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The hierarchical packaging of eukaryotic chromatin plays a central role in transcriptional regulation and other DNA-related biological processes. Here, we report the 11-angstrom-resolution cryogenic electron microscopy (cryo-EM) structures of 30-nanometer chromatin fibers reconstituted in the presence of linker histone H1 and with different nucleosome(More)
We describe the use of a unique DNA-modification-dependent restriction endonuclease AbaSI coupled with sequencing (Aba-seq) to map high-resolution hydroxymethylome of mouse E14 embryonic stem cells. The specificity of AbaSI enables sensitive detection of 5-hydroxymethylcytosine (5hmC) at low-occupancy regions. Bioinformatic analysis suggests 5hmCs in genic(More)
Fifteen single nucleotide polymorphism (SNP) markers were validated and characterized in the sea cucumber (Apostichopus japonicus). By assembling 5728 expressed sequence tags (EST), 4197 putative SNP were obtained from 330 contigs. Among 46 randomly selected putative SNPs, 15 were polymorphic. The minor allele frequency ranged from 0.209 to 0.500, and the(More)
Quinohemoprotein amine dehydrogenase (QHNDH) possesses a cysteine tryptophylquinone (CTQ) prosthetic group that catalyzes the oxidative deamination of primary amines. In addition to CTQ, two heme c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor. Steady-state kinetic(More)
Chronic kidney disease (CKD) is an intractable disease in which inflammation and oxidative stress are important. In the present study, the effect of simvastatin on inflammation and oxidative stress induced by angiotensin II (Ang II) in human mesangial cells (HMCs) and its corresponding mechanism was examined. In the in vitro experiment, HMCs were pretreated(More)
BACKGROUND/AIMS Age-related macular degeneration (AMD) appears to be a disease with increasing incidence in Western countries and may develop into acquired blindness. Choroidal neovascularization (CNV) is the most frequent cause for AMD, and is commonly induced by regional inflammation. Past studies have highlighted vascular endothelial growth factor A(More)
The complement system has been discovered in invertebrates and vertebrates, and plays a crucial role in the innate defense against common pathogens. As a central component in the complement system, complement component 3 (C3) is an intermediary between innate and adaptive immune system. In this study, a new isoform of C3 in the sea cucumber Apostichopus(More)
The echinoderm immunity system has been extensively investigated in adults in several classes such as echinoid and holothuroidea. However, the defense mechanism in embryos and larvae remains largely unexplored. To profile the immune-related genes expression in embryos and larvae and to monitor the stimulation of the innate immune response by(More)
Quinohemoprotein amine dehydrogenase (QHNDH) of Paracoccus denitrificans contains a peptidyl quinone cofactor, cysteine tryptophylquinone, as well as intrapeptidyl thioether cross-links between Cys and Asp/Glu residues within the smallestgamma-subunit of the alphabetagamma heterotrimeric protein. A putative [Fe-S]-cluster-binding protein (ORF2 protein)(More)
Methylamine dehydrogenase (MADH) is a tryptophan tryptophylquinone-dependent enzyme that catalyzes the oxidative deamination of primary amines. Native MADH exhibits a strong preference for methylamine over longer carbon chain amines. Residue alphaPhe(55) controls this substrate specificity. When alphaPhe(55) is replaced with Ala, this preference is reversed(More)