Genome-wide analysis of DNA methylation patterns in horse

Background: DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data are publically available the global DNA methylation data are yet to be known. Results: We report the first genome-wide DNA methylation characteristics data from skeletal muscle, heart, lung, and cerebrum tissues of thoroughbred (TH) and Jeju (JH) horses, an indigenous Korea breed, respectively by methyl-DNA immunoprecipitation sequencing. The analysis of the DNA methylation patterns indicated that the average methylation density was the lowest in the promoter region, while the density in the coding DNA sequence region was the highest. Among repeat elements, a relatively high density of methylation was observed in long interspersed nuclear elements compared to short interspersed nuclear elements or long terminal repeat elements. We also successfully identified differential methylated regions through a comparative analysis of corresponding tissues from TH and JH, indicating that the gene body regions showed a high methylation density. Conclusions: We provide report the first DNA methylation landscape and differentially methylated genomic regions (DMRs) of thoroughbred and Jeju horses, providing comprehensive DMRs maps of the DNA methylome. These data are invaluable resource to better understanding of epigenetics in the horse providing information for the further biological function analyses.open1

Genome-Wide Analysis of DNA Methylation before- and after Exercise in the Thoroughbred Horse with MeDIP-Seq

Athletic performance is an important criteria used for the selection of superior horses. However, little is known about exercise-related epigenetic processes in the horse. DNA methylation is a key mechanism for regulating gene expression in response to environmental changes. We carried out comparative genomic analysis of genome-wide DNA methylation profiles in the blood samples of two different thoroughbred horses before and after exercise by methylated-DNA immunoprecipitation sequencing (MeDIP-Seq). Differentially methylated regions (DMRs) in the pre- and post-exercise blood samples of superior and inferior horses were identified. Exercise altered the methylation patterns. After 30 min of exercise, 596 genes were hypomethylated and 715 genes were hypermethylated in the superior horse, whereas in the inferior horse, 868 genes were hypomethylated and 794 genes were hypermethylated. These genes were analyzed based on gene ontology (GO) annotations and the exercise-related pathway patterns in the two horses were compared. After exercise, gene regions related to cell division and adhesion were hypermethylated in the superior horse, whereas regions related to cell signaling and transport were hypermethylated in the inferior horse. Analysis of the distribution of methylated CpG islands confirmed the hypomethylation in the gene-body methylation regions after exercise. The methylation patterns of transposable elements also changed after exercise. Long interspersed nuclear elements (LINEs) showed abundance of DMRs. Collectively, our results serve as a basis to study exercise-based reprogramming of epigenetic traitsclose

Synthesis and Characterization of poly(2,5-benzimidazole) (ABPBI) Grafted CArbon Nanotubes

Single-walled carbon nanotube (SWCNT) and multi-walled carbon nanotube (MWCNT) were functionalized with 3,4-diaminobenzoic acid via "direct" Friedel-Crafts acylation reaction in PPA/P 2 O 5 to afford ortto-diamino-functionalized SWCNT (DIF-SWCNT) and MWCNT (DIF-MWCNT). The resultant DIF-SWCNT and DIF-MWCNT showed improved solubility and dispersibility. To improve interfacial adhesion between CNT and polymer matrix, the grafting of ABPBI onto the surface of DIF-SWCNT (10 wt%) or DIF-MWCNT (10 wt%) was conducted by simple in-situ polymerization of AB monomer, 3,4-diaminobenzoic acid dihydrochloride, in PPA. The resultant ABPBI-g-MWCNT and ABPBI-g-SWCNT showed improved the mechanical and electrical properties

Poly(2,5-benzoxazole)/carbon nanotube composites via in situ polymerization of 3-amino-4-hydroxybenzoic acid hydrochloride in a mild poly(phosphoric acid)

Poly(2,5-benzoxzole) (ABPBO)/carbon nanotube (CNT) composites were prepared via in situ polycondensation of "protonated" AB monomer, 3-amino-4-hydroxybenzoic acid hydrochloride, in a mildly acidic poly(phosphoric acid) medium. In situ generated hydrochloric acid during the dehydrochlorination process provided additional acidity to the reaction medium. The enhanced acidity was advantageous for both the purification and dispersion of CNTs. Specifically, it was evident for the purification of as-received single-walled carbon nanotube (SWCNT), which was contained a large portion of impurity (60-70 wt%). On the basis of the data obtained from elemental analysis (EA), thermogravimetric analysis (TGA), infrared spectroscopy (FT-IR), and X-ray diffraction (XRD) as well as scanning electron microscopy (SEM) and transmission electron microscopy (TEM), the resultant composites implicated that individual tube of multi-walled carbon nanotube (MWCNT) and bundles of SWCNT were homogeneously dispersed into the ABPBO matrix. After in situ polymerization in harsh temperature at 175 ??C and subsequent work-up processes, CNTs were remained structurally intact in a mild reaction medium. Thus, the PPA medium is indeed viable for the preparation of composite.close121

Multifunctional Poly(2,5-benzimidazole)/Carbon Nanotube Composite Films

The AB-monomer, 3,4-diaminobenzoic acid dihydrochloride, was recrystallized from an aqueous hydrochloric acid solution and used to synthesize high-molecular-weight poly(2,5-benzimidazole) (ABPBI). ABPBI/carbon nanotube (CNT) composites were prepared via in situ polymerization of the AB-monomer in the presence of single-walled carbon nanotube (SWCNT) or multiwalled carbon nanotube (MWCNT) in a mildly acidic polyphosphoric acid. The ABPBI/SWCNT and ABPBI/MWCNT composites displayed good solubility in methanesulfonic acid and thus, uniform films could be cast. The morphology of these composite films was studied by X-ray diffraction, scanning electron microscopy, transmission electron microscopy, and atomic force microscopy. The results showed that both types of CNTs were uniformly dispersed into the ABPBI matrix. Tensile properties of the composite films were significantly improved when compared with ABPBI, and their toughness (similar to 200 MPa) was close to the nature's toughest spider silk (similar to 215 MPa). The electrical conductivities of ABPBI/SWCNT and ABPBI/MWCNT composite films were 9.10 x 10(-5) and 2.53 x 10(-1) S/cm, respectively, whereas that of ABPBI film was 4.81 X 10(-6) S/cm. These values are similar to 19 and 52,700 times enhanced by the presence of SWCNT and MWCNT, respectively. Finally, without acid impregnation, the ABPBI film was nonconducting while the SWCNT- and MWCNT-based composites were proton conducting with maximum conductivities of 0.018 and 0.017 S/cm, respectively.close8

Expression of Human Endogenous Retrovirus env Genes in the Blood of Breast Cancer Patients

Human endogenous retroviruses (HERV) env proteins have been recently reported to be significantly up-regulated in certain cancers. Specifically, mRNA and protein levels of HERV-K (HML-2) are up-regulated in the blood plasma or serum of breast cancer patients. Here, we collected blood samples of 49 breast cancer patients and analyzed mRNA expressions of various HERVs env genes including HERV-R, HERV-H, HERV-K, and HERV-P by real-time PCR. The expression of env genes were significantly increased in the blood of primary breast cancer patients but were decreased in patients undergoing chemotherapy to a similar level with benign patients. When we compared the group currently undergoing chemotherapy and those patients undergoing chemotherapy simultaneously with radiotherapy, HERVs env genes were reduced more in the chemotherapy only group, suggesting that chemotherapy is more effective in reducing HERV env gene expression than is radiotherapy. Among chemotherapy groups, HERV env gene expression was the lowest in the taxotere- or taxol-treated group, suggesting that taxotere and taxol can reduce HERVs env expression. These data suggest the potential to use HERVs env genes as a diagnosis marker for primary breast cancer, and further studies are needed to identify the mechanism and physiological significance of the reduction of HERV env gene expression during chemotherapy