Are both agricultural intensification and farmland abandonment threats to biodiversity? A test with bird communities in paddy-dominated landscapes

Land-use changes, including agricultural intensification and farmland abandonment, influence biodiversity in agricultural landscapes. However, few studies have focused on how the two major land-use changes affect different types of species at landscape scales. This study examined the relationships between the richness and abundance of five bird groups (agricultural wetland species, agricultural land species, grassland species, edge species, and woodland species) as well as the total species richness and abundance, and intensification or abandonment in 28 square, 100-ha grid cells in paddy-dominated landscapes in the Tone River basin of central Japan. Rice-field intensification and abandonment were not completely segregated spatially: intensification occurred in both plain and hilly areas surrounded by forests, while abandonment tended to occur in hilly areas. The effects of intensification and abandonment differed among species groups and between seasons. The richness or abundance of agricultural wetland species in summer were negatively associated with both intensification and abandonment. While the abundance of agricultural land species in winter and grassland species in both seasons were positively associated with intensification and abandonment, respectively. The total species richness and abundance did not show clear association with intensification and abandonment due to a variety of responses of the five bird groups. Based on prefectural Red Data Books, agricultural wetland species, followed by grassland species, were more threatened than other three groups in both summer and winter. This study found that (1) the diversity of habitats (including consolidated and abandoned farmlands) provides buffer areas for the different bird groups on different times of the year and (2) agricultural wetland species that use flooded rice fields in summer, such as egrets and shorebirds, are particularly threatened by both intensification and abandonment.We thank Yoshinori Tokuoka, Susumu Yamada, Eun-Young Kim, and Shori Yamamoto for providing land-use data. We also appreciate two anonymous reviewers for their constructive comments and suggestions. This study was conducted as part of the research project “Developing management techniques for agricultural and aquatic ecosystems in river basins in pursuit of coexistence with nature,” funded by the Agriculture, Forestry and Fisheries Research Council of Japan. N.K. and T.O. were also financially supported by JSPS (Japan Society for the Promotion of Science) KAKENHI Grant Numbers 25830154 and 24710038, respectively. T.A. was supported by the European Commission’s Marie Curie International Incoming Fellowship Programme (PIIFGA-2011-303221).This is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.agee.2015.08.01

The cryoEM structure of cytochrome bd from C. glutamicum provides novel insights into structural properties of actinobacterial terminal oxidases

Cytochromes bd are essential for microaerobic respiration of many prokaryotes including a number of human pathogens. These enzymes catalyze the reduction of molecular oxygen to water using quinols as electron donors. Their importance for prokaryotic survival and the absence of eukaryotic homologs make these enzyme ideal targets for antimicrobial drugs. Here, we determined the cryoEM structure of the menaquinol-oxidizing cytochrome bd-type oxygen reductase of the facultative anaerobic Actinobacterium Corynebacterium glutamicum at a resolution of 2.7 Å. The obtained structure adopts the signature pseudosymmetrical heterodimeric architecture of canonical cytochrome bd oxidases formed by the core subunits CydA and CydB. No accessory subunits were identified for this cytochrome bd homolog. The two b-type hemes and the oxygen binding heme d are organized in a triangular geometry with a protein environment around these redox cofactors similar to that of the closely related cytochrome bd from M. tuberculosis. We identified oxygen and a proton conducting channels emerging from the membrane space and the cytoplasm, respectively. Compared to the prototypical enzyme homolog from the E. coli, the most apparent difference is found in the location and size of the proton channel entry site. In canonical cytochrome bd oxidases quinol oxidation occurs at the highly flexible periplasmic Q-loop located in the loop region between TMHs six and seven. An alternative quinol-binding site near heme b595 was previously identified for cytochrome bd from M. tuberculosis. We discuss the relevance of the two quinol oxidation sites in actinobacterial bd-type oxidases and highlight important differences that may explain functional and electrochemical differences between C. glutamicum and M. tuberculosis. This study expands our current understanding of the structural diversity of actinobacterial and proteobacterial cytochrome bd oxygen reductases and provides deeper insights into the unique structural and functional properties of various cytochrome bd variants from different phylae

Measurement of the cosmic-ray antiproton spectrum at solar minimum with a long-duration balloon flight over Antarctica

The energy spectrum of cosmic-ray antiprotons from 0.17 to 3.5 GeV has been measured using 7886 antiprotons detected by BESS-Polar II during a long-duration flight over Antarctica near solar minimum in December 2007 and January 2008. This shows good consistency with secondary antiproton calculations. Cosmologically primary antiprotons have been investigated by comparing measured and calculated antiproton spectra. BESS-Polar II data show no evidence of primary antiprotons from evaporation of primordial black holes.Comment: 4 pages, 4 figures, submitted to Physical Review Letter

Structure and mechanism of human DNA polymerase η

The variant form of the human syndrome xeroderma pigmentosum (XPV) is caused by a deficiency in DNA polymerase eta (Pol eta), a DNA polymerase that enables replication through ultraviolet-induced pyrimidine dimers. Here we report high-resolution crystal structures of human Pol eta at four consecutive steps during DNA synthesis through cis-syn cyclobutane thymine dimers. Pol eta acts like a 'molecular splint' to stabilize damaged DNA in a normal B-form conformation. An enlarged active site accommodates the thymine dimer with excellent stereochemistry for two-metal ion catalysis. Two residues conserved among Pol eta orthologues form specific hydrogen bonds with the lesion and the incoming nucleotide to assist translesion synthesis. On the basis of the structures, eight Pol eta missense mutations causing XPV can be rationalized as undermining the molecular splint or perturbing the active-site alignment. The structures also provide an insight into the role of Pol eta in replicating through D loop and DNA fragile sites