A Tentative Review of the Studies on the Environmental History of Ancient China

The existing research findings of our environmental history fail to attach due importance to the environmental history of ancient China. The studies of China’s environmental history should extend the time scope further to more ancient times and raise interdisciplinary research awareness. Such studies can help us trace our sources of culture and ecology, and better understand the current world and humanity itself. Studies on the environmental history of ancient China also need to be equipped with corresponding research concepts, orientation and approaches

DNA methylation and regulatory elements during chicken germline stem cell differentiation

Funding for Open Access provided by the UMD Libraries' Open Access Publishing Fund.The production of germ cells in vitro would open important new avenues for stem biology and human medicine, but the mechanisms of germ cell differentiation are not well understood. The chicken, as a great model for embryology and development, was used in this study to help us explore its regulatory mechanisms. In this study, we reported a comprehensive genome-wide DNA methylation landscape in chicken germ cells, and transcriptomic dynamics was also presented. By uncovering DNA methylation patterns on individual genes, some genes accurately modulated by DNA methylation were found to be associated with cancers and virus infection, e.g., AKT1 and CTNNB1. Chicken-unique markers were also discovered for identifying male germ cells. Importantly, integrated epigenetic mechanisms were explored during male germ cell differentiation, which provides deep insight into the epigenetic processes associated with male germ cell differentiation and possibly improves treatment options to male infertility in animals and humans

Elucidation of the hierarchical structure of natural eumelanins

Eumelanin is one of the most ubiquitous pigments in living organisms and plays an important role in coloration and UV protection. Because eumelanin is highly cross-linked and insoluble in solvents, the chemical structure is still not completely known. In this study, we used atomic force microscopy, X-ray photoelectron spectroscopy and solid-state nuclear magnetic resonance (NMR) to compare intact eumelanosomes (pigment granules mostly made of eumelanin) from four phylogentically distant species: cuttlefish (Sepia officinalis) inks, black fish crow (Corvus ossifragus) feathers, iridescent wild turkey (Melleagris gallopavo) feathers and black human hair. We found that eumelanosomes from all four species are composed of subunit nanoparticles with a length of 10-60 nm, consistent with earlier observations in eumelanosomes from the sepia ink and human hair. The solid-state NMR results indicate the presence of quinone methide tautomers in all four eumelanins. We also found clear differences in the UV absorbance, the ratio of 5,6-dihydroxyindole-2-carboxylic acid/5,6-dihydroxyindole and protonated aryl carbon ratios in sepia eumelanin relative to the other three. This comparison of natural eumelanin across a phylogenetically broad group of organisms provides insights into the change in the eumelanin structure over the evolutionary history and enables the production of synthetic eumelanin with properties that are similar to natural eumelanin

DNMT gene expression and methylome in Marek’s disease resistant and susceptible chickens prior to and following infection by MDV

Marek’s disease (MD) is characterized as a T cell lymphoma induced by a cell-associated α-herpesvirus, Marek’s disease virus type 1 (MDV1). As with many viral infectious diseases, DNA methylation variations were observed in the progression of MD; these variations are thought to play an important role in host-virus interactions. We observed that DNA methyltransferase 3a (DNMT3a) and 3b (DNMT3b) were differentially expressed in chicken MD-resistant line 6(3) and MD-susceptible line 7(2) at 21 d after MDV infection. To better understand the role of methylation variation induced by MDV infection in both chicken lines, we mapped the genome-wide DNA methylation profiles in each line using Methyl-MAPS (methylation mapping analysis by paired-end sequencing). Collectively, the data sets collected in this study provide a more comprehensive picture of the chicken methylome. Overall, methylation levels were reduced in chickens from the resistant line 6(3) after MDV infection. We identified 11,512 infection-induced differential methylation regions (iDMRs). The number of iDMRs was larger in line 7(2) than in line 6(3), and most of iDMRs found in line 6(3) were overlapped with the iDMRs found in line 7(2). We further showed that in vitro methylation levels were associated with MDV replication, and found that MDV propagation in the infected cells was restricted by pharmacological inhibition of DNA methylation. Our results suggest that DNA methylation in the host may be associated with disease resistance or susceptibility. The methylation variations induced by viral infection may consequentially change the host transcriptome and result in diverse disease outcomes

Functional Genomic Analysis of Variation on Beef Tenderness Induced by Acute Stress in Angus Cattle

Beef is one of the leading sources of protein, B vitamins, iron, and zinc in human food. Beef palatability is based on three general criteria: tenderness, juiciness, and flavor, of which tenderness is thought to be the most important factor. In this study, we found that beef tenderness, measured by the Warner-Bratzler shear force (WBSF), was dramatically increased by acute stress. Microarray analysis and qPCR identified a variety of genes that were differentially expressed. Pathway analysis showed that these genes were involved in immune response and regulation of metabolism process as activators or repressors. Further analysis identified that these changes may be related with CpG methylation of several genes. Therefore, the results from this study provide an enhanced understanding of the mechanisms that genetic and epigenetic regulations control meat quality and beef tenderness

miRNA-dysregulation associated with tenderness variation induced by acute stress in Angus cattle

miRNAs are a class of small, single-stranded, non-coding RNAs that perform post-transcriptional repression of target genes by binding to 3’ untranslated regions. Research has found that miRNAs involved in the regulation of many metabolic processes. Here we uncovered that the beef quality of Angus cattle sharply diversified after acute stress. By performing miRNA microarray analysis, 13 miRNAs were significantly differentially expressed in stressed group compared to control group. Using a bioinformatics method, 135 protein-coding genes were predicted as the targets of significant differentially expressed miRNAs. Gene Ontology (GO) term and Ingenuity Pathway Analysis (IPA) mined that these target genes involved in some important pathways, which may have impact on meat quality and beef tenderness.https://doi.org/10.1186/2049-1891-3-1

Histone modifications induced by MDV infection at early cytolytic and latency phases

Marek’s disease (MD) is a highly contagious, lymphomatous disease of chickens induced by a herpesvirus, Marek’s disease virus (MDV) that is the cause of major annual losses to the poultry industry. MD pathogenesis involves multiple stages including an early cytolytic phase and latency, and transitions between these stages are governed by several host and environmental factors. The success of vaccination strategies has led to the increased virulence of MDV and selective breeding of naturally resistant chickens is seen as a viable alternative. While multiple gene expression studies have been performed in resistant and susceptible populations, little is known about the epigenetic effects of infection. In this study, we investigated temporal chromatin signatures induced by MDV by analyzing early cytolytic and latent phases of infection in the bursa of Fabricius of MD-resistant and –susceptible birds. Major global variations in chromatin marks were observed at different stages of MD in the two lines. Differential H3K27me3 marks were associated with immune-related pathways, such as MAP kinase signaling, focal adhesion and neuroactive ligand receptor interaction, and suggested varying degrees of silencing in response to infection. Immune-related microRNAs, e.g. gga-miR-155 and gga-miR-10b, bore chromatin signatures, which suggested their contribution to MD-susceptibility. Finally, several members of the focal adhesion pathway, e.g. THBS4 and ITGA1, showed marked concordance between gene expression and chromatin marks indicating putative epigenetic regulation in response to MDV infection. Our comprehensive analysis of chromatin signatures, therefore, revealed further clues about the epigenetic effects of MDV infection although further studies are necessary to elucidate the functional implications of the observed variations in histone modifications.https://doi.org/10.1186/s12864-015-1492-

Local microstructure evolution at shear bands in metallic glasses with nanoscale phase separation.

At room temperature, plastic flow of metallic glasses (MGs) is sharply localized in shear bands, which are a key feature of the plastic deformation in MGs. Despite their clear importance and decades of study, the conditions for formation of shear bands, their structural evolution and multiplication mechanism are still under debate. In this work, we investigate the local conditions at shear bands in new phase-separated bulk MGs containing glassy nanospheres and exhibiting exceptional plasticity under compression. It is found that the glassy nanospheres within the shear band dissolve through mechanical mixing driven by the sharp strain localization there, while those nearby in the matrix coarsen by Ostwald ripening due to the increased atomic mobility. The experimental evidence demonstrates that there exists an affected zone around the shear band. This zone may arise from low-strain plastic deformation in the matrix between the bands. These results suggest that measured property changes originate not only from the shear bands themselves, but also from the affected zones in the adjacent matrix. This work sheds light on direct visualization of deformation-related effects, in particular increased atomic mobility, in the region around shear bands.Financial support for this research is gratefully acknowledged: for J.H. from the Alexander von Humboldt Foundation, the National Natural Science Foundation of China (Grant No. 51374194 and 51574216) and the Natural Science Foundation of Liaoning Province of China (Grant No.2015020172); for J.E. and I.K. from the German Federal Ministry of Education and Science (Project No 05K12OD1) and the German Science Foundation under the Leibniz Program (Grant EC 111/26-1); for D.H.K. from the Global Research Laboratory Program of the Korean Ministry of Education, Science and Technology; and for A.L.G. from the Engineering and Physical Sciences Research Council (UK) and the World Premier International Research Center Initiative (WPI), MEXT, Japan.This is the author accepted manuscript. It is currently under an indefinite embargo pending publication by Nature Publishing Group

Genomic Analyses Reveal Mutational Signatures and Frequently Altered Genes in Esophageal Squamous Cell Carcinoma

Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers worldwide and the fourth most lethal cancer in China. However, although genomic studies have identified some mutations associated with ESCC, we know little of the mutational processes responsible. To identify genome-wide mutational signatures, we performed either whole-genome sequencing (WGS) or whole-exome sequencing (WES) on 104 ESCC individuals and combined our data with those of 88 previously reported samples. An APOBEC-mediated mutational signature in 47% of 192 tumors suggests that APOBEC-catalyzed deamination provides a source of DNA damage in ESCC. Moreover, PIK3CA hotspot mutations (c.1624G>A [p.Glu542Lys] and c.1633G>A [p.Glu545Lys]) were enriched in APOBEC-signature tumors, and no smoking-associated signature was observed in ESCC. In the samples analyzed by WGS, we identified focal (<100 kb) amplifications of CBX4 and CBX8. In our combined cohort, we identified frequent inactivating mutations in AJUBA, ZNF750, and PTCH1 and the chromatin-remodeling genes CREBBP and BAP1, in addition to known mutations. Functional analyses suggest roles for several genes (CBX4, CBX8, AJUBA, and ZNF750) in ESCC. Notably, high activity of hedgehog signaling and the PI3K pathway in approximately 60% of 104 ESCC tumors indicates that therapies targeting these pathways might be particularly promising strategies for ESCC. Collectively, our data provide comprehensive insights into the mutational signatures of ESCC and identify markers for early diagnosis and potential therapeutic targets