University of Hyogo

The crystal structure of bovine heart cytochrome c oxidase at 2.8 A resolution with an R value of 19.9 percent reveals 13 subunits, each different from the other, five phosphatidyl ethanolamines, three phosphatidyl glycerols and two cholates, two hemes A, and three copper, one magnesium, and one zinc. Of 3606 amino acid residues in the dimer, 3560 have been converged to a reasonable structure by refinement. A hydrogen-bonded system, including a propionate of a heme A (heme a), part of peptide backbone, and an imidazole ligand of CuA, could provide an electron transfer pathway between CuA and heme a. Two possible proton pathways for pumping, each spanning from the matrix to the cytosolic surfaces, were identified, including hydrogen bonds, internal cavities likely to contain water molecules, and structures that could form hydrogen bonds with small possible conformational change of amino acid side chains. Possible channels for chemical protons to produce H2O, for removing the produced water, and for O2, respectively, were identified.

The high resolution three-dimensional x-ray structure of the metal sites of bovine heart cytochrome c oxidase is reported. Cytochrome c oxidase is the largest membrane protein yet crystallized and analyzed at atomic resolution. Electron density distribution of the oxidized bovine cytochrome c oxidase at 2.8 A resolution indicates a dinuclear copper center with an unexpected structure similar to a [2Fe-2S]-type iron-sulfur center. Previously predicted zinc and magnesium sites have been located, the former bound by a nuclear encoded subunit on the matrix side of the membrane, and the latter situated between heme a3 and CuA, at the interface of subunits I and II. The O2 binding site contains heme a3 iron and copper atoms (CuB) with an interatomic distance of 4.5 A; there is no detectable bridging ligand between iron and copper atoms in spite of a strong antiferromagnetic coupling between them. A hydrogen bond is present between a hydroxyl group of the hydroxyfarnesylethyl side chain of heme a3 and an OH of a tyrosine. The tyrosine phenol plane is immediately adjacent and perpendicular to an imidazole group bonded to CuB, suggesting a possible role in intramolecular electron transfer or conformational control, the latter of which could induce the redox-coupled proton pumping. A phenyl group located halfway between a pyrrole plane of the heme a3 and an imidazole plane liganded to the other heme (heme a) could also influence electron transfer or conformational control.

Recently, dye-sensitized solar cells have attracted much attention relevant to global environmental issues. Thus far, ruthenium(II) bipyridyl complexes have proven to be the most efficient TiO(2) sensitizers in dye-sensitized solar cells. However, a gradual increment in the highest power conversion efficiency has been recognized in the past decade. More importantly, considering that ruthenium is a rare metal, novel dyes without metal or using inexpensive metal are desirable for highly efficient dye-sensitized solar cells. Large pi-aromatic molecules, such as porphyrins, phthalocyanines, and perylenes, are important classes of potential sensitizers for highly efficient dye-sensitized solar cells, owing to their photostability and high light-harvesting capabilities that can allow applications in thinner, low-cost dye-sensitized solar cells. Porphyrins possess an intense Soret band at 400 nm and moderate Q bands at 600 nm. Nevertheless, the poor light-harvesting properties relative to the ruthenium complexes have limited the cell performance of porphyrin-sensitized TiO(2) cells. Elongation of the pi conjugation and loss of symmetry in porphyrins cause broadening and a red shift of the absorption bands together with an increasing intensity of the Q bands relative to that of the Soret band. On the basis of the strategy, the cell performance of porphyrin-sensitized solar cells has been improved intensively by the enhanced light absorption. Actually, some push-pull-type porphyrins have disclosed a remarkably high power conversion efficiency (6-7%) that was close to that of the ruthenium complexes. Phthalocyanines exhibit strong absorption around 300 and 700 nm and redox features that are similar to porphyrins. Moreover, phthalocyanines are transparent over a large region of the visible spectrum, thereby enabling the possibility of using them as "photovoltaic windows". However, the cell performance was poor, owing to strong aggregation and lack of directionality in the excited state. Novel unsymmetrical zinc phthalocyanine sensitizers with "push" and "pull" groups have made it possible to reduce the aggregation on a TiO(2) surface, tune the level of the excited state, and strengthen the electronic coupling between the phthalocyanine core and the TiO(2) surface. As a result, the power conversion efficiency of up to 3.5% has been achieved. Perylenes are well-known as chemically, thermally, and photophysically stable dyes and have been used in various optical devices and applications. Nevertheless, the power conversion efficiency remained low compared to other organic dyes. The origin of such limited cell performance is the poor electron-donating abilities of the perylenes, which makes it difficult to inject electrons from the excited singlet state of the perylenes to the conduction band of the TiO(2) electrode efficiently. Strongly electron-donating perylene carboxylic acid derivatives with amine substituents at their perylene core have allowed us to increase the power conversion efficiency of up to approximately 7% in perylene-sensitized solar cells. The efficiency of large pi-aromatic molecule-sensitized solar cells could be improved significantly if the dyes with larger red and near-infrared absorption could be developed.

OBJECTIVE: To compare the relative validity of food group intakes derived from a comprehensive self-administered diet history questionnaire (DHQ) and a brief-type DHQ (BDHQ) developed for the assessment of Japanese diets during the previous month using semi-weighed dietary records (DR) as a reference method. DESIGN: Between November 2002 and September 2003, a 4 d DR (covering four non-consecutive days), a DHQ (150-item semi-quantitative questionnaire) and a BDHQ (fifty-eight-item fixed-portion-type questionnaire) were completed four times (once per season) at 3-month intervals. SETTING: Three areas in Japan: Osaka, Nagano and Tottori. SUBJECTS: Ninety-two Japanese women aged 31-69 years and ninety-two Japanese men aged 32-76 years. RESULTS: Median food group intakes were estimated well for approximately half of the food groups. No statistically significant differences were noted between a 16 d DR and the first DHQ (DHQ1) or between the DR and the first BDHQ (BDHQ1) in fifteen (44 %) and fifteen (52 %) food items for women and in fourteen (41 %) and sixteen (55 %) food items for men, respectively, indicating that both questionnaires estimated median values reasonably well. Median Spearman's correlation coefficients with the DR were 0·43 (range: -0·09 to 0·77) for DHQ1 and 0·44 (range: 0·14 to 0·82) for BDHQ1 in women, with respective values of 0·44 (range: 0·08 to 0·87) and 0·48 (range: 0·22 to 0·83) in men, indicating reasonable ranking ability. Similar results were observed for mean values of the four DHQ and BDHQ. CONCLUSIONS: In terms of food intake estimates, both the DHQ and the BDHQ showed reasonable validity.

BACKGROUND: A comprehensive self-administered diet history questionnaire (DHQ: 150-item semi-quantitative questionnaire) and a brief self-administered DHQ (BDHQ: 58-item fixed-portion-type questionnaire) were developed for assessing Japanese diets. We compared the relative validity of nutrient intake derived from DHQ with that from the BDHQ, using semi-weighed 16-day dietary records (DRs) as reference. METHODS: Ninety-two Japanese women aged 31 to 69 years and 92 Japanese men aged 32 to 76 years completed a 4-nonconsecutive-day DR, a DHQ, and a BDHQ 4 times each (once per season) in 3 areas of Japan (Osaka, Nagano, and Tottori). RESULTS: No significant differences were seen in estimates of energy-adjusted intakes of 42 selected nutrients (based on the residual method) between the 16-day DRs and the first DHQ (DHQ1) or between the DR and the first BDHQ (BDHQ1) for 18 (43%) and 14 (33%) nutrients, respectively, among women and for 4 (10%) and 21 (50%) nutrients among men. The median (interquartile range) Pearson correlation coefficients with the DR for energy-adjusted intakes of the 42 nutrients were 0.57 (0.50 to 0.64) for the DHQ1 and 0.54 (0.45 to 0.61) for the BDHQ1 in women; in men, the respective values were 0.50 (0.42 to 0.59) and 0.56 (0.41 to 0.63). Similar results were observed for the means of the 4 DHQs and BDHQs. CONCLUSIONS: The DHQ and BDHQ had satisfactory ranking ability for the energy-adjusted intakes of many nutrients among the present Japanese population, although these instruments were satisfactory in estimating mean values for only a small number of nutrients.

BACKGROUND: Rheumatoid factor (RF) and autoantibodies against cyclic citrullinated peptide (CCP) are markers that might help physicians diagnose rheumatoid arthritis. PURPOSE: To determine whether anti-CCP antibody more accurately identifies patients with rheumatoid arthritis and better predicts radiographic progression than does RF. DATA SOURCES: MEDLINE through September 2006 and reference lists of retrieved studies and review articles. STUDY SELECTION: Studies in any language that enrolled at least 10 participants and that examined the role of anti-CCP antibody and RF in the diagnosis or prognosis of known or suspected rheumatoid arthritis. DATA EXTRACTION: Two authors independently evaluated studies for inclusion, rated methodological quality, and abstracted relevant data. DATA SYNTHESIS: The DerSimonian-Laird random-effects method was used to summarize sensitivities, specificities, and positive and negative likelihood ratios from 37 studies of anti-CCP antibody and 50 studies of RF. The pooled sensitivity, specificity, and positive and negative likelihood ratios for anti-CCP antibody were 67% (95% CI, 62% to 72%), 95% (CI, 94% to 97%), 12.46 (CI, 9.72 to 15.98), and 0.36 (CI, 0.31 to 0.42), respectively. For IgM RF, the values were 69% (CI, 65% to 73%), 85% (CI, 82% to 88%), 4.86 (CI, 3.95 to 5.97), and 0.38 (CI, 0.33 to 0.44). Likelihood ratios among IgM RF, IgG RF, and IgA RF seemed to be similar. Results from studies of patients with early rheumatoid arthritis were similar to those from all studies. Three of 4 studies found that risk for radiographic progression was greater with anti-CCP antibody positivity than with IgM RF positivity. LIMITATIONS: Many studies had methodological limitations. Studies of RF were heterogeneous and had wide ranges of sensitivity and specificity. CONCLUSIONS: Anti-CCP antibodies are more specific than RF for diagnosing rheumatoid arthritis and may better predict erosivedisease.

An indoline dye (D205), the synthesis method of which is disclosed in this report, gave high-efficiency organic dye-sensitized solar cells (9.52%) using an anti-aggregation reagent (chenodeoxycholic acid).

The bulk of the comet 81P/Wild 2 (hereafter Wild 2) samples returned to Earth by the Stardust spacecraft appear to be weakly constructed mixtures of nanometer-scale grains, with occasional much larger (over 1 micrometer) ferromagnesian silicates, Fe-Ni sulfides, Fe-Ni metal, and accessory phases. The very wide range of olivine and low-Ca pyroxene compositions in comet Wild 2 requires a wide range of formation conditions, probably reflecting very different formation locations in the protoplanetary disk. The restricted compositional ranges of Fe-Ni sulfides, the wide range for silicates, and the absence of hydrous phases indicate that comet Wild 2 experienced little or no aqueous alteration. Less abundant Wild 2 materials include a refractory particle, whose presence appears to require radial transport in the early protoplanetary disk.

Abstract Surface-supported isolated atoms in single-atom catalysts (SACs) are usually stabilized by diverse defects. The fabrication of high-metal-loading and thermally stable SACs remains a formidable challenge due to the difficulty of creating high densities of underpinning stable defects. Here we report that isolated Pt atoms can be stabilized through a strong covalent metal-support interaction (CMSI) that is not associated with support defects, yielding a high-loading and thermally stable SAC by trapping either the already deposited Pt atoms or the PtO 2 units vaporized from nanoparticles during high-temperature calcination. Experimental and computational modeling studies reveal that iron oxide reducibility is crucial to anchor isolated Pt atoms. The resulting high concentrations of single atoms enable specific activities far exceeding those of conventional nanoparticle catalysts. This non defect-stabilization strategy can be extended to non-reducible supports by simply doping with iron oxide, thus paving a new way for constructing high-loading SACs for diverse industrially important catalytic reactions.

refers to the microscale processes that affect cloud and precipitation particles and is a key linkage among the various components of Earth's atmospheric water and energy cycles. The representation of microphysical processes in models continues to pose a major challenge leading to uncertainty in numerical weather forecasts and climate simulations. In this paper, the problem of treating microphysics in models is divided into two parts: (i) how to represent the population of cloud and precipitation particles, given the impossibility of simulating all particles individually within a cloud, and (ii) uncertainties in the microphysical process rates owing to fundamental gaps in knowledge of cloud physics. The recently developed Lagrangian particle-based method is advocated as a way to address several conceptual and practical challenges of representing particle populations using traditional bulk and bin microphysics parameterization schemes. For addressing critical gaps in cloud physics knowledge, sustained investment for observational advances from laboratory experiments, new probe development, and next-generation instruments in space is needed. Greater emphasis on laboratory work, which has apparently declined over the past several decades relative to other areas of cloud physics research, is argued to be an essential ingredient for improving process-level understanding. More systematic use of natural cloud and precipitation observations to constrain microphysics schemes is also advocated. Because it is generally difficult to quantify individual microphysical process rates from these observations directly, this presents an inverse problem that can be viewed from the standpoint of Bayesian statistics. Following this idea, a probabilistic framework is proposed that combines elements from statistical and physical modeling. Besides providing rigorous constraint of schemes, there is an added benefit of quantifying uncertainty systematically. Finally, a broader hierarchical approach is proposed to accelerate improvements in microphysics schemes, leveraging the advances described in this paper related to process modeling (using Lagrangian particle-based schemes), laboratory experimentation, cloud and precipitation observations, and statistical methods.

Sb2S3 layers were inserted at the interface between TiO2 and CH3NH3PbI3 perovskite to create CH3NH3PbI3 solar cells using inorganic hole transporting material (CuSCN). The CH3NH3PbI3 layer was spin-coated by a one-drop method onto the nanocrystalline TiO2 layer. The photoenergy conversion efficiencies were improved with Sb2S3 layers (the best efficiency: 5.24%). During the light exposure test without encapsulation, the CH3NH3PbI3 solar cells without Sb2S3 deteriorated to zero efficiency in 12 h and were completely changed from black to yellow because the perovskite CH3NH3PbI3 was changed to hexagonal PbI2. With Sb2S3, on the other hand, the CH3NH3PbI3 solar cells became stable against light exposure without encapsulation, which did not change the crystal structure or the wavelength edges of absorption and IPCE. Therefore, it was believed that degradation can occur at the interface between TiO2 and CH3NH3PbI3.

Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.

By extending our previous study by Maehara et al. (2012), we searched for superflares on G-type dwarfs (solar type stars) using Kepler data for a longer period (500 days) than that (120 days) in our previous study. As a result, we found 1547 superflares on 279 G-type dwarfs, which are much more than previous 365 superflares on 148 stars. Using these new data, we studied the statistical properties of occurrence frequency of superflares, and basically confirmed the previous results, i.e., the occurrence frequency (dN/dE) of superflares vs flare energy (E) shows power-law distribution with dN/dE \propto E^{-\alpha}, where \alpha ~ 2. It is interesting that this distribution is roughly on the same line as that for solar flares. In the case of the Sun-like stars (with surface temperature 5600-6000K and slowly rotating with a period longer than 10 days), the occurrence frequency of superflares with energy of 10^34 -10^35 erg is once in 800-5000 years. We also studied long term (500 days) stellar brightness variation of these superflare stars, and found that in some G-type dwarfs the occurrence frequency of superflares was extremely high, ~ 57 superflares in 500 days (i.e., once in 10 days). In the case of Sun-like stars, the most active stars show the frequency of one superflares (with 10^34 erg) in 100 days. There is evidence that these superflares have extremely large starspots with a size about 10 times larger than that of the largest sunspot. We argue that the physical origin of extremely high occurrence frequency of superflares in these stars may be attributed to the existence of extremely large starspots.

In order to develop an optical method for pressure determination in the multimegabar region, the first-order Raman spectra of diamond anvils were investigated at pressures up to 310GPa. The high-frequency edge of the Raman band, which corresponds to the Raman shift of the anvil culet due to the normal stress, was calibrated against the sample pressure derived from the equation of state of Pt. The obtained pressure dependence of the edge frequency demonstrates the reliability of this diamond anvil Raman gauge. Up to the maximum pressure of this study, the relation between Raman frequency and normal stress at the diamond anvil culet is formally similar to the equation of state of a hydrostatically compressed isotropic elastic body having a bulk modulus of K0=547(11)GPa and a pressure derivative of the bulk modulus K0′=3.75(20).

Abstract Lead sulfide (PbS) and cadmium sulfide (CdS) quantum dots (QDs) are prepared over mesoporous TiO 2 films by a successive ionic layer adsorption and reaction (SILAR) process. These QDs are exploited as a sensitizer in solid‐state solar cells with 2,2′,7,7′‐tetrakis( N , N ‐di‐ p ‐methoxyphenylamine)‐9,9′‐spirobifluorene (spiro‐OMeTAD) as a hole conductor. High‐resolution transmission electron microscopy (TEM) images reveal that PbS QDs of around 3 nm in size are distributed homogeneously over the TiO 2 surface and are well separated from each other if prepared under common SILAR deposition conditions. The pore size of the TiO 2 films and the deposition medium are found to be very critical in determining the overall performance of the solid‐state QD cells. By incorporating promising inorganic QDs (PbS) and an organic hole conductor spiro‐OMeTAD into the solid‐state cells, it is possible to attain an efficiency of over 1% for PbS‐sensitized solid‐state cells after some optimizations. The optimized deposition cycle of the SILAR process for PbS QDs has also been confirmed by transient spectroscopic studies on the hole generation of spiro‐OMeTAD. In addition, it is established that the PbS QD layer plays a role in mediating the interfacial recombination between the spiro‐OMeTAD + cation and the TiO 2 conduction band electron, and that the lifetime of these species can change by around 2 orders of magnitude by varying the number of SILAR cycles used. When a near infrared (NIR)‐absorbing zinc carboxyphthalocyanine dye (TT1) is added on top of the PbS‐sensitized electrode to obtain a panchromatic response, two signals from each component are observed, which results in an improved efficiency. In particular, when a CdS‐sensitized electrode is first prepared, and then co‐sensitized with a squarine dye (SQ1), the resulting color change is clearly an addition of each component and the overall efficiencies are also added in a more synergistic way than those in PbS/TT1‐modified cells because of favorable charge‐transfer energetics.

Pre-MicroRNA Export Machinery Micro (mi) RNAs play a role in the regulation of many biological processes. Long transcripts are initially processed in the nucleus to yield pre-miRNAs that are translocated through the nuclear pore complex and further processed to mature miRNAs in the cytoplasm. Okada et al. (p. 1275 ; see the Perspective by Stewart ) describe the crystal structure of pre-miRNA complexed with the exportin Exp5 and the small nuclear GTPase RanGTP. The structure shows that Exp5 and RanGTP protect the miRNA from degradation by nucleases, as well as facilitate transport to the cytoplasm. RNA recognition is mainly through ionic interactions that are sequence independent, and model-building suggests that this nuclear export machinery could accommodate other small-structured RNAs.

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTReaction Mechanism of Cytochrome c OxidaseShinya Yoshikawa* and Atsuhiro ShimadaView Author Information Picobiology Institute, Graduate School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan*E-mail: [email protected]Cite this: Chem. Rev. 2015, 115, 4, 1936–1989Publication Date (Web):January 20, 2015Publication History Received19 May 2014Published online20 January 2015Published inissue 25 February 2015https://pubs.acs.org/doi/10.1021/cr500266ahttps://doi.org/10.1021/cr500266areview-articleACS PublicationsCopyright © 2015 American Chemical SocietyRequest reuse permissionsArticle Views9396Altmetric-Citations368LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Bioinorganic chemistry,Chemical structure,Peptides and proteins,Reaction mechanisms,X-rays Get e-Alerts

Mitochondrial cytochrome c oxidase plays an essential role in aerobic cellular respiration, reducing dioxygen to water in a process coupled with the pumping of protons across the mitochondrial inner membrane. An aspartate residue, Asp-51, located near the enzyme surface, undergoes a redox-coupled x-ray structural change, which is suggestive of a role for this residue in redox-driven proton pumping. However, functional or mechanistic evidence for the involvement of this residue in proton pumping has not yet been obtained. We report that the Asp-51 --> Asn mutation of the bovine enzyme abolishes its proton-pumping function without impairment of the dioxygen reduction activity. Improved x-ray structures (at 1.8/1.9-A resolution in the fully oxidized/reduced states) show that the net positive charge created upon oxidation of the low-spin heme of the enzyme drives the active proton transport from the interior of the mitochondria to Asp-51 across the enzyme via a water channel and a hydrogen-bond network, located in tandem, and that the enzyme reduction induces proton ejection from the aspartate to the mitochondrial exterior. A peptide bond in the hydrogen-bond network critically inhibits reverse proton transfer through the network. A redox-coupled change in the capacity of the water channel, induced by the hydroxyfarnesylethyl group of the low-spin heme, suggests that the channel functions as an effective proton-collecting region. Infrared results indicate that the conformation of Asp-51 is controlled only by the oxidation state of the low-spin heme. These results indicate that the low-spin heme drives the proton-pumping process.

Significance Marine sediment covers 70% of Earth’s surface and harbors as much biomass as seawater. However, the global taxonomic diversity of marine sedimentary communities, and the spatial distribution of that diversity remain unclear. We investigated microbial composition from 40 globally distributed sampling locations, spanning sediment depths of 0.1 to 678 m. Statistical analysis reveals that oxygen presence or absence and organic carbon concentration are key environmental factors for defining taxonomic composition and diversity of marine sedimentary communities. Global marine sedimentary taxonomic richness predicted by species–area relationship models is 7.85 × 10 3 to 6.10 × 10 5 for Archaea and 3.28 × 10 4 to 2.46 × 10 6 for Bacteria as amplicon sequence variants, which is comparable to the richness in seawater and that in topsoil.

Abstract If global policies intended to promote forest conservation continue to use the definition of “forest” adopted in 2001 by the United Nations Framework Convention on Climate Change (an area of >0.05–1 ha with >10–30% cover of plants >2–5 m tall at maturity), great quantities of carbon and other environmental values will be lost when natural forests are severely degraded or replaced by plantations but technically remain “forests.” While a definition of “forest” that is globally acceptable and appropriate for monitoring using standard remote sensing options will necessarily be based on a small set of easily measured parameters, there are dangers when simple definitions are applied locally. At the very least, we recommend that natural forest be differentiated from plantations and that for defining “forest” the lower height limit defining “trees” be set at more than 5 m tall with the minimum cover of trees be set at more than 40%. These changes will help reduce greenhouse gas emissions from what is now termed forest “degradation” without increasing monitoring costs. Furthermore, these minor changes in the definition of “forest” will promote the switch from degradation to responsible forest management, which will help mitigate global warming while protecting biodiversity and contributing to sustainable development.