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There is no standard software, programming language, or library used for computing and graphing biological data. The R language is commonly used for statistical work, but Python (in conjunction with the SciPy stack) and C++ also gets used a lot. Before going further, I should point out you are asking two questions. One about computation and the other about ...


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The accuracy of CRISPR to its target is not necessarily a problem at this time, because scientists have developed a more accurate version of it, CRISPR hf, which has almost no off target effects. Here's a report on a study with a very accurate version of CRISPR


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Repeats aren't the problem with CRISPR. They stop you from editing repeats and repeat-like sequences, but in principle they can be worked around through careful design of guide RNA. CRISPR techniques right now do have problems with off target effects, but these problems may yet be solved. The CRISP/Cas approach to gene editing already has a lot of different ...


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Regulatable promoter means that the expression of the gene downstream of this promoter can be either induced or repressed. Met3 is an example of such regulatable promoters and it is regulated by the addition of methionine to the media. In yeast, Met3 gene encodes for ATP sulphurylase, an enzyme in the methionine biosynthetic pathway. Upon the addition of ...


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Not sure if this question is still valid, but it was marked as unanswered and frequently viewed, so here's a go :) These days most polymerases (certainly for Real Time PCR) are so-called Hot Start enzymes (ask your manufacturer, because they save you a whole lot of trouble!). They are modified with a protein that prevents them from working until activated ...


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The situation that you presented in which an entity A inhibits the production of another entity B which in turn inhibits A, is a positive feedback. In a network path or a loop the overall sign of the loop/path is the product of the signs of individual edges (interactions). In this case it is negative times negative which gives a positive sign to the loop. ...


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You should read this paper. Here is the just of what you are interested in: Because most point mutations are deleterious or neutral7, the random point mutation rate must be low8 and the accumulation of beneficial mutations and the evolution of a desired function is relatively slow in such experiments. For example, the evolution of a fucosidase from a ...


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Although the situation you describe involves amplification rather than homeostasis it is not a positive feedback loop under the standard definition of the latter: In a a positive feedback loop: An increase in A leads (directly or indirectly) to an increase in B. The increase in B leads (directly or indirectly) to an increase in A. This repeats step 1., ...


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I know of an example in development biology. Here is an example where noise in retinoic acid gradients is required for the boundaries in the developing hindbrain to sharpen. A related result is that the zebrafish hindbrain has a protein to modulate noise, but does not reduce the noise to zero. Together these results show that noise in the retinoic acid ...


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Well, you already mentioned it. Random mutagenesis (with UV or chemical mutagens) targets the entire genome and you select the organism for certain traits. In a directed evolution experiment, you are just targeting a gene or a group of genes. With the progress of synthetic biology, it might be possible to synthesize small genomes (already shown by Craig ...


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DNA shuffling would be more efficient if you already have a big repertoire of variants (which have a lot of point differences among them; see Cohen, 2001). When you do not have that, then introducing point mutations using error prone PCR would be better. A detailed mathematical framework to compare these two methods, is not available. However there are many ...


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The photolysis of water is coupled to the reduction of plastaquinone (Q) in photosystem II (PSII) as summarized in this diagram, adapted from Berg et al.: The overall reaction (which balances) is: 2 H2O + 2 Q + 4 H+ = O2 + 2 QH2 + 4 H+ But the 4 H+ on both sides of the equation are not the same. The generation of the hydrogen ions in the thylakoid lumen ...


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The renowned biologist JBS Haldane was concerned with the problem of size and wrote about it in his essay of "On being the right size". Two situations he discusses may be of interest. The first is that large animals are not just scaled-up versions of smaller ones. He calculates the weight-bearing ability of bones to show that the increase in cross-section ...


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Partial answer: As for a book on the topic of mathematical modeling of coupled neural oscillators, you can start with: Wilson, H. R. (1999) Spikes, Decisions & Actions: Dynamical Foundations of Neuroscience, Oxford University Press, Oxford UK. author's copy, amz


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There is indeed a gene, called nusG which is believed to be antiterminator of RNA transcription. NusG binds to RNA polymerase which leads to increased RNA elongation rate, decreased time in which the polymerase is into short-lived paused states, and suppressed long-lived stabilized pause states 1. NusG has been shown to be important for natural product ...


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I have searched for information on this topic as I used to work in the area of protein biosynthesis, but without success. However one argument against there being a tendency for ribosomes to fall off mRNA is the very specific mechanism for ribosome release after the stop codon has been reached (described here). There are other possible problems with very ...


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In general, point mutations are introduced in the proteins of interest during directed evolution. These can be specific mutations in the active site of an enzyme if you would like to change its specificity towards a new substrate, for example. The point mutations can be introduced with primers when you amplify your gene of interest. However, if you don't ...


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"To me it seems like both clone based sequencing and shotgun sequencing could have been used together," I believe they were. The public project cut up the genome into BACs and shotgunned every BAC, and then put the BACs together, while Venter used some sequence position information from the public effort to help him place his shotgun pieces. ...


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Yeast strains have two mating types MATa (since it secretes a pheromone named 'a factor'), MATα (secretes pheromone 'α factor'). Both MATa and MATα strains are haploid and when they fuse together they form diploid zygote. A haploid yeast has only one set of genes and utilize chemicals like histidine and tryptophan (amino acids) and adenine (part of DNA, ATP ...


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Just a thought, have you tried eluting the DNA in Molecular Grade Water instead of TE? For DNA which are supposed to be used in downstream applications like sequencing or transformation, elution with Water instead of TE buffer is frequently done. I agree longer genomic DNA can be sticky upon elution, but if by chance the DNA is not entirely dissolved ...



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