Taylor Makela Journal Week 3

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Taylor Makela Week 3

Purpose

  • The purpose of this assignment was to gain experience with reading and analyzing primary scientific sources to better develop these skills that will be used in future assignments. By reading the primary source article, a better understanding of the similarities and differences between 2019-nCoV and SARS-CoV was provided.

Definitions of Biological Terms I Did Not Know

  1. Phylogenetic Analysis: study of the evolutionary relationships between genes, populations, species, etc., usually by constructing phylogenetic trees (Cammack, Atwood, Campbell, Parish, Smith, Vella, Stirling, 2006).
  2. Intermediate Host: the animal, insect, or occasionally human in which an infectious pathogen passes a developmental stage preceding the adult stage (Porta, Last, 2018).
  3. Animal Model: study of a disease or its determinants that is conducted with laboratory animals, using conditions, processes, etc. that mimic as far as feasible those occurring in humans (Porta, Last, 2018).
  4. Infectivity: the capability of a disease agent to invade, survive, and multiply in a host (Porta, Last, 2018).
  5. Orthologue: a gene, protein, or biopolymeric sequence that is evolutionarily related to another by descent from a common ancestor (Cammack, Atwood, Campbell, Parish, Smith, Vella, Stirling, 2006).
  6. Neighbor-Joining Method: a method for inferring phylogenetic trees based on the principle of minimum evolution (Cammack, Atwood, Campbell, Parish, Smith, Vella, Stirling, 2006).#
  7. Glutamine: the trivial name for the γ-amide of glutamic acid (Cammack, Atwood, Campbell, Parish, Smith, Vella, Stirling, 2006).
  8. Phylogeny: the evolutionary history of an organism or group of related organisms (Cammack, Atwood, Campbell, Parish, Smith, Vella, Stirling, 2006).
  9. Asparagine: trivial name for the β-amide of aspartic acid (Cammack, Atwood, Campbell, Parish, Smith, Vella, Stirling, 2006).
  10. Threonine: the trivial name for α-amino-β-hydroxybutyric acid (Cammack, Atwood, Campbell, Parish, Smith, Vella, Stirling, 2006).

Article Outline

  • What is the importance or significance of this work?
    • This research is significant because due to the outbreak of and the pandemic surrounding 2019-nCoV, research on the virus is of great importance. This work serves to provide information regrading the framework of 2019-nCoV as well as the potential origin species.
  • What were the goals and results of previous studies that led them to perform this work?
    • Due to the outbreak of SARS-CoV in 2002, extensive research on the structure, receptor usage, and transmission of the virus has since been conducted. This understanding of SARS-CoV prompted the researchers to perform this work because of the notable similarities between SARS-CoV and 2019-nCoV.
  • What is the main result presented in this paper?
    • The main result presented in this paper is that the similarities in sequencing of SARS-CoV and 2019-nCoV suggest that 2019-nCoV has the same receptor as SARS-CoV -- ACE2.
  • What were the methods used in this study?
    • Structural and phylogenetic analysis in addition to sequence alignment were used in this study. Structural analysis was done through the use of the software Coot and PyMol. Phylogenetic analysis was done by using Geneious Prime to create the phylograms, and then these phylograms were rendered using Adoble Illustrator. Sequence alignment was done using Clustal Omega.
  • Briefly state the results shown in each of the figures and tables, not just the ones you are presenting.
    • Figure 1A: Shows the overall structure of SARS-CoV including ACE2, RBD, and RBM.
    • Figure 1B: Shows the changes in the residue in the receptor-binding motif's of both 2019-nCoV and SARS-CoV.
    • Figure 1C: Shows the experimentally determined structure of the interface between a SARS-CoV receptor-binding domain optimized for human ACE2 recognition and human ACE2.
    • Figure 1D: Shows the structure of the interface between the 2019-nCoV receptor-binding domain and human ACE2.
    • Figure 2: Shows the phylogenetic tree for the β-genus lineage b coronaviruses.
    • Figure 3A: Shows the sequences of both SARS-CoV and 2019-nCoV for comparison.
    • Figure 3B: Shows the similarities between the sequencing of SARS-CoV and 2019-nCoV in the receptor-binding domain, receptor-binding motif, and spike protein.
    • Figure 3C: Shows the similarities between the sequencing of MERS-CoV and HKU4 in the receptor-binding domain, receptor-binding motif, and spike protein.
    • Figure 4A: Shows the difference between the virus containing residues of ACE2 in various host species.
    • Figure 4B: Shows the experimentally determined structure of the interface between a SARS-CoV receptor-binding domain optimized for civet ACE2 recognition and civet ACE2.
    • Figure 4C: Shows the structure of the interface between the SARS-CoV receptor-binding domain and civet ACE2.
  • What light does their work shed on the origin of the SARS-CoV-2 virus?
    • Their work showed that the critical receptor-binding motif residues of SARS-CoV were adapted to both human and civet ACE2, thus promoting cross-species transmission. Furthermore, SARS-CoV was found in palm civets, thus bats and other wild animals native to Wuhan should be tested for both SARS-CoV and 2019-nCoV.
  • What are the important implications of this work?
    • Their work showed that both SARS-CoV and 2019-nCoV use ACE2 as its host receptor, however, 2019-nCoV does so less efficiently.
  • What future directions should the authors take?
    • In the future, I think that the authors should use pigs, ferrets, and cats to further research and to determine whether these species could be used as either intermediate hosts or animal models for 2019-nCoV.
  • Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any limitations or major flaws to the paper?
    • I think that the authors did a great job of supporting their conclusions with data. Furthermore, I appreciated how clearly all the figures were labeled, making them much easier to interpret.

Scientific Conclusion

  • This assignment allowed us to become familiar with primary scientific sources by first having us find words in the article that we did not understand and then define them. Doing this made the article much easier to comprehend when reading it for the second time. Furthermore, the reading of the primary source provided a lot of information regarding the infamous COVID-19 (2019-nCoV) and how it is similar/different from SARS-CoV.

Acknowledgments

  • I acknowledge my homework partner Anna Horvath who I contacted regarding syntax and questions regarding our assigned figures.
  • I acknowledge Nida Patel, who I contacted regarding the formatting of the assignment.

Except for what is noted above, this individual entry was completed by me and not copied from another source. Taylor Makela (talk) 00:00, 24 September 2020 (PDT)

References

  1. Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (2006). Oxford Dictionary of Biochemistry and Molecular Biology. Oxford, England: Oxford University Press. Retrieved 23 September 2020 from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-15563?rskey=Nb1mqA&result=1
  2. Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (2006). Oxford Dictionary of Biochemistry and Molecular Biology. Oxford, England: Oxford University Press. Retrieved 23 September 2020 from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-14381?rskey=wfrucn&result=1
  3. Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (2006). Oxford Dictionary of Biochemistry and Molecular Biology. Oxford, England: Oxford University Press. Retrieved 23 September 2020 from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-13398?rskey=ZcDbT1&result=1
  4. Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (2006). Oxford Dictionary of Biochemistry and Molecular Biology. Oxford, England: Oxford University Press. Retrieved 23 September 2020 from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-8081?rskey=T12cRh&result=1
  5. Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (2006). Oxford Dictionary of Biochemistry and Molecular Biology. Oxford, England: Oxford University Press. Retrieved 23 September 2020 from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-1603?rskey=bpZ9CL&result=1
  6. Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (2006). Oxford Dictionary of Biochemistry and Molecular Biology. Oxford, England: Oxford University Press. Retrieved 23 September 2020 from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-19518?rskey=5m6Hc2&result=1
  7. Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (2006). Oxford Dictionary of Biochemistry and Molecular Biology. Oxford, England: Oxford University Press. Retrieved 23 September 2020 from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-15566?rskey=l3dHXg&result=4
  8. Porta, M., & Last, J. (2018). Oxford Dictionary of Public Health. Oxford, England: Oxford University Press. Retrieved 23 September 2020 from https://www.oxfordreference.com/view/10.1093/acref/9780191844386.001.0001/acref-9780191844386-e-2341?rskey=uMvvmH&result=3
  9. Porta, M., & Last, J. (2018). Oxford Dictionary of Public Health. Oxford, England: Oxford University Press. Retrieved 23 September 2020 from https://www.oxfordreference.com/view/10.1093/acref/9780191844386.001.0001/acref-9780191844386-e-197?rskey=JhV8WO&result=1
  10. Porta, M., & Last, J. (2018). Oxford Dictionary of Public Health. Oxford, England: Oxford University Press. Retrieved 23 September 2020 from https://www.oxfordreference.com/view/10.1093/acref/9780191844386.001.0001/acref-9780191844386-e-2265?rskey=wtfWEr&result=1
  11. Wan, Y., Shang, J., Graham, R., Baric, R., & Li, F. (2020). Journal of Virology, 94 (7) e00127-20; DOI: 10.1128/JVI.00127-20
  12. OpenWetWare. (2020). BIOL368/F20:Week 3. Accessed 23 September 2020 from https://openwetware.org/wiki/BIOL368/F20:Week_3

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