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10

Overview Modelling has come on leaps and bounds over the last decade or so and in many cases has acted as a sometimes viable, and inexpensive substitute for experimental structures. How do you know when you get it right? Ultimately, one still needs experimental evidence to know when a model generated in silico is right. But there are ways of scoring ...


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It is called conditional mutation. You flox (put lox sites around) gene of interest and express Cre recombinase driven by tissue-of-interest-specific promoter. Illustration from here: Using chemically-activatable variant of Cre recombinase (cre-ER) you can create knock-out in some cells of tissue of interest, not every. Addition: a bit weird but still ...


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My understanding of those three words as follows: sequence is a generic name describing order of biological letters (DNA/RNA or amino acids). Both contigs and reads are DNA/RNA or aa sequences reads are just a short hand for sequenced reads. Usually sequenced reads refer to somewhat digital information obtained from the sequencing machine (for example ...


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According to my book Molecular Biology Principles of Genome Function by Craig et al, eukaryotic RNA degradation does not have an initiation, as in bacteria where pyrophoasphate hydrolase hydrolyses the 5'-triphosphate to 5'-monophosphate, and is therefore the initiatior. In eukaryotes the polyA-tail is shortened by a deadenylase enzyme complex which ...


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I'm going to say the same thing as @Serine but in a slightly different context. Let's take an example where you want to compare smoking persons against non-smokers. In this context, you'd want to take a DNA sequence of smoking persons. However, due to technology limitation you won't get a single DNA sequence from the sequencing machine. You'll get millions ...


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I think that the OP was asking about relevance of using urea with respect to the FASP method. In the FASP method, the primary denaturant is SDS . Protein are denatured with a ~4% SDS solution (buffered to pH 7.5 - 8.0). Then 8 M urea solution is used to replace the SDS. Urea serves two purposes here, first it keeps the protein denatured and in solutions as ...


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Actually, whether polyadenylation protects an mRNA or makes it susceptible to degradation depends on the organism. From Dreyfus and R├ęgnier 2002: In eukaryotes, poly(A) tails usually act as stabilizers of intact mRNAs, whereas in E. coli they serve to accelerate the destruction of fragments. This is due to different protection mechanisms in prokaryotes ...


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Often genes or other DNA fragments are inserted into an expression vector and used to transform bacteria or other cells. When a mixture of vectors is used containing various DNA fragments (e.g. a chopped-up genome), then individual (bacterial) colonies need to be isolated to make sure they carry only one insert. This can be done, e.g., by plating the ...


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You are a bit confused with your terms here. Remember, when you are talking about natural regulation of a transcriptome, you can control it at the level of the genome, transcriptome and the epigenome. The Repressor protein is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator or associated silencers. ...


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Not necessarily, they can be enzymes, but they include a lot more (the whole proteome). It takes a FASTA format file containing a set of query protein sequences from a single organism (a partial or complete proteome) and identifies those sequences that are likely to participate in any of its supported metabolic pathways Path-A predicts the ...


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Reliability comes from the fact that in Sanger sequencing (AFAIK) the synthesis of the new strand to the template and the actual reading of the sequence is separated. As you may know Sanger seq uses capillary gel elfo. thus separating the newly produced DNA fragments on a single nucleotide difference, and the reading is done by fluorescence detectors (then ...


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I'm interpreting "durability" as the DNA's resistance to physical stress, such as shearing. The Bustamante lab at UC Berkeley does a lot of very cool single-molecule biophysics looking at forces involved in protein-protein interactions and protein-DNA interactions. This Bustamante et al. review paper, Single-molecule studies of DNA mechanics includes a look ...


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Macrophages and dendritic cells generally recognize large foreign complexes. They often do this through the recognition of pathogen or damage-associated molecular patterns (PAMPs or DAMPs). Otherwise, cell-mediated pathways involve cyto/chemokines which direct macrophages and the like in the region. We also have to consider, does the compound in question ...



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