A novel technique for retrospective genetic analysis of the response to vaccination or infection using cell-free DNA from archived sheep serum and plasma.

Genetic variation is associated with differences in disease resistance and susceptibility among individuals within a population. To date, molecular genetic analyses of host responses have relied on extraction of genomic DNA from whole blood or tissue samples. However, such samples are not routinely collected during large-scale field studies. We demonstrate that cell-free genomic DNA (cfDNA) may be extracted and amplified from archived plasma samples, allowing retrospective analysis of host genetic diversity. This technique was also applicable to archived serum samples up to 35 years old and to different ruminant species. As proof of concept, we used this cfDNA approach to genotype the major histocompatibility complex (MHC) class II DRB1 locus of 224 Merino sheep which had participated in field trials of a commercial Haemonchus contortus vaccine, Barbervax®, in Australia. This identified a total of 51 different DRB1 alleles and their relative frequencies. This is the first study to examine host MHC diversity using DNA extracted from archived plasma samples, an approach that may be applied to retrospective analyses of genetic diversity and responses to vaccination or infection across different species and populations.

Structural and functional diversity arising from intra- and inter-haplotype combinations of duplicated DQA and B loci within the ovine MHC.

In sheep, the A and B loci encoding the α and ß chains of the classical class II MHC molecules are DRA and DRB and DQA and DQB. Previous analyses described the duplication of the DQA and DQB genes. The majority of haplotypes include DQA1 and DQA2 loci, however, in a number of haplotypes, DQA1 appears absent and these haplotypes have been described as DQA1 null. In these haplotypes, the DQA2 locus is found in combination with a second locus which appeared more closely related to DQA2 than DQA1, hence the description of this locus as DQA2-like. Here we combine our previous analysis of the DQA transcripts with an analysis of the associated DQB transcripts in ten haplotypes from MHC homozygous animals. This allows the potential for surface expression of different haplotype combinations of DQA and B genes and the functional significance of DQA2-like and its predicted DQB partner to be determined. Atypical DQB transcripts (DQB2-like) were identified in haplotypes classified as DQA1-null and conserved DQB2-like orthologues were identified in other Bovidae indicating trans-species conservation of the allelic lineage. Functional combinations detected by co-transfection of DQ1, DQ2 and DQ2-like genes demonstrates the potential for a wide range of DQ molecules derived from both intra- and inter-haplotype as well as inter-locus combinations. We provide evidence that DQA2-like and B2-like genes form an evolutionary conserved pair which generates structurally distinct class II molecules that are likely to present a distinct range of peptides to CD4+ T cells.

Evidence-based practice guidelines for prescribing home modifications for clients with bariatric care needs.

BACKGROUND/AIM: Home modifications maintain people's functional independence and safety. No literature exists to guide the prescription of home modifications for clients with bariatric care needs. With Australia's increasing obesity rate, more evidence is needed to support home modification prescribers. This study aimed to map Australian home modification prescribing practices for clients with bariatric care needs and to establish and evaluate a clinical resource for this prescription process. METHODS: The study included two phases. Phase 1 conducted a cross-sectional survey of therapists practicing in Australia, and Australian industry partners who prescribe or install home modifications for clients with bariatric care needs. Phase 2 included design, implementation and evaluation of a clinical resource. Data were analysed with means and frequencies; multivariable regression analysis was used to explore prescribing habits. RESULTS: Therapists surveyed (n = 347) reported 11 different bariatric weight definitions. Less than 3% constantly or regularly prescribed home modifications for these clients; rails were most commonly prescribed. Many therapists (n = 171, 58%) 'never' or 'rarely' knew rail load capacity. Therapists' knowledge of rail load capacity was associated with previous experience prescribing home modifications (P = 0.009); rail manufacturer's advice (P = 0.016) and not using advice from builders (P = 0.001). Clinical resources were used by 11% (n = 26) of therapists to support their prescription, and industry sporadically relied on therapists to specify modification design requirements (n = 5, 45%). Post-implementation of a clinical resource increased consensus regarding understanding of the term bariatric and increased consultation with builders and manufacturers. CONCLUSION: There was a lack of consistency in bariatric terminology, uncertainty of rail load capacities and minimal use of clinical practice guidelines. Additional resources will assist with consistency in prescribing practices to maximise occupational performance for clients with bariatric care needs.

Alcelaphine herpesvirus 1 glycoprotein B: recombinant expression and antibody recognition.

The gammaherpesvirus alcelaphine herpesvirus 1 (AlHV-1) causes fatal malignant catarrhal fever (MCF) in susceptible species including cattle, but infects its reservoir host, wildebeest, without causing disease. Pathology in cattle may be influenced by virus-host cell interactions mediated by the virus glycoproteins. Cloning and expression of a haemagglutinin-tagged version of the AlHV-1 glycoprotein B (gB) was used to demonstrate that the AlHV-1-specific monoclonal antibody 12B5 recognised gB and that gB was the main component of the gp115 complex of AlHV-1, a glycoprotein complex of five components identified on the surface of AlHV-1 by immunoprecipitation and radiolabelling. Analysis of AlHV-1 virus particles showed that the native form of gB was detected by mAb 12B5 as a band of about 70 kDa, whilst recombinant gB expressed by transfected HEK293T cells appeared to be subject to additional cleavage and incomplete post-translational processing. Antibody 12B5 recognised an epitope on the N-terminal furin-cleaved fragment of gB on AlHV-1 virus particles. It could be used to detect recombinant and virus-expressed gB on western blots and on the surface of infected cells by flow cytometry, whilst recombinant gB was detected on the surface of transfected cells by immunofluorescence. Recombinant gB has potential as an antigen for ELISA detection of MCF virus infection and as a candidate vaccine antigen.

An ancient interlocus recombination increases class II MHC DQA diversity in sheep and other Bovidae.

Animals with fully characterised major histocompatibility complex (MHC) regions are often used to explore the molecular interactions that control the induction of adaptive immunity. The ovine MHC includes two DQA loci, termed DQA1 and DQA2. However, in a minority of haplotypes the DQA1 locus appears absent (DQA1 null) and is replaced by a second locus termed, DQA2-like. This raises a number of questions regarding the origins and function of the DQA2-like sequences. To address this, we have analysed DQA diversity associated with 10 MHC haplotypes, including two classified as DQA1 null. Pair-wise comparison between full-length DQA transcripts from each haplotype identified unique diversity throughout the DQA2-like sequences. Conserved orthologues of the DQA2-like sequences were identified in cattle and goat, and phylogenetic analysis clustered exons 1 and 2 with DQA2 whereas the remainder of the sequence clustered with DQA1. The DQA2-like allelic lineage appears functional and to have arisen from an ancient interlocus recombination between DQA1 and DQA2 loci which predates Bovidae speciation.

The effect of the TLR9 ligand CpG-oligodeoxynucleotide on the protective immune response to alcelaphine herpesvirus-1-mediated malignant catarrhal fever in cattle.

We wished to determine the effect of of CpG ODN adjuvant on the magnitude and duration of protective immunity against alcelaphine herpesvirus-1 (AlHV-1) malignant catarrhal fever (MCF), a fatal lymphoproliferative disease of cattle. Immunity was associated with a mucosal barrier of virus-neutralising antibody. The results showed that CpG ODN included either with emulsigen adjuvant and attenuated AlHV-1 (atAlHV-1) or alone with atAlHV-1 did not affect the overall protection from clinical disease or duration of immunity achieved using emulsigen and atAlHV-1. This is in contrast to other similar studies in cattle with BoHV-1 or cattle and pigs with various other immunogens. In addition to this, several other novel observations were made, not reported previously. Firstly, we were able to statistically verify that vaccine protection against MCF was associated with virus-neutralising antibodies (nAbs) in nasal secretions but was not associated with antibodies in blood plasma, nor with total virus-specific antibody (tAb) titres in either nasal secretions or blood plasma. Furthermore, CpG ODN alone as adjuvant did not support the generation of virus-neutralising antibodies. Secondly, there was a significant boost in tAb in animals with MCF comparing titres before and after challenge. This was not seen with protected animals. Finally, there was a strong IFN-γ response in animals with emulsigen and atAlHV-1 immunisation, as measured by IFN-γ secreting PBMC in culture (and a lack of IL-4) that was not affected by the inclusion of CpG ODN. This suggests that nAbs at the oro-nasal-pharyngeal region are important in protection against AlHV-1 MCF.

Large scale transcriptional analysis of MHC class I haplotype diversity in sheep.

Domestic sheep (Ovis aries) have been an important component of livestock agricultural production for thousands of years. Preserving genetic diversity within livestock populations maintains a capacity to respond to changing environments and rapidly evolving pathogens. MHC genetic diversity can influence immune functionality at individual and population levels. Here, we focus on defining functional MHC class I haplotype diversity in a large cohort of Scottish Blackface sheep pre-selected for high levels of MHC class II DRB1 diversity. Using high-throughput amplicon sequencing with three independent sets of barcoded primers we identified 134 MHC class I transcripts within 38 haplotypes. Haplotypes were identified with between two and six MHC class I genes, plus variable numbers of conserved sequences with very low read frequencies. One or two highly transcribed transcripts dominate each haplotype indicative of two highly polymorphic, classical MHC class I genes. Additional clusters of medium, low, and very low expressed transcripts are described, indicative of lower transcribed classical, non-classical and genes whose function remains to be determined.

A novel spliced gene in alcelaphine herpesvirus 1 encodes a glycoprotein which is secreted in vitro.

Herpesviruses often contain cryptic, spliced genes that are not obvious from the initial in silico annotation. Alcelaphine herpesvirus 1 (AlHV-1) contains 72 annotated ORFs but there are also a number of gaps between these that may have protein-coding potential. Comparative analysis of coding potential between AlHV-1 and the related ovine herpesvirus 2 (OvHV-2) revealed a putative novel spliced gene that we have termed A9.5. Analysis of cDNA clones from AlHV-1-infected cells revealed three overlapping clones corresponding to A9.5 and the coding sequence was confirmed by reverse transcription PCR of RNA from AlHV-1-infected cattle tissues. The A9.5 gene was predicted to encode a secreted glycoprotein with molecular mass 19 kDa. Empirical analysis showed that a recombinant haemagglutinin-tagged A9.5 fusion protein was secreted from transfected cells and had a molecular mass of 45 kDa, which was reduced to 20 kDa by endoglycosidase F treatment, confirming that A9.5 was a secreted glycoprotein. In situ RNA hybridization showed that A9.5 was expressed in cells associated with malignant catarrhal fever (MCF) lesions in infected cattle. Detailed analysis of the available OvHV-2 sequences revealed an homologous gene (Ov9.5) with conserved splicing signals and predicted amino acid sequence features in both sequenced isolates of this related virus. We have therefore identified a novel spliced gene in two related macaviruses that is expressed in MCF lesions. Future work will determine its importance for the pathogenesis of disease.

Duration of protective immunity and antibody responses in cattle immunised against alcelaphine herpesvirus-1-induced malignant catarrhal fever.

Protection of cattle from alcelaphine herpesvirus-1 (AlHV-1)-induced malignant catarrhal fever (MCF) has been described previously, using an attenuated virus vaccine in an unlicensed adjuvant. The vaccine was hypothesised to induce a protective barrier of virus-neutralising antibody in the oro-nasal region, supported by the observation of high titre neutralising antibodies in nasal secretions of protected animals. Here we describe further analysis of this vaccine strategy, studying the effectiveness of the vaccine formulated with a licensed adjuvant; the duration of immunity induced; and the virus-specific antibody responses in plasma and nasal secretions. The results presented here show that the attenuated AlHV-1 vaccine in a licensed adjuvant protected cattle from fatal intranasal challenge with pathogenic AlHV-1 at three or six months. In addition, animals protected from MCF had significantly higher initial anti-viral antibody titres than animals that succumbed to disease; and these antibody titres remained relatively stable after challenge, while titres in vaccinated animals with MCF increased significantly prior to the onset of clinical disease. These data support the view that a mucosal barrier of neutralising antibody blocks infection of vaccinated animals and suggests that the magnitude of the initial response may correlate with long-term protection. Interestingly, the high titre virus-neutralising antibody responses seen in animals that succumbed to MCF after vaccination were not protective.

Efficacy of high-throughput transthoracic ultrasonographic screening for on-farm detection of ovine pulmonary adenocarcinoma.

BACKGROUND: The aim of this study was to evaluate the efficacy of high-throughput on-farm transthoracic ultrasound (TUS) to screen for ovine pulmonary adenocarcinoma (OPA), an infectious ovine disease of increasing concern. No other routine diagnosis of preclinical OPA is available, or any vaccine or treatment. METHODS: More than 80,000 rapid TUS scans were applied on farms with a history of OPA. The TUS results from a convenience sample of 171 TUS-negative and 269 TUS-positive sheep were compared with postmortem histology/immunohistochemistry results, the 'gold standard' reference test for OPA diagnosis. These results, together with new data on within-flock prevalence, allowed estimation of the efficacy of rapid TUS screening to identify OPA (defined as tumours of larger than 1 cm) on-farm. RESULTS: The TUS screening had an estimated specificity of 0.998 (95% confidence interval [CI]: 0.998-0.999) and an estimated sensitivity of between 0.76 (95% CI: 0.72-0.79) and 0.99 (95% CI: 0.97-0.99) depending on the presumed false-negative rate applied to the calculation. CONCLUSION: High-throughput TUS should be considered for screening to identify individual sheep with OPA and has potential application to indicate flocks at low risk of OPA. However, lower efficacy is likely if conducted by less experienced persons.

"I see salt everywhere": A qualitative examination of the utility of arts-based participatory workshops to study noncommunicable diseases in Tanzania and Malawi.

The burden of noncommunicable diseases (NCDs) including hypertension, diabetes, and cancer, is rising in Sub-Saharan African countries like Tanzania and Malawi. This increase reflects complex interactions between diverse social, environmental, biological, and political factors. To intervene successfully, new approaches are therefore needed to understand how local knowledges and attitudes towards common NCDs influence health behaviours. This study compares the utility of using a novel arts-based participatory method and more traditional focus groups to generate new understandings of local knowledges, attitudes, and behaviours towards NCDs and their risk factors. Single-gender arts-based participatory workshops and focus group discussions were conducted with local communities in Tanzania and Malawi. Thematic analysis compared workshop and focus group transcripts for depth of content and researcher-participant hierarchies. In addition, semiotic analysis examined the contribution of photographs of workshop activities to understanding participants' experiences and beliefs about NCD risk factors. The arts-based participatory workshops produced in-depth, vivid, emotive narratives of participants' beliefs about NCDs and their impact (e.g., "… it spreads all over your body and kills you-snake's poison is similar to diabetes poison"), while the focus groups provided more basic accounts (e.g., "diabetes is a fast killer"). The workshops also empowered participants to navigate activities with autonomy, revealing their almost overwhelmingly negative beliefs about NCDs. However, enabling participants to direct the focus of workshop activities led to challenges, including the perpetuation of stigma (e.g., comparing smells associated with diabetes symptoms with sewage). Semiotic analysis of workshop photographs provided little additional insight beyond that gained from the transcripts. Arts-based participatory workshops are promising as a novel method to inform development of culturally relevant approaches to NCD prevention in Tanzania and Malawi. Future research should incorporate more structured opportunities for participant reflection during the workshops to minimise harm from any emerging stigma.

Intramammary Immunisation Provides Short Term Protection Against Mannheimia haemolytica Mastitis in Sheep.

Mastitis affects both dairy and meat/wool sheep industries with losses due to reductions in milk quality and quantity, increased treatment costs and restricted lamb growth. Effective vaccines would be important tools for mastitis control. However, the development of vaccines against mastitis has proved challenging due to the failure to target protective immunity to the mammary gland. In order to target responses to the mammary gland, this study tested whether local administration directly into the gland through the teat canal or in the udder skin confers protection against an intramammary infection. In this study, we tested a vaccine that confers protection against respiratory disease caused by Mannheimia haemolytica to determine if it also protects against intramammary infection by the same organism. No evidence of protection was observed in animals that received a subcutaneous immunisation in the udder skin, however, intramammary immunisation provided almost complete protection against an experimental challenge administered 7 days post immunisation but not if the challenge was delivered 14 days post immunisation. To investigate further the nature of this variation in response, the somatic cell count and concentration of cytokines Interleukin-1ß, Interleukin-10 and Interleukin-17A was determined in milk over the course of each study. Intramammary immunisation induced an inflammatory response within the mammary gland, characterised by increases in SCC and in the production of cytokines IL-1ß, IL-10, and IL-17A. This response was similar to that observed in un-vaccinated control animals post challenge. The SCC and cytokine levels had returned to levels comparable with un-vaccinated controls prior to challenge at both 7 and 14 days post immunisation. The transient nature of the protective effect is consistent with the priming of an innate antibacterial response within the mammary gland which provides protection against challenge at 7 days but is diminished by 14 days post-vaccination. Further studies are planned to determine the nature of the innate immune mechanisms associated with the protective effect described here to determine whether it may be exploited to improve ruminant udder health.

Analysis of immune responses to attenuated alcelaphine herpesvirus 1 formulated with and without adjuvant.

The experimental vaccine for bovine malignant catarrhal fever consists of viable attenuated alcelaphine herpesvirus 1 (AlHV-1) derived by extensive culture passage, combined with an oil-in-water adjuvant, delivered intramuscularly. This immunisation strategy was over 80% effective in previous experimental and field trials and protection appeared to be associated with induction of virus-neutralising antibodies. Whether the vaccine virus is required to be viable at the point of immunisation and whether adjuvant is required to induce the appropriate immune responses remains unclear. To address these issues two studies were performed, firstly to analyse immune responses in the presence and absence of adjuvant and secondly, to investigate immune responses to vaccines containing adjuvant plus viable or inactivated AlHV-1. The first study showed that viable attenuated AlHV-1 in the absence of adjuvant induced virus-specific antibodies but the titres of virus-neutralising antibodies were significantly lower than those induced by vaccine containing viable virus and adjuvant, suggesting adjuvant was required for optimal responses. In contrast, the second study found that the vaccine containing inactivated (>99.9%) AlHV-1 induced similar levels of virus-neutralising antibody to the equivalent formulation containing viable AlHV-1. Together these studies suggest that the MCF vaccine acts as an antigen depot for induction of immune responses, requiring adjuvant and a suitable antigen source, which need not be viable virus. These observations may help in directing the development of alternative MCF vaccine formulations for distribution in the absence of an extensive cold chain.

An official nomenclature for the major histocompatibility complex allele sequences from the domestic goat (Capra hircus).

Official allelic nomenclature and corresponding databases of validated major histocompatibility complex (MHC) alleles from most of the major species of farmed livestock are now represented on the IPD-MHC Database. The major exception is the domestic goat (Capra hircus) which can lead to confusion in the research community. Here, we propose to start the process of developing such a resource which will support the research community's interests in livestock population genetics, infectious disease research, vaccine development and comparative studies. In this manuscript, we assign the official nomenclature for the major transcribed and highly polymorphic MHC class II DRB1 locus. Additional class II loci including DRA and DQ and MHC class I loci will be added in the future.

Koeleria macrantha: performance and distribution in relation to soil and plant calcium and magnesium.

• The reported sensitivity of Koeleria macrantha (Poaceae) to soil magnesium, resulting in its absence from South Wales dolomitic limestone, was examined here in relation to varying ionic Ca to Mg ratios, and by cultivation in different limestone soils. • In a growth cabinet experiment, shoot and root Ca and Mg concentration and dry weight yield were determined for five edaphically varied populations of K. macrantha grown from tillers, over a range of Ca : Mg concentrations. The influence of relative concentrations of other nutrients was also investigated. In addition, K. macrantha plants were cultivated on Carboniferous, Magnesian and dolomitic limestone soils. • Total plant Ca: Mg ranged from 0.3 to > 20 mille-equivalents. Optimal substrate ratios (from 25 : 1 to 0.1 : 1), and response to different concentrations of nutrients varied between the populations. Cultivation on dolomitic limestone soil produced the highest yields. • The adverse effect on yields of all populations with low substrate Ca: Mg was much lower than predicted. Results suggest K. macrantha has a higher substrate Mg tolerance than other members of the Poaceae: its reported absence from the South Wales dolomitic limestone is unlikely to be due to soil magnesium sensitivity.

Production of a bovine IL-12p40 probe and application using in situ hybridization on ruminant fixed tissues.

Pro-inflammatory cytokines (particularly IL-12) are important for initiating protective T helper 1 (Th1)-type immune responses and hence vital for combating intracellular infections and tumours. In situ hybridization (ISH) provides a powerful diagnostic tool allowing the identification and localization of cells producing these mediators in fixed tissues. The objective of this work was to produce a bovine IL-12p40 probe that allows detection of IL-12p40 mRNA in fixed tissues from different ruminant species. The RNA probe sequence is 447bp in length and from a region with high cross-species-sequence homology (>97.3% homology) to the ovine, cervine, caprine and bubaline IL-12p40 genes. ISH was carried out on paraformaldehyde fixed tissues collected from cattle, sheep and goats. The probe was efficient in identifying IL-12p40 expressing cells in fixed tissues from all these species. In conclusion, the IL-12p40 probe was efficient in identifying and localizing cells that express IL-12p40, and provides a good immuno-diagnostic technique to characterize immune responses in fixed tissues.

Host gene expression changes in cattle infected with Alcelaphine herpesvirus 1.

Malignant catarrhal fever is a lymphoproliferative disease of cattle and other ungulates caused by infection with gamma-herpesviruses of the genus Macavirus. These viruses do not establish a productive infection but instead replicate in a cell-associated fashion in T lymphocytes, leading to systemic immune dysregulation and a generally fatal outcome. Despite significant progress in understanding the pathology of this disease, its pathogenesis remains unclear. To identify genes and pathways affected in clinical MCF, sixteen bovine GeneCHIP microarrays were used to assay RNA from kidney and lymph node of four MCF-affected and four control Bos taurus steers. This is the first expression study of AlHV-1-MCF in the bovine host. Over 250 genes showed significant changes in gene expression in either lymph node or kidney, while expression of 35 genes was altered in both tissues. Pathway and annotation analysis of the microarray data showed that immune response and inflammatory genes were up-regulated in the kidney while proliferation-associated transcripts were additionally increased in the lymph node. The genes that showed the largest expression rises in both diseased tissues included cytotoxic enzymes and pro-inflammatory chemokines. These data are consistent with disease-induced stimulation of inflammatory responses involving interferon-γ, including cytotoxic T cell recruitment and activation in peripheral tissues containing virus-infected cells. However it remains unclear whether the tissue damage in MCF lesions is due entirely to the activity of infected cells or whether uninfected T cells, recruited and activated at lesion sites through the action of infected cells, contribute to the pathogenesis of MCF.

A useful approach to identify novel small-molecule inhibitors of Wnt-dependent transcription.

The Wnt signaling pathway is frequently deregulated in cancer due to mutations in genes encoding APC, beta-catenin, and axin. To identify small-molecule inhibitors of Wnt signaling as potential therapeutics, a diverse chemical library was screened using a transcription factor reporter cell line in which the activity of the pathway was induced at the level of Disheveled protein. A series of deconvolution studies was used to focus on three compound series that selectively killed cancer cell lines with constitutive Wnt signaling. Activities of the compounds included the ability to induce degradation of beta-catenin that had been stabilized by a glycogen synthase kinase-3 (GSK-3) inhibitor. This screen illustrates a practical approach to identify small-molecule inhibitors of Wnt signaling that can seed the development of agents suitable to treat patients with Wnt-dependent tumors.

The human desmin locus: gene organization and LCR-mediated transcriptional control.

Locus control regions (LCRs) are defined by their ability to confer reproducible physiological levels of transgene expression in mice and therefore thought to possess the ability to generate dominantly a transcriptionally active chromatin structure. We report the first characterization of a muscle-cell-specific LCR, which is linked to the human desmin gene (DES). The DES LCR consists of five regions of muscle-specific DNase I hypersensitivity (HS) localized between -9 and -18 kb 5' of DES and reproducibly drives full physiological levels of expression in all muscle cell types. The DES LCR DNase I HS regions are highly conserved between humans and other mammals and can potentially bind a broad range of muscle-specific and ubiquitous transcription factors. Bioinformatics and direct molecular analysis show that the DES locus consists of three muscle-specific (DES) or muscle preferentially expressed genes (APEG1 and SPEG, the human orthologue of murine striated-muscle-specific serine/threonine protein kinase, Speg). The DES LCR may therefore regulate expression of SPEG and APEG1 as well as DES.