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Systems Dynamics

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https://www.readbyqxmd.com/read/28931065/chlamydomonas-fap265-is-a-tubulin-polymerization-promoting-protein-essential-for-flagellar-reassembly-and-hatching-of-daughter-cells-from-the-sporangium
#1
Damayanti Tammana, Trinadh Venkata Satish Tammana
Tubulin polymerization promoting proteins (TPPPs) belong to a family of neomorphic moon lighting proteins, involved in various physiological and pathological conditions. In physiological conditions, TPPPs play an important role in microtubule dynamics regulating mitotic spindle assembly and in turn cell proliferation. In pathological situations, TPPPs interact with α-synuclein and β-amyloid and promote their aggregation leading to Parkinson's disease and multiple system atrophy. Orthologs of TPPP family proteins were identified in ciliary proteomes from various organisms including Chlamydomonas but their role in ciliogenesis was not known...
2017: PloS One
https://www.readbyqxmd.com/read/28931032/a-microtubule-based-minimal-model-for-spontaneous-and-persistent-spherical-cell-polarity
#2
Panayiotis Foteinopoulos, Bela M Mulder
We propose a minimal model for the spontaneous and persistent generation of polarity in a spherical cell based on dynamic microtubules and a single mobile molecular component. This component, dubbed the polarity factor, binds to microtubules nucleated from a centrosome located in the center of the cell, is subsequently delivered to the cell membrane, where it diffuses until it unbinds. The only feedback mechanism we impose is that the residence time of the microtubules at the membrane increases with the local density of the polarity factor...
2017: PloS One
https://www.readbyqxmd.com/read/28930998/in-vitro-ovule-cultivation-for-live-cell-imaging-of-zygote-polarization-and-embryo-patterning-in-arabidopsis-thaliana
#3
Daisuke Kurihara, Yusuke Kimata, Tetsuya Higashiyama, Minako Ueda
In most flowering plants, the zygote and embryo are hidden deep in the mother tissue, and thus it has long been a mystery of how they develop dynamically; for example, how the zygote polarizes to establish the body axis and how the embryo specifies various cell fates during organ formation. This manuscript describes an in vitro ovule culture method to perform live-cell imaging of developing zygotes and embryos of Arabidopsis thaliana. The optimized cultivation medium allows zygotes or early embryos to grow into fertile plants...
September 11, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28930991/using-an-adapted-microfluidic-olfactory-chip-for-the-imaging-of-neuronal-activity-in-response-to-pheromones-in-male-c-elegans-head-neurons
#4
Douglas K Reilly, Daniel E Lawler, Dirk R Albrecht, Jagan Srinivasan
The use of calcium indicators has greatly enhanced our understanding of neural dynamics and regulation. The nematode Caenorhabditis elegans, with its completely mapped nervous system and transparent anatomy, presents an ideal model for understanding real-time neural dynamics using calcium indicators. In combination with microfluidic technologies and experimental designs, calcium-imaging studies using these indicators are performed in both free-moving and trapped animals. However, most previous studies utilizing trapping devices, such as the olfactory chip described in Chronis et al...
September 7, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28930972/study-of-protein-protein-interactions-in-autophagy-research
#5
Secil Erbil-Bilir, Nur M Kocaturk, Melih Yayli, Devrim Gozuacik
Protein-protein interactions are important for understanding cellular signaling cascades and identifying novel pathway components and protein dynamics. The majority of cellular activities require physical interactions between proteins. To analyze and map these interactions, various experimental techniques as well as bioinformatics tools were developed. Autophagy is a cellular recycling mechanism that allows the cells to cope with different stressors, including nutrient deprivation, chemicals, and hypoxia. In order to better understand autophagy-related signaling events and to discover novel factors that regulate protein complexes in autophagy, we performed protein-protein interaction screens...
September 9, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28930543/eeg-and-erp-biomarkers-of-alzheimer-s-disease-a-critical-review
#6
Andras Horvath, Anna Szucs, Gabor Csukly, Anna Sakovics, Gabor Stefanics, Anita Kamondi
Here we critically review studies that used electroencephalography (EEG) or event-related potential (ERP) indices as a biomarker of Alzheimer's disease. In the first part we overview studies that relied on visual inspection of EEG traces and spectral characteristics of EEG. Second, we survey analysis methods motivated by dynamical systems theory (DST) as well as more recent network connectivity approaches. In the third part we review studies of sleep.  Next, we compare the utility of early and late ERP components in dementia research...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28930459/interfacial-insights-into-a-carbon-capture-system-co2-uptake-to-an-aqueous-monoethanolamine-surface
#7
Laura E McWilliams, Nicholas Valley, Nina Vincent, Geraldine L Richmond
Monoethanolamine (MEA) is a benchmark scrubber for CO2 gas emissions reductions. Preliminary studies have indicated surface monoethanolamine could influence the greater chemistry of CO2 uptake. MEA is known to be surface active and orients at aqueous surfaces such that its nitrogen lone pair electrons are pointing toward the gas phase. This MEA orientation has the potential to facilitate CO2 surface chemistry, however a thorough description of the chemistry at play during this important carbon capture reaction is lacking...
September 20, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28930437/c-and-n-metalated-nitriles-the-relationship-between-structure-and-selectivity
#8
Xun Yang, Fraser F Fleming
Metalated nitriles are exceptional nucleophiles capable of forging highly hindered stereocenters in cases where enolates are unreactive. The excellent nucleophilicity emanates from the powerful inductive stabilization of adjacent negative charge by the nitrile, which has a miniscule steric demand. Inductive stabilization is the key to understanding the reactivity of metalated nitriles because this permits a continuum of structures that range from N-metalated ketenimines to nitrile anions. Solution and solid-state analyses reveal two different metal coordination sites, the formally anionic carbon and the nitrile nitrogen, with the site of metalation depending intimately on the solvent, counterion, temperature, and ligands...
September 20, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28930070/rapid-whole-brain-imaging-of-neural-activity-in-freely-behaving-larval-zebrafish-danio-rerio
#9
Lin Cong, Zeguan Wang, Yuming Chai, Wei Hang, Chunfeng Shang, Wenbin Yang, Lu Bai, Jiulin Du, Kai Wang, Quan Wen
The internal brain dynamics that link sensation and action are arguably better studied during natural animal behaviors. Here we report on a novel volume imaging and 3D tracking technique that monitors whole brain neural activity in freely swimming larval zebrafish (Danio rerio). We demonstrated the capability of our system through functional imaging of neural activity during visually evoked and prey capture behaviors in larval zebrafish.
September 20, 2017: ELife
https://www.readbyqxmd.com/read/28929969/cellnetvis-a-web-tool-for-visualization-of-biological-networks-using-force-directed-layout-constrained-by-cellular-components
#10
Henry Heberle, Marcelo Falsarella Carazzolle, Guilherme P Telles, Gabriela Vaz Meirelles, Rosane Minghim
BACKGROUND: The advent of "omics" science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organization of biological pathways. Biomolecular interaction networks, or graphs, are simple abstract representations where the components of a cell (e.g. proteins, metabolites etc.) are represented by nodes and their interactions are represented by edges. An appropriate visualization of data is crucial for understanding such networks, since pathways are related to functions that occur in specific regions of the cell...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28929810/dynamic-contrast-enhanced-perfusion-area-detector-ct-preliminary-comparison-of-diagnostic-performance-for-n-stage-assessment-with-fdg-pet-ct-in-non-small-cell-lung-cancer
#11
Yoshiharu Ohno, Yasuko Fujisawa, Naoki Sugihara, Yuji Kishida, Shinichiro Seki, Hisanobu Koyama, Takeshi Yoshikawa
OBJECTIVE: The objective of our study was to directly compare the capability of dynamic first-pass contrast-enhanced (CE) perfusion area-detector CT (ADCT) and FDG PET/CT for differentiation of metastatic from nonmetastatic lymph nodes and assessment of N stage in patients with non-small cell lung carcinoma (NSCLC). SUBJECTS AND METHODS: Seventy-seven consecutive patients, 45 men (mean age ± SD, 70.4 ± 5.9 years) and 32 women (71.2 ± 7.7 years), underwent dynamic first-pass CE-perfusion ADCT at two or three different positions for covering the entire thorax, FDG PET/CT, surgical treatment, and pathologic examination...
September 20, 2017: AJR. American Journal of Roentgenology
https://www.readbyqxmd.com/read/28929737/two-dimensional-magnetic-semiconductor-in-feroxyhyte-%C3%AE-feooh
#12
Imran Khan, Arqum Hashmi, M Umar Farooq, Jisang Hong
A few years ago, it was claimed that the two-dimensional (2D) feroxyhyte (δ-FeOOH) layer could possess a net magnetic moment and it could be applied for potential spintronics application because it showed a band gap. However, the exact crystal structure is still unknown. Hereby, we investigate the crystal structure, electronic band structure, magnetic and optical properties of 2D δ-FeOOH using density functional calculations. Based on the experimental observation and dynamical stability calculations, we propose that the 2D δ-FeOOH originates from a bulk Fe(OH)2 via oxidation...
September 20, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28929144/symmetry-and-dynamics-of-fhf-anion-in-vacuum-in-cd2cl2-and-in-ccl4-ab-initio-md-study-of-fluctuating-solvent-solute-hydrogen-and-halogen-bonds
#13
S A Pylaeva, H Elgabarty, D Sebastiani, P M Tolstoy
FHF(-) anion is a classic example of a central-symmetric strongly hydrogen bonded system that has been intensively investigated both experimentally and theoretically. In this paper we focus on solvent effects on symmetry, structure and dynamics of the anion. The FHF(-) anion is studied in vacuum, dissolved in CH2Cl2 and dissolved in CCl4 by ab initio molecular dynamics simulations. We show that CH2Cl2 molecules form CHF hydrogen bonds with lone pairs of fluorine atoms, while CCl4 molecules form halogen bonds...
September 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28929140/real-time-probing-of-granular-dynamics-with-magnetic-resonance
#14
Alexander Penn, Takuya Tsuji, David O Brunner, Christopher M Boyce, Klaas P Pruessmann, Christoph R Müller
Granular dynamics govern earthquakes, avalanches, and landslides and are of fundamental importance in a variety of industries ranging from energy to pharmaceuticals to agriculture. Nonetheless, our understanding of the underlying physics is poor because we lack spatially and temporally resolved experimental measurements of internal grain motion. We introduce a magnetic resonance imaging methodology that provides internal granular velocity measurements that are four orders of magnitude faster compared to previous work...
September 2017: Science Advances
https://www.readbyqxmd.com/read/28929133/assembling-oppositely-charged-lock-and-key-responsive-colloids-a-mesoscale-analog-of-adaptive-chemistry
#15
Adriana M Mihut, Björn Stenqvist, Mikael Lund, Peter Schurtenberger, Jérôme J Crassous
We have seen a considerable effort in colloid sciences to copy Nature's successful strategies to fabricate complex functional structures through self-assembly. This includes attempts to design colloidal building blocks and their intermolecular interactions, such as creating the colloidal analogs of directional molecular interactions, molecular recognition, host-guest systems, and specific binding. We show that we can use oppositely charged thermoresponsive particles with complementary shapes, such as spherical and bowl-shaped particles, to implement an externally controllable lock-and-key self-assembly mechanism...
September 2017: Science Advances
https://www.readbyqxmd.com/read/28928719/the-green-berry-consortia-of-the-sippewissett-salt-marsh-millimeter-sized-aggregates-of-diazotrophic-unicellular-cyanobacteria
#16
Elizabeth G Wilbanks, Verena Salman-Carvalho, Ulrike Jaekel, Parris T Humphrey, Jonathan A Eisen, Daniel H Buckley, Stephen H Zinder
Microbial interactions driving key biogeochemical fluxes often occur within multispecies consortia that form spatially heterogeneous microenvironments. Here, we describe the "green berry" consortia of the Sippewissett salt marsh (Falmouth, MA, United States): millimeter-sized aggregates dominated by an uncultured, diazotrophic unicellular cyanobacterium of the order Chroococcales (termed GB-CYN1). We show that GB-CYN1 is closely related to Crocosphaera watsonii (UCYN-B) and "Candidatus Atelocyanobacterium thalassa" (UCYN-A), two groups of unicellular diazotrophic cyanobacteria that play an important role in marine primary production...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28928649/changes-in-electroencephalography-complexity-using-a-brain-computer-interface-motor-observation-training-in-chronic-stroke-patients-a-fuzzy-approximate-entropy-analysis
#17
Rui Sun, Wan-Wa Wong, Jing Wang, Raymond Kai-Yu Tong
Entropy-based algorithms have been suggested as robust estimators of electroencephalography (EEG) predictability or regularity. This study aimed to examine possible disturbances in EEG complexity as a means to elucidate the pathophysiological mechanisms in chronic stroke, before and after a brain computer interface (BCI)-motor observation intervention. Eleven chronic stroke subjects and nine unimpaired subjects were recruited to examine the differences in their EEG complexity. The BCI-motor observation intervention was designed to promote functional recovery of the hand in stroke subjects...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28928409/modelling-sequences-and-temporal-networks-with-dynamic-community-structures
#18
Tiago P Peixoto, Martin Rosvall
In evolving complex systems such as air traffic and social organisations, collective effects emerge from their many components' dynamic interactions. While the dynamic interactions can be represented by temporal networks with nodes and links that change over time, they remain highly complex. It is therefore often necessary to use methods that extract the temporal networks' large-scale dynamic community structure. However, such methods are subject to overfitting or suffer from effects of arbitrary, a priori-imposed timescales, which should instead be extracted from data...
September 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28928389/spatiotemporal-dynamics-in-excitable-homogeneous-random-networks-composed-of-periodically-self-sustained-oscillation
#19
Yu Qian, Fei Liu, Keli Yang, Ge Zhang, Chenggui Yao, Jun Ma
The collective behaviors of networks are often dependent on the network connections and bifurcation parameters, also the local kinetics plays an important role in contributing the consensus of coupled oscillators. In this paper, we systematically investigate the influence of network structures and system parameters on the spatiotemporal dynamics in excitable homogeneous random networks (EHRNs) composed of periodically self-sustained oscillation (PSO). By using the dominant phase-advanced driving (DPAD) method, the one-dimensional (1D) Winfree loop is exposed as the oscillation source supporting the PSO, and the accurate wave propagation pathways from the oscillation source to the whole network are uncovered...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28928147/disconnecting-structure-and-dynamics-in-glassy-thin-films
#20
Daniel M Sussman, Samuel S Schoenholz, Ekin D Cubuk, Andrea J Liu
Nanometrically thin glassy films depart strikingly from the behavior of their bulk counterparts. We investigate whether the dynamical differences between a bulk and thin film polymeric glass former can be understood by differences in local microscopic structure. Machine learning methods have shown that local structure can serve as the foundation for successful, predictive models of particle rearrangement dynamics in bulk systems. By contrast, in thin glassy films, we find that particles at the center of the film and those near the surface are structurally indistinguishable despite exhibiting very different dynamics...
September 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
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