Crystallization and crystal-packing studies of \u3ci\u3eChlorella\u3c/i\u3e virus deoxyuridine triphosphatase

The 141-amino-acid deoxyuridine triphosphatase (dUTPase) from the algal Chlorella virus IL-3A and its Glu81Ser/Thr84Arg-mutant derivative Mu-22 were crystallized using the hanging-drop vapor-diffusion method at 298 K with polyethylene glycol as the precipitant. An apo IL-3A dUTPase with an aminoterminal T7 epitope tag and a carboxy-terminal histidine tag yielded cubic P213 crystals with unit-cell parameter a = 106.65 A . In the presence of dUDP, the enzyme produced thin stacked orthorhombic P222 crystals with unit-cell parameters a = 81.0, b = 96.2, c = 132.8 A. T7-histidine-tagged Mu-22 dUTPase formed thin stacked rectangular crystals. Amino-terminal histidine-tagged dUTPases did not crystallize but formed aggregates. Glycyl-seryl-tagged dUTPases yielded cubic P213 IL-3A crystals with unit-cell parameter a = 105.68 A and hexagonal P63 Mu-22 crystals with unit-cell parameters a = 132.07, c = 53.45 A , ƴ = 120°. Owing to the Thr84Arg mutation, Mu-22 dUTPase had different monomer-to-monomer interactions to those of IL-3A dUTPase

Crystallization and crystal-packing studies of \u3ci\u3eChlorella\u3c/i\u3e virus deoxyuridine triphosphatase

The 141-amino-acid deoxyuridine triphosphatase (dUTPase) from the algal Chlorella virus IL-3A and its Glu81Ser/Thr84Arg-mutant derivative Mu-22 were crystallized using the hanging-drop vapor-diffusion method at 298 K with polyethylene glycol as the precipitant. An apo IL-3A dUTPase with an aminoterminal T7 epitope tag and a carboxy-terminal histidine tag yielded cubic P213 crystals with unit-cell parameter a = 106.65 A . In the presence of dUDP, the enzyme produced thin stacked orthorhombic P222 crystals with unit-cell parameters a = 81.0, b = 96.2, c = 132.8 A. T7-histidine-tagged Mu-22 dUTPase formed thin stacked rectangular crystals. Amino-terminal histidine-tagged dUTPases did not crystallize but formed aggregates. Glycyl-seryl-tagged dUTPases yielded cubic P213 IL-3A crystals with unit-cell parameter a = 105.68 A and hexagonal P63 Mu-22 crystals with unit-cell parameters a = 132.07, c = 53.45 A , ƴ = 120°. Owing to the Thr84Arg mutation, Mu-22 dUTPase had different monomer-to-monomer interactions to those of IL-3A dUTPase

Searches for New Milky Way Satellites from the First Two Years of Data of the Subaru/Hyper Suprime-Cam Survey: Discovery of Cetus~III

We present the results from a search for new Milky Way (MW) satellites from the first two years of data from the Hyper Suprime-Cam (HSC) Subaru Strategic Program (SSP) $\sim 300$~deg$^2$ and report the discovery of a highly compelling ultra-faint dwarf galaxy candidate in Cetus. This is the second ultra-faint dwarf we have discovered after Virgo~I reported in our previous paper. This satellite, Cetus~III, has been identified as a statistically significant (10.7$\sigma$) spatial overdensity of star-like objects, which are selected from a relevant isochrone filter designed for a metal-poor and old stellar population. This stellar system is located at a heliocentric distance of 251$^{+24}_{-11}$~kpc with a most likely absolute magnitude of $M_V = -2.4 \pm 0.6$~mag estimated from a Monte Carlo analysis. Cetus~III is extended with a half-light radius of $r_h = 90^{+42}_{-17}$~pc, suggesting that this is a faint dwarf satellite in the MW located beyond the detection limit of the Sloan Digital Sky Survey. Further spectroscopic studies are needed to assess the nature of this stellar system. We also revisit and update the parameters for Virgo~I finding $M_V = -0.33^{+0.75}_{-0.87}$~mag and $r_h = 47^{+19}_{-13}$~pc. Using simulations of $\Lambda$-dominated cold dark matter models, we predict that we should find one or two new MW satellites from $\sim 300$~deg$^2$ HSC-SSP data, in rough agreement with the discovery rate so far. The further survey and completion of HSC-SSP over $\sim 1,400$~deg$^2$ will provide robust insights into the missing satellites problem.Comment: 12 pages, 12 figures, accepted for publication in PASJ special issu

X-ray structures of Na-GST-1 and Na-GST-2 two glutathione s-transferase from the human hookworm Necator americanus

<p>Abstract</p> <p>Background</p> <p>Human hookworm infection is a major cause of anemia and malnutrition of adults and children in the developing world. As part of on-going efforts to control hookworm infection, The Human Hookworm Vaccine Initiative has identified candidate vaccine antigens from the infective L3 larval stages and adult stages of the parasite. Adult stage antigens include the cytosolic glutathione-S-transferases (GSTs). Nematode GSTs facilitate the inactivation and degradation of a variety of electrophilic substrates (drugs) via the nucleophilic addition of reduced glutathione. Parasite GSTs also play significant roles in multi-drug resistance and the modulation of host-immune defense mechanisms.</p> <p>Results</p> <p>The crystal structures of <it>Na</it>-GST-1 and <it>Na</it>-GST-2, two major GSTs from <it>Necator americanus </it>the main human hookworm parasite, have been solved at the resolution limits of 2.4 Å and 1.9 Å respectively. The structure of <it>Na</it>-GST-1 was refined to R-factor 18.9% (R-free 28.3%) while that of <it>Na</it>-GST-2 was refined to R-factor 17.1% (R-free 21.7%). Glutathione usurped during the fermentation process in bound in the glutathione binding site (G-site) of each monomer of <it>Na</it>-GST-2. <it>Na</it>-GST-1 is uncomplexed and its G-site is abrogated by Gln 50. These first structures of human hookworm parasite GSTs could aid the design of novel hookworm drugs.</p> <p>Conclusion</p> <p>The 3-dimensional structures of <it>Na</it>-GST-1 and <it>Na</it>-GST-2 show two views of human hookworm GSTs. While the GST-complex structure of <it>Na</it>-GST-2 reveals a typical GST G-site that of <it>Na</it>-GST-1 suggests that there is some conformational flexibility required in order to bind the substrate GST. In addition, the overall binding cavities for both are larger, more open, as well as more accessible to diverse ligands than those of GSTs from organisms that have other major detoxifying mechanisms. The results from this study could aid in the design of novel drugs and vaccine antigens.</p

Bo\"otes IV: A New Milky Way Satellite Discovered in the Subaru Hyper Suprime-Cam Survey and Implications for the Missing Satellite Problem

We report on the discovery of a new Milky Way (MW) satellite in Bo\"otes based on data from the on-going Hyper Suprime-Cam (HSC) Subaru Strategic Program (SSP). This satellite, named Bo\"otes IV, is the third ultra-faint dwarf that we have discovered in the HSC-SSP. We have identified a statistically significant (32.3$\sigma$) overdensity of stars having characteristics of a metal-poor, old stellar population. The distance to this stellar system is $D_{\odot}=209^{+20}_{-18}$ kpc with a $V$-band absolute magnitude of $M_V=-4.53^{+0.23}_{-0.21}$ mag. Bo\"otes IV has a half-light radius of $r_h=462^{+98}_{-84}$ pc and an ellipticity of $0.64^{+0.05}_{-0.05}$, which clearly suggests that this is a dwarf satellite galaxy. We also found another overdensity that appears to be a faint globular cluster with $M_V=-0.20^{+0.59}_{-0.83}$ mag and $r_h=5.9^{+1.5}_{-1.3}$ pc located at $D_{\odot}=46^{+4}_{-4}$ kpc. Adopting the recent prediction for the total population of satellites in a MW-sized halo by Newton et al. (2018), which combined the characteristics of the observed satellites by SDSS and DES with the subhalos obtained in $\Lambda$CDM models, we estimate that there should be about two MW satellites at $M_V\le0$ in the $\sim676$ deg$^2$ covered by HSC-SSP, whereas that area includes six satellites. Thus, the observed number of satellites is larger than the theoretical prediction. On the face of it, we have a problem of too many satellites, instead of the well-known missing satellites problem whereby the $\Lambda$CDM theory overpredicts the number of satellites in a MW-sized halo. This may imply that the models need more refinements for the assignment of subhalos to satellites such as considering those found by the current deeper survey. [abridged]Comment: 13 pages, 11 figures, 2 tables, accepted for publication in PAS

Modeling Retinal Degeneration Using Patient-Specific Induced Pluripotent Stem Cells

Retinitis pigmentosa (RP) is the most common inherited human eye disease resulting in night blindness and visual defects. It is well known that the disease is caused by rod photoreceptor degeneration; however, it remains incurable, due to the unavailability of disease-specific human photoreceptor cells for use in mechanistic studies and drug screening. We obtained fibroblast cells from five RP patients with distinct mutations in the RP1, RP9, PRPH2 or RHO gene, and generated patient-specific induced pluripotent stem (iPS) cells by ectopic expression of four key reprogramming factors. We differentiated the iPS cells into rod photoreceptor cells, which had been lost in the patients, and found that they exhibited suitable immunocytochemical features and electrophysiological properties. Interestingly, the number of the patient-derived rod cells with distinct mutations decreased in vitro; cells derived from patients with a specific mutation expressed markers for oxidation or endoplasmic reticulum stress, and exhibited different responses to vitamin E than had been observed in clinical trials. Overall, patient-derived rod cells recapitulated the disease phenotype and expressed markers of cellular stresses. Our results demonstrate that the use of patient-derived iPS cells will help to elucidate the pathogenic mechanisms caused by genetic mutations in RP

Thin film deposition of metal oxides in resistance switching devices: electrode material dependence of resistance switching in manganite films.

The electric-pulse-induced resistance switching in layered structures composed of polycrystalline Pr1-xCaxMnO3 (PCMO) sandwiched between Pt bottom electrode and top electrodes of various metals (metal/PCMO/Pt) was studied by direct current current-voltage (I-V) measurements and alternating current impedance spectroscopy. The I-V characteristics showed nonlinear, asymmetric, and hysteretic behavior in PCMO-based devices with top electrode of Al, Ni, and Ag, while no hysteretic behavior was observed in Au/PCMO/Pt devices. The PCMO-based devices with hysteretic I-V curves exhibited an electric-pulse-induced resistance switching between high and low resistance states. Impedance spectroscopy was employed to study the origin of the resistance switching. From comparison of the impedance spectra between the high and low resistance states, the resistance switching in the PCMO-based devices was mainly due to the resistance change in the interface between the film and the electrode. The electronic properties of the devices showed stronger correlation with the oxidation Gibbs free energy than with the work function of the electrode metal, which suggests that the interface impedance is due to an interfacial oxide layer of the electrode metal. The interface component observed by impedance spectroscopy in the Al/PCMO/Pt device might be due to Al oxide layer formed by oxidation of Al top electrode. It is considered that the interfacial oxide layer plays a dominant role in the bipolar resistance switching in manganite film-based devices

Spatial changes in the vertical distribution of calanoid copepods down to great depths in the North Pacific

Background Despite its ecological importance, little information is available regarding the spatial and vertical changes in the calanoid copepod community over large geographical regions. This study investigated the spatial and vertical patterns in calanoid copepod abundance and community structure using zooplankton samples collected between depths of 0 and 2,615 m across the North Pacific from 0° to 56°N. Results A total of 211 calanoid copepod species belonging to 66 genera and 24 families were identified. Calanoid copepod abundance decreased with increasing depth, and few latitudinal differences were detected. Across the entire region, species diversity peaked near 500 to 2,000 m in depth. The calanoid copepod community was separated into seven groups with distinct spatial and vertical distributions. For all groups, the number of species was low (28 to 37 species) in the subarctic region (north of 40°N) and high (116 to 121 species) in the subtropical-tropical region. The deepest group in the subtropical-tropical region was composed of cosmopolitan species, and this group was also observed in deep water in the subarctic region. Conclusions In deep water, most of the calanoid copepod community consisted of cosmopolitan species, while an endemic community was observed in the subarctic region. Because the food of deep-sea calanoid copepods originates from the surface layer, sufficient and excess flux in the eutrophic subarctic region may be responsible for maintaining the endemic species in the region

Biotic and Abiotic Factors Affecting the Structures of Ground Invertebrate Communities in Japanese Cedar Dominant Forests

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