Comparative Gene Expression Profiling of In Vivo-Derived Expanded and Hatched Porcine Blastocyst-Stage Embryos.
Bibliographic record
Abstract
During the pre-implantation period of embryonic development, the mammalian embryo exhibits dramatic changes and many key events take place. The developmental stage at which porcine embryos are most commonly manipulated is the blastocyst, and the quality of the embryos used is critical to the success of reproductive technologies such as embryo transfer. Despite the importance of this critical period, our ability to determine early embryonic quality based on morphological criteria is limited. As an alternative, characterization of the gene expression profile of the early porcine embryo could identify gene markers of embryonic quality. The objective of this study was to perform comparative gene expression profiling analysis of in vivo-derived expanded and hatched porcine blastocysts using two-colored microarray (Pig-Oligo Array, USDA Pig Genome Consortium). Microarray data were interpreted using WebArray and DAVID functional annotation tools. The microarray results identified 1783 genes that were commonly expressed in both expanded and hatched porcine blastocysts. A further 148 genes were differentially expressed (p<0.05) and in comparison to expanded blastocysts, 35 genes were down-regulated and 113 genes were up-regulated after hatching. Many of the differentially expressed genes are related to important molecular mechanisms, such as macromolecule metabolism and energy related pathways. A total of 14 genes of interest (LDHA, LDHB, SLC16A7 (previously known as MCT2), BSG, SLC2A1, SLC2A3, SLC2A5, POU5F1 (previously known as OCT4), ACTB, GAPDH, GRB2, SETX, SPG7, and YWHAZ) were selected from the gene list generated by the microarray analysis, and their expressions were verified using SYBR Green-based real-time PCR. For the genes tested, the real-time PCR results were consistent with the microarray results. The differences detected in the gene expression profiles between in vivo-derived expanded and hatched porcine blastocysts increases our understanding of the molecular mechanisms involved in the hatching process and identifies potential candidate gene markers of 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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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".