The study of bovine mammary gland functional genomics requires appropriate cDNA library collections to access gene expression patterns from different developmental and physiological stages. The present study was undertaken with the objective to identify candidate genes involved in the process of increased milk synthesis following 0, 48 and 96 h of recombinant bovine somatotropin (rbST) treatment to Surti buffalo (Bubalus bubalis) through differential display reverse transcriptase PCR (DDRT-PCR). Of a total 50 sequenced DD bands, 64% of ESTs were differentially expressed (appeared only in post-treatment samples, i.e. 48 h and 96 h) and 36% were up-regulated after rbST treatment. Of the ESTs 32%were found to be located on Bos taurus chromosome 24 (equivalent to buffalo chromosome 22), whereas 16% of ESTs could not be mapped, indicating that they are specific to buffalo. Quantitative real time PCR assay of 15 ESTs revealed transcript level surge in 13 ESTs, and decline in one EST, while one showed up-regulation in expression level at 48 h while down-regulation at 96 h. This study indicates more than 30 novel transcripts, with unknown function, involved in increased milk synthesis and also the involvement of many more genes in the physiology of milk production than once thought.

The lower termite, Coptotermes gestroi (Isoptera: Rhinotermitidae), is originally from Southeast Asia and has become a pest in Brazil. The main goal of this study was to survey C. gestroi transcriptome composition. To accomplish this, we sequenced and analyzed 3003 expressed sequence tags (ESTs) isolated from libraries of worker heads. After assembly, 695 uniESTs were obtained from which 349 have similarity with known sequences. Comparison with insect genomes demonstrated similarity, primarily with genes from Apis mellifera (28%), Tribolium castaneum (28%) and Aedes aegypti (10%). Notably, we identified two endogenous cellulases in the sequences, which may be of interest for biotechnological applications. The results presented in this work represent the first genomic study of the Asian subterranean termite, Coptotermes gestroi.

To date, there are only a few sequenced-tagged site (STS) markers associated with genes controlling fruit quality in watermelon. A normalized cDNA library for watermelon fruit (Citrullus lanatus var. lanatus) was constructed. Sequence analysis of the cDNA clones resulted in the development of 4700 non-redundant ESTs (EST unigenes) expressed in watermelon fruit (http://www.ncbi.nlm.nih.gov, http://www.icugi.org). One hundred of these EST unigenes [including 40 EST unigenes that contain simple sequence repeat (SSR) motives (EST-SSRs) and 60 customary EST unigenes (not containing SSR motives)] were used for designing primer pairs for PCR experiments. The EST primer pairs were tested in PCR experiments with genomic DNA of 25 watermelon heirloom cultivars and 13 United States Plant Introductions (US PIs) of Citrullus sp., including four C. lanatus var. lanatus, five C. lanatus var. citroides PIs and four Citrullus colocynthis PIs. The 40 EST-SSR and 60 EST primer pairs produced 108 and 142 EST-PCR markers, respectively, among the Citrullus PIs and watermelon cultivars. A large number of the EST-PCR markers were polymorphic between the Citrullus PIs and the watermelon cultivars, but significantly less polymorphic among the cultivars. Of the 108 EST-PCR markers associated with EST-SSRs, 103 exist in the Citrullus PIs and 64 in the cultivars. Of these 64 markers, 45 (70.3%) were polymorphic among the cultivars. Of the 142 EST-PCR markers associated with customary ESTs, 134 exist in the Citrullus PIs and 108 in the cultivars. Of these 108 markers, 86 (79.6%) were polymorphic among cultivars. The results in this study indicate that polymorphism exists in coding regions of genes expressed in fruits of watermelon cultivars. In total, 131 polymorphic EST-PCR markers (45 associated with EST-SSRs and 86 associated with customary ESTs) related to watermelon fruit genes were generated using the above data. These markers should be useful for DNA fingerprinting of cultivars and breeding lines, for assessing genetic relationships and for genetic mapping of watermelon.

The adenophorean nematodes are evolutionarily distant from other species in the phylum Nematoda. Interspecific comparisons of predicted proteins have supported such an ancient divergence. Accordingly, Trichinella spiralis represents a basal nematode representative for genome sequencing focused on gaining a deeper insight into the evolutionary biology of nematodes. In addition, molecular characteristics that are conserved across the phylum could be of great value for control strategies with broad application. In this review, we describe and summarize progress that has been made on the sequencing and analysis of the T. spiralis genome. The genome sequence was used in preliminary analyses for the investigation of specific questions relating to the biology of T. spiralis and, more generally, to parasitic nematodes. For instance, we evaluated an unusually large DNase II-like protein family, predicted proteins of prospective interest in the parasite-host muscle cell interaction, anthelmintic targets and prospective intestinal genes, the encoded proteins (potentially) linked to immunological control against other nematodes. The results are discussed in relation to characteristics that are broadly conserved among evolutionary distant nematodes. The results lead to expectations that this genome sequence will contribute to advances in research on T. spiralis and other parasitic nematodes.

The avian egg is a nutritious food and also a major source of biologically active compounds that are beneficial for human health. These biologically active molecules are widely used by pharmaceutical, cosmetic and food industries. Egg proteins were previously studied using classical biochemical techniques such as chromatographic and electrophoretic separation and Edman sequence analysis. The development of molecular biology in the late 80's and the recent publication of the chicken genome sequence are major scientific advances leading to identification and characterization of a number of minor egg components that were not previously identified. Using recent data on the characterization of egg white and eggshell matrix proteins, we illustrate in this review recent developments in the biochemistry of the egg (proteomics) and in the molecular biology of the egg (cDNA and ESTs libraries, bioinformatic analysis of the chicken genome, transcriptomics). These methods have allowed the identification of hundreds of minor egg protein components with potential applications for industry. Functional studies to identify the biological activities of these novel egg protein components and to exploit their potential will form the next frontier of egg science.

In order to reveal the molecular basis of heterosis, Large White (LW), an introduced European pig breed, and Meishan (MS), a Chinese indigenous pig breed, were selected to hybridize directly and reciprocally in the present experiment. mRNA differential display (DD) technique was performed to identify genes that were differentially expressed in the backfat tissues of hybrids (LW×MS, MS×LW) and purebred (LW×LW, MS×MS) pigs. The ten anchor primers in combination with ten arbitrary primers (100 sets in total) were used and nearly 1500 reproducible bands were observed in polyacrylamide gels. The 40 differentially displayed bands were selected for cloning and sequencing. Thirty-six out of 40 expressed sequence tags (ESTs) proved to be novel and the sequences were submitted to GenBank (accession No. CV507051-CV507087); the other four showed similarity to known genes published in GenBank. Three among 36 novel ESTs were chosen for further identification with semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR). The result showed that two ESTs were differentially expressed, and the third showed no obvious difference between hybrids and purebreds. In order to reduce the percentage of false-positive DD, RNA pools of four types of pigs were constructed, by mixing samples from six pigs of the same genotype, and subjected to DD. Stringent annealing temperature was applied and only bands that could be repeated in duplicate PCR were used for further study. The results showed that the expression pattern of these 36 ESTs differed among the four genotypes of pigs, suggesting that the genes corresponding to these differentially expressed ESTs might be related to the heterosis occurring in fat tissue.

The construction of two cDNA libraries from young shoots of tea plant [Camellia sinensis cv. Longjing 43 and Anji Baicha], the sequencing of Longjing 43 cDNA clones and the analysis of expressed sequence tags (ESTs) are reported. Totally, 4320 clones from the cDNA library of Longjing 43 were sequenced, and 2963 useful sequences were obtained, corresponding to 68.6% of clones. A total of 416 clones shorter than 150 bp and 863 repeated clones were excluded, the first 1684 valid tea plant ESTs were generated. Most of the ESTs were between 300 and 700 bp, with an average of 478 bp. Six hundred and seven ESTs with known function or putative function were identified by BlastN searches against the National Center of Biotechnology Institute (NCBI) non-redundant nucleotide databases, corresponding to more than 130 functional genes in the tea plant. The rest, 1077 ESTs, were novel gene partial or full sequences. The results indicated that EST sequencing was a rapid and effective approach to identification of novel functional genes for tea plant.

Progress in the selection of production traits in the poultry industry has been dramatic over the past 75 years. Genetic progress has its biological limits and these may be reached in the next 20 years. The poultry industry will need to adapt with more emphasis on the needs of the consumer (e.g. product quality, health and animal welfare), as well as the needs of the breeders/producers (e.g. lower feed costs and higher fertility). These new traits are difficult and costly to measure by conventional genetic selection methods - the application of genomics is a possible solution. Poultry genomics has benefited from the rapid technological advances in the genetics of model organisms and human. A number of resources and approaches are now well established, including genetic markers and maps (both genetic and physical), QTL mapping, comparative mapping, EST and BAC resources. In addition, the next phase of gene discovery - Functional Genomics is underway. How the poultry industry can benefit and get access to these new technologies is discussed.

The phylum Apixomplexa includes obligate intracellular parasites that are of enormous medical and veterinary significance, as they are responsible for a wide variety of diseases including malaria, toxoplasmosis, coccidiosis, cryptosporidiosis, theileriosis and babesiosis. The EST sequencing projects in Toxoplasma gondii and the Plasmodium falciparum genome sequencing project have greatly accelerated gene discovery, revealing for example novel coding sequences restricted to the Apicomplexa. However, easy acquisition of sequence is almost useless if the function of any given gene cannot be tested. The establishment of transfection systems in Toxoplasma gondii, Neospora and in several Plasmodium species has provided us with the reverse genetics methods appropriate to the functional analysis of genes. Over the past few years, the discovery of novel genes coupled to the ability to introduce or modify genes has already contributed to a better understanding of cell biology and pathogenesis of these obligate intracellular parasites. Some insights into the complex processes of parasite invasion, differentiation, regulation of gene expression and protein trafficking are emerging although identification of the exact functional roles for many molecules is still awaiting more investigation. This review summarizes progress in this area. It also emphasises the tight link and synergy between Toxoplasma and malaria research. The use of reverse genetics does not guarantee the answer to gene function, so we can learn from both failed and successful experiments about how better and more efficiently to use ‘genomics’ to accelerate discoveries relevant to the understanding of parasitism by Apicomplexa.