recent breakthroughs on pattern-based biclustering enabled efficient searches without the restrictions that state-of-the-art biclustering algorithms place on the structure and homogeneity of biclusters. As a result, pattern-based biclustering provides the unprecedented opportunity to discover non-trivial yet meaningful biological modules with putative functions, whose coherency and tolerance to noise can be tuned and made problem-specific. To enable the effective use of pattern-based biclustering by the scientific community, we developed BicPAMS (Biclustering based on PAttern Mining Software), a software that: 1) makes available state-of-the-art pattern-based biclustering algorithms (BicPAM (Henriques and Madeira, Alg Mol Biol 9:27, 2014), BicNET (Henriques and Madeira, Alg Mol Biol 11:23, 2016), BicSPAM (Henriques and Madeira, BMC Bioinforma 15:130, 2014), BiC2PAM (Henriques and Madeira, Alg Mol Biol 11:1-30, 2016), BiP (Henriques and Madeira, IEEE/ACM Trans Comput Biol Bioinforma, 2015), DeBi (Serin and Vingron, AMB 6:1-12, 2011) and BiModule (Okada et al., IPSJ Trans Bioinf 48(SIG5):39-48, 2007)); 2) consistently integrates their dispersed contributions; 3) further explores additional accuracy and efficiency gains; and 4) makes available graphical and application programming interfaces. Results on both synthetic and real data confirm the relevance of BicPAMS for biological data analysis, highlighting its essential role for the discovery of putative modules with non-trivial yet biologically significant functions from expression and network data. BicPAMS is the first biclustering tool offering the possibility to: 1) parametrically customize the structure, coherency and quality of biclusters; 2) analyze large-scale biological networks; and 3) tackle the restrictive assumptions placed by state-of-the-art biclustering algorithms. These contributions are shown to be key for an adequate, complete and user-assisted unsupervised analysis of biological data. BicPAMS and its tutorial available in http://www.bicpams.com .

Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis.

PubMed

Yi, Ming; Mudunuri, Uma; Che, Anney; Stephens, Robert M

2009-06-29

One of the challenges in the analysis of microarray data is to integrate and compare the selected (e.g., differential) gene lists from multiple experiments for common or unique underlying biological themes. A common way to approach this problem is to extract common genes from these gene lists and then subject these genes to enrichment analysis to reveal the underlying biology. However, the capacity of this approach is largely restricted by the limited number of common genes shared by datasets from multiple experiments, which could be caused by the complexity of the biological system itself. We now introduce a new Pathway Pattern Extraction Pipeline (PPEP), which extends the existing WPS application by providing a new pathway-level comparative analysis scheme. To facilitate comparing and correlating results from different studies and sources, PPEP contains new interfaces that allow evaluation of the pathway-level enrichment patterns across multiple gene lists. As an exploratory tool, this analysis pipeline may help reveal the underlying biological themes at both the pathway and gene levels. The analysis scheme provided by PPEP begins with multiple gene lists, which may be derived from different studies in terms of the biological contexts, applied technologies, or methodologies. These lists are then subjected to pathway-level comparative analysis for extraction of pathway-level patterns. This analysis pipeline helps to explore the commonality or uniqueness of these lists at the level of pathways or biological processes from different but relevant biological systems using a combination of statistical enrichment measurements, pathway-level pattern extraction, and graphical display of the relationships of genes and their associated pathways as Gene-Term Association Networks (GTANs) within the WPS platform. As a proof of concept, we have used the new method to analyze many datasets from our collaborators as well as some public microarray datasets. This tool provides a new pathway-level analysis scheme for integrative and comparative analysis of data derived from different but relevant systems. The tool is freely available as a Pathway Pattern Extraction Pipeline implemented in our existing software package WPS, which can be obtained at http://www.abcc.ncifcrf.gov/wps/wps_index.php.

Multiparametric Analyses Reveal the pH-Dependence of Silicon Biomineralization in Diatoms

PubMed Central

Hervé, Vincent; Derr, Julien; Douady, Stéphane; Quinet, Michelle; Moisan, Lionel; Lopez, Pascal Jean

2012-01-01

Diatoms, the major contributors of the global biogenic silica cycle in modern oceans, account for about 40% of global marine primary productivity. They are an important component of the biological pump in the ocean, and their assemblage can be used as useful climate proxies; it is therefore critical to better understand the changes induced by environmental pH on their physiology, silicification capability and morphology. Here, we show that external pH influences cell growth of the ubiquitous diatom Thalassiosira weissflogii, and modifies intracellular silicic acid and biogenic silica contents per cell. Measurements at the single-cell level reveal that extracellular pH modifications lead to intracellular acidosis. To further understand how variations of the acid-base balance affect silicon metabolism and theca formation, we developed novel imaging techniques to measure the dynamics of valve formation. We demonstrate that the kinetics of valve morphogenesis, at least in the early stages, depends on pH. Analytical modeling results suggest that acidic conditions alter the dynamics of the expansion of the vesicles within which silica polymerization occurs, and probably its internal pH. Morphological analysis of valve patterns reveals that acidification also reduces the dimension of the nanometric pores present on the valves, and concurrently overall valve porosity. Variations in the valve silica network seem to be more correlated to the dynamics and the regulation of the morphogenesis process than the silicon incorporation rate. These multiparametric analyses from single-cell to cell-population levels demonstrate that several higher-level processes are sensitive to the acid-base balance in diatoms, and its regulation is a key factor for the control of pattern formation and silicon metabolism. PMID:23144697

Model for the role of auxin polar transport in patterning of the leaf adaxial-abaxial axis.

PubMed

Shi, Jianmin; Dong, Jiaqiang; Xue, Jingshi; Wang, Hua; Yang, Zhongnan; Jiao, Yuling; Xu, Lin; Huang, Hai

2017-11-01

Leaf adaxial-abaxial polarity refers to the two leaf faces, which have different types of cells performing distinct biological functions. In 1951, Ian Sussex reported that when an incipient leaf primordium was surgically isolated by an incision across the vegetative shoot apical meristem (SAM), a radialized structure without an adaxial domain would form. This led to the proposal that a signal, now called the Sussex signal, is transported from the SAM to emerging primordia to direct leaf adaxial-abaxial patterning. It was recently proposed that instead of the Sussex signal, polar transport of the plant hormone auxin is critical in leaf polarity formation. However, how auxin polar transport functions in the process is unknown. Through live imaging, we established a profile of auxin polar transport in and around young leaf primordia. Here we show that auxin polar transport in lateral regions of an incipient primordium forms auxin convergence points. We demonstrated that blocking auxin polar transport in the lateral regions of the incipient primordium by incisions abolished the auxin convergence points and caused abaxialized leaves to form. The lateral incisions also blocked the formation of leaf middle domain and margins and disrupted expression of the middle domain/margin-associated marker gene WUSCHEL-RELATED HOMEOBOX 1 (SlWOX1). Based on these results we propose that the auxin convergence points are required for the formation of leaf middle domain and margins, and the functional middle domain and margins ensure leaf adaxial-abaxial polarity. How middle domain and margins function in the process is discussed. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Formation of banded vegetation patterns resulted from interactions between sediment deposition and vegetation growth.

PubMed

Huang, Tousheng; Zhang, Huayong; Dai, Liming; Cong, Xuebing; Ma, Shengnan

2018-03-01

This research investigates the formation of banded vegetation patterns on hillslopes affected by interactions between sediment deposition and vegetation growth. The following two perspectives in the formation of these patterns are taken into consideration: (a) increased sediment deposition from plant interception, and (b) reduced plant biomass caused by sediment accumulation. A spatial model is proposed to describe how the interactions between sediment deposition and vegetation growth promote self-organization of banded vegetation patterns. Based on theoretical and numerical analyses of the proposed spatial model, vegetation bands can result from a Turing instability mechanism. The banded vegetation patterns obtained in this research resemble patterns reported in the literature. Moreover, measured by sediment dynamics, the variation of hillslope landform can be described. The model predicts how treads on hillslopes evolve with the banded patterns. Thus, we provide a quantitative interpretation for coevolution of vegetation patterns and landforms under effects of sediment redistribution. Copyright © 2018. Published by Elsevier Masson SAS.

Evaporation-induced patterns from droplets containing motile and nonmotile bacteria.

PubMed

Nellimoottil, Tittu Thomas; Rao, Pinjala Nagaraju; Ghosh, Siddhartha Sankar; Chattopadhyay, Arun

2007-08-14

In this letter, we report the observations of specific pattern formation from the evaporation of aqueous droplets containing motile and nonmotile bacteria. We found that when motile bacteria were present the droplet evaporated into disclike patterned deposits of bacteria. However, when the bacteria were made nonmotile by treatment with liquid nitrogen, the droplet evaporated into ringlike deposits. We also observed that bacteria with higher motility produced more uniformly deposited disclike patterns. Furthermore, we propose a model with numerical simulations to explain the mechanism of formation of these patterns. The model is based on the advective fluid flow from the center of the droplet toward the edge due to enhanced evaporation from the edge of the pinned droplet in comparison to that from the free surface. For the case of motile bacteria, we have added another velocity parameter toward the axis of the droplet and directed against the fluid flow in order to account for the disclike pattern formation. The numerical simulations match the experimental observations well. The present work, by qualitative and quantitative understanding of the evaporation of bacteria droplets, demonstrates that the inherent bacterial motility is primarily responsible for the formation of these differential patterns.

Dynamics of spiral patterns in gas discharge detected by optical method

NASA Astrophysics Data System (ADS)

Yang, Fan; Wang, Mingyi; Liu, Shuhua

2016-09-01

The dynamics behavior of spiral patterns is investigated in gas discharge using optical method. Rich kinks of spiral patterns are obtained and the formation and evolution process is investigated. The process of pattern formation is breakdown -> hexagon -> bee comb-like -> strip -> spiral -> chaos. Spiral pattern always formed after the strip pattern. It is found that the temperature of the water electrodes plays an important role in the spiral patterns formation. When it exceeds 20°C no spiral has been obtained. The discharge current waveform and the emission spectrum of the discharge have been measured when the filaments self-organized in spiral pattern. Electron excited temperature of forming spiral pattern is calculated using intensity ratio method. It is found that the electron excited temperature of spiral pattern increase as the power supply frequency increased. Relation between wavelength and discharge parameter has been measured. It shows that the wavelength of spiral pattern increases as the discharge gap increases, and decreases as the air ratio mixed in argon increases. Accompanying measurements proved that the wavelength is approximately linear to the square root of the spiral rotating period .This work has useful reference value for studying pattern dynamics.

Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation

DOE PAGES

Sobel, Sabrina G.; Hastings, Harold M.; Testa, Matthew

2009-01-01

Imore » mperfect mixing is a concern in industrial processes, everyday processes (mixing paint, bread machines), and in understanding salt water-fresh water mixing in ecosystems. The effects of imperfect mixing become evident in the unstirred ferroin-catalyzed Belousov-Zhabotinsky reaction, the prototype for chemical pattern formation. Over time, waves of oxidation (high ferriin concentration, blue) propagate into a background of low ferriin concentration (red); their structure reflects in part the history of mixing in the reaction vessel. However, it may be difficult to separate mixing effects from reaction effects. We describe a simpler model system for visualizing density-driven pattern formation in an essentially unmixed chemical system: the reaction of pale yellow Fe 3 + with colorless SCN − to form the blood-red Fe ( SCN ) 2 + complex ion in aqueous solution. Careful addition of one drop of Fe ( NO 3 ) 3 to KSCN yields striped patterns after several minutes. The patterns appear reminiscent of Rayleigh-Taylor instabilities and convection rolls, arguing that pattern formation is caused by density-driven mixing.« less

Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sobel, Sabrina G.; Hastings, Harold M.; Testa, Matthew

Imore » mperfect mixing is a concern in industrial processes, everyday processes (mixing paint, bread machines), and in understanding salt water-fresh water mixing in ecosystems. The effects of imperfect mixing become evident in the unstirred ferroin-catalyzed Belousov-Zhabotinsky reaction, the prototype for chemical pattern formation. Over time, waves of oxidation (high ferriin concentration, blue) propagate into a background of low ferriin concentration (red); their structure reflects in part the history of mixing in the reaction vessel. However, it may be difficult to separate mixing effects from reaction effects. We describe a simpler model system for visualizing density-driven pattern formation in an essentially unmixed chemical system: the reaction of pale yellow Fe 3 + with colorless SCN − to form the blood-red Fe ( SCN ) 2 + complex ion in aqueous solution. Careful addition of one drop of Fe ( NO 3 ) 3 to KSCN yields striped patterns after several minutes. The patterns appear reminiscent of Rayleigh-Taylor instabilities and convection rolls, arguing that pattern formation is caused by density-driven mixing.« less

Remodeling a tissue: subtraction adds insight.

PubMed

Axelrod, Jeffrey D

2012-11-27

Sculpting a body plan requires both patterning of gene expression and translating that pattern into morphogenesis. Developmental biologists have made remarkable strides in understanding gene expression patterning, but despite a long history of fascination with the mechanics of morphogenesis, knowledge of how patterned gene expression drives the emergence of even simple shapes and forms has grown at a slower pace. The successful merging of approaches from cell biology, developmental biology, imaging, engineering, and mathematical and computational sciences is now accelerating progress toward a fuller and better integrated understanding of the forces shaping morphogenesis.

New immature hominin fossil from European Lower Pleistocene shows the earliest evidence of a modern human dental development pattern

PubMed Central

Bermúdez de Castro, José María; Martinón-Torres, María; Prado, Leyre; Gómez-Robles, Aida; Rosell, Jordi; López-Polín, Lucía; Arsuaga, Juan Luís; Carbonell, Eudald

2010-01-01

Here we present data concerning the pattern of dental development derived from the microcomputed tomography (microCT) study of a recently discovered immature hominin mandible with a mixed dentition recovered from the TD6 level of the Gran Dolina Lower Pleistocene cave site in Sierra de Atapuerca, northern Spain. These data confirm our previous results that nearly 1 million years ago at least one European hominin species had a fully modern pattern of dental development with a clear slowdown in the development of the molar field regarding the anterior dental field. Furthermore, using available information about enamel formation times and root extension rates in chimpanzees, early hominins, and modern humans, we have estimated that the formation time of the upper and lower first molars of individual 5 (H5) from TD6, which had just erupted at the time of the death of this individual, ranges between 5.3 and 6.6 y. Therefore, the eruption time of the first permanent molars (M1) in the TD6 hominins was within the range of variation of modern human populations. Because the time of M1 eruption in primates is a robust marker of life history, we suggest, as a working hypothesis, that these hominins had a prolonged childhood in the range of the variation of modern humans. If this hypothesis is true, it implies that the appearance in Homo of this important developmental biological feature and an associated increase in brain size preceded the development of the neocortical areas leading to the cognitive capabilities that are thought to be exclusive to Homo sapiens. PMID:20547843

Effects of polymer surface energy on morphology and properties of silver nanowire fabricated via nanoimprint and E-beam evaporation

NASA Astrophysics Data System (ADS)

Zhao, Zhi-Jun; Hwang, Soon Hyoung; Jeon, Sohee; Jung, Joo-Yun; Lee, Jihye; Choi, Dae-Geun; Choi, Jun-Hyuk; Park, Sang-Hu; Jeong, Jun-Ho

2017-10-01

In this paper, we demonstrate that use of different nanoimprint resins as a polymer pattern has a significant effect on the morphology of silver (Ag) nanowires deposited via an E-beam evaporator. RM-311 and Ormo-stamp resins are chosen as a polymer pattern to form a line with dimensions of width (100 nm) × space (100 nm) × height (120 nm) by using nanoimprint lithography (NIL). Their contact angles are then measured to evaluate their surface energies. In order to compare the properties of the Ag nanowires deposited on the various polymer patterns with different surface energies, hydrophobic surface treatment of the polymer pattern surface is implemented using self-assembled monolayers. In addition, gold and aluminum nanowires are fabricated for comparison with the Ag nanowires, with the differences in the nanowire morphologies being determined by the different atomic properties. The monocrystalline and polycrystalline structures of the various Ag nanowire formations are observed using transmission electron microscopy. In addition, the melting temperatures and optical properties of four kinds of Ag nanowire morphologies deposited on various polymer patterns are evaluated using a hot plate and an ultraviolet-visible (UV-vis) spectrometer, respectively. The results indicate that the morphology of the Ag nanowire determines the melting temperature and the transmission. We believe that these findings will greatly aid the development of NIL, along with physical evaporation and chemical deposition techniques, and will be widely employed in optics, biology, and surface wettability applications.

Identifying Ant-Mirid Spatial Interactions to Improve Biological Control in Cacao-Based Agroforestry System.

PubMed

Bagny Beilhe, Leïla; Piou, Cyril; Tadu, Zéphirin; Babin, Régis

2018-06-06

The use of ants for biological control of insect pests was the first reported case of conservation biological control. Direct and indirect community interactions between ants and pests lead to differential spatial pattern. We investigated spatial interactions between mirids, the major cocoa pest in West Africa and numerically dominant ant species, using bivariate point pattern analysis to identify potential biological control agents. We assume that potential biological control agents should display negative spatial interactions with mirids considering their niche overlap. The mirid/ant data were collected in complex cacao-based agroforestry systems sampled in three agroecological areas over a forest-savannah gradient in Cameroon. Three species, Crematogaster striatula Emery (Hymenoptera: Formicidae), Crematogaster clariventris Mayr (Hymenoptera: Formicidae), and Oecophylla longinoda Latreille (Hymenoptera: Formicidae) with high predator and aggressive behaviors were identified as dominant and showed negative spatial relationships with mirids. The weaver ant, O. longinoda was identified as the only potential biological control agent, considering its ubiquity in the plots, the similarity in niche requirements, and the spatial segregation with mirids resulting probably from exclusion mechanisms. Combining bivariate point pattern analysis to good knowledge of insect ecology was an effective method to identify a potentially good biological control agent.

Soft lithographic functionalization and patterning oxide-free silicon and germanium.

PubMed

Bowers, Carleen M; Toone, Eric J; Clark, Robert L; Shestopalov, Alexander A

2011-12-16

The development of hybrid electronic devices relies in large part on the integration of (bio)organic materials and inorganic semiconductors through a stable interface that permits efficient electron transport and protects underlying substrates from oxidative degradation. Group IV semiconductors can be effectively protected with highly-ordered self-assembled monolayers (SAMs) composed of simple alkyl chains that act as impervious barriers to both organic and aqueous solutions. Simple alkyl SAMs, however, are inert and not amenable to traditional patterning techniques. The motivation for immobilizing organic molecular systems on semiconductors is to impart new functionality to the surface that can provide optical, electronic, and mechanical function, as well as chemical and biological activity. Microcontact printing (μCP) is a soft-lithographic technique for patterning SAMs on myriad surfaces. Despite its simplicity and versatility, the approach has been largely limited to noble metal surfaces and has not been well developed for pattern transfer to technologically important substrates such as oxide-free silicon and germanium. Furthermore, because this technique relies on the ink diffusion to transfer pattern from the elastomer to substrate, the resolution of such traditional printing is essentially limited to near 1 μm. In contrast to traditional printing, inkless μCP patterning relies on a specific reaction between a surface-immobilized substrate and a stamp-bound catalyst. Because the technique does not rely on diffusive SAM formation, it significantly expands the diversity of patternable surfaces. In addition, the inkless technique obviates the feature size limitations imposed by molecular diffusion, facilitating replication of very small (<200 nm) features. However, up till now, inkless μCP has been mainly used for patterning relatively disordered molecular systems, which do not protect underlying surfaces from degradation. Here, we report a simple, reliable high-throughput method for patterning passivated silicon and germanium with reactive organic monolayers and demonstrate selective functionalization of the patterned substrates with both small molecules and proteins. The technique utilizes a preformed NHS-reactive bilayered system on oxide-free silicon and germanium. The NHS moiety is hydrolyzed in a pattern-specific manner with a sulfonic acid-modified acrylate stamp to produce chemically distinct patterns of NHS-activated and free carboxylic acids. A significant limitation to the resolution of many μCP techniques is the use of PDMS material which lacks the mechanical rigidity necessary for high fidelity transfer. To alleviate this limitation we utilized a polyurethane acrylate polymer, a relatively rigid material that can be easily functionalized with different organic moieties. Our patterning approach completely protects both silicon and germanium from chemical oxidation, provides precise control over the shape and size of the patterned features, and gives ready access to chemically discriminated patterns that can be further functionalized with both organic and biological molecules. The approach is general and applicable to other technologically-relevant surfaces.

A Theoretical Model of Jigsaw-Puzzle Pattern Formation by Plant Leaf Epidermal Cells.

PubMed

Higaki, Takumi; Kutsuna, Natsumaro; Akita, Kae; Takigawa-Imamura, Hisako; Yoshimura, Kenji; Miura, Takashi

2016-04-01

Plant leaf epidermal cells exhibit a jigsaw puzzle-like pattern that is generated by interdigitation of the cell wall during leaf development. The contribution of two ROP GTPases, ROP2 and ROP6, to the cytoskeletal dynamics that regulate epidermal cell wall interdigitation has already been examined; however, how interactions between these molecules result in pattern formation remains to be elucidated. Here, we propose a simple interface equation model that incorporates both the cell wall remodeling activity of ROP GTPases and the diffusible signaling molecules by which they are regulated. This model successfully reproduces pattern formation observed in vivo, and explains the counterintuitive experimental results of decreased cellulose production and increased thickness. Our model also reproduces the dynamics of three-way cell wall junctions. Therefore, this model provides a possible mechanism for cell wall interdigitation formation in vivo.

Improving signal to noise in labeled biological specimens using energy-filtered TEM of sections with a drift correction strategy and a direct detection device.

PubMed

Ramachandra, Ranjan; Bouwer, James C; Mackey, Mason R; Bushong, Eric; Peltier, Steven T; Xuong, Nguyen-Huu; Ellisman, Mark H

2014-06-01

Energy filtered transmission electron microscopy techniques are regularly used to build elemental maps of spatially distributed nanoparticles in materials and biological specimens. When working with thick biological sections, electron energy loss spectroscopy techniques involving core-loss electrons often require exposures exceeding several minutes to provide sufficient signal to noise. Image quality with these long exposures is often compromised by specimen drift, which results in blurring and reduced resolution. To mitigate drift artifacts, a series of short exposure images can be acquired, aligned, and merged to form a single image. For samples where the target elements have extremely low signal yields, the use of charge coupled device (CCD)-based detectors for this purpose can be problematic. At short acquisition times, the images produced by CCDs can be noisy and may contain fixed pattern artifacts that impact subsequent correlative alignment. Here we report on the use of direct electron detection devices (DDD's) to increase the signal to noise as compared with CCD's. A 3× improvement in signal is reported with a DDD versus a comparably formatted CCD, with equivalent dose on each detector. With the fast rolling-readout design of the DDD, the duty cycle provides a major benefit, as there is no dead time between successive frames.

Comprehensive proteomic profiling of adult Angiostrongylus costaricensis, a human parasitic nematode.

PubMed

Rebello, Karina M; Barros, Juliana S L; Mota, Ester M; Carvalho, Paulo C; Perales, Jonas; Lenzi, Henrique L; Neves-Ferreira, Ana G C

2011-08-24

Angiostrongylus costaricensis is a nematode helminth that causes an intestinal acute inflammatory process known as abdominal angiostrongyliasis, which is a poorly understood human disease occurring in Latin America. Our aim was to study the proteomic profiles of adult parasites focusing on immunogenic proteins. Total cellular extracts from both genders showed similar 2-DE profiles, with 60% of all protein spots focused between pH 5-7 and presenting molecular masses from 20.1 to 66 kDa. A total of 53 different dominant proteins were identified in our dataset and were mainly associated with the following over-represented Gene Ontology Biological Process terms: "macromolecule metabolic process", "developmental process", "response to stress", and "biological regulation". Female and male immunoblots showed similar patterns of reactive proteins. Immunoreactive spots identified by MALDI-PSD were found to represent heat shock proteins, a putative abnormal DAuer Formation family member, and galectins. To date, very few biochemical analyses have focused on the nematode Angiostrongylus costaricensis. As such, our results contribute to a better understanding of its biology and the mechanisms underlying the host-parasite relationship associated with this species. Moreover, our findings represent a first step in the search for candidate proteins for diagnostic assays and the treatment of this parasitic infection. Copyright © 2011 Elsevier B.V. All rights reserved.

Adolescent Sleep Patterns: Biological, Social, and Psychological Influences.

ERIC Educational Resources Information Center

Carskadon, Mary A., Ed.

Noting that healthy, adequate sleep fosters longevity and the optimal use of waking hours, and that adolescents, although rarely included in previous studies of sleep, are among the most sleep-deprived populations, this book explores the genesis and development of sleep patterns during adolescence, including biological and cultural factors that…

Pattern identification in time-course gene expression data with the CoGAPS matrix factorization.

PubMed

Fertig, Elana J; Stein-O'Brien, Genevieve; Jaffe, Andrew; Colantuoni, Carlo

2014-01-01

Patterns in time-course gene expression data can represent the biological processes that are active over the measured time period. However, the orthogonality constraint in standard pattern-finding algorithms, including notably principal components analysis (PCA), confounds expression changes resulting from simultaneous, non-orthogonal biological processes. Previously, we have shown that Markov chain Monte Carlo nonnegative matrix factorization algorithms are particularly adept at distinguishing such concurrent patterns. One such matrix factorization is implemented in the software package CoGAPS. We describe the application of this software and several technical considerations for identification of age-related patterns in a public, prefrontal cortex gene expression dataset.

Introduction to the Focus Issue: Chemo-Hydrodynamic Patterns and Instabilities

NASA Astrophysics Data System (ADS)

De Wit, A.; Eckert, K.; Kalliadasis, S.

2012-09-01

Pattern forming instabilities are often encountered in a wide variety of natural phenomena and technological applications, from self-organization in biological and chemical systems to oceanic or atmospheric circulation and heat and mass transport processes in engineering systems. Spatio-temporal structures are ubiquitous in hydrodynamics where numerous different convective instabilities generate pattern formation and complex spatiotemporal dynamics, which have been much studied both theoretically and experimentally. In parallel, reaction-diffusion processes provide another large family of pattern forming instabilities and spatio-temporal structures which have been analyzed for several decades. At the intersection of these two fields, "chemo-hydrodynamic patterns and instabilities" resulting from the coupling of hydrodynamic and reaction-diffusion processes have been less studied. The exploration of the new instability and symmetry-breaking scenarios emerging from the interplay between chemical reactions, diffusion and convective motions is a burgeoning field in which numerous exciting problems have emerged during the last few years. These problems range from fingering instabilities of chemical fronts and reactive fluid-fluid interfaces to the dynamics of reaction-diffusion systems in the presence of chaotic mixing. The questions to be addressed are at the interface of hydrodynamics, chemistry, engineering or environmental sciences to name a few and, as a consequence, they have started to draw the attention of several communities including both the nonlinear chemical dynamics and hydrodynamics communities. The collection of papers gathered in this Focus Issue sheds new light on a wide range of phenomena in the general area of chemo-hydrodynamic patterns and instabilities. It also serves as an overview of the current research and state-of-the-art in the field.

Neointimal patterns obtained by optical coherence tomography correlate with specific histological components and neointimal proliferation in a swine model of restenosis.

PubMed

Kim, Jung-Sun; Afari, Maxwell E; Ha, Jinyong; Tellez, Armando; Milewski, Krzysztof; Conditt, Gerard; Cheng, Yanping; Hua Yi, Geng; Kaluza, Greg L; Granada, Juan F

2014-03-01

Although optical coherence tomography (OCT) is capable to detect microscopic peri-strut changes that seem to be related to neointimal inhibition and healing, its ability to characterize these components is still limited. In this study, we aimed to compare different OCT morphological characteristics with different in-stent neointimal tissue types analysed by histology. A total of 69 stents (39 drug eluting and 30 bare metal stents) were implanted in coronary arteries of 27 swine. By OCT, neointimal type was classified as homogeneous, heterogeneous, or layered according to its pattern of backscatter and optical intensity. The resulting optical patterns were correlated with several histological findings [external elastic lamina (EEL) disruption, fibrin deposition, circumferential rim of peri-strut inflammatory cell infiltration, and fibrous connective deposition] in every single cross-section (CS) analysed. A total of 197 matched OCT and histological CS were analysed. The heterogeneous (0.44 ± 0.21 mm) and layered (0.65 ± 0.16 mm) patterns had a significantly higher degree of neointimal thickness compared with the homogeneous pattern (0.25 ± 0.16 mm, P < 0.001). Fibrous connective tissue deposition was more frequently present in the homogeneous pattern (71.6%, P < 0.001), whereas significant fibrin deposits were more commonly seen in the heterogeneous pattern (56.9%, P = 0.007). Peri-strut inflammation was less frequently found in the homogeneous pattern (19.8%, P < 0.001) in comparison with the layered (73.9%) or heterogeneous patterns (43.1%). The presence of EEL rupture was also more commonly seen in layered (73.9%) and heterogeneous (46.6%) patterns than in the homogeneous pattern (22.4%, P < 0.001). The optical characteristics of neointimal formation seen in OCT properly correlated with the presence of several histological findings involved in stent healing. The biological implications of these findings in clinical outcomes require further investigation.

Pbx proteins cooperate with Engrailed to pattern the midbrain-hindbrain and diencephalic-mesencephalic boundaries

PubMed Central

Erickson, Timothy; Scholpp, Steffen; Brand, Michael; Moens, Cecilia B.; Waskiewicz, Andrew Jan

2007-01-01

Pbx proteins are a family of TALE-class transcription factors that are well characterized as Hox co-factors acting to impart segmental identity to the hindbrain rhombomeres. However, no role for Pbx in establishing more anterior neural compartments has been demonstrated. Studies done in Drosophila show that Engrailed requires Exd (Pbx orthologue) for its biological activity. Here, we present evidence that zebrafish Pbx proteins cooperate with Engrailed to compartmentalize the midbrain by regulating the maintenance of the midbrain-hindbrain boundary (MHB) and the diencephalic-mesencephalic boundary (DMB). Embryos lacking Pbx function correctly initiate midbrain patterning, but fail to maintain eng2a, pax2a, fgf8, gbx2, and wnt1 expression at the MHB. Formation of the DMB is also defective as shown by a caudal expansion of diencephalic epha4a and pax6a expression into midbrain territory. These phenotypes are similar to the phenotype of an Engrailed loss-of-function embryo, supporting the hypothesis that Pbx and Engrailed act together on a common genetic pathway. Consistent with this model, we demonstrate that zebrafish Engrailed and Pbx interact in vitro, and that this interaction is required for both the eng2a overexpression phenotype and Engrailed’s role in patterning the MHB. Our data support a novel model of midbrain development in which Pbx and Engrailed proteins cooperatively pattern the mesencephalic region of the neural tube. PMID:16959235

Pbx proteins cooperate with Engrailed to pattern the midbrain-hindbrain and diencephalic-mesencephalic boundaries.

PubMed

Erickson, Timothy; Scholpp, Steffen; Brand, Michael; Moens, Cecilia B; Waskiewicz, Andrew Jan

2007-01-15

Pbx proteins are a family of TALE-class transcription factors that are well characterized as Hox co-factors acting to impart segmental identity to the hindbrain rhombomeres. However, no role for Pbx in establishing more anterior neural compartments has been demonstrated. Studies done in Drosophila show that Engrailed requires Exd (Pbx orthologue) for its biological activity. Here, we present evidence that zebrafish Pbx proteins cooperate with Engrailed to compartmentalize the midbrain by regulating the maintenance of the midbrain-hindbrain boundary (MHB) and the diencephalic-mesencephalic boundary (DMB). Embryos lacking Pbx function correctly initiate midbrain patterning, but fail to maintain eng2a, pax2a, fgf8, gbx2, and wnt1 expression at the MHB. Formation of the DMB is also defective as shown by a caudal expansion of diencephalic epha4a and pax6a expression into midbrain territory. These phenotypes are similar to the phenotype of an Engrailed loss-of-function embryo, supporting the hypothesis that Pbx and Engrailed act together on a common genetic pathway. Consistent with this model, we demonstrate that zebrafish Engrailed and Pbx interact in vitro and that this interaction is required for both the eng2a overexpression phenotype and Engrailed's role in patterning the MHB. Our data support a novel model of midbrain development in which Pbx and Engrailed proteins cooperatively pattern the mesencephalic region of the neural tube.

The acquisition of biological knowledge during childhood: Cognitive conflict or tabula rasa?

NASA Astrophysics Data System (ADS)

Lawson, Anton E.

Clinical interviews were conducted with three elementary school children, who varied in age but not in family or school environment, to determine the extent to which they held naive misconceptions about important biological topics and to determine agewise trends in the development of biological knowledge. Does early biological knowledge acquisition follow a pattern of spontaneous naive theory construction and cognitive conflict or does it follow a pattern of gradual accretion to an initially blank slate? Contrary to findings in the physical sciences, little evidence was found for biological misconceptions as knowledge acquisition appeared to more directly follow the gradual accretion hypothesis with the primary source of that knowledge adult authority rather than personal experience. However, conceptual change teaching is still advocated due to its ability to provoke students to consider and test alternative conceptions (even if they are not their own) as a means of encouraging the development of important general reasoning patterns utilized in the testing of causal hypotheses.

Hormone-Mediated Pattern Formation in Seedling of Plants: a Competitive Growth Dynamics Model

NASA Astrophysics Data System (ADS)

Kawaguchi, Satoshi; Mimura, Masayasu; Ohya, Tomoyuki; Oikawa, Noriko; Okabe, Hirotaka; Kai, Shoichi

2001-10-01

An ecologically relevant pattern formation process mediated by hormonal interactions among growing seedlings is modeled based on the experimental observations on the effects of indole acetic acid, which can act as an inhibitor and activator of root growth depending on its concentration. In the absence of any lateral root with constant hormone-sensitivity, the edge effect phenomenon is obtained depending on the secretion rate of hormone from the main root. Introduction of growth-stage-dependent hormone-sensitivity drastically amplifies the initial randomness, resulting in spatially irregular macroscopic patterns. When the lateral root growth is introduced, periodic patterns are obtained whose periodicity depends on the length of lateral roots. The growth-stage-dependent hormone-sensitivity and the lateral root growth are crucial for macroscopic periodic-pattern formation.

Self-organized surface ripple pattern formation by ion implantation

NASA Astrophysics Data System (ADS)

Hofsäss, Hans; Zhang, Kun; Bobes, Omar

2016-10-01

Ion induced ripple pattern formation on solid surfaces has been extensively studied in the past and the theories describing curvature dependent ion erosion as well as redistribution of recoil atoms have been very successful in explaining many features of the pattern formation. Since most experimental studies use noble gas ion irradiation, the incorporation of the ions into the films is usually neglected. In this work we show that the incorporation or implantation of non-volatile ions also leads to a curvature dependent term in the equation of motion of a surface height profile. The implantation of ions can be interpreted as a negative sputter yield; and therefore, the effect of ion implantation is opposite to the one of ion erosion. For angles up to about 50°, implantation of ions stabilizes the surface, whereas above 50°, ion implantation contributes to the destabilization of the surface. We present simulations of the curvature coefficients using the crater function formalism and we compare the simulation results to the experimental data on the ion induced pattern formation using non-volatile ions. We present several model cases, where the incorporation of ions is a crucial requirement for the pattern formation.

Availability, health-care costs, and utilization patterns of biologics in Taiwan.

PubMed

Hsieh, Chee-Ruey; Liu, Ya-Ming

2012-01-01

To provide an overview of the use of biologics in Taiwan, including the access to new biologics, the impact of this access on the growth of health-care expenditure, and the utilization patterns. We first conducted a market-level analysis to investigate the availability of global biologics in Taiwan as well as the growth and concentration of aggregate spending on biologics. We then conducted a patient-level analysis to investigate the costs and utilization patterns for selected new biologics. We found that the concentration index is such that the 20 leading biologics in Taiwan account for more than 90% of the total spending on biologics. In our patient-level study on four biologics, the annual cost of treatment per patient ranged from NT$100,000 to NT$400,000. The prevalence rate of the user was between 6.5 and 37.2 per 100,000 of population. The treatment costs were inversely related to the prevalence rate of users. We also found that physicians in larger and public hospitals were more likely to prescribe new biologics to their patients compared with their counterparts practicing in smaller and private hospitals. In addition, we found that physicians were more likely to prescribe biologics to patients with more severe diseases and higher comorbidities. We conclude that public spending on biologics in Taiwan is highly targeted toward about 20 products with higher annual expenditures and growth rates and that the utilization of these biologics is targeted at a small number of patients. In addition, the access to these costly biologics is not uniform among patients in a country with universal coverage for prescription drugs. Copyright © 2012 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Is pigment patterning in fish skin determined by the Turing mechanism?

PubMed

Watanabe, Masakatsu; Kondo, Shigeru

2015-02-01

More than half a century ago, Alan Turing postulated that pigment patterns may arise from a mechanism that could be mathematically modeled based on the diffusion of two substances that interact with each other. Over the past 15 years, the molecular and genetic tools to verify this prediction have become available. Here, we review experimental studies aimed at identifying the mechanism underlying pigment pattern formation in zebrafish. Extensive molecular genetic studies in this model organism have revealed the interactions between the pigment cells that are responsible for the patterns. The mechanism discovered is substantially different from that predicted by the mathematical model, but it retains the property of 'local activation and long-range inhibition', a necessary condition for Turing pattern formation. Although some of the molecular details of pattern formation remain to be elucidated, current evidence confirms that the underlying mechanism is mathematically equivalent to the Turing mechanism. Copyright © 2014 Elsevier Ltd. All rights reserved.

From Patterns to Function in Living Systems: Dryland Ecosystems as a Case Study

NASA Astrophysics Data System (ADS)

Meron, Ehud

2018-03-01

Spatial patterns are ubiquitous in animate matter. Besides their intricate structure and beauty they generally play functional roles. The capacity of living systems to remain functional in changing environments is a question of utmost importance, but its intimate relationship to pattern formation is largely unexplored. Here, we address this relationship using dryland vegetation as a case study. Following a brief introduction to pattern-formation theory, we describe a mathematical model that captures several mechanisms of vegetation pattern formation and discuss ecological contexts that showcase different mechanisms. Using this model, we unravel the different vegetation patterns that keep dryland ecosystems viable along the rainfall gradient, identify multistability ranges where fronts separating domains of alternative stable states exist, and highlight the roles of front dynamics in mitigating or reversing desertification. The utility of satellite images in testing model predictions is discussed. An outlook on outstanding open problems concludes this paper.

PpNAC1, a main regulator of phenylalanine biosynthesis and utilization in maritime pine.

PubMed

Pascual, María Belén; Llebrés, María-Teresa; Craven-Bartle, Blanca; Cañas, Rafael A; Cánovas, Francisco M; Ávila, Concepción

2018-05-01

The transcriptional regulation of phenylalanine metabolism is particularly important in conifers, long-lived species that use large amounts of carbon in wood. Here, we show that the Pinus pinaster transcription factor, PpNAC1, is a main regulator of phenylalanine biosynthesis and utilization. A phylogenetic analysis classified PpNAC1 in the NST proteins group and was selected for functional characterization. PpNAC1 is predominantly expressed in the secondary xylem and compression wood of adult trees. Silencing of PpNAC1 in P. pinaster results in the alteration of stem vascular radial patterning and the down-regulation of several genes associated with cell wall biogenesis and secondary metabolism. Furthermore, transactivation and EMSA analyses showed that PpNAC1 is able to activate its own expression and PpMyb4 promoter, while PpMyb4 is able to activate PpMyb8, a transcriptional regulator of phenylalanine and lignin biosynthesis in maritime pine. Together, these results suggest that PpNAC1 is a functional ortholog of the ArabidopsisSND1 and NST1 genes and support the idea that key regulators governing secondary cell wall formation could be conserved between gymnosperms and angiosperms. Understanding the molecular switches controlling wood formation is of paramount importance for fundamental tree biology and paves the way for applications in conifer biotechnology. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

In Vitro Experimental Model for the Long-Term Analysis of Cellular Dynamics During Bronchial Tree Development from Lung Epithelial Cells

PubMed Central

Maruta, Naomichi; Marumoto, Moegi

2017-01-01

Lung branching morphogenesis has been studied for decades, but the underlying developmental mechanisms are still not fully understood. Cellular movements dynamically change during the branching process, but it is difficult to observe long-term cellular dynamics by in vivo or tissue culture experiments. Therefore, developing an in vitro experimental model of bronchial tree would provide an essential tool for developmental biology, pathology, and systems biology. In this study, we succeeded in reconstructing a bronchial tree in vitro by using primary human bronchial epithelial cells. A high concentration gradient of bronchial epithelial cells was required for branching initiation, whereas homogeneously distributed endothelial cells induced the formation of successive branches. Subsequently, the branches grew in size to the order of millimeter. The developed model contains only two types of cells and it facilitates the analysis of lung branching morphogenesis. By taking advantage of our experimental model, we carried out long-term time-lapse observations, which revealed self-assembly, collective migration with leader cells, rotational motion, and spiral motion of epithelial cells in each developmental event. Mathematical simulation was also carried out to analyze the self-assembly process and it revealed simple rules that govern cellular dynamics. Our experimental model has provided many new insights into lung development and it has the potential to accelerate the study of developmental mechanisms, pattern formation, left–right asymmetry, and disease pathogenesis of the human lung. PMID:28471293

Plasmodesmata: channels for intercellular signaling during plant growth and development.

PubMed

Sevilem, Iris; Yadav, Shri Ram; Helariutta, Ykä

2015-01-01

Plants have evolved strategies for short- and long-distance communication to coordinate plant development and to adapt to changing environmental conditions. Plasmodesmata (PD) are intercellular nanochannels that provide an effective pathway for both selective and nonselective movement of various molecules that function in diverse biological processes. Numerous non-cell-autonomous proteins (NCAP) and small RNAs have been identified that have crucial roles in cell fate determination and organ patterning during development. Both the density and aperture size of PD are developmentally regulated, allowing formation of spatial symplastic domains for establishment of tissue-specific developmental programs. The PD size exclusion limit (SEL) is controlled by reversible deposition of callose, as well as by some PD-associated proteins. Although a large number of PD-associated proteins have been identified, many of their functions remain unknown. Despite the fact that PD are primarily membranous structures, surprisingly very little is known about their lipid composition. Thus, future studies in PD biology will provide deeper insights into the high-resolution structure and tightly regulated functions of PD and the evolution of PD-mediated cell-to-cell communication in plants.

Plant-mediated synthesis of silver nanoparticles using parsley ( Petroselinum crispum) leaf extract: spectral analysis of the particles and antibacterial study

NASA Astrophysics Data System (ADS)

Roy, Kaushik; Sarkar, C. K.; Ghosh, C. K.

2015-12-01

Synthesis of nanomaterials may involve various routes including physical, chemical and biological approaches. Here, the biological green route was chosen to prepare silver nanoparticles from silver salts to avoid the requirement of costly instruments and involvement of hazardous chemicals as well. To make the process clean and green, leaf extract of parsley ( Petroselinum crispum) was used to synthesize Ag nanoparticles at room temperature. The formation of Ag-nanoparticles was monitored by UV-Vis spectroscopy. The presence of silver in the sample and its crystalline nature were verified by X-ray diffraction (XRD) analysis. The size distribution profile and particle size in the suspension were manipulated from dynamic light scattering (DLS) pattern. The shape, size and morphology of the biogenic nanoparticles were studied using high resolution transmission electron microscope (TEM). Fourier transform infra-red spectroscopy was used to detect the biomolecules responsible for reduction of silver ions. These biogenic Ag-nanoparticles showed appreciable antibacterial efficacy against three bacteria— Klebsiella pneumoniae, Escherichia coli and Staphylococcus aureus.

Aryldiones incorporating a [1,4,5]oxadiazepane ring. Part 2: chemistry and biology of the cereal herbicide pinoxaden.

PubMed

Muehlebach, Michel; Cederbaum, Fredrik; Cornes, Derek; Friedmann, Adrian A; Glock, Jutta; Hall, Gavin; Indolese, Adriano F; Kloer, Daniel P; Le Goupil, Gael; Maetzke, Thomas; Meier, Hans; Schneider, Rudolf; Stoller, André; Szczepanski, Henry; Wendeborn, Sebastian; Widmer, Hansjuerg

2011-12-01

Pinoxaden is a new cereal herbicide that provides outstanding levels of post-emergence activity against a broad spectrum of grass weed species for worldwide selective use in both wheat and barley. Factors influencing activity and tolerance to pinoxaden were in part linked to distinct structural parts of the active ingredient. Three complementary contributions that decisively impact upon the herbicidal potency against grasses were identified: a preferred 2,6-diethyl-4-methyl aromatic substitution pattern, a dione area suitable for proherbicide formation and beneficial adjuvant effects. The uptake and translocation pattern of pinoxaden when coapplied with its tailored adjuvant were analysed by autoradiography, indicating extensive and rapid penetration, followed by effective distribution throughout the plant. Crop injury reduction on incorporation of the [1,4,5]oxadiazepane ring into the aryldione template was reinforced with safener technology. Comparative studies on the behaviour of pinoxaden applied either alone or in combination with the safener cloquintocet-mexyl demonstrated that addition of the safener resulted in significant enhancement of metabolic degradation in wheat and barley, providing excellent crop tolerance and a substantial selectivity margin without adverse effects on weed control. The biological potential of pinoxaden and its active principle pinoxaden dione in terms of grass weed control and tolerance in cereals was fully exploited by inclusion of the safener cloquintocet-mexyl in the formulation in combination with a specific and tailor-made tank-mix adjuvant based on methylated rape seed oil. Copyright © 2011 Society of Chemical Industry.

Dental morphology and ancestry in Albuquerque, New Mexico Hispanics.

PubMed

Willermet, C M; Edgar, H J H

2009-01-01

The term "Hispanic" groups people from Central and South America and the Caribbean, combining disparate cultures, languages, and ancestry, and masking biological differences. Historical and current admixture patterns within these populations and with indigenous and European-, African-, and/or Asian- derived populations complicate the biological picture. Although "Hispanic" has little biological meaning, it is used widely in epidemiology, disease management, and forensics as a biologically significant group. An interdisciplinary approach combining historical, cultural, and biological data can characterize regional and temporal differences between Hispanic populations. We examined biological distances with a population of central New Mexico Hispanics, as a case study of the local specificity of population history. We collected dental morphological trait frequencies from samples of recent Albuquerque-area Hispanic Americans and several ancestral and contemporary groups. To explore regional admixture patterns we calculated biological distances using the modified Mahalanobis D(2) statistic. Our results indicate that Albuquerque Hispanics are more similar to their European and African ancestral groups than to Native Americans in New Mexico. Additionally, their affinity to Native Americans is greater with prehistoric rather than contemporary samples. We argue that these results reflect a local rather than pan-Hispanic admixture pattern; they underscore that populations are better understood at the local and regional levels. It is undesirable to make sweeping biological generalizations for groups known to be geographically and genetically disparate. This research is part of a growing trend in biological research concerning Hispanics and other groups-an emphasis on local samples, informed by historical, cultural, and biological factors.

Formative Assessment and Increased Student Involvement Increase Grades in an Upper Secondary School Biology Course

ERIC Educational Resources Information Center

Granbom, Martin

2016-01-01

This study shows that formative methods and increased student participation has a positive influence on learning measured as grades. The study was conducted during the course Biology A in a Swedish Upper Secondary School. The students constructed grade criteria and defined working methods and type of examination within a given topic, Gene…

A stochastic multicellular model identifies biological watermarks from disorders in self-organized patterns of phyllotaxis

PubMed Central

Refahi, Yassin; Brunoud, Géraldine; Farcot, Etienne; Jean-Marie, Alain; Pulkkinen, Minna; Vernoux, Teva; Godin, Christophe

2016-01-01

Exploration of developmental mechanisms classically relies on analysis of pattern regularities. Whether disorders induced by biological noise may carry information on building principles of developmental systems is an important debated question. Here, we addressed theoretically this question using phyllotaxis, the geometric arrangement of plant aerial organs, as a model system. Phyllotaxis arises from reiterative organogenesis driven by lateral inhibitions at the shoot apex. Motivated by recurrent observations of disorders in phyllotaxis patterns, we revisited in depth the classical deterministic view of phyllotaxis. We developed a stochastic model of primordia initiation at the shoot apex, integrating locality and stochasticity in the patterning system. This stochastic model recapitulates phyllotactic patterns, both regular and irregular, and makes quantitative predictions on the nature of disorders arising from noise. We further show that disorders in phyllotaxis instruct us on the parameters governing phyllotaxis dynamics, thus that disorders can reveal biological watermarks of developmental systems. DOI: http://dx.doi.org/10.7554/eLife.14093.001 PMID:27380805

Patterns in Parent-Child Conversations about Animals at a Marine Science Center

ERIC Educational Resources Information Center

Rigney, Jennifer C.; Callanan, Maureen A.

2011-01-01

Parent-child conversations are a potential source of children's developing understanding of the biological domain. We investigated patterns in parent-child conversations that may inform children about biological domain boundaries. At a marine science center exhibit, we compared parent-child talk about typical sea animals with faces (fish) with…

A Theoretical Model of Jigsaw-Puzzle Pattern Formation by Plant Leaf Epidermal Cells

PubMed Central

Higaki, Takumi; Kutsuna, Natsumaro; Akita, Kae; Takigawa-Imamura, Hisako; Yoshimura, Kenji; Miura, Takashi

2016-01-01

Plant leaf epidermal cells exhibit a jigsaw puzzle–like pattern that is generated by interdigitation of the cell wall during leaf development. The contribution of two ROP GTPases, ROP2 and ROP6, to the cytoskeletal dynamics that regulate epidermal cell wall interdigitation has already been examined; however, how interactions between these molecules result in pattern formation remains to be elucidated. Here, we propose a simple interface equation model that incorporates both the cell wall remodeling activity of ROP GTPases and the diffusible signaling molecules by which they are regulated. This model successfully reproduces pattern formation observed in vivo, and explains the counterintuitive experimental results of decreased cellulose production and increased thickness. Our model also reproduces the dynamics of three-way cell wall junctions. Therefore, this model provides a possible mechanism for cell wall interdigitation formation in vivo. PMID:27054467

Pattern formation in a monolayer of magnetic spheres

NASA Astrophysics Data System (ADS)

Stambaugh, Justin; Lathrop, Daniel P.; Ott, Edward; Losert, Wolfgang

2003-08-01

Pattern formation is investigated for a vertically vibrated monolayer of magnetic spheres. The spheres of diameter D encase cylindrical magnetic cores of length l. For large D/l, we find that the particles form a hexagonal-close-packed pattern in which the particles’ dipole vectors assume a macroscopic circulating vortical pattern. For smaller D/l, the particles form concentric rings. The static configurational magnetic energy (which depends on D/l) appears to be a determining factor in pattern selection even though the experimental system is driven and dissipative.

Do Houseflies Think? Patterns of Induction and Biological Beliefs in Development.

ERIC Educational Resources Information Center

Gutheil, Grant; Vera, Alonzo; Keil, Frank C.

1998-01-01

Examined preschoolers' inductive inferences across biological and non-biological kinds. Found support for gradual-enrichment model of conceptual change. Four-year-olds had a limited, coherent, independent biological theory which may form the basis of mature understanding of biological kinds. Explored results in terms of multiple explanatory…

Splitting a droplet for femtoliter liquid patterns and single cell isolation.

PubMed

Li, Huizeng; Yang, Qiang; Li, Guannan; Li, Mingzhu; Wang, Shutao; Song, Yanlin

2015-05-06

Well-defined microdroplet generation has attracted great interest, which is important for the high-resolution patterning and matrix distribution for chemical reactions and biological assays. By sliding a droplet on a patterned superhydrophilic/superhydrophobic substrate, tiny microdroplet arrays low to femtoliter were achieved with uniform volume and composition. Using this method, cells were successfully isolated, resulting in a single cell array. The droplet-splitting method is facile, sample-effective, and low-cost, which will be of great potential for the development of microdroplet arrays for biological analysis as well as patterning system and devices.

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data

PubMed Central

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H. L.; Onami, Shuichi

2015-01-01

Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Contact: sonami@riken.jp Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:25414366

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

PubMed

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H L; Onami, Shuichi

2015-04-01

Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Molecular biomimetics: utilizing nature's molecular ways in practical engineering.

PubMed

Tamerler, Candan; Sarikaya, Mehmet

2007-05-01

In nature, proteins are the machinery that accomplish many functions through their specific recognition and interactions in biological systems from single-celled to multicellular organisms. Biomolecule-material interaction is accomplished via molecular specificity, leading to the formation of controlled structures and functions at all scales of dimensional hierarchy. Through evolution, molecular recognition and, consequently, functions developed through successive cycles of mutation and selection. Using biology as a guide, we can now understand, engineer and control peptide-material interactions and exploit these to tailor novel materials and systems for practical applications. We adapted combinatorial biology protocols to display peptide libraries, either on the cell surface or on phages, to select short peptides specific to a variety of practical materials systems. Following the selection step, we determined the kinetics and stability of peptide binding experimentally to understand the bound peptide structure via modeling and its assembly via atomic force microscopy. The peptides were further engineered to have multiple repeats or their amino acid sequences varied to tailor their function. Both nanoparticles and flat inorganic substrates containing multimaterials patterned at the nano- and microscales were used for self-directed immobilization of molecular constructs. The molecular biomimetic approach opens up new avenues for the design and utilization of multifunctional molecular systems with wide ranging applications, from tissue engineering, drug delivery and biosensors, to nanotechnology and bioremediation. Here we give examples of protein-mediated functional materials in biology, peptide selection and engineering with affinity to inorganics, demonstrate potential utilizations in materials science, engineering and medicine, and describe future prospects.

Geostatistics and spatial analysis in biological anthropology.

PubMed

Relethford, John H

2008-05-01

A variety of methods have been used to make evolutionary inferences based on the spatial distribution of biological data, including reconstructing population history and detection of the geographic pattern of natural selection. This article provides an examination of geostatistical analysis, a method used widely in geology but which has not often been applied in biological anthropology. Geostatistical analysis begins with the examination of a variogram, a plot showing the relationship between a biological distance measure and the geographic distance between data points and which provides information on the extent and pattern of spatial correlation. The results of variogram analysis are used for interpolating values of unknown data points in order to construct a contour map, a process known as kriging. The methods of geostatistical analysis and discussion of potential problems are applied to a large data set of anthropometric measures for 197 populations in Ireland. The geostatistical analysis reveals two major sources of spatial variation. One pattern, seen for overall body and craniofacial size, shows an east-west cline most likely reflecting the combined effects of past population dispersal and settlement. The second pattern is seen for craniofacial height and shows an isolation by distance pattern reflecting rapid spatial changes in the midlands region of Ireland, perhaps attributable to the genetic impact of the Vikings. The correspondence of these results with other analyses of these data and the additional insights generated from variogram analysis and kriging illustrate the potential utility of geostatistical analysis in biological anthropology. (c) 2008 Wiley-Liss, Inc.

Biomimetic approaches to control soluble concentration gradients in biomaterials.

PubMed

Nguyen, Eric H; Schwartz, Michael P; Murphy, William L

2011-04-08

Soluble concentration gradients play a critical role in controlling tissue formation during embryonic development. The importance of soluble signaling in biology has motivated engineers to design systems that allow precise and quantitative manipulation of gradient formation in vitro. Engineering techniques have increasingly moved to the third dimension in order to provide more physiologically relevant models to study the biological role of gradient formation and to guide strategies for controlling new tissue formation for therapeutic applications. This review provides an overview of efforts to design biomimetic strategies for soluble gradient formation, with a focus on microfluidic techniques and biomaterials approaches for moving gradient generation to the third dimension. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spicule formation in calcareous sponges: Coordinated expression of biomineralization genes and spicule-type specific genes

PubMed Central

Voigt, Oliver; Adamska, Maja; Adamski, Marcin; Kittelmann, André; Wencker, Lukardis; Wörheide, Gert

2017-01-01

The ability to form mineral structures under biological control is widespread among animals. In several species, specific proteins have been shown to be involved in biomineralization, but it is uncertain how they influence the shape of the growing biomineral and the resulting skeleton. Calcareous sponges are the only sponges that form calcitic spicules, which, based on the number of rays (actines) are distinguished in diactines, triactines and tetractines. Each actine is formed by only two cells, called sclerocytes. Little is known about biomineralization proteins in calcareous sponges, other than that specific carbonic anhydrases (CAs) have been identified, and that uncharacterized Asx-rich proteins have been isolated from calcitic spicules. By RNA-Seq and RNA in situ hybridization (ISH), we identified five additional biomineralization genes in Sycon ciliatum: two bicarbonate transporters (BCTs) and three Asx-rich extracellular matrix proteins (ARPs). We show that these biomineralization genes are expressed in a coordinated pattern during spicule formation. Furthermore, two of the ARPs are spicule-type specific for triactines and tetractines (ARP1 or SciTriactinin) or diactines (ARP2 or SciDiactinin). Our results suggest that spicule formation is controlled by defined temporal and spatial expression of spicule-type specific sets of biomineralization genes. PMID:28406140

Fluorine-containing composition for forming anti-reflection film on resist surface and pattern formation method

DOEpatents

Nishi, Mineo; Makishima, Hideo

1996-01-01

A composition for forming anti-reflection film on resist surface which comprises an aqueous solution of a water soluble fluorine compound, and a pattern formation method which comprises the steps of coating a photoresist composition on a substrate; coating the above-mentioned composition for forming anti-reflection film; exposing the coated film to form a specific pattern; and developing the photoresist, are provided. Since the composition for forming anti-reflection film can be coated on the photoresist in the form of an aqueous solution, not only the anti-reflection film can be formed easily, but also, the film can be removed easily by rinsing with water or alkali development. Therefore, by the pattern formation method according to the present invention, it is possible to form a pattern easily with a high dimensional accuracy.

Pattern formation in a liquid-crystal light valve with feedback, including polarization, saturation, and internal threshold effects

NASA Astrophysics Data System (ADS)

Neubecker, R.; Oppo, G.-L.; Thuering, B.; Tschudi, T.

1995-07-01

The use of liquid-crystal light valves (LCLV's) as nonlinear elements in diffractive optical systems with feedback leads to the formation of a variety of optical patterns. The spectrum of possible spatial instabilities is shown to be even richer when the LCLV's capability for polarization modulation is utilized and internal threshold and saturation effects are considered. We derive a model for the feedback system based on a realistic description of the LCLV's internal function and coupling to a polarizer. Thresholds of pattern formation are compared to the common Kerr-type approximation and show transitions involving rolls, squares, hexagons, and tiled patterns. Numerical and experimental results confirm our theoretical predictions and unveil how patterns and their typical length scales can be easily controlled by changes of the parameters.

Patterning in time and space: HoxB cluster gene expression in the developing chick embryo.

PubMed

Gouveia, Analuce; Marcelino, Hugo M; Gonçalves, Lisa; Palmeirim, Isabel; Andrade, Raquel P

2015-01-01

The developing embryo is a paradigmatic model to study molecular mechanisms of time control in Biology. Hox genes are key players in the specification of tissue identity during embryo development and their expression is under strict temporal regulation. However, the molecular mechanisms underlying timely Hox activation in the early embryo remain unknown. This is hindered by the lack of a rigorous temporal framework of sequential Hox expression within a single cluster. Herein, a thorough characterization of HoxB cluster gene expression was performed over time and space in the early chick embryo. Clear temporal collinearity of HoxB cluster gene expression activation was observed. Spatial collinearity of HoxB expression was evidenced in different stages of development and in multiple tissues. Using embryo explant cultures we showed that HoxB2 is cyclically expressed in the rostral presomitic mesoderm with the same periodicity as somite formation, suggesting a link between timely tissue specification and somite formation. We foresee that the molecular framework herein provided will facilitate experimental approaches aimed at identifying the regulatory mechanisms underlying Hox expression in Time and Space.

Patterning in time and space: HoxB cluster gene expression in the developing chick embryo

PubMed Central

Gouveia, Analuce; Marcelino, Hugo M; Gonçalves, Lisa; Palmeirim, Isabel; Andrade, Raquel P

2015-01-01

The developing embryo is a paradigmatic model to study molecular mechanisms of time control in Biology. Hox genes are key players in the specification of tissue identity during embryo development and their expression is under strict temporal regulation. However, the molecular mechanisms underlying timely Hox activation in the early embryo remain unknown. This is hindered by the lack of a rigorous temporal framework of sequential Hox expression within a single cluster. Herein, a thorough characterization of HoxB cluster gene expression was performed over time and space in the early chick embryo. Clear temporal collinearity of HoxB cluster gene expression activation was observed. Spatial collinearity of HoxB expression was evidenced in different stages of development and in multiple tissues. Using embryo explant cultures we showed that HoxB2 is cyclically expressed in the rostral presomitic mesoderm with the same periodicity as somite formation, suggesting a link between timely tissue specification and somite formation. We foresee that the molecular framework herein provided will facilitate experimental approaches aimed at identifying the regulatory mechanisms underlying Hox expression in Time and Space. PMID:25602523

Noise reduction in the intracellular pom1p gradient by a dynamic clustering mechanism.

PubMed

Saunders, Timothy E; Pan, Kally Z; Angel, Andrew; Guan, Yinghua; Shah, Jagesh V; Howard, Martin; Chang, Fred

2012-03-13

Chemical gradients can generate pattern formation in biological systems. In the fission yeast Schizosaccharomyces pombe, a cortical gradient of pom1p (a DYRK-type protein kinase) functions to position sites of cytokinesis and cell polarity and to control cell length. Here, using quantitative imaging, fluorescence correlation spectroscopy, and mathematical modeling, we study how its gradient distribution is formed. Pom1p gradients exhibit large cell-to-cell variability, as well as dynamic fluctuations in each individual gradient. Our data lead to a two-state model for gradient formation in which pom1p molecules associate with the plasma membrane at cell tips and then diffuse on the membrane while aggregating into and fragmenting from clusters, before disassociating from the membrane. In contrast to a classical one-component gradient, this two-state gradient buffers against cell-to-cell variations in protein concentration. This buffering mechanism, together with time averaging to reduce intrinsic noise, allows the pom1p gradient to specify positional information in a robust manner. Copyright © 2012 Elsevier Inc. All rights reserved.

Determining environmental causes of biological effects: the need for a mechanistic physiological dimension in conservation biology.

PubMed

Seebacher, Frank; Franklin, Craig E

2012-06-19

The emerging field of Conservation Physiology links environmental change and ecological success by the application of physiological theory, approaches and tools to elucidate and address conservation problems. Human activity has changed the natural environment to a point where the viability of many ecosystems is now under threat. There are already many descriptions of how changes in biological patterns are correlated with environmental changes. The next important step is to determine the causative relationship between environmental variability and biological systems. Physiology provides the mechanistic link between environmental change and ecological patterns. Physiological research, therefore, should be integrated into conservation to predict the biological consequences of human activity, and to identify those species or populations that are most vulnerable.

Role of high molecular mass organics in colour formation during biological treatment of pulp and paper wastewater.

PubMed

Milestone, C B; Stuthridge, T R; Fulthorpe, R R

2007-01-01

This paper forms part of series of biological treatment colour behaviour studies. Surveys across a range of mills have observed colour increases in aerated stabilisation basins of 20-45%. Much of the colour formation has been demonstrated to occur in high molecular mass effluent organic constituents (HMM) present in bleach plant effluents. Removing material greater than 3000 Da essentially eliminated the colour forming ability in both E and D stage wastewaters. We have also shown that pulp and paper sludges contain anaerobic bacteria capable of reducing humic like materials. Colour formation was correlated to the anoxic conditions and the availability of readily biodegradable organic constituents during the wastewater treatment process. Overall, these studies suggest that colour formation in pulp and paper biological treatment systems may be caused by anaerobic bacteria using HMM material from the bleaching effluents as an electron acceptor for growth. This leads to the reduction of the material, which in turn leads to non-reversible internal changes, such as intra-molecular polymerisation or formation of chromophoric functional groups.

Implementing the Biological ConditionGradient Framework for Management of Estuaries and Coasts

EPA Science Inventory

The Biological Condition Gradient (BCG) is a conceptual scientific framework for interpreting biological response to increasing effects of stressors on aquatic ecosystems (U.S. EPA 2016). The framework was developed from common patterns of biological response to stressors observe...

Interconnected Cavernous Structure of Bacterial Fruiting Bodies

DOE PAGES

Harvey, Cameron W.; Du, Huijing; Xu, Zhiliang; ...

2012-12-27

The formation of spore-filled fruiting bodies by myxobacteria is a fascinating case of multicelular self-organization by bacteria. The organization of Myxococcus xanthus into fruiting bodies has long been studied not only as an important example of collective motion of bacteria, but also as a simplified model for developmental morphogenesis. Sporulation within the nascent fruiting body requires signaling between moving cells in order that the rod-shaped self-propelled cells differentiate into spores at the appropriate time. Probing the three-dimensional structure of myxobacteria fruiting bodies has previously presented a challenge due to Imitations at different imaging methods. A new technique using Infrared Opticalmore » Coherence Tomography (OCT) revealed previously unknown details of the Internal structure of M. xanthus fruiting bodies consisting of interconnected pockets of relative nigh and low spore density regions. Here, to make sense of the experimentally observed structure, modeling and computer simulations were used to test a hypothesized mechanism that could produce high density pockets of spores. The mechanism consists of self-propelled cells aligning with each other and signaling by end-to-end contact to coordinate the process of differentiation resulting in a pattern of clusters observed in the experiment. The Integration of novel OCT experimental techniques with computational simulations can provide new insight Into the mechanisms that can give rise to the pattern formation seen In other biological systems such as dlctyostelids, social amoeba known to form multicellular aggregates observed as slugs under starvation conditions.« less

Integument pattern formation involves genetic and epigenetic controls: feather arrays simulated by digital hormone models

PubMed Central

Jiang, Ting-Xin; Widelitz, Randall B.; Shen, Wei-Min; Will, Peter; Wu, Da-Yu; Lin, Chih-Min; Jung, Han-Sung; Chuong, Cheng-Ming

2015-01-01

Pattern formation is a fundamental morphogenetic process. Models based on genetic and epigenetic control have been proposed but remain controversial. Here we use feather morphogenesis for further evaluation. Adhesion molecules and/or signaling molecules were first expressed homogenously in feather tracts (restrictive mode, appear earlier) or directly in bud or inter-bud regions (de novo mode, appear later). They either activate or inhibit bud formation, but paradoxically co-localize in the bud. Using feather bud reconstitution, we showed that completely dissociated cells can reform periodic patterns without reference to previous positional codes. The patterning process has the characteristics of being self-organizing, dynamic and plastic. The final pattern is an equilibrium state reached by competition, and the number and size of buds can be altered based on cell number and activator/inhibitor ratio, respectively. We developed a Digital Hormone Model which consists of (1) competent cells without identity that move randomly in a space, (2) extracellular signaling hormones which diffuse by a reaction-diffusion mechanism and activate or inhibit cell adhesion, and (3) cells which respond with topological stochastic actions manifested as changes in cell adhesion. Based on probability, the results are cell clusters arranged in dots or stripes. Thus genetic control provides combinational molecular information which defines the properties of the cells but not the final pattern. Epigenetic control governs interactions among cells and their environment based on physical-chemical rules (such as those described in the Digital Hormone Model). Complex integument patterning is the sum of these two components of control and that is why integument patterns are usually similar but non-identical. These principles may be shared by other pattern formation processes such as barb ridge formation, fingerprints, pigmentation patterning, etc. The Digital Hormone Model can also be applied to swarming robot navigation, reaching intelligent automata and representing a self-re-configurable type of control rather than a follow-the-instruction type of control. PMID:15272377

Easy Fabrication of Thin Membranes with Through Holes. Application to Protein Patterning

PubMed Central

Arasi, Bakya; Gauthier, Nils; Viasnoff, Virgile

2012-01-01

Since protein patterning on 2D surfaces has emerged as an important tool in cell biology, the development of easy patterning methods has gained importance in biology labs. In this paper we present a simple, rapid and reliable technique to fabricate thin layers of UV curable polymer with through holes. These membranes are as easy to fabricate as microcontact printing stamps and can be readily used for stencil patterning. We show how this microfabrication scheme allows highly reproducible and highly homogeneous protein patterning with micron sized resolution on surfaces as large as 10 cm2. Using these stencils, fragile proteins were patterned without loss of function in a fully hydrated state. We further demonstrate how intricate patterns of multiple proteins can be achieved by stacking the stencil membranes. We termed this approach microserigraphy. PMID:22952944

Drying bacterial biosaline patterns capable of vital reanimation upon rehydration: novel hibernating biomineralogical life formations.

PubMed

Gómez Gómez, José María; Medina, Jesús; Hochberg, David; Mateo-Martí, Eva; Martínez-Frías, Jesús; Rull, Fernando

2014-07-01

Water is the fundamental molecule for life on Earth. Thus, the search for hibernating life-forms in waterless environments is an important research topic for astrobiology. To date, however, the organizational patterns containing microbial life in extremely dry places, such as the deserts of Earth, the Dry Valleys of Antarctica, or Mars analog regolith, have been poorly characterized. Here, we report on the formation of bacterial biosaline self-organized drying patterns formed over plastic surfaces. These emerge during the evaporation of sessile droplets of aqueous NaCl salt 0.15 M solutions containing Escherichia coli cells. In the present study, scanning electron microscopy (SEM) and energy dispersive X-ray spectrometry (EDS) analyses indicated that the bacterial cells and the NaCl in these biosaline formations are organized in a two-layered characteristic 3-D architectural morphology. A thin filmlike top layer formed by NaCl conjugated to, and intermingled with, "mineralized" bacterial cells covers a bottom layer constructed by the bulk of the nonmineralized bacterial cells; both layers have the same morphological pattern. In addition, optical microscopic time-lapsed movies show that the formation of these patterns is a kinetically fast process that requires the coupled interaction between the salt and the bacterial cells. Apparently, this mutual interaction drives the generative process of self-assembly that underlies the drying pattern formation. Most notably, the bacterial cells inside these drying self-assembled patterns enter into a quiescent suspended anhydrobiotic state resistant to complete desiccation and capable of vital reanimation upon rehydration. We propose that these E. coli biosaline drying patterns represent an excellent experimental model for understanding different aspects of anhydrobiosis phenomena in bacteria as well as for revealing the mechanisms of bacterially induced biomineralization, both highly relevant topics for the search of life in extraterrestrial locations.

Biologic meshes are not superior to synthetic meshes in ventral hernia repair: an experimental study with long-term follow-up evaluation.

PubMed

Ditzel, M; Deerenberg, E B; Grotenhuis, N; Harlaar, J J; Monkhorst, K; Bastiaansen-Jenniskens, Y M; Jeekel, J; Lange, J F

2013-10-01

In laparoscopic incisional hernia repair, direct contact between the prosthesis and the abdominal viscera is inevitable, which may lead to an inflammatory reaction resulting in abdominal adhesion formation. This study compared five different synthetic and biologic meshes in terms of adhesion formation, shrinkage, incorporation, and histologic characteristics after a period of 30 and 90 days. In 85 rats, a mesh was positioned intraperitoneally in direct contact with the viscera. Five different meshes were implanted: Prolene (polypropylene), Parietex composite (collagen-coated polyester), Strattice (porcine dermis, non-cross-linked), Surgisis (porcine small intestine submucosa, non-cross-linked), and Permacol (porcine dermis, cross-linked). The meshes were tested in terms of adhesion formation, shrinkage, and incorporation after a period of 30 and 90 days. Additionally, collagen formation after 90 days was determined. Significantly less adhesion formation was observed with Parietex composite (5 %; interquartile range [IQR], 2-5 %) and Strattice (5 %; IQR, 4-10 %) in the long term. In contrast, organs were attached to Permacol with four of seven meshes (57 %), and adhesion coverage of Surgisis mesh was present in 66 % (IQR, 0-100 %) of the cases. After 90 days, the best incorporation was seen with the Parietex composite mesh (79 %; IQR, 61-83 %). After 90 days, major alterations in adhesion formation were seen compared with 30 days. Histologically, Strattice and Parietex composite showed a new mesothelial layer on the visceral side of the mesh. Microscopic degradation and new collagen formation were seen in the Surgisis group. Parietex composite mesh demonstrated the best long-term results compared with all the other meshes. The biologic non-cross-linked mesh, Strattice, showed little adhesion formation and moderate shrinkage but poor incorporation. Biologic meshes are promising, but varying results require a more detailed investigation and demonstrate that biologic meshes are not necessarily superior to synthetic meshes. The significant changes that take place between 30 and 90 days should lead to careful interpretation of short-term experimental results.

Microfasciculation: a morphological pattern in leprosy nerve damage.

PubMed

Antunes, Sérgio L G; Medeiros, Mildred F; Corte-Real, Suzana; Jardim, Márcia R; Nery, José A da Costa; Hacker, Mariana A V B; Valentim, Vânia da Costa; Amadeu, Thaís Porto; Sarno, Euzenir N

2011-01-01

To study Microfasciculation, a perineurial response found in neuropathies, emphasizing its frequency, detailed morphological characteristics and biological significance in pure neural leprosy (PNL), post-treatment leprosy neuropathy (PTLN) and non-leprosy neuropathies (NLN). Morphological characteristics of microfascicles were examined via histological staining methods, immunohistochemical expression of neural markers and transmission electronmicroscopy. The detection of microfasciculation in 18 nerve biopsy specimens [12 PNL, six PTLN but not in the NLN group, was associated strongly with perineurial damage and the presence of a multibacillary inflammatory process in the nerves, particularly in the perineurium. Immunoreactivity to anti-S100 protein, anti-neurofilament, anti-nerve growth receptor and anti-myelin basic protein immunoreactivity was found within microfascicles. Ultrastructural examination of three biopsies showed that fibroblast-perineurial cells were devoid of basement membrane despite perineurial-like NGFr immunoreactivity. Morphological evidence demonstrated that multipotent pericytes from inflammation-activated microvessels could be the origin of fibroblast-perineurial cells. A microfasciculation pattern was found in 10% of leprosy-affected nerves. The microfascicles were composed predominantly of unmyelinated fibres and denervated Schwann cells (SCs) surrounded by fibroblast-perineurial cells. This pattern was found more frequently in leprosy nerves with acid-fast bacilli (AFB) and perineurial damage while undergoing an inflammatory process. Further experimental studies are necessary to elucidate microfascicle formation. © 2011 Blackwell Publishing Limited.

Micro-patterned agarose gel devices for single-cell high-throughput microscopy of E. coli cells.

PubMed

Priest, David G; Tanaka, Nobuyuki; Tanaka, Yo; Taniguchi, Yuichi

2017-12-21

High-throughput microscopy of bacterial cells elucidated fundamental cellular processes including cellular heterogeneity and cell division homeostasis. Polydimethylsiloxane (PDMS)-based microfluidic devices provide advantages including precise positioning of cells and throughput, however device fabrication is time-consuming and requires specialised skills. Agarose pads are a popular alternative, however cells often clump together, which hinders single cell quantitation. Here, we imprint agarose pads with micro-patterned 'capsules', to trap individual cells and 'lines', to direct cellular growth outwards in a straight line. We implement this micro-patterning into multi-pad devices called CapsuleHotel and LineHotel for high-throughput imaging. CapsuleHotel provides ~65,000 capsule structures per mm 2 that isolate individual Escherichia coli cells. In contrast, LineHotel provides ~300 line structures per mm that direct growth of micro-colonies. With CapsuleHotel, a quantitative single cell dataset of ~10,000 cells across 24 samples can be acquired and analysed in under 1 hour. LineHotel allows tracking growth of > 10 micro-colonies across 24 samples simultaneously for up to 4 generations. These easy-to-use devices can be provided in kit format, and will accelerate discoveries in diverse fields ranging from microbiology to systems and synthetic biology.

Full Transcriptome Analysis of Early Dorsoventral Patterning in Zebrafish

PubMed Central

Horváth, Balázs; Molnár, János; Nagy, István; Tóth, Gábor; Wilson, Stephen W.; Varga, Máté

2013-01-01

Understanding the molecular interactions that lead to the establishment of the major body axes during embryogenesis is one of the main goals of developmental biology. Although the past two decades have revolutionized our knowledge about the genetic basis of these patterning processes, the list of genes involved in axis formation is unlikely to be complete. In order to identify new genes involved in the establishment of the dorsoventral (DV) axis during early stages of zebrafish embryonic development, we employed next generation sequencing for full transcriptome analysis of normal embryos and embryos lacking overt DV pattern. A combination of different statistical approaches yielded 41 differentially expressed candidate genes and we confirmed by in situ hybridization the early dorsal expression of 32 genes that are transcribed shortly after the onset of zygotic transcription. Although promoter analysis of the validated genes suggests no general enrichment for the binding sites of early acting transcription factors, most of these genes carry “bivalent” epigenetic histone modifications at the time when zygotic transcription is initiated, suggesting a “poised” transcriptional status. Our results reveal some new candidates of the dorsal gene regulatory network and suggest that a plurality of the earliest upregulated genes on the dorsal side have a role in the modulation of the canonical Wnt pathway. PMID:23922899

Focal high cell density generates a gradient of patterns in self-organizing vascular mesenchymal cells.

PubMed

Cheng, Henry; Reddy, Aneela; Sage, Andrew; Lu, Jinxiu; Garfinkel, Alan; Tintut, Yin; Demer, Linda L

2012-01-01

In embryogenesis, structural patterns, such as vascular branching, may form via a reaction-diffusion mechanism in which activator and inhibitor morphogens guide cells into periodic aggregates. We previously found that vascular mesenchymal cells (VMCs) spontaneously aggregate into nodular structures and that morphogen pairs regulate the aggregation into patterns of spots and stripes. To test the effect of a focal change in activator morphogen on VMC pattern formation, we created a focal zone of high cell density by plating a second VMC layer within a cloning ring over a confluent monolayer. After 24 h, the ring was removed and pattern formation monitored by phase-contrast microscopy. At days 2-8, the patterns progressed from uniform distributions to swirl, labyrinthine and spot patterns. Within the focal high-density zone (HDZ) and a narrow halo zone, cells aggregated into spot patterns, whilst in the outermost zone of the plate, cells formed a labyrinthine pattern. The area occupied by aggregates was significantly greater in the outermost zone than in the HDZ or halo. The rate of pattern progression within the HDZ increased as a function of its plating density. Thus, focal differences in cell density may drive pattern formation gradients in tissue architecture, such as vascular branching. Copyright © 2012 S. Karger AG, Basel.

Contribution to the understanding of how principal component analysis-derived dietary patterns emerge from habitual data on food consumption.

PubMed

Schwedhelm, Carolina; Iqbal, Khalid; Knüppel, Sven; Schwingshackl, Lukas; Boeing, Heiner

2018-02-01

Principal component analysis (PCA) is a widely used exploratory method in epidemiology to derive dietary patterns from habitual diet. Such dietary patterns seem to originate from intakes on multiple days and eating occasions. Therefore, analyzing food intake of study populations with different levels of food consumption can provide additional insights as to how habitual dietary patterns are formed. We analyzed the food intake data of German adults in terms of the relations among food groups from three 24-h dietary recalls (24hDRs) on the habitual, single-day, and main-meal levels, and investigated the contribution of each level to the formation of PCA-derived habitual dietary patterns. Three 24hDRs were collected in 2010-2012 from 816 adults for an European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam subcohort study. We identified PCA-derived habitual dietary patterns and compared cross-sectional food consumption data in terms of correlation (Spearman), consistency (intraclass correlation coefficient), and frequency of consumption across all days and main meals. Contribution to the formation of the dietary patterns was obtained through Spearman correlation of the dietary pattern scores. Among the meals, breakfast appeared to be the most consistent eating occasion within individuals. Dinner showed the strongest correlations with "Prudent" (Spearman correlation = 0.60), "Western" (Spearman correlation = 0.59), and "Traditional" (Spearman correlation = 0.60) dietary patterns identified on the habitual level, and lunch showed the strongest correlations with the "Cereals and legumes" (Spearman correlation = 0.60) habitual dietary pattern. Higher meal consistency was related to lower contributions to the formation of PCA-derived habitual dietary patterns. Absolute amounts of food consumption did not strongly conform to the habitual dietary patterns by meals, suggesting that these patterns are formed by complex combinations of variable food consumption across meals. Dinner showed the highest contribution to the formation of habitual dietary patterns. This study provided information about how PCA-derived dietary patterns are formed and how they could be influenced.

Formative Assessment: Using Concept Cartoon, Pupils' Drawings, and Group Discussions to Tackle Children's Ideas about Biological Inheritance

ERIC Educational Resources Information Center

Chin, Christine; Teou, Lay-Yen

2010-01-01

This study was carried out in the context of formative assessment where assessment and learning were integrated to enhance both teaching and learning. The purpose of the study was to: (a) identify pupils' ideas about biological inheritance through the use of a concept cartoon, pupils' drawings and talk, and (b) devise scaffolding structures that…

An Evaluation of Two Hands-On Lab Styles for Plant Biodiversity in Undergraduate Biology

ERIC Educational Resources Information Center

Basey, John M.; Maines, Anastasia P.; Francis, Clinton D.; Melbourne, Brett

2014-01-01

We compared learning cycle and expository formats for teaching about plant biodiversity in an inquiry-oriented university biology lab class (n = 465). Both formats had preparatory lab activities, a hands-on lab, and a postlab with reflection and argumentation. Learning was assessed with a lab report, a practical quiz in lab, and a multiple-choice…

21 CFR 201.56 - Requirements on content and format of labeling for human prescription drug and biological products.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 4 2011-04-01 2011-04-01 false Requirements on content and format of labeling for human prescription drug and biological products. 201.56 Section 201.56 Food and Drugs FOOD AND DRUG... Contraindications Warnings and Precautions Adverse Reactions Drug Interactions Use in Specific Populations Full...

Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants

PubMed Central

Li, Shu-Fen; Su, Ting; Cheng, Guang-Qian; Wang, Bing-Xiao; Li, Xu; Deng, Chuan-Liang; Gao, Wu-Jun

2017-01-01

Chromosome evolution is a fundamental aspect of evolutionary biology. The evolution of chromosome size, structure and shape, number, and the change in DNA composition suggest the high plasticity of nuclear genomes at the chromosomal level. Repetitive DNA sequences, which represent a conspicuous fraction of every eukaryotic genome, particularly in plants, are found to be tightly linked with plant chromosome evolution. Different classes of repetitive sequences have distinct distribution patterns on the chromosomes. Mounting evidence shows that repetitive sequences may play multiple generative roles in shaping the chromosome karyotypes in plants. Furthermore, recent development in our understanding of the repetitive sequences and plant chromosome evolution has elucidated the involvement of a spectrum of epigenetic modification. In this review, we focused on the recent evidence relating to the distribution pattern of repetitive sequences in plant chromosomes and highlighted their potential relevance to chromosome evolution in plants. We also discussed the possible connections between evolution and epigenetic alterations in chromosome structure and repatterning, such as heterochromatin formation, centromere function, and epigenetic-associated transposable element inactivation. PMID:29064432

Discretization-dependent model for weakly connected excitable media

NASA Astrophysics Data System (ADS)

Arroyo, Pedro André; Alonso, Sergio; Weber dos Santos, Rodrigo

2018-03-01

Pattern formation has been widely observed in extended chemical and biological processes. Although the biochemical systems are highly heterogeneous, homogenized continuum approaches formed by partial differential equations have been employed frequently. Such approaches are usually justified by the difference of scales between the heterogeneities and the characteristic spatial size of the patterns. Under different conditions, for example, under weak coupling, discrete models are more adequate. However, discrete models may be less manageable, for instance, in terms of numerical implementation and mesh generation, than the associated continuum models. Here we study a model to approach discreteness which permits the computer implementation on general unstructured meshes. The model is cast as a partial differential equation but with a parameter that depends not only on heterogeneities sizes, as in the case of quasicontinuum models, but also on the discretization mesh. Therefore, we refer to it as a discretization-dependent model. We validate the approach in a generic excitable media that simulates three different phenomena: the propagation of action membrane potential in cardiac tissue, in myelinated axons of neurons, and concentration waves in chemical microemulsions.

Probing Mechanoregulation of Neuronal Differentiation by Plasma Lithography Patterned Elastomeric Substrates

NASA Astrophysics Data System (ADS)

Nam, Ki-Hwan; Jamilpour, Nima; Mfoumou, Etienne; Wang, Fei-Yue; Zhang, Donna D.; Wong, Pak Kin

2014-11-01

Cells sense and interpret mechanical cues, including cell-cell and cell-substrate interactions, in the microenvironment to collectively regulate various physiological functions. Understanding the influences of these mechanical factors on cell behavior is critical for fundamental cell biology and for the development of novel strategies in regenerative medicine. Here, we demonstrate plasma lithography patterning on elastomeric substrates for elucidating the influences of mechanical cues on neuronal differentiation and neuritogenesis. The neuroblastoma cells form neuronal spheres on plasma-treated regions, which geometrically confine the cells over two weeks. The elastic modulus of the elastomer is controlled simultaneously by the crosslinker concentration. The cell-substrate mechanical interactions are also investigated by controlling the size of neuronal spheres with different cell seeding densities. These physical cues are shown to modulate with the formation of focal adhesions, neurite outgrowth, and the morphology of neuroblastoma. By systematic adjustment of these cues, along with computational biomechanical analysis, we demonstrate the interrelated mechanoregulatory effects of substrate elasticity and cell size. Taken together, our results reveal that the neuronal differentiation and neuritogenesis of neuroblastoma cells are collectively regulated via the cell-substrate mechanical interactions.

RNA-DNA Triplex Formation by Long Noncoding RNAs.

PubMed

Li, Yue; Syed, Junetha; Sugiyama, Hiroshi

2016-11-17

Long noncoding RNAs (lncRNAs) play a pivotal role in the regulation of biological processes through various mechanisms that are not fully understood. Proposed mechanisms include regulation based on RNA-protein interactions, as well as RNA-RNA interactions and RNA-DNA interactions. Here, we focus on one possible mechanism that lncRNA might be using to impact biological function, the RNA-DNA triplex formation. We summarize currently available examples of lncRNA triplex formation and discuss the details surrounding orientation of triplex formation as one of the key properties guiding this process. We propose that symmetrical triplex-forming motifs, especially those in cis-acting lncRNAs, favor triplex formation. We also consider the effects of lncRNA structures, protein or ligand binding, and chromatin structures on the lncRNAs triplex formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Silicide induced ion beam patterning of Si(001).

PubMed

Engler, Martin; Frost, Frank; Müller, Sven; Macko, Sven; Will, Moritz; Feder, René; Spemann, Daniel; Hübner, René; Facsko, Stefan; Michely, Thomas

2014-03-21

Low energy ion beam pattern formation on Si with simultaneous co-deposition of Ag, Pd, Pb, Ir, Fe or C impurities was investigated by in situ scanning tunneling microscopy as well as ex situ atomic force microscopy, scanning electron microscopy, transmission electron microscopy and Rutherford backscattering spectrometry. The impurities were supplied by sputter deposition. Additional insight into the mechanism of pattern formation was obtained by more controlled supply through e-beam evaporation. For the situations investigated, the ability of the impurity to react with Si, i.e. to form a silicide, appears to be a necessary, but not a sufficient condition for pattern formation. Comparing the effects of impurities with similar mass and nuclear charge, the collision kinetics is shown to be not of primary importance for pattern formation. To understand the observed phenomena, it is necessary to assume a bi-directional coupling of composition and height fluctuations. This coupling gives rise to a sensitive dependence of the final morphology on the conditions of impurity supply. Because of this history dependence, the final morphology cannot be uniquely characterized by a steady state impurity concentration.

De-pinning of contact line of droplets on rough surfaces

NASA Astrophysics Data System (ADS)

Madhurima, V.; Nilavarasi, K.

2016-10-01

The present study reports the formation of self-assembled droplet pattern on the PDMS polymer coated over grooved side of DVD under saturated vapours of alcohols. Comparison of the results with breath figures formed over unconstrained side of DVD is made. Four different environments namely methanol, ethanol, 2-propanol and n-butanol are used for the analysis. It is observed that the pattern formation occurs with methanol and ethanol vapours and not with 2-propanol and n-butanol. The difference is pattern formation with different alcohols is attributed to the variation in chain length and the presence of hydrophobic groups in alcohols, as given by Traube's rule. The distortion of patterns over constrained surface is attributed to the depinning of contact lines.

Pattern formation based on complex coupling mechanism in dielectric barrier discharge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Weibo; College of Aeronautical Engineering, Binzhou University, Binzhou 256603; Dong, Lifang, E-mail: donglfhbu@163.com, E-mail: pyy1616@163.com

2016-08-15

The pattern formation of cinque-dice square superlattice pattern (CDSSP) is investigated based on the complex coupling mechanism in a dielectric barrier discharge (DBD) system. The spatio-temporal structure of CDSSP obtained by using an intensified-charge coupled device indicates that CDSSP is an interleaving of two kinds of subpatterns (mixture of rectangle and square, and dot-line square) which discharge twice in one half voltage, respectively. Selected by the complex coupling of two subpatterns, the CDSSP can be formed and shows good stability. This investigation based on gas discharge theory together with nonlinear theory may provide a deeper understanding for the nonlinear characteristicsmore » and even the formation mechanism of patterns in DBD.« less

Ground testing of bioconvective variables such as morphological characterizations and mechanisms which regulate macroscopic patterns

NASA Technical Reports Server (NTRS)

Johnson, Adriel D.

1992-01-01

Conditions simulating low- and high-gravity, reveal changes in macroscopic pattern formation in selected microorganisms, but whether these structures are gravity dependent is not clear. Two theories have been identified in the fluid dynamics community which support macroscopic pattern formation. The first one is gravity dependent (fluid density models) where small concentrated regions of organisms sink unstably, and the second is gravity independent (wave reinforcement theory) where organisms align their movements in concert, such that either their swimming strokes beat in phase or their vortices entrain neighbors to follow parallel paths. Studies have shown that macroscopic pattern formation is consistent with the fluid density models for protozoa and algae and wave reinforcement hypothesis for caprine spermatozoa.

Cranial suture biology of the Aleutian Island inhabitants.

PubMed

Cray, James; Mooney, Mark P; Siegel, Michael I

2011-04-01

Research on cranial suture biology suggests there is biological and taxonomic information to be garnered from the heritable pattern of suture synostosis. Suture synostosis along with brain growth patterns, diet, and biomechanical forces influence phenotypic variability in cranial vault morphology. This study was designed to determine the pattern of ectocranial suture synostosis in skeletal populations from the Aleutian Islands. We address the hypothesis that ectocranial suture synostosis pattern will differ according to cranial vault shape. Ales Hrdlicka identified two phenotypes in remains excavated from the Aleutian Island. The Paleo-Aleutians, exhibiting a dolichocranic phenotype with little prognathism linked to artifacts distinguished from later inhabitants, Aleutians, who exhibited a brachycranic phenotype with a greater amount of prognathism. A total of 212 crania representing Paleo-Aleuts and Aleutian as defined by Hrdlicka were investigated for suture synostosis pattern following standard methodologies. Comparisons were performed using Guttmann analyses. Results revealed similar suture fusion patterns for the Paleo-Aleut and Aleutian, a strong anterior to posterior pattern of suture fusion for the lateral-anterior suture sites, and a pattern of early termination at the sagittal suture sites for the vault. These patterns were found to differ from that reported in the literature. Because these two populations with distinct cranial shapes exhibit similar patterns of suture synostosis it appears pattern is independent of cranial shape in these populations of Homo sapiens. These findings suggest that suture fusion patterns may be population dependent and that a standardized methodology, using suture fusion to determine age-at-death, may not be applicable to all populations. Copyright © 2011 Wiley-Liss, Inc.

Coherent X-ray diffraction from collagenous soft tissues

PubMed Central

Berenguer de la Cuesta, Felisa; Wenger, Marco P. E.; Bean, Richard J.; Bozec, Laurent; Horton, Michael A.; Robinson, Ian K.

2009-01-01

Coherent X-ray diffraction has been applied in the imaging of inorganic materials with great success. However, its application to biological specimens has been limited to some notable exceptions, due to the induced radiation damage and the extended nature of biological samples, the last limiting the application of most part of the phasing algorithms. X-ray ptychography, still under development, is a good candidate to overcome such difficulties and become a powerful imaging method for biology. We describe herein the feasibility of applying ptychography to the imaging of biological specimens, in particular collagen rich samples. We report here speckles in diffraction patterns from soft animal tissue, obtained with an optimized small angle X-ray setup that exploits the natural coherence of the beam. By phasing these patterns, dark field images of collagen within tendon, skin, bone, or cornea will eventually be obtained with a resolution of 60–70 nm. We present simulations of the contrast mechanism in collagen based on atomic force microscope images of the samples. Simulations confirmed the ‘speckled’ nature of the obtained diffraction patterns. Once inverted, the patterns will show the disposition and orientation of the fibers within the tissue, by enhancing the phase contrast between protein and no protein regions of the sample. Our work affords the application of the most innovative coherent X-ray diffraction tools to the study of biological specimens, and this approach will have a significant impact in biology and medicine because it overcomes many of the limits of current microscopy techniques. PMID:19706395

Coherent X-ray diffraction from collagenous soft tissues.

PubMed

Berenguer de la Cuesta, Felisa; Wenger, Marco P E; Bean, Richard J; Bozec, Laurent; Horton, Michael A; Robinson, Ian K

2009-09-08

Coherent X-ray diffraction has been applied in the imaging of inorganic materials with great success. However, its application to biological specimens has been limited to some notable exceptions, due to the induced radiation damage and the extended nature of biological samples, the last limiting the application of most part of the phasing algorithms. X-ray ptychography, still under development, is a good candidate to overcome such difficulties and become a powerful imaging method for biology. We describe herein the feasibility of applying ptychography to the imaging of biological specimens, in particular collagen rich samples. We report here speckles in diffraction patterns from soft animal tissue, obtained with an optimized small angle X-ray setup that exploits the natural coherence of the beam. By phasing these patterns, dark field images of collagen within tendon, skin, bone, or cornea will eventually be obtained with a resolution of 60-70 nm. We present simulations of the contrast mechanism in collagen based on atomic force microscope images of the samples. Simulations confirmed the 'speckled' nature of the obtained diffraction patterns. Once inverted, the patterns will show the disposition and orientation of the fibers within the tissue, by enhancing the phase contrast between protein and no protein regions of the sample. Our work affords the application of the most innovative coherent X-ray diffraction tools to the study of biological specimens, and this approach will have a significant impact in biology and medicine because it overcomes many of the limits of current microscopy techniques.

XML-based approaches for the integration of heterogeneous bio-molecular data.

PubMed

Mesiti, Marco; Jiménez-Ruiz, Ernesto; Sanz, Ismael; Berlanga-Llavori, Rafael; Perlasca, Paolo; Valentini, Giorgio; Manset, David

2009-10-15

The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing. In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML. XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources.

Perspectives on the mathematics of biological patterning and morphogenesis

NASA Astrophysics Data System (ADS)

Garikipati, Krishna

2017-02-01

A central question in developmental biology is how size and position are determined. The genetic code carries instructions on how to control these properties in order to regulate the pattern and morphology of structures in the developing organism. Transcription and protein translation mechanisms implement these instructions. However, this cannot happen without some manner of sampling of epigenetic information on the current patterns and morphological forms of structures in the organism. Any rigorous description of space- and time-varying patterns and morphological forms reduces to one among various classes of spatio-temporal partial differential equations. Reaction-transport equations represent one such class. Starting from simple Fickian diffusion, the incorporation of reaction, phase segregation and advection terms can represent many of the patterns seen in the animal and plant kingdoms. Morphological form, requiring the development of three-dimensional structure, also can be represented by these equations of mass transport, albeit to a limited degree. The recognition that physical forces play controlling roles in shaping tissues leads to the conclusion that (nonlinear) elasticity governs the development of morphological form. In this setting, inhomogeneous growth drives the elasticity problem. The combination of reaction-transport equations with those of elasto-growth makes accessible a potentially unlimited spectrum of patterning and morphogenetic phenomena in developmental biology. This perspective communication is a survey of the partial differential equations of mathematical physics that have been proposed to govern patterning and morphogenesis in developmental biology. Several numerical examples are included to illustrate these equations and the corresponding physics, with the intention of providing physical insight wherever possible.

iTRAQ-Based Proteomic Analysis Reveals Potential Regulation Networks of IBA-Induced Adventitious Root Formation in Apple

PubMed Central

Lei, Chao; Fan, Sheng; Li, Ke; Meng, Yuan; Mao, Jiangping; Han, Mingyu; Zhao, Caiping; Bao, Lu; Zhang, Dong

2018-01-01

Adventitious root (AR) formation, which is controlled by endogenous and environmental factors, is indispensable for vegetative asexual propagation. However, comprehensive proteomic data on AR formation are still lacking. The aim of this work was to study indole-3-butyric acid (IBA)-induced AR formation in the dwarf apple rootstock ‘T337’. In this study, the effect of IBA on AR formation was analysed. Subsequent to treatment with IBA, both the rooting rate and root length of ‘T337’ increased significantly. An assessment of hormone levels in basal stem cuttings suggested that auxin, abscisic acid, and brassinolide were higher in basal stem cuttings that received the exogenous IBA application; while zeatin riboside, gibberellins, and jasmonic acid were lower than non-treated basal stem cuttings. To explore the underlying molecular mechanism, an isobaric tags for relative and absolute quantification (iTRAQ)-based proteomic technique was employed to identify the expression profiles of proteins at a key period of adventitious root induction (three days after IBA treatment). In total, 3355 differentially expressed proteins (DEPs) were identified. Many DEPs were closely related to carbohydrate metabolism and energy production, protein homeostasis, reactive oxygen and nitric oxide signaling, and cell wall remodeling biological processes; as well as the phytohormone signaling, which was the most critical process in response to IBA treatment. Further, RT-qPCR analysis was used to evaluate the expression level of nine genes that are involved in phytohormone signaling and their transcriptional levels were mostly in accordance with the protein patterns. Finally, a putative work model was proposed. Our study establishes a foundation for further research and sheds light on IBA-mediated AR formation in apple as well as other fruit rootstock cuttings. PMID:29495482

Challenges and Opportunities for Learning Biology in Distance-Based Settings

ERIC Educational Resources Information Center

Hallyburton, Chad L.; Lunsford, Eddie

2013-01-01

The history of learning biology through distance education is documented. A review of terminology and unique problems associated with biology instruction is presented. Using published research and their own teaching experience, the authors present recommendations and best practices for managing biology in distance-based formats. They offer ideas…

Nucleosomes suppress the formation of double-strand DNA breaks during attempted base excision repair of clustered oxidative damages.

PubMed

Cannan, Wendy J; Tsang, Betty P; Wallace, Susan S; Pederson, David S

2014-07-18

Exposure to ionizing radiation can produce multiple, clustered oxidative lesions in DNA. The near simultaneous excision of nearby lesions in opposing DNA strands by the base excision repair (BER) enzymes can produce double-strand DNA breaks (DSBs). This attempted BER accounts for many of the potentially lethal or mutagenic DSBs that occur in vivo. To assess the impact of nucleosomes on the frequency and pattern of BER-dependent DSB formation, we incubated nucleosomes containing oxidative damages in opposing DNA strands with selected DNA glycosylases and human apurinic/apyrimidinic endonuclease 1. Overall, nucleosomes substantially suppressed DSB formation. However, the degree of suppression varied as a function of (i) the lesion type and DNA glycosylase tested, (ii) local sequence context and the stagger between opposing strand lesions, (iii) the helical orientation of oxidative lesions relative to the underlying histone octamer, and (iv) the distance between the lesion cluster and the nucleosome edge. In some instances the binding of a BER factor to one nucleosomal lesion appeared to facilitate binding to the opposing strand lesion. DSB formation did not invariably lead to nucleosome dissolution, and in some cases, free DNA ends resulting from DSB formation remained associated with the histone octamer. These observations explain how specific structural and dynamic properties of nucleosomes contribute to the suppression of BER-generated DSBs. These studies also suggest that most BER-generated DSBs will occur in linker DNA and in genomic regions associated with elevated rates of nucleosome turnover or remodeling. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Pattern formation, logistics, and maximum path probability

NASA Astrophysics Data System (ADS)

Kirkaldy, J. S.

1985-05-01

The concept of pattern formation, which to current researchers is a synonym for self-organization, carries the connotation of deductive logic together with the process of spontaneous inference. Defining a pattern as an equivalence relation on a set of thermodynamic objects, we establish that a large class of irreversible pattern-forming systems, evolving along idealized quasisteady paths, approaches the stable steady state as a mapping upon the formal deductive imperatives of a propositional function calculus. In the preamble the classical reversible thermodynamics of composite systems is analyzed as an externally manipulated system of space partitioning and classification based on ideal enclosures and diaphragms. The diaphragms have discrete classification capabilities which are designated in relation to conserved quantities by descriptors such as impervious, diathermal, and adiabatic. Differentiability in the continuum thermodynamic calculus is invoked as equivalent to analyticity and consistency in the underlying class or sentential calculus. The seat of inference, however, rests with the thermodynamicist. In the transition to an irreversible pattern-forming system the defined nature of the composite reservoirs remains, but a given diaphragm is replaced by a pattern-forming system which by its nature is a spontaneously evolving volume partitioner and classifier of invariants. The seat of volition or inference for the classification system is thus transferred from the experimenter or theoretician to the diaphragm, and with it the full deductive facility. The equivalence relations or partitions associated with the emerging patterns may thus be associated with theorems of the natural pattern-forming calculus. The entropy function, together with its derivatives, is the vehicle which relates the logistics of reservoirs and diaphragms to the analog logistics of the continuum. Maximum path probability or second-order differentiability of the entropy in isolation are sufficiently strong interpretations of the second law of thermodynamics to define the approach to and the nature of patterned stable steady states. For many pattern-forming systems these principles define quantifiable stable states as maxima or minima (or both) in the dissipation. An elementary statistical-mechanical proof is offered. To turn the argument full circle, the transformations of the partitions and classes which are predicated upon such minimax entropic paths can through digital modeling be directly identified with the syntactic and inferential elements of deductive logic. It follows therefore that all self-organizing or pattern-forming systems which possess stable steady states approach these states according to the imperatives of formal logic, the optimum pattern with its rich endowment of equivalence relations representing the central theorem of the associated calculus. Logic is thus ``the stuff of the universe,'' and biological evolution with its culmination in the human brain is the most significant example of all the irreversible pattern-forming processes. We thus conclude with a few remarks on the relevance of the contribution to the theory of evolution and to research on artificial intelligence.

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.

PubMed

Beltrame, Luca; Calura, Enrica; Popovici, Razvan R; Rizzetto, Lisa; Guedez, Damariz Rivero; Donato, Michele; Romualdi, Chiara; Draghici, Sorin; Cavalieri, Duccio

2011-08-01

Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and 'wet lab' scientists. The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X.

Investigation of the mechanism of impurity assisted nanoripple formation on Si induced by low energy ion beam erosion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koyiloth Vayalil, Sarathlal, E-mail: sarathlal.koyilothvayalil@desy.de; UGC-DAE Consortium for Scientific Research, University Campus, Khandwa Road, Indore 452017; Gupta, Ajay

A detailed mechanism of the nanoripple pattern formation on Si substrates generated by the simultaneous incorporation of pure Fe impurities at low energy (1 keV) ion beam erosion has been studied. To understand and clarify the mechanism of the pattern formation, a comparative analysis of the samples prepared for various ion fluence values using two complimentary methods for nanostructure analysis, atomic force microscopy, and grazing incidence small angle x-ray scattering has been done. We observed that phase separation of the metal silicide formed during the erosion does not precede the ripple formation. It rather concurrently develops along with the ripple structure.more » Our work is able to differentiate among various models existing in the literature and provides an insight into the mechanism of pattern formation under ion beam erosion with impurity incorporation.« less

Spontaneous formation of linearly arranged microcraters on sol-gel-derived silica-poly(vinylpyrrolidone) hybrid films induced by Bénard-Marangoni convection.

PubMed

Uchiyama, Hiroaki; Mantani, Yuto; Kozuka, Hiromitsu

2012-07-10

Complex, sophisticated surface patterns on micrometer and nanometer scales are obtained when solvent evaporates from solutions containing nonvolatile solutes dropped on a solid substrate. Such evaporation-driven pattern formation has been utilized as a fabrication process of highly ordered patterns in thin films. Here, we suggested the spontaneous pattern formation induced by Bénard-Marangoni convection triggered by solvent evaporation as a novel patterning process of sol-gel-derived organic-inorganic hybrid films. Microcraters of 1.0-1.5 μm in height and of 100-200 μm in width were spontaneously formed on the surface of silica-poly(vinylpyrrolidone) hybrid films prepared via temperature-controlled dip-coating process, where the surface patterns were linearly arranged parallel to the substrate withdrawal direction. Such highly ordered micropatterns were achieved by Bénard-Marangoni convection activated at high temperatures and the unidirectional flow of the coating solution on the substrate during dip-coating.

Freshwater Biological Traits Database (Final Report)

EPA Science Inventory

EPA announced the release of the final report, Freshwater Biological Traits Database. This report discusses the development of a database of freshwater biological traits. The database combines several existing traits databases into an online format. The database is also...

Structure and formation of ant transportation networks

PubMed Central

Latty, Tanya; Ramsch, Kai; Ito, Kentaro; Nakagaki, Toshiyuki; Sumpter, David J. T.; Middendorf, Martin; Beekman, Madeleine

2011-01-01

Many biological systems use extensive networks for the transport of resources and information. Ants are no exception. How do biological systems achieve efficient transportation networks in the absence of centralized control and without global knowledge of the environment? Here, we address this question by studying the formation and properties of inter-nest transportation networks in the Argentine ant (Linepithema humile). We find that the formation of inter-nest networks depends on the number of ants involved in the construction process. When the number of ants is sufficient and networks do form, they tend to have short total length but a low level of robustness. These networks are topologically similar to either minimum spanning trees or Steiner networks. The process of network formation involves an initial construction of multiple links followed by a pruning process that reduces the number of trails. Our study thus illuminates the conditions under and the process by which minimal biological transport networks can be constructed. PMID:21288958

The Biophysics Microgravity Initiative

NASA Technical Reports Server (NTRS)

Gorti, S.

2016-01-01

Biophysical microgravity research on the International Space Station using biological materials has been ongoing for several decades. The well-documented substantive effects of long duration microgravity include the facilitation of the assembly of biological macromolecules into large structures, e.g., formation of large protein crystals under micro-gravity. NASA is invested not only in understanding the possible physical mechanisms of crystal growth, but also promoting two flight investigations to determine the influence of µ-gravity on protein crystal quality. In addition to crystal growth, flight investigations to determine the effects of shear on nucleation and subsequent formation of complex structures (e.g., crystals, fibrils, etc.) are also supported. It is now considered that long duration microgravity research aboard the ISS could also make possible the formation of large complex biological and biomimetic materials. Investigations of various materials undergoing complex structure formation in microgravity will not only strengthen NASA science programs, but may also provide invaluable insight towards the construction of large complex tissues, organs, or biomimetic materials on Earth.

Random scalar fields and hyperuniformity

NASA Astrophysics Data System (ADS)

Ma, Zheng; Torquato, Salvatore

2017-06-01

Disordered many-particle hyperuniform systems are exotic amorphous states of matter that lie between crystals and liquids. Hyperuniform systems have attracted recent attention because they are endowed with novel transport and optical properties. Recently, the hyperuniformity concept has been generalized to characterize two-phase media, scalar fields, and random vector fields. In this paper, we devise methods to explicitly construct hyperuniform scalar fields. Specifically, we analyze spatial patterns generated from Gaussian random fields, which have been used to model the microwave background radiation and heterogeneous materials, the Cahn-Hilliard equation for spinodal decomposition, and Swift-Hohenberg equations that have been used to model emergent pattern formation, including Rayleigh-Bénard convection. We show that the Gaussian random scalar fields can be constructed to be hyperuniform. We also numerically study the time evolution of spinodal decomposition patterns and demonstrate that they are hyperuniform in the scaling regime. Moreover, we find that labyrinth-like patterns generated by the Swift-Hohenberg equation are effectively hyperuniform. We show that thresholding (level-cutting) a hyperuniform Gaussian random field to produce a two-phase random medium tends to destroy the hyperuniformity of the progenitor scalar field. We then propose guidelines to achieve effectively hyperuniform two-phase media derived from thresholded non-Gaussian fields. Our investigation paves the way for new research directions to characterize the large-structure spatial patterns that arise in physics, chemistry, biology, and ecology. Moreover, our theoretical results are expected to guide experimentalists to synthesize new classes of hyperuniform materials with novel physical properties via coarsening processes and using state-of-the-art techniques, such as stereolithography and 3D printing.

Reaction-diffusion pattern in shoot apical meristem of plants.

PubMed

Fujita, Hironori; Toyokura, Koichi; Okada, Kiyotaka; Kawaguchi, Masayoshi

2011-03-29

A fundamental question in developmental biology is how spatial patterns are self-organized from homogeneous structures. In 1952, Turing proposed the reaction-diffusion model in order to explain this issue. Experimental evidence of reaction-diffusion patterns in living organisms was first provided by the pigmentation pattern on the skin of fishes in 1995. However, whether or not this mechanism plays an essential role in developmental events of living organisms remains elusive. Here we show that a reaction-diffusion model can successfully explain the shoot apical meristem (SAM) development of plants. SAM of plants resides in the top of each shoot and consists of a central zone (CZ) and a surrounding peripheral zone (PZ). SAM contains stem cells and continuously produces new organs throughout the lifespan. Molecular genetic studies using Arabidopsis thaliana revealed that the formation and maintenance of the SAM are essentially regulated by the feedback interaction between WUSHCEL (WUS) and CLAVATA (CLV). We developed a mathematical model of the SAM based on a reaction-diffusion dynamics of the WUS-CLV interaction, incorporating cell division and the spatial restriction of the dynamics. Our model explains the various SAM patterns observed in plants, for example, homeostatic control of SAM size in the wild type, enlarged or fasciated SAM in clv mutants, and initiation of ectopic secondary meristems from an initial flattened SAM in wus mutant. In addition, the model is supported by comparing its prediction with the expression pattern of WUS in the wus mutant. Furthermore, the model can account for many experimental results including reorganization processes caused by the CZ ablation and by incision through the meristem center. We thus conclude that the reaction-diffusion dynamics is probably indispensable for the SAM development of plants.

Reaction-Diffusion Pattern in Shoot Apical Meristem of Plants

PubMed Central

Fujita, Hironori; Toyokura, Koichi; Okada, Kiyotaka; Kawaguchi, Masayoshi

2011-01-01

A fundamental question in developmental biology is how spatial patterns are self-organized from homogeneous structures. In 1952, Turing proposed the reaction-diffusion model in order to explain this issue. Experimental evidence of reaction-diffusion patterns in living organisms was first provided by the pigmentation pattern on the skin of fishes in 1995. However, whether or not this mechanism plays an essential role in developmental events of living organisms remains elusive. Here we show that a reaction-diffusion model can successfully explain the shoot apical meristem (SAM) development of plants. SAM of plants resides in the top of each shoot and consists of a central zone (CZ) and a surrounding peripheral zone (PZ). SAM contains stem cells and continuously produces new organs throughout the lifespan. Molecular genetic studies using Arabidopsis thaliana revealed that the formation and maintenance of the SAM are essentially regulated by the feedback interaction between WUSHCEL (WUS) and CLAVATA (CLV). We developed a mathematical model of the SAM based on a reaction-diffusion dynamics of the WUS-CLV interaction, incorporating cell division and the spatial restriction of the dynamics. Our model explains the various SAM patterns observed in plants, for example, homeostatic control of SAM size in the wild type, enlarged or fasciated SAM in clv mutants, and initiation of ectopic secondary meristems from an initial flattened SAM in wus mutant. In addition, the model is supported by comparing its prediction with the expression pattern of WUS in the wus mutant. Furthermore, the model can account for many experimental results including reorganization processes caused by the CZ ablation and by incision through the meristem center. We thus conclude that the reaction-diffusion dynamics is probably indispensable for the SAM development of plants. PMID:21479227

Separating macroecological pattern and process: comparing ecological, economic, and geological systems.

PubMed

Blonder, Benjamin; Sloat, Lindsey; Enquist, Brian J; McGill, Brian

2014-01-01

Theories of biodiversity rest on several macroecological patterns describing the relationship between species abundance and diversity. A central problem is that all theories make similar predictions for these patterns despite disparate assumptions. A troubling implication is that these patterns may not reflect anything unique about organizational principles of biology or the functioning of ecological systems. To test this, we analyze five datasets from ecological, economic, and geological systems that describe the distribution of objects across categories in the United States. At the level of functional form ('first-order effects'), these patterns are not unique to ecological systems, indicating they may reveal little about biological process. However, we show that mechanism can be better revealed in the scale-dependency of first-order patterns ('second-order effects'). These results provide a roadmap for biodiversity theory to move beyond traditional patterns, and also suggest ways in which macroecological theory can constrain the dynamics of economic systems.

Analysis of Land-Use Effects on Landscape Patterns and Biological Diversity in Pacific North Forests: 1972-1991

NASA Technical Reports Server (NTRS)

Wallin, David O.; Cohen, Warren B.; Bradshaw, G. A.; Spies, T. A.; Hansen, A.; Huff, M. H.; Lehmkuhl, J. F.; Raphael, M. G.; Ripple, W. J.

1998-01-01

While there is widespread recognition of the importance of preserving biological diversity there is considerable uncertainty about how to map current patterns of diversity and monitor changes through time. Ground-based approaches are impractical for examining regional patterns of biological diversity, for monitoring change, and they may actually overlook important higher-order phenomena. Thus, there is a critical need for innovative techniques to examine land-use effects on biological diversity at the landscape and regional scales. In this project, we have used satellite-based remote sensing to examine land-use effects on forest ecosystems in the Pacific NorthWest region (PNW) of the U.S.A. Rates and patterns of forest change throughout the region were quantified for the period from 1972 to 1993. This information was then used to map changes in the abundance and distribution of potential habitat for selected vertebrate species. The results of this project will be useful for identifying "keystone" stands that are important in maintaining habitat connectivity at the regional scale and for evaluating the impact of future land-use on vertebrate diversity throughout the region. The approaches developed here will also be useful in other forested regions throughout the world.

Master stability functions reveal diffusion-driven pattern formation in networks

NASA Astrophysics Data System (ADS)

Brechtel, Andreas; Gramlich, Philipp; Ritterskamp, Daniel; Drossel, Barbara; Gross, Thilo

2018-03-01

We study diffusion-driven pattern formation in networks of networks, a class of multilayer systems, where different layers have the same topology, but different internal dynamics. Agents are assumed to disperse within a layer by undergoing random walks, while they can be created or destroyed by reactions between or within a layer. We show that the stability of homogeneous steady states can be analyzed with a master stability function approach that reveals a deep analogy between pattern formation in networks and pattern formation in continuous space. For illustration, we consider a generalized model of ecological meta-food webs. This fairly complex model describes the dispersal of many different species across a region consisting of a network of individual habitats while subject to realistic, nonlinear predator-prey interactions. In this example, the method reveals the intricate dependence of the dynamics on the spatial structure. The ability of the proposed approach to deal with this fairly complex system highlights it as a promising tool for ecology and other applications.

Sarcomeric Pattern Formation by Actin Cluster Coalescence

PubMed Central

Friedrich, Benjamin M.; Fischer-Friedrich, Elisabeth; Gov, Nir S.; Safran, Samuel A.

2012-01-01

Contractile function of striated muscle cells depends crucially on the almost crystalline order of actin and myosin filaments in myofibrils, but the physical mechanisms that lead to myofibril assembly remains ill-defined. Passive diffusive sorting of actin filaments into sarcomeric order is kinetically impossible, suggesting a pivotal role of active processes in sarcomeric pattern formation. Using a one-dimensional computational model of an initially unstriated actin bundle, we show that actin filament treadmilling in the presence of processive plus-end crosslinking provides a simple and robust mechanism for the polarity sorting of actin filaments as well as for the correct localization of myosin filaments. We propose that the coalescence of crosslinked actin clusters could be key for sarcomeric pattern formation. In our simulations, sarcomere spacing is set by filament length prompting tight length control already at early stages of pattern formation. The proposed mechanism could be generic and apply both to premyofibrils and nascent myofibrils in developing muscle cells as well as possibly to striated stress-fibers in non-muscle cells. PMID:22685394

Host cell recruitment patterns by bone morphogenetic protein-2 releasing hyaluronic acid hydrogels in a mouse subcutaneous environment.

PubMed

Todeschi, Maria R; El Backly, Rania M; Varghese, Oommen P; Hilborn, Jöns; Cancedda, Ranieri; Mastrogiacomo, Maddalena

2017-07-01

This study aimed to identify host cell recruitment patterns in a mouse model in response to rhBMP-2 releasing hyaluronic acid hydrogels and influence of added nano-hydroxyapatite particles on rhBMP-2 release and pattern of bone formation. Implanted gels were retrieved after implantation and cells were enzymatically dissociated for flow cytometric analysis. Percentages of macrophages, progenitor endothelial cells and putative mesenchymal stem cells were measured. Implants were evaluated for BMP-2 release by ELISA and by histology to monitor tissue formation. Hyaluronic acid+BMP-2 gels influenced the inflammatory response in the bone healing microenvironment. Host-derived putative mesenchymal stem cells were major contributors. Addition of hydroxyapatite nanoparticles modified the release pattern of rhBMP-2, resulting in enhanced bone formation.

Design and integration of a problem-based biofabrication course into an undergraduate biomedical engineering curriculum.

PubMed

Raman, Ritu; Mitchell, Marlon; Perez-Pinera, Pablo; Bashir, Rashid; DeStefano, Lizanne

2016-01-01

The rapidly evolving discipline of biological and biomedical engineering requires adaptive instructional approaches that teach students to target and solve multi-pronged and ill-structured problems at the cutting edge of scientific research. Here we present a modular approach to designing a lab-based course in the emerging field of biofabrication and biological design, leading to a final capstone design project that requires students to formulate and test a hypothesis using the scientific method. Students were assessed on a range of metrics designed to evaluate the format of the course, the efficacy of the format for teaching new topics and concepts, and the depth of the contribution this course made to students training for biological engineering careers. The evaluation showed that the problem-based format of the course was well suited to teaching students how to use the scientific method to investigate and uncover the fundamental biological design rules that govern the field of biofabrication. We show that this approach is an efficient and effective method of translating emergent scientific principles from the lab bench to the classroom and training the next generation of biological and biomedical engineers for careers as researchers and industry practicians.

[Prospects for Application of Gases and Gas Hydrates to Cryopreservation].

PubMed

Shishova, N V; Fesenko, E E

2015-01-01

In the present review, we tried to evaluate the known properties of gas hydrates and gases participating in the formation of gas hydrates from the point of view of the mechanisms of cryoinjury and cryoprotection, to consider the papers on freezing biological materials in the presence of inert gases, and to analyze the perspectives for the development of this direction. For the purpose, we searched for the information on the physical properties of gases and gas hydrates, compared processes occured during the formation of gas hydrates and water ice, analyzed the influence of the formation and growth of gas hydrates on the structure of biological objects. We prepared a short review on the biological effects of xenon, krypton, argon, carbon dioxide, hydrogen sulfide, and carbon monoxide especially on hypothermal conditions and probable application of these properties in cryopreservation technologies. The description of the existing experiments on cryopreservation of biological objects with the use of gases was analyzed. On the basis of the information we found, the most perspective directions of work in the field of cryopreservation of biological objects with the use of gases were outlined. An attempt was made to forecast the potential problems in this field.

Extraction of consensus protein patterns in regions containing non-proline cis peptide bonds and their functional assessment.

PubMed

Exarchos, Konstantinos P; Exarchos, Themis P; Rigas, Georgios; Papaloukas, Costas; Fotiadis, Dimitrios I

2011-05-10

In peptides and proteins, only a small percentile of peptide bonds adopts the cis configuration. Especially in the case of amide peptide bonds, the amount of cis conformations is quite limited thus hampering systematic studies, until recently. However, lately the emerging population of databases with more 3D structures of proteins has produced a considerable number of sequences containing non-proline cis formations (cis-nonPro). In our work, we extract regular expression-type patterns that are descriptive of regions surrounding the cis-nonPro formations. For this purpose, three types of pattern discovery are performed: i) exact pattern discovery, ii) pattern discovery using a chemical equivalency set, and iii) pattern discovery using a structural equivalency set. Afterwards, using each pattern as predicate, we search the Eukaryotic Linear Motif (ELM) resource to identify potential functional implications of regions with cis-nonPro peptide bonds. The patterns extracted from each type of pattern discovery are further employed, in order to formulate a pattern-based classifier, which is used to discriminate between cis-nonPro and trans-nonPro formations. In terms of functional implications, we observe a significant association of cis-nonPro peptide bonds towards ligand/binding functionalities. As for the pattern-based classification scheme, the highest results were obtained using the structural equivalency set, which yielded 70% accuracy, 77% sensitivity and 63% specificity.

Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex

PubMed Central

Dincâ, V; Wiklund, C; Lukhtanov, V A; Kodandaramaiah, U; Norén, K; Dapporto, L; Wahlberg, N; Vila, R; Friberg, M

2013-01-01

Molecular studies of natural populations are often designed to detect and categorize hidden layers of cryptic diversity, and an emerging pattern suggests that cryptic species are more common and more widely distributed than previously thought. However, these studies are often decoupled from ecological and behavioural studies of species divergence. Thus, the mechanisms by which the cryptic diversity is distributed and maintained across large spatial scales are often unknown. In 1988, it was discovered that the common Eurasian Wood White butterfly consisted of two species (Leptidea sinapis and Leptidea reali), and the pair became an emerging model for the study of speciation and chromosomal evolution. In 2011, the existence of a third cryptic species (Leptidea juvernica) was proposed. This unexpected discovery raises questions about the mechanisms preventing gene flow and about the potential existence of additional species hidden in the complex. Here, we compare patterns of genetic divergence across western Eurasia in an extensive data set of mitochondrial and nuclear DNA sequences with behavioural data on inter- and intraspecific reproductive isolation in courtship experiments. We show that three species exist in accordance with both the phylogenetic and biological species concepts and that additional hidden diversity is unlikely to occur in Europe. The Leptidea species are now the best studied cryptic complex of butterflies in Europe and a promising model system for understanding the formation of cryptic species and the roles of local processes, colonization patterns and heterospecific interactions for ecological and evolutionary divergence. PMID:23909947

Network patterns in exponentially growing two-dimensional biofilms

NASA Astrophysics Data System (ADS)

Zachreson, Cameron; Yap, Xinhui; Gloag, Erin S.; Shimoni, Raz; Whitchurch, Cynthia B.; Toth, Milos

2017-10-01

Anisotropic collective patterns occur frequently in the morphogenesis of two-dimensional biofilms. These patterns are often attributed to growth regulation mechanisms and differentiation based on gradients of diffusing nutrients and signaling molecules. Here, we employ a model of bacterial growth dynamics to show that even in the absence of growth regulation or differentiation, confinement by an enclosing medium such as agar can itself lead to stable pattern formation over time scales that are employed in experiments. The underlying mechanism relies on path formation through physical deformation of the enclosing environment.

Significance of the E3 ubiquitin protein UBR5 as an oncogene and a prognostic biomarker in colorectal cancer

PubMed Central

Xu, Xiaowen; Zhu, Yan; Guo, Aizhen; Shen, Xian; Cao, Fuao; Chang, Wenjun

2017-01-01

The E3 ubiquitin protein UBR5 has been implicated in the regulation of multiple biological functions and has recently emerged as a key regulator of the ubiquitin-proteasome system (UPS) in cancer. However, the clinical significance and biological function of UBR5 in colorectal cancer (CRC) are poorly understood. In this study, we compared the expression pattern of UBR5 between CRC and adjacent normal tissues and found that UBR5 expression was frequently elevated in CRC, possibly through chromosomal gains. Using three CRC patient cohorts, we found that patients with high UBR5 mRNA levels, UBR5 gene amplification, or high nuclear UBR5 protein levels had poor prognoses. Multivariate analysis showed that the alterations in UBR5 were independent predictors of CRC prognosis with the TNM stage as a confounding factor. Furthermore, knockdown of UBR5 prevented the proliferation, colony formation, migration, and invasion of CRC cells in cell culture models. An in vivo animal model further confirmed that UBR5 knockdown reduced the growth of CRC tumors. In conclusion, our study is the first to systematically investigate the clinical and biological significance of UBR5 and to conclude that an elevated UBR5 level plays an oncogenic role and may be a potential prognostic marker in CRC. PMID:29296225

Unicellular eukaryotes as models in cell and molecular biology: critical appraisal of their past and future value.

PubMed

Simon, Martin; Plattner, Helmut

2014-01-01

Unicellular eukaryotes have been appreciated as model systems for the analysis of crucial questions in cell and molecular biology. This includes Dictyostelium (chemotaxis, amoeboid movement, phagocytosis), Tetrahymena (telomere structure, telomerase function), Paramecium (variant surface antigens, exocytosis, phagocytosis cycle) or both ciliates (ciliary beat regulation, surface pattern formation), Chlamydomonas (flagellar biogenesis and beat), and yeast (S. cerevisiae) for innumerable aspects. Nowadays many problems may be tackled with "higher" eukaryotic/metazoan cells for which full genomic information as well as domain databases, etc., were available long before protozoa. Established molecular tools, commercial antibodies, and established pharmacology are additional advantages available for higher eukaryotic cells. Moreover, an increasing number of inherited genetic disturbances in humans have become elucidated and can serve as new models. Among lower eukaryotes, yeast will remain a standard model because of its peculiarities, including its reduced genome and availability in the haploid form. But do protists still have a future as models? This touches not only the basic understanding of biology but also practical aspects of research, such as fund raising. As we try to scrutinize, due to specific advantages some protozoa should and will remain favorable models for analyzing novel genes or specific aspects of cell structure and function. Outstanding examples are epigenetic phenomena-a field of rising interest. © 2014 Elsevier Inc. All rights reserved.

Patterns of fMRI activity dissociate overlapping functional brain areas that respond to biological motion.

PubMed

Peelen, Marius V; Wiggett, Alison J; Downing, Paul E

2006-03-16

Accurate perception of the actions and intentions of other people is essential for successful interactions in a social environment. Several cortical areas that support this process respond selectively in fMRI to static and dynamic displays of human bodies and faces. Here we apply pattern-analysis techniques to arrive at a new understanding of the neural response to biological motion. Functionally defined body-, face-, and motion-selective visual areas all responded significantly to "point-light" human motion. Strikingly, however, only body selectivity was correlated, on a voxel-by-voxel basis, with biological motion selectivity. We conclude that (1) biological motion, through the process of structure-from-motion, engages areas involved in the analysis of the static human form; (2) body-selective regions in posterior fusiform gyrus and posterior inferior temporal sulcus overlap with, but are distinct from, face- and motion-selective regions; (3) the interpretation of region-of-interest findings may be substantially altered when multiple patterns of selectivity are considered.

How can macromolecular crowding inhibit biological reactions? The enhanced formation of DNA nanoparticles

PubMed Central

Hou, Sen; Trochimczyk, Piotr; Sun, Lili; Wisniewska, Agnieszka; Kalwarczyk, Tomasz; Zhang, Xuzhu; Wielgus-Kutrowska, Beata; Bzowska, Agnieszka; Holyst, Robert

2016-01-01

In contrast to the already known effect that macromolecular crowding usually promotes biological reactions, solutions of PEG 6k at high concentrations stop the cleavage of DNA by HindIII enzyme, due to the formation of DNA nanoparticles. We characterized the DNA nanoparticles and probed the prerequisites for their formation using multiple techniques such as fluorescence correlation spectroscopy, dynamic light scattering, fluorescence analytical ultracentrifugation etc. In >25% PEG 6k solution, macromolecular crowding promotes the formation of DNA nanoparticles with dimensions of several hundreds of nanometers. The formation of DNA nanoparticles is a fast and reversible process. Both plasmid DNA (2686 bp) and double-stranded/single-stranded DNA fragment (66bp/nt) can form nanoparticles. We attribute the enhanced nanoparticle formation to the depletion effect of macromolecular crowding. This study presents our idea to enhance the formation of DNA nanoparticles by macromolecular crowding, providing the first step towards a final solution to efficient gene therapy. PMID:26903405

How can macromolecular crowding inhibit biological reactions? The enhanced formation of DNA nanoparticles.

PubMed

Hou, Sen; Trochimczyk, Piotr; Sun, Lili; Wisniewska, Agnieszka; Kalwarczyk, Tomasz; Zhang, Xuzhu; Wielgus-Kutrowska, Beata; Bzowska, Agnieszka; Holyst, Robert

2016-02-23

In contrast to the already known effect that macromolecular crowding usually promotes biological reactions, solutions of PEG 6k at high concentrations stop the cleavage of DNA by HindIII enzyme, due to the formation of DNA nanoparticles. We characterized the DNA nanoparticles and probed the prerequisites for their formation using multiple techniques such as fluorescence correlation spectroscopy, dynamic light scattering, fluorescence analytical ultracentrifugation etc. In >25% PEG 6k solution, macromolecular crowding promotes the formation of DNA nanoparticles with dimensions of several hundreds of nanometers. The formation of DNA nanoparticles is a fast and reversible process. Both plasmid DNA (2686 bp) and double-stranded/single-stranded DNA fragment (66 bp/nt) can form nanoparticles. We attribute the enhanced nanoparticle formation to the depletion effect of macromolecular crowding. This study presents our idea to enhance the formation of DNA nanoparticles by macromolecular crowding, providing the first step towards a final solution to efficient gene therapy.

Stimulation of Changes, Collective Commitment and The Patterns of Group Formation in Community Development in South Sulawesi

NASA Astrophysics Data System (ADS)

Saleh, Syafiuddin

2018-05-01

This study aims to examine the pattern of group formation, related to the stimulation of change through the empowerment of farmers and poor fishermen The pattern of group formation is the basis for sustainable development. The research method used is qualitative descriptive method and relevant research type such as case study and triangulasi. The results of the study showed that (1) stimulation of changes made through development programs or community empowerment in the areas studied both among farm households and poor fishermen households for some programs received positive response from farmers and fishermen. However, the collective commitment to the breeding is relatively weak, since the group formed in each program is not done through good planning and concepts. (2) there are two patterns of group formation that are natural and formed formations initiated by outsiders. Groups that are naturally formed are more institutionalized and have characteristics such as intense and relatively routine interaction, strong mutual trust, and have a common form or mechanism shared for common purposes. The group can form the basis for sustainable development in improving the welfare of the poor.

Biocatalytic Self-Assembly on Magnetic Nanoparticles.

PubMed

Conte, Maria P; Sahoo, Jugal Kishore; Abul-Haija, Yousef M; Lau, K H Aaron; Ulijn, Rein V

2018-01-24

Combining (bio)catalysis and molecular self-assembly provides an effective approach for the production and processing of self-assembled materials by exploiting catalysis to direct the assembly kinetics and hence controlling the formation of ordered nanostructures. Applications of (bio)catalytic self-assembly in biologically interfacing systems and in nanofabrication have recently been reported. Inspired by self-assembly in biological cells, efforts to confine catalysts on flat or patterned surfaces to exert spatial control over molecular gelator generation and nanostructure self-assembly have also emerged. Building on our previous work in the area, we demonstrate in this report the use of enzymes immobilized onto magnetic nanoparticles (NPs) to spatially localize the initiation of peptide self-assembly into nanofibers around NPs. The concept is generalized for both an equilibrium biocatalytic system that forms stable hydrogels and a nonequilibrium system that normally has a preset lifetime. Characterization of the hydrogels shows that self-assembly occurs at the site of enzyme immobilization on the NPs to give rise to gels with a "hub-and-spoke" morphology, where the nanofibers are linked through the enzyme-NP conjugates. This NP-controlled arrangement of self-assembled nanofibers enables both remarkable enhancements in the shear strength of hydrogel systems and a dramatic extension of the hydrogel stability in the nonequilibrium system. We are also able to show that the use of magnetic NPs enables the external control of both the formation of the hydrogel and its overall structure by application of an external magnetic field. We anticipate that the enhanced properties and stimuli-responsiveness of our NP-enzyme system will have applications ranging from nanomaterial fabrication to biomaterials and biosensing.

Probing the modulated formation of gold nanoparticles-beta-lactoglobulin corona complexes and their applications.

PubMed

Yang, Jiang; Wang, Bo; You, Youngsang; Chang, Woo-Jin; Tang, Ke; Wang, Yi-Cheng; Zhang, Wenzhao; Ding, Feng; Gunasekaran, Sundaram

2017-11-23

Understanding the interactions between proteins and nanoparticles (NPs) along with the underlying structural and dynamic information is of utmost importance to exploit nanotechnology for biomedical applications. Upon adsorption onto a NP surface, proteins form a well-organized layer, termed the corona, that dictates the identity of the NP-protein complex and governs its biological pathways. Given its high biological relevance, in-depth molecular investigations and applications of NPs-protein corona complexes are still scarce, especially since different proteins form unique corona patterns, making identification of the biomolecular motifs at the interface critical. In this work, we provide molecular insights and structural characterizations of the bio-nano interface of a popular food-based protein, namely bovine beta-lactoglobulin (β-LG), with gold nanoparticles (AuNPs) and report on our investigations of the formation of corona complexes by combined molecular simulations and complementary experiments. Two major binding sites in β-LG were identified as being driven by citrate-mediated electrostatic interactions, while the associated binding kinetics and conformational changes in the secondary structures were also characterized. More importantly, the superior stability of the corona led us to further explore its biomedical applications, such as in the smartphone-based point-of-care biosensing of Escherichia coli (E. coli) and in the computed tomography (CT) of the gastrointestinal (GI) tract through oral administration to probe GI tolerance and functions. Considering their biocompatibility, edible nature, and efficient excretion through defecation, AuNPs-β-LG corona complexes have shown promising perspectives for future in vitro and in vivo clinical settings.

The role of FGF2 in migration and tubulogenesis of endothelial progenitor cells in relation to pro-angiogenic growth factor production.

PubMed

Litwin, Monika; Radwańska, Agata; Paprocka, Maria; Kieda, Claudine; Dobosz, Tadeusz; Witkiewicz, Wojciech; Baczyńska, Dagmara

2015-12-01

In recent years, special attention has been paid to finding new pro-angiogenic factors which could be used in gene therapy of vascular diseases such as critical limb ischaemia (CLI). Angiogenesis, the formation of new blood vessels, is a complex process dependent on different cytokines, matrix proteins, growth factors and other pro- or anti-angiogenic stimuli. Numerous lines of evidence suggest that key mediators of angiogenesis, vascular endothelial growth factor (VEGF) and hepatocyte growth factor (HGF) together with fibroblast growth factor2 (FGF2) are involved in regulation of the normal and pathological process of angiogenesis. However, less information is available on the complex interactions between these and other angiogenic factors. The aim of this study was to characterise the effect of fibroblast growth factor2 on biological properties of human endothelial progenitor cells with respect to the expression level of other regulatory cytokines. Ectopic expression of FGF2 in EP cells stimulates their pro-angiogenic behaviour, leading to increased proliferation, migration and tube formation abilities. Moreover, we show that the expression profile of VEGF and other pro-angiogenic cytokines, such as HGF, MCP2, and interleukins, is affected differently by FGF2 in EPC. In conclusion, we provide evidence that FGF2 directly affects not only the biological properties of EP cells but also the expression pattern and secretion of numerous chemocytokines. Our results suggest that FGF2 could be applied in therapeutic approaches for CLI and other ischaemic diseases of the vascular system in vivo.

Inclusion Bodies Are a Site of Ebolavirus Replication

PubMed Central

Hoenen, Thomas; Shabman, Reed S.; Groseth, Allison; Herwig, Astrid; Weber, Michaela; Schudt, Gordian; Dolnik, Olga; Basler, Christopher F.; Becker, Stephan

2012-01-01

Inclusion bodies are a characteristic feature of ebolavirus infections in cells. They contain large numbers of preformed nucleocapsids, but their biological significance has been debated, and they have been suggested to be aggregates of viral proteins without any further biological function. However, recent data for other viruses that produce similar structures have suggested that inclusion bodies might be involved in genome replication and transcription. In order to study filovirus inclusion bodies, we fused mCherry to the ebolavirus polymerase L, which is found in inclusion bodies. The resulting L-mCherry fusion protein was functional in minigenome assays and incorporated into virus-like particles. Importantly, L-mCherry fluorescence in transfected cells was readily detectable and distributed in a punctate pattern characteristic for inclusion bodies. A recombinant ebolavirus encoding L-mCherry instead of L was rescued and showed virtually identical growth kinetics and endpoint titers to those for wild-type virus. Using this virus, we showed that the onset of inclusion body formation corresponds to the onset of viral genome replication, but that viral transcription occurs prior to inclusion body formation. Live-cell imaging further showed that inclusion bodies are highly dynamic structures and that they can undergo dramatic reorganization during cell division. Finally, by labeling nascent RNAs using click technology we showed that inclusion bodies are indeed the site of viral RNA synthesis. Based on these data we conclude that, rather than being inert aggregates of nucleocapsids, ebolavirus inclusion bodies are in fact complex and dynamic structures and an important site at which viral RNA replication takes place. PMID:22915810

Inclusion bodies are a site of ebolavirus replication.

PubMed

Hoenen, Thomas; Shabman, Reed S; Groseth, Allison; Herwig, Astrid; Weber, Michaela; Schudt, Gordian; Dolnik, Olga; Basler, Christopher F; Becker, Stephan; Feldmann, Heinz

2012-11-01

Inclusion bodies are a characteristic feature of ebolavirus infections in cells. They contain large numbers of preformed nucleocapsids, but their biological significance has been debated, and they have been suggested to be aggregates of viral proteins without any further biological function. However, recent data for other viruses that produce similar structures have suggested that inclusion bodies might be involved in genome replication and transcription. In order to study filovirus inclusion bodies, we fused mCherry to the ebolavirus polymerase L, which is found in inclusion bodies. The resulting L-mCherry fusion protein was functional in minigenome assays and incorporated into virus-like particles. Importantly, L-mCherry fluorescence in transfected cells was readily detectable and distributed in a punctate pattern characteristic for inclusion bodies. A recombinant ebolavirus encoding L-mCherry instead of L was rescued and showed virtually identical growth kinetics and endpoint titers to those for wild-type virus. Using this virus, we showed that the onset of inclusion body formation corresponds to the onset of viral genome replication, but that viral transcription occurs prior to inclusion body formation. Live-cell imaging further showed that inclusion bodies are highly dynamic structures and that they can undergo dramatic reorganization during cell division. Finally, by labeling nascent RNAs using click technology we showed that inclusion bodies are indeed the site of viral RNA synthesis. Based on these data we conclude that, rather than being inert aggregates of nucleocapsids, ebolavirus inclusion bodies are in fact complex and dynamic structures and an important site at which viral RNA replication takes place.

Interactome analysis of longitudinal pharyngeal infection of cynomolgus macaques by group A Streptococcus.

PubMed

Shea, Patrick R; Virtaneva, Kimmo; Kupko, John J; Porcella, Stephen F; Barry, William T; Wright, Fred A; Kobayashi, Scott D; Carmody, Aaron; Ireland, Robin M; Sturdevant, Daniel E; Ricklefs, Stacy M; Babar, Imran; Johnson, Claire A; Graham, Morag R; Gardner, Donald J; Bailey, John R; Parnell, Michael J; Deleo, Frank R; Musser, James M

2010-03-09

Relatively little is understood about the dynamics of global host-pathogen transcriptome changes that occur during bacterial infection of mucosal surfaces. To test the hypothesis that group A Streptococcus (GAS) infection of the oropharynx provokes a distinct host transcriptome response, we performed genome-wide transcriptome analysis using a nonhuman primate model of experimental pharyngitis. We also identified host and pathogen biological processes and individual host and pathogen gene pairs with correlated patterns of expression, suggesting interaction. For this study, 509 host genes and seven biological pathways were differentially expressed throughout the entire 32-day infection cycle. GAS infection produced an initial widespread significant decrease in expression of many host genes, including those involved in cytokine production, vesicle formation, metabolism, and signal transduction. This repression lasted until day 4, at which time a large increase in expression of host genes was observed, including those involved in protein translation, antigen presentation, and GTP-mediated signaling. The interactome analysis identified 73 host and pathogen gene pairs with correlated expression levels. We discovered significant correlations between transcripts of GAS genes involved in hyaluronic capsule production and host endocytic vesicle formation, GAS GTPases and host fibrinolytic genes, and GAS response to interaction with neutrophils. We also identified a strong signal, suggesting interaction between host gammadelta T cells and genes in the GAS mevalonic acid synthesis pathway responsible for production of isopentenyl-pyrophosphate, a short-chain phospholipid that stimulates these T cells. Taken together, our results are unique in providing a comprehensive understanding of the host-pathogen interactome during mucosal infection by a bacterial pathogen.

On the holistic approach in cellular and cancer biology: nonlinearity, complexity, and quasi-determinism of the dynamic cellular network.

PubMed

Waliszewski, P; Molski, M; Konarski, J

1998-06-01

A keystone of the molecular reductionist approach to cellular biology is a specific deductive strategy relating genotype to phenotype-two distinct categories. This relationship is based on the assumption that the intermediary cellular network of actively transcribed genes and their regulatory elements is deterministic (i.e., a link between expression of a gene and a phenotypic trait can always be identified, and evolution of the network in time is predetermined). However, experimental data suggest that the relationship between genotype and phenotype is nonbijective (i.e., a gene can contribute to the emergence of more than just one phenotypic trait or a phenotypic trait can be determined by expression of several genes). This implies nonlinearity (i.e., lack of the proportional relationship between input and the outcome), complexity (i.e. emergence of the hierarchical network of multiple cross-interacting elements that is sensitive to initial conditions, possesses multiple equilibria, organizes spontaneously into different morphological patterns, and is controlled in dispersed rather than centralized manner), and quasi-determinism (i.e., coexistence of deterministic and nondeterministic events) of the network. Nonlinearity within the space of the cellular molecular events underlies the existence of a fractal structure within a number of metabolic processes, and patterns of tissue growth, which is measured experimentally as a fractal dimension. Because of its complexity, the same phenotype can be associated with a number of alternative sequences of cellular events. Moreover, the primary cause initiating phenotypic evolution of cells such as malignant transformation can be favored probabilistically, but not identified unequivocally. Thermodynamic fluctuations of energy rather than gene mutations, the material traits of the fluctuations alter both the molecular and informational structure of the network. Then, the interplay between deterministic chaos, complexity, self-organization, and natural selection drives formation of malignant phenotype. This concept offers a novel perspective for investigation of tumorigenesis without invalidating current molecular findings. The essay integrates the ideas of the sciences of complexity in a biological context.

Rayleigh-Taylor instability and mushroom-pattern formation in a two-component Bose-Einstein condensate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sasaki, Kazuki; Suzuki, Naoya; Saito, Hiroki

2009-12-15

The Rayleigh-Taylor instability at the interface in an immiscible two-component Bose-Einstein condensate is investigated using the mean field and Bogoliubov theories. Rayleigh-Taylor fingers are found to grow from the interface and mushroom patterns are formed. Quantized vortex rings and vortex lines are then generated around the mushrooms. The Rayleigh-Taylor instability and mushroom-pattern formation can be observed in a trapped system.

Dynamical spike solutions in a nonlocal model of pattern formation

NASA Astrophysics Data System (ADS)

Marciniak-Czochra, Anna; Härting, Steffen; Karch, Grzegorz; Suzuki, Kanako

2018-05-01

Coupling a reaction-diffusion equation with ordinary differential equa- tions (ODE) may lead to diffusion-driven instability (DDI) which, in contrast to the classical reaction-diffusion models, causes destabilization of both, constant solutions and Turing patterns. Using a shadow-type limit of a reaction-diffusion-ODE model, we show that in such cases the instability driven by nonlocal terms (a counterpart of DDI) may lead to formation of unbounded spike patterns.

Tendon–bone contact pressure and biomechanical evaluation of a modified suture-bridge technique for rotator cuff repair

PubMed Central

Geyer, Michael; Büschken, Meike; Buchhorn, Gottfried H.; Spahn, Gunter; Klinger, Hans-Michael

2009-01-01

The aim of the study was to evaluate the time-zero mechanical and footprint properties of a suture-bridge technique for rotator cuff repair in an animal model. Thirty fresh-frozen sheep shoulders were randomly assigned among three investigation groups: (1) cyclic loading, (2) load-to-failure testing, and (3) tendon–bone interface contact pressure measurement. Shoulders were cyclically loaded from 10 to 180 N and displacement to gap formation of 5- and 10-mm at the repair site. Cycles to failure were determined. Additionally, the ultimate tensile strength and stiffness were verified along with the mode of failure. The average contact pressure and pressure pattern were investigated using a pressure-sensitive film system. All of the specimens resisted against 3,000 cycles and none of them reached a gap formation of 10 mm. The number of cycles to 5-mm gap formation was 2,884.5 ± 96.8 cycles. The ultimate tensile strength was 565.8 ± 17.8 N and stiffness was 173.7 ± 9.9 N/mm. The entire specimen presented a unique mode of failure as it is well known in using high strength sutures by pulling them through the tendon. We observed a mean contact pressure of 1.19 ± 0.03 MPa, applied on the footprint area. The fundamental results of our study support the use of a suture-bridge technique for optimising the conditions of the healing biology of a reconstructed rotator cuff tendon. Nevertheless, an individual estimation has to be done if using the suture-bridge technique clinically. Further investigation is necessary to evaluate the cell biological healing process in order to achieve further sufficient advancements in rotator cuff repair. PMID:19826786