In silico modification of suberoylanilide hydroxamic acid (SAHA) as potential inhibitor for class II histone deacetylase (HDAC)

<p>Abstract</p> <p>Background</p> <p>The cervical cancer is the second most prevalent cancer for the woman in the world. It is caused by the oncogenic human papilloma virus (HPV). The inhibition activity of histone deacetylase (HDAC) is a potential strategy for cancer therapy. Suberoylanilide hydroxamic acid (SAHA) is widely known as a low toxicity HDAC inhibitor. This research presents <it>in silico</it> SAHA modification by utilizing triazole, in order to obtain a better inhibitor. We conducted docking of the SAHA inhibitor and 12 modified versions to six class II HDAC enzymes, and then proceeded with drug scanning of each one of them.</p> <p>Results</p> <p>The docking results show that the 12 modified inhibitors have much better binding affinity and inhibition potential than SAHA. Based on drug scan analysis, six of the modified inhibitors have robust pharmacological attributes, as revealed by drug likeness, drug score, oral bioavailability, and toxicity levels.</p> <p>Conclusions</p> <p>The binding affinity, free energy and drug scan screening of the best inhibitors have shown that 1c and 2c modified inhibitors are the best ones to inhibit class II HDAC.</p

Analytic approximations, perturbation methods, and their applications

The paper summarizes the parallel session B3 {\em Analytic approximations, perturbation methods, and their applications} of the GR18 conference. The talks in the session reported notably recent advances in black hole perturbations and post-Newtonian approximations as applied to sources of gravitational waves.Comment: Summary of the B3 parallel session of the GR18 conferenc

Small anisotropy of the lower critical field and s±s_\pm-wave two-gap feature in single crystal LiFeAs

The in- and out-of-plane lower critical fields and magnetic penetration depths for LiFeAs were examined. The anisotropy ratio $\gamma_{H_{c1}}(0)$ is smaller than the expected theoretical value, and increased slightly with increasing temperature from 0.6$T_c$ to $T_c$. This small degree of anisotropy was numerically confirmed by considering electron correlation effect. The temperature dependence of the penetration depths followed a power law($\sim$$T^n$) below 0.3$T_c$, with $n$$>$3.5 for both $\lambda_{ab}$ and $\lambda_c$. Based on theoretical studies of iron-based superconductors, these results suggest that the superconductivity of LiFeAs can be represented by an extended $s_\pm$-wave due to weak impurity scattering effect. And the magnitudes of the two gaps were also evaluted by fitting the superfluid density for both the in- and out-of-plane to the two-gap model. The estimated values for the two gaps are consistent with the results of angle resolved photoemission spectroscopy and specific heat experiments.Comment: 10 pages, 5 figure

Non-conformal Hydrodynamics in Einstein-dilaton Theory

In the Einestein-dilaton theory with a Liouville potential parameterized by $\eta$, we find a Schwarzschild-type black hole solution. This black hole solution, whose asymptotic geometry is described by the warped metric, is thermodynamically stable only for $0 \le \eta < 2$. Applying the gauge/gravity duality, we find that the dual gauge theory represents a non-conformal thermal system with the equation of state depending on $\eta$. After turning on the bulk vector fluctuations with and without a dilaton coupling, we calculate the charge diffusion constant, which indicates that the life time of the quasi normal mode decreases with $\eta$. Interestingly, the vector fluctuation with the dilaton coupling shows that the DC conductivity increases with temperature, a feature commonly found in electrolytes.Comment: 27 pages and 2 figures, published in JHE

Bubble collision with gravitation

In this paper, we study vacuum bubble collisions with various potentials including gravitation, assuming spherical, planar, and hyperbolic symmetry. We use numerical calculations from double-null formalism. Spherical symmetry can mimic the formation of a black hole via multiple bubble collisions. Planar and especially hyperbolic symmetry describes two bubble collisions. We study both cases, when two true vacuum regions have the same field value or different field values, by varying tensions. For the latter case, we also test symmetric and asymmetric bubble collisions, and see details of causal structures. If the colliding energy is sufficient, then the vacuum can be destabilized, and it is also demonstrated. This double-null formalism can be a complementary approach in the context of bubble collisions.Comment: 31 pages, 19 figure

Nanostring-based multigene assay to predict recurrence for gastric cancer patients after surgery

10.1371/journal.pone.0090133PLoS ONE93-POLN

Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus, we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters (Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton