Direct Counting Analysis on Network Generated by Discrete Dynamics

A detail study on the In-degree Distribution (ID) of Cellular Automata is obtained by exact enumeration. The results indicate large deviation from multiscaling and classification according to ID are discussed. We further augment the transfer matrix as such the distributions for more complicated rules are obtained. Dependence of In-degree Distribution on the lattice size have also been found for some rules including R50 and R77.Comment: 8 pages, 11 figure

Cellular Ability to Sense Spatial Gradients in the Presence of Multiple Competitive Ligands

Many eukaryotic and prokaryotic cells can exhibit remarkable sensing ability under small gradient of chemical compound. In this study, we approach this phenomenon by considering the contribution of multiple ligands to the chemical kinetics within Michaelis-Menten model. This work was inspired by the recent theoretical findings from Bo Hu et al. [Phys. Rev. Lett. 105, 048104 (2010)], our treatment with practical binding energies and chemical potential provides the results which are consistent with experimental observations.Comment: 5 pages, 4 figure

The Use of Nanoscale Visible Light-Responsive Photocatalyst TiO2-Pt for the Elimination of Soil-Borne Pathogens

Exposure to the soil-borne pathogens Burkholderia pseudomallei and Burkholderia cenocepacia can lead to severe infections and even mortality. These pathogens exhibit a high resistance to antibiotic treatments. In addition, no licensed vaccine is currently available. A nanoscale platinum-containing titania photocatalyst (TiO2-Pt) has been shown to have a superior visible light-responsive photocatalytic ability to degrade chemical contaminants like nitrogen oxides. The antibacterial activity of the catalyst and its potential use in soil pathogen control were evaluated. Using the plating method, we found that TiO2-Pt exerts superior antibacterial performance against Escherichia coli compared to other commercially available and laboratory prepared ultraviolet/visible light-responsive titania photocatalysts. TiO2-Pt-mediated photocatalysis also affectively eliminates the soil-borne bacteria B. pseudomallei and B. cenocepacia. An air pouch infection mouse model further revealed that TiO2-Pt-mediated photocatalysis could reduce the pathogenicity of both strains of bacteria. Unexpectedly, water containing up to 10% w/v dissolved soil particles did not reduce the antibacterial potency of TiO2-Pt, suggesting that the TiO2-Pt photocatalyst is suitable for use in soil-contaminated environments. The TiO2-Pt photocatalyst exerted superior antibacterial activity against a broad spectrum of human pathogens, including B. pseudomallei and B. cenocepacia. Soil particles (<10% w/v) did not significantly reduce the antibacterial activity of TiO2-Pt in water. These findings suggest that the TiO2-Pt photocatalyst may have potential applications in the development of bactericides for soil-borne pathogens

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Exhumation of serpentinized peridotite in the northern Manila subduction zone inferred from forward gravity modeling

The Taiwan Integrated Geodynamic Research program (TAIGER) collected two wide-angle and reflection seismic transects across the northern Manila subduction zone that provide constraints on the seismic velocity structure of the crust. Two-dimensional gravity modeling along these two transects shows a significant, relatively high density (3.12 and 3.02 g/cm3) in the fore-arc region, at the interface between the subducting Eurasian Plate and the accretionary prism in front of the Luzon arc on the overriding Philippine Sea Plate. The anomalous density in this zone is higher than that in the fore-arc crust and the accretionary prism but lower than that in mantle. Numerous geophysical and geological data, together with numerical models, have indicated that serpentinization of the fore-arc mantle is both expected and observed. Serpentinization of mantle rocks can dramatically reduce their seismic velocity and therefore their seismic velocity in a density to velocity conversion. Therefore, the source of the high-density material could be serpentinized fore-arc mantle, with serpentinization caused by the dehydration of the subducting Eurasian Plate. We interpret that positive buoyancy combined with weak plate coupling forces in the northern Manila subduction zone is resulting in this serpentinized fore-arc mantle peridotite being exhumed. Key Points Two-dimensional gravity modeling shows a significant high-density structure in the fore-arc region Positive buoyancy and weak plate coupling result in serpentinized peridotite exhumed Exhumed serpentinized materials in the northern Manila subduction zone are foundWen-Bin Doo was supported by Ministry of Science and Technology of Taiwan (grant MOST 104-2111-M-008-006). H.K-C. was supported by National Science Council (grant NSC101-2116-M- 008-023-MY3). D. Brown acknowledges funding by MICINN grant CGL2013-43877-P.Peer reviewe

Linkage between Proximal and Distal Movements of P450cam Induced by Putidaredoxin

Putidaredoxin (Pdx) is the exclusive reductase and a structural effector for P450cam (CYP101A1). However, the mechanism of how Pdx modulates the conformational states of P450cam remains elusive. Here we report a putative communication pathway for the Pdx-induced conformational change in P450cam using results of double electron-electron resonance (DEER) spectroscopy and molecular dynamics simulations. Use of solution state DEER measurements allows us to observe subtle conformational changes in the internal helices in P450cam among closed, open, and P450cam-Pdx complex states. Molecular dynamics simulations and dynamic network analysis suggest that Pdx binding is coupled to small coordinated movements of several regions of P450cam, including helices C, B', I, G, and F. These changes provide a linkage between the Pdx binding site on the proximal side of the enzyme and helices F/G on the distal side and the site of the largest movement resulting from the Pdx-induced closed-to-open transition. This study provides a detailed rationale for how Pdx exerts its long-recognized effector function at the active site from its binding site on the opposite face of the enzyme