Population genomics of early events in the ecological differentiation of bacteria

Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observations of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.     

Analysis of the risk of introduction and spread of porcine reproductive and respiratory syndrome virus through importation of raw pigmeat into New Zealand

AIMS: To determine the frequency with which porcine reproductive and respiratory syndrome (PRRS) virus (PRRSv) would become established in a non-commercial pig herd in New Zealand due to illegal feeding of uncooked food waste containing virus-contaminated pigmeat. To determine the likelihood of a single incursion resulting in a multi-farm outbreak of the disease, and describe the spatio-temporal characteristics of such an outbreak.

METHODS: A Monte Carlo simulation model was constructed to determine the expected annual frequency of PRRSv infection being initiated in a non-commercial pig herd as a result of inadvertent feeding of pigmeat imported from countries endemically infected with the disease. Once the likelihood of PRRSv becoming established in a single pig herd was determined, stochastic spatially explicit infectious disease modelling software was utilised to model the temporal and spatial characteristics of the resulting epidemic.

RESULTS: Assuming the proportion of imported pigmeat remained at current levels, consumption patterns of pigmeat in households in New Zealand remained steady, and limited compliance with recently reintroduced regulations to prevent feeding of uncooked food waste, at least 4.3 pig herds per year were predicted to become infected with PRRSv. Simulation modelling of PRRSv epidemics related to initial infection of a non-commercial farm produced an estimate that 36% of these incursions would spread from the initial herd, and that these outbreaks would involve 93 herds on average in the first year. By increasing the estimated persistence of PRRSv infection in small herds, an average of 205 herds became infected in the first year.

CONCLUSIONS: Given a mean of 4.3 infected premises per year and a 36% probability of infection spreading beyond the initial infected herd, there was a 95% likelihood of a multi-farm PRRS outbreak occurring within 3 years.

CLINICAL RELEVANCE: Introduction of PRRSv through importation of virus-contaminated pigmeat presents a high risk for establishment of the disease in the pig industry in New Zealand.     

Prediction of enteric methane production from dairy cows

Abstract

The main objective of this study was to elucidate the potential for prediction of enteric methane (CH₄) emissions from dairy cows by using predicted rumen plus hindgut digested (fermented nutrients) and total tract digested nutrients (by using NorFor) as input variables. Twenty-one experiments (78 dietary treatments) were collected. The data-set was used to develop prediction models and to test their and extant models ability to predict enteric CH₄ emissions. Models were compared based on mean squared prediction error and concordance correlation coefficient (CCC) analysis. Fermented nutrients did not predict enteric CH₄ emissions adequately (CCC < 0.420). Including total digested (td) nutrients in the model [CH₄ (MJ/d) = ?2.13 + 1.64 tdOM (kg/d) ?9.74 tdFat (kg/d) + 1.64 tdNDF (kg/d)] predicted enteric CH₄ emissions more precisely (CCC = 0.733), and showed an improvement in the prediction of enteric CH₄ emissions over the extant models tested.     

Descriptive epidemiological study of the use of antimicrobial drugs by companion animal veterinarians in New Zealand

Abstract

AIM: To describe the patterns of use of antimicrobial drugs by veterinary surgeons treating commonly presented bacterial infections in companion animals in New Zealand.

METHODS: A postal survey of 800 randomly selected companion animal veterinarians practicing in New Zealand was conducted between August and December 2008. Data were collected regarding the antimicrobials prescribed for recent cases of skin, ear and urinary tract infections; the use of culture and susceptibility testing; and veterinarian characteristics such as proportion of time spent treating companion animals and recent attendance at continuing professional development (CPD) events. Potential associations within the data were explored using extended mosaic plots and multivariable regression models.

RESULTS:Completed surveys from 393 respondents were available for analysis, providing data on systemic antimicrobial drug use for 1,799 cases of presumptive bacterial infections. The most frequently prescribed drugs were amoxicillin-clavulanic acid (864 cases, 48%), cephalexin (558, 31%), and fluoroquinolones (198, 11%). Of 359 cases of canine superficial pyoderma, 157 (44%) were treated with amoxicillin-clavulanic acid and 155 (43%) were treated with cephalexin with median reported treatment durations of 7 and 10 days, for these two drugs respectively. Culture and susceptibility tests had been used in 376 of 1,984 (19%) of all reported cases and 160 (43%) of these were suspected urinary tract infections. Practitioners that spent 100% of their time treating companion animals and who had attended a CPD course related to companion animals within the 12 months prior to completing the survey were more likely to submit a sample for culture and susceptibility testing and to prescribe longer courses of antimicrobials for the treatment of canine pyoderma than practitioners who spent less than 100% of their time treating companion animals and had not attended a CPD course in the last 12 months.

CONCLUSIONS: Broad-spectrum drugs considered by the World Health Organisation to be critically important for human health, such as fluoroquinolones and amoxicillin-clavulanic acid, are amongst the most frequently prescribed antimicrobials in companion animal medicine, and these drugs are often prescribed without submitting a sample for culture and susceptibility testing.

CLINICAL RELEVANCE: Many cases of superficial pyoderma were treated for less than the recommended duration of 21 days, which may contribute to a higher rate of recurrent pyoderma and the development of drug resistance within the causal bacteria. Veterinarians should be aware that the use of fluoroquinolones, in particular, should be based upon the results of a culture and susceptibility test.     

Understanding foot-and-mouth disease virus transmission biology: identification of the indicators of infectiousness

The control of foot-and-mouth disease virus (FMDV) outbreaks in non-endemic countries relies on the rapid detection and removal of infected animals. In this paper we use the observed relationship between the onset of clinical signs and direct contact transmission of FMDV to identify predictors for the onset of clinical signs and identify possible approaches to preclinical screening in the field. Threshold levels for various virological and immunological variables were determined using Receiver Operating Characteristic (ROC) curve analysis and then tested using generalized linear mixed models to determine their ability to predict the onset of clinical signs. In addition, concordance statistics between qualitative real time PCR test results and virus isolation results were evaluated. For the majority of animals (71%), the onset of clinical signs occurred 3–4 days post infection. The onset of clinical signs was associated with high levels of virus in the blood, oropharyngeal fluid and nasal fluid. Virus is first detectable in the oropharyngeal fluid, but detection of virus in the blood and nasal fluid may also be good candidates for preclinical indicators. Detection of virus in the air was also significantly associated with transmission. This study is the first to identify statistically significant indicators of infectiousness for FMDV at defined time periods during disease progression in a natural host species. Identifying factors associated with infectiousness will advance our understanding of transmission mechanisms and refine intra-herd and inter-herd disease transmission models.     

Heat Shock Protein 70 and Sex Steroid Receptors in the Follicular Structures of Induced Ovarian Cysts

The purpose of this study was to estimate the expression and relative amounts of estrogen (ER) and progesterone receptors (PR) and their isoforms as well as heat shock protein 70 (HSP70) in ovaries of rats with induced cystic ovarian disease (COD). Primary, secondary, tertiary, atretic and cystic follicles were evaluated by immunohistochemistry and total ovarian proteins were analyzed by Western blot. In the granulosa layer, growing and cystic follicles in the treated group have a higher expression of ERα than growing follicles of control individuals. In the theca interna layer, tertiary follicles presented a significantly higher expression of ERα in the treated group. An increase in total ERα protein was detected in the treated group. Granulosa cells of all growing, atretic and cystic follicles show a lower expression of ERβ in animals with COD, and the total protein expression of ERβ was lower in this group. The expression of PR was lower in the granulosa cell layer of tertiary and cystic follicles in treated animals, and theca interna layer had less intense immunostaining in this group. Although there were no differences in the expression of PR-B by Western blotting, the expression of PR-A was higher and the expression of PR-C was smaller in the treated group. An intense HSP70 immunostaining was observed in the cells of cystic follicles. By Western blotting, higher protein expression of HSP70 was detected in the ovarian samples of the control group than those of the treated ones. Ovaries of animals with COD exhibited an altered steroid receptor expression and subtype balance as compared with control animals, and an increase in HSP70 immunoexpression.     

Predicting the solubility of Cd,Cu, Pb and Zn in uncontaminated Croatian soils under different land uses by applying established regression models

Soil pH, soil organic matter (SOM), dissolved organic carbon (DOC) and total trace metal concentration (M_(tot)) control the solubility of metals in the soil. Several regression models have included these soil chemical variables for the prediction of metal solubility and free metal ion (FMI) concentrations in contaminated soils. We hypothesize that models developed on contaminated soils (after optimization of the coefficients) can be used on samples from uncontaminated sites. Soil samples were collected from unpolluted agricultural and forest soils located in Eastern Croatia and extracted with water to determine the concentrations of Cd, Cu, Pb and Zn. We used these data to test the applicability of three regression models on existing conditions under different land uses. The same predictors issued in the three models and the same regression coefficients were utilized in the present study. The results showed a good correlation between the observed and predicted values of metal solubility. However, the models overestimate the total solution concentration (M_(sol)) and the concentrations of free metal ions (FMI) in solution, and therefore the same regression coefficients were optimized to fit our own observations. This was found to be very successful. The results showed that pH and DOC played a very important role in controlling metal solubility, while SOM and CEC were somewhat less significant. The impact of total soil concentration of metals (M_(tot)) was rather minor. However, we feel that to carry out good predictions of M_(sol) and FMI, the M_(tot) is needed in such regression models.     

Fast recession of a west antarctic glacier

Satellite radar interferometry observations of Pine Island Glacier, West Antarctica, reveal that the glacier hinge-line position retreated 1.2 +/- 0.3 kilometers per year between 1992 and 1996, which in turn implies that the ice thinned by 3.5 +/- 0.9 meters per year. The fast recession of Pine Island Glacier, predicted to be a possible trigger for the disintegration of the West Antarctic Ice Sheet, is attributed to enhanced basal melting of the glacier floating tongue by warm ocean waters.     

A mathematical verification of the reinforced-matrix hypothesis using the Mori-Tanaka theory

This article presents a theoretical verification of the reinforced-matrix hypothesis derived from tensor equations, σ ^W = σ ^f + σ ^m and ε ^W = ε ^f = ε ^m (Wood Sci Technol 32:171–182, 1998; Wood Sci Technol 33:311–325, 1999; J Biomech Eng 124:432–440, 2002), using classical Mori-Tanaka theory on the micromechanics of fiber-reinforced materials (Acta Metall 21:571–574, 1973; Micromechanics — dislcation and inclusions (in Japanese), pp 141–147, 1976). The Mori-Tanaka theory was applied to a small fragment of the cell wall undergoing changes in its physical state, such as those arising from sorption of moisture, maturation of wall components, or action of an external force, to obtain 〈σ ^A〉_D = ϕ·〈σ ^F〉_I + (1−ϕ)·〈σ ^M〉_D−I. When the constitutive equation of each constituent material was applied to the equation 〈σ ^A〉_D = ϕ·〈σ ^F〉_I + (1−ϕ)·〈σ ^M〉_D−I, the equations σ ^W = σ ^f + σ ^m and ε ^W = ε ^f = ε ^m were derived to lend support to the concept that two main phases, the reinforcing cellulose microfibril and the lignin-hemicellulose matrix, coexist in the same domain. The constitutive equations for the cell wall fragment were obtained without recourse to additional parameters such as Eshelby’s tensor S and Hill’s averaged concentration tensors A^F and A^M. In our previous articles, the coexistence of two main phases and σ ^W = σ ^f + σ ^m and ε ^W = ε ^f =ε ^m had been taken as our starting point to formulate the behavior of wood fiber with multilayered cell walls. The present article provides a rational explanation for both concepts.