Development and testing of a high-density cDNA microarray resource for cattle

Biomarker Discovery in Animal Health and Disease: The Application of Post-Genomic Technologies

The causes of many important diseases in animals are complex and multifactorial, which present unique challenges. Biomarkers indicate the presence or extent of a biological process, which is directly linked to the clinical manifestations and outcome of a particular disease. Identifying biomarkers or biomarker profiles will be an important step towards disease characterization and management of disease in animals. The emergence of post-genomic technologies has led to the development of strategies aimed at identifying specific and sensitive biomarkers from the thousands of molecules present in a tissue or biological fluid. This review will summarize the current developments in biomarker discovery and will focus on the role of transcriptomics, proteomics and metabolomics in biomarker discovery for animal health and disease.

A genomic study on mammary gland acclimatization to tropical environment in the Holstein cattle

This study aims at identifying mammary gland genes expressed in Brazilian Holstein cattle produced under tropical conditions, as compared to the Portuguese Holstein cattle produced in a temperate region. For this purpose, cDNA microarrays and real-time (RT) PCR transcriptomic techniques were utilized in 12 Holstein cows from the same lactating phase and management systems divided into two groups: Holstein Brazil (HB) originated from Brazil and Holstein Portugal (HP) from Portugal. The genomic results show that from a total of 4608 genes available from the microarray slide (Bovine Long Oligo (BLO) library), 65 transcripts were identified as differentially expressed in mammary glands. The genes associated with mammary gland development and heat stress responses showed greater expression in HB animals. In the HP group, upregulated genes related with apoptosis and vascular development and downregulated genes related with resistance to heat stress were observed. Validation of microarray results was done using RT-PCR. HB animals had higher blood levels of growth hormone than HP animals. Blood levels of prolactin and T₃ were similar for both groups and GH levels were increased in the HB group. The results suggest a gene change towards long-term acclimatization of Brazilian Holstein cattle to cope with tropical heat stress conditions.

Global Gene Expression Profiling: A Complement to Conventional Histopathologic Analysis of Neoplasia

Transcriptional profiling of entire tumors has yielded considerable insight into the molecular mechanisms of heterogeneous cell populations within different types of neoplasms. The data thus acquired can be further refined by microdissection methods that enable the analyses of subpopulations of neoplastic cells. Separation of the various components of a neoplasm (i.e., stromal cells, inflammatory infiltrates, and blood vessels) has been problematic, primarily because of a paucity of tools for accurate microdissection. The advent of laser capture microdissection combined with powerful tools of linear amplification of RNA and high-throughput microarray-based assays have allowed the transcriptional mapping of intricate and highly complex networks within pure populations of neoplastic cells. With this approach, specific “molecular signatures” can be assigned to tumors of distinct or even similar histomorphology, thereby aiding the desired objective of pattern recognition, tumor classification, and prognostication. This review highlights the potential benefits of global gene expression profiling of tumor cells as a complement to conventional histopathologic analyses.

Microarray evaluation of bovine hepatic gene response to fescue toxicosis

‘Fescue toxicosis’ is a disease in livestock caused by ingestion of ergot alkaloids produced by the fungal endophyte Neotyphodium coenophialum in tall fescue; it is estimated to cost 1 billion USD in damages per year to the beef industry alone. Clinical signs include decreased reproductive fitness, necrosis of extremities, and reduced average daily gain and milk production. Little is known about the cellular mechanisms that mediate these toxic sequelae. We evaluated the effects of ergovaline-based fescue toxicosis on gene expression via oligonucleotide microarray. Liver biopsies were obtained from steers (n=4) pre- and post-exposure (0 and 29 days) to feed containing 579 ng/g ergovaline. Analyses were performed using both ANOVA with false discovery rate correction and Storey's optimal discovery procedure. Overall, down-regulation of gene expression was observed; heart contraction and cardiac development, apoptosis, cell cycle control, and RNA processing genes represented the bulk of differentially expressed transcripts. 2 CYPs (CYP2E1 and CYP4F6) were amongst the significantly upregulated results. Thus, exposure of cattle to toxic levels of ergovaline caused widespread changes in hepatic gene expression, which can both help explain macroscopic clinical signs observed in ruminant animals, and reinforce previous findings in monogastric models.

Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources

Background

Gene expression profiling studies of mastitis in ruminants have provided key but fragmented knowledge for the understanding of the disease. A systematic combination of different expression profiling studies via meta-analysis techniques has the potential to test the extensibility of conclusions based on single studies. Using the program Pointillist, we performed meta-analysis of transcription-profiling data from six independent studies of infections with mammary gland pathogens, including samples from cattle challenged in vivo with S. aureus, E. coli, and S. uberis, samples from goats challenged in vivo with S. aureus, as well as cattle macrophages and ovine dendritic cells infected in vitro with S. aureus. We combined different time points from those studies, testing different responses to mastitis infection: overall (common signature), early stage, late stage, and cattle-specific.

Results

Ingenuity Pathway Analysis of affected genes showed that the four meta-analysis combinations share biological functions and pathways (e.g. protein ubiquitination and polyamine regulation) which are intrinsic to the general disease response. In the overall response, pathways related to immune response and inflammation, as well as biological functions related to lipid metabolism were altered. This latter observation is consistent with the milk fat content depression commonly observed during mastitis infection. Complementarities between early and late stage responses were found, with a prominence of metabolic and stress signals in the early stage and of the immune response related to the lipid metabolism in the late stage; both mechanisms apparently modulated by few genes, including XBP1 and SREBF1.

The cattle-specific response was characterized by alteration of the immune response and by modification of lipid metabolism. Comparison of E. coli and S. aureus infections in cattle in vivo revealed that affected genes showing opposite regulation had the same altered biological functions and provided evidence that E. coli caused a stronger host response.

Conclusions

This meta-analysis approach reinforces previous findings but also reveals several novel themes, including the involvement of genes, biological functions, and pathways that were not identified in individual studies. As such, it provides an interesting proof of principle for future studies combining information from diverse heterogeneous sources.

Development and application of bovine and porcine oligonucleotide arrays with protein-based annotation

The design of oligonucleotide sequences for the detection of gene expression in species with disparate volumes of genome and EST sequence information has been broadly studied. However, a congruous strategy has yet to emerge to allow the design of sensitive and specific gene expression detection probes. This study explores the use of a phylogenomic approach to align transcribed sequences to vertebrate protein sequences for the detection of gene families to design genomewide 70-mer oligonucleotide probe sequences for bovine and porcine. The bovine array contains 23,580 probes that target the transcripts of 16,341 genes, about 72% of the total number of bovine genes. The porcine array contains 19,980 probes targeting 15,204 genes, about 76% of the genes in the Ensembl annotation of the pig genome. An initial experiment using the bovine array demonstrates the specificity and sensitivity of the array.

Differentially expressed genes associated with Staphylococcus aureus mastitis in dairy goats

To study gene expression within the mammary glands of dairy goats with mastitis, mRNA was collected from milk somatic cells (MSCs) of left udder halves challenged with Staphylococcus aureus and right udder halves infused with PBS, as control, at different time points (0, 12, 24 and 48h post-infection). Transcriptional profiles were investigated using bovine cDNA microarrays; of the total 288 differentially expressed genes identified with ANOVA analysis (False Discovery Rate=0.05, 1.5-fold change), 26, 36 and 16 genes were down-regulated at 12, 24 and 48h post-infection, respectively, while 60, 141 and 9 genes were up-regulated at the same corresponding time points. The expression profiles clearly changed at 24h post-infection with 177 genes significantly altered, corresponding to a 10-fold increase of S. aureus bacterial count in milk from infected udders. Differential expression of selected genes (CD2BP2, BCAP31, MHCII, FOSL2, MAPK13, ILT5 and JUNB) was also confirmed by real-time PCR at the different time points considered, showing high correlation with the microarray measurements and high reliability of the microarray analyses. The most readily inducible classes of genes in caprine MSCs infected with S. aureus were pro-inflammatory cytokines, chemokines and their receptors; IL-1alpha, lymphotoxin alpha, granulocyte chemotactic protein (CXCL6), and IL-2 receptor gamma were all up-regulated in infected udders versus healthy controls. This study identified a number of differentially expressed genes induced by S. aureus intramammary infection and demonstrates the intricacy of the patterns of gene expression that influence host response to a complex pathogen of significant relevance to both human and veterinary medicine.

Comparison of skeletal muscle transcriptional profiles in dairy and beef breeds bulls

A cDNA microarray (18 263 probes) was used for transcriptome analysis of bovine skeletal muscle (m. semitendinosus) in 12-month-old bulls of the beef breed Limousin (LIM) and the typical dairy breed Holstein-Friesian (HF, used as a reference). We aimed to identify the genes whose expression may reflect the muscle phenotype of beef bulls. A comparison of muscle transcriptional profiles revealed significant differences in expression of 393 genes between HF and LIM. We classified biological functions of 117 genes with over 2-fold differences in expression between the examined breeds. Among them, 72 genes were up-regulated and 45 genes were down-regulated in LIM vs. HF. The genes were involved in protein metabolism and modifications (22 genes), signal transduction (15), nucleoside, nucleotide and nucleic acid metabolism (13), cell cycle (9), cell structure and motility (9), developmental processes (9), intracellular protein traffic (7), cell proliferation and differentiation (6), cell adhesion (6), lipid, fatty acid and steroid metabolism (5), transport (5), and other processes. For the purpose of microarray data validation, we randomly selected 4 genes: trip12, mrps30, pycrl, and c-erbb3. Real-time RT-PCR results showed similar trends in gene expression changes as those observed in microarray studies. Basing on results of the present study, we proposed a model of the regulation of skeletal muscle growth and differentiation, with a principal role of the somatotropic pathway. It may explain at least in part the development of muscle phenotype in LIM bulls. We assume that the growth hormone directly or indirectly (through IGF-1) activates the calcium-signaling pathway with calcineurin, which stimulates myogenic regulatory factors (MRFs) and inhibits early growth response gene. The inhibition results in indirect activation of MRFs and impaired activation of TGF-beta1 and myostatin, which finally facilitates terminal muscle differentiation.

Embryonic gene expression profiling using microarray analysis

Microarray technology enables the interrogation of thousands of genes at one time and therefore a systems level of analysis. Recent advances in the amplification of RNA, genome sequencing and annotation, and the lower cost of developing microarrays or purchasing them commercially, have facilitated the analysis of single preimplantation embryos. The present review discusses the components of embryonic expression profiling and examines current research that has used microarrays to study the effects of in vitro production and nuclear transfer.

Gene expression profiling of bovine preovulatory follicles: gonadotropin surge and prostanoid-dependent up-regulation of genes potentially linked to the ovulatory process

The molecular mechanisms of ovulation and luteinization have not been well established, partially due to lack of a comprehensive understanding of functionally significant genes up-regulated in response to an ovulatory stimulus and the signaling pathways involved. In the present study, transcripts increased in bovine preovulatory follicles following a GnRH-induced LH surge were identified using microarray technology. Increased expression of 368 and 878 genes was detected at 12 (368 genes) and 20 h (878 genes) following GnRH injection. The temporal, cell specific and prostanoid-dependent regulation of selected genes (ADAM10, DBI, CD36, MTSS1, TFG, and RABGAP1) identified from microarray studies and related genes (ADAM17 and AREG) of potential significance were also investigated. Expression of mRNA for DBI and CD36 was simultaneously up-regulated in theca and granulosa cells (GC) following the LH surge, whereas temporal regulation of ADAM10, MTSS1, TFG, and RABGAP1 was distinct in the two cell compartments and increased granulosa TFG and RABGAP1 mRNA were prostanoid dependent. AREG mRNA was increased in theca and GCs at 12 and 24 h following GnRH injection. ADAM17 mRNA was increased in theca, but reduced in GCs 24 h following GnRH injection. The increased ADAM17 and AREG mRNA were prostanoid dependent. ADAM10 and ADAM17 protein were increased specifically in the apex but not the base of preovulatory follicles and the increase in ADAM17 was prostanoid dependent. Results reveal novel information on the regulation of preovulatory gene expression and suggest a potential functional role for ADAM10 and ADAM17 proteins in the region of follicle rupture.

Identification of novel bovine cumulus cell molecular markers predictive of oocyte competence: functional and diagnostic implications

The present study was undertaken to discover molecular markers in bovine cumulus cells predictive of oocyte competence and to elucidate their functional significance. Differences in RNA transcript abundance in cumulus cells harvested from oocytes of adult versus prepubertal animals (a model of poor oocyte quality) were identified by microarray analysis. Four genes of interest encoding for the lysosomal cysteine proteinases cathepsins B, S, K, and Z and displaying greater transcript abundance in cumulus cells surrounding oocytes harvested from prepubertal animals were chosen for further investigation. Greater mRNA abundance for such genes in cumulus cells of prepubertal oocytes was confirmed by real-time RT-PCR. Elevated transcript abundance for cathepsins B, S, and Z also was observed in cumulus cells surrounding adult metaphase II oocytes that developed to the blastocyst stage at a low percentage following parthenogenetic activation versus those that developed at a high percentage. Functional significance of cumulus cell cathepsin expression to oocyte competence was confirmed by treatment of cumulus-oocyte complexes during in vitro oocyte maturation with a cell-permeable cysteine proteinase (cathepsin) inhibitor. Inhibitor treatment decreased apoptotic nuclei in the cumulus layer and enhanced development of parthenogenetically activated and in vitro-fertilized adult oocytes to the blastocyst stage. Stimulatory effects of inhibitor treatment during meiotic maturation on subsequent embryonic development were not observed when oocytes were matured in the absence of cumulus cells. The present results support a functional role for cumulus cell cathepsins in compromised oocyte competence and suggest that cumulus cell cathepsin mRNA abundance may be predictive of oocyte quality.

Invited review: genes involved in the bovine heat stress response

The cellular heat stress (HS) response is one component of the acute systemic response to HS. Gene networks within and across cells and tissues respond to environmental heat loads above the thermoneutral zone with both intra- and extracellular signals that coordinate cellular and whole-animal metabolism. Activation of these systems appears to be initiated at skin surface temperatures exceeding 35 degrees C as animals begin to store heat and rapidly increase evaporative heat loss (EVHL) mechanisms. Gene expression changes include 1) activation of heat shock transcription factor 1 (HSF1); 2) increased expression of heat shock proteins (HSP) and decreased expression and synthesis of other proteins; 3) increased glucose and amino acid oxidation and reduced fatty acid metabolism; 4) endocrine system activation of the stress response; and 5) immune system activation via extracellular secretion of HSP. If the stress persists, these gene expression changes lead to an altered physiological state referred to as "acclimation," a process largely controlled by the endocrine system. In the acclimated state, metabolism is adjusted to minimize detrimental effects of increased thermal heat load. The role of secreted HSP in feedback regulation of the immune and endocrine system has not yet been investigated. The variation in EVHL among animals and the central role that HSF1 has in coordinating thermal tolerance suggest that there is opportunity to improve thermal tolerance via gene manipulation. Determining the basis for altered energy metabolism during thermal stress will lead to opportunities for improved animal performance via altered nutritional management.

Characterization of a newly developed chicken 44K Agilent microarray

Background

The development of microarray technology has greatly enhanced our ability to evaluate gene expression. In theory, the expression of all genes in a given organism can be monitored simultaneously. Sequencing of the chicken genome has provided the crucial information for the design of a comprehensive chicken transcriptome microarray. A long oligonucleotide microarray has been manually curated and designed by our group and manufactured using Agilent inkjet technology. This provides a flexible and powerful platform with high sensitivity and specificity for gene expression studies.

Results

A chicken 60-mer oligonucleotide microarray consisting of 42,034 features including the entire Marek's disease virus, two avian influenza virus (H5N2 and H5N3), and 150 chicken microRNAs has been designed and tested. In an important validation study, total RNA isolated from four major chicken tissues: cecal tonsil (C), ileum (I), liver (L), and spleen (S) were used for comparative hybridizations. More than 95% of spots had high signal noise ratio (SNR > 10). There were 2886, 2660, 358, 3208, 3355, and 3710 genes differentially expressed between liver and spleen, spleen and cecal tonsil, cecal tonsil and ileum, liver and cecal tonsil, liver and ileum, spleen and ileum (P < 10^-7), respectively. There were a number of tissue-selective genes for cecal tonsil, ileum, liver, and spleen identified (95, 71, 535, and 108, respectively; P < 10^-7). Another highlight of these data revealed that the antimicrobial peptides GAL1, GAL2, GAL6 and GAL7 were highly expressed in the spleen compared to other tissues tested.

Conclusion

A chicken 60-mer oligonucleotide 44K microarray was designed and validated in a comprehensive survey of gene expression in diverse tissues. The results of these tissue expression analyses have demonstrated that this microarray has high specificity and sensitivity, and will be a useful tool for chicken functional genomics. Novel data on the expression of putative tissue specific genes and antimicrobial peptides is highlighted as part of this comprehensive microarray validation study. The information for accessing and ordering this 44K chicken array can be found at

Identification of differentially expressed genes in distinct skeletal muscles in cattle using cDNA microarray

The 788-gene microarray was manufactured using selected elements from three different cDNA libraries in order to identify molecular processes that determine phenotypic characteristics between loin (M. longissimus thoracis) and round (M. semimembranosus) muscles. Microarray analyses identified 24 differentially expressed genes between the two muscles investigated. Five of the genes were verified by quantitative RT-PCR and three of them were mapped on bovine chromosomes using 5,000 rad bovine radiation hybrid (RH) panel. The map locations indicated that they were mapped in the same chromosomal regions where IMF and growth QTLs were located, suggesting that they are most possible positional candidate genes for the traits.

Alternative splicing and expression profile analysis of expressed sequence tags in domestic pig

Domestic pig (Sus scrofa domestica) is one of the most important mammals to humans. Alternative splicing is a cellular mechanism in eukaryotes that greatly increases the diversity of gene products. Expression sequence tags (ESTs) have been widely used for gene discovery, expression profile analysis, and alternative splicing detection. In this study, a total of 712,905 ESTs extracted from 101 different non-normalized EST libraries of the domestic pig were analyzed. These EST libraries cover the nervous system, digestive system, immune system, and meat production related tissues from embryo, newborn, and adult pigs, making contributions to the analysis of alternative splicing variants as well as expression profiles in various stages of tissues. A modified approach was designed to cluster and assemble large EST datasets, aiming to detect alternative splicing together with EST abundance of each splicing variant. Much efforts were made to classify alternative splicing into different types and apply different filters to each type to get more reliable results. Finally, a total of 1,223 genes with average 2.8 splicing variants were detected among 16,540 unique genes. The overview of expression profiles would change when we take alternative splicing into account.

Technical Note: Bovine Oviduct and Endometrium Array Version 1: A Tailored Tool for Studying Bovine Endometrium Biology and Pathophysiology

Fertility problems are the main reason for slaughter of high-performance milk cows, because elongated calving intervals result in financial losses for the farmer and retard genetic progress. Genetic improvement of fertility would be of great benefit, but functional traits for effective selection are missing. Recent advances in functional genomics tools like DNA microarrays could be the key to identify gene expression patterns in the endometrium that correlate with maternal fertility. Therefore, a first version of a bovine oviduct and endometrium cDNA array was established that contains a set of 1,440 cDNA clones and long oligonucleotides representing 950 different genes. The major part of these genes has been identified in a series of differential gene expression studies in endometrium (different stages of the estrous cycle, d 18 pregnant vs. nonpregnant) and in oviduct epithelial cells (different stages of the estrous cycle) using a combination of subtracted cDNA libraries and cDNA array hybridization. Furthermore, cDNA clones of genes, which showed no changes in their mRNA levels in the analyzed tissues, were added as controls. Reproducibility of the array hybridization, a comparison with the Affymetrix bovine genome array, and confirmation of differential gene expression with reverse transcription-quantitative PCR is shown. Potential future applications include systematic studies of interactions between metabolic status and functionality of the endometrium to identify genes that could be used for differential diagnosis of fertility problems. Further, endometrium transcriptome profiles may serve as novel traits to improve fertility by genetic selection.

Use of gene expression microarrays for evaluating environmental stress tolerance at the cellular level in cattle

Selecting domestic animals for tolerance to thermal stress (TS) has been counterproductive, because acclimation involves reducing or diverting metabolizable energy from production to balance heat gain and loss. Ideally, simultaneous selection for increased production and improved thermotolerance is desirable, but to accomplish this at the genomic level the genes associated with acclimation, adaptation, and thermo-tolerance need to be identified. We evaluated the effects of TS on mammary development and gene expression in vitro using a bovine mammary epithelial cell collagen gel culture system. Acute TS was characterized by inhibition and regression of the ductal branches. Gene expression profiling revealed an overall upregulation of genes associated with the stress response and protein repair. In contrast, genes associated with cellular and mammary epithelial cell-specific biosynthesis, metabolism, and morphogenesis were generally downregulated by TS. Future studies will examine the impact of acclimation and adaptation on gene expression to identify those genes associated with acquisition of thermal tolerance.

Interpretation of microarray data: Trudging out of the abyss towards elucidation of biological significance1

The recent development of tools for expression profiling in livestock has availed reproductive biologists of new opportunities to examine global changes in gene expression during key developmental events, in response to hormonal or other treatments, and as a tool for phenotyping or predicting developmental potential. Such experiments often yield lists of tens to thousands of modulated genes, transcripts of interest, or both. Some argue that such technological advances signal a move from hypothesis-driven research to descriptive discovery research, resulting in information overload at the expense of biological significance. One can easily spend hours staring into the abyss, wondering if the results are real and what they mean. However, microarrays can be more than a high throughput and expensive screening tool. Many factors contribute to the success of expression profiling experiments and the yield of interpretable data, including the nature of the hypothesis or objective of the study, the microarray platform, the complexity of the tissue of interest, the experimental design, and the incorporation of the best available strategies for data analysis and interpretation of the biological themes. Although challenging due to the lack of extensive annotation or ontology classification for genes in livestock species, functional categories of coregulated genes and gene pathways can be determined, and hypotheses about common regulatory elements or the functional significance can be formulated. We have applied cDNA microarray technology to studies of follicular growth, oocyte quality, and the periovulatory period in cattle. Lessons learned from such experiments and a review of the available literature form the basis for the strategies described to facilitate successful application of microarray technology to studies of reproductive biology of livestock species.

Functional genomics studies of oocyte competence: evidence that reduced transcript abundance for follistatin is associated with poor developmental competence of bovine oocytes

Poor oocyte competence contributes to infertility in humans and livestock species. The molecular characteristics of such oocytes are generally unknown. Objectives of the present studies were to identify differences in RNA transcript abundance in oocytes and early embryos associated with reduced oocyte competence and development to the blastocyst stage. Microarray experiments were conducted using RNA isolated from germinal vesicle stage oocytes collected from adult versus prepubertal animals (model of poor oocyte competence). A total of 193 genes displaying greater mRNA abundance in adult oocytes and 223 genes displaying greater mRNA abundance in prepubertal oocytes were detected. Subsequent gene ontology analysis of microarray data revealed significant overrepresentation of transcripts encoding for genes in hormone secretion classification within adult oocytes and such genes were selected for further analysis. Real-time PCR experiments revealed greater abundance of mRNA for βA and βB subunits of inhibin/activin and follistatin, but not the α subunit in germinal vesicle stage oocytes collected from adult versus prepubertal animals. Cumulus cell follistatin and βB subunit mRNA abundance were similar in samples collected from prepubertal versus adult animals. A positive association between time of first cleavage (oocyte competence) and follistatin mRNA abundance was noted. Follistatin, βB, and α subunit mRNAs were temporally regulated during early bovine embryogenesis and peaked at the 16-cell stage. Collectively, results demonstrate a positive association of follistatin mRNA abundance with oocyte competence in two distinct models and dynamic regulation of follistatin, βB, and α subunit mRNAs in early embryos after initiation of transcription from the embryonic genome.

Capturing benefits from the bovine genome sequence

The bovine genome sequence in ‘draft’ form will be complete in 2007. The availability of the sequence and very large numbers of single nucleotide polymorphisms will have profound effects on livestock production. The dairy industry is well positioned to capture the benefits of this enormous and enabling resource because of its comprehensive databases containing phenotypic and pedigree data for large numbers of animals, intense utilisation of genetics in breeding programs and efficient management of reproductive performance. The bovine genome sequence will assist in the development of novel products, especially value-added products, and markedly enhance the rate of genetic gain in the Australian dairy population. The immediate challenge facing the industry is the integration of new technological capabilities into existing breeding programs and production systems.

Analysis of the bovine neutrophil transcriptome during glucocorticoid treatment

The objective of this study was to characterize a large portion of the bovine neutrophil transcriptome following treatment with the anti-inflammatory glucocorticoid dexamethasone (Dex). Total RNA was isolated from blood neutrophils of healthy cattle (5 castrated male Holsteins) immediately following cell purification (0 h) or after ex vivo aging for 4 h with or without added Dex. Additional neutrophils were cotreated with a glucocorticoid receptor (GR) antagonist (RU486) and Dex for 4 h. RNA was amplified, dye labeled (Cy3 or Cy5), and hybridized to a series of National Bovine Functional Genomics Consortium (NBFGC) microarrays. LOWESS data normalization followed by mixture model analyses showed that 11.15% of the spotted NBFGC cDNAs (2,036/18,263) were expressed in 4-h (untreated) neutrophils. Subsequent two-step mixed-model analysis detected ( P ≤ 0.05) 1,109 differentially expressed genes, of which contrast analysis indicated those that were independently responsive to aging (1,064), Dex (502), RU486 + Dex (141), or RU486 (357). In silico analysis revealed that 416 of the differentially expressed genes are unknown, 59 did not cluster well based on known function, and 634 clustered into 20 ontological categories. Independent validation of differential expression was done for 14 of the putatively Dex-responsive genes across these categories. Results showed that Dex induced rapid translocation of GR into the neutrophil nucleus and signaled dramatic alterations in expression of genes that delay apoptosis, enhance bactericidal activity, and promote tissue remodeling without inflammation or fibrosis. Thus these findings revealed hitherto unappreciated plasticity of blood neutrophils and potentially novel anti-inflammatory/wound-healing actions of glucocorticoids.

Novel algorithm for transcriptome analysis

A growing body of evidence implicates the oocyte as a key regulator of ovarian folliculogenesis and early embryonic development. We have screened bovine cDNA microarrays (containing expressed sequence tags representing >15,000 unique genes) with Cy3- and Cy5-labeled cDNA derived from bovine oocyte samples collected at two different stages of meiotic maturation (germinal vesicle vs. metaphase II; n = 3 samples per group). Here, we present a novel data analysis approach that uses all available information from above experiments to obtain and index the transcriptome of bovine oocytes and changes in transcriptome composition in response to meiotic maturation. Signal intensities (Fg) for all housekeeping genes were omitted prior to analysis. A local threshold for gene expression was computed as background intensity (Bg) plus 2 times the standard deviation of background and foreground signals. Within each array, data were normalized by the LOWESS procedure. Subsequently, a two-stage mixed model was fitted to remove systematic variations. In the first stage, the response was the LOWESS normalized Fg with treatment as a fixed effect. In stage 2, the residuals from stage 1 were analyzed in a gene-specific model that included treatment group and spots nested within patch and array. A test for the difference between least squares means for the treatment effect was performed. A false discovery rate (FDR) adjustment on the p values for the difference was carried out. This novel algorithm was compared with approaches that ignore the FDR and the threshold described herein and stark differences obtained.

A gene coexpression network for bovine skeletal muscle inferred from microarray data

We present the application of large-scale multivariate mixed-model equations to the joint analysis of nine gene expression experiments in beef cattle muscle and fat tissues with a total of 147 hybridizations, and we explore 47 experimental conditions or treatments. Using a correlation-based method, we constructed a gene network for 822 genes. Modules of muscle structural proteins and enzymes, extracellular matrix, fat metabolism, and protein synthesis were clearly evident. Detailed analysis of the network identified groupings of proteins on the basis of physical association. For example, expression of three components of the z-disk, MYOZ1, TCAP, and PDLIM3, was significantly correlated. In contrast, expression of these z-disk proteins was not highly correlated with the expression of a cluster of thick (myosins) and thin (actin and tropomyosins) filament proteins or of titin, the third major filament system. However, expression of titin was itself not significantly correlated with the cluster of thick and thin filament proteins and enzymes. Correlation in expression of many fast-twitch muscle structural proteins and enzymes was observed, but slow-twitch-specific proteins were not correlated with the fast-twitch proteins or with each other. In addition, a number of significant associations between genes and transcription factors were also identified. Our results not only recapitulate the known biology of muscle but have also started to reveal some of the underlying associations between and within the structural components of skeletal muscle.

Gene expression-based approaches to beef quality research

Advances in mammalian genomics have permitted the application of gene expression profiling approaches to gene discovery for meat quality traits in cattle. The first custom cDNA microarray based on the transcriptome of bovine muscle and fat tissue was developed and applied to animal experimentation and cell culture experimentation between 1999 and 2005. Complementary DNA microarray tools for beef quality research were developed in parallel with bioinformatics tools that permit the analysis of microarray data obtained from complex experimental designs commonly encountered in large animal research. In addition, tools were designed to link gene expression data with gene function in the bovine, such as in vitro models of bovine adipogenesis and bioinformatics tools to map gene networks from expression data. The application of these genomics tools to the study of beef quality has yielded novel knowledge of genes and molecules involved in the processes of intramuscular adipogenesis and protein turnover. This review summarises the current state of knowledge and important lessons derived from bovine genomics initiatives in Australia and around the world.

Advances in livestock genomics: Opening the barn door

Genome research in animals used in agriculture has progressed rapidly in recent years, moving from rudimentary genome maps to trait maps to gene discovery. These advances are the result of animal genome projects following closely in the footsteps of the Human Genome Project, which has opened the door to genome research in farm animals. In return, genome research in livestock species is contributing to our understanding of chromosome evolution and to informing the human genome. Enhancement of these contributions plus the much anticipated application of DNA-based tools to animal health and production can be expected as livestock genomics enters its sequencing era.

Construction and validation of a Bovine Innate Immune Microarray

BACKGROUND

Microarray transcript profiling has the potential to illuminate the molecular processes that are involved in the responses of cattle to disease challenges. This knowledge may allow the development of strategies that exploit these genes to enhance resistance to disease in an individual or animal population.

RESULTS

The Bovine Innate Immune Microarray developed in this study consists of 1480 characterised genes identified by literature searches, 31 positive and negative control elements and 5376 cDNAs derived from subtracted and normalised libraries. The cDNA libraries were produced from 'challenged' bovine epithelial and leukocyte cells. The microarray was found to have a limit of detection of 1 pg/microg of total RNA and a mean slide-to-slide correlation co-efficient of 0.88. The profiles of differentially expressed genes from Concanavalin A (ConA) stimulated bovine peripheral blood lymphocytes were determined. Three distinct profiles highlighted 19 genes that were rapidly up-regulated within 30 minutes and returned to basal levels by 24 h; 76 genes that were up-regulated between 2-8 hours and sustained high levels of expression until 24 h and 10 genes that were down-regulated. Quantitative real-time RT-PCR on selected genes was used to confirm the results from the microarray analysis. The results indicate that there is a dynamic process involving gene activation and regulatory mechanisms re-establishing homeostasis in the ConA activated lymphocytes. The Bovine Innate Immune Microarray was also used to determine the cross-species hybridisation capabilities of an ovine PBL sample.

CONCLUSION

The Bovine Innate Immune Microarray has been developed which contains a set of well-characterised genes and anonymous cDNAs from a number of different bovine cell types. The microarray can be used to determine the gene expression profiles underlying innate immune responses in cattle and sheep.

Microarrays in veterinary diagnostics

Microarrays have numerous applications in the clinical setting, and these uses are not confined to the study of common human diseases. Indeed, the high-throughput technology affects clinical diagnostics in a variety of contexts, and this is reflected in the increasing use of microarray-based tools in the development of diagnostic and prognostic tests and in the identification of novel therapeutic targets. While much of the value of microarray-based experimentation has been derived from the study of human disease, there is equivalent potential for its role in veterinary medicine. Even though the resources devoted to the study of animal molecular diagnostics may be less than those available for human research, there is nonetheless a growing appreciation of the value of genome-wide information as it applies to animal disease. Therefore, this review focuses on the basics of microarray experimentation, and how this technology lends itself to a variety of diagnostic approaches in veterinary medicine.

Transcriptional profiling of skeletal muscle tissue from two breeds of cattle

We used a 9.6 K cattle muscle/fat cDNA microarray to study gene expression differences between the longuissimus dorsi (LD) muscle of Japanese Black (JB) and Holstein (HOL) cattle. JB cattle exhibit an unusual ability to accumulate intramuscular adipose tissue with fat melting points lower than that in other breeds. The LD biopsies from three JB (Tajima strain) and three HOL animals were used in this breed comparison. Seventeen genes were identified as preferentially expressed in LD samples from JB and seven genes were found to be expressed more highly in HOL. The expression of six selected differentially expressed genes was confirmed by quantitative real-time PCR. The genes more highly expressed in JB are associated with unsaturated fatty acid synthesis, fat deposition, and the thyroid hormone pathway. These results are consistent with the increased amounts and proportions of monounsaturated fatty acids observed in the muscle of JB animals. By discovering as yet uncharacterized genes that are differentially regulated in this comparison, the work may lead us to a better understanding of the regulatory pathways involved in the development of intramuscular adipose tissue.

Molecular analyses of disease pathogenesis: application of bovine microarrays

The molecular analysis of disease pathogenesis in cattle has been limited by the lack of availability of tools to analyze both host and pathogen responses. These limitations are disappearing with the advent of methodologies such as microarrays that facilitate rapid characterization of global gene expression at the level of individual cells and tissues. The present review focuses on the use of microarray technologies to investigate the functional pathogenomics of infectious disease in cattle. We discuss a number of unique issues that must be addressed when designing both in vitro and in vivo model systems to analyze host responses to a specific pathogen. Furthermore, comparative functional genomic strategies are discussed that can be used to address questions regarding host responses that are either common to a variety of pathogens or unique to individual pathogens. These strategies can also be applied to investigations of cell signaling pathways and the analyses of innate immune responses. Microarray analyses of both host and pathogen responses hold substantial promise for the generation of databases that can be used in the future to address a wide variety of questions. A critical component limiting these comparative analyses will be the quality of the databases and the complete functional annotation of the bovine genome. These limitations are discussed with an indication of future developments that will accelerate the validation of data generated when completing a molecular characterization of disease pathogenesis in cattle.

The expanding role of microarrays in the investigation of macrophage responses to pathogens

In the last few years, microarray technology has emerged as the method of choice for large-scale gene expression studies. It provides an efficient and rapid method to investigate the entire transcriptome of a cell. No research field has benefited more from microarray technology than the study of the exquisite interplay between pathogens and hosts. Numerous microarray studies have now been published in this field, which have provided insights into the mechanisms of host defence and the tactics employed by pathogens to circumvent these protection strategies. These studies have led to a more comprehensive understanding of the host immune response and identified new avenues of research for potential control strategies against pathogens. In the past, research has concentrated on human and mouse microarrays to investigate host-pathogen interactions, regardless of the host species. This trend is changing with the ever-expanding sequence resources now available for many pathogen and host species, including livestock animals. The use of species-specific microarrays has furthered our understanding of host-pathogen interactions for particular organisms and aided in the annotation of unknown genes. Macrophages play a central role in the host's innate and adaptive immune responses to pathogens. These cells are in the first line of defence and interact with a wide range of pathogens; many of which have evolved strategies to circumvent the macrophage defence mechanisms and survive within these cells. In this report, we review the wealth of studies using microarray technology to investigate the response of macrophages to pathogens. These studies illustrate how microarray technology has expanded our understanding of the dialogue between macrophage and pathogen and provide examples of the benefits and pitfalls of using this technique. Furthermore, we discuss the resources available to use microarray analysis to study the immune response of a non-human, non-rodent species, the cow.

Generation of a bovine oocyte cDNA library and microarray: resources for identification of genes important for follicular development and early embryogenesis

The oocyte is a key regulator of ovarian folliculogenesis and early embryonic development. However, the composition of the oocyte transcriptome and identities and functions of key oocyte-specific genes involved in the above processes are relatively unknown. Using a PCR-based cDNA amplification method (SMART technology), we constructed a bovine oocyte cDNA library. Analysis of 230 expressed sequence tags (ESTs) from this library identified 102 unique sequences. Although some correspond to housekeeping genes (e.g., ribosomal protein L15) and some represent genes previously known to be expressed in oocytes and other tissues, most encode for genes whose expression in mammalian oocytes has not been reported previously (e.g., cocaine- and amphetamine-regulated transcript) or genes of unknown function. Sixteen did not show significant sequence similarity to any entries in the GenBank database and were classified as novel. Using over 2,000 unsequenced, randomly selected cDNA clones from the library, we constructed an oocyte microarray and performed experiments to identify genes preferentially expressed in fetal ovary (an enriched source of oocytes) relative to somatic tissues. Eleven clones were identified by microarray analysis with consistently higher expression in fetal ovaries (collected from animals at days 210-260 of gestation) compared with spleen and liver. DNA sequence analysis of these clones revealed that two correspond to JY-1, a novel bovine oocyte-specific gene. The remaining nine clones represent five identified genes and one additional completely novel gene. Increased abundance of mRNA in fetal ovary for five of the six genes identified was confirmed by real-time PCR. Results demonstrate the potential utility of these unique resources for identification of oocyte-expressed genes potentially important for reproductive function.

Validation and application of a high fidelity mRNA linear amplification procedure for profiling gene expression

The need for microgram quantities of RNA for microarray experiments has hindered application of this novel technology in cell types/tissue samples with limited abundance of RNA. In this study, potential application of T7-based linear RNA amplification was investigated for use in gene expression profiling experiments where starting material is limited. Yield and integrity of amplified antisense RNA (aaRNA), microarray hybridization intensities, and fidelity of differential gene expression detected were determined for arrays generated for unamplified versus amplified RNA from the same homogenous starting pools. Total RNA was extracted from bovine spleen and fetal ovary, serially diluted to concentrations ranging from 2 microg to 500 pg and amplified. Quality and quantity of total input RNA and aaRNA were assessed by spectrophotometry, gel electrophoresis and bioanalyzer. In experiment 1, we determined the optimal amounts of aaRNA generated from 20, 40, 200 ng and 2 microg input total RNA for use in cDNA synthesis, labeling and array hybridization that would yield robust and consistent hybridization signals on a bovine oocyte cDNA microarray. In experiment 2, comparison of microarray hybridization intensities and fidelity of differential gene expression between aaRNA generated from 2, 20 and 40 ng input total RNA versus unamplified RNA (uRNA) were conducted. The hybridization intensities for each of the 7000 spots per slide for microarrays conducted using aaRNA versus uRNA were highly correlated (2 ng = 0.84, 20 ng = 0.88, 40 ng = 0.90; P < 0.01). The false positive rate was low and similar (4.0% versus 4.4%) for arrays done with uRNA and aaRNA. Ninety-seven ESTs were detected as differentially expressed in the fetal ovary versus spleen at > 1.5- or < 0.5-fold using uRNA (P < 0.05). However, the number of genes detected in arrays using aaRNA was approximately 1.5-2.5 times greater than with uRNA. Approximately, 65-70% of differentially expressed genes were common between uRNA and aaRNA arrays. Relative fold-expression (Cy3/Cy5 ratios) for 25 overlapping abundant genes was comparable for uRNA versus aaRNA arrays with 2 and 20 ng total RNA as input. Results demonstrate that T7-based linear amplification of small amounts of input RNA and use of aaRNA in microarray experiments retains fidelity of detection of differential gene expression that is relatively comparable to experiments done with uRNA and provides a potentially viable approach to facilitate gene expression profiling using limited amounts of starting material.

A 7872 cDNA microarray and its use in bovine functional genomics

The strategy used to create and annotate a 7872 cDNA microarray from cattle placenta and spleen cDNA sequences is described. This microarray contains approximately 6300 unique genes, as determined by BLASTN and TBLASTX similarity search against the human and mouse UniGene and draft human genome sequence databases (build 34). Sequences on the array were annotated with gene ontology (GO) terms, thereby facilitating data analysis and interpretation. A total of 3244 genes were annotated with GO terms. The array is rich in sequences encoding transcription factors, signal transducers and cell cycle regulators. Current research being conducted with this array is described, and an overview of planned improvements in our microarray platform for cattle functional genomics is presented.

A collection of bovine cDNA probes for gene expression profiling in muscle

Array technology has been increasingly used to monitor global gene expression patterns in various tissues and cell types. However, applications to muscle development and pathology as well as meat production in livestock species have been hampered by the lack of appropriate cDNA collections. To overcome this problem, a directed cDNA library was constructed starting from 23 muscles of meat-producing bovines to derive a collection of 3573 clones. A preliminary sequence characterization of this collection indicated that the most abundant transcripts correspond to genes encoding proteins involved in energy metabolism (COX and NADH dehydrogenase subunits) and belonging to the contractile apparatus (myosin chains and troponin isoforms). From this cDNA library, we selected a set of 435 clones representing 340 unique genes, of which 24 were novel. This collection was subsequently completed with 75 specific cDNA probes for genes of interest already studied in our laboratory. The bovine 'muscle' cDNA repertoire thus designed was spotted onto a nylon membrane (macroarray) in order to test its utility to further investigate the transcriptome of bovine muscles in relation to meat quality traits. It is also anticipated that this type of collection might be useful for the study of chronic myologic diseases in other mammalian species, including humans.

Development and application of a bovine cDNA microarray for expression profiling of muscle and adipose tissue

In order to gain new knowledge of the genetic control of biochemical and developmental processes that contribute to beef quality, we constructed a bovine microarray of 9600 elements comprising about 2000 expressed sequence tags (ESTs) and 7300 anonymous cDNA clones from muscle and fat-derived cDNA libraries. The microarray was used in 2 animal experiments aimed at uncovering gene expression differences associated with adipogenesis and protein turnover. The results obtained so far show that expression profiling of bovine muscle using the microarray can reliably identify differentially expressed genes and confirm existing hypotheses. Moreover, the technique can provide new evidence on the detailed involvement of well-characterised genes and can identify genes that have not previously been described as having a role in these processes.