Comparative proteomics of uropathogenic Escherichia coli during growth in human urine identify UCA-like (UCL) fimbriae as an adherence factor involved in biofilm formation and binding to uroepithelial cells

Uropathogenic Escherichia coli (UPEC) are the primary cause of urinary tract infection (UTI) in humans. For the successful colonisation of the human urinary tract, UPEC employ a diverse collection of secreted or surface-exposed virulence factors including toxins, iron acquisition systems and adhesins. In this study, a comparative proteomic approach was utilised to define the UPEC pan and core surface proteome following growth in pooled human urine. Identified proteins were investigated for subcellular origin, prevalence and homology to characterised virulence factors. Fourteen core surface proteins were identified, as well as eleven iron uptake receptor proteins and four distinct fimbrial types, including type 1, P, F1C/S and a previously uncharacterised fimbrial type, designated UCA-like (UCL) fimbriae in this study. These pathogenicity island (PAI)-associated fimbriae are related to UCA fimbriae of Proteus mirabilis, associated with UPEC and exclusively found in members of the E. coli B2 and D phylogroup. We further demonstrated that UCL fimbriae promote significant biofilm formation on abiotic surfaces and mediate specific attachment to exfoliated human uroepithelial cells. Combined, this study has defined the surface proteomic profiles and core surface proteome of UPEC during growth in human urine and identified a new type of fimbriae that may contribute to UTI.

Using lead sulphate instead of lead oxide in flux growth of yttrium iron garnet(YIG) crystals

Crystal growth of YIG from fluxes containing lead sulphate in place of lead oxide in the usual lead oxide-lead fluoride-boron oxide flux system has been tried. Lead sulphate decomposes during crystal growth giving lead oxide and sulphur trioxide. Due to the influence of sulphur trioxide in the system the yield of crystals almost doubles. There is no change either in the morphology of the crystals or their lattice parameter. It is possible that solubility of YIG is different in the new flux and the changed solubility causes the increase in yield of crystals.

Rapid assessment of genotype-by-environment interactions and heritability for growth rate in aquaculture species using in vitro fertilisation and DNA tagging

Commercial environments may receive only a fraction of expected genetic gains for growth rate as predicted from the selection environment This fraction is the result of undesirable genotype-by-environment interactions (G x E) and measured by the genetic correlation (r(g)) of growth between environments. Rapid estimates of genetic correlation achieved in one generation are notoriously difficult to estimate with precision. A new design is proposed where genetic correlations can be estimated by utilising artificial mating from cryopreserved semen and unfertilised eggs stripped from a single female. We compare a traditional phenotype analysis of growth to a threshold model where only the largest fish are genotyped for sire identification. The threshold model was robust to differences in family mortality differing up to 30%. The design is unique as it negates potential re-ranking of families caused by an interaction between common maternal environmental effects and growing environment. The design is suitable for rapid assessment of G x E over one generation with a true 0.70 genetic correlation yielding standard errors as low as 0.07. Different design scenarios were tested for bias and accuracy with a range of heritability values, number of half-sib families created, number of progeny within each full-sib family, number of fish genotyped, number of fish stocked, differing family survival rates and at various simulated genetic correlation levels

Generalised growth models for aquatic species with an application to blacklip abalone (Haliotis rubra)

This paper presents a maximum likelihood method for estimating growth parameters for an aquatic species that incorporates growth covariates, and takes into consideration multiple tag-recapture data. Individual variability in asymptotic length, age-at-tagging, and measurement error are also considered in the model structure. Using distribution theory, the log-likelihood function is derived under a generalised framework for the von Bertalanffy and Gompertz growth models. Due to the generality of the derivation, covariate effects can be included for both models with seasonality and tagging effects investigated. Method robustness is established via comparison with the Fabens, improved Fabens, James and a non-linear mixed-effects growth models, with the maximum likelihood method performing the best. The method is illustrated further with an application to blacklip abalone (Haliotis rubra) for which a strong growth-retarding tagging effect that persisted for several months was detected

Stochastic growth models for analyzing crustacean data

The contemporary methodology for growth models of organisms is based on continuous trajectories and thus it hinders us from modelling stepwise growth in crustacean populations. Growth models for fish are normally assumed to follow a continuous function, but a different type of model is needed for crustacean growth. Crustaceans must moult in order for them to grow. The growth of crustaceans is a discontinuous process due to the periodical shedding of the exoskeleton in moulting. The stepwise growth of crustaceans through the moulting process makes the growth estimation more complex. Stochastic approaches can be used to model discontinuous growth or what are commonly known as "jumps" (Figure 1). However, in stochastic growth model we need to ensure that the stochastic growth model results in only positive jumps. In view of this, we will introduce a subordinator that is a special case of a Levy process. A subordinator is a non-decreasing Levy process, that will assist in modelling crustacean growth for better understanding of the individual variability and stochasticity in moulting periods and increments. We develop the estimation methods for parameter estimation and illustrate them with the help of a dataset from laboratory experiments. The motivational dataset is from the ornate rock lobster, Panulirus ornatus, which can be found between Australia and Papua New Guinea. Due to the presence of sex effects on the growth (Munday et al., 2004), we estimate the growth parameters separately for each sex. Since all hard parts are shed too often, the exact age determination of a lobster can be challenging. However, the growth parameters for the aforementioned moult processes from tank data being able to estimate through: (i) inter-moult periods, and (ii) moult increment. We will attempt to derive a joint density, which is made up of two functions: one for moult increments and the other for time intervals between moults. We claim these functions are conditionally independent given pre-moult length and the inter-moult periods. The variables moult increments and inter-moult periods are said to be independent because of the Markov property or conditional probability. Hence, the parameters in each function can be estimated separately. Subsequently, we integrate both of the functions through a Monte Carlo method. We can therefore obtain a population mean for crustacean growth (e. g. red curve in Figure 1). [GRAPHICS]

Latitudinal and seasonal effects on growth of the Australian eastern king prawn (Melicertus plebejus)

The growth of the Australian eastern king prawn (Melicertus plebejus) is understood in greater detail by quantifying the latitudinal effect. The latitudinal effect is the change in the species' growth rate during migration. Mark-recapture data (N = 1635, latitude 22.21 degrees S-34.00 degrees S) presents northerly movement of the eastern king prawn, with New South Wales prawns showing substantial average movement of 140 km (standard deviation: 176 km) north. A generalized von Bertalanffy growth model framework is used to incorporate the latitudinal effect together with the canonical seasonal effect. Applying this method to eastern king prawn mark-recapture data guarantees consistent estimates for the latitudinal and seasonal effects. For M. plebejus, it was found that growth rate peaks on 25 and 29 January for males and females, respectively; is at a minimum on 27 and 31 July, respectively; and that the shape parameter, k (per year), changes by -0.0236 and -0.0556 every 1 degree of latitude south increase for males and females, respectively.

Fatigue crack growth rates and fracture toughness in electroslag refined En 52 steel

En 52 steel has been electroslag refined and the resultant effects of refining on its mechanical properties have been assessed. It was found that refining caused a decrease in fatigue crack growth rates and increases in fatigue strength, fracture toughness, Charpy fracture energy and tensile ductility. Fatigue crack growth rates in region I and in region III were found to be considerably lower in the electroslag refined steel: they were unaffected in region II. The fracture toughness values for the electroslag refined steel are nearly twice those estimated for the unrefined steel. Measurements on heat-treated samples have shown that the electroslag refined steel has a better response to heat-treatment. The improvement in the mechanical properties is explained in terms of the removal of nonmetallic inclusions and a reduction in the sulphur content of the steel.

A maximum likelihood approach for estimating growth from tag–recapture data

The Fabens method is commonly used to estimate growth parameters k and l infinity in the von Bertalanffy model from tag-recapture data. However, the Fabens method of estimation has an inherent bias when individual growth is variable. This paper presents an asymptotically unbiassed method using a maximum likelihood approach that takes account of individual variability in both maximum length and age-at-tagging. It is assumed that each individual's growth follows a von Bertalanffy curve with its own maximum length and age-at-tagging. The parameter k is assumed to be a constant to ensure that the mean growth follows a von Bertalanffy curve and to avoid overparameterization. Our method also makes more efficient use nf thp measurements at tno and recapture and includes diagnostic techniques for checking distributional assumptions. The method is reasonably robust and performs better than the Fabens method when individual growth differs from the von Bertalanffy relationship. When measurement error is negligible, the estimation involves maximizing the profile likelihood of one parameter only. The method is applied to tag-recapture data for the grooved tiger prawn (Penaeus semisulcatus) from the Gulf of Carpentaria, Australia.

Accounting for individual variability in the von Bertalanffy growth model

Estimation of von Bertalanffy growth parameters has received considerable attention in fisheries research. Since Sainsbury (1980, Can. J. Fish. Aquat. Sci. 37: 241-247) much of this research effort has centered on accounting for individual variability in the growth parameters. In this paper we demonstrate that, in analysis of tagging data, Sainsbury's method and its derivatives do not, in general, satisfactorily account for individual variability in growth, leading to inconsistent parameter estimates (the bias does not tend to zero as sample size increases to infinity). The bias arises because these methods do not use appropriate conditional expectations as a basis for estimation. This bias is found to be similar to that of the Fabens method. Such methods would be appropriate only under the assumption that the individual growth parameters that generate the growth increment were independent of the growth parameters that generated the initial length. However, such an assumption would be unrealistic. The results are derived analytically, and illustrated with a simulation study. Until techniques that take full account of the appropriate conditioning have been developed, the effect of individual variability on growth has yet to be fully understood.

A simple method for estimating growth parameters from multiple length-frequency data in presence of continuous recruitment

The extended recruitment season for short-lived species such as prawns biases the estimation of growth parameters from length-frequency data when conventional methods are used. We propose a simple method for overcoming this bias given a time series of length-frequency data. The difficulties arising from extended recruitment are eliminated by predicting the growth of the succeeding samples and the length increments of the recruits in previous samples. This method requires that some maximum size at recruitment can be specified. The advantages of this multiple length-frequency method are: it is simple to use; it requires only three parameters; no specific distributions need to be assumed; and the actual seasonal recruitment pattern does not have to be specified. We illustrate the new method with length-frequency data on the tiger prawn Penaeus esculentus from the north-western Gulf of Carpentaria, Australia.

Growth curves with time-dependent explanatory variables

A class of growth models incorporating time-dependent factors and stochastic perturbations are introduced. The proposed model includes the existing growth models used in fisheries as special cases. Particular attention is given to growth of a population (in average weight or length) from which observations are taken randomly each time and the analysis of tag-recapture data. Two real data sets are used for illustration: (a) to estimate the seasonal effect and population density effect on growth of farmed prawn (Penaeus monodon) from weight data and (b) to assess the effect of tagging on growth of barramundi (Lates calcarifer)

Maximum likelihood estimation of mortality and growth with individual variability from multiple length-frequency data

We consider estimation of mortality rates and growth parameters from length-frequency data of a fish stock and derive the underlying length distribution of the population and the catch when there is individual variability in the von Bertalanffy growth parameter L-infinity. The model is flexible enough to accommodate 1) any recruitment pattern as a function of both time and length, 2) length-specific selectivity, and 3) varying fishing effort over time. The maximum likelihood method gives consistent estimates, provided the underlying distribution for individual variation in growth is correctly specified. Simulation results indicate that our method is reasonably robust to violations in the assumptions. The method is applied to tiger prawn data (Penaeus semisulcatus) to obtain estimates of natural and fishing mortality.

Population structure, mortality and growth of Pinna nobilis Linnaeus, 1758 (Mollusca, Bivalvia) at different depths in Moraira bay (Alicante, Western Mediterranean)

An investigation to characterize the causes of Pinna nobilis population structure in Moraira bay (Western Mediterranean) was developed. Individuals of two areas of the same Posidonia meadow, located at different depths (A1, -13 and A2, -6 m), were inventoried, tagged, their positions accurately recorded and monitored from July 1997 to July 2002. On each area, different aspects of population demography were studied (i.e. spatial distribution, size structure, displacement evidences, mortality, growth and shell orientation). A comparison between both groups of individuals was carried out, finding important differences between them. In A1, the individuals were more aggregated and mean and maximum size were higher (A1, 10.3 and A2, 6 individuals/100 m(2); A1, x = 47.2 +/- 9.9; A2, x = 29.8 +/- 7.4 cm, P < 0.001, respectively). In A2, growth rate and mortality were higher, the latter concentrated on the largest individuals, in contrast to A1, where the smallest individuals had the higher mortality rate [A1, L = 56.03(1 - e(-0.17t)); A2, L = 37.59(1 - e(-0.40t)), P < 0.001; mean annual mortality A1: 32 dead individuals out of 135, 23.7% and A2: 16 dead individuals out of 36, 44.4%, and total mortality coefficients (z), z(A1(-30)) = 0.28, z(A1(31-45)) = 0.05, z(A1(46-)) = 0.08; z(A2(-30)) = 0.15, z(A2(31-45)) = 0.25]. A common shell orientation N-S, coincident with the maximum shore exposure, was observed in A2. Spatial distribution in both areas showed not enough evidence to discard a random distribution of the individuals, despite the greater aggregation on the deeper area (A1) (A1, chi(2) = 0.41, df = 3, P > 0.5, A2, chi(2)= 0.98, df = 2 and 0.3 < P < 0.5). The obtained results have demonstrated that the depth-related size segregation usually shown by P. nobilis is mainly caused by differences in mortality and growth among individuals located at different depths, rather than by the active displacement of individuals previously reported in the literature. Furthermore, dwarf individuals are observed in shallower levels and as a consequence, the relationship between size and age are not comparable even among groups of individuals inhabiting the same meadow at different depths. The final causes of the differences on mortality and growth are also discussed.

Evaluation of growth and changes in body composition following neonatal diagnosis of cystic fibrosis

Early deficits in nutritional status that might require specific treatment and early response to nutritional therapy were studied longitudinally in 25 infants with cystic fibrosis (CF) diagnosed by neonatal screening, using anthropometric and research body composition methodology, and evaluation of pancreatic function. At the time of confirmed diagnosis (mean 5.4 weeks), body mass, length, total body fat (TBF), and total body potassium (TBK) were all significantly reduced. Following diagnosis and commencement of therapy there was a normalization of weight, length, and TBK by 6-12 months of age, indicating catch-up growth. But in some individuals the response was incomplete, and as a group, mean total body fat remained significantly lower than normal at 1 year of age. Seven of 25 (28%) were pancreatic sufficient at diagnosis, and all but one had evidence of declining pancreatic function requiring the institution of pancreatic enzyme therapy during the next 1-9 months. The median age of commencement of enzyme therapy was 10 weeks (range 5 weeks to 11 months). These longitudinal assessments emphasize the dynamic changes occurring in absorptive function, body composition, and nutritional status following neonatal diagnosis of cystic fibrosis and may reflect previously described abnormalities of energy metabolism in this age group. Abnormal body composition is evident in most CF infants following diagnosis by neonatal screening but pancreatic damage may still be evolving. We suggest that early active nutritional therapy and surveillance for changes in pancreatic function are warranted in CF infants diagnosed by neonatal screening.