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7

Note: In your PCR program you always set extension time. Case: Product length = 500bp PCR extension time = 50sec Assuming that polymerase adds 1000 nt/min Cycle 1: Strand that binds FP: extends ~800nt to the right (as per the polymerization rate): 300 bp ahead of RP complementary site. This product is lets say P1 Strand that binds RP: extends ~800nt ...


5

Code Golf! This is my Python script, avoiding regex and not at all prettified. def gettract(strand): #if strand is 1 then replace C with T and split on T #else replace A with G and split on G if strand==1: print 'top strand purine tracts:' aseq=seq.replace('C','T') tracts=aseq.split('T') elif strand==2: ...


4

According to this article, a single lacI gene copy gives rise to about 10 copies of lacI protein per cell, and we can conclude, therefore, that this is the amount required to keep a single lac operon repressed. The article also mentions the lacIQ mutation in the promoter of lacI that results in a ten-fold increase in the level of lacI protein. If a lac ...


4

These equations describe how the haplotype frequencies will change over time due to a combination of recombination and natural selection. Before I proceed, I need to change your four $\delta X_i$ formulas above. Lewontin and Kojima (1960) writes the equations as: $$\Delta X_i = \frac{X_i(w_i - \bar w) \pm Drw_{14}}{\bar w}$$ where the minus sign is used ...


4

That's a pretty neat video, I'll just give you some background information first. It's an illustration of the "trombone model" of DNA replication. The darker blue molecule is helicase, it unwinds the DNA and facilitates translocation (this is an ATP dependent process). The dark purple molecules are DNA polymerase, they catalyze DNA strand synthesis (an NTP ...


4

A tumor suppressor is an essential gene that regulates the cell cycle at different checkpoints. If one allele is lost due to a mutation then the function of that gene can be carried out by the other allele (There might be a less expression of that gene because of copy number reduction but it is not necessary in all cases- cases where there are feedback ...


4

NAD+ is important in this step, since it is co-factor for the glyceraldehyde-3-phosphate dehydrogenase (G3PDH), which acts as a acceptor for the hydrogen atom from the C1 (see below). If you look at the reaction, the aldehyde from the C1 is oxidized to a carboxylic acid which in a second step is turned into a phosphoester. To do so, a cysteine from the ...


4

I'm no expert at transcription but from what I can figure out here and here transcription requires a promoter region acting as a template-directed mechanism for allowing transcription, which presumably bear a certain sequence recognised by the RNA polymerase and associated complexes. However DNA polymerase requires primers to guide it to the correct location ...


4

I'm not completely clear when you say "what makes the replication terminate when the polymerase reaches the primer at the other end" since when you perform a PCR you go through three phases. The denaturation, whereby the two DNA strands become single stranded, then the annealing, which is when primers attach to their appropriate matching site (but the ...


3

Lets define the nomenclature first: An antigen is a large structure (protein, virus, bacteria and so an) which is recognized by the immune system as foreign. The word antigen derives from the abbreviation ANTIbody GENerator. Exposure of our immune system to an antigen results in an immune response and the generation of many antibodies. An epitope is a small ...


3

Since you said an internet sequence is good enough, I will propose a computer programming approach. The basic idea is to enter the sequence as a string of text and then have the program read the text, keeping track of the length of the current polypurine tract, and the longest encountered so far. When it's done, it reports the longest one. I'm not sure if ...


3

The question is slightly unclear since it fails to clarify whether the GPL-1 receptor is endogenous or is over-expressed. Also does the GLP-1 belong the same species that Min-6 originates from or it belongs to a different species? Those are important points since if the receptor is endogenous then the main problem is sensitivity of the detection method, ...


2

A possible solution is to use the DNA ZAP solution, which I know many people used in adjacent labs and were happy with for cleaning their DNA free workbench. The product sheet states When 500 ng of template DNA is dried down in a PCR tube, it is rendered unamplifiable upon treatment with DNA ZAP solutions. Additional experiments demonstrate that the DNA ...


2

Working with hot phenolic solutions is rarely been done due to the dangers of this. Phenol needs to be handled in the fume hood anyway, at higher temperatures it gets even more volatile. So if you plan to do this, do it with extra care to avoid injury. There is one paper that describes this method for bacteria, but this should work for other samples as ...


2

As @WYSIWYG mentioned, I think HLA type is probably the best way to claim specificity. Then the glycoprotein (fusion protein probably) on the virus fits only in an exact MHC class II molecule. If you want to hit some valid heavy science jargon, I recommend saying the virus was made with recombineering, using a bacterial artificial chromosome (BAC), with a ...


2

When you say RPKM do you mean crude RPKM or the estimates that you get using expectation maximization methods like cufflinks and eXpress? It is better if you get your RPKM or FPKM values from one of these programs because you can differentiate between transcript variants. I have mostly used cufflinks and eXpress. Cufflinks package is better for multiple ...


2

Did you try googling "splice site recognition sequences"? In general, the first two letters of the intron must be GT, the next three are often ARG. The last three letters of the acceptor site of the intron are virtually always YAG


1

Check this technique called Chromosome Conformation Capture (3C). Its variants exist such as 4C, Hi-C etc. Basically, the principle of this technique is based on the physical interaction between the enhancer and promoter that is bridged by a transcriptional modulator(protein). The chromatin is crosslinked DNA is sheared The protein is pulled down ...


1

Try rinsing the blot in TBS or PBS before treating. Shake it try and place on level dry surface. When I pour the a chemo reagent on there I just pour enough so the surface tension keeps the fluid on the paper not allowing it to run off. Other possibilities I see could be in your transfer. The temp could not be uniform in the buffer


1

Well usually in an ECL kit, one of the reagents is the substrate and the other one is hydrogen peroxide, which activates the substrate for breakdown using the HRP on your secondary antibody (Ab) so I genuinely doubt what you are seeing is the result of ratio difference. In order to make that conclusion you need to run your samples twice (on two separate ...


1

Why do you need to do this? This is pretty simple with the right computer tools and some knowledge of how to use regular expressions, but the fact that you are daunted by a 4.6 Mbase file suggests to me you don't have that. Using an old copy of E.coli DH10B, and Lasergene's SeqBuilder, I found a stretch of 29 Cs and T's, so in the reverse stand, that ...


1

Just search for /[AG/{30}]/ and if I didn't find it, I'd keep dropping the number until it hit - swbarnes2 Code for swbarnes2's method (will work on Linux terminal, Mac Console and cygwin terminal) Usually in a genome file a single fasta sequence will represent one chromosome. In E.coli there will be only one. You would need to pop the fasta header ...


1

Having looked into this question, I came across this paper, where they mixed biotin labelled EGFR-mutant-specific oligonucleotide and isolated the target using streptavidin beads followed by real-time TaqMan PCR allowing a 40 fold increase in detection sensitivity of the mutant allele, suggesting that biotin does not effect nucleotides in PCR based ...


1

I realize this question is about yeast, but I'm afraid that people may try to expand the answer to all systems, and beta galactosidase is not good for all systems, particularly for animal studies. I've seen too many gene therapy papers try to get away with using it. Beta galactosidase is not a good reporter gene for in vivo gene delivery studies. There is ...


1

I can make a rough analogy in terms of digital media storage. Our memories exist as a relationship between our perceptions and our sensations. Computers store input readily. However, humans store memories perceptually. This means who we are and how we remember an event permanently changes our recollection. If you look at the progression of lossy video ...



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