NUI Galway Logo

NUI Galway Home

NUI Galway Prospective Students NUI Galway Library
NUI Galway Logo NUI Galway Search NUI Galway Faculties & Departments NUI Galway Student Life
NUI Galway Logo NUI Galway University News NUI Galway Research NUI Galway Administration & Services
NUI Galway Logo
Home >> Research >> National Diagnostics Centre
Menu Header
Gene Regulation Group

Gene Regulation Group

The Gene Regulation Group (formerly the Molecular Biology Group) at the National Diagnostics Centre is engaged in research activities related to the investigation of differential gene expression in a range of mammalian and fish tissues. Our goal is to improve current understanding of factors that influence the quality and welfare of these species from the perspective of both the consumer and the animal itself. We are also involved in the development of CHO expression systems for the production of recombinant glycoproteins.

The group is made up of postgraduate students, research assistants and postdoctoral researchers. Several of the projects are collaborations with partners in other European countries including, France, Spain, Sweden and Britain. 

Research in the group focuses on the areas of:


   Animal Biotechnology  

   Mammalian Cell Culture  



Dr Michael Cairns
Team Leader Gene Regulation Group
National Diagnostics Centre
National University of Ireland, Galway
Ph: 353 91 524411 x2094: 353 91 492094 (direct)
Fax: 353 91 586570


There are currently three funded projects in the Gene Regulation Group related to Aquaculture.  

The overall aim of the project "A Functional Genomics Approach to Measuring Stress in Fish Aquaculture" is to identify in fish candidate genes associated with resistance to stress conditions and thus provide the physiological and genetic basis for new marker-assisted selection strategies. The stressful conditions of intensive aquaculture lead to an overall reduction in performance, including poor acclimatisation and growth performance, impaired reproduction and increased susceptibility to disease. The recent development of genomic tools, particularly microarray technology, allows systematic gene expression analysis of biological material and provides an integrated overview of the global response at the level of gene expression. The present study applies this new functional genomic approach to examine a complex physiological problem: analysis of the pattern of gene expression at tissue level in response to exposure to a stressor. 

The project is funded under EC Framework 5 and has as PIs: Patrick Prunet (Rennes, France), Tom Pottinger (CEFAS, Windermere), Chris Secombes (Aberdeen), Svante Winburg (Uppsala, Sweden), Michael Cairns (NUI, Galway) and Andrew Cossins (Liverpool). Patrick Prunet is the project coordinator and contact point. See also the official Stressgenes web site. NUI, Galway is responsible for preparing SSH cDNA libraries from liver, pituitary and brain from fish subjected to confinement stress.  

Figure 1 Salmon salar.  

We are also interested in the isolation of genes involved in the regulation of the immune system in commercially important salmonid species. Although numerous cytokines have been isolated from mammals, only a few cytokines have been identified in teleosts. In this project we are using the technique of Suppression Subtractive Hybridization (SSH) to isolate genes differentially expressed in response to mitogens, such as phytohaemaglutinin (PHA) and lipopolysaccharide (LPS).






Figure 2 : Printed clones from SSH libraries generated from "confinement stressed" Rainbow trout (O.mykiss) tissues (brain, liver & pituitary). The target is RNA extracted from a 2 hour stressed sample (liver).

In the project "Regulation of Acute Phase Response (APR) Proteins in Rainbow trout during Exposure to a Confinement Stressor" studies into stress in aquaculture are extended. The acute phase response (APR) is a physiological response of the body to injury, trauma or infection. The APR involves changes in the hepatic, neuroendocrine, hematopoietic, musculo-skeletal and immune systems. Many of the APPs (Acute Phase Proteins) involved in the APR are synthesised in the liver. Although the APR is typically induced by injury, trauma and infection in this project we are investigating whether the APR can also be induced in Rainbow trout by the confinement / overcrowding stress of the aquaculture environment. This project is funded by Enterprise Ireland

In a third project "Molecular Biology of Wild Atlantic Salmon", NUI, Galway researchers in the National Diagnostics Centre, the Martin Ryan Institute and the Department of Zoology, and their collaborators in the Marine Institute and University College Cork, are exploiting functional genomics, proteomics and population genetics approaches to an investigation of the molecular genetics of wild Atlantic salmon (Salmo salar). Building on the existing research interests and expertise of the participants, the major objective of this programme is to create the first comprehensive database of gene expression profiles and functional information associated with embryo development, smoltification and sexual maturation in wild Atlantic salmon. In a related project we have investigated thyroid stimulating hormone (TSH) and its role in smoltification in Atlantic salmon. The thyroid-pituitary axis is of major importance for the metabolic changes that occur during smoltification. In order to understand the regulation of hormonal changes in the Atlantic salmon during smoltification, we have investigated the cDNA sequences, genomic organisation and promoter sequence of the thyroid stimulating hormone b subunit and a GP subunits. The Wild Salmon project is funded by the Irish Higher Education Authority.  






Figure 3: Returning adult Atlantic salmon (Salmo salar)  



Animal Biotechnology

There are currently two funded projects in the Gene Regulation Group related to Animal Biotechnology.

In the project "New Gene Tools to Improve Pig Welfare and the Quality of Pork" the overall aim is to identify genes responsible for variation in pork meat quality, including the relationship with stress and animal welfare, in order to provide the basis for the development of new tools to improve raw material quality. This functional genomics approach requires phenotypic data that relates to a known genetic structure. The approach being adopted utilises novel genomics technologies such as cDNA microarrays and proteomics to analyse gene expression and gene products in muscle at the time of slaughter in order to relate this to differences in meat processing and eating quality.This project is supported by the EC under the Framework 5. For more information on this project and the partners involved please see qualityporkgenes

Figure 4: Sampling March 2003

A related project Analysis of Gene and Protein Expression for the Measurement of Beef Quality is funded through the Department of Agriculture, Food and Rural Development in Ireland  by Dr Anne Maria Mullen, (Coordinator).  The National Food Centre, Teagasc, Dublin, a collaboration with Dr Torres Sweeney, Faculty of Veterinary Medicine, University College Dublin. 

Although many advances have been made in controlling the growth and carcass composition of animals and the post slaughter conditioning of carcasses, factors that will ensure a product of consistent quality are still difficult to define.  Meat quality is an extremely complex set of properties, manifested as economically important phenotypic traits such as tenderness, nutrition and water holding capacity.  These are ultimately determined by the interaction of genetic factors, (through the expression of particular genes leading to the production of specific gene products (proteins)) with the environment. This project aims to make progress towards the identification of genes and proteins (and their expression levels) that confer the consistently high quality required by both the Irish and export markets. The importance of these genes and proteins in determining desirable meat quality will be assessed by analysing associations between quality traits and the expression of the identified genes and gene products. More information on meat quality can be obtained through Teagasc.

   Mammalian Cell Culture

It is important in producing recombinant glycoproteins for the human therapeutic and diagnostic markets that the covalent attachment of glycan/oligosaccharide chains to the protein is carried out correctly, as these structures are important for the in vivo functioning of the glycoprotein. The advantages of recombinant glycoprotein products over natural products, such as unlimited source, ease of large-scale production and purification as well as assurance of product safety and consistency, has led to the rapid growth in this sector of the biotechnology industry.  For authentic glycosylation, mammalian cell production systems, such as Chinese Hamster Ovary cells, must be used. The main objective of this project, which is a collaboration with Prof Terry Smith in the NCBES is to characterise novel regulatory elements (promoters, 3'UTRs and polyadenylation signal sequences) from CHO cells for use in high efficiency CHO expression systems.

Figure 5: Main room of the Gene Regulation Laboratory  


Procedures used in the Gene Regulation Group include:  

  •  RNA isolation and quality determination

  •  cDNA and SSH library construction and characterisation

  •  cDNA microarray analysis

  •  Q-PCR (Real time) to confirm differential expression   

  •  Cell culture reporter assays and promoter isolation  

Team Leader  

Michael Cairns, Ph.D.
TEL: +353-91-492094


Grace Davey Ph.D.,B.Sc.
TEL+353-91-524411; EXT:2815

Benoit Houeix M.Sc.,
TEL: +353-91-524411; EXT:2077 

Anita Talbot, B.Sc.,

TEL: +353-91-524411; EXT:2077  
Chris Mc Gee
TEL+353-91-524411; EXT:2816
Ph.D. Students


National Diagnostics Centre
National University of Ireland, Galway, University Road, Galway, Ireland.
Phone: +353 (0)91.512266 , Fax: +353 (0) 91.586570 , E-mail: