Direct targeting and rapid isolation of BAC clones spanning a defined chromosome region

To isolate genes of interest in plants, it is essential to construct bacterial artificial chromosome (BAC) libraries from specific genotypes. Construction and organisation of BAC libraries is laborious and costly, especially from organisms with large and complex genomes. In the present study, we developed the pooled BAC library strategy that allows rapid and low cost generation and screening of genomic libraries from any genotype of interest. The BAC library is constructed, directly organised into a few pools and screened for BAC clones of interest using PCR and hybridisation steps, without requiring organization into individual clones. As a proof of concept, a pooled BAC library of approximately 177,000 recombinant clones has been constructed from the barley cultivar Cebada Capa that carries the Rph7 leaf rust resistance gene. The library has an average insert size of 140 kb, a coverage of six barley genome equivalents and is organised in 138 pools of about 1,300 clones each. We rapidly established a single contig of six BAC clones spanning 230 kb at the Rph7 locus on chromosome 3HS. The described low-cost cloning strategy is fast and will greatly facilitate direct targeting of genes and large-scale intra- and inter-species comparative genome analysis.Edwige Isidore and Beatrice Scherrer contributed equally to the work.     

An alternative to radiation hybrid mapping for large-scale genome analysis in barley

The presence of a monosomic gametocidal chromosome (GC) in a barley chromosome addition line of common wheat generates structural aberrations in the barley chromosome as well as in the wheat chromosomes of gametes lacking the GC. A collection of structurally aberrant barley chromosomes is analogous to a panel of radiation hybrid (RH) mapping and is valuable for high-throughput physical mapping. We developed 90 common wheat lines (GC lines) containing aberrant barley 7H chromosomes induced by a gametocidal chromosome, 2C. DNAs isolated from these GC lines provided a panel of 7H chromosomal fragments in a wheat genetic background, comparable with RH mapping panels in mammals. We used this 7H GC panel and the methodology for RH mapping to physically map PCR-based barley markers, SSRs and AFLPs, onto chromosome 7H, relying on polymorphism between the 7H chromosome and the wheat genome. We call this method GC mapping. This study describes a novel adaptation and combination of methods of inducing chromosomal rearrangements to produce physical maps of markers. The advantages of the presented method are similar to RH mapping in that non-polymorphic markers can be used and the mapping panels can be relatively easily obtained. In addition, mapping results are cumulative when using the same mapping set with new markers. The GC lines will be available from the National Bioresources Project-KOMUGI (). Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

A trial platform to develop a tailored theory-based intervention to improve professional practice in the disclosure of a diagnosis of dementia: Study protocol [ISRCTN15871014]

Background

Despite the availability of clinical guidelines for the management of low back pain (LBP), there continues to be wide variation in general practitioners' (GPs') referral rates for lumbar spine x-ray (LSX). This study aims to explain variation in GPs' referral rates for LSX from their accounts of the management of patients with low back pain.

Methods

Qualitative, semi-structured interviews with 29 GPs with high and low referral rates for LSX in North East England. Thematic analysis used constant comparative techniques.

Results

Common and divergent themes were identified among high- and low-users of LSX. Themes that were similar in both groups included an awareness of current guidelines for the use of LSX for patients with LBP and the pressure from patients and institutional factors to order a LSX. Differentiating themes for the high-user group included: a belief that LSX provides reassurance to patients that can outweigh risks, pessimism about the management options for LBP, and a belief that denying LSX would adversely affect doctor-patient relationships. Two specific differentiating themes are considered in more depth: GPs' awareness of their use of lumbar spine radiology relative to others, and the perceived risks associated with LSX radiation.

Conclusion

Several key factors differentiate the accounts of GPs who have high and low rates of referral for LSX, even though they are aware of clinical guideline recommendations. Intervention studies that aim to increase adherence to guideline recommendations on the use of LSX by changing the ordering behaviour of practitioners in primary care should focus on these factors.     

Behavioural responses of invasive American mink Neovison vison to an eradication campaign, revealed by stable isotope analysis

1.  The detrimental impacts of invasive, non-native species on islands are widely acknowledged and it is often best to act rapidly against such species, even where uncertainty exists over the best way to proceed. If management actions are evaluated and refined, using information learnt from the biology of culled animals, this uncertainty can be gradually reduced, increasing the likelihood of a successful outcome.
2.  American mink Neovison vison carcasses were collected as part of an eradication campaign on several islands of the Outer Hebrides, Scotland, and stable isotope analysis was used to describe ecological variation in this invasive non-native predator.
3.  Isotope profiles from individual mink whiskers demonstrated how behaviour at a population level changed markedly over time. As the eradication campaign progressed, mink increased their reliance on marine food sources and focused their activity on the coastline. Stable isotope analyses also demonstrated sex-related changes in foraging and ranging behaviour in relation to food resource availability on the two main island complexes.
4.   Synthesis and applications. Our findings contribute to the refinement of a campaign to extend the successful eradication of mink from Uist and Harris, to the whole of the Outer Hebrides archipelago, UK. They also highlight the potential for stable isotope approaches to provide more detailed postmortem information that can inform adaptive management of wildlife populations for conservation objectives.     

Differential distribution of vanilloid receptors in the primary sensory neurons projecting to the dorsal skin and muscles

We examined transient receptor potential (TRP) V1 and TRPV2 expression in calcitonin gene-related peptide (CGRP) positive (+) primary sensory neurons projecting to the skin and skeletal muscles of the rat dorsum. Among the dorsal root ganglia at the levels from C2 to Th1, 34.9% of neurons projecting to the skin were positive for CGRP, and 32.6% or 21.6% of neurons projecting to the trapezius muscle or the longissimus muscle were positive for CGRP. Of the small CGRP+ neurons projecting to the skin, 53.5% were positive for TRPV1, 11.6% were positive for TRPV2. Of the small CGRP+ neurons projecting to the trapezius or the longissimus, 53.1 or 53.2% were positive for TRPV1, 8.8 or 8.3% were positive for TRPV2, respectively. In the periphery, 29.3% of CGRP+ nerve fibers were positive for TRPV1 in the skin, whereas 65.0 or 59.8% were positive in the trapezius or the longissimus. Therefore, the present study showed that the percentage of CGRP+ neurons projecting to the trapezius is higher than that to the longissimus, and that the co-localization percentage of CGRP and TRPV1 on the sensory nerves was also higher in the trapezius than in the longissimus and the skin.     

Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov.

Three Gram-positive bacterial strains, 7-3, 255-15 and 190-11, previously isolated from Siberian permafrost, were characterized and taxonomically classified. These microorganisms are rod-shaped, facultative aerobic, motile with peritrichous flagella and their growth ranges are from -2.5 to 40 degrees C. The chemotaxonomic markers indicated that the three strains belong to the genus Exiguobacterium. Their peptidoglycan type was A3alpha L-Lys-Gly. The predominant menaquinone detected in all three strains was MK7. The polar lipids present were phosphatidyl-glycerol, diphosphatidyl-glycerol and phosphatidyl-ethanolamine. The major fatty acids were iso-C13:0, anteiso-C13:0, iso-C15:0, C16:0 and iso-C17:0. Phylogenetic analysis based on 16S rRNA and six diverse genes, gyrB (gyrase subunit B), rpoB (DNA-directed RNA polymerase beta subunit), recA (homologous recombination), csp (cold shock protein), hsp70 (ClassI-heat shock protein-chaperonin) and citC (isocitrate dehydrogenase), indicated that the strains were closely related to Exiguobacterium undae (DSM 14481(T)) and Exiguobacterium antarcticum (DSM 14480(T)). On the basis of the phenotypic characteristics, phylogenetic data and DNA-DNA reassociation data, strain 190-11 was classified as E. undae, while the other two isolates, 7-3 and 255-15, comprise a novel species, for which the name Exiguobacterium sibiricum sp. nov. is proposed.     

Interaction of nucleoredoxin with protein phosphatase 2A

A trimeric protein phosphatase 2A (PP2A(T55)) composed of the catalytic (PP2Ac), structural (PR65/A), and regulatory (PR55/B) subunits was isolated from rabbit skeletal muscle by thiophosphorylase affinity chromatography, and contained two additional proteins of 54 and 55 kDa, respectively. The 54 kDa protein was identified as eukaryotic translation termination factor 1 (eRF1) and as a PP2A interacting protein. The 55 kDa protein is now identified as nucleoredoxin (NRX). The formation of a complex between GST-NRX, PP2A(C) and PP2A(D) was demonstrated by pull-down experiments with purified forms of PP2A, and by immunoprecipitation of HA-tagged NRX expressed in HEK293 cells complexed endogenous PP2A subunits. Analysis of PP2A activity in the presence of GST-NRX showed that NRX competed with polycations for both stimulatory and inhibitory effects on different forms of PP2A.     

Crystal structure of the PP2A phosphatase activator: implications for its PP2A-specific PPIase activity

PTPA, an essential and specific activator of protein phosphatase 2A (PP2A), functions as a peptidyl prolyl isomerase (PPIase). We present here the crystal structures of human PTPA and of the two yeast orthologs (Ypa1 and Ypa2), revealing an all alpha-helical protein fold that is radically different from other PPIases. The protein is organized into two domains separated by a groove lined by highly conserved residues. To understand the molecular mechanism of PTPA activity, Ypa1 was cocrystallized with a proline-containing PPIase peptide substrate. In the complex, the peptide binds at the interface of a peptide-induced dimer interface. Conserved residues of the interdomain groove contribute to the peptide binding site and dimer interface. Structure-guided mutational studies showed that in vivo PTPA activity is influenced by mutations on the surface of the peptide binding pocket, the same mutations that also influenced the in vitro activation of PP2Ai and PPIase activity.     

A trans-specific polymorphism in ZC3HAV1 is maintained by long-standing balancing selection and may confer susceptibility to multiple sclerosis

The human ZC3HAV1 gene encodes an antiviral protein. The longest splicing isoform of ZC3HAV1 contains a C-terminal PARP-like domain, which has evolved under positive selection in primates. We analyzed the evolutionary history of this same domain in humans and in Pan troglodytes. We identified two variants that segregate in both humans and chimpanzees; one of them (rs3735007) does not occur at a hypermutable site and accounts for a nonsynonymous substitution (Thr851Ile). The probability that the two trans-specific polymorphisms have occurred independently in the two lineages was estimated to be low (P = 0.0054), suggesting that at least one of them has arisen before speciation and has been maintained by selection. Population genetic analyses in humans indicated that the region surrounding the shared variants displays strong evidences of long-standing balancing selection. Selection signatures were also observed in a chimpanzee population sample. Inspection of 1000 Genomes data confirmed these findings but indicated that search for selection signatures using low-coverage whole-genome data may need masking of repetitive sequences. A case-control study of more than 1,000 individuals from mainland Italy indicated that the Thr851Ile SNP is significantly associated with susceptibility to multiple sclerosis (MS) (odds ratio [OR] = 1.47, 95% confidence intervals [CI]: 1.08-1.99, P = 0.011). This finding was confirmed in a larger sample of 4,416 Sardinians cases/controls (OR = 1.18, 95% CI: 1.037-1.344, P = 0.011), but not in a population from Belgium. We provide one of the first instances of human/chimpanzee trans-specific coding variant located outside the major histocompatibility complex region. The selective pressure is likely to be virus driven; in modern populations, this variant associates with susceptibility to MS, possibly via the interaction with environmental factors.