Stage-Specific Gene Expression Profile Differences During Early Porcine Embryonic Development.
Bibliographic record
Abstract
During the pre-implantation period of embryonic development, the porcine embryo exhibits dramatic morphological changes associated with key developmental events such as compaction, differentiation, blastocyst formation and hatching. However, the molecular mechanisms underlying these events are mostly unknown. To better elucidate these mechanisms at the gene expression level, a comparative transcriptomic analysis of in vivo-derived porcine embryos representing 4 different developmental stages (4-cell, morula (MOR), expanded blastocyst (EXB) and hatched blastocyst (HB)) was performed with a custom designed porcine embryo-specific microarray (http://embryogene.ca/). In this study, total RNA samples were extracted from pools of 5 embryos of each embryonic stage and 3 biological replicates from each stage were utilized. They were compared to a reference sample consisting of pooled total RNA from 8 different porcine embryonic stages (GV, MII, 2-cell, 4-cell, 8-cell, MOR, EXB and HB). Microarray data were analyzed with the Flexarray1.6.1 software. The PANTHER (http://www.pantherdb.org/) and Ingenuity Pathway analysis software were used for the biological process and pathway analysis. The results of this comparative analysis across the four embryonic stages revealed 1517, 1286, 1286 and 1813 differentially expressed genes across stages from 4-cell, MOR, EXB and HB stages respectively. Further analysis was conducted to identify genes that were differentially expressed uniquely in one of the four embryonic stages evaluated and this revealed that 768, 228, 133 and 412 genes were specifically differentially expressed in the 4-cell, MOR, EXB, and HB embryos respectively. Among these stage-specific differentially expressed genes, 46, 17, 17 and 50 were found to be related to specific developmental processes. These genes were primarily involved with biological processes such as embryonic development, pattern specification processes (such as anterior/posterior and dorsal/ventral axis specification) and system development. It was also determined that several genes involved in homeostatic processes were uniquely differentially expressed in the 4-cell (ATP1A1, PTPN23), MOR (NUCB2) and HB embryos (ATP8B1, PTPRK, AGR2 and PSAP). Further analysis identified 10 genes related to homeostatic processes that showed differential expression across the four evaluated stages, 5 of them (AGR2, ATP1A1, ATP2B1, ATP8B1 and NUCB2) were related to cellular calcium ion homeostasis, 3 (PTPN23, PTPRK and SOCS5) were related to cellular glucose homeostasis and 2 (AGR2 and PSAP) were related to the regulation of liquid surface tension. In comparison with the 4-cell stage, 5 genes (AGR2, ATP1A1, ATP2B1, ATP8B1 and SOCS5) were down-regulated in MOR stage embryos and continued to be down-regulated at the EXB and HB stages. Two other genes (ATP12A, NUCB2) were up-regulated in MOR and then down-regulated in the EXB. Fluid accumulation in the embryo, caused by homeostatic mechanism, is critical for a morula to develop to a blastocyst and forth hatching process of that blastocyst. The regulation of homeostasis-related genes in morula and expanded blastocyst stage embryos may play an important role during blastocyst formation and hatching. This study has identified potential gene markers of early embryonic quality in pigs and increases our understanding of the molecular mechanisms involved in early embryonic development.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| 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) | 0.000 | 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 teacher head, 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".