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African trypanosomes are protozoan parasites, most species of which are transmitted by tsetse flies. They reside in the mammalian bloodstream and evade the immune system by periodically switching the major protein on their surface — a phenomenon called antigenic variation, mediated by gene rearrangements in the trypanosome genome. The trypanosomes eventually enter the central nervous system and cause a fatal disease, commonly called ngana in domestic cattle and sleeping sickness in humans. Two sub-species of Trypanosoma brucei infect humans ( T. b. rhodesiense and T. b. gambiense ) and one sub-species does not survive in humans ( T. b. brucei ) because it is lysed by the human-specific serum protein, apolipoprotein L-I. Wild animals in Africa have other (less well understood) molecular mechanisms of suppressing the number of African trypanosomes in the blood, and some indigenous breeds of African cattle also display a partial “trypanotolerance” whose genetic loci have recently been mapped.

Economic losses due to ticks and tick-borne disease of livestock fall disproportionately on developing countries. Currently, tick control relies mostly on pesticides and parasite-resistant cattle. Release of a commercial recombinant vaccine against Boophilus microplus in Australia in 1994 showed that anti-tick vaccines are a feasible alternative. For vaccines, it is important to understand the efficacy needed for a beneficial outcome. In this, it is relevant that some tick antigens affect multiple tick species; that existing vaccines could be improved by the inclusion of additional tick antigens; and that vaccination against ticks can have an impact on tick-borne disease. Practically, although recombinant vaccine manufacture involves relatively few steps, issues of intellectual property rights (IPR) and requirements for registration of a product may affect economic viability of manufacture. Hence practical vaccines for the developing world will require both successful science and a creative “business solution” for delivery in a cost-effective way.

Rinderpest is an economically devastating disease of cattle (cattle plague), but a live-attenuated vaccine has been very successfully used in a global rinderpest eradication campaign. As a consequence, the endemic focus of the virus has been reduced to an area in eastern Africa known as the Kenya-Somali ecosystem. Although the vaccine is highly effective, it has a drawback in that vaccinated animals are serologically indistinguishable from those that have recovered from natural infection. In the final stages of the eradication campaign, when vaccination to control the spread of disease will only be used in emergencies to contain an outbreak, a marker vaccine would be a very useful tool to monitor possible wild virus spread outside the vaccination area. Marker vaccines for rinderpest, and other viruses with negative-sense RNA genomes, can now be produced using reverse genetics, and the development of such marker vaccines for rinderpest virus is described.

Since the implementation in 1988 of the foot-and-mouth disease (FMD) eradication programme in South America (PHEFA), significant advances have been made in the control of the disease. Particularly relevant has been the progress attained in one of the three subregions, the Southern Cone, where during the late 1990s most areas were recognized as FMD-free by OIE, with or without vaccination. To achieve PHEFA goals, development and implementation of diagnostic tools to trace for potential sources of infection was of utmost importance. Accordingly, priority was given to the identification of genetic links among circulating strains and, in relevant areas, to the systematic sero-epidemiological monitoring of persistent viral activity, regardless of vaccination condition. A genetic database of representative strains from South America, constructed at the Pan American Foot-and-Mouth Disease Center, constituted the basis for the phylogenetic analysis of viruses types O and A recorded recently in endemic regions, and during the emergencies in FMD-free areas of the Southern Cone. The genetic data placed all variants from the Southern Cone in a single lineage, which clearly differed from the evolutionary nodes that included the isolates in the Andean subregion, reflecting two independent production systems and livestock trade circuits. To complement the search for potential sources of infection, serosurveillance became an important adjunct. To this end, new tools to infer viral circulation within and between herds, irrespective of vaccination, were developed and validated. The diagnostic approach, based on an immunoenzymatic system that detects antibodies against non-capsid proteins, was particularly useful in support of epidemiological investigations after episodes and to confirm absence of viral activity in regions to be recognized as FMD-free, being especially important prior to the suspension of vaccination. Results of samplings in the Southern Cone during the 1990s strongly suggested that emergencies in this subregion did not originate from residual persistent activity in the areas declared FMD-free, but most probably from trade activities involving “hot spots” within the subregion.

Microbial infections are highly dynamic. Viruses have evolved two main strategies against the host response: interaction or evasion. Interaction is typical of complex DNA viruses. Their genomes encode a number of proteins that exert modulatory functions that alter the immune response of the host. Evasion strategy is used mainly by RNA viruses, and is based on high mutation rates and quasispecies dynamics. The complexity of viral populations demands research on new antiviral strategies that take into consideration the adaptive potential of viruses, in particular RNA viruses.

Improving microbial degradation of plant cell wall polysaccharides remains one of the highest priority goals for all livestock enterprises, including the cattle herds and draught animals of developing countries. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created to promote the sequencing and comparative analysis of rumen microbial genomes, offering the potential to fully assess the genetic potential in a functional and comparative fashion. It has been found that the Fibrobacter succinogenes genome encodes many more endoglucanases and cellodextrinases than previously isolated, and several new processive endoglucanases have been identified by genome and proteomic analysis of Ruminococcus albus , in addition to a variety of strategies for its adhesion to fibre. The ramifications of acquiring genome sequence data for rumen micro-organisms are profound, including the potential to elucidate and overcome the biochemical, ecological or physiological processes that are rate limiting for ruminal fibre degradation.

Significant advances in the establishment of the methodologies required for the molecular breeding of temperate forage grasses ( Lolium and Festuca species ) and legumes ( Trifolium and Medicago species) are reviewed. Examples of current products and approaches for the application of these methodologies to forage grass and legume improvement are outlined. The plethora of new technologies and tools now available for high-throughput gene discovery and genome-wide expression analysis have opened up opportunities for innovative applications in the identification, functional characterization and use of genes of value in forage production systems and beyond. Selected examples of current work in pasture plant genomics, xenogenomics, symbiogenomics and micro-array-based molecular phenotyping are discussed.

Acacia angustissima has been proposed as a protein supplement in countries where availability of high quality fodder for grazing animals is a problem due to extreme, dry climates. While A. angustissima thrives in harsh environments and provides valuable nutrients required by ruminants, it has also been found to contain anti-nutritive factors that currently preclude its widespread application. A number of non-protein amino acids have been identified in the leaves of A. angustissima and in the past these have been linked to toxicity in ruminants. The non-protein amino acid 4-n-acetyl-2,4-diaminobutyric acid (ADAB) had been determined to be the major non-protein amino acid in the leaves of A. angustissima . Thus, in this study, the aim was to identify micro-organisms from the rumen environment capable of degrading ADAB. Using an ADAB-containing plant extract, a mixed enrichment culture was obtained that exhibited substantial ADAB-degrading ability. Attempts to isolate an ADAB-degrading micro-organism were carried out, but no isolates were able to degrade ADAB in pure culture. The mixed microbial community of the ADAB-degrading enrichment culture was further examined through the use of pure-culture-independent techniques. Fluorescence in situ hybridization (FISH) was employed to investigate the diversity within this sample. In addition two bacterial 16S rDNA clone libraries were constructed in an attempt to further elucidate the members of the microbial population. The clone libraries were constructed from serial dilutions of the enrichment culture, a 10^−5 dilution where complete degradation of ADAB occurred, and a 10^−7 dilution where ADAB degradation did not occur. Through the comparison of these two libraries it was hypothesized that clones belonging to the Firmicutes phylum were involved in ADAB degradation. A FISH probe, ADAB1268, was then designed to target these clones and was applied to the enrichment cultures to investigate their relative abundance within the sample.

Ruminant livestock populations in developing countries are increasing in response to increasing demand for meat and milk. These animals are a major global source of methane, a greenhouse gas produced during the degradation of organic matter by micro-organisms in the foregut of ruminant livestock. Chemical inhibition of methanogenic micro-organisms has been reported; however, associated improvements in feed digestion and livestock productivity have not been consistently demonstrated. Gene-based technologies have the potential to contribute new knowledge of the rumen microbial populations involved in these processes, which will assist in identifying feeding practices that lead to methane abatement and improved livestock productivity. For small-scale farmers, feeding interventions that achieve greenhouse gas abatement need also to be associated with improved feed conversion efficiency and enterprise profitability. During the adoption of methane abatement technologies, other regionally important issues such as poverty, food security, sustainable agriculture production systems and environmental management must also be addressed.

A gas syringe method was used to evaluate the effect of secondary compounds from plant materials on in vitro fermentation products and microbial biomass. The experiment used Pennisetum purpureum, Morinda citrifolia fruit, Nothopanax scutellarium leaves, Sesbania sesban LS (low saponins type), Sesbania sesban HS (high saponins type) and Sapindus rarak fruit as substrates. The incubation was conducted with and without polyethylene glycol 6000 (PEG) addition for 24 hours. Gas production and short-chain fatty acids (SCFA) were analysed. Prokaryotic and eukaryotic concentrations were measured by quantifying 16S and 18S rRNA. The percentage increase in gas production due to PEG was very small (<5%) for all plant materials, which indicated that the biological effect of tannin in these plant materials is limited. TLC analysis revealed that all materials contained saponin, but only S. rarak , followed by S. sesban , contained a high diversity of saponins. S. sesban gave the highest (234 ml/g) while S. rarak gave the lowest gas production (115 ml/g). S. rarak gave the lowest SCFA production (3.57 mmole/g) and also the lowest ratio of acetate to propionate (1.76), indicating a change in pattern of SCFA production. Total elimination of eukaryotic concentration was evident from the absence of the 18S rRNA band when S. rarak and S. sesban were used as sole substrates. S. rarak also reduced the prokaryotic concentration. To use S. rarak as a defaunating agent without affecting prokaryotes, a crude saponin extract was prepared from S. rarak for further experiment. Different concentrations of crude saponins in a methanol extract of S. rarak fruit dissolved in rumen buffer were added to a substrate consisting of elephant grass and wheat bran (7:3 w/w). Microbial biomass yield was quantified by gravimetry and using rRNA as a marker. Addition of crude saponin extract from S. rarak to a high-roughage diet increased microbial biomass (MB) yield to 1.07 and 1.14 times MB yield of the control, estimated by gravimetry and using rRNA as a marker, respectively. A significant, although low, correlation between these methods was found, suggesting that both methods can possibly be used to study the effect of saponin. However, due to the limited correlation between these two methods (r = 0.5793), more studies are warranted, using a greater number of samples. Using rRNA as a marker for estimating microbial biomass would be advantageous as the same RNA can be used for further microbial community analysis.