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HIV-1 CRF02_AG intra-patient evolution in relation to disease progression rate

Rodriguez Fernandez, Veronica (2011) MOBM15 20111
Degree Projects in Molecular Biology
Abstract
Abstract

To analyze the HIV-1 CRF02_AG viral diversity and evolution during the course of disease, the V1-V3 region of the env gene of sequential blood plasma samples from eight patients from Guinea-Bissau was studied. The patients were divided into two different groups, fast and slow progressors (FP and SP), according to the time between seroconversion and development of AIDS. The RNA of the virus was extracted from plasma samples from three or more time points, and was amplified and cloned. Based on the results from RNA extraction and PCR amplification, the success rate was inversely correlated with the year of sampling, with a PCR success rate that increased linearly from 0% in samples collected 1993-1995 to 100% in samples... (More)
Abstract

To analyze the HIV-1 CRF02_AG viral diversity and evolution during the course of disease, the V1-V3 region of the env gene of sequential blood plasma samples from eight patients from Guinea-Bissau was studied. The patients were divided into two different groups, fast and slow progressors (FP and SP), according to the time between seroconversion and development of AIDS. The RNA of the virus was extracted from plasma samples from three or more time points, and was amplified and cloned. Based on the results from RNA extraction and PCR amplification, the success rate was inversely correlated with the year of sampling, with a PCR success rate that increased linearly from 0% in samples collected 1993-1995 to 100% in samples collected after 2005. From the diversity analysis, we found that six of eight patients included in this study showed a decline in diversity 3-6 years after seroconversion, while it continued to increase in the other two. Among those that showed a decline in diversity, four patients developed AIDS between 1-2 years after the diversity peak. Our results suggest that diversity and divergence for HIV-1 CRF02_AG follow the same tendency as reported for HIV-1 subtype B in previous studies.

Popular science summary:

SEWAGE IN SEAWATER TRACKED BY MANGANESE

Manganese is a trace element that easily changes oxidation state and is essential for humans and other organisms in order to develop and maintain health. Through sewage, manganese enters the oceanic environment from variety of anthropogenic sources, and like every chemical, it can cause toxicity when it exceeds certain concentrations. The main objective of present study was to find out whether manganese could be used as a tracer for sewage from ocean outfalls in Kollafjörður, southwest of Iceland. Kollafjörður is the fjord receiving the entire sewage from Reykjavík and nearby communities. Manganese was analyzed in seawater surface samples during spring in Kollafjörður, around the effluents from two sewage treatment plants, which are located on the northern shore of Reykjavík. Analyzed manganese was the Mn2+ ion, both dissolvable and dissolved. The analytical method used for the determination of manganese concentration is based on the catalytic effect of Mn2+ on the oxidation of the leuco base of malachite green by IO4- and in order to increase the method sensitivity, experiments with an activator ligand, nitrilotriacetic acid, were carried out. Observations lead to the conclusion that introducing the nitrilotriacetic acid increased the sensitivity significantly but was not practical for the current observations considering the concentration range.

At this time of year, total dissolvable manganese proved to be a better as a tracer for urban effluents than dissolved inorganic silicate, which in an earlier winter study had been found to be a suitable tracer. However, the behaviour of measured manganese indicates that it is non-conservative at the sampling site in Kollafjörður. The conclusion can be made that the manganese in excess of background levels measured at the water surface is mainly from the sewage effluent. The observed salinity range was rather small, illustrating the effective dilution processes of sewage at the site. In addition, it can also be concluded that sewage is mixing with coastal seawater at salinity at and above 34.6. Regarding the marine ecosystem around the sewage effluent one can conclude that the manganese concentration measured will not cause harm to living resources. This assumption can be made from the range of natural ambient manganese concentration in seawater, toxicity values and the fact that manganese is unlikely to biomagnify in the food chain. (Less)
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author
Rodriguez Fernandez, Veronica
supervisor
organization
course
MOBM15 20111
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
2206407
date added to LUP
2013-02-22 10:55:57
date last changed
2013-03-26 14:16:35
@misc{2206407,
  abstract     = {Abstract 

To analyze the HIV-1 CRF02_AG viral diversity and evolution during the course of disease, the V1-V3 region of the env gene of sequential blood plasma samples from eight patients from Guinea-Bissau was studied. The patients were divided into two different groups, fast and slow progressors (FP and SP), according to the time between seroconversion and development of AIDS. The RNA of the virus was extracted from plasma samples from three or more time points, and was amplified and cloned. Based on the results from RNA extraction and PCR amplification, the success rate was inversely correlated with the year of sampling, with a PCR success rate that increased linearly from 0% in samples collected 1993-1995 to 100% in samples collected after 2005. From the diversity analysis, we found that six of eight patients included in this study showed a decline in diversity 3-6 years after seroconversion, while it continued to increase in the other two. Among those that showed a decline in diversity, four patients developed AIDS between 1-2 years after the diversity peak. Our results suggest that diversity and divergence for HIV-1 CRF02_AG follow the same tendency as reported for HIV-1 subtype B in previous studies.

Popular science summary:

SEWAGE IN SEAWATER TRACKED BY MANGANESE

Manganese is a trace element that easily changes oxidation state and is essential for humans and other organisms in order to develop and maintain health. Through sewage, manganese enters the oceanic environment from variety of anthropogenic sources, and like every chemical, it can cause toxicity when it exceeds certain concentrations. The main objective of present study was to find out whether manganese could be used as a tracer for sewage from ocean outfalls in Kollafjörður, southwest of Iceland. Kollafjörður is the fjord receiving the entire sewage from Reykjavík and nearby communities. Manganese was analyzed in seawater surface samples during spring in Kollafjörður, around the effluents from two sewage treatment plants, which are located on the northern shore of Reykjavík. Analyzed manganese was the Mn2+ ion, both dissolvable and dissolved. The analytical method used for the determination of manganese concentration is based on the catalytic effect of Mn2+ on the oxidation of the leuco base of malachite green by IO4- and in order to increase the method sensitivity, experiments with an activator ligand, nitrilotriacetic acid, were carried out. Observations lead to the conclusion that introducing the nitrilotriacetic acid increased the sensitivity significantly but was not practical for the current observations considering the concentration range. 

At this time of year, total dissolvable manganese proved to be a better as a tracer for urban effluents than dissolved inorganic silicate, which in an earlier winter study had been found to be a suitable tracer. However, the behaviour of measured manganese indicates that it is non-conservative at the sampling site in Kollafjörður. The conclusion can be made that the manganese in excess of background levels measured at the water surface is mainly from the sewage effluent. The observed salinity range was rather small, illustrating the effective dilution processes of sewage at the site. In addition, it can also be concluded that sewage is mixing with coastal seawater at salinity at and above 34.6. Regarding the marine ecosystem around the sewage effluent one can conclude that the manganese concentration measured will not cause harm to living resources. This assumption can be made from the range of natural ambient manganese concentration in seawater, toxicity values and the fact that manganese is unlikely to biomagnify in the food chain.},
  author       = {Rodriguez Fernandez, Veronica},
  language     = {eng},
  note         = {Student Paper},
  title        = {HIV-1 CRF02_AG intra-patient evolution in relation to disease progression rate},
  year         = {2011},
}