Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells

The huge amount of data acquired by high-throughput sequencing requires data reduction for effective analysis. Here we give a clustering algorithm for genome-wide open chromatin data using a new data reduction method. This method regards the genome as a string of $1$s and $0$s based on a set of peaks and calculates the Hamming distances between the strings. This algorithm with the systematically optimized set of peaks enables us to quantitatively evaluate differences between samples of hematopoietic cells and classify cell types, potentially leading to a better understanding of leukemia pathogenesis.Comment: 24 pages, 17 figure

A Case of a Giant Congenital Melanocytic Nevus Treated by Curettage with the Application of Cultured Epidermal Autografts before 6 Months of Age

Curettage is common in the treatment of a giant congenital melanocytic nevus (GCMN) in infants and should generally be performed before 6 months of age. Post-curettage retarded epithelialization often interferes with the ability to perform multiple operations within a short interval, and thus, it is difficult to treat large lesions in the neonatal period. We herein report a case of a GCMN comprising 20% of the total body surface area, which required multi-stage curettage, in which a cultured epithelial autograft was used to promote epithelialization of the post-curettage wound. The patient was a 1-month-old boy with a GCMN in his head, neck, chest, back, buttock, left upper arm, and a few satellite lesions. A four-stage operation was performed between 3 and 6 months of age; the cultured epithelial autograft took well after each operation, and complete epithelialization was observed at postoperative days 20, 23, 27, and 12, respectively. Seven months after the last surgery, hypertrophic scar formation was only observed in a small area of the left upper arm without axillary contracture. The color of the treated area improved, except for slight partial re-pigmentation. A skin biopsy was obtained from the re-pigmented area. The results demonstrated that nevus cells remained in the basal layer of the epidermis, hair follicles, and deep layer of the remaining dermis, suggesting that the recurrent nevus cells in the regenerated epidermis migrated from hair follicles. We conclude that the combination of curettage and the application of a cultured epithelial autograft is a promising option for GCMN treatment

Palmitate induces reactive oxygen species production and β-cell dysfunction by activating nicotinamide adenine dinucleotide phosphate oxidase through Src signaling.

[Aims/Introduction]Chronic hyperlipidemia impairs pancreatic β-cell function, referred to as lipotoxicity. We have reported an important role of endogenous reactive oxygen species (ROS) overproduction by activation of Src, a non-receptor tyrosine kinase, in impaired glucose-induced insulin secretion (GIIS) from diabetic rat islets. In the present study, we investigated the role of ROS production by Src signaling in palmitate-induced dysfunction of β-cells. [Materials and Methods]After rat insulinoma INS-1D cells were exposed to 0.6 mmol/L palmitate for 24 h (palmitate exposure); GIIS, ROS production and nicotinamide adenine dinucleotide phosphate oxidase (NOX) activity were examined with or without exposure to10 μmol/L 4-amino-5-(4-chlorophenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine (PP2), a Src inhibitior, for 30 or 60 min. [Results]Exposure to PP2 recovered impaired GIIS and decreased ROS overproduction as a result of palmitate exposure. Palmitate exposure increased activity of NOX and protein levels of NOX2, a pathological ROS source in β-cells. Palmitate exposure increased the protein level of p47phox, a regulatory protein of NOX2, in membrane fraction compared with control, which was reduced by PP2. Transfection of small interfering ribonucleic acid of p47phox suppressed the augmented p47phox protein level in membrane fraction, decreased augmented ROS production and increased impaired GΙIS by palmitate exposure. In addition, exposure to PP2 ameliorated impaired GIIS and decreased ROS production in isolated islets of KK-Ay mice, an obese diabetic model with hyperlipidemia. [Conclusions]Activation of NOX through Src signaling plays an important role in ROS overproduction and impaired GΙIS caused by chronic exposure to palmitate, suggesting a lipotoxic mechanism of β-cell dysfunction of obese mice

Novel missense mutation in the FH gene in familial renal cell cancer patients lacking cutaneous leiomyomas

BACKGROUND: Hereditary leiomyomatosis and renal cell cancer (HLRCC) is a rare tumor predisposition syndrome characterized by cutaneous and uterine leiomyomas and papillary type 2 renal cell cancer. Germline mutation of the fumarate hydratase (FH) gene is known to be associated with HLRCC. CASE PRESENTATION: We describe a 64-year-old father and his 39-year-old son with HLRCC who developed papillary type 2 RCCs lacking cutaneous leiomyomas at any site. A common missense mutation in the FH gene, (c.1021G > A, p.D341N) in exon 7, was detected in the 2 cases. Functional prediction with the bioinformatics programs, SIFT and Polyphen-2, reported “damaging (SIFT score 0.00)” and “probably damaging (PSIC score 1.621)” values, respectively. In 162 healthy individuals, there were no cases of a G transition to any base. Finally, (c.1021G > A) in exon 7, was identified as a point mutation. CONCLUSION: We report a family with HLRCC in which a novel missense mutation was detected. A familial papillary type 2 renal cancer should be considered HLRCC unless typical cutaneous leiomyomas do not occur

First Results of Axion Dark Matter Search with DANCE

Axions are one of the well-motivated candidates for dark matter, originally proposed to solve the strong CP problem in particle physics. Dark matter Axion search with riNg Cavity Experiment (DANCE) is a new experimental project to broadly search for axion dark matter in the mass range of $10^{-17}~\mathrm{eV} < m_a < 10^{-11}~\mathrm{eV}$. We aim to detect the rotational oscillation of linearly polarized light caused by the axion-photon coupling with a bow-tie cavity. The first results of the prototype experiment, DANCE Act-1, are reported from a 24-hour observation. We found no evidence for axions and set 95% confidence level upper limit on the axion-photon coupling $g_{a \gamma} \lesssim 8 \times 10^{-4}~\mathrm{GeV^{-1}}$ in $10^{-14}~\mathrm{eV} < m_a < 10^{-13}~\mathrm{eV}$. Although the bound did not exceed the current best limits, this optical cavity experiment is the first demonstration of polarization-based axion dark matter search without any external magnetic field.Comment: 9 pages, 8 figure

Spatio-Temporal Expression Profile of Stem Cell-Associated Gene LGR5 in the Intestine during Thyroid Hormone-Dependent Metamorphosis in Xenopus laevis

The intestinal epithelium undergoes constant self-renewal throughout adult life across vertebrates. This is accomplished through the proliferation and subsequent differentiation of the adult stem cells. This self-renewal system is established in the so-called postembryonic developmental period in mammals when endogenous thyroid hormone (T3) levels are high.The T3-dependent metamorphosis in anurans like Xenopus laevis resembles the mammalian postembryonic development and offers a unique opportunity to study how the adult stem cells are developed. The tadpole intestine is predominantly a monolayer of larval epithelial cells. During metamorphosis, the larval epithelial cells undergo apoptosis and, concurrently, adult epithelial stem/progenitor cells develop de novo, rapidly proliferate, and then differentiate to establish a trough-crest axis of the epithelial fold, resembling the crypt-villus axis in the adult mammalian intestine. The leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5) is a well-established stem cell marker in the adult mouse intestinal crypt. Here we have cloned and analyzed the spatiotemporal expression profile of LGR5 gene during frog metamorphosis. We show that the two duplicated LGR5 genes in Xenopus laevis and the LGR5 gene in Xenopus tropicalis are highly homologous to the LGR5 in other vertebrates. The expression of LGR5 is induced in the limb, tail, and intestine by T3 during metamorphosis. More importantly, LGR5 mRNA is localized to the developing adult epithelial stem cells of the intestine.These results suggest that LGR5-expressing cells are the stem/progenitor cells of the adult intestine and that LGR5 plays a role in the development and/or maintenance of the adult intestinal stem cells during postembryonic development in vertebrates

Aqueous/Aqueous Micro Phase Separation: Construction of an Artificial Model of Cellular Assembly

To artificially construct a three-dimensional cell assembly, we investigated the availability of long-duration microdroplets that emerged near a critical point in an aqueous two-phase system (ATPS) with the hydrophilic binary polymers, polyethylene glycol (PEG), and dextran (DEX), as host containers. We found that erythrocytes (horse red blood cells; RBCs) and NAMRU mouse mammary gland epithelial cells (NMuMG cells) were completely and spontaneously entrapped inside DEX-rich microdroplets. RBCs and NMuMG cells were located in the interior and at the periphery of the droplets at PEG/DEX = 5%:5%. In contrast, the cells exhibited opposite localizations at PEG/DEX = 10%:5%, where, interestingly, NMuMG cells apparently assembled to achieve cell adhesion. We simply interpreted such specific localizations by considering the alternative responses of these cells to the properties of the PEG/DEX interfaces with different gradients in polymer concentrations