54

Using your example, the gene doesn't know anything. Mutations cause some of the offspring of the red frog to turn green, some to turn blue, some to turn fluorescent yellow, and some stay red. Birds can't see the green ones as well as the others, so more green frogs survive and make more green frogs. The red frogs, the fluorescent yellow ones, the blue ones, ...


36

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 ...


31

The first modern humans evolved about 200.000 years ago in Africa. When they lost their body hair (or at least most of it), they needed some other protection of their skin from the sun - otherwise they are prone to develop melanoma. Melanin is such a protection, and the rate of melanoma is much lower in dark skinned people. There is also a nice correlation ...


19

According to wikipedia, "comparisons between known skin pigmentation genes in chimpanzees and modern Africans show that dark skin evolved along with the loss of body hair about 1.2 million years ago and is the ancestral state of all humans." This is several million years after after the time estimated for the last common human-chimpanzee ancestor, but at ...


16

This language is called the genetic code. But before talking about this specific code, it is important to talk about how the code is read. Please note that the below answer is a simplification of the reality. Mechanism by which the code is read To make things easier (reality is a little more complicated), DNA is "formatted" into RNA which is then "...


11

You can validate the interactions by knockding down (KD) or overexpressing (OE) a gene and checking the change in expression levels of the downstream nodes. You can do this in a high throughput fashion using microarray or RNAseq. For protein you can do an LC-MS. However this method cannot help you in: Differentiating direct vs indirect interactions Finding ...


11

...would then be his offspring at risk? Why? No. Generally speaking, fathers do not pass on their mtDNA (Mitochondrial DNA). Why? Because the mitochondria present in oocytes (egg cell) is the mother's, as every oocyte directly inherits the mother's mitochondria when they are made in the reproductive organs. The mitochondria that the sperm from the father ...


9

Yes, these sequences exist and they are called "silencers" (surprising, right?). There are different mechanisms by which this silencing of genes can happen. In the "classical" way the silencer is bound by a transcription factor which either passively suppress the gene by hindering the binding of specific transcription factors or by actively preventing the ...


9

Yes there are reports of RNA directly inhibiting transcription. RNA induced transcriptional silencing (RITS) is a well known pathway in Schizosaccharomyces pombe (fission yeast). Initial heterochromatinization is dependent on the RNA (as a DNA identfication module) that guides other functional proteins to the target (Also see Djupedal et al., 2009). piRNA ...


8

I understand this in the following way: For each probe you have two sets of measurements, one for ER+ and one for ER-. What you do is a T-test (to my understanding is that the "parametric" just emphasizes that T-test is a parametric test) on these two sets, testing if their mean is significantly different (they refer to this as "separated"). You repeat this ...


8

If you transfect cells with plasmid then these plasmids need to go into the nucleus (otherwise they wouldn't be transcribed). Getting the plasmid either happens during cell division (when the nucleus is not present) or by adding a signal sequence to the plasmid which induces the import into the nucleus through nuclear pores. The SV40 sequence is an example ...


8

I can think of at least 3 reasons in addition to the one you gave: 1: As mentioned in the comments, RNA splicing takes place on most messenger RNA encoding proteins in eukaryotes. Sections of the mRNA may be spliced out, therefore multiple mRNAs with different codon sequence can encode the same gene. 2: Translation is a stateful process, since it depends ...


7

It is a Benjamini-Hochberg q-value, similar to a p-value corrected for multiple hypothesis testing using the false discovery rate.


7

The technique described here is called microarray. Your question has given me an opportunity to put forth one of my opinions about certain problems of gene expression studies. Gene expression is a measure of the activity of any gene. If the gene performs its activity in the form of a protein, then its expression should be a measure of the protein. If a gene ...


7

The first differentiation in human embryogenesis is from early blastomeres into trophoblast, which forms the outer layer of the blastocyst, and inner cell mass (ICM). It may be unsurprising then that cells on the inside of the 8-16 cell stage morula differentiate into ICM whereas those on the outside differentiate into trophoblast. However it is currently ...


7

That really depends on your system. At least for yeast the difference influences the strength of the activation ("Analysis of Transcriptional Activation at a Distance in Saccharomyces cerevisiae"). For bacteria such long distance regulations have recently been identified. Before that it was thought that this does happen only in eukaryotes. See the paper: "...


7

There are some databases in which you can search for E.coli gene expression data: GenExpDB: E. coli Gene Expression Database Many Microbe Microarrays Database (M3D): A resource of microbial gene expression data Stanford MicroArray Database (use the search tool to find relevant organisms) Colombos (COLlection Of Microarrays for Bacterial OrganismS) ...


7

Introductory textbooks will not get into the details of the lac operon. Basically, the operon is expressed constitutively at a low level that means that Beta Galactosidase and Lactose Permease are expressed at low levels by the bacterium. This is because it takes a little bit of time to build up the concentration of LacI in the cell before it can start to ...


6

I'm not personally familiar with Illumina arrays, but I can give some notes here. This link is a paper which describes the array quality controls specifically. This presentation describes the calculation of the intensities in bioconductor. The answer is yes: you will find negative numbers sometimes. They should be rare. The Intensities numbers from a ...


6

There are a large number of ways a protein variant can be produced by post translational modification. The question may seem obvious, but its really quite broad. I can start this out. I doubt I know all the ways a single transcript can produce variant proteins. A detailed description might be more like a review article than an answer here. First, ...


6

There's no rule that says a transcription factor must be either a repressor or an activator. The lambda repressor (CI) is in fact a repressor and activator of transcription, depending on where it is bound and to what promoter you are referring to. I know your question isn't directly about lambda phage, but I think this mechanism may be best explained in the ...


6

In RNA sequencing, the RNA is fragmented, DNA is synthesized complementary to the RNA fragments, which is followed by a complementary strand synthesis. Fragmentation can be done after the cDNA synthesis too. This DNA is then amplified to form a cluster that is sequenced. Most Next-Gen sequencing approaches sequence a short segment of the DNA (it has ...


6

Handedness has, like many traits, a non zero heritability. You now should read the post Why is a heritability coefficient not an index of how “genetic” something is? to understanding what heritability mean. In short, yes part of the variance in handedness seen in the human population is due to genetic variance. You will note that footedness is highly ...


5

It's a probe to detect external 'Alien' RNA standard, a synthetic mRNA commercialized by Stratagene/Agilent. The Alien RNA transcript is a ~500-nt, polyadenylated RNA molecule that is synthesized by in vitro transcription. The Alien RNA transcript is nonhomologous to all known nucleic acid sequences currently in public databases, as determined by ...


5

Unfortunately, protein and gene name mapping is one of the most annoying problems in modern computational biology. There is no surefire way of doing this. Especially from hopeless gene names as the one in the paper you cite. Here are a few services you can try though: General, text search, useful if you have a gene description (as in the case described in ...


5

A group of tightly linked genes that are involved in similar molecular pathway is called a supergene. For the pleasure to formulate a slight opposition to @shigeta's answer, I will give some examples of supergenes in eukaryotes. In Primula, heterostyly is controlled by a supergene. In Papilio memno, mimicry is controlled by a supergene. In some species of ...


5

The answer is not simple - @shigeta mentioned a few mechanisms leading to single gene-to-multi protein relationships - and the answer is certainly not short (there are thousands of these genes). But anyway "alternative splicing" seems to be the primary mechanism according to this article, so rather than listing all alternatively splicing genes, here are the ...


5

I'm tempted to say, "It's complicated." CI does indeed act as both a repressor and activator. Transcription regulation in the lambda bacteriophage is quite complex for such a small system, so some confusion is understandable. Lewis et al. gives a rough description in a relatively recent paper (1): The CI protein autoregulates its synthesis. At low ...


5

Wobble pairing is just a phenomenon and not a hard and fast rule. There are some justifications for why it should exist and that is why it is still called a hypothesis. And this statement is not true:"the base on the third position of the codon and that on the anticodon need not be complementary". The anticodon residue corresponding to the third residue of ...


5

TL;DR: Ubiquitin. Occasional occurrence of paternal inheritance of mtDNA has been suggested in mammals including humans. Clearly, spermatozoa have mitochondria; they make the energy needed for motility. Paternal mitochondrial DNA (mtDNA) does enter oocytes. It is a persisting fallacy that only maternal mtDNA is present in humans because only oocyte ...


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