Epigenetics in Traditional Chinese Pharmacy: A Bioinformatic Study at Pharmacopoeia Scale

Epigenetics is a phenomenon of heritable changes in the chromatin structure of a genomic region, resulting in a transcriptional silent or active state of the region over cell mitosis. Mounting evidence has demonstrated phenotypic consequence of alternations in the patterns of DNA methylation and histone modifications, two of the well-studied epigenetic mechanisms. The epigenome thus represents an interesting therapeutic target. Traditional Chinese medicine (TCM) is a system of therapies that has developed through empiricism for over 2100 years and has remained a popular alternative medicine in some Far East Asian populations. We searched 3294 TCM medicinals (TCMMs) containing 48 491 chemicals for chemicals that interact with the epigenetics-related proteins and found that 29.8% of the TCMMs are epigenome- and miRNA-modulating via, mainly, interactions with Polycomb group and methyl CpG-binding proteins. We analyzed 200 government-approved TCM formulas (TCMFs) and found that a statistically significant proportion (99%) of them are epigenome- and miRNA-interacting. The epigenome and miRNA interactivity of the Monarch medicinals is found to be most prominent. Histone modifications are heavily exploited by the TCMFs, many of which are tonic. Furthermore, epigenetically, the Assistant medicinals least resemble the Monarch. We quantified the role of epigenetics in TCM prescription and found that epigenome- and miRNA-interaction information alone determined, to an extent of 20%, the clinical application areas of the TCMFs. Our results provide (i) a further support for the notion of the epigenomes as a drug target and (ii) a new set of tools for the design of TCM prescriptions

Hydrodynamical Simulations of the Barred Spiral Galaxy NGC 1097

NGC 1097 is a nearby barred spiral galaxy believed to be interacting with the elliptical galaxy NGC 1097A located to its northwest. It hosts a Seyfert 1 nucleus surrounded by a circumnuclear starburst ring. Two straight dust lanes connected to the ring extend almost continuously out to the bar. The other ends of the dust lanes attach to two main spiral arms. To provide a physical understanding of its structural and kinematical properties, two-dimensional hydrodynamical simulations have been carried out. Numerical calculations reveal that many features of the gas morphology and kinematics can be reproduced provided that the gas flow is governed by a gravitational potential associated with a slowly rotating strong bar. By including the self-gravity of the gas disk in our calculation, we have found the starburst ring to be gravitationally unstable which is consistent with the observation in \citet{hsieh11}. Our simulations show that the gas inflow rate is 0.17 M_\sun yr$^{-1}$ into the region within the starburst ring even after its formation, leading to the coexistence of both a nuclear ring and a circumnuclear disk.Comment: 32 pages, 14 figures, 1 table, accepted for publication in the Ap

Effects of Gas on Formation and Evolution of Stellar Bars and Nuclear Rings in Disk Galaxies

We run self-consistent simulations of Milky Way-sized, isolated disk galaxies to study formation and evolution of a stellar bar as well as a nuclear ring in the presence of gas. We consider two sets of models with cold or warm disks that differ in the radial velocity dispersions, and vary the gas fraction $f_{\rm gas}$ by fixing the total disk mass. A bar forms earlier and more strongly in the cold disks with larger $f_{\rm gas}$, while gas progressively delays the bar formation in the warm disks . The bar formation enhances a central mass concentration which in turn makes the bar decay temporarily, after which it regrows in size and strength, eventually becoming stronger in models with smaller $f_{\rm gas}$. Although all bars rotate fast in the beginning, they rapidly turn to slow rotators. In our models, only the gas-free, warm disk undergoes rapid buckling instability, while other disks thicken more gradually via vertical heating. The gas driven inward by the bar potential readily forms a star-forming nuclear ring. The ring is very small when it first forms and grows in size over time. The ring star formation rate is episodic and bursty due to feedback, and well correlated with the mass inflow rate to the ring. Some expanding shells produced by star formation feedback are sheared out in the bar regions and collide with dust lanes to appear as filamentary interbar spurs. The bars and nuclear rings formed in our simulations have properties similar to those in the Milky Way