Reflections

Roxanne Burger

Before this project I had never heard of grid computing, so I was really surprised to hear that you could contribute to research by just downloading some software onto your computer. The moment I saw that HIV/AIDS was an option, I knew that's the topic I wanted to do. HIV is a continuing medical and moral/ethical issue in the united states. Through this project I have learned more about the personal struggles that those affected by this disease face every day of their life. Conducting the interview, was probably the most impactful to me, especially hearing Rashaan and Kaylon's testimonies about the continuous fight against prejudice and the push for a cure not just treatment. I am very thankful to have had the opportunity to meet those fantastic men and moving forward I will try to spread their cause.

Sara Ficenec

In the beginning of this semester I was less than excited to hear I had another service learning project. I currently volunteer in a long term service position and did not want a new service learning project to interfere with that. Hearing that for this project we simply had to run a program on our computers I was excited, but a little hesitant at first. Researching grid-computing it was amazing to hear that we could be helping important scientific research simply by running a program in the background, we could even track the progress being made. This seemed like a very worthwhile project and my group decided to research HIV. At this time this seemed like as good a topic as any to research but after the interview the research became much more meaningful. I was personally unable to attend the interview but just from reading what of the individuals being interviewed had to say, it was clear this was a very important topic. This is a disease that personally impacts many individuals as well as their families, and unfortunately it is also an illness that carries many negative stereotypes and stigmas. After learning about grid-computing it is great knowing that there is something that I can being doing to help this cause. I do believe this project was a worthwhile use of my time and am thankful for the opportunity to work on this project.

Christiana Hayden

When I began this project, I was nervous because it had to deal with technology which is a little out of my comfort zone. But as time progressed, I started to feel more comfortable about it. I was the one who had the program downloaded on my computer, so it was neat to watch the performance it was doing. I also liked how we were helping the greater scientific community. It was cool to a part of something so big and contribute to various projects.  I also got to learn about HIV. I did not really know much about it until this project. Not only did I learn about it, but it became a more personable topic with the interview. I am very happy that I got to experience this type of service learning, especially since it relates to field I feel so passionate about. 

Kelsey Lee

This service learning project introduced me to a new kind of service that I had no idea existed. It has been an interesting experience to contribute in a new way to the scientific community through grid computing. In terms of learning about HIV, it was nice to get a well rounded view on the virus, particularly from the interview with the KC Care Clinic. As a science major of course it was interesting to learn about the virology, but it was also very interesting to learn about the misconceptions and stigmas the public has about the disease and how they influence what kind of efforts are being made to find a cure. This experience definitely raised my awareness for HIV/AIDS. Just because it is not necessarily a death sentence does not mean it doesn't deserve the awareness and funding that other diseases such as cancer receive from the public. It affects people's everyday lives in more ways than just having to take a cocktail of pills. There are even legal issues that infiltrate the private life of diagnosed individuals, which can be emotionally debilitating. Overall this service learning project was a valuable experience that I am grateful to have participated in! 

Shereen Salfity 

Upon participating in this service learning project, I found that I learned a lot about HIV and grid computing. Coming into this class, I had no idea that one could do service by participating in these grid computing programs. This was a very cool service opportunity that was both useful for the scientific community, as well as incredibly easy and convenient to do on the computer. In terms of learning about HIV, I feel that I have truly gained a comprehensive perspective on the virus, and I have learned a lot coming out of this class. Perhaps the learning experience that most resonated with me was the opportunity we had to interview HIV experts at KC Care clinic. During our interview experience, we got to learn about the problems that Kansas City faces, the policies, misconceptions, and even the legal issues associated with HIV. In short, we all came out of that interview with a better appreciation of HIV beyond just the strict biology. This service project was a fantastic opportunity to learn and contribute to the understanding of HIV, this has been a very valuable experience :)

Total Credit: 29,233

Projects/Applications Contributed to: "Quantum Chemistry", "Molecular Dynamics for CPU and AMD GPUs, and Nathaniel's PhD, along with others. 

Reviewing "The evolution of HIV-1 and the origin of AIDS" by Paul Sharp and Beatrice H. Hayn

If you are interested in reading the paper that correlates to these questions and following along please go to this link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935100/

1. What is phylogeography? How were the authors able to use phylogenetics and phylogeography to localize the origin of HIV strains?

Phylogeography is the study of the genetic and geographic structure of populations and species. Phylogeography generally uses genetic information to examine genealogical history and patterning within species and populations.

The authors were able to localize the origin of the HIV strain through a series of tests in various primates to determine which species had been infected and which carried viruses that closely resembled HIV (Types O, M and N). To begin, the authors first tested a wide range of primates and began identifying SIV’s (simian immunodeficiency virus), a 1920 test had shown M type HIV in Kinshassa, Democratic Republic of Congo and this is where they began looking for similar SIVs. The first break through was in the discovery of SIVcpz in 1989, this chimpanzee SIV was very similar to HIV-1 which is the most prevalent type of HIV and thus of the most interest to the authors. After the discovery of the SIVcpz there was a huge push to test as many chimpanzees as possible to learn more about the origin of the species, this push only resulted in a couple more cases being found. In 2002, a new method of testing was developed and allowed fecal samples of wild chimpanzees to be analyzed; through these tests it was found that SIVcpz was very prevalent among the central and eastern chimpanzees. The similarity and prevalence of SIVcpz in these subspecies of chimpanzees shows that they are the source for HIV-1.

Once all of this data was gathered they were able to add the SIV and HIV strains into a phylogenetic tree and see how the strains are related to each other. Using this phylogenetic tree, they identified that the HIV type M and N were transferred directly from the chimpanzees. The HIV type O, however required several cross species transfers to come to humans. The SIVcpz was first transferred to gorillas before coming to humans. These crosses were supported by looking at the mutations of SIV and HIV in specific geographic locations. These locations line up with the intra-species crosses suggested in the phylogenetic tree.

2. How do they know that most HIV transmissions are intraspecific? Explain.

The multiple strains of SIVs were characterized from a single species; they generally formed a monophyletic clade, which indicated that the majority of transmissions are intraspecific.

3. What do the env, vpu, and nef genes code for in HIV? Would you then expect high levels of mutation rates to be tolerated in these genes?

The env gene codes for the env viral protein. This protein assists in the formation of the viral envelope. It is also common for retroviruses, and helps retroviruses target and attach to cells. In addition, it helps the virus gain access to the cell membrane of a target cell. Vpu is a protein that is involved in the degradation of CD4. It also assists in the virion release from the membrane of infected cells. Nef is a protein encoded by primate lentivirsuses. It assists in manipulating the host cell’s machinery, which ultimately helps with infection. High levels of mutation rates would not be tolerated in these genes as they code for proteins that provide essential functions for the HIV virus to infect cells.

4. Apply Darwin’s postulates to the adaptation of the recombinant virus to the human host population.

1. The individuals within a population differ from one another.

HIVs and SIVs interact with many host proteins. Many of those host proteins have diverged since the common ancestor of old world monkeys and apes. There is variance within the HIV population.

2. The differences are, at least in part, passed from parent to offspring.

When inside of a host, HIV replicates itself and passes it’s genetic information on to its offspring.

3. Some individuals are more successful at surviving and reproducing than others.

Tetherin is a mammalian protein with antiviral activity by preventing the release of the virus into the cytoplasm. Only SIV or HIV-1 that are resistant to tetherin survive and reproduce.

4. Individuals with more favorable adaptations are more likely to survive and reproduce.

SIVcpz uses the Nef protein to counteract tetherin, while HIV-1 uses Vpu. This is because human tetherin has diverged from the chimpanzee protein. As a result, SIVcpz Nef protein is not active against human tetherin. This would have placed strong selection pressure on HIV-1, which resulted in the reaquisition of anti-tetherin activity by Vpu. HIV-1 viruses that were active against human tetherin would be more successful at surviving and reproducing. 

5. What evidence does this study provide that we share an immediate common ancestor with Pan troglodytes?

The study states that humans and Pan troglodytes share very similar gene sequences. The differences between the two are at less than two percent of all nucleotides. The evidence that they come from a common ancestor can be seen with how easily the SIVcpz transferred to humans. 

6. On the next page you will find a figure from Science entitled “Application and Accuracy of Molecular Phylogenies” (Hillis et al. 1994; Vol. 264: 671-677). In the study referenced, the authors considered the allegations of 7 patients (A-G) that they had contracted HIV from their dentist. Were their allegations correct? Describe how the authors might have generated this tree.

Yes, the dentist did transmit HIV to his patients. HIV tends to have an A to G nucleotide base change, but there are other nucleotide base changes that can occur. The researchers probably looked at those other changes and documented which ones these patients had.  Though, they also took into account all other transversions and transitions because they need to have a thorough phylogenic tree.Taking into account all the possible changes, they might have looked at the number of times those specific nucleotide base changes occurred. The researchers would then take into account which of these changes was most similar to the that of the dentist. 

KC Care Interview and Reflection

Interview: We had the opportunity to interview two HIV experts at the Kansas City Care Clinic, D. Rashaan Gilmore, the Principle Community Liaison, and Kaylon Sanders, a PEER at the clinic, who is HIV positive.

Questions:

Why did you choose this field? 

Sanders: Kaylon first became involved by participating in a project, entitled Visual AIDS, which was a photographic exhibition geared toward establishing positive images for HIV positive men. From there, Kaylon was inspired by his interest in helping others, and his passion for this issue, to continue to be involved and make a difference. 
The following link provides more information on the Visual AIDS project: http://fox4kc.com/2014/06/06/visual-aids-aims-to-reduce-stigma-for-black-men-who-are-hiv-positive/
Gilmore: Rashaan became involved at the KC Care Clinic after being offered a position to work on a CDC funded project. 

In what ways have we progressed as a community in terms of how we deal with HIV and AIDS? In what ways do we need to improve as a community?​
In 2009, for the first time in Kansas City, the transmission rates of HIV from African American men aged 16-29, was higher than any other transmission rates for any group of Caucasian men. There had been a lot of attention placed on AIDS as a "white gay man disease". As a result from this statistic, people became more optimistic with these numbers that are showing that HIV transmission is decreasing. However, this is misleading because for young African American men, the numbers are skyrocketing. We need to allocate more attention to all of those affected by HIV. In terms of the improvement, Kansas City has clinics such as KC Care, churches, and agencies that 

Do you believe there is enough time and funding going into HIV research?
There is not enough time being invested in a cure. However, there are a lot of drugs being produced that are designed for treatment. Some companies are advertising "treatment is the cure" for HIV, however, this is a fallacy. The reason why there is less of a focus on a cure may be in part due to the weaker campaign, or push, for finding a cure. For example, for Breast Cancer, the campaign for finding a cure has been focused on all types of women, and is insistent on fighting cancer and finding a cure. With slogans like "Find a cure", the awareness and support raised for this issue has been tremendous. However, with HIV/AIDS, people do not seem to be optimistic about finding a cure, as it has been regarded as a "death sentence disease". In addition, while this has improved since the 1980s, HIV/AIDS was considered to be a gay man's disease. Thus, there is a stigma for the people who are traditionally regarded as suffering from this disease. These two reasons are important factors for why the time and funding for a cure has not been sufficient. 

Can you tell us more about the LTC HIV support program?

LTC is linkage to care, it is a short term 90 day program that is centered around providing information to those who have just been diagnosed with HIV. The goal is help the individual understand what this means, and arrange for a confirmatory test (a full blood draw). When this happens, a peer will become involved and provide support for the individual. In addition, LTC includes providing information about medicine, future changes that will be necessary, etc. 

What do you do as a PEER at KC Care? How does your diagnosis help you to mentor others? 

I work with those who have been diagnosed, or those returning for care, and help them along their journey ( providing support, guidance, etc.) While anyone can offer sympathy or empathy, only a person who has experienced the same diagnosis can truly understand what it feels like to find out that you are HIV positive. Therefore, I can help mentor people from my experience, as I understand what this can be like, and I have experienced first hand how life changing this is. 

What has been the most rewarding part of your career? 

As a PEER at KC Care, the most rewarding part of my job is finding out that one of my clients has become undetectable. This term refers having less than 20 copies of viral loads, or having a CD4 level above 200. Most of the clients that I have worked with are now undetectable. Once someone has become undetectable, the chance that he or she will pass on the virus with an HIV negative individual drops from 98% to 2%. 

Are you currently on medication for HIV? If so what is the medication routine like (number of times taken a day, has it changed over time, etc.)? 
My medication regimen has changed three times, this has been due to allergic reactions that I have have with Truvada. Truvada is a PrEP (Pre-Exposure Prophylaxis), which is a method for people who are HIV negative, but at high risk for getting it, it prevents HIV infection. Truvada is also used for HIV positive individuals to try to help treat them to have less than 20 copies of viral loads, and thus be undetectable. I am currently on Stribild, which has 3 medications with one booster. All regimens have a standard of at least three medications. 

More on Medication:
As a result of the evolution of the virus, the way in which we select the medicine that people use is influenced. When a person is diagnosed, he or she will take a genotype test. This test will test your own virus with every type of medication that is available. If the test comes up as green, it means that your strain of HIV is sensitive. If the result comes up as yellow, it means there is partial resistance, and if it is red, it means that it is highly resistant. By taking that blood test, information may be gathered about someone's personal HIV, and from there, a cocktail can be hand picked. The process of carefully selecting medication that works for your HIV, as well as consistently taking that medication is important to prevent the likelihood that the virus will become resistant. 

On Missouri Law: 
Missouri and 19 other states have laws about HIV transmission and exposure. If you are positive and are about to engage in sex, whether or not you are virally suppressed, you are required to disclose your status. There have been many unfortunate cases in which people have taken advantage of this law. For example, a man and his partner were involved for seven years. This partner was aware of his status and even accompanied him to medical visits. However, once they broke up, he prosecuted his ex partner, and claimed that he was unaware of his status. Although they had the proof of the medical visits, this individual was found guilty. In another case, an HIV positive woman who was undetectable spit on an officer. She was charged with assault on a police officer and was sentenced to 37 years in prison. It would take exposure to 2 gallons of saliva for someone to become infected.

Reflection: 
Upon learning more about HIV/AIDS, we have all become so much more aware of the issues that still affect many people today. We were particularly surprised to learn about the rising numbers of transmission among African American men, compared to the numbers with Caucasian men. It was also interesting to see the evolution principles that we have learned about being put into action. The genotype test that patients use for determining what type of medication is best for that individual is based on the fact that individuals have different types of HIV, which all have different resistances to different medications. Perhaps the most eye-opening was learning about the HIV laws that Missouri has. It was heart breaking to hear about the cases in which people took advantage of this law in order to criminalize HIV positive individuals. While being positive within itself is not easy, we have learned that there is so much more to it than the health issues. There is the stigma, the difficult commitment to one's health (like taking a pill everyday for the rest of your life), as well as the law. In fact, HIV is the only chronic illness for which you are required to disclose your status. As a result of having the opportunity of speaking with Rashaan and Kaylon, we have a better appreciation for the project, as we know have a better idea of how HIV changes lives, beyond from just the physical bodily consequences. In closing, we thank Rashaan and Kaylon for their willingness to share their insightful thoughts on HIV/AIDS. We are all also more aware of the KC Care clinic, and its dedication to support HIV individuals. Below are some of the  pamphlets that are currently being circulated at the Clinic

What is Grid Computing? What is HIV?

Grid Computing Introduction: 

           A variety of different professionals, ranging from scientists to businessmen, may work online and use grid computing in order to accomplish their online goals. According to Jonathan Strickland, an expert in this field, grid computing essentially involves a computer network that consists of various computers that share information. This information includes memory, data, and processing power. Another expert in grid computing describes a computer grid as a “grouping of computer resources for use as a single, powerful computer” (Coppola, 1). In short, grid computing forms a super computer, consisting of different devices from different locations that collectively work on certain tasks.
         In terms of the practical applications of grid computing, there are many potential uses for this technology. In this class, the service project that students will complete involves the usage of computing projects like GPUGRID. According to their website, this project is a volunteer-based research endeavor that utilizes graphic cards in order to construct various biomolecular simulations. The research that is performed in GPUGRID and other similar computing based projects may require a supercomputer. With the help of volunteers who are willing to donate computing power (i.e. set up their computer with the project), these scientists may continue their research without the need of an expensive super computer.

HIV: 

  1.2 million people in the United States alone have it. 1 in 7 of those people are unaware that they have it. Making a controversial debut in the 1980s, HIV, Human Immunodeficiency Virus, has changed the lives of millions. This virus causes the immune system to deteriorate, and could possible lead to AIDS, or acquired immune deficiency syndrome. Unfortunately, a person cannot get rid of HIV. Once a person has HIV, there is no way to get rid of it (CDC 2014). HIV received it's name in 1983. There were disagreements about who found it first, but in 1987, France and the United States reached an agreement that allowed both countries to take credit. 
 

Below is an image of HIV's structure.

HIV Structure

https://hivskeptic.wordpress.com/tag/electron-microscopy-of-hiv/

HIV's structure is crucial to it's replication process. Below is a video that describes the replication process. 

HIV Replication 3D Medical Animation

HIV Transmission 

HIV is transmitted through blood, breast milk, seminal, vaginal and rectal fluids, when these fluids come into contact with a mucous membrane the virus is able to pass from the carrier into its next host.  In the United States, HIV is usually passed by having unprotected sex or sharing needles with someone who has HIV. Less commonly, HIV can also be passed from an infected mother to an infant during birth and breast feeding. It is important to note that HIV does not survive outside a body for long and thus it cannot be transmitted through air, water, insects, shaking hands or having casual contact with someone who is infected.

To minimize your risk of getting HIV you should practice safe sex consistently and correctly as well as limiting the number of sexual partners you have.

Total Credit: 5,590
Recent Average Credit: 481.37

References

Coppola, Jay. “Grid Computing and its Applications in the Biomedical Informatics Domain.”         Biomedical Informatics 2008. University of Connecticut, Storrs, CT, online.

"HIV Basics." Centers for Disease Control and Prevention. Centers for Disease Control and    Prevention,    15 Oct. 2014. Web. 21 Jan. 2015.  http://www.cdc.gov/hiv/basics/index.html
"In Their Own Words." In Their Own Words. NIH, n.d. Web. 21 Jan. 2015.                                http://history.nih.gov/NIHInOwnWords/index.html             

"U.S. Statistics." U.S. Statistics. U.S. Department of Health & Human Services, n.d. Web. 20    Jan. 2015.   <https://www.aids.gov/hiv-aids-basics/hiv-aids-101/statistics/>.