Mutagen X and chlorinated tap water are recombinagenic in yeast

This study determines the effects of a water disinfection by-product, 3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (also known as mutagen X or MX) and chlorinated tap water on genomic instability in the yeast Saccharomyces cerevisiae. Tap water samples collected from Cherepovets (Russia) and Boston (MA, USA), were extracted using XAD absorption and ethyl acetate elution. MX and these water extracts were then tested for their ability to induce intrachromosomal recombination (deletions or DEL events), interchromosomal recombination (ICR) and aneuploidy (ANEU) using the yeast DEL assay. MX strongly induced DEL, ICR and ANEU events with a positive dose response and no threshold. Cherepovets tap water induced DEL and ICR events while evidence of ANEU induction was weak. The DEL induction potencies were stronger at higher concentrations. The estimated contribution of MX to DEL induction varied from over 50% at low concentrations (which is comparable to a typical contribution of MX to Ames mutagenicity of tap water) to between 2 and 10% at highest concentrations. For Boston tap water, there was only weak evidence of DEL induction and no evidence of ICR and ANEU induction. This is consistent with the results of other studies, which reported much higher concentrations of MX and stronger Ames mutagenicity in Cherepovets tap water than in Boston tap water.     

Nest orientation and hatching success in the tree pipit Anthus trivialis

Many open-nesting bird species orient their nests relative to surrounding vegetation to avoid adverse environmental conditions. In eastern England, tree pipit Anthus trivialis nests predominantly faced east, an orientation that provided shelter from prevailing WSW winds, allowed warming by the morning sun and which, together with relatively high field layer cover, shaded nest contents from the midday sun. Mean orientation moved from south to north through the breeding season as temperatures increased, suggesting that solar radiation was a key influence on nest placement for tree pipits in the study area. Tree pipit nests with eastward orientations experienced better hatching success than those in less-preferred orientations and it is suggested that this was due to their thermal advantages. In contrast, nest orientation had no influence on nestling survival.     

Urban and coastal breeding lesser black-backed gulls (Larus fuscus) segregate by foraging habitat

Despite urbanization's general erosion of biodiversity, towns and cities provide novel opportunities for some species. During the 20th century, gulls (Laridae) colonized urban areas around the world where they flourished. At the same time, some coastal populations declined. The reasons for this difference are not fully understood, partly because little is known about any ecological differences between urban and non-urban gulls, such as their foraging ecology. Here we compare the movement ecology and habitat selection of Lesser Black-backed Gulls Larus fuscus graellsii breeding at two neighbouring colonies – one urban and one coastal – in north-west England. We used bird-borne GPS loggers to first compare colony-level movement behaviour and habitat selection and then investigated individual-level habitat use. We observed clear colony-level habitat segregation: urban breeders preferentially foraged in urban areas whereas coastal breeders foraged primarily in coastal habitats and avoided urban areas. Coastal breeders also had larger core and home-ranges than urban breeders, possibly due to differences in colony size. However, we also found inter-individual differences in habitat use, which may have important management implications. These findings suggest a link between nesting and foraging ecology, and thus management or environmental change altering food availability will impact gulls at the coastal and urban sites differently.     

Constrained peptides mimic a viral suppressor of RNA silencing

The design of high-affinity, RNA-binding ligands has proven very challenging. This is due to the unique structural properties of RNA, often characterized by polar surfaces and high flexibility. In addition, the frequent lack of well-defined binding pockets complicates the development of small molecule binders. This has triggered the search for alternative scaffolds of intermediate size. Among these, peptide-derived molecules represent appealing entities as they can mimic structural features also present in RNA-binding proteins. However, the application of peptidic RNA-targeting ligands is hampered by a lack of design principles and their inherently low bio-stability. Here, the structure-based design of constrained α-helical peptides derived from the viral suppressor of RNA silencing, TAV2b, is described. We observe that the introduction of two inter-side chain crosslinks provides peptides with increased α-helicity and protease stability. One of these modified peptides (B3) shows high affinity for double-stranded RNA structures including a palindromic siRNA as well as microRNA-21 and its precursor pre-miR-21. Notably, B3 binding to pre-miR-21 inhibits Dicer processing in a biochemical assay. As a further characteristic this peptide also exhibits cellular entry. Our findings show that constrained peptides can efficiently mimic RNA-binding proteins rendering them potentially useful for the design of bioactive RNA-targeting ligands.     

Orphanin FQ/Nociceptin Modulation of Mesolimbic Dopamine Transmission Determined by Microdialysis

Orphanin FQ has been reported to suppress extracellular dopamine levels in the nucleus accumbens after intracerebroventricular administration. This study sought to provide evidence for an intra-ventral tegmental site of action for this effect using a dual-probe microdialysis experimental design. Orphanin FQ was applied to the ventral tegmental area of anesthetized rats by reverse dialysis while extracellular dopamine was sampled with a second dialysis probe in the nucleus accumbens. Orphanin FQ at a probe concentration of 1 mM (but not at 0.1 mM) significantly reduced nucleus accumbens dialysate dopamine levels. The receptor-inactive analogue, des-Phe1-orphanin FQ (1 mM), produced a small but significant increase in nucleus accumbens dialysate dopamine levels. Simultaneous measurement of ventral tegmental area dialysate amino acid content revealed significant increases in both GABA and glutamate during infusion of orphanin FQ (1 mM). To determine if increased GABA overflow mediates the action of orphanin FQ on mesolimbic neurons, orphanin FQ (10 nmol) was microinjected directly into the ventral tegmental area in the presence or absence of the GABA(A) receptor antagonist, bicuculline (1 nmol). Bicuculline transiently blocked the suppressive action of orphanin FQ on accumbens dialysate dopamine levels. These data indicate that orphanin FQ decreases dopamine transmission in the nucleus accumbens by inhibiting dopamine neuronal activity in the ventral tegmental area through a mechanism that may involve an increased overflow of GABA.     

The contribution of 'omic'-based approaches to the study of enhanced biological phosphorus removal microbiology

The role that microorganisms play in the biological removal of phosphate from wastewater streams has received sustained interest since its initial observation over 30 years ago. Recent advances in 'omic'-based approaches have greatly advanced our knowledge in this field and facilitated a refinement of existing enhanced biological phosphate removal (EBPR) models, which were primarily based on culture-dependent approaches that had predominantly been used to investigate the process. This minireview will focus on the recent advances made in our overall understanding of the EBPR process resulting from the use of 'omic'-based methodologies.     

An arctic community of symbiotic fungi assembled by long‐distance dispersers: phylogenetic diversity of ectomycorrhizal basidiomycetes in Svalbard based on soil and sporocarp DNA

Aim Current evidence from temperate studies suggests that ectomycorrhizal (ECM) fungi require overland routes for migration because of their obligate symbiotic associations with woody plants. Despite their key roles in arctic ecosystems, the phylogenetic diversity and phylogeography of arctic ECM fungi remains little known. Here we assess the phylogenetic diversity of ECM communities in an isolated, formerly glaciated, high arctic archipelago, and provide explanations for their phylogeographic origins. Location Svalbard. Methods We generated and analysed internal transcribed spacer (ITS) nuclear ribosomal DNA sequences from both curated sporocarp collections (from Svalbard) and soil polymerase chain reaction (PCR) clone libraries (from Svalbard and the North American Arctic), compared these with publicly available sequences in GenBank, and estimated the phylogenetic diversity of ECM fungi in Svalbard. In addition, we conducted coalescent analyses to estimate migration rates in selected species. Results Despite Svalbard’s geographic isolation and arctic climate, its ECM fungi are surprisingly diverse, with at least 72 non‐singleton operational taxonomic units (soil) and 109 phylogroups (soil + sporocarp). The most species‐rich genera are Thelephora/Tomentella, Cortinarius and Inocybe, followed by Hebeloma, Russula, Lactarius, Entoloma, Sebacina, Clavulina, Laccaria, Leccinum and Alnicola. Despite the scarcity of available reference data from other arctic regions, the majority of the phylogroups (73.4%) were also found outside Svalbard. At the same time, all putative Svalbard ‘endemics’ were newly sequenced taxa from diverse genera with massive undocumented diversity. Overall, our results support long‐distance dispersal more strongly than vicariance and glacial survival. However, because of the high variation in nucleotide substitution rates among fungi, allopatric persistence since the Pliocene, although unlikely, cannot be statistically rejected. Results from the coalescent analyses suggest recent gene flow among different arctic areas. Main conclusions Our results indicate numerous recent colonization events and suggest that long‐distance, transoceanic dispersal is widespread in arctic ECM fungi, which differs markedly from the currently prevailing view on the dispersal capabilities of ECM fungi. Our molecular evidence indicates that long‐distance dispersal has probably played a major role in the phylogeographic history of some ECM fungi in the Northern Hemisphere. Our results may have implications for studies on the biodiversity, ecology and conservation of arctic fungi in general.     

Serological and molecular diversity in the cattle MHC class I region

Information on major histocompatibility complex (MHC) diversity in cattle is important to aid our understanding of immune responses and may contribute to maintenance of healthy cattle populations. Equally, understanding the mechanisms involved in generating this diversity may shed light on the complex nature of mammalian MHC evolution. The aim of this study was to assess molecular and serological variation within cattle MHC class I molecules and to study the mechanisms generating diversity. To address this aim, sequence variation was examined in 12 serologically assigned alleles from three putative loci and correlated with monoclonal antibody (mAb) binding data. The results demonstrate that both alloantisera and mAbs often fail to distinguish gene products that differ by a significant number of amino acids. Conversely, some mAbs could distinguish alleles differing by only one or two amino acids. Examination of the sequences demonstrates sharing of motifs between alleles, some encoded at distinct loci, supporting the occurrence of interlocus recombination within the cattle MHC class I region. The implications of this for MHC sequence diversity, and functional capability, are discussed.     

Yeast DEL assay detects clastogens

Chromosomal rearrangements, including DNA deletions are involved in carcinogenesis. The deletion (DEL) assay scoring for DNA deletions in the yeast Saccharomyces cerevisiae is able to detect a wide range of carcinogens. Among approximately 60 compounds of known carcinogenic activity, the DEL assay detected 86% correctly whereas the Ames Salmonella assay detected only 30% correctly [R.J. Brennan, R.H. Schiestl, Detecting carcinogens with the yeast DEL assay, Methods Mol. Biol. 262 (2004) 111-124]. Since the DEL assay is highly inducible by DNA double strand breaks, this study examined the utility of the DEL assay for detecting clastogens. Ten model compounds, with varied mechanisms of genotoxicity, were examined for their effect on the frequency of DNA deletions with the DEL assay. The compounds tested were: actinomycin D, camptothecin, methotrexate and 5-fluorodeoxyuridine, which are anticancer agents, noscapine and furosemide are therapeutics, acridine, methyl acrylate and resorcinol are industrial chemicals and diazinon is an insecticide. The in vitro micronucleus assay (IVMN) in CHO cells, a commonly used tool for detection of clastogens, was performed on the same compounds and the results of the two assays were compared. The results of our study show that there is 70% concordance in the presence of metabolic activation (rat liver S9) and 80% concordance in the absence of metabolic activation between the DEL assay and the standard in vitro micronucleus assay. The lack of cytotoxicity observed for four of the ten compounds examined indicates limited diffusion of lipophilic compounds across the yeast cell wall. Thus, the development of a more permeable yeast tester strain is expected to greatly improve concordance of the DEL assay with the IVMN assay. The yeast DEL assay is inexpensive, amenable to automation and requires less expertise to perform than the IVMN. Thus, it has a strong potential as a robust, fast and economical screen for detecting clastogens in vitro.