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13

I'd like to know what is the reference for amoebic learning. I cannot comment directly on this, but there is some evidence for "adaptive anticipation" in both prokaryotes and single-celled Eukaryotes which do not have a nervous system. In the case of E. coli, it has been shown that the bacteria can anticipate the environment it is about to enter. E. coli ...


9

I don't believe anything should change in the majority of DNA->RNA transcription. DNA methylation typically occurs on the non-watson crick side of Cytosine so it shouldn't affect the base-pairing. However, there are a few hypothetical situations that would result in alterations of the transcribed RNA. The sponatneous deamination of the 4' amine would ...


9

The techniques used to do this are ChIP-seq and ChIP-chip. Basically, you let the pathogen bind to the (highly replicated) DNA cut up the DNA into little random pieces by sonication enrich (“pull down”) the pathogen-bound DNA fragments by using a known antibody which binds to the pathogen sequence the thus enriched DNA map the sequenced fragments back to ...


9

Methylation is increasingly seen as a consequence of gene activity rather than a regulatory mechanism. There are cases where methylation is controlled because of gene regulatory control, especially at the famous H19/Igf2 locus[1]. Here is a generally good recent review[2], note they mention that DNA methylation does not cause transcriptional silencing, and ...


9

The NF-κB family of transcription factors is very modular, with different combinations having different effects. The active (nuclear, DNA-bound) TF is a dimer, composed variously of RelA/p65, RelB, c-rel, NFKB1/p50, and/or NFKB2/p52 subunits. For example, the "canonical" p65/p50 dimer is activated in response to stimulants like TNF-α (tumor necrosis factor ...


8

This question is closely related, and the fascinating link posted by @JohnSmith is a good read. In short, with a four-base system, and a codon size of 1, you get four possible amino acids. Silly system. A codon size of 2 gives 16. Not too shabby, but not a lot of room for growth, and not enough for those 20 amino acids. Codons of size 3 gives 64 - ...


7

In addition to the excellent response up top (by Poshpaws), one can also imagine how these systems work by looking at recent synthetic examples of single-celled organism memory. It is possible to design various bistable switches using protein pathways, RNAi, or other means that will latch a particular state. In that way, an organism could effectively ...


7

There are two mechanisms of transcriptional termination in prokaryotes. The one shown here is "rho-dependent" because it involves rho, a DNA-RNA helicase that loads on and unwinds the RNA from the DNA, terminating the elongation by the polymerase. Check out [1] which shows a model for how rho multimers move through the RNA. The other mechanism involves ...


6

Still if you change your question as (If histidine is abundant, HisP's job is to stop the histidine pathway as a "repressor." If HisP binds less tightly to promotors, the pathway should not produce as much histidine.) Then it should be under another assumption that what is the effect of HisP binding promoter of enzyme's gene. Is it suppressing the ...


6

As the number of human TFs have been discussed by the previous answers, I'll limit myself to Anopheles gambiae. In the same issue of Science in which Holt et al. published a genome sequence for Anopheles gambiae (1), Zdobnov et al. published a comparison of the A. gambiae and Drosophila melanogaster genomes.(2) While the two species diverged about 250 ...


5

A large number of prokaryotes do indeed have nucleosome-like structures. The most well studied is H-NS in E. coli, Salmonella and some other deltaproteobacteria. H-NS like molecules have also been found in mycoplasma (Lsr2). One of its roles is to bind AT-rich DNA and silence transcription. The binding is usually to suppress the expression of foreign DNA ...


5

As you pointed out, the repressor gene lacI is transcribed as a one mRNA, and three structural genes: lacZ, lacY and lacA are transcribed into a single polycistronic mRNA. The two mRNAs are translated independently of one another. The polycisronic mRNA is not broken into pieces. Rather, it is translated by ribosomes (at least three, explanation below), ...


5

Yes. For an example, see this list of targets of NF-kB (a transcription factor). Many other transcription factors are included there. As for a TF that does nothing except activate another, single TF? I don't know that those exist - TFs tend to modulate multiple genes.


5

From the wikipedia article on TFs: In molecular biology and genetics, a transcription factor (sometimes called a sequence-specific DNA-binding factor) is a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to messenger RNA. The nature of the gene affected is irrelevant, a ...


5

This is the Curated database of mouse and human transcription factors. And this is the paper in which they describe how they curated the database. In summary, there are 3230 putative mouse TF, 1200 of which are described in scientific papers.


4

A quick search on T7 cysteines gave some clues: Bacteriophage T7-induced DNA polymerase is composed of a 1: 1 complex of phage-induced gene 5 protein and Escherichia coli thioredoxin. Preparation of active subunits in the absence of sulfhydryl reagents indicates the reduced form of thioredoxin is sufficient for formation of the active ...


4

Someone is almost sure to prove me wrong about 30 seconds after I post this, but I don't think that the mechanistic aspects of learning are really all that well known in these study systems. The idea that it is occurring at all is recent enough (I've enjoyed Tanya Latty's Ph.D. work on this, for instance: http://www.tanyalatty.com/Home/research) that I ...


4

There seems to be some solid evidence that transcription promotes mutation because the untranscribed strand is able to form secondary structures which expose bases to chemical mutagenesis. Here is a recent paper about transcription-associated mutagenesis: Kim H et al.(2010) Transcription-associated mutagenesis increases protein sequence diversity more ...


4

ChIP-exo does seem to be the "ChIP-seq killer." I've seen Dr. Pugh present it a few times, and the audience is pretty much always impressed. One thing I'd do if I were of the "experimental bent" would be to add random degenerate barcodes in the library prep to control for potential PCR artifacts. I imagine that since the "peaks" in ChIP-exo seem to be quite ...


4

Both the DNA and the RNA polymerase complexes moves along the DNA molecule like it was a track. While the new mRNA is big, it would never be as big as the whole genome, so the reference point is the DNA molecule. Plus, the functioning of the movement of this enzymes is quite similar to other proteins that move "climbing" long polymers, such as actin polymers ...


4

Hutchinson–Gilford progeria syndrome is almost always due to to a de novo mutation (i.e. not an inherited mutation) in the lamin A gene (LMNA). The mutation responsible is a C-to-T substitution at position 1824. Remarkably this doesn't change the encoded amino acid but rather creates a new splice donor site in the RNA transcript. When this splice site is ...


4

The answer to this question depends upon the definition of the word 'promoter'. In the simplest possible model of prokaryotic transcription the promoter is the site where RNA polymerase binds to the DNA before initiating RNA synthesis. In this process the σ factor recognises the core promoter elements directing the polymerase to bind to the DNA to ...


4

The amount of transfected plasmid does not correlate at all with the protein expression level. After transfction, usually each cell is going to get and keep only one copy of the plasmid. Once the plasmid is in the cell, it will be replicated and the cell will contain X copies of it, depending on the plasmid copy number. In general, plasmids with low copy ...


4

Pretty interesting question. There are a few numbers out, I remember that round about 10% of the human genes are coding for transcription factors (unfortunately I don'T remember the source for that). This paper from 2002 estimates between 2000 and 3000 factors: Signal transduction and the control of gene expression. This paper from 2009 states a number ...


4

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: ...


3

There was a paper published in Cell last year that has shown that the binding motif of a Hox transcription factor will change depending on whether there's a co-factor bound to the Hox. link to paper


3

If gene B makes a protein product, you can try designing a morpholino against the 5'-UTR of gene B. This can prevent translation initiation at the ribosome as the morpholino occludes mRNA entry into the ribosome. You can detect this by western blotting. If gene B makes some sort of regulator RNA, you will need to target expression of gene B at the DNA ...


3

How well is gene A annotated? Do you have the gene A sequence (after post-transcriptional modifications)? If you do, you can order it from a company like DNA2.0 and they will synthesize it for you for like $0.35/base. Then you can transform the cells with this plasmid and do a knockout of gene B by inserting some sequence at the ~200bases overlap. Also, I ...


3

Inferring transcriptional / regulatory networks from empirical data is an active area of research, and to my knowledge there aren't many mature tools for this type of analysis. I see mostly mathematicians, statisticians, and engineers working on this problem, probably because of the intense quantitative theory involved. Even if mature tools do exist, I doubt ...


3

So what you need is basically your data expressed as counts instead of proportions. Even if you do not have the matrix of counts as raw data, these proportions only needs to be multiplied by the total number of binding sites used in the study (e.g. the number of sequences that have been analysed) to get the counts (since proportion = count/total number of ...



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