Assignments

Weekly Assigments

Class Journal Assigments

Purpose

The purpose of the paper was to evaluate the change in CD4 T cells and its impact/correlation, if any, to the progression in genetic diversity and divergence in 15 subjects over a long period of time.

Vocabulary

Seroconverting
1. vb. to produce specific antibodies in response to the presence of an antigen (e.g. a vaccine or a virus). In HIV-positive patients, seroconversion occurs within about two weeks of the initial infection (Oxford reference,2020)
Serocoversion
1. mmunological jargon for having responded to immunization by producing antibody, becoming seropositive (Oxford Dictionary of Biomedicine, 2020)
PCPR
1. a technique of molecular genetics in which a particular sequence of DNA can be isolated and amplified sufficiently to enable genetic analysis. The technique may be utilized, for example, in the identification of viruses in tissue samples, e.g. human papillomavirus in cervical smears.(Oxford reference,2020)
Divergence
1. in molecular biology, the percent difference between nucleotide sequences of two related DNA segments or between amino acid sequences of the two related polypeptide chains. (Oxford A Dictionary of Genetics,2013)
Epitope
1. The structure on the surface of an antigen that is recognized by and can bind to a specific antibody. Its shape is generally complementary to that of the antibody's antigen-binding site(Oxford reference,2020)
Synonymous mutation
1. do not change the amino acid sequence of the gene product, and can therefore be silent mutations that have no effect on the function of the encoded protein (Oxford A Dictionary of Genetics,2013)
Nonsynonymous mutation
1. A nucleotide substitution in a protein‐coding gene that results in an amino acid substitution in the translation product. The ratio of nonsynonymous to synonymous substitutions may be used to detect positive Darwinian selection(Oxford reference,2020)
Viral Load
1. a measurement of the amount of a virus in an organism, typically in the bloodstream, usually stated in virus particles per milliliter. (New Oxford American Dictionary,2010)
Cohort
1. a group of individuals of similar age within a population.(Oxford A Dictionary of Genetics,2013)
PBMC
1. Peripheral blood mononuclear cells. The mononuclear cells of the blood: monocytes and lymphocytes.(Oxford reference,2020)

Journal

What is the importance or significance of this work?

By studying the evolution of the diversity within the HIV-1 could help identifies and what is making the virus evolve and how the virus adapting.

What were the limitations in previous studies that led them to perform this work?

Previous work of the evolution of the HIV-1 was performed with small cohorts of infected patients, additionally, did not study the sequences patter. Moreover, there were limited by the number of time check-ins with each patient.

How did they overcome these limitations?

They studied 15 subjects since seroconversion, collecting data frequently and over a 4 years period of time.

What is the main result presented in this paper?

they discovered different patterns of selection among the three categories they divided the subjects; nonprogressor, moderate and rapid progressors. Additionally, progression in this study was associated with a frequency-dependent selection. Differentiating, from previous studies that associated higher levels of diversity with a rapid CD4T cells.

What were the methods used in the study?

The study of population
- Chose 15 participants from the AIDS linked to Intravenous Experiences (ALIVE) study in Baltimore. Dived them into 3 groups according to their different levels of CD4T cells.
  - Rapid Progressor less than 200 CD4 T Cells within 2 years of seroconversion.
  - Moderate Progressor CD4 T Cells declines to 200-650 for 4 years
  - Nonprogressor maintained CD4 T cells levels above 650 throughout the study.

Sequencing of HIV-1 env Genes.
- PCR was used to amplify a 285-bp region of the env gene from the PBMC. Then. the amplified sequences were clone into pUC19. even at the lowest dilution, the analysis revealed a great input of copy of the viral DNA, could be concluded that all of the copies derived from the amplification of PCR come from a unique viral genome template.

Plasma Viral Load
- this was determined by reverse transcription.

Generation of Phylogenetic trees.
- to show the time each strain was isolated and the number of identical replicates sampled.

Correlation Analysis
- This analysis was done to show the correlation between diversity and divergence.

Determination of dS/dN Ratios
- Comparing and finding the difference between two strains, and classified as synonymous or nonsynonymous.

Examination of Source of Greater Initial Visit Diversity in Subject 9 and 15
- Due to high genetic variation, subject 9 and 15 were examined to determine if they have been infected by two different viruses.

Comparison of the Rate of Change of Divergence and Diversity
- For each subject this study fits a regression line of divergence over time and diversity over time.

The result shown in each of the figures and tables.

Figure 1
- shows the CD4 T cells count record in each visit, showing diversity and divergence

Figure 2
- A and B compare the mean slope per year of each of the groups. A shows the viral genetic diversity. B shows the percent of nucleotides that diverged from the original sequences.

Figure 3
- Phylogenetic tree of subject 3, showed a single mutation. Therefore infected by one virus.

Figure 4
- Phylogenetic trees of subject 5, 7, 8, 14. Reflects single mutation, and an interruption of the braches at different locations, use to interpret diversity and divergence.

Table 1
- Summary table of the data of all subjects. Include: the changes in CD4 levels, nucleotide diversity, and percent of nucleotide divergence.

How do the results of this study compare to the results of previous studies?

The results of this study support the idea that nonprogressors have a possible selection against amino acid change. Previous studies and models support the idea that "most fit" viral strain is the cause of proliferation.

How do the results of this study support published HIV evolution models?

This study is inconsistent with the model that supports the idea of progression is caused by a high proliferation of a "most fit" viral strain. Additionally, this study is consistent with the model of Nowak, which showed the correlation of CD4 T cells declines to an increase in genetic diversity.

What are the important implications of this work?

The results of this study showed new insight into the correlation of CD4 T cells declines to an increase in genetic diversity. Additionally, it showed a pattern of non-progressors to a selection against amino acid sequence change to reduce the risk to create a strain that could be recognized by the immune system. Moreover, it suggests the immune system has failed to eradicate the HIV virus due to not broadly attack all the viruses present and instead is targeting the most frequent virus.

What future directions should the authors take?

Researchers could focus on ways the immune system could attack all the strains present in an HIV virus infection.

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 would like to see more information about the statics analysis, the process that gave rise to their conclusions. Additionally, I would like to see a more detail explanation of the divergence role in their results. Overall, the paper was well written.

Conclusion

The research study showed a correlation in the decline of CD4 T cells and the progression of diversity and divergence. Additionally, it showed a pattern in non-progressors to possible resist amino acid change, and the progressor could possible select for change.

Acknowledgements

I worked with my partner Sahil Patel in class.
I followed the protocol on the Week 3
I used the following online dictionaries for vocabulary: Biology-Online Dictionary and Oxford Dictionary.
I analyzed and discussed the paper: Markham et. al - Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline.
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Lurbinah (talk) 23:06, 5 February 2020 (PST)

References

seroconvert. Oxford Reference. Retrieved 6 Feb. 2020, from https://www.oxfordreference.com/view/10.1093/oi/authority.20110803100456151

Lackie, J. seroconversion. In Nation, B. (Ed.), A Dictionary of Biomedicine. : Oxford University Press. Retrieved 6 Feb. 2020, from https://www.oxfordreference.com/view/10.1093/acref/9780191829116.001.0001/acref-9780191829116-e-8464.

polymerase chain reaction. Oxford Reference. Retrieved 6 Feb. 2020, from https://www.oxfordreference.com/view/10.1093/oi/authority.20110803100335693.

King, R., Mulligan, P., & Stansfield, W. (2013). divergence. In A Dictionary of Genetics. : Oxford University Press. Retrieved 6 Feb. 2020, from https://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444-e-1830.

epitope. Oxford Reference. Retrieved 6 Feb. 2020, from https://www.oxfordreference.com/view/10.1093/oi/authority.20110803095755256.

nonsynonymous mutation. Oxford Reference. Retrieved 6 Feb. 2020, from https://www.oxfordreference.com/view/10.1093/oi/authority.20110803100238383.

OpenWetWare. (2020). BIOL368/S20:Week 1. Retrieved January 16, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_1

King, R., Mulligan, P., & Stansfield, W. (2013). synonymous mutation. In A Dictionary of Genetics. : Oxford University Press. Retrieved 6 Feb. 2020, from https://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444-e-6654.

(2010). viral load. In Stevenson, A., & Lindberg, C. (Eds.), New Oxford American Dictionary. : Oxford University Press. Retrieved 6 Feb. 2020, from https://www.oxfordreference.com/view/10.1093/acref/9780195392883.001.0001/m_en_us1304355.

King, R., Mulligan, P., & Stansfield, W. (2013). cohort. In A Dictionary of Genetics. : Oxford University Press. Retrieved 6 Feb. 2020, from https://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444-e-1304

PBMC. Oxford Reference. Retrieved 6 Feb. 2020, from https://www.oxfordreference.com/view/10.1093/oi/authority.20110803100317873.

Markham, R. B., Wang, W. C., Weisstein, A. E., Wang, Z., Munoz, A., Templeton, A., ... & Yu, X. F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proceedings of the National Academy of Sciences, 95(21), 12568-12573. doi: 10.1073/pnas.95.21.12568

Lurbinah Week 3

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