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

Edge-Termination and Core-Modification Effects of Hexagonal Nanosheet Graphene

[[abstract]]Optimized geometries and electronic structures of two different hexagonal grapheme nanosheets (HGNSs), with armchair (n-A-HGNS, n = 3–11) and zigzag (n-Z-HGNS, n = 1–8) edges have been calculated by using the GGA/PBE method implemented in the SIESTA package, with the DZP basis set, where n represents the number of peripheral rings. The computed HOMO-LUMO energy gap (Eg = ELUMO − EHOMO) decreases for fully H-terminated A- and Z-HGNSs with increasing n, i.e., with increasing nanosheet size and pπ-orbitals being widely delocalized over the sheet surface. The full terminations, calculated with various functional groups, including the electron-withdrawing (F-, Cl-, and CN-) and -donating (OH-, and SH-) substitutions, were addressed. Significant lowering of EHOMO and ELUMO was obtained for CN-terminated HGNS as compared to those for H-terminated ones due to the mesomeric effect. The calculated Eg value decreases with increasing n for all terminations, whereby for the SH-termination in HGNS, the termination effect becomes less significant with increasing n. Further, the calculation results for stabilities of HGNS oxides support the tendency toward the oxidative reactivity at the edge site of the sheet, which shows most pronounced C-C bond length alternation, by chemical modification. Physical properties of HGNSs with various numbers of the core-defects, which can be obtained by strong oxidation, were also investigated. Their structures can change drastically from planar to saddle-like shapes. These conformations could be used as stationary phases with controlled interaction in the separation methods such as HPLC and the other chemical analysis techniques.[[notice]]補正完畢[[incitationindex]]SCI[[booktype]]電子

Location-based Data Analysis of Visitor Structure for Recreational Area Management

This work presents a location-based data analysis framework for profiling visitors structures. In terms of recreational area management, understanding visitors’ structure and popularity is important. Traditionally, visitors monitoring with automatic counting devices has drawbacks of inaccurate visitors counting. In this work, compared to automatic counting devices, we use Wi-Fi tracking as the main method to count visitors, which provides a fairly precise picture of visitor structures. Moreover, we deliver rich analytic functions in this framework and we present the functionality with visitor data collected from Guanyinshan Visitor Center. This framework not only standardizes visitor counting process but also facilitates a profound analysis of visitor structures. Key Words: Guanyinshan Visitor Center, Wi-Fi trackin

Epidemiology of acute otitis media among young children: A multiple database study in Taiwan

Background/PurposeAcute otitis media (AOM) is a common complication of upper respiratory tract infection (URTI) among children. The purpose of this study was to evaluate the epidemiology of AOM among young children in Taiwan, including the age incidence and seasonality by combining multiple databases.MethodsTwo country-based questionnaire survey studies had been conducted to evaluate the experience of otitis media (OM) among young children: one in 2007 and the other between 2005 and 2010. The number of OM cases (5% of population younger than 7 years) in 2005 and annual visiting rates for URTI from 2005 to 2010 obtained from the National Health Insurance Research Database of Taiwan were collected and comprised the third database. The fourth database comprised ambulatory visits of children with OM to a medical center in central Taiwan between 2005 and 2010.ResultsData from a total of 1099 questionnaires were entered into Database I in 2007, and data from 9705 questionnaires between 2005 and 2010 comprised Database II. There were 86,702 children (younger than 7 years, representing 5% of the whole population for this age group) retrieved from Database III in 2007, and 5,904 cases of OM in children between 2005 and 2010 in a hospital. In Database I, 7.46% children experienced at least one episode of AOM compared with 9.21% in Database II for children aged 5 years and younger. In Database III, 13.2% children younger than 7 years had AOM in 2005. The peak season of AOM among children was from March to May (Databases III and IV).ConclusionAOM was thought to be a very common disease among children; however, this comparative analysis showed that the overall prevalence of AOM among children younger than 5 years was only 20%, much lower than in other countries. AOM was more prevalent during the spring season, and still was similarly common after age 2 years

Coalescence of RAGE in Lipid Rafts in Response to Cytolethal Distending Toxin-Induced Inflammation

The receptor for advanced glycation end products (RAGE) interacts with various molecules in the cell membrane to induce an inflammatory response. The cytolethal distending toxin (CDT) produced by Campylobacter jejuni contains three subunits: CdtA, CdtB, and CdtC. Amongst, CdtA and CdtC interact with membrane lipid rafts, by which CdtB enters the nucleus to induce pathogenesis. In this study, we first explored the relationships between RAGE, lipid rafts, and inflammation in gastrointestinal epithelial cells exposed to CDT. Our results showed that CDT activated the expression of RAGE and high mobility group box 1 (HMGB1), followed by the recruitment of RAGE into lipid rafts. In contrast, RAGE antagonist inhibited CDT-induced inflammation via the RAGE-HMGB1 axis. Disruption of lipid rafts decreased CDT-induced downstream signaling, which in turn attenuated the inflammatory response. Furthermore, in vivo studies revealed severe inflammation and upregulation of RAGE and IL-1β in the intestinal tissues of CDT-treated mice. These results demonstrate that mobilization of RAGE to lipid rafts plays a crucial role in CDT-induced inflammation

Cytolethal Distending Toxin Enhances Radiosensitivity in Prostate Cancer Cells by Regulating Autophagy

Cytolethal distending toxin (CDT) produced by Campylobacter jejuni contains three subunits: CdtA, CdtB, and CdtC. Among these three toxin subunits, CdtB is the toxic moiety of CDT with DNase I activity, resulting in DNA double-strand breaks (DSB) and, consequently, cell cycle arrest at the G2/M stage and apoptosis. Radiation therapy is an effective modality for the treatment of localized prostate cancer (PCa). However, patients often develop radioresistance. Owing to its particular biochemical properties, we previously employed CdtB as a therapeutic agent for sensitizing radioresistant PCa cells to ionizing radiation (IR). In this study, we further demonstrated that CDT suppresses the IR-induced autophagy pathway in PCa cells by attenuating c-Myc expression and therefore sensitizes PCa cells to radiation. We further showed that CDT prevents the formation of autophagosomes via decreased high-mobility group box 1 (HMGB1) expression and the inhibition of acidic vesicular organelle (AVO) formation, which are associated with enhanced radiosensitivity in PCa cells. The results of this study reveal the detailed mechanism of CDT for the treatment of radioresistant PCa

Prescriptions of Traditional Chinese Medicine Are Specific to Cancer Types and Adjustable to Temperature Changes

Targeted cancer therapies, with specific molecular targets, ameliorate the side effect issue of radiation and chemotherapy and also point to the development of personalized medicine. Combination of drugs targeting multiple pathways of carcinogenesis is potentially more fruitful. Traditional Chinese medicine (TCM) has been tailoring herbal mixtures for individualized healthcare for two thousand years. A systematic study of the patterns of TCM formulas and herbs prescribed to cancers is valuable. We analysed a total of 187,230 TCM prescriptions to 30 types of cancer in Taiwan in 2007, a year's worth of collection from the National Health Insurance reimbursement database (Taiwan). We found that a TCM cancer prescription consists on average of two formulas and four herbs. We show that the percentage weights of TCM formulas and herbs in a TCM prescription follow Zipf's law with an exponent around 0.6. TCM prescriptions to benign neoplasms have a larger Zipf's exponent than those to malignant cancers. Furthermore, we show that TCM prescriptions, via weighted combination of formulas and herbs, are specific to not only the malignancy of neoplasms but also the sites of origins of malignant cancers. From the effects of formulas and natures of herbs that were heavily prescribed to cancers, that cancers are a ‘warm and stagnant’ syndrome in TCM can be proposed, suggesting anti-inflammatory regimens for better prevention and treatment of cancers. We show that TCM incorporated relevant formulas to the prescriptions to cancer patients with a secondary morbidity. We compared TCM prescriptions made in different seasons and identified temperatures as the environmental factor that correlates with changes in TCM prescriptions in Taiwan. Lung cancer patients were among the patients whose prescriptions were adjusted when temperatures drop. The findings of our study provide insight to TCM cancer treatment, helping dialogue between modern western medicine and TCM for better cancer care

Variations in TCM prescriptions between seasons.

<p>(A) A cancer prescription is represented by a point in the three dimensional space spanned by the first three PCs, that together account for 55% of the data variation as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031648#pone.0031648.s007" target="_blank">Figure S7</a>. The points come from prescriptions made in spring. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031648#pone.0031648.s008" target="_blank">Figures S8</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031648#pone.0031648.s009" target="_blank">S9</a>, and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031648#pone.0031648.s010" target="_blank">S10</a> show the prescriptions made in summer, autumn and winter, in the space defined by the same three PCs. (B) Differences between autumn- and winter-prescriptions are plotted against cancers. Cancer color codes follow those of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031648#pone-0031648-g002" target="_blank">Figure 2</a>.</p

Heatmap and hierarchical clustering of cancers and TCM categories, natures, and flavors.

<p>The effect of a TCM formula is classified into one of the 21 TCM categories. The average percentage weight of a category in the prescriptions to each cancer is calculated. In (A) shows the heatmap of the cancer by category weights. Similarly, an herb is designated its TCM nature and TCM flavor. The heatmaps of the cancer by nature and cancer by flavor weight matrices are shown in (B) and (C).</p