The application of radiography to the study of fish nutrition

The measurement of individual food consumption rates of fish held in groups using radiography has enabled the development of a new approach to fish nutrition trials. In order to compare diets, groups of individually numbered fish are fed different experimental diets over extended periods of time (similar to standard nutrition trials) and food consumption rates are measured regularly over the course of the experiment. Analysis of covariance is then used to compare regression coefficients, obtained from mean consumption-growth relationships, from each diet. The advantages of the approach are several: (1) differences in appetite between fish fed different diets are monitored; (2) fewer fish are needed to establish consumption-growth curves over a large range of consumption rates; (3) measured food consumption rates, not ration levels, are used to calculate 'true' growth efficiencies; and (4) other factors, such as absorption efficiency, trypsin activity, the concentration of free amino acids in tissues and protein turnover can be measured for individual fish and related to differences in food consumption between fish in the same group. The approach has been used successfully with a variety of species to compare the growth response of groups fed two or more diets.     

Purification and characterization of Thermus thermophilus UvrD

The DNA helicase UvrD (helicase II) protein plays an important role in nucleotide excision repair, mismatch repair, rolling circular plasmid replication, and in DNA replication. A homologue of the Escherichia coli uvrD gene was previously identified in Thermus thermophilus; however, to date, a UvrD helicase has not been purified and characterized from a thermophile. Here we report the purification and characterization of a UvrD protein from Thermus thermophilus HB8. The purified UvrD has a temperature range from 10 degrees to >65 degrees C, with an optimum of 50 degrees C, within the temperature limits of the assay. The enzyme had a requirement for divalent metal ions and nucleoside triphosphates which related to enzyme activity in the order ATP > dATP > dGTP > GTP > CTP > dCTP > UTP. A simple real-time helicase assay was developed that should facilitate detailed kinetic studies of the enzyme. Evaluation of helicase substrates using this assay showed that the enzyme was highly active on a double-stranded DNA with 5' recessed ends in comparison with substrates with 3' recessed or blunt ends, and supports enzyme translocation in a 3'-5' direction relative to the strand bound by the enzyme.     

Apple 1-aminocyclopropane-1-carboxylate synthase in complex with the inhibitor L-aminoethoxyvinylglycine. Evidence for a ketimine intermediate

The 1.6-A crystal structure of the covalent ketimine complex of apple 1-aminocyclopropane-1-carboxylate (ACC) synthase with the potent inhibitor l-aminoethoxyvinylglycine (AVG) is described. ACC synthase catalyzes the committed step in the biosynthesis of ethylene, a plant hormone that is responsible for the initiation of fruit ripening and for regulating many other developmental processes. AVG is widely used in plant physiology studies to inhibit the activity of ACC synthase. The structural assignment is supported by the fact that the complex absorbs maximally at 341 nm. These results are not in accord with the recently reported crystal structure of the tomato ACC synthase AVG complex, which claims that the inhibitor only associates noncovalently. The rate constant for the association of AVG with apple ACC synthase was determined by stopped-flow spectrophotometry (2.1 x 10(5) m(-1) s(-1)) and by the rate of loss of enzyme activity (1.1 x 10(5) m(-1) s(-1)). The dissociation rate constant determined by activity recovery is 2.4 x 10(-6) s(-1). Thus, the calculated K(d) value is 10-20 pm.     

Spatially-correlated extinction in a metapopulation model of Leadbeater's Possum

The importance of considering spatially-correlated extinction in metapopulation viability analyses was investigated using a model of the population dynamics of Gymnobelideus leadbeateri McCoy (Leadbeater's Possum). Fire caused local extinction of G. leadbeateri and induced changes in the suitability of the habitat over a period of decades and centuries. Spatially-correlated fires, in which the correlation between the incidence of fire declines with distance, and uniformly-correlated fires were simulated. The predicted risk of metapopulation extinction increased: (i) as the variance in the number of fires each year increased, (ii) as the mean fire interval decreased, and (iii) as the mean dispersal distance decreased. Incorporating spatial correlation in the incidence of fires between patches had little effect on the results, provided the variance in the number of fires per year remained the same and fires modified habitat quality. The predicted risk of metapopulation extinction was greater for spatially-correlated fires than for uniformly-correlated fires when fires only caused local extinction but did not change habitat suitability. Incorporating spatial correlation in the incidence of fire within patches, which allowed partial burning of patches, reduced the predicted risk of extinction. This effect was only slight when patches were smaller than about 50 ha. The results of our simulations demonstrate the importance of considering correlations in disturbance regimes in metapopulation models, especially if these models are used to assist the design of nature reserves.     

Movement and habitat shift responses of juvenile Atlantic Salmon (Salmo salar) to annually permanent stream flooding

Reservoir formation in a river system changes a lotic environment to more lacustrine conditions, with impacts throughout the ecosystem. In this study, a river reach containing typical salmonid riffle/run habitat was flooded to create a large, deep pool from June to September in each of 3 years. We test the hypothesis that juvenile Atlantic salmon (Salmo salar) with their preference for run/riffle habitats will respond to the transformation to a lentic environment by moving into adjacent lotic environments. Movements of juvenile Atlantic salmon were monitored using a combination of biotelemetry (radio- and passive integrated transponder-tagging) and electrofishing. Results showed that no tracked fish moved away from the created pool habitat. Mass-specific growth rates showed the created pool habitat resulted in net growth of juveniles. The results confirm that fish may not immediately (i.e., at least for an approximate 2 months) respond to rapid, large-scale habitat alterations by moving to find similar habitat conditions outside the altered habitat. This is most probably related to plasticity of behavior and habitat use, and no change in biological conditions to a point that would negatively impact fish growth and survival, for example food availability, competition, or predation. The results also support the hypothesis that the relative importance of physical habitat variables is not universal among streams and populations, therefore limiting the value of applying standard habitat suitability criteria and use.     

Campylobacter infection of broiler chickens in a free-range environment

Campylobacter jejuni is the most common cause of bacterial gastroenteritis worldwide, with contaminated chicken meat considered to represent a major source of human infection. Biosecurity measures can reduce C. jejuni shedding rates of housed chickens, but the increasing popularity of free-range and organic meat raises the question of whether the welfare benefits of extensive production are compatible with food safety. The widespread assumption that the free-range environment contaminates extensively reared chickens has not been rigorously tested. A year-long survey of 64 free-range broiler flocks reared on two sites in Oxfordshire, UK, combining high-resolution genotyping with behavioural and environmental observations revealed: (i) no evidence of colonization of succeeding flocks by the C. jejuni genotypes shed by preceding flocks, (ii) a high degree of similarity between C. jejuni genotypes from both farm sites, (iii) no association of ranging behaviour with likelihood of Campylobacter shedding, and (iv) higher genetic differentiation between C. jejuni populations from chickens and wild birds on the same farm than between the chicken samples, human disease isolates from the same region and national samples of C. jejuni from chicken meat.     

Improved Detection of Common Variants Associated with Schizophrenia by Leveraging Pleiotropy with Cardiovascular-Disease Risk Factors

Several lines of evidence suggest that genome-wide association studies (GWASs) have the potential to explain more of the “missing heritability” of common complex phenotypes. However, reliable methods for identifying a larger proportion of SNPs are currently lacking. Here, we present a genetic-pleiotropy-informed method for improving gene discovery with the use of GWAS summary-statistics data. We applied this methodology to identify additional loci associated with schizophrenia (SCZ), a highly heritable disorder with significant missing heritability. Epidemiological and clinical studies suggest comorbidity between SCZ and cardiovascular-disease (CVD) risk factors, including systolic blood pressure, triglycerides, low- and high-density lipoprotein, body mass index, waist-to-hip ratio, and type 2 diabetes. Using stratified quantile-quantile plots, we show enrichment of SNPs associated with SCZ as a function of the association with several CVD risk factors and a corresponding reduction in false discovery rate (FDR). We validate this “pleiotropic enrichment” by demonstrating increased replication rate across independent SCZ substudies. Applying the stratified FDR method, we identified 25 loci associated with SCZ at a conditional FDR level of 0.01. Of these, ten loci are associated with both SCZ and CVD risk factors, mainly triglycerides and low- and high-density lipoproteins but also waist-to-hip ratio, systolic blood pressure, and body mass index. Together, these findings suggest the feasibility of using genetic-pleiotropy-informed methods for improving gene discovery in SCZ and identifying potential mechanistic relationships with various CVD risk factors.     

Loss of Bard1, the heterodimeric partner of the Brca1 tumor suppressor,results in early embryonic lethality and chromosomal instability

The BRCA1 tumor suppressor has been implicated in many cellular pathways, but the mechanisms by which it suppresses tumor formation are not fully understood. In vivo BRCA1 forms a heterodimeric complex with the related BARD1 protein, and its enzymatic activity as a ubiquitin ligase is largely dependent upon its interaction with BARD1. To explore the genetic relationship between BRCA1 and BARD1, we have examined the phenotype of Bard1-null mice. These mice become developmentally retarded and die between embryonic day 7.5 (E7.5) and E8.5. Embryonic lethality results from a severe impairment of cell proliferation that is not accompanied by increased apoptosis. In the absence of p53, the developmental defects associated with Bard1 deficiency are partly ameliorated, and the lethality of Bard1; p53-nullizygous mice is delayed until E9.5. This result, together with the increased chromosomal aneuploidy of Bard1 mutant cells, indicates a role for Bard1 in maintaining genomic stability. The striking similarities between the phenotypes of Bard1-null, Brca1-null, and double Bard1; Brca1-null mice provide strong genetic evidence that the developmental functions of Brca1 and Bard1 are mediated by the Brca1/Bard1 heterodimer.