We have created a global map of the effects of polymorphism on gene expression in 400 children from families recruited through a proband with asthma. We genotyped 408,273 SNPs and identified expression quantitative trait loci from measurements of 54,675 transcripts representing 20,599 genes in Epstein-Barr virus-transformed lymphoblastoid cell lines. We found that 15,084 transcripts (28%) representing 6,660 genes had narrow-sense heritabilities (H2) > 0.3. We executed genome-wide association scans for these traits and found peak lod scores between 3.68 and 59.1. The most highly heritable traits were markedly enriched in Gene Ontology descriptors for response to unfolded protein (chaperonins and heat shock proteins), regulation of progression through the cell cycle, RNA processing, DNA repair, immune responses and apoptosis. SNPs that regulate expression of these genes are candidates in the study of degenerative diseases, malignancy, infection and inflammation. We have created a downloadable database to facilitate use of our findings in the mapping of complex disease loci.

Pulmonary research requires models that represent the physiology of alveolar epithelium but concerns with reproducibility, consistency and the technical and ethical challenges of using primary or stem cells has resulted in widespread use of continuous cancer or other immortalized cell lines. The A549 ‘alveolar’ cell line has been available for over four decades but there is an inconsistent view as to its suitability as an appropriate model for primary alveolar type II (ATII) cells. Since most work with A549 cells involves short term culture of proliferating cells, we postulated that culture conditions that reduced proliferation of the cancer cells would promote a more differentiated ATII cell phenotype. We examined A549 cell growth in different media over long term culture and then used microarray analysis to investigate temporal regulation of pathways involved in cell cycle and ATII differentiation; we also made comparisons with gene expression in freshly isolated human ATII cells. Analyses indicated that long term culture in Ham’s F12 resulted in substantial modulation of cell cycle genes to result in a quiescent population of cells with significant up-regulation of autophagic, differentiation and lipidogenic pathways. There were also increased numbers of up- and down-regulated genes shared with primary cells suggesting adoption of ATII characteristics and multilamellar body (MLB) development. Subsequent Oil Red-O staining and Transmission Electron Microscopy confirmed MLB expression in the differentiated A549 cells. This work defines a set of conditions for promoting ATII differentiation characteristics in A549 cells that may be advantageous for studies with this cell line.

In-gel protein kinase assays using myelin basic protein (MBP) as substrate have been used to demonstrate that abscisic acid (ABA) activates an MBP kinase (AMBP kinase) in epidermal peels prepared from leaves of the Argenteum mutant of pea, Pisum sativum L. AMBP kinase has the characteristics of a mitogen-activated protein kinase (MAPK): it utilizes MBP preferentially as an artificial substrate, it is rapidly and transiently activated, it is of the appropriate size (molecular weight c. 45 kDa), requires tyrosine phosphorylation for activity and is tyrosine phosphorylated upon activation. Reverse transcription-PCR was used to generate a previously-cloned MAPK from guard cells, epidermis and mesophyll and immunoblotting using an antibody raised against a mammalian MAPK detected MAPK-related proteins, including one of 45 kDa, in epidermal peels, mesophyll and guard cells. Inhibition of AMBP kinase activation by PD98059, a specific inhibitor of MAPK kinase, and thus MAPK activation, correlated with PD98059-inhibition of ABA-induced stomatal closure and dehydrin gene expression, suggesting that ABA effects in pea epidermal peels require MAPK activation. AMBP kinase was not activated by ABA in guard cells isolated by enzyme treatment. However, a protein kinase of c. 43 kDa was activated by ABA in isolated guard cells, but not in mesophyll or epidermal tissue.

The eects of a number of treatments, both in planta and in vitro, on the accumulation of mRNA encoding dehydrin, an abscisic acid (ABA)-inducible protein, were determined for guard cells and mesophyll cells prepared from leaves of the Argenteum mutant of Pisum sativum L. Guard cells and mesophyll cells treated for 10 d with ABA in planta accumulated dehydrin mRNA. However, after 1 or 3 d treatment, dehydrin mRNA was induced only in guard cells. Wilting induced dehydrin mRNA accumulation in leaves and epidermal cells. Induction of mRNA in epidermal cells was correlated with an increased ABA content after either ABA application or following wilting. Isolated mesophyll and guard cells responded to ABA in vitro by the induction of dehydrin mRNA. However, osmotic stress, imposed by incubation in mannitol, had no eect on ABA and dehydrin mRNA synthesis in mesophyll cells, and only a slight eect on guard cells. Both protein phosphorylation and dephosphorylation were shown to be required for ABA-induced dehydrin gene expression and stomatal movements. Inhibitors of protein kinases (K-252a) and protein phosphatases 1/2A (okadaic acid) and protein phosphatase 2B (cyclosporin A) all inhibited ABA-induced dehydrin mRNA accumulation. They also reduced the inhibitory eects of ABA on stomatal opening, as did the protein kinase activator phorbol myristate acetate (PMA). While K-252a, cyclosporin A and PMA also inhibited ABA-induced stomatal closure, okadaic acid enhanced the ABA eect, indicating the involvement of multiple protein phosphorylation/dephosphorylation steps in ABA signal transduction in guard cells.Abbreviations: ABA = abscisic acid; DAPI = 4¢,6¢-diamidino-2-phenylindole dihydrochloride; DMSO = dimethylsulfoxide; FDA =¯uorescein diacetate; PKC = protein kinase C; PMA = phorbol myristate acetate; PP = protein phosphatase; RIA = radioimmunoassay Correspondence to: S.J. Neill; Fax: 44 (117) 976 3871

Studies of historical isolates inform on the evolution and emergence of important pathogens and phenotypes, including antimicrobial resistance. Crucial to studying antimicrobial resistance are isolates that predate the widespread clinical use of antimicrobials. The Murray collection of several hundred bacterial strains of pre-antibiotic era Enterobacteriaceae is an invaluable resource of historical strains from important pathogen groups. Studies performed on the Collection to date merely exemplify its potential, which will only be realised through the continued effort of many scientific groups. To enable that aim, we announce the public availability of the Murray collection through the National Collection of Type Cultures, and present associated metadata with whole genome sequence data for over half of the strains. Using this information we verify the metadata for the collection with regard to subgroup designations, equivalence groupings and plasmid content. We also present genomic analyses of population structure and determinants of mobilisable antimicrobial resistance to aid strain selection in future studies. This represents an invaluable public resource for the study of these important pathogen groups and the emergence and evolution of antimicrobial resistance.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-015-0222-7) contains supplementary material, which is available to authorized users.