EST-based identification of genes expressed in the liver of adult Atlantic salmon (Salmo salar)

Trypsin gene expression in adults and larvae of tropical gar Atractosteus tropicus

Trypsin gene (try) expression levels were quantified in different organs of wild and captive tropical gar (Atractosteus tropicus) adults, and changes in expression during initial ontogeny of the species were determined. RNA was extracted from the pancreas, and cDNA was synthesized and later amplified by endpoint PCR using oligonucleotides designed from different try sequences of fish registered in GenBank. Subsequently, specific oligonucleotides were designed from the partial sequences. Gene expression was measured after RNA extraction and synthesis of the cDNA of 11 organs (liver, pancreas, stomach, esophagus, intestine, pyloric caeca, brain, muscle, gills, gonad, and kidney) of captive and wild adults. Likewise, samples of A. tropicus larvae were taken on days 0 (embryo), 5, 10, 15, 20, 25, and 30 days after hatching (DAH), the RNA was extracted, and the synthesis of cDNA was carried out to measure real-time gene expression (qPCR). The results showed that the highest relative try expression occurred mainly in the esophagus, liver, stomach, and pancreas of both wild and captive adult fish; however, captive organisms had a higher try expression level than wild fish. Although try expression during initial ontogeny was high in embryos (0 DAH), it did not reach the maximum value until 15 DAH. It was concluded that try expression levels in captive adults are due to the high protein content in the balanced feed (trout diet). The highest try expression level during larviculture was detected at 15 DAH, which indicates that A. tropicus larvae have a mature digestive system and can efficiently hydrolyze proteins from feed at this developmental stage.

Transcriptome analysis of the critically endangered Dabry's sturgeon (Acipenser dabryanus) head kidney response to Aeromonas hydrophila

Dabry's sturgeon (Acipenser dabryanus), as a living fossil, is considered a critically endangered aquatic animal in China. To date, the immune system of this species remains largely unknown, with limited available sequence information. In addition, increasing incidence of bacterial pathogenic diseases has been reported. Hence, the present study aimed to characterize comprehensively transcriptome profile of the head kidney from Dabry's sturgeon infected with Aeromonas hydrophila using Illumina platform. Over 42 million high-quality reads were obtained and de novo assembled into a final set of 195240 unique transcript fragments (unigenes), with an average length of 564 bp. Approximately 41702 unigenes were annotated in the NR NCBI database. Dabry's sturgeon unigenes had the highest number of hits with 14365 (34.45%) to Lepisosteus oculatus. The 195240 unigenes were assigned to three Gene Ontology (GO) categories: biological process, cellular component, and molecular function. Among them, 27770 unigenes were clustered into 26 Eukaryotic Orthologous Group (KOG) functional categories, and 36031 unigenes were mapped to 335 known Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. After A. hydrophila administration, 1728 differentially expressed unigenes were identified, including 980 upregulated and 748 downregulated unigenes. Further KEGG enrichment analysis of these unigenes identified 16 immune-related pathways, including the Toll-like receptor signaling pathway, chemokine signaling pathway, complement and coagulation pathway, RIG-I-like receptor signaling pathway, and NOD-like receptor signaling pathway. 20 DEGs were selected and their expression patterns are largely consistent with the transcriptome profile analysis, which clearly validated the reliability of the DEGs in transcriptome analysis. This work revealed novel gene expression patterns of Dabry's sturgeon host defense and contributes to a better understanding of the immune system and defense mechanisms of Dabry's sturgeon in response to bacterial infection. The results provide valuable references for studies in sturgeons that lack complete genomic sequences, and could also be helpful for the analyzing evolution among cartilaginous and teleost fish.

Transcriptome analysis revealed changes of multiple genes involved in immunity in Cynoglossus semilaevis during Vibrio anguillarum infection

Half-smooth tongue sole (Cynoglossus semilaevis) is one of the most valuable marine aquatic species in Northern China. Given to the rapid development of aquaculture industry, the C. semilaevis was subjected to disease-causing bacteria Vibrio anguillarum. It therefore is indispensable and urgent to understand the mechanism of C. semilaevis host defense against V. anguillarum infection. In the present study, the extensively analysis at the transcriptome level for V. Anguillarum disease in tongue sole was carried out. In total, 94,716 high quality contigs were generated from 75,884,572 clean reads in three libraries (HOSG, NOSG, and CG). 22,746 unigenes were identified when compared with SwissProt, an NR protein database and NT nucleotide database. 954 genes exhibiting the differentially expression at least one pair of comparison in all three libraries were identified. GO enrichment for these genes revealed gene response to biotic stimulus, immune system regulation, and immune response and cytokine production. Further, the pathways such as complement and coagulation cascades and Vibrio cholerae infection pathways were enriched in defensing of pathogen. Besides, 13,428 SSRs and 118,239 SNPs were detected in tongue sole, providing further support for genetic variation and marker-assisted selection in future. In summary, this study identifies several putative immune pathways and candidate genes deserving further investigation in the context of development of therapeutic regimens and lays the foundation for selecting resistant lines of C. semilaevis against V. anguillarum.

Transcriptome and expression profiling analysis of the hemocytes reveals a large number of immune-related genes in mud crab Scylla paramamosain during Vibrio parahaemolyticus infection

BACKGROUND

Mud crab Scylla paramamosain is an economically important marine species in China. However, frequent outbreaks of infectious diseases caused by marine bacteria, such as Vibrio parahaemolyticus, result in great economic losses.

METHODOLOGY/PRINCIPAL FINDINGS

Comparative de novo transcriptome analysis of S. paramamosain infected with V. parahaemolyticus was carried out to investigate the molecular mechanisms underlying the immune response to pathogenic bacteria by using the Illumina paired-end sequencing platform. A total of 52,934,042 clean reads from the hemocytes of V. parahaemolyticus-infected mud crabs and controls were obtained and assembled into 186,193 contigs. 59,120 unigenes were identified from 81,709 consensus sequences of mud crabs and 48,934 unigenes were matched proteins in the Nr or Swissprot databases. Among these, 10,566 unigenes belong to 3 categories of Gene Ontology, 25,349 to 30 categories of KEGG, and 15,191 to 25 categories of COG database, covering almost all functional categories. By using the Solexa/Illumina's DGE platform, 1213 differentially expressed genes (P<0.05), including 538 significantly up-regulated and 675 down-regulated, were detected in V. parahaemolyticus-infected crabs as compared to that in the controls. Transcript levels of randomly-chosen genes were further measured by quantitative real-time PCR to confirm the expression profiles. Many differentially expressed genes are involved in various immune processes, including stimulation of the Toll pathway, Immune Deficiency (IMD) pathway, Ras-regulated endocytosis, and proPO-activating system.

CONCLUSIONS/SIGNIFICANCE

Analysis of the expression profile of crabs under infection provides invaluable new data for biological research in S. paramamosain, such as the identification of novel genes in the hemocytes during V. parahaemolyticus infection. These results will facilitate our comprehensive understanding of the mechanisms involved in the immune response to bacterial infection and will be helpful for diseases prevention in crab aquaculture.

The Expression Analysis of Complement Component C3 during Early Developmental Stages in Olive Flounder (Paralichthys olivaceus)

Fish larvae are immediately exposed to microbes from hatching to maturation of their lymphoid organs, therefore effective innate mechanisms is very important for survival in such an environment. The key component of innate immune system, C3 is central protein of all activation pathways of the complement system, leading to inflammatory reactions, such as opsonisation, chemotaxis, and cell lysis of pathogens. Although, innate mechanisms is essential for survival in the early stage of development, little is known about defence mechanisms. In this study, the alignment analysis showed that amino acid sequence of C3 from olive flounder liver EST homologous to other known C3 sequences with 73-99% identity. Also, we examined the tissue distribution of olive flounder C3 and analyzed expression pattern from the fertilized egg until 28 days post hatching. As a result, olive flounder C3 mRNA was expressed only in the liver and the mRNA level more increased as developmental proceed during the early stage. These results may suggest that olive flounder C3 plays an important function in the early immune response of olive flounder larvae.

Transcriptomics for understanding marine fish larval development1This review is part of a virtual symposium on current topics in aquaculture of marine fish and shellfish

The larval phase is a crucial period in the life of marine fish. During this phase, the organism will acquire the phenotype of an adult fish through the development of tissues and organs and the maturation of some of the principal physiological functions. Many biological processes (differentiation, cellular proliferation, growth, etc.) are regulated during this period. These regulations take place at different biological levels and particularly concern the expression of genes involved in larval ontogenesis processes. The development of bioinformatic resources (DNA or cDNA sequences) and molecular tools enabling high throughput gene expression analysis (microarrays) have allowed the transcriptome of marine fish species to be studied. In the present review, we summarize the main findings from transcriptomic investigations of development of marine fish larvae. Special attention is paid to investigations of transcriptomic patterns during postembryonic development and to the impact of environmental or nutritional factors on the transcriptome of marine fish larvae. Transcriptomic approaches will be especially useful in the future for investigating the effect of temperature and water acidification (or pH) on the development of different fish species in the context of global climate change.

Targeted SNP discovery in Atlantic salmon (Salmo salar) genes using a 3'UTR-primed SNP detection approach

Background

Single nucleotide polymorphisms (SNPs) represent the most widespread type of DNA variation in vertebrates and may be used as genetic markers for a range of applications. This has led to an increased interest in identification of SNP markers in non-model species and farmed animals. The in silico SNP mining method used for discovery of most known SNPs in Atlantic salmon (Salmo salar) has applied a global (genome-wide) approach. In this study we present a targeted 3'UTR-primed SNP discovery strategy that utilizes sequence data from Salmo salar full length sequenced cDNAs (FLIcs). We compare the efficiency of this new strategy to the in silico SNP mining method when using both methods for targeted SNP discovery.

Results

The SNP discovery efficiency of the two methods was tested in a set of FLIc target genes. The 3'UTR-primed SNP discovery method detected novel SNPs in 35% of the target genes while the in silico SNP mining method detected novel SNPs in 15% of the target genes. Furthermore, the 3'UTR-primed SNP discovery strategy was the less labor intensive one and revealed a higher success rate than the in silico SNP mining method in the initial amplification step. When testing the methods we discovered 112 novel bi-allelic polymorphisms (type I markers) in 88 salmon genes [dbSNP: ss179319972-179320081, ss250608647-250608648], and three of the SNPs discovered were missense substitutions.

Conclusions

Full length insert cDNAs (FLIcs) are important genomic resources that have been developed in many farmed animals. The 3'UTR-primed SNP discovery strategy successfully utilized FLIc data to detect novel SNPs in the partially tetraploid Atlantic salmon. This strategy may therefore be useful for targeted SNP discovery in several species, and particularly useful in species that, like salmonids, have duplicated genomes.

Sequencing the genome of the Atlantic salmon (Salmo salar)

The International Collaboration to Sequence the Atlantic Salmon Genome (ICSASG) will produce a genome sequence that identifies and physically maps all genes in the Atlantic salmon genome and acts as a reference sequence for other salmonids.

Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection

BACKGROUND

The large yellow croaker (Pseudosciaena crocea) is an economically important marine fish in China suffering from severe outbreaks of infectious disease caused by marine bacteria such as Aeromonas hydrophila (A. hydrophila), resulting in great economic losses. However, the mechanisms involved in the immune response of this fish to bacterial infection are not fully understood. To understand the molecular mechanisms underlying the immune response to such pathogenic bacteria, we used high-throughput deep sequencing technology to investigate the transcriptome and comparative expression profiles of the large yellow croaker infected with A. hydrophila.

RESULTS

A total of 13,611,340 reads were obtained and assembled into 26,313 scaffolds in transcriptional responses of the A. hydrophila-infected large yellow croaker. Via annotation to the NCBI database, we obtained 8216 identified unigenes. In total, 5590 (68%) unigenes were classified into Gene Ontology, and 3094 unigenes were found in 20 KEGG categories. These genes included representatives from almost all functional categories. By using Solexa/Illumina's DeepSAGE, 1996 differentially expressed genes (P value < 0.05) were detected in comparative analysis of the expression profiles between A. hydrophila-infected fish and control fish, including 727 remarkably upregulated genes and 489 remarkably downregulated genes. Dramatic differences were observed in genes involved in the inflammatory response. Bacterial infection affected the gene expression of many components of signaling cascades, including the Toll-like receptor, JAK-STAT, and MAPK pathways. Genes encoding factors involved in T cell receptor (TCR) signaling were also revealed to be regulated by infection in these fish.

CONCLUSION

Based on our results, we conclude that the inflammatory response may play an important role in the early stages of infection. The signaling cascades such as the Toll-like receptor, JAK-STAT, and MAPK pathways are regulated by A. hydrophila infection. Interestingly, genes encoding factors involved in TCR signaling were revealed to be downregulated by infection, indicating that TCR signaling was suppressed at this early period. These results revealed changes of multiple signaling pathways involved in immunity during A. hydrophila infection, which will facilitate our comprehensive understanding of the mechanisms involved in the immune response to bacterial infection in the large yellow croaker.

Molecular evolution of the duplicated TFIIAgamma genes in Oryzeae and its relatives

Background

Gene duplication provides raw genetic materials for evolutionary novelty and adaptation. The evolutionary fate of duplicated transcription factor genes is less studied although transcription factor gene plays important roles in many biological processes. TFIIAγ is a small subunit of TFIIA that is one of general transcription factors required by RNA polymerase II. Previous studies identified two TFIIAγ-like genes in rice genome and found that these genes either conferred resistance to rice bacterial blight or could be induced by pathogen invasion, raising the question as to their functional divergence and evolutionary fates after gene duplication.

Results

We reconstructed the evolutionary history of the TFIIAγ genes from main lineages of angiosperms and demonstrated that two TFIIAγ genes (TFIIAγ1 and TFIIAγ5) arose from a whole genome duplication that happened in the common ancestor of grasses. Likelihood-based analyses with branch, codon, and branch-site models showed no evidence of positive selection but a signature of relaxed selective constraint after the TFIIAγ duplication. In particular, we found that the nonsynonymous/synonymous rate ratio (ω = d_N/d_S) of the TFIIAγ1 sequences was two times higher than that of TFIIAγ5 sequences, indicating highly asymmetric rates of protein evolution in rice tribe and its relatives, with an accelerated rate of TFIIAγ1 gene. Our expression data and EST database search further indicated that after whole genome duplication, the expression of TFIIAγ1 gene was significantly reduced while TFIIAγ5 remained constitutively expressed and maintained the ancestral role as a subunit of the TFIIA complex.

Conclusion

The evolutionary fate of TFIIAγ duplicates is not consistent with the neofunctionalization model that predicts that one of the duplicated genes acquires a new function because of positive Darwinian selection. Instead, we suggest that subfunctionalization might be involved in TFIIAγ evolution in grasses. The fact that both TFIIAγ1 and TFIIAγ5 genes were effectively involved in response to biotic or abiotic factors might be explained by either Dykhuizen-Hartl effect or buffering hypothesis.

Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar)

Background

Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs) are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP), the number of sequences where the full-length of the cDNA insert has been determined has been small.

Results

High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank: BT043497 - BT044056]. Five hundred and ten (91%) of the transcripts were annotated using Gene Ontology (GO) terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS). The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. Finally, conserved 7-mers in the 3'UTRs were identified, of which some were identical to miRNA target sequences.

Conclusion

This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We have demonstrated that many FLIcs contained a complete coding sequence (cCDS). This suggests that the remaining cDNA libraries generated by SGP represent a valuable cCDS FLIc source. The conservation of 7-mers in 3'UTRs indicates that these motifs are functionally important. Identity between some of these 7-mers and miRNA target sequences suggests that they are miRNA targets in Salmo salar transcripts as well.

Profiling of infection specific mRNA transcripts of the European seabass Dicentrarchus labrax

Background

The European seabass (Dicentrarchus labrax), one of the most extensively cultured species in European aquaculture productions, is, along with the gilthead sea bream (Sparus aurata), a prospective model species for the Perciformes which includes several other commercially important species. Massive mortalities may be caused by bacterial or viral infections in intensive aquaculture production. Revealing transcripts involved in immune response and studying their relative expression enhances the understanding of the immune response mechanism and consequently also the creation of vaccines. The analysis of expressed sequence tags (EST) is an efficient and easy approach for gene discovery, comparative genomics and for examining gene expression in specific tissues in a qualitative and quantitative way.

Results

Here we describe the construction, analysis and comparison of a total of ten cDNA libraries, six from different tissues infected with V. anguillarum (liver, spleen, head kidney, gill, peritoneal exudates and intestine) and four cDNA libraries from different tissues infected with Nodavirus (liver, spleen, head kidney and brain). In total 9605 sequences representing 3075 (32%) unique sequences (set of sequences obtained after clustering) were obtained and analysed. Among the sequences several immune-related proteins were identified for the first time in the order of Perciformes as well as in Teleostei.

Conclusion

The present study provides new information to the Gene Index of seabass. It gives a unigene set that will make a significant contribution to functional genomic studies and to studies of differential gene expression in relation to the immune system. In addition some of the potentially interesting genes identified by in silico analysis and confirmed by real-time PCR are putative biomarkers for bacterial and viral infections in fish.

A description of the origins, design and performance of the TRAITS-SGP Atlantic salmon Salmo salar L. cDNA microarray

The origins, design, fabrication and performance of an Atlantic salmon microarray are described. The microarray comprises 16 950 Atlantic salmon-derived cDNA features, printed in duplicate and mostly sourced from pre-existing expressed sequence tag (EST) collections [SALGENE and salmon genome project (SGP)] but also supplemented with cDNAs from suppression subtractive hybridization libraries and candidate genes involved in immune response, protein catabolism, lipid metabolism and the parr-smolt transformation. A preliminary analysis of a dietary lipid experiment identified a number of genes known to be involved in lipid metabolism. Significant fold change differences (as low as 1.2x) were apparent from the microarray analysis and were confirmed by quantitative real-time polymerase chain reaction analysis. The study also highlighted the potential for obtaining artefactual expression patterns as a result of cross-hybridization of similar transcripts. Examination of the robustness and sensitivity of the experimental design employed demonstrated the greater importance of biological replication over technical (dye flip) replication for identification of a limited number of key genes in the studied system. The TRAITS (TRanscriptome Analysis of Important Traits of Salmon)-salmon genome project microarray has been proven, in a number of studies, to be a powerful tool for the study of key traits of Atlantic salmon biology. It is now available for use by researchers in the wider scientific community.

Evolution of CC chemokines in teleost fish: a case study in gene duplication and implications for immune diversity

Chemokines are a superfamily of cytokines responsible for regulating cell migration under both inflammatory and physiological conditions. CC chemokines are the largest subfamily of chemokines, with 28 members in humans. A subject of intense study in mammalian species, the known functional roles of CC chemokines ligands in both developmental and disease conditions continue to expand. They are also an important family for the study of gene copy number variation and tandem duplication in mammalian species. However, little is known regarding the evolutionary origin and status of these ligands in primitive vertebrates such as teleost fish. In this paper, we review the evolution of the teleost fish CC chemokine gene family, noting evidence of widespread tandem gene duplications and examining the implications of this phenomenon on immune diversity. Through extensive phylogenetic analysis of the CC chemokine sets of four teleost species, zebrafish, catfish, rainbow trout, and Atlantic salmon, we identified seven large groups of CC chemokines. It appeared that several major groups of CC chemokines are highly related including the CCL19/21/25 group, the CCL20 group, CCL27/28 group, and the fish-specific group. In the three remaining groups that contained the largest number of members, the CCL17/22 group, the MIP group, and the MCP group, similarities among species members were obscured by rapid, tandem duplications that may contribute to immune diversity.

Transcriptional analysis of LPS-stimulated activation of trout (Oncorhynchus mykiss) monocyte/macrophage cells in primary culture treated with cortisol

Primary immune responses to pathogen invasion are mediated by the innate immune system in which tissue macrophages play a key role. During infectious processes glucocorticoids generally may function to dampen inflammatory responses. In this study, the ability of cortisol to directly modulate the transcriptional response of rainbow trout macrophages to the cellular activator lipopolysaccharide (LPS) was investigated. The results indicate that cortisol significantly inhibits the well-described LPS-dependent induction of the expression of TNF-alpha2, a pro-inflammatory cytokine. In order to further characterize the molecular effects of LPS and the immunomodulatory role of cortisol, the in vitro macrophage response to LPS in the absence or presence of 12-h cortisol exposure was analyzed utilizing a salmonid-specific microarray platform. Genes that were stimulated or inhibited with LPS plus cortisol fell into several major functional groups. The first, a general "response" group comprising genes within ontology classes including the response to external stimuli, stress, humoral immunity and apoptosis, exhibited a significant increase after LPS stimulation, whereas suppression of this response was observed in the presence of cortisol. LPS stimulated other genes in a second group involved in cell signalling and also genes in a third group involved in the activation of transcription. Categories activated with cortisol were mainly related to various aspects of metabolism (including protein biosynthesis, binding and transport of ions) and structural proteins (mainly cytoskeleton and microtubules). The immunomodulatory action of cortisol on LPS-stimulated macrophages therefore appears more complex than simply the antagonism of LPS-induced transcriptional responses.

An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar)

Background

The Atlantic salmon is an important aquaculture species and a very interesting species biologically, since it spawns in fresh water and develops through several stages before becoming a smolt, the stage at which it migrates to the sea to feed. The dramatic change of habitat requires physiological, morphological and behavioural changes to prepare the salmon for its new environment. These changes are called the parr-smolt transformation or smoltification, and pre-adapt the salmon for survival and growth in the marine environment. The development of hypo-osmotic regulatory ability plays an important part in facilitating the transition from rivers to the sea. The physiological mechanisms behind the developmental changes are largely unknown. An understanding of the transformation process will be vital to the future of the aquaculture industry. A knowledge of which genes are expressed prior to the smoltification process is an important basis for further studies.

Results

In all, 2974 unique sequences, consisting of 779 contigs and 2195 singlets, were generated for Atlantic salmon from two cDNA libraries constructed from the gills and the intestine, accession numbers [Genbank: CK877169-CK879929, CK884015-CK886537 and CN181112-CN181464]. Nearly 50% of the sequences were assigned putative functions because they showed similarity to known genes, mostly from other species, in one or more of the databases used. The Swiss-Prot database returned significant hits for 1005 sequences. These could be assigned predicted gene products, and 967 were annotated using Gene Ontology (GO) terms for molecular function, biological process and/or cellular component, employing an annotation transfer procedure.

Conclusion

This paper describes the construction of two cDNA libraries from pre-smolt Atlantic salmon (Salmo salar) and the subsequent EST sequencing, clustering and assigning of putative function to 1005 genes expressed in the gills and/or intestine.

Identification of genes differentially expressed in Atlantic salmon (Salmo salar) in response to infection by Aeromonas salmonicida using cDNA microarray technology

The response of Atlantic salmon, Salmo salar, to infection by the bacterial pathogen Aeromonas salmonicida (the causative agent of furunculosis), was investigated using a cohabitation model and a custom Atlantic salmon cDNA microarray consisting of over 4000 different amplicons. Pooled samples of each of three immune-relevant tissues (spleen, head kidney and liver) were obtained from fish exposed to infected salmon for 13 days. Reverse transcription-PCR assays were used to verify the differential expression of 12 candidate genes uncovered by microarray analysis. Among the differentially expressed genes were several previously revealed by suppression subtractive hybridization and EST surveys and that are recognized to encode humoral components of the innate immune system. Other genes identified in this study were not previously associated with infection. In addition, a number of genes with no known homologs were uncovered. Determination of their specific roles during infection may lead to a better understanding of innate immunity.

Analysis of gene expression in the bovine corpus luteum through generation and characterisation of 960 ESTs

To gain new insights into gene identity and gene expression in the bovine corpus luteum (CL) a directionally cloned CL cDNA library was constructed, screened with a total CL cDNA probe and clones representing abundant and rare mRNA transcripts isolated. The 5'-terminal DNA sequence of 960 cDNA clones, composed of 192 abundant and 768 rare mRNA transcripts was determined and clustered into 351 non-redundant expressed sequence tag (EST) groups. Bioinformatic analysis revealed that 309 (88%) of the ESTs showed significant homology to existing sequences in the protein and nucleotide public databases. Several previously unidentified bovine genes encoding proteins associated with key aspects of CL function including extracellular matrix remodelling, lipid metabolism/steroid biosynthesis and apoptosis, were identified. Forty-two (12%) of the ESTs showed homology with human or with other uncharacterised ESTs, some of these were abundantly expressed and may therefore play an important role in primary CL function. Tissue-specificity and temporal CL gene expression of selected clones previously unidentified in bovine CL tissue was also examined. The most interesting finds indicated that mRNA encoding squalene epoxidase was constitutively expressed in CL tissue throughout the oestrous cycle and 7-fold down-regulated (P < 0.05) in late luteal tissue, concomitant with the disappearance of systemic progesterone, suggesting that de novo cholesterol biosynthesis plays an important role in steroidogenesis. The mRNA encoding the growth factor, insulin-like growth factor-binding protein-related protein 1 (IGFBP-rP1), remained constant during the oestrous cycle and was 1.8-fold up-regulated (P < 0.05) in late luteal tissue implying a role in CL regression.

EST-based identification of genes expressed in the hypothalamus of adult tilapia, Oreochromis mossambicus

The hypothalamus is involved in many physiological functions in teleosts. To accelerate the molecular analysis of hypothalamic functions, a list of transcripts expressed in the hypothalamus of adult tilapia, Oreochromis mossambicus, was compiled using the expressed sequence tag (EST) strategy. Of 161 clones, 130 clones were unique genes and 31 clones were found to be redundant. Of 130 unique genes, 32.3% (42/130 ESTs) were identified as known genes and 67.7% (88/130 ESTs) as unknown genes. The functional categorization of the known genes was analyzed. Bioinformatic analysis revealed that 62 of 88 unknown genes (62/130 ESTs, 47.7%) showed a significant homology to neither nucleotide nor translated peptide sequences in the public database. These genes might be particularly expressed in the tilapia hypothalamus.