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2

If they are available, talk to the people who analysed your data. Using their knowledge is intelligent. I will assume two critical steps are completed. First that your results have been searched correctly. I will also assume that the peptide and protein identifications have been filtered to provide a false discovery rate of 1:100 at each level. You can ...


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It's not the size that counts, it's how you pack it (sorry couldn't help myself). Wild-type bidensoviruses do a lot of interesting things to pack genome like splitting its genome into two virions(1), inverted terminal repeats (ITRs) that form panhandles that can stack instead of hairpins (2), and overlapping positive and negative ssDNA strand ends (2 and 3) ...


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During cell-division centrioles move towards opposite 'poles' and finally get attached to cell-membrane. Different factors influence & drives this process, most still not discovered. So this mechanism is largely unknown. From the scientific literatures published on this matter till recently we can say that this process should include, 1. A structure ...


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As others have mentioned poly-A seems to be favoured because of higher concentrations of ATP with respect to other NTPs, due to its ubiquitous role. There is no real proof for this like most "why" questions. However, the ubiquitous presence of ATP is itself an evidence for a random selection of ATP and a subsequent expansion of its role. There is no ...


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Most probably because the concentration of ATP in cells is much higher than that of the other nucleoside triphosphates and there was no functional requirement for a particular base in the tail. Its main function seems to be to work with an appropriate nuclease system to regulate the mRNA lifetime (see, e.g. Wikipedia article).


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The term ‘pseudogene’ was originally coined to described genomic sequences related to protein-coding genes, but which contained: “defects… which would completely prevent the production of functional protein.” (Quoted from review by Jeffreys and Harris, 1984.) There are two distinct types of pseudogene: Duplicative Pseudogenes As their name implies, ...


2

A subset of pseudogenes can have a function - even if not translated: For one possibility see the official record for PTENP1, which acts as a tumor suppressor by providing a decoy for PTEN targeting miRNAs A subset of pseudogenes can be translated. There is a selection for preserving the length of the reading frame, which suggests (but does not formally show)...


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This is a good question as, although in higher eukaroyotes codon usage does not necessarily correlate with translational efficiency, it does to a large extent in Escherichia coli (see e.g. Boël et al., 2016). The answer is not simple, but the following may contribute. To optimize the strength of base pairing Although in particular circumstances ‘wobble’ ...


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Codon usage is not necessarily associated with translation efficiency, as your example would illustrate. Though control of translational efficiency and accuracy is one of the well known reasons for the existence of codon usage there have been other hypotheses that link it with asymmetric mutagenesis rates and overall GC content (See "Why does codon usage ...


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If you are lucky and live in a university town with student shops, which are run by student organizations, I would recommend you to visit one of those shops. Often they sell used microscopes, which are no longer needed. If you do not mind that these microscopes have been used before, you will get a much better quality for less money. If you go to such a ...


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So there are a couple of things you should ask yourself: a) how 'small' do you want to see b) what are you trying to study - (microspores can differ depending on that. Examples: Microbiology - (bacteriology), Plant biology...) 200 dollars for a 'proper prof. microscope'I do not think is enough. However I do not think that is what you are looking for (For ...


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Run it out on a gel after digestion and extract the vector only. Treat with a phosphatase after digestion. This will prevent religation since you need at least one of your fragments to be phosphorylated for the ligation to work. (A must regardless) sequence several colonies at the end. I recommend doing all three. Edit: option 4: digest with a third ...


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Definitely not. There is a ton of variation from gene to gene, otherwise, as you say, regulation wouldn't work. That said, the word "promoter" sometimes gets used in different ways. Especially in eukaryotic systems, people will sometimes say "promoter" to mean the entire region upstream of the gene where transcription factors can bind (for yeast, typically ...


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This is not my area, but as nobody has answered yet I'll start the ball rolling to try to encourage a more authoratative response. Long, long ago, before the internet, when I was a post-doc and the emphasis was on bacterial rather than eukaryotic gene expression, I remember hearing something about specific sigma factors differentially controlling initiation ...


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It requires two genetic constructs to create a conditional KO organism. One parent with a transgene that expresses a DNA recombinase (such as Cre) after the promoter of a gene that is ONLY expressed in your tissue of interest. The other parent contains a modified gene of interest to be removed in the presence of said DNA recombinase but is fully functional ...


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There are several ways you can try to get legal access to publications that are not open access. First, and most simple, subscribe to the medium or pay for the single publication. This is usually very expensive, so you might want to look for other ways. Second, you can try to get access by your/an institution by logging in over your institutes network. ...


9

1x is the final working concentration of the solution (it could be anything depending on the type of the solution). Stock solutions are made at a higher concentration; if it is 10 times more concentrated than the working solution then it is 10x. Why 50x TAE but 10x TBE? The salts in TBE precipitate at higher concentrations. In other words, the salts ...


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The easiest answer would be to ask the authors of the patent. Several other possibilities (see comments) were excluded, such as: restriction sites which interfere with cloning signal peptide proteolytic cleavage Although it's just a theory, removing part of the N-terminus might improve protein stability and half-life time because the first 30-40 amino ...


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It's going to be hard for you to generate an RPKM or RPM value without % aligning to the genome, or the transcriptome. Your read counts will have no context.


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Formaldehyde forms adducts with RNA and can also make it more susceptible to degradation. It can also cause crosslinks to form between RNA and proteins (or possibly other RNAs). For all these reasons extraction of high quality RNA from formaldehyde fixed samples is very difficult and the yields are low (Howat and Wilson, 2014). Have a look at this article ...


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The plasmid won't religate efficiently if the ends are not compatible. However, it's possible that very rarely your plasmids may re-ligate, perhaps because of a tiny level of contamination with exonuclease that trims back the ends to be blunt. Or there may be spontaneous blunt breaks or other strange events. This may happen in a tiny fraction of the ...


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As @WYSIWYG said in comments, there is no effect of change in nitrogenous base on the third phosphate. Why? Simple, they are too far to directly influence each other's stability. See the diagram (of ATP) below from wikipedia: and of GTP from here: What one can clearly interpret from these diagrams is that there would be no effect on the energy released ...


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Cognate means of common origin. In molecular biology, cognate is used to refer to known interacting pairs of functional entities. For example, cognate receptor of a ligand means the primary (default) receptor with which this ligand interacts. Similarly, cognate sites (which also includes enhancer) of a transcription factor (TF) refers to the well known and ...


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You could be measuring outside the dynamic range of the assay (you can only add so much / so little BSA to a certain amount of reagent). You could be outside the linear range of your spectrophotometer, usually under 1 is fine, although some old/crappy ones might not even be reliable over 0.5. If you're fast you're measuring your different concentrations ...


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If you look at the DNA sequence in the patent, you will see that it does not start with ATG and does not end with a stop codon. The disclosed sequence has some additional bases in it, therefore the discrepancy in protein and DNA length. Those additional bases almost always occur in cDNA, e.g. because of polyadenylation, Kozak sequences, etc.


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If you're expressing the gene in E. coli, then you're almost certain to be using a plasmid or other ectopic gene vector. There are a wide variety of plasmids available, with many different promoters. With a commercial plasmid, you're not adding in the promoter sequence, but the gene sequence. You pick the promoter you want and then clone your gene sequence ...


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It depends on how much time elapsed between adding the concentrated antibodies to the diluting solution and adding the diluted antibodies to the slide. If it was just a couple of seconds, then I can abolutely see there being a difference. Even if it was longer - say 30-90 seconds, even - there potentially could be antibody gradients in the solution without ...



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