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基因調控網路與Sox32和Sox17之內胚層斑馬魚發育次基因調控網路

為了解決Yamaha mixer的問題，作者詹子民 這樣論述：

The process of development is a result of cascades made by gene regulated interaction,which operates mainly through the regulated expression of genes encoding transcription factorsand signaling pathways. In this thesis, I first integrated preexist bioinformatics data, combininggene expression patte

rn from ZFIN website and the interrelationship between genes fromprevious literatures. We established a database, and then constructed the genomic regulatorynetworks in zebrafish embryogenesis by using BioTapestry. We focused on the endodermformation and dorsoanterior–ventroposterior patterning. Thi

s is the first part of this thesis.In vertebrate development, the process of gastrulation leads to three germ layers: ectoderm,endoderm, and mesoderm. The endoderm originates from the most marginal blastomeres ofblastula stage embryos in zebrafish (Danio rerio). The most important signaling molecule

in theendoderm formation is Nodal. Upon binding to its receptors, Nodal leads to the activation ofgata5, bon and og9x, which then activate sox32 to promote the expression of sox17 and activatethe endoderm differentiation. In the second part of this thesis, we established the subcircuits ofsox32 and

sox17 using morpholinos against sox32 and sox17, measured certain gene expressionprofiles by real time RT-PCR and validation by in situ hybridization. We identified severalinteresting functional motifs that are important building blocks in zebrafish developmental generegulatory networks (GRNs). At

the early stage, Sox32 and sox17 provide an autoregulatory lockon the endodermal fate of cells. Early activation turns to late repression for Sox32 to sox32 itself,and for Otx2 to sox17. Late transcription factors repress early activators: e.g., Gata5 activatessox17 and then Sox17 represses gata5; G

bx1 activates sox32 and then Sox32 represses gbx1. Wefound Sox32 and Sox17 repress many early transcription factors such as foxh1, and sox17represses itself at a later stage. This interaction network extends from the two importantendoderm transcription factors and provides in-depth understanding of

the complex regulatoryarchitecture in early embryonic development.In the third part of this thesis, we further analyzed cis-regulatory element and directly testedfor the existence of functional modules. The sox17 gene is a key marker of endodermal cell inthe zebrafish. According to the predictions o

f the GRNs, based on perturbation experiment andliterature search, the sox17 gene is engaged with two other regulatory genes, sox32 and pou5f1,however the regulatory inputs of sox17 at the genomic sequence level are not known. I analyzedthe regulatory modules and transcription factor binding sites o

n the sox17 gene, and discoveredthree evolutionary conserved region, A, B, and C, are positive regulatory modules with asynergistic effect among them. I revealed the functionality for Pou5f1-transcription factorbinding site on the B module, and Sox32-transcription factor binding site on the C module

, andthose two transcription factors work synergistically to positively regulate sox17. Furthermore, anevolutionarily non-conserved R module exhibits a repressive effect on both the ventral and dorsalside of the ectoderm. My research provides new insight into the complexity of endodermformation. Thi

s is the first elucidated node in the zebrafish endoderm GRN`s which has beenproved directly by their structural and functional relationships. It may serve as a landmark fordecipher the complete endoderm gene regulatory network.