Matthew K. Oki Individual Journal 8

Preparation for Week 9 Journal Club

Biological Terms

1. glycoprotein
   • "One of a group of compounds consisting of a protein combined with a carbohydrate (such as galactose or mannose). Examples of glycoproteins are certain enzymes, hormones, and antigens."
   • http://www.oxfordreference.com/view/10.1093/oi/authority.20110803095856565
2. Simulated Annealing Algorithm
   • "A technique used in data mining to select an optimal set of data from a large space of solutions. The term comes from the fact that the techniques uses a process similar to that found when metals are cooled slowly."
   • http://www.oxfordreference.com/view/10.1093/oi/authority.20110803100507504
3. Chemokine co-receptors
   • "Any one of a group of small proteins that guide leucocytes to sites of infection and are vital for immune function. They fall into two main classes, CC chemokines and CXC chemokines; receptors (denoted R) are named after the class that bind to them, and subtypes of each class are indicated by numbers (e.g. CCR5)."
   • http://www.oxfordreference.com/view/10.1093/oi/authority.20110803095605484
4. Immunochemical
   • "any specific immunological reagent that consists of or incorporates an antigen or an antibody, especially one of commerce."
   • http://www.oxfordreference.com/view/10.1093/oi/authority.20110803095958733
5. X-ray crystallography
   • "The study of the geometric forms of crystals by X‐ray diffraction."
   • http://www.oxfordreference.com/view/10.1093/oi/authority.20110803125218110
6. Transient
   • "Lasting only for a short period of time."
   • http://www.oxfordreference.com/view/10.1093/acref/9780199641666.001.0001/acref-9780199641666-e-8368?rskey=tPcmHs&result=2
7. Dihedrals
   • "An angle formed by the intersection of two planes (e.g. two faces of a polyhedron). The dihedral angle is the angle formed by taking a point on the line of intersection and drawing two lines from this point, one in each plane, perpendicular to the line of intersection."
   • http://www.oxfordreference.com/view/10.1093/oi/authority.20110803095718396
8. Immunogenic
   • "Capable of stimulating an immune response."
   • http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444-e-3321?rskey=tZbOkd&result=1
9. Collating
   • "An ordering of the internal character set, used in alphabetic and alphanumeric sorting."
   • http://www.oxfordreference.com/search?q=collating%20sequence
10. glycosylated
    • "The process of adding sugar units such as in the addition of glycan chains to proteins. An occurrence where a carbohydrate is added to a protein molecule, which can occur in the golgi apparatus."
    • http://www.biology-online.org/dictionary/Glycosylation

Outline

Questions

1. What is the main result (message) presented in this paper?
2. What is the importance or significance of this work?
3. What were the limitations in previous studies that led them to perform this work?
4. What were the methods used in the study?
5. Briefly state the result shown in each of the figures and tables.
6. How do the results of this study compare to the results of previous studies.

Acknowledgements

• I would like to thank my partners, Mia Huddleston, Zachary T. Goldstein, and Welliam P. Fuchs, for the assistance on this weeks project both in the understanding of our paper in class and completion of the powerpoint outside of class
• I would also like to thank Kam D. Dahlquist, Ph.D. for providing the instructions and information for this assignment both in class and on this document: BIOL368/F16:Week 8.
• Even though I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
• Matthew K. Oki 17:44, 19 October 2016 (EDT):

References

1. BIOL368/F16:Week 8
2. Andrianov, A. M., & Anishchenko, I. V. (2009). Computational model of the HIV-1 subtype A V3 loop: Study on the conformational mobility for structure-based anti-AIDS drug design. Journal of Biomolecular Structure and Dynamics, 27(2), 179-193. DOI: 10.1080/07391102.2009.10507308

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