Fossil biotas from the Okanagan Highlands, southern British Columbia and northeastern Washington State: climates and ecosystems across an Eocene landscape

The late Early to early Middle Eocene Okanagan Highlands fossil sites, spanning -1000 km north-south (northeastern Washington State, southern British Columbia) provide an opportunity to reconstruct biotic communities across a broad upland landscape during the warmest part of the Cenozoic. Plant taxa from these fossil sites are characteristic of the modern eastern North American deciduous forest zone, principally the mixed mesophytic forest, but also include extinct taxa, taxa known only from eastern Asian mesothermal forests, and a small number of taxa restricted to the present-day North American west coast coniferous biome. In this preliminary report, paleoclimates and forest types are reconstructed using collections from Republic in Washington State, USA., and Princeton, Quilchena, Falkland, McAbee, Hat Creek, Horsefly, and Driftwood Canyon in British Columbia, Canada. Both leaf margin analysis (LMA) and quantitative bioclimatic analysis of identified nearest living relatives of megaflora indicated upper microthermal to lower mesothermal moist environments (MAT -10-15 degrees C, CMMT > 0 degrees C, MAP > 100 cm/year). Some taxa common to most sites suggest cool conditions (e.g., Abies, other Pinaceae; Alnus, other Betulaceae). However, all floras contain a substantive broadleaf deciduous element (e.g., Fagaceae, Juglandaceae) and conifers (e.g., Metasequoia) with the bioclimatic analysis yielding slightly higher MAT than LMA. Thermophilic (principally mesothermal) taxa include various insects, the aquatic fern Azolla, palms, the banana relative Ensete, taxodiaceous conifers, Eucommia and Gordonia, taxa which may have occurred near their climatic limits. The mixture of thermophilic and temperate insect and plant taxa indicates low-temperature seasonality (i.e., highly equable climate).

Monitoring PAHs in the Brisbane River and Moreton Bay, Australia, using semipermeable membrane devices and EROD activity in yellowfin bream, Acanthopagrus australis

Two water quality monitoring strategies designed to sample hydrophobic organic contaminants have been applied and evaluated across an expected concentration gradient in PAHs in the Moreton region. Semipermeable membrane devices (SPMDs) that sequester contaminants via passive diffusion across a membrane were used to evaluate the concentration of PAHs at four and five sites in spring and summer 2001/2002, respectively. In addition, induction of hepatic cytochrome P4501, EROD activity, in yellowfin bream, Acanthopagrus australis, captured in the vicinity of SPMD sampling sites following deployment in summer was used as a biomarker of exposure to PAHs and related chemicals. SPMDs identified a clear and reproducible gradient in PAH contamination with levels increasing from east to west in Moreton Bay and upstream in the Brisbane River. The highest PAH concentrations expressed as B(a)P-toxicity equivalents (TEQs) were found in urban areas, which were also furthest upstream and experienced the least flushing. Cytochrome P4501 induction in A. australis was similar at all sites. The absence of clear trends in EROD activity may be attributable to factors not measured in this study or variable residency time of A. australis in contaminated areas. It is also possible that fish in the Moreton region are displaying enzymatic adaptation, which has been reported previously for fish subjected to chronic exposure to organic contaminants. These potential interferences complicate interpretation of EROD activity from feral biota. It is, therefore, suggested that future monitoring combine the two methods by applying passive sampler extracts to in vitro EROD assays. (C) 2004 Elsevier Ltd. All rights reserved.

An automated failure mode and effect analysis based on high-level design specificication with behavior trees

Formal methods have significant benefits for developing safety critical systems, in that they allow for correctness proofs, model checking safety and liveness properties, deadlock checking, etc. However, formal methods do not scale very well and demand specialist skills, when developing real-world systems. For these reasons, development and analysis of large-scale safety critical systems will require effective integration of formal and informal methods. In this paper, we use such an integrative approach to automate Failure Modes and Effects Analysis (FMEA), a widely used system safety analysis technique, using a high-level graphical modelling notation (Behavior Trees) and model checking. We inject component failure modes into the Behavior Trees and translate the resulting Behavior Trees to SAL code. This enables us to model check if the system in the presence of these faults satisfies its safety properties, specified by temporal logic formulas. The benefit of this process is tool support that automates the tedious and error-prone aspects of FMEA.

Identification of the essential histidine residue for high-affinity binding of AlbA protein to albicidin antibiotics

The albA gene from Klebsiella oxytoca encodes a protein that binds albicidin phytotoxins and antibiotics with high affinity. Previously, it has been shown that shifting pH from 6 to 4 reduces binding activity of AlbA by about 30%, indicating that histidine residues might be involved in substrate binding. In this study, molecular analysis of the albA coding region revealed sequence discrepancies with the albA sequence reported previously, which were probably due to sequencing errors. The albA gene was subsequently cloned from K oxytoca ATCC 13182(T) to establish the revised sequence. Biochemical and molecular approaches were used to determine the functional role of four histidine residues (His(78), HiS(125), HiS(141) and His(189)) in the corrected sequence for AlbA. Treatment of AlbA with diethyl pyrocarbonate (DEPC), a histidine-specific alkylating reagent, reduced binding activity by about 95%. DEPC treatment increased absorbance at 240-244 nm by an amount indicating conversion to N-carbethoxyhistidine of a single histidine residue per AlbA molecule. Pretreatment with albicidin protected AlbA against modification by DEPC, with a 1 : 1 molar ratio of albicidin to the protected histidine residues. Based on protein secondary structure and amino acid surface probability indices, it is predicted that HiS125 might be the residue required for albicidin binding. Mutation of HiS125 to either alanine or leucine resulted in about 32% loss of binding activity, and deletion of HiS125 totally abolished binding activity. Mutation of HiS125 to arginine and tyrosine had no effect. These results indicate that HiS125 plays a key role either in an electrostatic interaction between AlbA and albicidin or in the conformational dynamics of the albicidin-binding site.

Flavivirus isolations from mosquitoes collected from Saibai Island in the Torres Strait, Australia, during an incursion of Japanese encephalitis virus

Adult mosquitoes (Diptera: Culicidae) were collected in January and February 2000 from Saibai Island in the Torres Strait of northern Australia, and processed for arbovirus isolation during a period of Japanese encephalitis (JE) virus activity on nearby Badu Island. A total of 84 2 10 mosquitoes were processed for virus isolation, yielding six flavivirus isolates. Viruses obtained were single isolates of JE and Kokobera (KOK) and four of Kunjin (KUN). All virus isolates were from members of the Culex sitiens Weidemann subgroup, which comprised 53.1 % of mosquitoes processed. Nucleotide sequencing and phylogenetic analysis of the pre-membrane region of the genome of JE isolate TS5313 indicated that it was closely related to other isolates from a sentinel pig and a pool of Cx. gelidus Theobald from Badu Island during the same period. Also molecular analyses of part of the envelope gene of KUN virus isolates showed that they were closely related to other KUN virus strains from Cape York Peninsula. The results indicate that flaviviruses are dynamic in the area, and suggest patterns of movement south from New Guinea and north from the Australian mainland.

The impact of changes to heroin supply on blood-borne virus notifications and injecting related harms in New South Wales, Australia

Background: In early 2001 Australia experienced a sudden and unexpected disruption to heroin availability, know as the 'heroin shortage'. This 'shortage has been linked to a decrease in needle and syringe output and therefore possibly a reduction in injecting drug use. We aimed to examine changes, if any, in blood-borne viral infections and presentations for injecting related problems related to injecting drug use following the reduction heroin availability in Australia, in the context of widespread harm reduction measures. Methods: Time series analysis of State level databases on HIV, hepatitis B, hepatitis C notifications and hospital and emergency department data. Examination of changes in HIV, hepatitis B, hepatitis C notifications and hospital and emergency department admissions for injection-related problems following the onset of the heroin shortage; non-parametric curve-fitting of number of hepatitis C notifications among those aged 15 - 19 years. Results: There were no changes observed in hospital visits for injection-related problems. There was no change related to the onset heroin shortage in the number of hepatitis C notifications among persons aged 15 - 19 years, but HCV notifications have subsequently decreased in this group. No change occurred in HIV and hepatitis B notifications. Conclusion: A marked reduction in heroin supply resulted in no increase in injection-related harm at the community level. However, a delayed decrease in HCV notifications among young people may be related. These changes occurred in a setting with widespread, publicly funded harm reduction initiatives.

Interpretation of the temperature dependence of rate constants in biosensor studies

A comparison is made between Arrhenius and transition-state analyses of the temperature dependence of rate constants reported in four published biosensor studies. Although the Eyring transition-state theory seemingly affords a more definitive solution to the problem of characterizing the activation energetics, the analysis is equivocal because of inherent assumptions about reaction mechanism and the magnitude of the transmission coefficient. In view of those uncertainties it is suggested that a preferable course of action entails reversion to the empirical Arrhenius analysis with regard to the energy of activation and a preexponential factor. The former is essentially equivalent to the enthalpy of activation, whereas the magnitude of the latter indicates directly the extent of disparity between the frequency of product formation and the universal frequency factor (temperature multiplied by the ratio of the Boltzmann and Planck constants) and hence the likelihood of a more complicated kinetic mechanism than that encompassed by the Eyring transition-state theory. (C) 2004 Elsevier Inc. All rights reserved.

MHC promoter polymorphism in grey wolves and domestic dogs

A functional immune system requires a tight control over major histocompatibility complex (MHC) gene transcription, as the abnormal MHC expression patterns of severe immunodeficiency and autoimmune diseases demonstrate. Although the regulation of MHC expression has been well documented in humans and mice, little is known in other species. In this study, we detail the level of polymorphism in wolf and dog MHC gene promoters. The promoter regions of the DRB, DQA and DQB locus were sequenced in 90 wolves and 90 dogs. The level of polymorphism was high in the DQB promoters, with variation found within functionally relevant regions, including binding sites for transcription factors. Clear associations between DQB promoters and exon 2 alleles were noted in wolves, indicating strong linkage disequilibrium in this region. Low levels of polymorphism were found within the DRB and DQA promoter regions. However, a variable site was identified within the T box, a TNF-alpha response element, of the DQA promoter. Furthermore, we identified a previously unrecognised 18-base-pair deletion within exon 1 of the DQB locus.