The genes within the genome (genetic code) of cattle need to be identified and defined before variability of these genes among cattle (individuals and breeds) can be identified. One goal is to determine whether such variations when found are associated with enhanced or decreased resistance to infectious diseases. The cattle genome has been largely sequenced (that is, the genetic code 'read'), and now one of the purposes of the international community effort is to annotate the bovine genome (define genes within the genetic code). The subgroup addressing this began their efforts with a workshop in Iowa to teach the participating groups about the Apollo or other computer software needed for proper gene annotation techniques. This is a subset of what is known as 'bioinformatics'.
We use genome information from humans, other primates, mice and other livestock species to help us first highlight the potential bovine genes among the large amount of sequence information (make the "model genes" or "gene model" as it is known). This is possible since there is a great deal of conservation of gene sequences among mammals. The predictions made this way are later confirmed by us in a wetlab as part of this project. That is, we will show that the predicted genes are actually expressed (used as a template to make proteins) by cattle cells. This validation is necessary because there are a number of reasons why the bioinformatics approach (which generates gene models) is not sufficient alone. The sequence of genes that are expressed by bovine cells validate the gene model if they match or largely match, since there will be variation among animals. To do this, specific cells or tissues are obtained from cattle and their gene expression evaluated. This is accomplished by: first, obtaining the message for the expressed gene (called mRNA) and, then, obtaining the sequence of this, and subsequently comparing it to that predicted by the gene model. In some cases the genes may be non-functional (known as pseudogenes) and will not be expressed. Once we have validated a gene's expression, the sequence information can be compared among individual cattle of the same or varying breeds.
The variations can be assessed according to the animal's susceptibility or resistance to particular infections with bacteria, viruses and parasites. Identifying genes that correlate with the outcome of exposure to infection will eventually facilitate programs to breed resistant animals. Our laboratory is focusing on genes within the immune system. The immune system can provide the host with both immediate resistance (known as innate immunity) and long-term resistance in the form of responses to vaccines (for example). However, the immune system is very complex; it has many different cell types and their products which interact though a network. We are focusing on defining the genes expressed by the immune system cells known as gamma delta T lymphocytes. We are interested in their receptors that detect the presence of infectious agents as well as the molecules these cells may produce to communicate with other cells in the immune system (known as cytokines or interleukins).