Validation of the suppressive subtractive hybridization method in Mycoplasma agalactiae species by the comparison of a field strain with the type strain PG2

The subtractive suppressive hybridization (SSH), a method that allows the identification of sequences that are present in one genome (tester) but not in the other (driver), is a promising technique for the comparison of Mycoplasma agalactiae pathogenic strains. The optimal conditions for SSH were established by subtracting the M. agalactiae type strain PG2 DNA from the M. agalactiae strain 5632 DNA. Because these two strains possess different vpma gene repertoires, 5632-specific vpma sequences (and possibly other 5632-specific sequences) were predicted to be retrieved by SSH. The subtracted tester DNA was PCR-amplified and cloned into the pGEM-T easy E. coli vector. Two independent libraries were generated and used to prepare individual probes that were tested by Southern blot with genomic DNA from various field isolates and mycoplasma reference strains. Sequence analysis of two overlapping clones showed that they potentially code for a large carboxyterminal portion of a new vpma ORF. Several DNA fragments homologous to insertion sequences were also found in 5632 and related strains. These preliminary data suggest that SSH is a powerful method to investigate differences between mycoplasma strains, and may be applied to molecular epidemiology, diagnostic, and host specificity or pathogenicity determinant discovery.     

Chuukese travellers and the idea of horizon

Travelling, as movement, has always been a tradition of atoll islanders. Their travels continue to identify the ways in which atoll peoples understand, appropriate, and manipulate space and boundaries. This paper argues that travelling is as relevant to islanders today as in the past and examines meanings in Chuuk islanders' travel. ‘Horizon’, the space ‘out there’, is a metaphorical model of space for atoll peoples with many traditions of travel. ‘Horizon’ is also a dual concept. The horizon is the space within which the islander traveller is located that is ‘strange’ and ‘foreign’. It is also the horizon, as a defined space, that locates and brings those strange and foreign forces into the places of atoll residents and across familiar boundaries. The narrative traditions of Chuuk islanders will be used to explore these dual formulations of horizon and the different terms for travelling among an atoll people. Discussion will focus on how islanders define the boundaries of their horizon in their travels and the meanings that these boundaries give travelling or movements.     

Seasonal and diurnal variation of downstream fish movement at four small-scale hydropower plants

Hydropower structures hinder the movement and migration of fishes, impairing their life cycles. Additionally, downstream moving fish are often at risk of being injured during turbine passage. To improve hydropower production towards more fish-friendly techniques and management, knowledge on timing and extent of natural patterns of fish downstream movement is necessary. So far, migration behaviour of long-distance migrators such as eel or salmon has been well studied, but little is known about seasonal and diurnal movement patterns of nonmigratory species or medium-distance migrators. In this study, movement patterns of 39 fish species captured by stownets while transiting hydropower facilities in four impounded rivers were assessed and compared with the fish community composition directly upstream of the hydropower plants assessed by electrofishing. Strong differences between the fish community composition inhabiting the upstream sides of the dams and the fish detected in downstream passage were evident. In each study river, the downstream moving fish community composition differed significantly between spring and autumn. On average, significantly more fish were caught during the night (2.9 fish/hr) than during the day (1.3 fish/hr). Topmouth gudgeon, European grayling and pike-perch mostly moved downstream during the night, whereas roach, spirlin and bleak were the most frequent downstream moving fish during daytime. Downstream fish movement was positively related with turbidity, water temperature and discharge. The strong differences in seasonal and diurnal fish movement patterns suggest that fish damage can be strongly reduced by adaptive turbine and corridor management, for example by shutting down turbines at peak movements.     

Mantophasmatodea: a new insect order with extant members in the Afrotropics

A new insect order, Mantophasmatodea, is described on the basis of museum specimens of a new genus with two species: Mantophasma zephyra gen. et sp. nov. (one female from Namibia) and M. subsolana sp. nov. (one male from Tanzania). This is the first time since 1914 that a newly described extant insect taxon has proved unplaceable within a recognized order. Mantophasmatodeans are apterous carnivores. Their closest phylogenetic relationships may be to Grylloblattodea (ice-crawlers) and/or Phasmatodea (stick insects), but the morphological evidence is ambiguous. Raptophasma Zompro from Baltic amber is assigned to the Mantophasmatodea, revealing a wider previous range for the lineage.     

Review of History and Recent Development of Organic Farming Worldwide

The history of the organic farming worldwide was reviewed in this paper. The development of the organic farming worldwide had gone through three stages, emergence, expansion, and growth. The contributors and their thoughts during the different development stages of the organic farming were briefly introduced. And the development status of the organic farming worldwide was reviewed from the aspects of land area under organic management, land area under organic management in percentage of total agricultural area, and world markets for organic products. Besides, the main existing problems for the further development of the world＇s organic farming, as well as the development status, problems and strategies of the Chinese organic farming were discussed.     

The structure of a pH-sensing mycobacterial adenylyl cyclase holoenzyme

Class III adenylyl cyclases contain catalytic and regulatory domains, yet structural insight into their interactions is missing. We show that the mycobacterial adenylyl cyclase Rv1264 is rendered a pH sensor by its N-terminal domain. In the structure of the inhibited state, catalytic and regulatory domains share a large interface involving catalytic residues. In the structure of the active state, the two catalytic domains rotate by 55 degrees to form two catalytic sites at their interface. Two alpha helices serve as molecular switches. Mutagenesis is consistent with a regulatory role of the structural transition, and we suggest that the transition is regulated by pH.     

HIV-1 proviral DNA excision using an evolved recombinase

HIV-1 integrates into the host chromosome and persists as a provirus flanked by long terminal repeats (LTRs). To date, treatment regimens primarily target the virus enzymes or virus-cell fusion, but not the integrated provirus. We report here the substrate-linked protein evolution of a tailored recombinase that recognizes an asymmetric sequence within an HIV-1 LTR. This evolved recombinase efficiently excised integrated HIV proviral DNA from the genome of infected cells. Although a long way from use in the clinic, we speculate that this type of technology might be adapted in future antiretroviral therapies, among other possible uses.     

Effects of nitrogen supply on growth and nitrogen uptake by Miscanthus sinensis during establishment

The effect of nitrogen (N) supply on growth and N uptake of Miscanthus sinensis during the establishment was determined. Seven different N addition regimes were compared in a nutrient solution experiment. In the treatments N111 (severe deficient), N222 (moderate deficient), N333 and N444 (optimal for maximum growth) different N concentration ranges were held constant during the entire growing season. In the treatments N144, N414 and N441 plants were subjected to low (1) N concentration in one of three experimental periods, whereas the N concentration was high (4) in the other two periods. Depending on the N demand of the plants, N concentrations were adjusted to 250–500 μM (N1), 500–1000 μM (N2), 1250–2500 μM (N3) and 2500–5000 μM (N4) when the N concentration in the N222 treatment had dropped below 100 μM. The other elements in the solution were replenished according to the estimated element ratios in the plants. As a reference the potassium concentration in the solution was measured regularly. During the first year plants with a non-limited N supply (N444) produced new tillers and increased the length of individual tillers until the end of the growing season. This resulted in a 48% shoot dry matter increase late in the growing season between August and October and a linear increase of cumulative N uptake between July and October. Limited N supply during the entire growing season (N111, N222) caused lower shoot yields but rhizome and particularly root dry weights were less affected. Significant final yield losses were also observed when the N supply was limited only during the first 7 weeks of growth (N144). By contrast, final shoot yield was hardly affected when the plants were exposed to limited N supply over a period of 9 weeks at the end of the growing season (N441). In the second year regrowth of shoots in spring was affected by the previous year's N supply, since five weeks after the beginning of regrowth, shoot dry matter was significantly positively correlated with N contents in rhizomes and shoots in the previous October. Our results show, that N supply at the beginning of the growing season has a major effect on final yield in the first establishment year of M. sinensis. However, from the second year on, the capacity of N reserves in rhizomes and roots affects spring growth much more than current N supply.