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Really interesting question: The lethal yellow mutation (also abbreviated Ay) affects the agouti signalling protein which plays a major role in pigmentation. Heterozygous expression of it leads to the dominant expression of pheomelanin (which is yellow), causing the mice to express this color (among other effects). To understand why it is homozygous ...


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What is Protein Expression Level? This was the original title of the post, which I edited myself because I regard the answer as trivial, but the question as more substantial. To deal with the trivial first: ‘Level’ is not a scientific unit, and can only be used unambiguously as a scientific term in its English sense in relation to liquids, e.g. “The level ...


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A methylated nucleotide is the same nucleotide, for the purposes of base-pairing events. The methylated base will be paired with its Watson-Crick opposite after replication, for instance (and methylation will even persist after replication).


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If I understand your question and graph correctly, your Y-axis is log(x/REF), where REF is some external standard. Your "Ref" on the x-axis you expect to be the same as REF, so that log(Ref/REF) "should be" zero, but you find it is not. However, it looks like the mean(log(Ref/REF)) is still approximately zero. This is what I would expect: ...


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Gene expression can be very well described by Hill functions, i.e.: $$c_Y(c_X) = \frac{c_X^n}{1+c_X^n}$$ when $X$ activates $Y$ and $$c_Y(c_X) = \frac{1}{1+c_X^n}$$ when $X$ represses $Y$ (omitting units and all sorts of constants for simplicity). For the common case that $n>1$, these functions look like this: As you can see, they are far from linear, ...


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Yes, Agrobacterium is indeed a very widely used vector in plants. So it wouldn't be wrong to consider bacteria as vectors. Just to add, it's worth noting that in recent times, bacterial vector options have been explored in the case of humans also, especially in the case of gene therapy for cancer treatment, though its success hasn't been demonstrated yet. ...


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Your question is very broad, but I'll try to address each of your points briefly. It would be nearly impossible to edit the genes in every cell of a human being or other complex organism simply due to the number (and accessibility) of cells. A full-grown human has in the neighborhood of 30 trillion cells - 30,000,000,000,000. Cells in locations such as the ...


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The characteristic(or trait) which is visible in an organism is called its phenotype. The ratio of the phenotypes of the progeny produced in a cross of trait(s) gives us the phenotypic ratio. A dihybrid cross refers to a cross in which plants having two contrasting characters are crossed with each other. For example, crossing round and yellow seeds with ...


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There are technologies available for inducing higher (or lower) gene expression in cultured mammalian/human cells as well as in bacteria. The state of the art is CRISPR-mediated gene activation/repression, where you fuse a transcription activation domain to a Cas gene in a CRISPR-Cas system (usually Cas9), and provide a guide RNA to target genes of interest. ...


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First, it's been estimated that the narrow-sense heritability of facial morphology is about ~60-90% (Martinez-Abadias et al 2009, Weinberg et al 2013, Liu et al 2012), so genetics is likely to be a greater influence than environment. But actually, the molecular genetic understanding of cranio-facial morphology is quite poor relative to other quantitative ...


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Heterogeneity is a noun meaning: the fact of consisting of parts or things that are very different from each other In scientific use the context determines what is differing. The context here is gene expression in individual embryonic stem cells (presumably single-cell RNASeq). Here the heterogeneity in expression would be for the genes …(Neurod1, Klf4, ...


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What you are looking at there is a microarray dataset (see the description here). Microarrays are chips that have many sequence specific probes on them and sometimes they have multiple probes for the same gene. Readout differences between the probes of the same gene could be caused by either noise in the data or biological effects like expression differences ...


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It is entirely possible that different cell-lines express the same genes at drastically different levels. The proteinatlas provides data and analyses on differences between certain tissues or cell types / cell-lines. If your cells are of the same line/tissue, then they might still differ dependent on the cell-cycle, age and external factors. There are ...


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Looking at the article, I think they could leave out the word "targeted". I think they used it because what is being enriched is not a promoter DNA, but the section of promoter DNA bound to the protein and antibody. I suppose they could use "...enriched 4.1-fold more FOLR1 Promoter DNA-CIC protein complex,..." It is a little awkward or ...


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I think you need to clarify what kind of research you are doing. Breeding and genetic modification might both produce the desired result, but in research it is likely not the main point (but instead getting to this result in a certain way and obtaining the insights from doing this). There are many studies on coloring of zebrafish and guppies, producing all ...


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Just to expand on @Wrzlprmft's great answer with a concrete example: Sticking to your simple gene circuit with $X$, $Y$, and $Z$, now consider the possibility that $Y$ also activates its own expression via a positive feedback loop: $X \to \underset{\circlearrowright}Y \to Z$ Here activation of $Y$ will be only minimally dependent on $X$. Once $Y$ is ...


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$\gamma$-irradiation produces single- and double-strand DNA breaks, depending on the dosage, and activates DNA damage repair pathways like p53. During this time, the cell cycle arrests and most if not all mRNA production ceases. For sub-lethal doses of $\gamma$ rays, I would expect to see newly-produced mRNA levels drop off fairly quickly with time following ...


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I lack the knowledge to fully answer your question but I can give some potentially useful pieces of information: In theory you can easily in-silico reverse translate a peptide sequence to an unambiguous nucleotide sequence using the GMOs optimized codon usage. I can share a Python script for that. Also you could easily search for the 'real' nucleotide ...


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Agrobacterium tumefaciens and Agrobacterium rhizogenes are soil-based plant pathogenic bacterial strains containing plasmid. This plasmid is known as Ti plasmid and is responsible for inducing tumor. Part of this plasmid called T-DNA can be integrated into the host chromosomes. So, this bacterium plasmid act as vector, but not the whole bacterial cell. (...


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Yes, Sodium phenylbutyrate can upregulate the transcription of silenced genes by inhibiting the activity of Histone deacetylases (HDACs). Histone acetylation performed by Histone acetyltransferases (HATs) helps in activation of genes, while deacetylation performed by HDACs is responsible for gene silencing. This makes HDACs a potent drug target to treat ...


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A sequence is executed with transcriptase. To double amount of signaling or some protein production try doubling the sequence occurrence.


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If you are after large amounts of a particular protein, search "recombinant protein production". It is a huge field.


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The Methylation will change the individual nucleotide(s) and persist after replication. However the order of the base pairs does not change, so the information in the DNA will still remain , and the base pairs remain with their same partners.For an analogy consider a hardcover book as the DNA . Then the author of the book signs the cover. The signature is ...


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The gene isn't specified here, but the general idea expressed is variegation. There are individual hairs (it could be larger regions) that are controlled by one of the two genes, but there is some randomization of which one. An easy system to picture this in would be the X chromosome. One X chromosome is inactivated in the female, and the other is not. If ...


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It depends on the definition of housekeeping genes. ENCODE recently released RNA-seq of 17 tissues at 8 developmental stages. A list of housekeeping genes was also provided. They are not exactly constant. They just are less variable than other genes.


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