Crystallization of Adenylylsulfate Reductase from Desulfovibrio gigas: A Strategy Based on Controlled Protein Oligomerization

Adenylylsulfate reductase (adenosine 5′-phosphosulfate reductase, APS reductase or APSR, E.C.1.8.99.2) catalyzes the conversion of APS to sulfite in dissimilatory sulfate reduction. APSR was isolated and purified directly from massive anaerobically grown Desulfovibrio gigas, a strict anaerobe, for structure and function investigation. Oligomerization of APSR to form dimers–α_2β_2, tetramers–α_4β_4, hexamers–α_6β_6, and larger oligomers was observed during purification of the protein. Dynamic light scattering and ultracentrifugation revealed that the addition of adenosine monophosphate (AMP) or adenosine 5′-phosphosulfate (APS) disrupts the oligomerization, indicating that AMP or APS binding to the APSR dissociates the inactive hexamers into functional dimers. Treatment of APSR with β-mercaptoethanol decreased the enzyme size from a hexamer to a dimer, probably by disrupting the disulfide Cys156—Cys162 toward the C-terminus of the β-subunit. Alignment of the APSR sequences from D. gigas and A. fulgidus revealed the largest differences in this region of the β-subunit, with the D. gigas APSR containing 16 additional amino acids with the Cys156—Cys162 disulfide. Studies in a pH gradient showed that the diameter of the APSR decreased progressively with acidic pH. To crystallize the APSR for structure determination, we optimized conditions to generate a homogeneous and stable form of APSR by combining dynamic light scattering, ultracentrifugation, and electron paramagnetic resonance methods to analyze the various oligomeric states of the enzyme in varied environments

A four dukkha state-space model for hand tracking

In this paper, we propose a hand tracking method which was inspired by the notion of the four dukkha: birth, aging, sickness and death (BASD) in Buddhism. Based on this philosophy, we formalize the hand tracking problem in the BASD framework, and apply it to hand track hand gestures in isolated sign language videos. The proposed BASD method is a novel nature-inspired computational intelligence method which is able to handle complex real-world tracking problem. The proposed BASD framework operates in a manner similar to a standard state-space model, but maintains multiple hypotheses and integrates hypothesis update and propagation mechanisms that resemble the effect of BASD. The survival of the hypothesis relies upon the strength, aging and sickness of existing hypotheses, and new hypotheses are birthed by the fittest pairs of parent hypotheses. These properties resolve the sample impoverishment problem of the particle filter. The estimated hand trajectories show promising results for the American sign language

Planar Dirac Electron in Coulomb and Magnetic Fields: a Bethe ansatz approach

The Dirac equation for an electron in two spatial dimensions in the Coulomb and homogeneous magnetic fields is an example of the so-called quasi-exactly solvable models. The solvable parts of its spectrum was previously solved from the recursion relations. In this work we present a purely algebraic solution based on the Bethe ansatz equations. It is realised that, unlike the corresponding problems in the Schr\"odinger and the Klein-Gordon case, here the unknown parameters to be solved for in the Bethe ansatz equations include not only the roots of wave function assumed, but also a parameter from the relevant operator. We also show that the quasi-exactly solvable differential equation does not belong to the classes based on the algebra $sl_2$.Comment: LaTex, 12 pages, no figure

Optimal Choices of Reference for a Quasi-local Energy: Spherically Symmetric Spacetimes

For a given timelike displacement vector the covariant Hamiltonian quasi-local energy expression requires a proper choice of reference spacetime. We propose a program for determining the reference by embedding a neighborhood of the two-sphere boundary in the dynamic spacetime into a Minkowski reference, so that the two sphere is embedded isometrically, and then extremizing the energy to determine the embedding variables. Applying this idea to Schwarzschild spacetime, we found that for each given future timelike displacement vector our program gives a unique energy value. The static observer measures the maximal energy. Applied to the Friedmann-Lemaitre-Robertson-Walker spacetime, we find that the maximum energy value is nonnegative; the associated displacement vector is the unit dual mean curvature vector, and the expansion of the two-sphere boundary matches that of its reference image. For these spherically symmetric cases the reference determined by our program is equivalent to isometrically matching the geometry at the two-sphere boundary and taking the displacement vector to be orthogonal to the spacelike constant coordinate time hypersurface, like the timelike Killing vector of the Minkowski reference.Comment: 12 page

Bose-Einstein condensation in an optical lattice: A perturbation approach

We derive closed analytical expressions for the order parameter $\Phi (x)$ and for the chemical potential $\mu$ of a Bose-Einstein Condensate loaded into a harmonically confined, one dimensional optical lattice, for sufficiently weak, repulsive or attractive interaction, and not too strong laser intensities. Our results are compared with exact numerical calculations in order to map out the range of validity of the perturbative analytical approach. We identify parameter values where the optical lattice compensates the interaction-induced nonlinearity, such that the condensate ground state coincides with a simple, single particle harmonic oscillator wave function

Conversion of Polyethylenes into Fungal Secondary Metabolites

Waste plastics represent major environmental and economic burdens due to their ubiquity, slow breakdown rates, and inadequacy of current recycling routes. Polyethylenes are particularly problematic, because they lack robust recycling approaches despite being the most abundant plastics in use today. We report a novel chemical and biological approach for the rapid conversion of polyethylenes into structurally complex and pharmacologically active compounds. We present conditions for aerobic, catalytic digestion of polyethylenes collected from post‐consumer and oceanic waste streams, creating carboxylic diacids that can then be used as a carbon source by the fungus Aspergillus nidulans. As a proof of principle, we have engineered strains of A. nidulans to synthesize the fungal secondary metabolites asperbenzaldehyde, citreoviridin, and mutilin when grown on these digestion products. This hybrid approach considerably expands the range of products to which polyethylenes can be upcycled

Inhibition of Tau Aggregation by Three Aspergillus nidulans Secondary Metabolites: 2,ω-Dihydroxyemodin, Asperthecin, and Asperbenzaldehyde

This is the published version. Copyright 2014 George Theime Verlag. All rights reserved.The aggregation of the microtubule-associated protein tau is a significant event in many neurodegenerative diseases including Alzheimerʼs disease. The inhibition or reversal of tau aggregation is therefore a potential therapeutic strategy for these diseases. Fungal natural products have proven to be a rich source of useful compounds having wide varieties of biological activity. We have screened Aspergillus nidulans secondary metabolites containing aromatic ring structures for their ability to inhibit tau aggregation in vitro using an arachidonic acid polymerization protocol and the previously identified aggregation inhibitor emodin as a positive control. While several compounds showed some activity, 2,ω-dihydroxyemodin, asperthecin, and asperbenzaldehyde were potent aggregation inhibitors as determined by both a filter trap assay and electron microscopy. In this study, these three compounds were stronger inhibitors than emodin, which has been shown in a prior study to inhibit the heparin induction of tau aggregation with an IC50 of 1–5 µM. Additionally, 2,ω-dihydroxyemodin, asperthecin, and asperbenzaldehyde reduced, but did not block, tau stabilization of microtubules. 2,ω-Dihydroxyemodin and asperthecin have similar structures to previously identified tau aggregation inhibitors, while asperbenzaldehyde represents a new class of compounds with tau aggregation inhibitor activity. Asperbenzaldehyde can be readily modified into compounds with strong lipoxygenase inhibitor activity, suggesting that compounds derived from asperbenzaldehyde could have dual activity. Together, our data demonstrates the potential of 2,ω-dihydroxyemodin, asperthecin, and asperbenzaldehyde as lead compounds for further development as therapeutics to inhibit tau aggregation in Alzheimerʼs disease and neurodegenerative tauopathies

Damping in 2D and 3D dilute Bose gases

Damping in 2D and 3D dilute gases is investigated using both the hydrodynamical approach and the Hartree-Fock-Bogoliubov (HFB) approximation . We found that the both methods are good for the Beliaev damping at zero temperature and Landau damping at very low temperature, however, at high temperature, the hydrodynamical approach overestimates the Landau damping and the HFB gives a better approximation. This result shows that the comparison of the theoretical calculation using the hydrodynamical approach and the experimental data for high temperature done by Vincent Liu (PRL {\bf21} 4056 (1997)) is not proper. For two-dimensional systems, we show that the Beliaev damping rate is proportional to $k^3$ and the Landau damping rate is proportional to $T^2$ for low temperature and to $T$ for high temperature. We also show that in two dimensions the hydrodynamical approach gives the same result for zero temperature and for low temperature as HFB, but overestimates the Landau damping for high temperature.Comment: 11 pages, 4 figure