E1-Like Activating Enzyme Atg7 Is Preferentially Sequestered into p62 Aggregates via Its Interaction with LC3-I

p62 is constitutively degraded by autophagy via its interaction with LC3. However, the interaction of p62 with LC3 species in the context of the LC3 lipidation process is not specified. Further, the p62-mediated protein aggregation's effect on autophagy is unclear. We systemically analyzed the interactions of p62 with all known Atg proteins involved in LC3 lipidation. We find that p62 does not interact with LC3 at the stages when it is being processed by Atg4B or when it is complexed or conjugated with Atg3. p62 does interact with LC3-I and LC3-I:Atg7 complex and is preferentially recruited by LC3-II species under autophagic stimulation. Given that Atg4B, Atg3 and LC3-Atg3 are indispensable for LC3-II conversion, our study reveals a protective mechanism for Atg4B, Atg3 and LC3-Atg3 conjugate from being inappropriately sequestered into p62 aggregates. Our findings imply that p62 could potentially impair autophagy by negatively affecting LC3 lipidation and contribute to the development of protein aggregate diseases. © 2013 Gao et al

Viscoelastic evaluation of biological soft tissue in crush process at subsonic level for anti-bird strike technology of airplane

Miniaturization and lightening of airplane are advanced to improve its economic efficiency, and the safety technology of airplane design becomes difficult while the accident of bird-strike is increasing year by year. Then a system of shock impact test by using airsoft rifle is developed to evaluate the design technology of anti-bird strike structure of airplane. The viscoelastic characteristics of specimen is evaluated by analyzing stress response using the modified Hertz contact theory and the wave equation at the moment when simple ball bullet is shot to specimen by the airsoft rifle. In the results of experiment, the obvious relationship is observed subjectively between quasi-static and impact responses of specimen. The evaluated viscoelastic relationship is applied to simulate the impact test by using LSDYNA with fundamental viscoelastic constitutive equation and the material parameters derived from the impact test, and the well similar behavior has been simulated by the constitutive equation. By using the developed technology here, the phantom imitating real bird will be developed as standard specimen for an anti-bird strike test in future

Delayed particles in EAS at Akeno

Using two 2.25 square meter fast scintillation detectors, delayed particles in cosmic ray showers (CRS) have been observed at Akeno Observatory. These are set under 1 m concrete and 2.5 cm lead plates respectively. About 2500 CRS are analyzed. The lateral distribution of delayed particles for the CRS size 10 to the 7th power is flatter than that for to the 7th power. The lateral density of delayed particles is almost constant for the size range 2.2 X 10 to the 5th power approx. 10 to the 7th power and increases rapidly above 10 to the 7th power. These facts may suggest change of nuclear interaction at 10 to the 7th power and substantially the existence of heavy particles with long life

Simultaneously optimizing the interdependent thermoelectric parameters in Ce(Ni1−x_{1-x}Cux_x)2_2Al3_3

Substitution of Cu for Ni in the Kondo lattice system CeNi$_2$Al$_3$ results in a simultaneous optimization of the three interdependent thermoelectric parameters: thermoelectric power, electrical and thermal conductivities, where the electronic change in conduction band induced by the extra electron of Cu is shown to be crucial. The obtained thermoelectric figure of merit $zT$ amounts to 0.125 at around 100 K, comparable to the best values known for Kondo compounds. The realization of ideal thermoelectric optimization in Ce(Ni$_{1-x}$Cu$_x$)$_2$Al$_3$ indicates that proper electronic tuning of Kondo compounds is a promising approach to efficient thermoelectric materials for cryogenic application.Comment: 4 pages, 4 figures. Accepted for publication in Physical Review

A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions

The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental challenge in this domain is the reconstruction of a protein-protein subnetwork that underlies a process of interest from a genome-wide screen of associated genes. Despite intense work in this area, current algorithmic approaches are largely limited to analyzing a single screen and are, thus, unable to account for information on condition-specific genes, or reveal the dynamics (over time or condition) of the process in question. Here we propose a novel formulation for network reconstruction from multiple-condition data and devise an efficient integer program solution for it. We apply our algorithm to analyze the response to influenza infection in humans over time as well as to analyze a pair of ER export related screens in humans. By comparing to an extant, single-condition tool we demonstrate the power of our new approach in integrating data from multiple conditions in a compact and coherent manner, capturing the dynamics of the underlying processes.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Rotational predissociation of extremely weakly bound atom-molecule complexes produced by Feshbach resonance association

We study the rotational predissociation of atom - molecule complexes with very small binding energy. Such complexes can be produced by Feshbach resonance association of ultracold molecules with ultracold atoms. Numerical calculations of the predissociation lifetimes based on the computation of the energy dependence of the scattering matrix elements become inaccurate when the binding energy is smaller than the energy width of the predissociating state. We derive expressions that represent accurately the predissociation lifetimes in terms of the real and imaginary parts of the scattering length and effective range for molecules in an excited rotational state. Our results show that the predissociation lifetimes are the longest when the binding energy is positive, i.e. when the predissociating state is just above the excited state threshold.Comment: 17 pages, 5 figure

Superexchange in Dilute Magnetic Dielectrics: Application to (Ti,Co)O_2

We extend the model of ferromagnetic superexchange in dilute magnetic semiconductors to the ferromagnetically ordered highly insulating compounds (dilute magnetic dielectrics). The intrinsic ferromagnetism without free carriers is observed in oxygen-deficient films of anatase TiO_2 doped with transition metal impurities in cation sublattice. We suppose that ferromagnetic order arises due to superexchange between complexes [oxygen vacancies + magnetic impurities], which are stabilized by charge transfer from vacancies to impurities. The Hund rule controls the superexchange via empty vacancy related levels so that it becomes possible only for the parallel orientation of impurity magnetic moments. The percolation threshold for magnetic ordering is determined by the radius of vacancy levels, but the exchange mechanism does not require free carriers. The crucial role of the non-stoichiometry in formation of the ferromagnetism makes the Curie temperatures extremely sensitive to the methods of sample preparation.Comment: 18 pages, 2 figure

Autophagosome formation is initiated at phosphatidylinositol synthase‐enriched ER subdomains

The autophagosome, a double‐membrane structure mediating degradation of cytoplasmic materials by macroautophagy, is formed in close proximity to the endoplasmic reticulum (ER). However, how the ER membrane is involved in autophagy initiation and to which membrane structures the autophagy‐initiation complex is localized have not been fully characterized. Here, we were able to biochemically analyze autophagic intermediate membranes and show that the autophagy‐initiation complex containing ULK and FIP200 first associates with the ER membrane. To further characterize the ER subdomain, we screened phospholipid biosynthetic enzymes and found that the autophagy‐initiation complex localizes to phosphatidylinositol synthase (PIS)‐enriched ER subdomains. Then, the initiation complex translocates to the ATG9A‐positive autophagosome precursors in a PI3P‐dependent manner. Depletion of phosphatidylinositol (PI) by targeting bacterial PI‐specific phospholipase C to the PIS domain impairs recruitment of downstream autophagy factors and autophagosome formation. These findings suggest that the autophagy‐initiation complex, the PIS‐enriched ER subdomain, and ATG9A vesicles together initiate autophagosome formation

Functions of sensor 1 and sensor 2 regions of Saccharomyces cerevisiae Cdc6p in vivo and in vitro

Cdc6p is a key regulator of the cell cycle in eukaryotes and is a member of the AAA(+) (ATPases associated with a variety of cellular activities) family of proteins. In this family of proteins, the sensor 1 and sensor 2 regions are important for their function and ATPase activity. Here, site-directed mutagenesis has been used to examine the role of these regions of Saccharomyces cerevisiae Cdc6p in controlling the cell cycle progression and initiation of DNA replication. Two important amino acid residues (Asn(263) in sensor 1 and Arg(332) in sensor 2) were identified as key residues for Cdc6p function in vivo. Cells expressing mutant Cdc6p (N263A or R332E) grew slowly and accumulated in the S phase. In cells expressing mutant Cdc6p, loading of the minichromosome maintenance (MCM) complex of proteins was decreased, suggesting that the slow progression of S phase in these cells was due to inefficient MCM loading on chromatin. Purified wild type Cdc6p but not mutant Cdc6p (N263A and R332E) caused the structural modification of origin recognition complex proteins. These results are consistent with the idea that Cdc6p uses its ATPase activity to change the conformation of origin recognition complex, and then together they recruit the MCM complex

Autophagy in the Thymic Epithelium Is Dispensable for the Development of Self-Tolerance in a Novel Mouse Model

The thymic epithelium plays critical roles in the positive and negative selection of T cells. Recently, it was proposed that autophagy in thymic epithelial cells is essential for the induction of T cell tolerance to self antigens and thus for the prevention of autoimmune diseases. Here we have tested this hypothesis using mouse models in which autophagy was blocked specifically in epithelial cells expressing keratin 14 (K14), including the precursor of thymic epithelial cells. While the thymic epithelial cells of mice carrying the floxed Atg7 gene (ATG7 f/f) showed a high level of autophagy, as determined by LC3 Western blot analysis and fluorescence detection of the recombinant green fluorescent protein (GFP)-LC3 reporter protein on autophagosomes, autophagy in the thymic epithelium was efficiently suppressed by deletion of the Atg7 gene using the Cre-loxP system (ATG7 f/f K14-Cre). Suppression of autophagy led to the massive accumulation of p62/sequestosome 1 (SQSTM1) in thymic epithelial cells. However, the structure of the thymic epithelium as well as the organization and the size of the thymus were not altered in mutant mice. The ratio of CD4 to CD8-positive T cells, as well as the frequency of activated (CD69+) CD4 T cells in lymphoid organs, did not differ between mice with autophagy-competent and autophagy-deficient thymic epithelium. Inflammatory infiltrating cells, potentially indicative of autoimmune reactions, were present in the liver, lung, and colon of a similar fraction of ATG7 f/f and ATG7 f/f K14-Cre mice. In contrast to previously reported mice, that had received an autophagy-deficient thymus transplant, ATG7 f/f K14-Cre mice did not suffer from autoimmunity-induced weight loss. In summary, the results of this study suggest that autophagy in the thymic epithelium is dispensable for negative selection of autoreactive T cells