Identification and Characterization of Novel Genes from Blastocyst-Stage Porcine Embryos Using 454 Sequencing.
Notice bibliographique
Résumé
During the pre-implantation period of embryonic development, the mammalian embryo exhibits dramatic morphological changes and many key developmental events take place. Due to physiological similarities between pig and human, there is strong interest in producing large quantities of pre-implantation embryos through assisted reproductive technologies for biomedical and biological research purposes. The developmental stage at which porcine embryos are most commonly manipulated is the blastocyst, and the quality of the embryos utilized is critical to the success of reproductive technologies such as embryo transfer. Despite the importance of this critical developmental period, our ability to determine early embryonic quality based on morphological criteria is limited. As an alternative, characterization of the early porcine embryo transcriptome could identify gene markers of embryonic quality. 454 sequencing is a powerful ultra-high-throughput method of gene expression profiling which is able to characterize the expression of both known and novel genes. In this study, 454 sequencing was performed on a cDNA library constructed from 15 in vivo-derived porcine blastocysts using a whole transcriptome amplification method (Ribo-SPIA, NuGen) in order to identify and characterize novel genes from blastocyst-stage embryos. A total of 19,438 reads were generated from a 1/8 plate run using GS FLX Titanium reagent kit (454 Technology, Roche), resulting in 18,338 quality ESTs (expression sequence tags) after filtering using 454 Replicate Filter (http://microbiomes.msu.edu/replicates/), of which approximately 1.1% (202 ESTs) were identified as unknown ESTs with significant matches in the porcine EST database (http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=9823). A consensus sequence of those porcine EST matches was identified for each unknown EST query using the Seqman module of DNAstar software (http://www.dnastar.com). The consensus sequences were further compared with the NCBI nucleotide database using the NCBI BLAST tool (http://blast.ncbi.nlm.nih.gov/Blast.cgi), and 41 of the sequences had significant matches with porcine refseq RNA records. An additional 156 sequences were identified as novel genes and were further analyzed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) functional annotation tool (http://david.abcc.ncifcrf.gov/tools.jsp). The results indicate that many of these newly identified genes are involved with pathways important to embryonic development, such as pathways related to differentiation, apoptosis, cell survival and proliferation. The findings from this study increase our understanding of the molecular mechanisms involved in early porcine embryonic development, and may help to identify candidate gene markers of early porcine embryo quality. This research was supported by the Natural Sciences and Engineering Research Council (NSERC) and is a part of the activities of the EmbryoGENE NSERC Strategic Research Network. (poster)
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Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule tête enseignante, pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».