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The several panels show what happens in each cycle. Each cycle consists of a denaturation step at a temperature higher than the melting temperature of the duplex DNA (e.g. 95 oC ), then an annealing step at a temperature below the melting temperature for the primer-template (e.g. 55 oC), followed by extension of the primer by DNA polymerase using dNTPs provided in the reaction. This is done at the temperature optimum for the DNA polymerase (e.g. 70 oC for a thermostable polymerase). Thermocylers are commercially available for carrying out many cycles quickly and reliably
- Denature
- Annealing primer
- Synthesize new DNA with polymerase
-
- High speed
- Extreme sensitivity
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- Jul 2021
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www.biorxiv.org www.biorxiv.org
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- Jun 2021
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www.cell.com www.cell.com
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Zhao, H., Wu, D., Nguyen, A., Li, Y., Adão, R. C., Valkov, E., Patterson, G. H., Piszczek, G., & Schuck, P. (2021). Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. IScience, 24(6), 102523. https://doi.org/10.1016/j.isci.2021.102523
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- May 2021
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- Apr 2021
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- Feb 2021
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- Jan 2021
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www.theatlantic.com www.theatlantic.com
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Proteins are made up of building blocks called amino acids. N501Y means that the 501st amino acid was originally an N, which stands for the amino acid asparagine, but has been changed to a Y, which stands for tyrosine.
The takeaway: Amino acids, represented by single letters such as N or Y make up proteins which are part of the coronavirus (as well as other biology such as animals, plants, microorganisms, etc.). Mutations are written with the original amino acid letter followed by the number of the amino acid and the new amino acid letter.
The claim: Proteins are made up of building blocks called amino acids. N501Y means that the 501st amino acid was originally an N, which stands for the amino acid asparagine, but has been changed to a Y, which stands for tyrosine.
The evidence:
Coronavirus is made up of greater than 20 proteins (1). The spike protein helps coronavirus attach and enter human cells which leads to infection and disease (1). The spike protein on SARS-CoV-2, the virus that causes COVID-19, is the target of many antibodies produced by the human body to fight the SARS-CoV-2 infection (2). Changes in the spike protein sequence may necessitate a change in the human immune system to produce antibodies which stop SARS-CoV-2 from infecting human cells. Changes in the amino acid sequence are written as was stated in the claim: original amino acid, number of the amino acid in the sequence, new amino acid.
Sources:
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- Nov 2020
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www.healthline.com www.healthline.com
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Schleiss says a better analogy for COVID-19 is the mumps. For more than 45 years, we’ve had a very effective vaccine for measles, mumps, and rubella (which are also RNA viruses).
The takeaway: Even though mutations happen in all virus, vaccines still work. Current evidence about SARS-CoV-2 indicates that an effective COVID-19 vaccine can be obtained, and that it should be able to provide immunity against the virus.
The claim: A better analogy for COVID-19 is the mumps. For more than 45 years, we’ve had a very effective vaccine for measles, mumps, and rubella (which are also RNA viruses).
The evidence: We are all imperfect and we all make mistakes. For a virus, a mistake means the introduction of a mutation in its sequence, and RNA viruses (like the flu, mumps, measles virus, and SARS-CoV-2) have the highest error rates in nature. Mutations are indispensable for viral survival and evolution; this property is believed to benefit the viral population, allowing it to adapt and respond to different complex environments encountered during spread between hosts, within organs and tissues, and in response to the pressure of the host immune response [1]. How fast a virus is changing can be estimated by measuring its mutation rate, and then they can be classified as changing fast – high mutation rate – like HIV or Influenza, or as stable, like measles or mumps virus. SARS-CoV-2 has a mutation rate three times slower than the flu virus [2], but it's still changing faster than the mumps virus (the mutation rate of influenza is more than 10 times higher than mumps) [3]. Of course, how fast a virus can change has implications in the efficacy of treatments and vaccines, but it's not the only determinant. Even though mutations happen in all viruses, vaccines still work. A great example is the measles virus, as the antigenic composition of the vaccine (the molecules that “wake up” the immune system) used to prevent it has remained efficient since it was developed, in the 1960s, and confers protection against the 24 circulating genotypes [4]. The same is true for the mumps virus, with a vaccine that has been efficient for many decades [5]. Sequencing data suggest that coronaviruses change more slowly than most other RNA viruses, probably because of a viral ‘proofreading’ activity that corrects all the copying mistakes [6]. Taken together, all this evidence indicates that an effective COVID-19 vaccine can be obtained, and that it should be able to provide lasting immunity against the virus.
Sources:<br> 1
2 SARS-CoV-2 mutation rate: 1.26 x 10-3 substitutions/site/year
3 Influenza (flu-virus) mutation rate: 3.68 x 10-3 substitutions/site/year. Mumps mutation rate: 2.98 × 10−4 substitutions/site/year
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- Oct 2020
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core-genomics.blogspot.com core-genomics.blogspot.com
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Kits rock! But understanding what is going on at each stage of the protocol provided with the kit really helps with troubleshooting and modification.
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