The rulB gene of plasmid pWW0 is a hotspot for the site-specific insertion of integron-like elements found in the chromosomes of environmental Pseudomonas fluorescens group bacteria

The rulAB operon of Pseudomonas spp. confers fitness traits on the host and has been suggested to be a hotspot for insertion of mobile elements that carry avirulence genes. Here, for the first time, we show that rulB on plasmid pWW0 is a hotspot for the active site-specific integration of related integron-like elements (ILEs) found in six environmental pseudomonads (strains FH1–FH6). Integration into rulB on pWW0 occurred at position 6488 generating a 3 bp direct repeat. ILEs from FH1 and FH5 were 9403 bp in length and contained eight open reading frames (ORFs), while the ILE from FH4 was 16 233 bp in length and contained 16 ORFs. In all three ILEs, the first 5.1 kb (containing ORFs 1–4) were structurally conserved and contained three predicted site-specific recombinases/integrases and a tetR homologue. Downstream of these resided ORFs of the ‘variable side’ with structural and sequence similarity to those encoding survival traits on the fitness enhancing plasmid pGRT1 (ILEFH1 and ILEFH5) and the NR-II virulence region of genomic island PAGI-5 (ILEFH4). Collectively, these ILEs share features with the previously described type III protein secretion system effector ILEs and are considered important to host survival and transfer of fitness enhancing and (a)virulence genes between bacteria.

Origin and evolution of 3'UTR of flaviviruses: long direct repeats as a basis for the formation of secondary structures and their significance for virus transmission

The 3' untranslated regions (3'UTRs) of flaviviruses are reviewed and analyzed in relation to short sequences conserved as direct repeats (DRs). Previously, alignments of the 3'UTRs have been constructed for three of the four recognized flavivirus groups, namely mosquito-borne, tick-borne, and nonclassified flaviviruses (MBFV, TBFV, and NCFV, respectively). This revealed (1) six long repeat sequences (LRSs) in the 3'UTR and open-reading frame (ORF) of the TBFV, (2) duplication of the 3'UTR of the NCFV by intramolecular recombination, and (3) the possibility of a common origin for all DRs within the MBFV. We have now extended this analysis and review it in the context of all previous published analyses. This has been achieved by constructing a robust alignment between all flaviviruses using the published DRs and secondary RNA structures as "anchors" to reveal additional homologies along the 3'UTR. This approach identified nucleotide regions within the MBFV, NKV (no-known vector viruses), and NCFV 3'UTRs that are homologous to different LRSs in the TBFV 3'UTR and ORF. The analysis revealed that some of the DRs and secondary RNA structures described individually within each flavivirus group share common evolutionary origins. The 3'UTR of flaviviruses, and possibly the ORF, therefore probably evolved through multiple duplication of an RNA domain, homologous to the LRS previously identified only in the TBFV. The short DRs in all virus groups appear to represent the evolutionary remnants of these domains rather than resulting from new duplications. The relevance of these flavivirus DRs to evolution, diversity, 3'UTR enhancer function, and virus transmission is reviewed.

Estrogen regulation of chicken riboflavin carrier protein gene is mediated by ERE half sites without direct binding of estrogen receptor

Estrogen is an important steroid hormone that mediates most of its effects on regulation of gene expression by binding to intracellular receptors. The consensus estrogen response element (ERE) is a 13 bp palindromic inverted repeat with a three nucleotide spacer. However, several reports suggest that many estrogen target genes are regulated by diverse elements, such as imperfect EREs and ERE half sites (ERE 1/2), which are either the proximal or the distal half of the palindrome. To gain more insight into ERE half site-mediated gene regulation, we used a region from the estrogen-regulated chicken riboflavin carrier protein (RCP) gene promoter that contains ERE half sites. Using moxestrol, an analogue of estrogen and transient transfection of deletion and mutation containing RCP promoter/reporter constructs in chicken hepatoma (LMH2A) cells, we identified an estrogen response unit (ERU) composed of two consensus ERE 1/2 sites and one non-consensus ERE 1/2 site. Mutation of any of these sites within this ERU abolishes moxestrol response. Further, the ERU is able to confer moxestrol responsiveness to a heterologous promoter. Interestingly, RCP promoter is regulated by moxestrol in estrogen responsive human MCF-7 cells, but not in other cell lines such as NIH3T3 and HepG2 despite estrogen receptor-alpha (ER-�) co transfection. Electrophoretic mobility shift assays (EMSAs) with promoter regions encompassing the half sites and nuclear extracts from LMH2A cells show the presence of a moxestrol-induced complex that is abolished by a polyclonal anti-ER� antibody. Surprisingly, estrogen receptor cannot bind to these promoter elements in isolation. Thus, there appears to be a definite requirement for some other factor(s) in addition to estrogen receptor, for the generation of a suitable response of this promoter to estrogen. Our studies therefore suggest a novel mechanism of gene regulation by estrogen, involving ERE half sites without direct binding of ER to the cognate elements.

Aerosol Direct Radiative Impact Experiment (ADRIEX) overview

The Aerosol Direct Radiative Experiment (ADRIEX) took place over the Adriatic and Black Seas during August and September 2004 with the aim of characterizing anthropogenic aerosol in these regions in terms of its physical and optical properties and establishing its impact on radiative balance. Eight successful flights of the UK BAE-146 Facility for Atmospheric Airborne Measurements were completed together with surface-based lidar and AERONET measurements, in conjunction with satellite overpasses. This paper outlines the motivation for the campaign, the methodology and instruments used, describes the synoptic situation and provides an overview of the key results. ADRIEX successfully measured a range of aerosol conditions across the northern Adriatic, Po Valley and Black Sea. Generally two layers of aerosol were found in the vertical: in the flights over the Black Sea and the Po Valley these showed differences in chemical and microphysical properties, whilst over the Adriatic the layers were often more similar. Nitrate aerosol was found to be important in the Po Valley region. The use of new instruments to measure the aerosol chemistry and mixing state and to use this information in determining optical properties is demonstrated. These results are described in much more detail in the subsequent papers of this special issue.

Direct radiative effect of aerosols emitted by transport from road, shipping and aviation

Aerosols and their precursors are emitted abundantly by transport activities. Transportation constitutes one of the fastest growing activities and its growth is predicted to increase significantly in the future. Previous studies have estimated the aerosol direct radiative forcing from one transport sub-sector, but only one study to our knowledge estimated the range of radiative forcing from the main aerosol components (sulphate, black carbon (BC) and organic carbon) for the whole transportation sector. In this study, we compare results from two different chemical transport models and three radiation codes under different hypothesis of mixing: internal and external mixing using emission inventories for the year 2000. The main results from this study consist of a positive direct radiative forcing for aerosols emitted by road traffic of +20±11 mW m−2 for an externally mixed aerosol, and of +32±13 mW m−2 when BC is internally mixed. These direct radiative forcings are much higher than the previously published estimate of +3±11 mW m−2. For transport activities from shipping, the net direct aerosol radiative forcing is negative. This forcing is dominated by the contribution of the sulphate. For both an external and an internal mixture, the radiative forcing from shipping is estimated at −26±4 mW m−2. These estimates are in very good agreement with the range of a previously published one (from −46 to −13 mW m−2) but with a much narrower range. By contrast, the direct aerosol forcing from aviation is estimated to be small, and in the range −0.9 to +0.3 mW m−2.