Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity

<p>Abstract</p> <p>Background</p> <p>Computational comparison of two protein structures is the starting point of many methods that build on existing knowledge, such as structure modeling (including modeling of protein complexes and conformational changes), molecular replacement, or annotation by structural similarity. In a commonly used strategy, significant effort is invested in matching two sets of atoms. In a complementary approach, a global descriptor is assigned to the overall structure, thus losing track of the substructures within.</p> <p>Results</p> <p>Using a small set of geometric features, we define a reduced representation of protein structure, together with an optimizing function for matching two representations, to provide a pre-filtering stage in a database search. We show that, in a straightforward implementation, the representation performs well in terms of resolution in the space of protein structures, and its ability to make new predictions.</p> <p>Conclusions</p> <p>Perhaps unexpectedly, a substantial discriminating power already exists at the level of main features of protein structure, such as directions of secondary structural elements, possibly constrained by their sequential order. This can be used toward efficient comparison of protein (sub)structures, allowing for various degrees of conformational flexibility within the compared pair, which in turn can be used for modeling by homology of protein structure and dynamics.</p

The effects of low frequency electrical stimulation on satellite cell activity in rat skeletal muscle during hindlimb suspension

<p>Abstract</p> <p>Background</p> <p>The ability of skeletal muscle to grow and regenerate is dependent on resident stem cells called satellite cells. It has been shown that chronic hindlimb unloading downregulates the satellite cell activity. This study investigated the role of low-frequency electrical stimulation on satellite cell activity during a 28 d hindlimb suspension in rats.</p> <p>Results</p> <p>Mechanical unloading resulted in a 44% reduction in the myofiber cross-sectional area as well as a 29% and 34% reduction in the number of myonuclei and myonuclear domains, respectively, in the soleus muscles (<it>P </it>< 0.001 <it>vs </it>the weight-bearing control). The number of quiescent (M-cadherin⁺), proliferating (BrdU⁺and myoD⁺), and differentiated (myogenin⁺) satellite cells was also reduced by 48-57% compared to the weight-bearing animals (<it>P </it>< 0.01 for all). Daily application of electrical stimulation (2 × 3 h at a 20 Hz frequency) partially attenuated the reduction of the fiber cross-sectional area, satellite cell activity, and myonuclear domain (<it>P </it>< 0.05 for all). Extensor digitorum longus muscles were not significantly altered by hindlimb unloading.</p> <p>Conclusion</p> <p>This study shows that electrical stimulation partially attenuated the decrease in muscle size and satellite cells during hindlimb unloading. The causal relationship between satellite cell activation and electrical stimulation remain to be established.</p

Constraints on the DGP Model from Recent Supernova Observations and Baryon Acoustic Oscillations

Although there is mounting observational evidence that the expansion of our universe is undergoing a late-time acceleration, the mechanism for this acceleration is yet unknown. In the so-called Dvali-Gabadadze-Porrati (DGP) model this phenomena is attributed to gravitational leakage into extra dimensions. In this work, we mainly focus our attention to the constraints on the model from the gold sample of type Ia supernovae (SNeIa), the first year data from the Supernova Legacy Survey (SNLS) and the baryon acoustic oscillation (BAO) peak found in the Sloan Digital Sky Survey (SDSS). At 99.73% confidence level, the combination of the three databases provides Omega_m=0.270^{+0.018}_{-0.017} and Omega_{r_c}=0.216^{+0.012}_{-0.013} (hence a spatially closed universe with Omega_k=-0.350^{+0.080}_{-0.083}), which seems to be in contradiction with the most recent WMAP results indicating a flat universe. Based on this result, we also estimated the transition redshift (at which the universe switches from deceleration to acceleration) to be 0.70 < z_{q=0} < 1.01, at 2 sigma confidence level.Comment: 16 pages, 5 figures, AASLaTeX, Accepted for publication in Ap

Seasonal variation of total carotenoids content in the tissues of male and female golden noble scallops Chlamys nobilis

The noble scallop Chlamys nobilis is an economically important edible marine bivalve that has been cultivated in the Southern Sea of China since the 1980s. Noble scallops, particularly the golden scallops, are rich in carotenoids, are of interest for their potential beneficial uses in human healthcare, food processing and pharmaceuticals. However, very little is known about the seasonal variation of total carotenoids content (TCC) in the golden scallops. Therefore, present study was conducted to determine the seasonal variation of TCC in the tissues of male and female of golden scallops. The results of present study revealed that the TCC in adductor, mantle and gonads of golden scallops were ranged from 16.79 to 138.86 μg/ g, 92.86 to 312.98 μg/ g, and 71.5 to 750.0 μg/ g, respectively. Generally, the gonads of golden scallops contain the highest TCC, followed by the mantle and adductor. In comparison of male and female scallops, TCC in the same tissue (except for gonad) was not statistically significant. However, female gonads contain much higher TCC than male gonads. The temporal variation of the TCC in golden scallops showed the highest in March to April and the lowest in October. The findings of current study can be very useful for scallop farmers and industry to determine the best harvest time to obtain the highest quality of golden scallops with high TCC

Effects of Vanadium doping on BaFe2As2

We report an investigation of the structural, magnetic and electronic properties of Ba(Fe(1-x)V(x))2As2 using x-ray, transport, magnetic susceptibility and neutron scattering measurements. The vanadium substitutions in Fe sites are possible up to 40\%. Hall effect measurements indicate strong hole-doping effect through V doping, while no superconductivity is observed in all samples down to 2K. The antiferromagnetic and structural transition temperature of BaFe2As2 is gradually suppressed to finite temperature then vanishes at x=0.245 with the emergence of spin glass behavior, suggesting an avoided quantum critical point (QCP). Our results demonstrate that the avoided QCP and spin glass state which were previously reported in the superconducting phase of Co/Ni-doped BaFe2As2 can also be realized in non-superconducting Ba(Fe(1-x)V(x))2As2.Comment: 5 pages, 6 figure

Superconductivity in the cobalt-doped V3Si A15 intermetallic compound

The A15 structure of superconductors is a prototypical type-II superconductor that has generated considerable interest since the early history of superconducting materials. This paper discusses the superconducting properties of previously unreported V3-xCoxSi alloys. It is found that the lattice parameter decreases with increasing cobalt-doped content and leads to an increased residual resistivity ratio (RRR) value of the V3-xCoxSi system. Meanwhile, the superconducting transition temperature (Tc) cobalt-doped content. Furthermore, the fitted data show that the increase of cobalt-doped content also reduces the lower/upper critical fields of the V3-xCoxSi system. Type-II superconductivity is demonstrated on all V3-xCoxSi samples. With higher Co-doped content, V3-xCoxSi alloys may have superconducting and structural phase transitions at low-temperature regions. As the electron/atom (e/a) ratio increases, the Tc variation trend of V3Si is as pronounced as in crystalline alloys and monotonically follows the trend observed for amorphous superconductors.Comment: 20 pages, 7 figure

Cytochrome P450-mediated co-metabolism of fluoroquinolones by Haematococcus lacustris for simultaneously promoting astaxanthin and lipid accumulation

Microalgae-based antibiotic removal treatment has attracted attention because of its low carbon and sustainable advantages. The microalgal co-metabolism system with a suitable carbon source leads to enhanced performance of pollutant removal. However, currently, limited knowledge is available for the removal of fluoroquinolone using a microalgae-mediated co-metabolism system. In this study, we first investigated that the biotic processes by alga Haematococcus lacustris in the co-metabolism system by adding glycerol would be the main contributors responsible for the removal of 10 mg/L ofloxacin (OFL) with the efficiency of 79.73% and the removal of 10 mg/ L enrofloxacin (ENR) with the efficiency of 54.10%, respectively. Furthermore, we found that pyruvate from glycerol was converted into substrates and precursors, thereby resulting in the significant accumulations of microalgal astaxanthin and lipid. The astaxanthin content of H. lacustris was achieved at 4.81% and 4.69% treated with OFL and ENR in the presence of glycerol, with 16.04% and 14.55% of lipid content, respectively. The proposed metabolites and pathways were identified to plausibly explain the biodegradation of fluoroquinolone by H. lacustris. The molecular analyses demonstrated that cytochrome P450 (CYP450) enzymes are responsible for the biodegradation of fluoroquinolone, and it was further verified that fluoroquinolones might insert into CYP450 to finally form an efficient and tight binding conformation by molecular dynamic simulation. These findings provide a microalgae-based route for feasible and sustainable biodegradation of antibiotics using a co-metabolism strategy comprising glycerol as a carbon source, with the synergistic accumulation of valuable products.peer-reviewe