Screening for immune biomarkers associated with infection or protection against Ehrlichia ruminantium by RNA-sequencing analysis.

Heartwater is one of the most economically important tick-borne fatal diseases of livestock. The disease is caused by the bacteria Ehrlichia ruminantium transmitted by Amblyomma ticks. Although there is evidence that interferon-gamma controls E. ruminantium growth and that cellular immune responses are protective, an effective recombinant vaccine for this disease is lacking. Analyses of markers associated with infection as well as protection will lead to a better understanding of the E. ruminantium immune response and corresponding pathways induced in sheep peripheral blood mononuclear cells (PBMC) will assist in development of such a vaccine. In this study, Biomarkers of infection (BMI) were identified as uniquely expressed genes during primary infection and biomarkers of protection (BMP) associated with immune to heartwater were identified post challenge. Sheep were experimentally infected and challenged with E. ruminantium infected ticks. The immune phenotypic and transcriptome profile of their PBMC were compared to their own naïve PBMC collected before infection. The study revealed 305 differentially expressed genes (DEGs) as BMI, of these 17 were upregulated at all three time-points investigated. These DEGs, form part of the bacterial invasion of epithelial cells Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway, and others detected from day 1 post infection and are considered predictive markers for early heartwater infection in ruminants. Similarly, a total of 332 DEGs were identified as BMP, of these 100 were upregulated and 75 were downregulated at all three time-points investigated. However, at D1PC most DEGs were downregulated (n = 1312) that correlated with a reduction in the % CD4 and CD8 T cells detected with flow cytometry. KEGG pathway analyses showed complete down regulation of T cell specific pathways possibly due to homing of immune cells to the site of infection after acquired immunity developed. At D4PC, expression levels of most of these downregulated genes increased and by D6PC they were upregulated. This indicates that the sampling time-point for biomarker analyses is important when results for acquired immune responses are inferred. This data identified DEGs that could be considered as biomarkers of protective immunity that can be used for identification of vaccine antigens and provides a strong foundation to further development of heartwater recombinant vaccines.

Visual parameter optimisation for biomedical image processing.

BACKGROUND: Biomedical image processing methods require users to optimise input parameters to ensure high-quality output. This presents two challenges. First, it is difficult to optimise multiple input parameters for multiple input images. Second, it is difficult to achieve an understanding of underlying algorithms, in particular, relationships between input and output. RESULTS: We present a visualisation method that transforms users' ability to understand algorithm behaviour by integrating input and output, and by supporting exploration of their relationships. We discuss its application to a colour deconvolution technique for stained histology images and show how it enabled a domain expert to identify suitable parameter values for the deconvolution of two types of images, and metrics to quantify deconvolution performance. It also enabled a breakthrough in understanding by invalidating an underlying assumption about the algorithm. CONCLUSIONS: The visualisation method presented here provides analysis capability for multiple inputs and outputs in biomedical image processing that is not supported by previous analysis software. The analysis supported by our method is not feasible with conventional trial-and-error approaches.

Protection of Cattle Elicited Using a Bivalent Lumpy Skin Disease Virus-Vectored Recombinant Rift Valley Fever Vaccine.

Lumpy skin disease and Rift Valley fever are two high-priority livestock diseases which have the potential to spread into previously free regions through animal movement and/or vectors, as well as intentional release by bioterrorists. Since the distribution range of both diseases is similar in Africa, it makes sense to use a bivalent vaccine to control them. This may lead to the more consistent and sustainable use of vaccination against Rift Valley fever through a more cost-effective vaccine. In this study, a recombinant lumpy skin disease virus was constructed in which the thymidine kinase gene was used as the insertion site for the Gn and Gc protective glycoprotein genes of Rift Valley fever virus using homologous recombination. Selection markers, the enhanced green fluorescent protein and Escherichia coli guanidine phosphoribosyl transferase (gpt), were used for selection of recombinant virus and in a manner enabling a second recombination event to occur upon removal of the gpt selection-pressure allowing the removal of both marker genes in the final product. This recombinant virus, LSD-RVF.mf, was selected to homogeneity, characterized and evaluated in cattle as a vaccine to show protection against both lumpy skin disease and Rift Valley fever in cattle. The results demonstrate that the LSD-RVF.mf is safe, immunogenic and can protect cattle against both diseases.

Genetics of schizophrenia in the South African Xhosa.

Africa, the ancestral home of all modern humans, is the most informative continent for understanding the human genome and its contribution to complex disease. To better understand the genetics of schizophrenia, we studied the illness in the Xhosa population of South Africa, recruiting 909 cases and 917 age-, gender-, and residence-matched controls. Individuals with schizophrenia were significantly more likely than controls to harbor private, severely damaging mutations in genes that are critical to synaptic function, including neural circuitry mediated by the neurotransmitters glutamine, γ-aminobutyric acid, and dopamine. Schizophrenia is genetically highly heterogeneous, involving severe ultrarare mutations in genes that are critical to synaptic plasticity. The depth of genetic variation in Africa revealed this relationship with a moderate sample size and informed our understanding of the genetics of schizophrenia worldwide.

Ticks and tick-borne pathogens from wildlife in the Free State Province, South Africa.

Eight ixodid tick species, associated with 59 free-ranging mammals belonging to 10 species, were collected at five different localities in the Free State Province, South Africa. Four of the study areas were nature reserves (Willem Pretorius, Sandveld, Tussen-die-Riviere, and Soetdoring), and one site was a private farm located in Senekal district. The collection was performed from March 2006 until June 2006. Ticks (n=569) and tissues from animals (n=52) were analyzed by polymerase chain reaction, reverse line blot, and sequencing for various tick-borne pathogens belonging to the genera Babesia, Theileria, Anaplasma, and Ehrlichia. Rhipicephalus (Boophilus) microplus, the known vector of Babesia bovis responsible for Asiatic redwater in South Africa, was found for the first time in the Free State Province. Rhipicephalus warburtoni [corrected] also was collected in areas in the Free State where it has not been previously described. Anaplasma marginale was detected for the first time in a gemsbok (Oryx gazella gazella). Gene sequences recovered in this study were 98-100% homologous with GenBank sequences for Anaplasma bovis, Theileria separata, and Theileria sp. Malelane sable antelope.

The composite interleukin-1 genotype in South Africa.

OBJECTIVE: The objective of this study was to evaluate the association between the interleukin-1 composite gene polymorphism and the severity of periodontal disease in the Xhosa population of South Africa. BACKGROUND: Periodontitis is a bacterially-induced chronic inflammatory disease that destroys the tooth supporting tissues. A specific pattern of interleukin-1 polymorphisms (known as the composite IL-1 genotype) has been found to influence the severity of chronic periodontitis in some ethnic groups. METHODS: Ninety-nine subjects, 35-60 years of age, of Xhosa descent, who were non-smokers and free of systemic disease, were enrolled in a case-control study depending on their periodontal status (healthy to mild vs. moderate to severe disease). A buccal smear was obtained from each subject; the DNA was isolated then amplified using the polymerase chain reaction (PCR). Allele identification was either by real-time PCR or by size fractionation following restriction digestion and separation on a polyacrylamide gel. RESULTS: The prevalence of the composite genotype was only 6% in the 99 subjects of the study population, which occurred more frequently in "cases" (8.2%) than in "controls" (4%). The frequency of IL-1A +4845 allele 2 genotype was 47% in cases and 22% in controls (p = 0.009), and that for IL-1B +3954 was 14.3% in cases and 20% in controls (p = 0.595). CONCLUSIONS: This study demonstrated that the IL-1 composite polymorphism occurred among only few subjects in the Xhosa population of South Africa, and so was not significantly associated with the severity of chronic periodontitis in this population.

A multi-epitope DNA vaccine co-administered with monophosphoryl lipid A adjuvant provides protection against tick transmitted Ehrlichia ruminantium in sheep.

Previously, a heartwater experimental DNA vaccine provided 100% protection following laboratory challenge with Ehrlichia ruminantium administered by needle but not against an E. ruminantium tick challenge in the field. A multi-epitope DNA vaccine incorporating both CD4+ and CD8+ cytotoxic T lymphocytes epitopes could provide a better alternative. In this study, we investigated the use of multi-epitope DNA vaccines against an E. ruminantium experimental tick challenge in sheep. The multi-epitope DNA vaccines were delivered via the intramuscular route and intradermal route using the gene gun in the presence of monophosphoryl lipid A (MPL) adjuvant, which was either applied topically to the gene gun inoculation site or co-administered with the vaccine via the intramuscular route. Initially two constructs namely, pSignal plus and pLamp were tested with MPL applied topically only and no protection was obtained in this formulation. However, when pLamp was co-administered with MPL via the intramuscular route in addition to topical application, its protective efficiency improved to protect 60% of the sheep against tick challenge. In this formulation, the vaccine induced enhanced activation of memory T cell responses both before and after challenge with variations amongst the different sheep possibly due to their different genetic backgrounds. In conclusion, this study showed that a heartwater multi-epitope DNA vaccine, co-administered with MPL adjuvant can protect sheep following a laboratory E. ruminantium tick challenge.

Identification and characterisation of conserved epitopes of E. ruminantium that activate Th1 CD4+ T cells: Towards the development of a multi-epitope vaccine.

Several studies have shown that cytotoxic T lymphocytes (CTL) require CD4 + Th1 epitopes to generate strong immune responses to intracellular pathogens. However, not much is known about Ehrlichia ruminantium epitopes, particularly those that can be considered potential candidates for inclusion in a multi-epitope vaccine. In order to identify CD4+ Th1 epitopes that induce IFNγ, a number of proteins previously identified as immunogenic were first screened to determine if they induce cellular immunity in tick infected immune sheep PBMC. Significant IFN-γ production and other Th1 cytokines were evident for 10 recombinant proteins in all sheep tested. Secondly, peptides (n = 246) derived from the top 10 E. ruminantium vaccine candidate proteins were assayed using enzyme linked immunospot (ELISPOT) assay, quantitative real-time PCR and flow cytometry. Of the 246 peptides, 23 peptides, Erum0660 (p0660-42), Erum1150 (p1150-18, p1150-19), Erum2540 (p2540-6, p2540-16, p2540-19, p2540-20, p2540-21), Erum5420 (p5420-13, p5420-14), Erum7140 (p7140-6, p7140-7, p7140-12, p7140-13, p7140-20), Erum7320 (p7320-8, p7320-9, p7320-21), Erum7350 (p7350-9), Erum7360 (p7360-8), Erum7620 (p7620-2, p7620-12) and Erum8010 (p8010-8) were identified that stimulate the best and different cell mediated immune responses. Amino acid sequences of these peptides except for p7140-12, p7140-13, p7140-20, and p7350-9 were conserved between 13 different local strains. These peptides could efficiently induce memory CD4+ T cells to rapidly proliferate and significantly increase IFN-γ production in immune sheep PBMC. The upregulation of pro-inflammatory cytokines, which include, IL-1α, IL-2, IL-12p40, TNF-α, IFN-γ, inducible nitric oxide synthase (iNOS) and granulocyte-macrophage colony stimulating factor (GM-CSF) was also detected. Our results show that these peptides could serve as promising candidates for a multi-epitope vaccine against E. ruminantium.

Ehrlichia ruminantium antigens and peptides induce cytotoxic T cell responses in vitro.

Since CD8+ T cells play an important role in resistance to infection with heartwater, effective vaccines against this disease will likely require identification of antigens that contain CD8+ T cell epitopes responsible for cytotoxic T lymphocyte (CTL) responses. With the use of the fluorescent antigen-transfected target cell (FATT)-CTL assay, IFN-γ ELISPOT and flow cytometry, peptides that induce CTL, proliferation of CD8 + T cells and IFN-γ production were identified as possible target antigens for vaccine development. Of particular relevance was the finding that different peptides from different antigens were able to elicit varied cytotoxic activities by immune peripheral blood mononuclear cells (PBMC) from heartwater immune tick-infected sheep. Several peptides derived from Erum0660, Erum2330, Erum2540, Erum2580 and Erum5000 induced CTL in immune sheep PBMC. Peptide Erum2540-6 was the only peptide that induced significant CTL, CD8+CD45RO+ and CD8+IFN-γ+ by PBMC from all three sheep, and Erum2540 and p2540-20 induced the highest % CTL response in all three outbred sheep. These results suggest that these epitopes may be of major importance in heartwater recombinant vaccine development.

A quantitative real-time PCR assay for Ehrlichia ruminantium using pCS20.

Heartwater is a tick borne disease that affects ruminants and wild animals in Africa south of the Sahara. It is caused by Ehrlichia ruminantium and transmitted by the tick Amblyomma hebraeum. The protocols currently used to detect heartwater take several days to complete. Here, we describe the development of a pCS20 quantitative real-time PCR TaqMan probe assay to detect E. ruminantium in livestock blood and ticks from the field. The assay is based on the conserved pCS20 gene region of E. ruminantium that contains two overlapping genes, rnc and ctaG [Collins, N.E., Liebenberg, J., De Villiers, E.P., Brayton, K.A., Louw, E., Pretorius, A., Faber, F.E., Van Heerden, H., Josemans, A., Van Kleef, M., Steyn, H.C., Van Strijp, M.F., Zweygarth, E., Jongejan, F., Maillard, J.C., Berthier, D., Botha, M., Joubert, F., Corton, C.H., Thomson, N.R., Allsopp, M.T., Allsopp, B.A., 2005. The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number. PNAS 102, 838-843]. The pCS20 quantitative real-time PCR TaqMan probe was compared to the currently used pCS20 PCR and PCR/32P-probe test with regards to sensitivity, specificity and the ability to detect DNA in field samples and in blood from experimentally infected sheep. This investigation showed that the pCS20 quantitative real-time PCR TaqMan probe was the most sensitive assay detecting seven copies of DNA/mul of cell culture. All three assays, however, cross react with Ehrlichia canis and Ehrlichia chaffeensis. The pCS20 real-time PCR detected significantly more positive field samples. Both the PCR and pCS20 real-time PCR could only detect E. ruminantium parasites in the blood of experimentally infected sheep during the febrile reaction. The PCR/32P-probe assay, however, detected the parasite DNA 1 day before and during the febrile reaction. Thus, because this new quantitative pCS20 real-time PCR TaqMan probe assay was the most sensitive and can be performed within 2h it is an effective assay for epidemiological surveillance and monitoring of infected animals.

Innate immune transcriptomic evaluation of PBMC isolated from sheep after infection with E. ruminantium Welgevonden strain.

Heartwater is a tick-borne non-infectious fatal disease of wild and domestic ruminants caused by the bacterium Ehrlichia ruminantium, transmitted by Amblyomma ticks. Although there is evidence that interferon-gamma (IFN-γ) controls E. ruminantium growth and that cellular immune responses could be protective, an effective recombinant vaccine for this disease is lacking. An overall analysis of which immune pathways are up- or down-regulated in sheep peripheral blood mononuclear cells is expected to lead to a better understanding of the global immune response of sheep to E. ruminantium infection. Therefore, a systems biology oriented approach following the infection with E. ruminantium was investigated from peripheral blood mononuclear cells to aid recombinant vaccine development. In this study, heartwater naïve sheep were infected and challenged by allowing E. ruminantium infected ticks to feed on them. After primary infection, all the animals were treated with antibiotic during the resulting febrile response. Blood was collected daily for E. ruminantium detection by qPCR (pCS20 assay). The pCS20 assay only detected the pathogen in the blood one day prior to and during the febrile stage of infection confirming infection of the sheep. IFN-γ real-time PCR indicated that this cytokine was expressed at specific time points: post infection, during the febrile stage of the disease and after challenge. These were used as a guide to select samples for transcriptome sequencing. This paper focuses on transcripts that are associated with innate activating pathways that were identified to be up- and down-regulated after primary infection and the subsequent challenge. These included the CD14 monocyte marker, toll-like receptor (TLR), nod-like receptor, chemokine, cytosolic and cytokine-cytokine interaction receptor pathways. In particular, TLR4, TLR9 and CD14 were activated together with DNA detection pathways, suggesting that vaccine formulations may be improved if CpG motifs and lipopolysaccharides are included. This data indicates that innate immune activation, perhaps by using adjuvants, should be an important component for consideration during future heartwater recombinant vaccine development.

Visual analysis of multivariate state transition graphs.

We present a new approach for the visual analysis of state transition graphs. We deal with multivariate graphs where a number of attributes are associated with every node. Our method provides an interactive attribute-based clustering facility. Clustering results in metric, hierarchical and relational data, represented in a single visualization. To visualize hierarchically structured quantitative data, we introduce a novel technique: the bar tree. We combine this with a node-link diagram to visualize the hierarchy and an arc diagram to visualize relational data. Our method enables the user to gain significant insight into large state transition graphs containing tens of thousands of nodes. We illustrate the effectiveness of our approach by applying it to a real-world use case. The graph we consider models the behavior of an industrial wafer stepper and contains 55 043 nodes and 289 443 edges.

Immune gene expression profiling of PBMC isolated from horses vaccinated with attenuated African horsesickness virus serotype 4.

Development of African horsesickness (AHS) subunit vaccines will have to include a rational approach that uses knowledge of how the virus interacts with the host immune system. The global in vivo immune response induced by attenuated AHSV serotype 4 in horses was characterised using transcriptome sequencing. PBMC were collected with 24h intervals for four days after inoculation and four days after a second boost, 21 days later. Transcriptome data were normalised to the day 0 naïve transcriptome and up- or down-regulated immune genes identified using the CLC workbench. Peak expression was observed 24h after each inoculation. Innate immunity was up-regulated after both inoculations and was characterised by type-1 interferon activation via the RIG-1/MDA5 pathway and the up-regulation of complement cascade components. After the second boost an adaptive immune response could be identified that included the production of cytokines indicative of T helper (Th)1, Th2 and Th17 responses.

African horse sickness virus serotype 4 antigens, VP1-1, VP2-2, VP4, VP7 and NS3, induce cytotoxic T cell responses in vitro.

It was shown in a previous study that proliferating CD8+ T cells could be detected in immune horse peripheral blood mononuclear cells (PBMC) when stimulated with African horse sickness virus serotype 4 (AHSV4). In this study the cytotoxicity of CD8+ T cells were tested by using the fluorescent antigen-transfected target cells-cytotoxic T lymphocytes (FATT-CTL) assay, for both the virus and its individual proteins expressed in Escherichia coli. This CTL assay measures the killing of viral protein expressing cells. AHSV proteins were successfully expressed in E. coli using the pET102/D-TOPO expression vector and the effector cells were stimulated with these recombinant proteins or with live viable virulent AHSV4. The AHSV genes were amplified and cloned into the pIRES-hrGFP II (pGFPempty) vector and these plasmid vectors encoding antigen-green fluorescent protein (GFP) fusion proteins were used to nucleofect PBMC, the target cells. The elimination of antigen-GFP expressing cells by CTL was quantified by flowcytometry. VP1-1, VP2-2, VP4, VP7 and NS3, antigen-specific CD8+ T cells resulted in cell lysis suggesting that CTL may play a role in the immune response induced against the AHSV4 vaccine strain.

Sequencing of a 15-kb Ehrlichia ruminantium clone and evaluation of the cpg1 open reading frame for protection against heartwater.

A 1.2 kb polymorphic fragment from the Gardel isolate of Ehrlichia (formerly Cowdria) ruminantium was used to isolate a 15kb clone from the E. ruminantium Welgevonden LambdaGEM-11 library. This clone, WL2EL1, was subcloned and sequenced. Eight open reading frames (ORFs) were identified. The ORF in WL2EL1 which contained the Welgevonden homologue of the 1.2 kb polymorphic fragment was designated Cowdria polymorphic gene 1 (cpg1). The cpg1 ORF was cloned into pCMViUB, a genetic vaccine vector. Mice and sheep were immunized with pCMViUB/cpg1 by intramuscular injection and gene gun inoculation. Although all of the immunized mice died, there was a trend for mice that received larger amounts of pCMViUB/cpg1 DNA to survive longer. Four out of five sheep immunized with the construct survived lethal challenge.

Rift Valley fever virus: a seroepidemiologic study of small terrestrial vertebrates in South Africa.

Epizootics of Rift Valley fever (RVF) are often associated with periods of heavy rainfall, which are favorable for mosquito vectors. However, in seasons with normal or low rainfall, enzootic circulation occurs, suggesting the existence of a natural host that can act as a cryptic carrier during interepizootic periods. To confirm the role of heavy rainfall in epizootic circulation, and to identify a possible natural host of RVF virus, serum samples from small terrestrial mammals in the Free State and Northern Cape regions of South Africa were collected before and after the 1988 floods. These areas are known to support epizootic circulation of RVF virus. The samples were tested for the presence of RVF virus-specific IgG using an ELISA and positive sera were confirmed by a neutralization test. Forty-seven (15%) of 312 Aethomys namaquensis (Namaqua rock rat) had antibodies to RVF virus. Of these positive sera, nine (6%) of 141 were collected before the floods of 1988 and 38 (22%) of 171 were collected afterwards (P = 0.001). Naive A. namaquensis were inoculated with RVF virus and developed a viremia, but no clinical symptoms, suggesting that they can act as temporary asymptomatic carriers of the virus. These results suggest a role for A. namaquensis as a cryptic carrier for RVF virus during interepizootic periods and support the results of other studies suggesting an amplifying role for heavy rainfall in the circulation of RVF virus.

Preliminary evidence for a fourth phosphoglucomutase (PGM) locus in the dog.

The PGM polymorphisms were investigated in starch gel electrophoresis in a total of 34 dogs. After prolonged incubation, a zone located 5-6 cm anodal to PGM3 was found in which two clear bands were identified. Two dogs had only the faster band, and two dogs had only the slower band. This provides preliminary evidence for the existence of a fourth PGM locus in dogs. A series of exclusion experiments indicates that the newly found bands contain PGM activity.

Development of improved attenuated and nucleic acid vaccines for heartwater.

Heartwater, an economically important tickborne disease of wild and domestic ruminants, is caused by the intracellular rickettsia Ehrlichia (formerly Cowdria) ruminantium. The only commercially available immunization procedure is more than 50 years old and uses an infection and treatment regimen using a preparation of virulent organisms in cryopreserved sheep blood. Much research has been conducted into the development of attenuated, inactivated, and nucleic acid vaccines over the last half-century, with relatively little success until recently. We describe here the development of two new experimental vaccines, a live attenuated vaccine and a nucleic acid vaccine. The attenuation of virulent E. ruminantium was achieved by growing the organisms in a continuous canine macrophage-monocyte cell line. After more than 125 passages the cultures produced no disease when inoculated into mice or sheep, and the animals were completely protected against a subsequent lethal homologous needle challenge. The nucleic acid vaccine consists of a cocktail of four E. ruminantium genes, from a genetic locus involved in nutrient transport, cloned in a DNA vaccine vector. Sheep immunized with this cocktail were completely protected against a subsequent lethal needle challenge, either with the homologous isolate or with any one of five different virulent heterologous isolates. Protection against a field challenge in a heartwater endemic area, however, was relatively poor. Genetic characterization of the E. ruminantium genotypes in the challenge area did not identify any having major differences from those used in the heterologous needle challenge experiments, so lack of cross-immunity between the vaccine genotype and those in the field was unlikely to be the main reason for the lack of protection. We believe that a needle challenge is far less severe than a tick challenge, and that the immunity engendered by the DNA vaccine alone was not sufficient to protect against the natural route of infection. Boosting with live organisms after DNA vaccination results in much higher levels of protection against tick challenge than DNA vaccination alone, suggesting that improved methods of boosting could lead to more effective immunization.

The binding potential of commercial antibody conjugates with sera of various small terrestrial mammals.

Infectious diseases of wild animals are of increasing importance, both from an economic viewpoint and because several of these diseases are pathogenic to man. However, serosurveys to determine the circulation of infectious organisms in wildlife are complicated by the fact that antibodies to species-specific immunoglobulins are not available for use in serological assays such as enzyme-linked immunosorbent assays (ELISAs) or immunofluorescence assays. To determine the binding potential of four commercially available antibody conjugates with the sera of wild animals, sera from 27 species of small terrestrial mammals were allowed to react with alkaline phosphatase-labelled protein A, anti-rabbit IgG, anti-mouse IgG and anti-human IgG by by the use of an ELISA. It was found that sera from some species of the order Lagomorpha bound optimally to anti-rabbit IgG, while anti-mouse IgG could be used for most species of Rodentia. For all Carnivora, Insectivora, Macroscelidea, Hyracoidea and other Rodentia, staphylococcal protein A demonstrated optimal binding. None of the sera that was tested bound to anti-human IgG. These results demonstrate that commercial conjugates can be used in serological assays in which wild animal sera are used, and should be useful for future serosurveys to determine the circulation of infectious agents in small terrestrial mammals.