Guidelines for evaluating performance of oyster habitat restoration should include tidal emersion: reply to Baggett et al.

Baggett et al. (2015) identified a set of three universal environmental variables to be monitored for evaluating all oyster habitat restoration projects: salinity, temperature, and dissolved oxygen. Perhaps evidencing a bias toward subtidal reefs, this set of parameters omits another first-order environmental factor, tidal emersion. Intertidal oyster reefs can be the dominant reef habitat in estuaries, with clear zonation in oyster performance across the intertidal exposure gradient. Therefore, we propose to include tidal emersion as a fourth universal environmental parameter when designing and evaluating oyster restoration projects to better encompass the whole environmental spectrum along which reefs occur

Evaluation of updated Feed Saved breeding values developed in Australian Holstein dairy cattle.

Although selection for increased milk production traits has led to a genetic increase in body weight (BW), the genetic gain in milk production has exceeded the gain in BW, so gross feed efficiency has improved. Nonetheless, greater gains may be possible by directly selecting for a measure of feed efficiency. Australia first introduced Feed Saved (FS) estimated breeding value (EBV) in 2015. Feed Saved combines residual feed intake (RFI) genomic EBV and maintenance requirements calculated from mature BW EBV. The FS EBV was designed to enable the selection of cows for reduced energy requirements with similar milk production. In this study, we used a reference population of 3,711 animals in a multivariate analysis including Australian heifers (AUSh), Australian cows (AUSc), and overseas cows (OVEc) to update the Australian EBV for lifetime RFI (i.e., a breeding value that incorporated RFI in growing and lactating cows) and to recalculate the FS EBV in Australian Holstein bulls (AUSb). The estimates of genomic heritabilities using univariate (only AUSc or AUSh) to trivariate (including the OVEc) analyses were similar. Genomic heritabilities for RFI were estimated as 0.18 for AUSc, 0.27 for OVEc, and 0.36 for AUSh. The genomic correlation for RFI between AUSc and AUSh was 0.47 and that between AUSc and OVEc was 0.94, but these estimates were associated with large standard errors (range: 0.18-0.28). The reliability of lifetime RFI (a component of FS) in the trivariate analysis (i.e., including OVEc) increased from 11% to 20% compared with the 2015 model and was greater, by 12%, than in a bivariate analysis in which the reference population included only AUSc and AUSh. By applying the prediction equation of the 2020 model, the average reliability of the FS EBV in 20,816 AUSb that were born between 2010 and 2020 improved from 33% to 43%. Previous selection strategies-that is, using the predecessor of the Balanced Performance Index (Australian Profit Ranking index) that did not include FS-have resulted in an unfavorable genetic trend in FS. However, this unfavorable trend has stabilized since 2015, when FS was included in the Balanced Performance Index, and is expected to move in a favorable direction with selection on Balanced Performance Index or the Health Weighted Index. Doubling the reference population, particularly by incorporating international data for feed efficiency, has improved the reliability of the FS EBV. This could lead to increased genetic gain for feed efficiency in the Australian industry

Guidelines for evaluating performance of oyster habitat restoration should include tidal emersion: Reply to Baggett et al.

Baggett et al. (2015) identified a set of three universal environmental variables to be monitored for evaluating all oyster habitat restoration projects: salinity, temperature, and dissolved oxygen. Perhaps evidencing a bias toward subtidal reefs, this set of parameters omits another first-order environmental factor, tidal emersion. Intertidal oyster reefs can be the dominant reef habitat in estuaries, with clear zonation in oyster performance across the intertidal exposure gradient. Therefore, we propose to include tidal emersion as a fourth universal environmental parameter when designing and evaluating oyster restoration projects to better encompass the whole environmental spectrum along which reefs occur

Sharing of either phenotypes or genetic variants can increase the accuracy of genomic prediction of feed efficiency.

BACKGROUND Sharing individual phenotype and genotype data between countries is complex and fraught with potential errors, while sharing summary statistics of genome-wide association studies (GWAS) is relatively straightforward, and thus would be especially useful for traits that are expensive or difficult-to-measure, such as feed efficiency. Here we examined: (1) the sharing of individual cow data from international partners; and (2) the use of sequence variants selected from GWAS of international cow data to evaluate the accuracy of genomic estimated breeding values (GEBV) for residual feed intake (RFI) in Australian cows. RESULTS GEBV for RFI were estimated using genomic best linear unbiased prediction (GBLUP) with 50k or high-density single nucleotide polymorphisms (SNPs), from a training population of 3797 individuals in univariate to trivariate analyses where the three traits were RFI phenotypes calculated using 584 Australian lactating cows (AUSc), 824 growing heifers (AUSh), and 2526 international lactating cows (OVE). Accuracies of GEBV in AUSc were evaluated by either cohort-by-birth-year or fourfold random cross-validations. GEBV of AUSc were also predicted using only the AUS training population with a weighted genomic relationship matrix constructed with SNPs from the 50k array and sequence variants selected from a meta-GWAS that included only international datasets. The genomic heritabilities estimated using the AUSc, OVE and AUSh datasets were moderate, ranging from 0.20 to 0.36. The genetic correlations (rg) of traits between heifers and cows ranged from 0.30 to 0.95 but were associated with large standard errors. The mean accuracies of GEBV in Australian cows were up to 0.32 and almost doubled when either overseas cows, or both overseas cows and AUS heifers were included in the training population. They also increased when selected sequence variants were combined with 50k SNPs, but with a smaller relative increase. CONCLUSIONS The accuracy of RFI GEBV increased when international data were used or when selected sequence variants were combined with 50k SNP array data. This suggests that if direct sharing of data is not feasible, a meta-analysis of summary GWAS statistics could provide selected SNPs for custom panels to use in genomic selection programs. However, since this finding is based on a small cross-validation study, confirmation through a larger study is recommended

Sites of persistence of Fusobacterium necrophorum and Dichelobacter nodosus: a paradigm shift in understanding the epidemiology of footrot in sheep

Sites of persistence of bacterial pathogens contribute to disease dynamics of bacterial diseases. Footrot is a globally important bacterial disease that reduces health and productivity of sheep. It is caused by Dichelobacter nodosus, a pathogen apparently highly specialised for feet, while Fusobacterium necrophorum, a secondary pathogen in footrot is reportedly ubiquitous on pasture. Two prospective longitudinal studies were conducted to investigate the persistence of D. nodosus and F. necrophorum in sheep feet, mouths and faeces, and in soil. Molecular tools were used to detect species, strains and communities. In contrast to the existing paradigm, F. necrophorum persisted on footrot diseased feet, and in mouths and faeces; different strains were detected in feet and mouths. D. nodosus persisted in soil and on diseased, but not healthy, feet; similar strains were detected on both healthy and diseased feet of diseased sheep. We conclude that D. nodosus and F. necrophorum depend on sheep for persistence but use different strategies to persist and spread between sheep within and between flocks. Elimination of F. necrophorum would be challenging due to faecal shedding. In contrast D. nodosus could be eliminated if all footrot-affected sheep were removed and fade out of D. nodosus occurred in the environment before re-infection of a foot

Ventricular septal defect in a child with Alport syndrome: a case report

<p>Abstract</p> <p>Background</p> <p>Alport syndrome (AS) is a rare inherited disorder characterized by an inflammation of the kidneys and damage to the glomerular capillaries, ultimately leading to renal failure at an early age. To date, rare reports of cardiac involvement in AS have been described, due in the majority of cases to the higher risk of heart conduction abnormalities in these patients, at times requiring implantation of a transcutaneous pacemaker. An increased risk of hypertension is likewise commonly featured.</p> <p>Case presentation</p> <p>We report the case of a 17-year-old female affected by a very severe early form of AS. A previously unreported association of the syndrome with congenital heart disease (CHD), (in this case membranous ventricular septal defect), is also reported. A possible pathophysiological mechanism underlying the concomitant manifestation of these two disorders is suggested. Complications implicated in surgical treatment of CHD are described. Clinical and therapeutic management of AS with cardiovascular involvement are discussed, and a short literature review performed.</p> <p>Conclusions</p> <p>This first report of a cardiovascular association highlights the possible involvement of collagen mutations in the two pathologies. Even when drug-resistance appears to be responsible for the failure to control secondary hypertension in AS, clonidine may represent a safe, effective option in the normalization of high blood pressure.</p

A method for single pair mating in an obligate parasitic nematode

Parasitic nematode species have extremely high levels of genetic diversity, presenting a number of experimental challenges for genomic and genetic work. Consequently, there is a need to develop inbred laboratory strains with reduced levels of polymorphism. The most efficient approach to inbred line development is single pair mating, but this is challenging for obligate parasites where the adult sexual reproductive stages are inside the host, and thus difficult to experimentally manipulate. This paper describes a successful approach to single pair mating of a parasitic nematode, Haemonchus contortus. The method allows for polyandrous mating behaviour and involves the surgical transplantation of a single adult male worm with multiple immature adult females directly into the sheep abomasum. We used a panel of microsatellite markers to monitor and validate the single pair mating crosses and to ensure that the genotypes of progeny and subsequent filial generations were consistent with those expected from a mating between a single female parent of known genotype and a single male parent of unknown genotype. We have established two inbred lines that both show a significant overall reduction in genetic diversity based on microsatellite genotyping and genome-wide single nucleotide polymorphism. There was an approximately 50% reduction in heterozygous SNP sites across the genome in the MHco3.N1 line compared with the MoHco3(ISE) parental strain. The MHco3.N1 inbred line has subsequently been used to provide DNA template for whole genome sequencing of H. contortus. This work provides proof of concept and methodologies for forward genetic analysis of obligate parasitic nematodes

Effectiveness analysis of resistance and tolerance to infection

<p>Abstract</p> <p>Background</p> <p>Tolerance and resistance provide animals with two distinct strategies to fight infectious pathogens and may exhibit different evolutionary dynamics. However, few studies have investigated these mechanisms in the case of animal diseases under commercial constraints.</p> <p>Methods</p> <p>The paper proposes a method to simultaneously describe (1) the dynamics of transmission of a contagious pathogen between animals, (2) the growth and death of the pathogen within infected hosts and (3) the effects on their performances. The effectiveness of increasing individual levels of tolerance and resistance is evaluated by the number of infected animals and the performance at the population level.</p> <p>Results</p> <p>The model is applied to a particular set of parameters and different combinations of values. Given these imputed values, it is shown that higher levels of individual tolerance should be more effective than increased levels of resistance in commercial populations. As a practical example, a method is proposed to measure levels of animal tolerance to bovine mastitis.</p> <p>Conclusions</p> <p>The model provides a general framework and some tools to maximize health and performances of a population under infection. Limits and assumptions of the model are clearly identified so it can be improved for different epidemiological settings.</p

Development of a cDNA microarray for the measurement of gene expression in the sheep scab mite Psoroptes ovis

Background: Sheep scab is caused by the ectoparasitic mite Psoroptes ovis which initiates a profound cutaneous inflammatory response, leading to the development of the skin lesions which are characteristic of the disease. Existing control strategies rely upon injectable endectocides and acaricidal dips but concerns over residues, eco-toxicity and the development of acaricide resistance limit the sustainability of this approach. In order to identify alternative means of disease control, a deeper understanding of both the parasite and its interaction with the host are required. Methods: Herein we describe the development and utilisation of an annotated P. ovis cDNA microarray containing 3,456 elements for the measurement of gene expression in this economically important ectoparasite. The array consists of 981 P. ovis EST sequences printed in triplicate along with 513 control elements. Array performance was validated through the analysis of gene expression differences between fed and starved P. ovis mites. Results: Sequences represented on the array include homologues of major house dust mite allergens and tick salivary proteins, along with factors potentially involved in mite reproduction and xenobiotic metabolism. In order to validate the performance of this unique resource under biological conditions we used the array to analyse gene expression differences between fed and starved P. ovis mites. These analyses identified a number of house dust mite allergen homologues up-regulated in fed mites and P. ovis transcripts involved in stress responses, autophagy and chemosensory perception up-regulated in starved mites. Conclusion: The P. ovis cDNA microarray described here has been shown to be both robust and reproducible and will enable future studies to analyse gene expression in this important ectoparasite