Reflection and Data from Grid Computing

Fight Against Malaria

Statistics
Our group selected the malariacontrol.net grid computing project run with BOINC. It simulates models of transmission dynamics and health effects of malaria. This grid can be used to determine optimal strategies for delivering mosquito nets, chemotherapy, or new vaccines, which are currently in development testing. The malaria grid process is extremely computer extensive, but the results generated are very helpful.

The grid started a new project every 3 or so hours. It worked on 4 tasks at a time. Our grid completed 12,280 units of work. Total time elapsed was approximately 552 hours.

Reflections

Sean:
        This service learning project was very interesting because it incorporated grid computing, which I had never heard about prior to this class. Grid computing is a very interesting way to research prevalent topics throughout the world. It also allowed me to better understand Malaria (thanks to the interview with Dr. Cooper) and how the transmission occurs, as well as how it affects those worldwide. It is amazing that we can use the extra computer power on our laptops to help understand something as complex as protein folding in Malaria.

David:
        This is by far the simplest and most effective service project I have ever been a part of. Grid computing allows us to be a part of malaria research that is unlike anything we can do in the classroom. Our interview with Dr. Cooper broadened our understanding of malaria, including the transmitted and evolutionary effects.  The questions about the malaria paper made us relate our knowledge of evolution to malaria.  This grid computing project has made me realize how common malaria is in certain parts of  the world and that evolution drastically alters the effects of drugs and vaccines on malaria. I am very grateful for the opportunity to learn from grid computing while contributing to malaria research along the way. I believe grid computing will only improve and become more widely utilized in future research.

Drew:
        After being exposed to the benefits of grid computing, I believe that more people should be informed about the advantages of helping out other by simply running a program on your computer. Malaria is a widespread and serious threat across the world. Millions of cases arise each year and hundreds of thousands of people die from the illness. I also think that more people need to be informed about the disease itself, as plenty of people think it is a simple bacterial or viral infection. If more people were informed about grid computing and how easy it is to help out causes such as these, I think that the potential for a cure or vaccine would be much easier to reach. Im glad to have helped the cause, if only by a small margin.

Malaria Paper Questions

1. According to another paper (PNAS “Systemic lupus erythematosus-associated defects in the inhibitory receptor FcyRIIb reduce susceptibility to malaria” by Clatworthy et al. 2007), systemic lupus confers some immunity to malaria.  Geographically, where would you expect the disease alleles to be common, and why?  Considering what you know about sickle cell anemia, how do you hypothesize that this immunity is conferred?

The alleles for systemic lupus most likely would occur in areas of Africa, Asia, and South America. They may be common because those that survive after a infection of Malaria can then pass on those same genes on to their children. A survivor that has systemic lupus also has better immunity to Malaria making them have overall better fitness (ability to pass on their genes through reproduction) in those areas where Malaria is deadly. 

Our original hypothesis was that the parasite cannot live as well on sickle cells than on the regular re blood cells or non-sickle cell carriers. This may not allow the parasites to infect as many cells and would reduce the overall infection. However, after doing some research we found that the "heme oxygenase-1 (HO-1), an enzyme whose expression is strongly induced by sickle hemoglobin. This enzyme, that produces the gas carbon monoxide, had been previously shown by the laboratory of Miguel Soares to confer protection against cerebral malaria" (Ferreira, 2011). The research done by this group showed that the carbon monoxide protects the host against cerebral Malaria, which in many cases can become deadly. 

     2.  In an evolutionary sense, why is it informative to study malaria and its implications in mice?

It is important to study malaria in mice because it can allow us to determine which methods may or may not work according to how the parasite reacts. Studying the mice allows for us to see how quickly the parasite evolves. Studying malaria in mice allows a controlled environment that allows scientist to collect consistent data in a host with a well-known genetic sequence.

3. Apply Darwin’s four postulates to within-host Plasmodium virulence and transmission success.

Individuals within species vary- some Plasmodium individuals have higher virulence and better transmission rates and therefore vary.

Some of these variations are passed on to offspring- The individuals that have a higher virulence and a higher rate of transmission are more likely to pass their genes on to their offspring due to a higher fitness level. Those individuals that have the highest virulence have a better chance of passing on their prominent genes.

Individuals vary in their fitness.

Most favorable adaptations are most likely to survive and reproduce.

4. On page 973, the authors assert that “drug resistance becomes a problem within 5-30 years of first using a drug” and that this “is indicative of their potential to evolve rapidly.”  What does this tell you about the efficacy of vaccines?  Why should your Tropical Medicine physician know about evolution?

This tells us that vaccines are lacking the ability to block all aspects of malaria. It also shows that malaria is evolving rapidly and developing ways to get around vaccines. A Tropical Medicine physician should know how evolution works and keep in mind the effects of it as well. They should know of selection, mutations, and variation among populations. 

  

      5. If, as the authors suggest, more virulent strains have a competitive advantage within their mouse host, why do they conclude that “parasites evolve some intermediate level of virulence”?  What mode of selection on this quantitative trait does this exemplify?

The optimal level of virulence is determined by the selective pressures at both the host and population levels. Natural populations are characterized by a distribution of parasite strains, shaped by parasite traits and selective pressures experienced by parasites. Evolutionary actions also have a vital effect on virulence evolution. The trade-off between the two leads to maximum parasite fitness at intermediate levels of virulence. This is a prime example of stabilizing selection where fitness increases at the intermediate level.

     6. Why is it important to study protein folding/misfolding in malaria, even though we know its  cause?

It is important to study the protein folding and misfolding because it can show how the mutations can change the protein sequence. These changes in protein sequence or changes in protein folding can change how the protein acts.

1. Ana Ferreira, Ivo Marguti, Ingo Bechmann, Viktória Jeney, Ângelo Chora, Nuno R. Palha, Sofia Rebelo, Annie Henri, Yves Beuzard, Miguel P. Soares. Sickle Hemoglobin Confers Tolerance to Plasmodium Infection. Cell, Volume 145, Issue 3, 398-409, 29 April 2011 DOI: 10.1016/j.cell.2011.03.049

Interview Response

   Interview Response

We decided to interview Dr. Janet Cooper, a professor at Rockhurst University, who teaches courses such as Cell Biology and Microbiology.

Q1: Why should a researcher studying Malaria know about evolution?

The organism is going to change over time and in order to come up with medicines or vaccines, you need to be able to track those changes and understand that those changes are going to happen.

Q2: What do you think that grid computing can do for research, specifically malaria?

 I think that using grid computing would be beneficial in being able to find something that would match up with a protein on the malarial parasite and would be very helpful in terms of finding a new drug or vaccine. The possibilities are pretty good with grid computing.

Q3: Why do you think that Malaria is so difficult to treat?

Organisms that end up entering the cell are always much trickier to get out. You need a whole new approach to treatment with this occurs.

Q4: Why do you think that Malaria is so much more common in rural areas, particularly Africa?

I think that a lot of it has to do with mosquito control. It used to be in the United States and they were able to, with the help of eradication programs, get rid of most of the infected mosquitos. This was one of the things that the CDC was originally tasked to do in the late 1800's- early 1900's. But today with global travel, there will always be a chance that it can return. I think that Africa just doesn't have the health infrastructure that the United States has.

Q5: Do you think that a more adequate solution to the Malaria problem is the eradication of the infected mosquitos or the prevention of the disease in humans with a vaccine?

I feel that the vaccine would have a much better chance in preventing the disease in humans. Actually, one of the big things that the Bill Gates foundation is currently working on is a vaccine for malaria. I saw not too long ago that they were working on trials for vaccine testing, so hopefully we can see the results of their testing soon.

We want to thank Dr. Cooper for her time and input on Malaria.


 After talking with Dr. Cooper, our feelings towards the project were reassured. Malaria is a big deal, and hopefully our efforts can make an impact on trying to aid in the fight against Malaria. We all feel that a disease like this needs to be at the forefront for combating diseases throughout the world, because it has such a large impact. We also discussed that it is not as prevalent in the United States, but we should still work hard to fight this disease.
     After the interview, we gained a better understanding of how this grid computing project can aid in the fight against Malaria. Dr. Cooper helped to explain that Malaria is like an endless cycle, and that a vaccine would be most beneficial way to fight Malaria. It is incredible to know how many people are affected by Malaria around the world, and that a vaccine could dramatically affect the lives of millions of people.
    The interview changed the way we thought about Malaria and how the process of Malaria infects humans. We also gained a better understanding of why it is so popular in African nations and other areas. It also makes us realize how fortunate we are in America to have such a good medical system compared to other places around the world.
    Malaria evolves just as every living thing does. Recently, drug resistant Malaria has taken form. This form of Malaria is a huge problem and studying evolution can help to better understand the evolutionary process behind it. Hopefully, we can learn about this and make a change to prevent such occurrences.
   

Fight against Malaria

1/23/15 Fight against Malaria   Drew Baum, David Baldwin and Sean Badock

Intro to our service-learning project:

            Our service-learning project uses grid computing, which is a way to divide a huge amount of data throughout a network of computers to solve an issue or problem. Grid computing is a much quicker and more efficient way than using just one super computer to do all of the data analysis on one machine. By downloading and running software, grid computing uses unused computer power on a daily basis by a large network of computers that each solves tasks or analyzes data in order to find the solution to the overall problem.

Help Fight Malaria:

            Our group decided to choose a grid computing system that helps to find a cure to Malaria, which “infects 216 million people and kills 650,000 each year”(http://www.fight-malaria.org). Stats like these should not be overlooked. Malaria results in high fever, chills, and flu-like symptoms. In many cases we ask ourselves what can we do about a problem like Malaria. Well, grid computing allows us to help find a cure.

Malaria is a mosquito carried parasite, (Plasmodium falciparum), that infects humans, most commonly in African nations and southern Asia. Malaria is a cycle that seems endless between mosquitoes and humans. It is carried by parasites in mosquitos that are not affected by the parasite, however, the parasite is released into the blood stream of an individual that is bit by a mosquito. The individual will show symptoms after the parasites have reproduced in the liver and infected the red blood cells of the human host. The blood stream is then infected and another uninfected mosquito may bite an individual and the process begins all over again.

http://www.cdc.gov/malaria/about/index.html

 Malaria can be fatal and the parasite can even mutate, making Malarial drugs useless.  Running this program will help provide information to find the specific protein within the parasite that needs to be targeted along with other useful information regarding Malaria. The website and program we used is called malariacontrol.net. In an effort to help stop the vicious cycle of Malaria, we hope that we can aid the discovery of a better way to fight this disease. 

Malaria-endemic_countries_eastern_hemisphere-CDC.png

http://www.cdc.gov/malaria/about/index.html