Sequence Information Encoded in DNA that May Influence Long-Range Chromatin Structure Correlates with Human Chromosome Functions.

Little is known about the possible function of the bulk of the human genome. We have recently shown that long-range regular oscillation in the motif non-T, A/T, G (VWG) existing at ten-nucleotide multiples influences large-scale nucleosome array formation. In this work, we have determined the locations of all 100 kb regions that are predicted to form distinctive chromatin structures throughout each human chromosome (except Y). Using these data, we found that a significantly greater fraction of 300 kb sequences lacked annotated transcripts in genomic DNA regions ≥300 kb that contained nearly continuous chromatin organizing signals than in control regions. We also found a relationship between the meiotic recombination frequency and the presence of strong VWG chromatin organizing signals. Large (≥300 kb) genomic DNA regions having low average recombination frequency are enriched in chromatin organizing signals. As additional controls, we show using chromosome 1 that the VWG motif signals are not enriched in randomly selected DNA regions having the mean size of the recombination coldspots, and that non-VWG motif sets do not generate signals that are enriched in recombination coldspots. We also show that tandemly repeated alpha satellite DNA contains strong VWG signals for the formation of distinctive nucleosome arrays, consistent with the low recombination activity of centromeres. Our correlations cannot be explained simply by variations in the GC content. Our findings suggest that a specific set of periodic DNA motifs encoded in genomic DNA, which provide signals for chromatin organization, influence human chromosome function

The northernmost record of Eriostethus rufus (Uchida, 1932) (Hymenoptera, Ichneumonidae) with an indication of new host, Trichonephila clavata (Koch, 1878) (Araneae, Araneidae) and its web manipulation

Eriostethus rufus (Uchida, 1932) is a polysphinctine ectoparasitoid of araneid spiders (Neoscona spp.) and is endemic to Japan. An individual was collected in Yamagata Prefecture (38º46' N), northern Japan, the northernmost record of the species and also the genus. Its identification was confirmed by morphology and by DNA barcoding. The cocoon was found in a large modified web, which is unique in that the web structure is shaped like an inverted triangle extending to over 50 cm with the cocoon hanging from an ill-defined part of the cocoon web without any organized structure surrounding the cocoon. The host spider of this individual appears to be Trichonephila clavata (Koch, 1878) (Araneidae, Nephilinae) based on several circumstantial evidences. The structure of the modified web suggests that the pre-existing web was partly reused, the orb web was completely removed, and sustaining threads of the barrier web would be newly moored to the substrates. This record means that E. rufus parasitises host spiders of two subfamilies, which is unusual for the group

Pathologically Proven Intraocular Infiltration With Adult T-Cell Leukemia/Lymphoma: Two New Cases With Either Vitreous Opacity or Aqueous Hypopyon and Literature Review of 16 Cases

This study reported 2 new patients and 16 historical cases with pathologically proven intraocular infiltration with adult T-cell leukemia and lymphoma (ATLL) to know the timing of intraocular infiltration in the disease course. The first case was a 67-year-old woman who developed bilateral vitreous opacity about half a year after the onset of acute type of ATLL that had been unresponsive to chemotherapy. She underwent vitrectomy combined with cataract surgery in both eyes. She had bilateral optic disc atrophy and localized retinal white infiltrates in both eyes. Cytological examination of vitreous aspirates demonstrated medium-sized cells with aberrant flower-like convoluted nuclei, positive for CD3, and thus indicative of T-cells. The second case was a 38-year-old man who was diagnosed acute type of ATLL at the presentation of acute kidney injury. About half a year after initial chemotherapy and allogeneic hematopoietic stem cell transplantation, he developed aqueous hypopyon in the right eye, concurrent with cutaneous and central nervous system relapse. Aqueous tap disclosed class V abnormal cells. The aqueous “pseudohypopyon” resolved in response to another round of chemotherapy with mogamulizumab. In review of 18 patients, intraocular infiltration with ATLL was diagnosed by vitrectomy in 9, aqueous tap in 3, chorioretinal biopsy in 3, and autopsy in 3. The intraocular infiltration developed concurrently with systemic diagnosis of ATLL in 5 patients, but developed later after chemotherapy in 13. In conclusion, intraocular infiltration with ATLL appears rare, and pathological diagnosis by vitrectomy and aqueous tap would help determine therapeutic plan in relapse after chemotherapy

Direct measurements of the nucleosome-forming preferences of periodic DNA motifs challenge established models

Several periodic motifs have been implicated in facilitating the bending of DNA around the histone core of the nucleosome. For example, di-nucleotides AA/TT/TA and GC at ∼10-bp periods, but offset by 5 bp, are found with higher-than-expected occurrences in aligned nucleosomal DNAs in vitro and in vivo. Additionally, regularly oscillating period-10 trinucleotide motifs non-T, A/T, G and their complements have been implicated in the formation of regular nucleosome arrays. The effects of these periodic motifs on nucleosome formation have not been systematically tested directly by competitive reconstitution assays. We show that, in general, none of these period-10 motifs, except TA, in certain sequence contexts, facilitates nucleosome formation. The influence of periodic TAs on nucleosome formation is appreciable; with some of the 200-bp DNAs out-competing bulk nucleosomal DNA by more than 400-fold. Only the nucleotides immediately flanking TA influence its nucleosome-forming ability. Period-10 TA, when flanked by a pair of permissive nucleotides, facilitates DNA bending through compression of the minor groove. The free energy change for nucleosome formation decreases linearly with the number of consecutive TAs, up to eight. We suggest how these data can be reconciled with previous findings

The changing use of the ovipositor in host shifts by ichneumonid ectoparasitoids of spiders (Hymenoptera, Ichneumonidae, Pimplinae)

Accurate egg placement into or onto a living host is an essential ability for many parasitoids, and changes in associated phenotypes, such as ovipositor morphology and behaviour, correlate with significant host shifts. Here, we report that in the ichneumonid group of koinobiont spider-ectoparasitoids ("polysphinctines"), several putatively ancestral taxa (clade I here), parasitic on ground-dwelling RTA-spiders (a group characterised by retrolateral tibial apophysis on male palpal tibiae), lay their eggs in a specific way. They tightly bend their metasoma above the spider's cephalothorax, touching the carapace with the dorsal side of the ovipositor apically ("dorsal-press"). The egg slips out from the middle part of the ventral side of the ovipositor and moves towards its apex with the parted lower valves acting as rails. Deposition occurs as the parasitoid draws the ovipositor backwards from under the egg. Oviposition upon the tough carapace of the cephalothorax, presumably less palatable than the abdomen, is conserved in these taxa, and presumed adaptive through avoiding physical damage to the developing parasitoid. This specific way of oviposition is reversed in the putatively derived clade of polysphinctines (clade II here) parasitic on Araneoidea spiders with aerial webs, which is already known. They bend their metasoma along the spider's abdomen, grasping the abdomen with their fore/mid legs, pressing the ventral tip of the metasoma and the lower valves of the ovipositor against the abdomen ("ventral-press"). The egg is expelled through an expansion of the lower valves, which is developed only in this clade and evident in most species, onto the softer and presumably more nutritious abdomen

Transformed diffuse large B-cell lymphoma from marginal zone lymphoma in the anterior mediastinum: A case report and review of the literature

Marginal zone lymphoma (MZL) arising from the anterior mediastinum is rare. In the majority of reported cases, the tumor was incidentally discovered, reflecting its indolent clinical features. We present a 38-year-old woman who had no medical history, and presented with a bulky anterior mediastinal tumor complicated by life-threatening compression of the vasculature and bronchi. Biopsy specimens of the neoplasm suggested transformed diffuse large B-cell lymphoma (DLBCL) from MZL. To our best knowledge, this is the first case report of anterior mediastinum MZL associated with an aggressive clinical course and life-threatening complications likely due to transformation to DLBCL

Hachisuka Mochiaki’s Overseas Achievements

Hachisuka Mochiaki (1846-1918) was the last lord of the Awa (Tokushima) domain, and he became a successful businessman and a statesman after the Meiji Restoration. He went to the UK to study when he was 25 years old, and stayed there for seven years, during which he graduated from college at the Balliol College, University of Oxford. Three years after returning to Japan, he was appointed to an envoy extraordinary and minister plenipotentiary of Japan in France (also serving as a minister in Spain, Portugal, Switzerland and Belgium) and he stayed in Paris three years. Despite ten years of foreign life, little has been known about his overseas activities. In this study, we investigated his overseas activities using digital archives of European libraries, and could find information from British Newspaper Archive, Welsh Newspaper Online, and Gallica. He began to attend public events in the UK after graduating from the Oxford University. He received in an audience by Queen Victoria and the Prince of Wales in 1877 and 1878, and attended to parties hosted by the Ministry of Foreign Affairs. He also participated in the launching ceremony of three Japanese warships Kongo, Fuso, and Hiei in 1877. He worked variously as a diplomat in Paris during 1884-1886. He signed three treaties, the Geneva Convention, the treaty on remittance by postal money order, and the International Meter Convention. Conpared with signing the Geneva Convention remaining two have not received much attention so far. In this study we found that he encouraged the Japanese government to join the International Meter Convention and negotiated with the Comité International des Poids et Mesures many times. He organized Japanese exhibition at a museum to introduce Japanese culture to Parisians, and he contributed to the academic exchange between France and Japan with the Geographical Society. And he and his wife Yoriko participated in many social events, and they held parties, concerts and theaters in Paris and Brussels. Several French newspapers mentioned elegant behavior of his wife Yoriko at those parties. And He focused on politics and business after returning to Japan, but also worked to promote exchange with foreign countries. In particular, he established the Welcome Society, which was the first organization in Japan for attracting and accommodating foreign tourists, with other of founders, and became the chairman of the organization. His abundant overseas experience and wide-ranging personal connections helped to establish this association

Climate of High-obliquity Exoterrestrial Planets with a Three-dimensional Cloud System Resolving Climate Model

Planetary climates are strongly affected by planetary orbital parameters such as obliquity, eccentricity, and precession. In exoplanetary systems, exoterrestrial planets should have various obliquities. High-obliquity planets would have extreme seasonal cycles due to the seasonal change of the distribution of the insolation. Here, we introduce the Non-hydrostatic ICosahedral Atmospheric Model (NICAM), a global cloud-resolving model, to investigate the climate of high-obliquity planets. This model can explicitly simulate a three-dimensional cloud distribution and vertical transports of water vapor. We simulated exoterrestrial climates with high resolution using the supercomputer FUGAKU. We assumed aqua-planet configurations with 1 bar of air as a background atmosphere, with four different obliquities (0°, 23.5°, 45°, and 60°). We ran two sets of simulations: (1) low resolution (∼220 km mesh as the standard resolution of a general circulation model for exoplanetary science) with parameterization for cloud formation, and (2) high resolution (∼14 km mesh) with an explicit cloud microphysics scheme. Results suggest that high-resolution simulations with an explicit treatment of cloud microphysics reveal warmer climates due to less low cloud fraction and a large amount of water vapor in the atmosphere. It implies that treatments of cloud-related processes lead to a difference between different resolutions in climatic regimes in cases with high obliquities