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## ‣ The coronin-like protein POD-1 is required for anterior–posterior axis formation and cellular architecture in the nematode Caenorhabditis elegans

Rappleye, Chad A.; Paredez, Alexander R.; Smith, Carol W.; McDonald, Kent L.; Aroian, Raffi V.
Fonte: Cold Spring Harbor Laboratory Press Publicador: Cold Spring Harbor Laboratory Press
Tipo: Artigo de Revista Científica
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Establishment of anterior–posterior (a-p) polarity in the Caenorhabditis elegans embryo depends on filamentous (F-) actin. Previously, we isolated an F-actin-binding protein that was enriched in the anterior cortex of the one-cell embryo and was hypothesized to link developmental polarity to the actin cytoskeleton. Here, we identify this protein, POD-1, as a new member of the coronin family of actin-binding proteins. We have generated a deletion within the pod-1 gene. Elimination of POD-1 from early embryos results in a loss of physical and molecular asymmetries along the a-p axis. For example, PAR-1 and PAR-3, which themselves are polarized and required for a-p polarity, are delocalized in pod-1 mutant embryos. However, unlike loss of PAR proteins, loss of POD-1 gives rise to the formation of abnormal cellular structures, namely large vesicles of endocytic origin, membrane protrusions, unstable cell divisions, a defective eggshell, and deposition of extracellular material. We conclude that, analogous to coronin, POD-1 plays an important role in intracellular trafficking and organizing specific aspects of the actin cytoskeleton. We propose models to explain how the role of POD-1 in basic cellular processes could be linked to the generation of polarity along the embryonic a-p axis.

## ‣ Diffusion in Cytoplasm: Effects of Excluded Volume Due to Internal Membranes and Cytoskeletal Structures

Novak, Igor L.; Kraikivski, Pavel; Slepchenko, Boris M.
Fonte: The Biophysical Society Publicador: The Biophysical Society
Tipo: Artigo de Revista Científica
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The intricate geometry of cytoskeletal networks and internal membranes causes the space available for diffusion in cytoplasm to be convoluted, thereby affecting macromolecule diffusivity. We present a first systematic computational study of this effect by approximating intracellular structures as mixtures of random overlapping obstacles of various shapes. Effective diffusion coefficients are computed using a fast homogenization technique. It is found that a simple two-parameter power law provides a remarkably accurate description of effective diffusion over the entire range of volume fractions and for any given composition of structures. This universality allows for fast computation of diffusion coefficients, once the obstacle shapes and volume fractions are specified. We demonstrate that the excluded volume effect alone can account for a four-to-sixfold reduction in diffusive transport in cells, relative to diffusion in vitro. The study lays the foundation for an accurate coarse-grain formulation that would account for cytoplasm heterogeneity on a micron scale and binding of tracers to intracellular structures.

## ‣ Increased Activity of the Vacuolar Monosaccharide Transporter TMT1 Alters Cellular Sugar Partitioning, Sugar Signaling, and Seed Yield in Arabidopsis1[OA]

Wingenter, Karina; Schulz, Alexander; Wormit, Alexandra; Wic, Stefan; Trentmann, Oliver; Hoermiller, Imke I.; Heyer, Arnd G.; Marten, Irene; Hedrich, Rainer; Neuhaus, H. Ekkehard
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Português
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The extent to which vacuolar sugar transport activity affects molecular, cellular, and developmental processes in Arabidopsis (Arabidopsis thaliana) is unknown. Electrophysiological analysis revealed that overexpression of the tonoplast monosaccharide transporter TMT1 in a tmt1-2::tDNA mutant led to increased proton-coupled monosaccharide import into isolated mesophyll vacuoles in comparison with wild-type vacuoles. TMT1 overexpressor mutants grew faster than wild-type plants on soil and in high-glucose (Glc)-containing liquid medium. These effects were correlated with increased vacuolar monosaccharide compartmentation, as revealed by nonaqueous fractionation and by chlorophyllab-binding protein1 and nitrate reductase1 gene expression studies. Soil-grown TMT1 overexpressor plants respired less Glc than wild-type plants and only about half the amount of Glc respired by tmt1-2::tDNA mutants. In sum, these data show that TMT activity in wild-type plants limits vacuolar monosaccharide loading. Remarkably, TMT1 overexpressor mutants produced larger seeds and greater total seed yield, which was associated with increased lipid and protein content. These changes in seed properties were correlated with slightly decreased nocturnal CO2 release and increased sugar export rates from detached source leaves. The SUC2 gene...

## ‣ Advances in Light-based Imaging of Three-Dimensional Cellular Ultrastructure

Kanchanawong, Pakorn; Waterman, Clare M.
Tipo: Artigo de Revista Científica
Português
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Visualization methods are key to gaining insights into cellular structure and function. Since diffraction has long confined optical microscopes to a resolution no better than hundreds of nanometers, the observation of ultrastructural features has traditionally been the domain of electron microscopes (EM). In the past decade, however, advances in super-resolution fluorescence microscopy have considerably expanded the capability of light-based imaging techniques. Advantages of fluorescent labeling such as high sensitivity, specificity, and multichannel capability, can now be exploited to dissect ultrastructural features of cells. With recent methods capable of imaging specific proteins with a resolution on the order of a few tens of nanometers in 3-dimensions, this has made it possible to elucidate the molecular organization of many complex cellular structures.

## ‣ Confocal laser scanning microscopic photoconversion: a new method to stabilize fluorescently labeled cellular elements for electron microscopic analysis

Colello, Raymond J.; Tozer, Jordan; Henderson, Scott C.
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
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Photoconversion, the method by which a fluorescent dye is transformed into a stable, osmiophilic product that can be visualized by electron microscopy, is the most widely used method to enable the ultrastructural analysis of fluorescently-labeled cellular structures. Nevertheless, the conventional method of photoconversion using widefield fluorescence microscopy requires long reaction times and results in low resolution cell targeting. Accordingly, we have developed a photoconversion method that ameliorates these limitations by adapting confocal laser scanning microscopy to the procedure. We have found that this method greatly reduces photoconversion times as compared to conventional wide field microscopy. Moreover, region of interest scanning capabilities of a confocal microscope facilitate the targeting of the photoconversion process to individual cellular or subcellular elements within a fluorescent field. This reduces the area of the cell exposed to light energy, thereby reducing the ultrastructural damage common to this process when widefield microscopes are employed.

## ‣ A Microfluidic-Enabled Mechanical Microcompressor for the Immobilization of Live Single- and Multi-Cellular Specimens

Yan, Yingjun; Jiang, Liwei; Aufderheide, Karl J.; Wright, Gus A.; Terekhov, Alexander; Costa, Lino; Qin, Kevin; McCleery, W. Tyler; Fellenstein, John J.; Ustione, Alessandro; Robertson, J. Brian; Johnson, Carl Hirschie; Piston, David W.; Hutson, M. Shane;
Tipo: Artigo de Revista Científica
Português
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A microcompressor is a precision mechanical device that flattens and immobilizes living cells and small organisms for optical microscopy, allowing enhanced visualization of sub-cellular structures and organelles. We have developed an easily fabricated device, which can be equipped with microfluidics, permitting the addition of media or chemicals during observation. This device can be used on both upright and inverted microscopes. The apparatus permits micrometer precision flattening for nondestructive immobilization of specimens as small as a bacterium, while also accommodating larger specimens, such as Caenorhabditis elegans, for long-term observations. The compressor mount is removable and allows easy specimen addition and recovery for later observation. Several customized specimen beds can be incorporated into the base. To demonstrate the capabilities of the device, we have imaged numerous cellular events in several protozoan species, in yeast cells, and in Drosophila melanogaster embryos. We have been able to document previously unreported events, and also perform photobleaching experiments, in conjugating Tetrahymena thermophila.

## ‣ Structures and Dynamics in Live Bacteria Revealed by Super-Resolution Fluorescence Microscopy

Wang, Wenqin
Fonte: Harvard University Publicador: Harvard University
Tipo: Thesis or Dissertation
Português
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Light microscopy, in particular fluorescence microscopy, is a widely used imaging method in biological research due to its noninvasive nature and molecular specificity. The resolution of conventional fluorescence microscopy is limited to a few hundred nanometers by the diffraction of light, leaving many biological structures too small to be optically resolved. Stochastic Optical Reconstruction Microscopy (STORM) technique overcomes this limit by localizing single photoswitchable fluorophores separated in time. We further extended the then two-dimensional capability to three-dimensional (3D) STORM by determining both axial and lateral positions of individual fluorophores with nanometer accuracy using optical astigmatism. Iterative, stochastic activation of photo-switchable probes enables high-precision 3D localization of each probe and thus the construction of a 3D image without scanning the sample. We achieved an image resolution of 20 - 30 nm in the lateral dimensions and 50 - 60 nm in the axial dimension. This development allowed us to resolve the 3D morphology of nanoscopic cellular structures. Enabled by the super-resolution imaging capability, we used 3D STORM in conjunction with biochemical assays to study structures and dynamics in live bacteria. Bacterial chromosomes are confined in submicron-sized nucleoids. Chromosome organization is facilitated by nucleoid-associated proteins (NAPs)...

## ‣ Astrocytic Mitochondrial Membrane Hyperpolarization following Extended Oxygen and Glucose Deprivation

Korenić, Andrej; Boltze, Johannes; Deten, Alexander; Peters, Myriam; Andjus, Pavle; Radenović, Lidija
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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Astrocytes can tolerate longer periods of oxygen and glucose deprivation (OGD) as compared to neurons. The reasons for this reduced vulnerability are not well understood. Particularly, changes in mitochondrial membrane potential (Δψm) in astrocytes, an indicator of the cellular redox state, have not been investigated during reperfusion after extended OGD exposure. Here, we subjected primary mouse astrocytes to glucose deprivation (GD), OGD and combinations of both conditions varying in duration and sequence. Changes in Δψm, visualized by change in the fluorescence of JC-1, were investigated within one hour after reconstitution of oxygen and glucose supply, intended to model in vivo reperfusion. In all experiments, astrocytes showed resilience to extended periods of OGD, which had little effect on Δψm during reperfusion, whereas GD caused a robust Δψm negativation. In case no Δψm negativation was observed after OGD, subsequent chemical oxygen deprivation (OD) induced by sodium azide caused depolarization, which, however, was significantly delayed as compared to normoxic group. When GD preceded OD for 12 h, Δψm hyperpolarization was induced by both GD and subsequent OD, but significant interaction between these conditions was not detected. However...

## ‣ LMKB/MARF1 Localizes to mRNA Processing Bodies, Interacts with Ge-1, and Regulates IFI44L Gene Expression

Bloch, Donald B.; Li, Pingcheng; Bloch, Emily G.; Berenson, Daniel F.; Galdos, Rita L.; Arora, Pankaj; Malhotra, Rajeev; Wu, Connie; Yang, Weihong
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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The mRNA processing body (P-body) is a cellular structure that regulates the stability of cytoplasmic mRNA. MARF1 is a murine oocyte RNA-binding protein that is associated with maintenance of mRNA homeostasis and genomic stability. In this study, autoantibodies were used to identify Limkain B (LMKB), the human orthologue of MARF1, as a P-body component. Indirect immunofluorescence demonstrated that Ge-1 (a central component of the mammalian core-decapping complex) co-localized with LMKB in P-bodies. Two-hybrid and co-immunoprecipitation assays were used to demonstrate interaction between Ge-1 and LMKB. The C-terminal 120 amino acids of LMKB mediated interaction with Ge-1 and the N-terminal 1094 amino acids of Ge-1 were required for interaction with LMKB. LMKB is the first protein identified to date that interacts with this portion of Ge-1. LMKB was expressed in human B and T lymphocyte cell lines; depletion of LMKB increased expression of IFI44L, a gene that has been implicated in the cellular response to Type I interferons. The interaction between LMKB/MARF1, a protein that contains RNA-binding domains, and Ge-1, which interacts with core-decapping proteins, suggests that LMKB has a role in the regulation of mRNA stability. LMKB appears to have different functions in different cell types: maintenance of genomic stability in developing oocytes and possible dampening of the inflammatory response in B and T cells.

## ‣ Plasticity and damage analysis of metal hollow sphere structures under dynamic compressive loading

Cunda, Luiz Antonio Bragança da; Oliveira, Branca Freitas de; Creus, Guillermo Juan
Tipo: Artigo de Revista Científica
Português
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Purpose – As compared with homogeneous metals and alloys, cellular metals provide low density, high specific stiffness, high energy absorption and good damping, thus being interesting alternatives to employ as protection against shock and impact. Impact energy is dissipated through cell bending, buckling or fracture. The knowledge and computational modelling of the mechanical behaviour of metal foams structures is thus of great importance for real life applications. The purpose of this paper is to increase the knowledge of the differences in metallic hollow sphere structures’ (MHSS) behaviour under dynamic loading, as compared with the corresponding behaviour under static loading and to determine the influence of inertia and loading rate. Design/methodology/approach – Computational dynamical finite element analyses of representative volume elements (RVE) of MHSS have been performed considering varying loading rates. Partially bonded geometries are considered and the effect of the spheres’ distribution is also taken into account. Findings – The results of the numerical examples presented show that inertia plays an important role in the dynamic behaviour of this kind of energy-absorbing structure. When compared with the corresponding values in the quasi-static case...

## ‣ Neural Network architectures design by Cellular Automata evolution

Galván, Inés M.; Isasi, Pedro; Molina, José M.; Sanchis, Araceli
Tipo: Conferência ou Objeto de Conferência Formato: application/pdf
Relevância na Pesquisa
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The design of the architecture is a crucial step in the successful application of a neural network. However, the architecture design is basically, in most cases, a human experts job. The design depends heavily on both, the expert experience and on a tedious trial-and-error process. Therefore, the development of automatic methods to determine the architecture of feedforward neural networks is a field of interest in the neural network community. These methods are generally based on search techniques, as genetic algorithms, simulated annealing or evolutionary strategies. Most of the designed methods are based on direct representation of the parameters of the network. This representation does not allow scalability, so to represent large architectures very large structures are required. In this work, an indirect constructive encoding scheme is proposed to find optimal architectures of feed-forward neural networks. This scheme is based on cellular automata representations in order to increase the scalability of the method.; 4th Conference of Systemics Cybernetics and Informatics. Orlando, 23-26 July 2000

## ‣ Isomorphisms of Additive Cellular Automata on Finite Groups

Bulitko, Valeriy
Tipo: Artigo de Revista Científica
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We study sources of isomorphisms of additive cellular automata on finite groups (called index-group). It is shown that many isomorphisms (called regular) of automata are reducible to the isomorphisms of underlying algebraic structures (such as the index-group, monoid of automata rules, and its subgroup of reversible elements). However for some groups there exist not regular automata isomorphisms. A complete description of linear automorphisms of the monoid is obtained. These automorphisms cover the most part of all automata isomorphisms for small groups and are represented by reversible matrices M such that for any index-group circulant C the matrix M^{-1}CM is an index-group circulant.; Comment: 24 pages

## ‣ Reversible boolean networks II: Phase transition, oscillation, and local structures

Coppersmith, S. N.; Kadanoff, Leo P.; Zhang, Zhitong
Tipo: Artigo de Revista Científica
Português
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## ‣ On the Use of Cellular Automata in Symmetric Cryptography

Fuster-Sabater, Amparo; Caballero-Gil, Pino
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
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In this work, pseudorandom sequence generators based on finite fields have been analyzed from the point of view of their cryptographic application. In fact, a class of nonlinear sequence generators has been modelled in terms of linear cellular automata. The algorithm that converts the given generator into a linear model based on automata is very simple and is based on the concatenation of a basic structure. Once the generator has been linearized, a cryptanalytic attack that exploits the weaknesses of such a model has been developed. Linear cellular structures easily model sequence generators with application in stream cipher cryptography.; Comment: 25 pages, 0 figures

## ‣ Splitting instability of cellular structures in the Ginzburg-Landau model under the feedback control

Sakaguchi, Hidetsugu
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
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We study numerically a Ginzburg-Landau type equation for micelles in two dimensions. The domain size and the interface length of a cellular structure are controlled by two feedback terms. The deformation and the successive splitting of the cellular structure are observed when the controlled interface length is increased. The splitting instability is further investigated using coupled mode equations to understand the bifurcation structure.; Comment: 4 pages, 4 figures

## ‣ Quantum Algorithms of Solving the Backtracking of One-dimensional Cellular Automata

Chang, Weng-Long; Feng, Mang; Lin, Kawuu Weicheng; Wang, Chih-Chiang; Chen, Ju-Chin
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
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In [Wolfram 1982; Wolfram 1983; Wolfram 2002], the backtracking of one-dimensional cellular automata is to find out which of the 2n possible initial configurations of width n evolve to a specific configuration. In this paper, in one-dimensional cellular automata for a specific configuration of width n, its unique initial configuration can be found by mean of the proposed quantum algorithm with polynomial quantum gates, polynomial quantum bits and the successful probability that is the same as that of Shor's quantum order-finding algorithm in [Shor 1994].; Comment: 14 pages, 2 figures

## ‣ The X-rule: universal computation in a non-isotropic Life-like Cellular Automaton

Soto, José Manuel Gómez; Wuensche, Andrew
Tipo: Artigo de Revista Científica
Português
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We present a new Life-like cellular automaton (CA) capable of logic universality -- the X-rule. The CA is 2D, binary, with a Moore neighborhood and $\lambda$ parameter similar to the game-of-Life, but is not based on birth/survival and is non-isotropic. We outline the search method. Several glider types and stable structures emerge spontaneously within X-rule dynamics. We construct glider-guns based on periodic oscillations between stable barriers, and interactions to create logical gates.; Comment: 34 pages, 45 figures, to appear in "Journal of Cellular Automata"

## ‣ Nonsynchronous updating in the multiverse of cellular automata

Reia, Sandro M.; Kinouchi, Osame
Tipo: Artigo de Revista Científica