• Confirmation of the Dietary Background of Beef from its Stable Isotope Signature

      Moloney, Aidan P; Bahar, Bojlul; Schmidt, Olaf; Scrimgeour, C.M.; Begley, I.S.; Monahan, Frank J (Teagasc, 2009-11-01)
      Consumers are increasingly demanding information on the authenticity and source of the food they purchase. Molecular DNA-based technology allows animal identification, but without certification or a “paper-trail” but does not provide information about feed history or the production system under which the animal was reared. The stable isotopes of chemical elements (e.g.13C/12C, 15N/14N) are naturally present in animal tissue and reflect the isotopic composition of the diet. The overall aim of this project was to determine the feasibility of using the stable isotopic composition as an intrinsic, biochemical marker to gain information about feed components used in the production of beef. Factors likely to affect the isotopic signature such as source of tissue, duration of feeding and production systems were examined. It is expected that this highly innovative and original technique will permit the identification of country of origin and dietary history of beef and so greatly assist efforts to market Irish beef, particularly in lucrative European markets. Sequential sampling and stable isotope analysis of bovine tail hair and hoof revealed that the two tissues can provide a detailed and continuous record of animal dietary history. Because hair can be sampled repeatedly and noninvasively, we anticipate that this approach will also prove useful for the investigation of short-term wildlife movements and changes in dietary preferences.
    • Long-term stability of RNA in post-mortem bovine skeletal muscle, liver and subcutaneous adipose tissues

      Bahar, Bojlul; Monahan, Frank J; Moloney, Aidan P; Schmidt, Olaf; MacHugh, David E; Sweeney, Torres; National Development Plan 2000-2006; Teagasc Walsh Fellowship Programme (Biomed Central, 2007-11-29)
      Background: Recovering high quality intact RNA from post-mortem tissue is of major concern for gene expression studies in animals and humans. Since the availability of post-mortem tissue is often associated with substantial delay, it is important that we understand the temporal variation in the stability of total RNA and of individual gene transcripts so as to be able to appropriately interpret the data generated from such studies. Hence, the objective of this experiment was to qualitatively and quantitatively assess the integrity of total and messenger RNA extracted from bovine skeletal muscle, subcutaneous adipose tissue and liver stored at 4°C at a range of time points up to 22 days post-mortem. These conditions were designed to mimic the environment prevailing during the transport of beef from the abattoir to retail outlets. Results: The 28S and 18S rRNA molecules of total RNA were intact for up to 24 h post-mortem in liver and adipose tissues and up to 8 days post-mortem in skeletal muscle. The mRNA of housekeeping genes (GAPDH and ACTB) and two diet-related genes (RBP5 and SCD) were detectable up to 22 days post-mortem in skeletal muscle. While the mRNA stability of the two housekeeping genes was different in skeletal muscle and liver, they were similar to each other in adipose tissue. After 22 days post-mortem, the relative abundance of RBP5 gene was increased in skeletal muscle and in adipose tissue and decreased in liver. During this period, the relative abundance of SCD gene also increased in skeletal muscle whereas it decreased in both adipose tissue and liver. Conclusion: Stability of RNA in three tissues (skeletal muscle, subcutaneous adipose tissue and liver) subjected to long-term post-mortem storage at refrigeration temperature indicated that skeletal muscle can be a suitable tissue for recovering biologically useful RNA for gene expression studies even if the tissue is subjected to post-mortem storage for weeks, whereas adipose tissue and liver should be processed within 24 hours post-mortem.
    • Variation in the Ovine Abomasal Lymph Node Transcriptome between Breeds Known to Differ in Resistance to the Gastrointestinal Nematode

      Ahmed, Albin M.; Good, Barbara; Hanrahan, James P; McGettigan, Paul; Browne, John A; Keane, Orla M; Bahar, Bojlul; Mehta, Jai; Markey, Bryan; Lohan, Amanda; et al. (PLoS, 2015-05-15)
      Texel lambs are known to be more resistant to gastrointestinal nematode (GIN) infection than Suffolk lambs, with a greater ability to limit infection. The objectives of this study were to: 1) profile the whole transcriptome of abomasal lymph node tissue of GIN-free Texel and Suffolk lambs; 2) identify differentially expressed genes and characterize the immune-related biological pathways and networks associated with these genes. Abomasal lymph nodes were collected from Texel (n = 6) and Suffolk (n = 4) lambs aged 19 weeks that had been GIN-free since 6 weeks of age. Whole transcriptome profiling was performed using RNA-seq on the Illumina platform. At the time of conducting this study, a well annotated Ovine genome was not available and hence the sequence reads were aligned with the Bovine (UMD3.1) genome. Identification of differentially expressed genes was followed by pathway and network analysis. The Suffolk breed accounted for significantly more of the differentially expressed genes, (276 more highly expressed in Suffolk v 162 in Texel; P < 0.001). The four most significant differentially expressed pathways were all related to immunity and were classified as: Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses, Activation of IRF by Cytosolic Pattern Recognition Receptors, Role of RIG-I-like Receptors in Antiviral Innate Immunity, and Interferon Signaling. Of significance is the fact that all of these four pathways were more highly expressed in the Suffolk. These data suggest that in a GIN-free environment, Suffolk lambs have a more active immune profile relative to the Texel: this immune profile may contribute to the poorer efficiency of response to a GIN challenge in the Suffolk breed compared to the Texel breed.