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Embryogenesis is the stage of the life cycle after fertilization: the development of the embryo, from the zygote (fertilized egg). Organisms can differ significantly in the way the embryo develops, particularly when they belong to different phyla. For example, embryonic development in placental mammals begins with the cleavage of the zygote into eight uncommitted cells, which then form a ball (morula). The external cells become the trophectoderm or trophoblast, which will form, in combination with the maternal uterine endometrial tissue, the placenta, necessary for nourishing the fetus via maternal blood, while the internal cells become the internal cell mass which will form all the fetal organs (the bridge between these two certain parts ultimately form the umbilical cord). In contrast, the fruit fly zygote first forms a sausage-shaped syncytium, which is still one cell but with many cell nuclei.[18]

Patterning is important in determining which cells develop into which organs. This is mediated by signaling between adjacent cells by proteins on their surface and by gradients of secreted signaling molecules.[19] An example is retinoic acid, which forms a gradient in the direction from head to tail in animals. Retinoic acid enters cells and activates Hox genes in a concentration-dependent manner. Hox genes differ in the amount of retinoic acid they require for activation and will thus show differential rostral expression boundaries, collinear with their genomic order. As Hox genes encode transcription factors, this causes different activated combinations of Hox and other genes in discrete anteroposterior transverse segments of the neural tube (neuromeres) and associated patterns in surrounding tissues, such as the branchial arches, the lateral mesoderm, the neural crest, the skin. and the endodermis, in the direction from head to tail. This is important, for example, for spine segmentation in vertebrates.

Embryonic development does not always proceed correctly and errors can lead to birth defects or miscarriage. The reason is often genetic (mutation or chromosomal abnormality), but there may be environmental influence (such as teratogens) or stochastic events. Abnormal development caused by mutation is also of evolutionary interest because it provides a mechanism for changing the body plan (see evolutionary developmental biology).

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