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1

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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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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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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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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At this point, it must be verified experimentally. In this foldit research paper, they use software and user input to design essentially an enhanced version of a naturally occurring protein, but they then physically make their new protein and determine its structure experimentally, using x-ray crystallography. Overall, they use a lot of trial and error ...


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No not necessarily. Cancer can also be caused by bacteria and viruses in your body The regulation of cancerous tumor development is converged upon by multiple pathways and factors. Besides environmental factors, gastrointestinal (GI) tract cancer can be caused by chronic inflammation, which is generally induced by bacteria, viruses, and parasites. The ...


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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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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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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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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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The length of Okazaki fragments is not necessarily a tight distribution. The lengths are determined by the spacing between adjacent sites where DNA primase has synthesized a short RNA primer on the lagging strand at an active DNA replication fork. In E. coli, as I recall, this occurs on an average of once per 1000 nt. DNA polymerase holoenzyme then uses ...


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Macrophages take up pathogens to present them to other specific immune cells. The things they take up via phagocytosis have specific markers on them called PAMPs (Pathogen Associated Molecular Patterns). Hence they won't phagocytose locally injected substances (until and unless it has a PAMP like region).


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I have used both Gibson assembly (what you mean by assembly?) and LCR as replacements for blunt or sticky ended cloning. LCR has, for me, worked better in that a higher proportion of constructs that come out have been assembled correctly and I have noticed no mutations after LCR while I have seen them somewhat often with Gibson.


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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. ...


1

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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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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The optimization done by service providers like IDT should be fine because they weigh in multiple factors like avoiding mRNA secondary structures and specified restriction endonucleases. Even I was considering manual editing but then some research on the internet revealed that codon usage is not the only factor involved :)


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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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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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Being no expert on pain, I will share some thoughts on the issue. According to the following site(http://www.helpforpain.com/arch2000dec.htm), there are two types of pain: nociceptive and neuropathic pain. Neuropathic pain involves the central and peripheral nervous system, a possibility I would discount due to no apparent link to suffocation. Thus, it is ...



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