A single nucleotide polymorphism in the coding region of ABL and its effects on sensitivity to imatinib.

We have identified a gene polymorphism (K247R) within or close to the P-loop of BCR-ABL, which leads to the substitution of arginine for lysine. We investigated the allelic frequency of K247R by screening 157 CML patients and 213 healthy blood donors with conventional sequencing, restriction enzyme digest and single strand conformational polymorphism analysis, and found the arginine allele to be rare. Three out of five CML patients with the arginine allele of K247R failed to achieve a major cytogenetic response to imatinib, suggesting that the arginine allele may have reduced sensitivity. However, despite K247R's position in or near to the P-loop, biochemical and cellular assays of imatinib and dasatinib sensitivity showed no alteration compared to wild type. Clinicians should be aware that possession of the arginine allele of K247R does not reflect a mutation that necessitates a change in the therapeutic strategy, unless there are other signs of inadequate response to drug.

Catalytic domains of tyrosine kinases determine the phosphorylation sites within c-Cbl.

Catalytic (SH1) domains of protein tyrosine kinases (PTKs) demonstrate specificity for peptide substrates. Whether SH1 domains differentiate between tyrosines in a physiological substrate has not been confirmed. Using purified proteins, we studied the ability of Syk, Fyn, and Abl to differentiate between tyrosines in a common PTK substrate, c-Cbl. We found that each kinase produced a distinct pattern of c-Cbl phosphorylation, which altered the phosphotyrosine-dependent interactions between c-Cbl and CrkL or phosphatidylinositol 3'-kinase (PI3-K). Our data support the concept that SH1 domains determine the final sites of phosphorylation once PTKs reach their target proteins.

Responses of butterflies to twentieth century climate warming: implications for future ranges.

We analyse distribution records for 51 British butterfly species to investigate altitudinal and latitudinal responses to twentieth century climate warming. Species with northern and/or montane distributions have disappeared from low elevation sites and colonized sites at higher elevations during the twentieth century, consistent with a climate explanation. We found no evidence for a systematic shift northwards across all species, even though 11 out of 46 southerly distributed species have expanded in the northern part of their distributions. For a subset of 35 species, we model the role of climate in limiting current European distributions and predict potential future distributions for the period 2070-2099. Most northerly distributed species will have little opportunity to expand northwards and will disappear from areas in the south, resulting in reduced range sizes. Southerly distributed species will have the potential to shift northwards, resulting in similar or increased range sizes. However, 30 out of 35 study species have failed to track recent climate changes because of lack of suitable habitat, so we revised our estimates accordingly for these species and predicted 65% and 24% declines in range sizes for northern and southern species, respectively. These revised estimates are likely to be more realistic predictions of future butterfly range sizes.

Rapid responses of British butterflies to opposing forces of climate and habitat change.

Habitat degradation and climate change are thought to be altering the distributions and abundances of animals and plants throughout the world, but their combined impacts have not been assessed for any species assemblage. Here we evaluated changes in the distribution sizes and abundances of 46 species of butterflies that approach their northern climatic range margins in Britain-where changes in climate and habitat are opposing forces. These insects might be expected to have responded positively to climate warming over the past 30 years, yet three-quarters of them declined: negative responses to habitat loss have outweighed positive responses to climate warming. Half of the species that were mobile and habitat generalists increased their distribution sites over this period (consistent with a climate explanation), whereas the other generalists and 89% of the habitat specialists declined in distribution size (consistent with habitat limitation). Changes in population abundances closely matched changes in distributions. The dual forces of habitat modification and climate change are likely to cause specialists to decline, leaving biological communities with reduced numbers of species and dominated by mobile and widespread habitat generalists.

Phenotypic and genotypic heterogeneity among cultivable pathogen-related oral spirochetes and Treponema vincentii.

Recent findings challenge the assumption that pathogen-related oral spirochetes (PROS) are related to Treponema pallidum. Treponema vincentii, grown in OMIZ-Pat media, cross-reacted with monoclonal antibody H9-2 against T. pallidum, and cultivable PROS had 16S rRNA gene sequences similar to those of T. vincentii (C.-B. Choi, C. Wyss, and U. B. Göbel. J. Clin. Microbiol. 34:1922-1925, 1996). Aims of the present study were to determine whether antigen phenotypes of oral treponemas were influenced by growth conditions and to evaluate the genetic relatedness of cultivable PROS to T. pallidum and T. vincentii. Results show that three T. pallidum monoclonal antibodies (H9-1, H9-2, and F5) cross-reacted with whole cells from four Treponema species grown in modified OMIZ-Pat medium, but not with treponemas grown in NOS medium. Only H9-2 reacted in immunoblots with reduced proteins from cultivable PROS and T. vincentii. Three of five PROS isolates were amplified by T. vincentii-specific PCR, and one was amplified by Treponema medium-specific PCR. None were amplified by T. pallidum-specific PCR. Three of five PROS isolates had 16S ribosomal DNA restriction fragment length polymorphism patterns identical to that of T. vincentii, and the patterns of two isolates resembled that of T. medium. Arbitrarily primed-PCR profiles from whole genomic DNA were distinct among five PROS isolates and two T. vincentii strains. Thus, PROS isolates represent a heterogeneous group of treponemas that share some 16S rRNA gene sequences with T. vincentii and T. medium, but not with T. pallidum. It is proposed that the PROS nomenclature be dropped.

Identification of seven Treponema species in health- and disease-associated dental plaque by nested PCR.

Species-specific nested PCR was used to detect Treponema amylovorum, Treponema denticola, Treponema maltophilum, Treponema medium, Treponema pectinovorum, Treponema socranskii, and Treponema vincentii in dental plaque. Subjects with periodontitis harbored all species, but T. pectinovorum and T. vincentii were not found in plaque from disease-free subjects.

Phylogenetic and physiological diversity of sulphate-reducing bacteria isolated from a salt marsh sediment.

The phylogenetic and physiological diversity of sulphate-reducing bacteria inhabiting a salt marsh rhizosphere were investigated. Sulphate-reducing bacteria were isolated from a salt marsh rhizosphere using enrichment cultures with electron donors thought to be prevalent in the rhizosphere of Spartina alterniflora. The relationship between phylogeny and nutritional characteristics of 10 strains was investigated. None of the isolates had 16S rRNA sequences identical to other delta subclass sulphate-reducers, sharing 85.3 to 98.1% sequence similarity with 16S rRNA sequences of their respective closest relatives. Phylogenetic analysis placed two isolates, obtained with ethanol as an electron donor, within the Desulfovibrionaceae. Seven isolates, obtained with acetate, butyrate, propionate, or benzoate, were placed within the Desulfobacteriaceae. One isolate, obtained with butyrate, fell within the Desulfobulbus assemblage, which is currently considered part of the Desulfobacteriaceae family. However, due to the phylogenetic breadth and physiological traits of this group, we propose that it be considered a new family, the "Desulfobulbusaceae." The isolates utilised an array of electron donors similar to their closest relatives with a few exceptions. As a whole, the phylogenetic and physiological data indicate isolation of several sulphate-reducing bacteria which might be considered as new species and representative of new genera. Comparison of the Desulfobacteriaceae isolates' 16S rRNA sequences to environmental clones originating from the same study site revealed that none shared more than 86% sequence similarity. The results provide further insight into the diversity of sulphate-reducing bacteria inhabiting the salt marsh ecosystem, as well as supporting general trends in the phylogenetic coherence of physiological traits of delta Proteobacteria sulphate reducers.

Genome sizes of Desulfovibrio desulfuricans, Desulfovibrio vulgaris, and Desulfobulbus propionicus estimated by pulsed-field gel electrophoresis of linearized chromosomal DNA.

Pulsed-field gel electrophoresis (PFGE) of linearized, full-length chromosomal DNA was used to estimate the genome sizes of three species of sulfate-reducing bacteria. Genome sizes of Desulfovibrio desulfuricans, Desulfovibrio vulgaris, and Desulfobulbus propionicus were estimated to be 3.1, 3.6, and 3.7 Mb, respectively. These values are double the genome sizes previously determined for two Desulfovibrio species by two-dimensional agarose gel electrophoresis of DNA cut with restriction enzymes. PFGE of full-length chromosomal DNA could provide a generally applicable method to rapidly determine bacterial genome size and organization.

Phylogenetic and physiological comparisons of PAH-degrading bacteria from geographically diverse soils.

The diversity of bacteria isolated from creosote- contaminated soils in the United States, Norway, and Germany was determined by comparing their ability to degrade polycyclic aromatic hydrocarbons (PAHs), their phospholipid ester-linked fatty acid (GC-FAME) profiles, sole carbon source utilization patterns (Biolog assays), and 16S rRNA sequences. Bacteria were initially obtained by enrichment with phenanthrene and fluoranthene. Many were capable of degrading a broad range of the PAHs found in creosote. Phenanthrene- or fluoranthene-degraders were abundant in most of the soils tested. Several of the fluoranthene-degrading isolates clustered with Sphingomonas (formerly Pseudomonas) paucimobilis strain EPA505 in the GC-FAME and Biolog analyses and three of the isolates examined by 16S rRNA sequence comparisons showed a close relationship with Sphingomonas. In addition, the Sphingomonas strains showed the most extensive degradation of 4- & 5-ring PAHs in creosote. Burkholderia cepacia strains isolated on phenanthrene from PAH-contaminated soils had limited ability to attack higher molecular weight PAHs either individually or in creosote. Thus, degradation capabilities appeared to be associated with members of certain taxa, independent of the origin of the soils from which the bacteria were isolated.