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

Vortex structures and zero energy states in the BCS-to-BEC evolution of p-wave resonant Fermi gases

Multiply quantized vortices in the BCS-to-BEC evolution of p-wave resonant Fermi gases are investigated theoretically. The vortex structure and the low-energy quasiparticle states are discussed, based on the self-consistent calculations of the Bogoliubov-de Gennes and gap equations. We reveal the direct relation between the macroscopic structure of vortices, such as particle densities, and the low-lying quasiparticle state. In addition, the net angular momentum for multiply quantized vortices with a vorticity $\kappa$ is found to be expressed by a simple equation, which reflects the chirality of the Cooper pairing. Hence, the observation of the particle density depletion and the measurement of the angular momentum will provide the information on the core-bound state and $p$-wave superfluidity. Moreover, the details on the zero energy Majorana state are discussed in the vicinity of the BCS-to-BEC evolution. It is demonstrated numerically that the zero energy Majorana state appears in the weak coupling BCS limit only when the vortex winding number is odd. There exist the $\kappa$ branches of the core bound states for a vortex state with vorticity $\kappa$, whereas only one of them can be the zero energy. This zero energy state vanishes at the BCS-BEC topological phase transition, because of interference between the core-bound and edge-bound states.Comment: 15 pages, 9 figures, published versio

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

Effect of Quadratic Zeeman Energy on the Vortex of Spinor Bose-Einstein Condensates

The spinor Bose-Einstein condensate of atomic gases has been experimentally realized by a number of groups. Further, theoretical proposals of the possible vortex states have been sugessted. This paper studies the effects of the quadratic Zeeman energy on the vortex states. This energy was ignored in previous theoretical studies, although it exists in experimental systems. We present phase diagrams of various vortex states taking into account the quadratic Zeeman energy. The vortex states are calculated by the Gross-Pitaevskii equations. Several new kinds of vortex states are found. It is also found that the quadratic Zeeman energy affects the direction of total magnetization and causes a significant change in the phase diagrams.Comment: 6 pages, 5 figures. Published in J. Phys. Soc. Jp

Semiflexible Filamentous Composites

Inspired by the ubiquity of composite filamentous networks in nature we investigate models of biopolymer networks that consist of interconnected floppy and stiff filaments. Numerical simulations carried out in three dimensions allow us to explore the microscopic partitioning of stresses and strains between the stiff and floppy fractions c_s and c_f, and reveal a non-trivial relationship between the mechanical behavior and the relative fraction of stiff polymer: when there are few stiff polymers, non-percolated stiff ``inclusions`` are protected from large deformations by an encompassing floppy matrix, while at higher fractions of stiff material the stiff network is independently percolated and dominates the mechanical response.Comment: Phys. Rev. Lett, to appear (4 pages, 2 figures

Asymmetric Fermi superfluid with different atomic species in a harmonic trap

We study the dilute fermion gas with pairing between two species and unequal concentrations in a harmonic trap using the mean field theory and the local density approximation. We found that the system can exhibit a superfluid shell structure sandwiched by the normal fermions. This superfluid shell structure occurs if the mass ratio is larger then certain critical value which increases from the weak-coupling BCS region to the strong-coupling BEC side. In the strong coupling BEC regime, the radii of superfluid phase are less sensitive to the mass ratios and are similar to the case of pairing with equal masses. However, the lighter leftover fermions are easier to mix with the superfluid core than the heavier ones. A partially polarized superfluid can be found if the majority fermions are lighter, whereas phase separation is still found if they are heavier.Comment: 12 pages, 7 figure

Following autophagy step by step

Autophagy is an evolutionarily conserved lysosomal degradation route for soluble components of the cytosol and organelles. There is great interest in identifying compounds that modulate autophagy because they may have applications in the treatment of major diseases including cancer and neurodegenerative disease. Hundeshagen and colleagues describe this month in BMC Biology a screening assay based on flow cytometry that makes it possible to track distinct steps in the autophagic process and thereby identify novel modulators of autophagy

Majorana edge modes of superfluid 3He A-phase in a slab

Motivated by a recent experiment on the superfluid 3He A-phase with a chiral p-wave pairing confined in a thin slab, we propose designing a concrete experimental setup for observing the Majorana edge modes that appear around the circumference edge region. We solve the quasi-classical Eilenberger equation, which is quantitatively reliable, to evaluate several observables. To derive the property inherent to the Majorana edge state, the full quantum mechanical Bogoliubov-de Gennes equation is solved in this setting. On the basis of the results obtained, we perform decisive experiments to check the Majorana nature.Comment: 5 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

Superfluid 3He in a restricted geometry with a perpendicular magnetic field

We theoretically investigate the role of surface Andreev bound states (SABSs) on the phase diagram and spin susceptibilities of superfluid 3He confined to a restricted geometry. We first explicitly derive the dispersion of the SABS in 3He-B in the presence of a magnetic field, where the Majorana Ising spin and the spin susceptibility contributed from the SABS are associated with the SO(3) order parameter manifold. Subsequently, based on the quasiclassical Eilenberger theory with Fermi liquid corrections, we discuss the nonlinear effect of a magnetic field on the SABS, where the magnetic field is perpendicular to the specular surface. It is directly demonstrated that a gapped SABS strongly enhances the magnetization density and spin susceptibility at the surface, compared with that in the normal 3He. To capture the characteristics of the SABS, we show the field- and temperature-dependences of the spatially averaged susceptibility which is detectable through NMR experiments. It turns out that the contribution of the SABS leads to nonmonotonic temperature-dependence of the spin susceptibility. Furthermore, we present the superfluid phase diagram, where the B-phase undergoes a first-order (second-order) phase transition to A-phase or planar phase at low (high) temperatures.Comment: 18 pages, 12 figure