Identification of the Axin and Frat binding region of glycogen synthase kinase-3.

Glycogen synthase kinase-3 (GSK-3) is a key component of several signaling pathways including those regulated by Wnt and insulin ligands. Specificity in GSK-3 signaling is thought to involve interactions with scaffold proteins that localize GSK-3 regulators and substrates. This report shows that GSK-3 forms a low affinity homodimer that is disrupted by binding to Axin and Frat. Based on the crystal structure of GSK-3, we have used surface-scanning mutagenesis to identify residues that differentially affect GSK-3 interactions. Mutations that disrupt Frat and Axin cluster at the dimer interface explaining their effect on homodimer formation. Loss of the Axin binding site blocks the ability of dominant negative GSK-3 to cause axis duplication in Xenopus embryos. The Axin binding site is conserved within all GSK-3 proteins, and its loss affects both cell motility and gene expression in the nonmetazoan, Dictyostelium. Surprisingly, we find no genetic interaction between a non-Axin-binding GSK-3 mutant and T-cell factor activity, arguing that Axin interactions alone cannot explain the regulation of T-cell factor-mediated gene expression.     

A vegetation analysis of the pastoral landscapes of upland Wales,UK

Abstract. The upland moorlands of Wales are situated on the oceanic fringe of western Europe, and have experienced a long history of pastoral management. Recent vegetation data are analysed to assess the relative contribution of abiotic and anthropogenic factors to variation in habitat composition among the major upland ranges of this region. From a numerical analysis of plant community cover data, recorded from 65 sites covering 260 000 ha, a six‐cluster site classification emerged with striking biogeographical coherence. Direct gradient analysis and variance partitioning revealed strong correlation between vegetation composition and spatially‐structured climatic gradients, in particular temperature, rainfall and oceanicity; differences in bedrock geology appear to have a lesser role. The analysis also indicates a close correlation between habitat variation and anthropogenic parameters, especially grazing intensity, burning frequency, and sulphur and nitrogen deposition levels. At this regional scale, anthropogenic impacts appear to have accentuated, rather than obscured, vegetation patterns which are primarily determined by climate and other abiotic variables. The findings have considerable relevance for conservation planning and also for predictive studies on the consequences of climatic change for the biota of the uplands of southern Britain.     

Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals.

We propose a framework for modeling sequence motifs based on the maximum entropy principle (MEP). We recommend approximating short sequence motif distributions with the maximum entropy distribution (MED) consistent with low-order marginal constraints estimated from available data, which may include dependencies between nonadjacent as well as adjacent positions. Many maximum entropy models (MEMs) are specified by simply changing the set of constraints. Such models can be utilized to discriminate between signals and decoys. Classification performance using different MEMs gives insight into the relative importance of dependencies between different positions. We apply our framework to large datasets of RNA splicing signals. Our best models out-perform previous probabilistic models in the discrimination of human 5' (donor) and 3' (acceptor) splice sites from decoys. Finally, we discuss mechanistically motivated ways of comparing models.     

Genome Sequence of Multidrug-Resistant Escherichia coli EC302/04, Isolated from a Human Tracheal Aspirate

Escherichia coli is an important etiologic agent of lower respiratory tract infections (LRTI). Multidrug-resistant E. coli EC302/04 was isolated from a tracheal aspirate, and its genome sequence is expected to provide insights into antimicrobial resistance as well as adaptive and virulence mechanisms of E. coli involved in LRTI.     

Termination of second trimester pregnancy with laminaria and intramuscular 16 phenoxy-ω-17,18,19,20 tetranor PGE2 methylsuldonylamide (sulprostone) — A randomised study

16 phenoxy-ω-17,18,19,20 tetranor PGE₂ methylsulfonylamide (Sulprostone) was used for termination of second trimester pregnancy in four groups of 30 patients. The drug was administered in intramuscular doses of either 0.5 mg four hourly or 1.0 mg 8 hourly. In two groups of 30 patients a medium size sterile laminaria was inserted into the cervical canal eight hours before the start of prostaglandin treatment. In the group treated with 1.0 mg sulprostone eight hourly, 96.7% of those with laminaria and 86.7% without laminaria aborted in respective mean times of 11.2 hrs and 17.5 hrs. All 30 patients (100%) in the laminaria group treated with 0.5 mg sulprostone four hourly aborted within 30 hours in a mean time of 10.4 hours compared with 26 patients (86.7%) in a mean time of 16.7 hours in the group without laminaria.One patient receiving 0.5 mg sulprostone four hourly (no laminaria) sustained a cervical tear requiring repair. The incidence of nausea, vomiting, diarrhoea, cold and shivering was low and similar in the four groups.     

Cloning and sequencing of complement component C9 and its linkage to DOC-2 in the pufferfish Fugu rubripes

The Japanese pufferfish Fugu rubripes has a 400 Mb genome with high gene density and minimal non-coding complexity, and is therefore an ideal vertebrate model for sequence comparison. The identification of regions of conserved synteny between Fugu and humans would greatly accelerate the mapping and ordering of genes. Fugu C9 was cloned and sequenced as a first step in an attempt to characterize the region in Fugu homologous to human chromosome 5p13. The 11 exons of the Fugu C9 gene share 33% identity with human C9 and span 2.9 kb of genomic DNA. By comparison, human C9 spans 90 kb, representing a 30-fold difference in size. We have also determined by cosmid sequence scanning that DOC-2, a tumour suppresser gene which also maps to human 5p13, lies 6–7 kb from C9 in a head-to-head or 5′ to 5′ orientation. These results demonstrate that the Fugu C9/DOC-2 locus is a region of conserved synteny. Sequence scanning of overlapping cosmids has identified two other genes, GAS-1 and FBP, both of which map to human chromosome 9q22, and lie adjacent to the Fugu C9/DOC-2 locus, indicating the boundary between two syntenic regions.     

Amine group of guanine enhances the binding of norfloxacin antibiotics to DNA.

The binding mode of norfloxacin, a quinolone antibacterial agent, in the synthetic polynucleotides poly[d(G-C)2], poly[d(I-C)2] and poly[d(A-T)2] was studied using polarized light spectroscopy, fluorescence spectroscopy and melting profiles. The absorption, circular and linear dichroism properties of norfloxacin are essentially the same for all the complexes, and the angle of electric transition dipole moment I and II of norfloxacin relative to the DNA helix axis is measured as 68-75 degrees for all complexes. These similarities indicate that the binding mode of norfloxacin is similar for all the polynucleotides. The decrease in the linear dichroism (LD) magnitude at 260 nm upon binding norfloxacin, which is strongest for the norfloxacin-poly[d(G-C)2] complex, and the identical melting temperature of poly[d(A-T)2] and poly[d(I-C)2] in the presence and absence of norfloxacin rule out the possibility of classic intercalation and minor groove binding. However, the characteristics of the fluorescence emission spectra of norfloxacin bound to poly[d(A-T)2] and to poly[d(I-C)2] are similar but are different to that of norfloxacin bound to poly[d(G-C)2]. As the amine group of the guanine base protrudes to the minor groove, this result strongly suggests that norfloxacin binds in the minor groove of B-form DNA in a nonclassic manner.