A unique family of proteins associated with internalized membranes in protein storage vacuoles of the Brassicaceae

The protein storage vacuole (PSV) is a specialized organelle in plant seeds that accumulates storage proteins and phytate during seed development. In many plant species, such as tomato and tobacco, the PSV contains two types of microscopically visible intra-organellar inclusions: a large crystalline lattice of membranes and proteins, the crystalloid, and one or a few large phytate crystals, the globoids. In seeds of the family Brassicaceae, the PSVs lack visible crystalloids and have many small globoids dispersed throughout. We biochemically fractionated PSVs from Brassica napus and defined a crystalloid-like fraction that contained integral membrane protein markers found in crystalloids of other plants. Protein analyses identified a previously undescribed family of proteins, the Brassicaceae PSV-embedded proteins (BPEPs), associated with 'crystalloid' and globoid fractions. The defining characteristics of the BPEPs are an N-terminal signal peptide and tandem MATH domains, which may mediate protein-protein interactions. Database analyses indicated that the BPEPs are unique to Brassicaceae. Immunofluorescence studies using anti-BPEP antibodies and antibodies to other biochemical markers to label B. napus and Arabidopsis thaliana seed sections localized the BPEPs to structures within the PSVs, whose appearance was consistent with a diffuse network of internalized membranes and globoids. These results demonstrate that Brassicaceae PSVs contain internalized membranes, and raise the possibility that BPEPs modify these internal membrane structures to yield a PSV morphology different from that of tomato or tobacco.     

Structural and functional characterization of CFE88: evidence that a conserved and essential bacterial protein is a methyltransferase

CFE88 is a conserved essential gene product from Streptococcus pneumoniae. This 227-residue protein has minimal sequence similarity to proteins of known 3D structure. Sequence alignment models and computational protein threading studies suggest that CFE88 is a methyltransferase. Characterization of the conformation and function of CFE88 has been performed by using several techniques. Backbone atom and limited side-chain atom NMR resonance assignments have been obtained. The data indicate that CFE88 has two domains: an N-terminal domain with 163 residues and a C-terminal domain with 64 residues. The C-terminal domain is primarily helical, while the N-terminal domain has a mixed helical/extended (Rossmann) fold. By aligning the experimentally observed elements of secondary structure, an initial unrefined model of CFE88 has been constructed based on the X-ray structure of ErmC' methyltransferase (Protein Data Bank entry 1QAN). NMR and biophysical studies demonstrate binding of S-adenosyl-L-homocysteine (SAH) to CFE88; these interactions have been localized by NMR to the predicted active site in the N-terminal domain. Mutants that target this predicted active site (H26W, E46R, and E46W) have been constructed and characterized. Overall, our results both indicate that CFE88 is a methyltransferase and further suggest that the methyltransferase activity is essential for bacterial survival.     

Temporal Changes between Ecological Regimes in a Range of Primary and Secondary Salinised Wetlands

Many rivers and wetlands in south-western Australia are threatened by salinisation due to rising saline watertables, which have resulted from land clearing and the replacement of deep-rooted perennial species with shallow-rooted annual species. A four to six weekly sampling program of water quality, submerged macrophytes and macroinvertebrates was undertaken at six wetlands, from September 2002 to February 2004, to investigate seasonal variation in a range of primary and secondary saline systems. The wetlands dried and filled at different times in response to local rainfall patterns, and salinities varied accordingly with evapoconcentration and dilution. Two types of clear-water wetlands were recognised; those dominated by submerged aquatic macrophytes (Ruppia, Lepilaena and Lamprothamnium) and those dominated by benthic microbial communities. Two types of turbid wetlands were also recognised; those with high concentrations of phytoplankton and those with high concentrations of suspended sediments. A primary saline lake and two lakes that have only recently been affected by secondary salinisation persisted in a clear, macrophyte-dominated regime throughout most of the study period, except during drying and filling. Two lakes with a long history of secondary salinisation (70 years) moved between regimes over the study period. A clear, benthic microbial community – dominated regime only persisted at the wetland which contained permanent water throughout the study period. The turbid regimes were only present during drying and refilling phases. A richer and more abundant macroinvertebrate fauna was associated with the clear, macrophyte- dominated wetlands. Our results suggest that the development of management guidelines that recognise the presence of different ecological regimes and that consider the interactions between water regime, salinity, and primary and secondary production will be more useful in protecting biodiversity and ecological function in these systems than managing salinity as a single factor.     

Relations in biomedical ontologies

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.     

Phenotypic and genotypic characterization of encapsulated Escherichia coli isolated from blooms in two Australian lakes

Escherichia coli has long been used as an indicator organism for water quality assessment. Recently there has been an accumulation of evidence that suggests some strains of this organism are able to proliferate in the environment, a characteristic that would detract from its utility as an indicator of faecal pollution. Phenotypic and genotypic characterization of E. coli isolated from blooms in two Australian lakes, separated by a distance of approximately 200 km, identified that the blooms were dominated by three E. coli strains. A major phenotypic similarity among the three bloom strains was the presence of a group 1 capsule. Genetic characterization of a conserved region of the cps gene cluster, which encodes group 1 capsules, identified a high degree of genetic variation within the bloom isolates. This differs from previously described encapsulated E. coli strains which are highly conserved at the cps locus. The phenotypic or genotypic profiles of the bloom strains were not identified in 435 E. coli strains isolated from vertebrates. The occurrence of these encapsulated strains suggests that some E. coli have evolved a free-living lifestyle and do not require a host in order to proliferate. The presence of the same three strains in bloom events in different geographical regions of a temperate climate, and at different times, indicates that free-living E. coli strains are able to persist in these water reservoirs. This study provides further evidence of circumstances where caution is required in using E. coli as an indicator organism for water quality.     

Whole-genome patenting

Gene patenting is now a familiar commercial practice, but there is little awareness that several patents claim ownership of the complete genome sequence of a prokaryote or virus. When these patents are analysed and compared to those for other biological entities, it becomes clear that genome patents seek to exploit the genome as an information base and are part of a broader shift towards intangible intellectual property in genomics.     

Protein kinase A as a therapeutic target for memory disorders: rationale and challenges

cAMP-dependent protein kinase A (PKA) signaling has a key role in memory processes and has been identified as a potential therapeutic target for memory disorders. The activation of PKA signaling is crucial for the consolidation of long-term memories dependent on the hippocampus and/or the amygdala, By contrast, initial studies indicate that cAMP-PKA activation might impair the working memory and executive functions of the prefrontal cortex. Furthermore, PKA activation in the nucleus accumbens might increase sensitivity to addiction. These complexities must be heeded when designing medications aimed at altering PKA activity. PKA might be most practical as a therapeutic target in disorders with global alterations in cAMP-PKA activity due to genetic or environmental factors.     

Emerging therapeutic approaches for osteogenesis imperfecta

Osteogenesis imperfecta (OI) is an incurable genetic brittle-bone disease. Although drug therapy, surgery and physiotherapy represent current treatments for OI, the search is ongoing for effective and innovative new therapies targeting the underlying causes of the disease. In this regard, recent advances in the fields of gene and stem-cell therapies have been considerable. In spite of the many challenges that remain, potential new therapies for OI, which have been tested in cell culture systems, animal models and patients, offer hope for the future development of successful therapies. Recent progress in the field is reviewed here.