Grid-Computing Results

Our group has been running a grid for Malaria for the past three months on one member's laptop. Our average number of credits for each session was 15 with a total of 3,146 for the semester. The program we used was titled BOINC.

Article Question Responses

1. step 1. splitting participants into groups

- the article did this by splitting participants into 3 populations samples based on their descent: Afro-Caribbean group, Afro-German group, and a healthy European expatriates, they were then screened for sickle cell disease and beta-thalassaemia by hemoglobin electrophoresis. There was then a 4th group called HbSS which were affected British individuals with sickle cell anemia

- in the QTL paper, mice were collected and tested for their PPI responses and then split into groups based on high or low response levels

step 2. phenotyping

- in the QTL paper, they kind of put steps 1 and 2 together by splitting participants into groups based on their phenotyping results which was their PPI responses

- in the article the participants were phenotyped based on their levels of fetal hemoglobin, and the F cell levels were determined by flow cytometry. The HbSS patients were routinely measured for HbF levels in the clinic

step 3. genotyping

- in the QTL paper, they collected DNA markers called "microsatellites"  which are short stretches of repeat DNA sequences with high mutation rates. this was another way to assign individuals to different groups based on what microsatellites were present in their DNA. used computational model to detect QTL signals across whole genome to identify potential contributions to different PPI responses

- in the article, geneotyping was performed by PCR/restiction enzyme analysis and was used for all HMIP-2 markers. This genotyping was used to find different HMIP-2 markers and haplotypes related to these different ethnic groups.

step 4. statistical analysis

- in the QLT paper, computational models were used to extract more detailed information on possible genetic contributions to PPI responses. Once the gene was identified, they tested the transcription levels for that gene in the different groups of mice. The researchers then performed a complementation test to provide evidence that their gene was one of the genes responsible for the PPI-QTL signal on chromosome 10

- in the sickle cell article, they ran statistical analysis on the association of FC and HbF traits with HMIP-2 marker alleles and investigated the linkage disequilibrium between markers and marker haplotypes. They also calculated the effective number of haplotypes.They then tested the haplotypes (11 SNPs) to see which ones had a strong association in all ethnic types in the study. By showing an influence of HMIP-2 locus to healthy and affected individuals of African origin, they believe this can lead to more powerful approaches for identifying the loci involved in the determination of HbF persistence. 

2. The article states that, "the number of HbF carrying cells, referred to as F cells...shows 89% heritability". This leads us to believe that VG would contribute more to the variance of the HbF and F cell phenotype. Since the variation is due to inheritance and genetics, if we were to draw a linear regression scatterplot for this trait, the slope of the line would be closer to 1. The offspring phenotype is going to more closely reflect the phenotypes of their parents. This leaves only about 11% of the variation of this phenotype up to environmental factors. This is understandable since sickle cell is an inherited disease.

3. There are 4 general causes of linkage disequilibrium (LD). They are physical linkage, selection, genetic drift, and population admixture. Physical linkage is when the loci are located on the same chromosome and near enough to each other such that cross-over between the loci rarely occurs. They are so close that they basically can't be separated through crossing-over. Selection is probably the most common cause of linkage disequilibrium, and most likely plays a role in our paper. This is when alleles at one locus affect the phenotype at a second locus. This means that one locus will affect the frequency of a second locus. If the first locus is advantageous, it will be selected for, and no matter if the second allele is advantageous or disadvantageous, it will also be selected for. Genetic drift leading to LD is when sampling error a mutation at one locus creates coupling of the new, mutated allele with specific-alleles at physically-linked loci. So this cause plays back into the first cause, which was physical linkage. This just makes new alleles linked because one of the alleles is mutated. The final cause of LD is population admixture, which also plays a role in our paper. This is when the combination of two populations, each of which are in linkage equilibrium (like the African population and the other ethnic populations), can create a single population that is in linkage disequilibrium. 

If we are trying to guess what happened in our article to make HMIP-2 locus in LD, I would say in the African population, a mutated HMIP-2 locus probably became advantageous. This is the locus that influences your number of F cells, your F cells are what carry HbF which is what sickle cell patients tend to have higher levels of. So the African population was probably in linkage equilibrium with a higher frequency of HMIP-2 mutated allele and then population admixture probably occurred with Europeans or people in the Caribbean, where HMIP-2 is at linkage equilibrium for a normal allele and then population admixture occurred. 

4. Our focal disease, malaria, is a disease which infects red blood cells and that is the site were they multiply within the body. After multiplying the disease can then destroy the red blood cells and lead to anemia. These also results in large amounts of free hemoglobin being released into the bloodstream. Malaria is a prominent disease in many African countries. At some point, there was probably a mutation in the SNPs at the HMIP-2 locus that lead to mutant haplotypes that led to sickle cell anemia. This turned into an advantageous trait because the malaria parasite cannot affect sickle shaped cells. This would lead to either a cure for the disease or at least a less severe form of the disease. Since less blood cells would be affected, less red blood cells would be destroyed and would lead to less free hemoglobin in the blood and better circulation of oxygen to the body. 

Bonus: The functional difference between HbF and HbA is that HbF binds less tightly to 2,3-BPG than does HbA. 2,3-BPG is a molecule that binds to hemoglobin and lowers its affinity for oxygen and promotes oxygen release. Higher levels of 2,3-DPG in the blood allows the delivery of more oxygen to tissues even under low oxygen tension (high altitiudes). This difference between fetal and adult hemoglobin is what accounts for the leftward shift of the oxygen saturation curve of fetal Hb compared to adult Hb. 

Scientific Paper

Genetic Variation on Chromosome 6 Influences F Cell Levels in Healthy Individuals of African Descent and HbF Levels in Sickle Cell Patients

Lisa E. Creary¹, Pinar Ulug¹, Stephan Menzel¹, Colin A. McKenzie², Neil A. Hanchard², Veronica Taylor³, Martin Farrall⁴, Terrence E. Forrester², Swee Lay Thein^1,5*

Abstract Top

Fetal haemoglobin (HbF) is a major ameliorating factor in sickle cell disease. We investigated if a quantitative trait locus on chromosome 6q23 was significantly associated with HbF and F cell levels in individuals of African descent. Single nucleotide polymorphisms (SNPs) in a 24-kb intergenic region, 33-kb upstream of the HBS1L gene and 80-kb upstream of the MYB gene, were typed in 177 healthy Afro-Caribbean subjects (AC) of approximately 7% European admixture, 631 healthy Afro-Germans (AG, a group of African and German descendents located in rural Jamaica with about 20% European admixture), 87 West African and Afro-Caribbean individuals with sickle cell anaemia (HbSS), as well as 75 Northern Europeans, which served as a contrasting population. Association with a tag SNP for the locus was detected in all four groups (AC, P = 0.005, AG, P = 0.002, HbSS patients, P = 0.019, Europeans, P = 1.5×10⁻⁷). The association signal varied across the interval in the African-descended groups, while it is more uniform in Europeans. The 6q QTL for HbF traits is present in populations of African origin and is also acting in sickle cell anaemia patients. We have started to distinguish effects originating from European and African ancestral populations in our admixed study populations.

Rest of study can be found at 

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0004218

Josh's Interview Reflection

1) Describe your feeling about or response to the interview.

           Going into the interview I expected it to go very well considering I am currently in Invertebrate Zoology with Dr. Haskins and know she is very knowledgeable about the topic. Seeing as our group had a fairly good understanding of the cause of malaria going into the interview Dr. Haskins was able to provide us with even more additional information. This made for a very interesting interview because it was not full of  that same old material you can find in a textbook. Dr. Haskins was able to make the topic even more interesting by making it easier to relate to, which is very important because malaria is not encountered in the United States like it is in some countries.     

2) What changes occurred for you as a result of the interview?

           Going into the medical field for my future occupation and wanting to participate in medical service trips this has altered my view on parasites. Living in the United States really isolates us from many parasites that other less fortunate countries suffer from, whether it be due just to location or having the proper medical care available. This interview sparked a little desire in me to make sure I have a good base knowledge of parasites that way I might be able to identify the symptoms of a parasitic infection in the future.    

3) Did anything about it disturb you?

           The most disturbing thing to me would have to be the lack of knowledge individuals have when referring to parasites, especially malaria. It seems as though like with other illnesses individuals do not have any interest or become concerned with them until they have or their loved ones have become affected by it. This is unfortunate because sometimes if something is discovered too late in the game then the effects are irreversible.

4) Discuss the connection you found between the interview and your research/classwork.
           The biggest connection that I can make between the interview and my research/classwork would have to be malaria's connection to sickle cell. An individual that is heterozygous for sickle cell, have sickle cell trait, is in some areas more fit then individuals who do not. These areas include areas greatly affected by malaria. The advantage to having the sickle cell trait is that an individual only has half the normal hemoglobin, which means Plasmodium (cause of malaria) is only able to attach to half of the hemoglobin because it is not able to attach to the folded hemoglobin (sickle shaped) seen in sickle cell trait individuals. This leads to these individuals experiencing mild if any symptoms from malaria. This relationship has been briefly covered in my previous general biology classes I have taken, but it was not until this year that this relationship has sprung to life. I have encountered this relationship in Evolution, Invertebrate Zoology, and Advance Principles of Biology.


                                                                                                                          Josh Linton  

Riley's Interview Reflection

1. Describe your feelings about or response to the interview.

Overall, the interview was great. It actually went well over the time that I thought would be needed simply because Dr. Haskins had so much information to share with us. Her stories and knowledge of the topic meshed extremely well and she provided us with great insight that we had never before thought of. Dr. Haskins was the perfect person for us to interview.

2. What changes occurred for you as a result of the interview?

The main change that this interview had on me was the overall impact that malaria can have. Dr. Haskins provided many facts such as a single company losing over 5,000 work days per year with employees being out sick. I never really had a grasp on the seriousness of this disease until we interviewed her.

3. Did anything about it disturb you?

Nothing really disturbed me about the interview as a whole. As said in questions 2, I was more surprised about the severity of malaria than anything.

4. Describe the connections you found between the interview and your research/classwork.

The biggest connection that I found between the interview and classwork/research was actually the lack of knowledge about grid computing. Dr. Haskins had never heard of this until I mentioned that my computer was running on a grid for malaria. This surprised me because I initially had never heard about it until starting the Evolution course. I feel that if this was a better known concept then more people would be willing to sign their computers onto different grids allowing for more research to take place at a much cheaper cost.

Nina's Interview Reflection

1. Describe your feeling about or response to the interview.

I was really pleased with the outcome of the interview. I was really nervous we were going to run out of things to talk about very quickly and I was scared the questions we had prepared were not going to be very good questions. We ended up talking to Dr. Haskins for 45 minutes though and we definitely got on topics and subjects I didn't expect the interview to go in to. I had Dr. Haskins for invert zoology last year so I knew she was knowledgeable on the Plasmodium parasite but I was really surprised at how knowledgeable she was on the socioeconomic results Plasmodium and malaria can have on not only the economies of countries where malaria is a problem but also on our own economy. 

2. What changes occurred for you as a result of the interview?

The thing that changed most for me was just the idea of how big of an economical effect a parasite can have. When Dr. Haskins talked about how a company can lose almost 5000 days of work a year from being out sick it really shed a new light on the situation and why these impoverished and diseased countries have a hard time with health and economy and how they can be intertwined. 

3. Did anything about the interview disturb you?

We did get into talking about how there are studies being done with parasites controlling the habits of the organisms they inhabit. This was a little disturbing because one of the studies is about humans and if a parasite can cause sexual promiscuity or bad driving. 

4. What connections can be made between research and classwork?

The biggest connection that can be made between research and classwork I feel is the evolutionary advantage of sickle cell anemia. Just a single missense substitution mutation became selected for and now, in certain populations, being heterozygotic for sickle cell anemia is advantageous to having a completely normal hemoglobin protein. Dr. Haskins believes researchers are starting to look into the coevolution of other mutations and diseases as well. 

Dr. Haskins' Interview

For the next step in our project towards understanding malaria, we decided to interview Dr. Haskins. Dr. Haskins is a professor at Rockhurst who teaches classes such as Invertebrate Zoology and Parasitology, in which she talks about malaria in both classes. We were able to ask her questions that expanded on the background information we found, and what research and prevention methods are being used now.

We started off the interview by asking Dr. Haskins to more or less explain what the general public does or should know about malaria, if she thinks American physicians know enough about malaria, and what preventative measures are currently being used in the fight against malaria. Dr. Haskins believes that American physicians don't get enough training in the field of parasitology in general but if she had to guess which parasite they knew the most about it would be malaria. She thinks malaria is the best known parasite in the general public also. She thinks malaria is the parasite most easily diagnosed because of its prominent fever/chill cycle. The first step is for doctors to rule out the flu and then with the 24, 48, or 72 hour chill/fever cycle. She thinks that doctors knowing how to diagnose it is not enough though. Dr. Haskins thinks that the general public does not know enough about malaria. She thinks it is something the public is scared of but they do not understand the world-wide impact of the disease. Most Americans think malaria is a disease confined to third world countries in Central America and Africa. What Dr. Haskins thinks people need to realize is that the disease has world wide repercussions.
When asked to elaborate on repercussions, her main example was products being produced in countries affected by malaria. In one year, a company can lose up to 5,000 days of work because of people out sick. When people are out sick, productivity decreases drastically. When productivity decreases, it is more expensive to make products and then more expensive to sell them. Although Dr. Haskins still thinks the number one reason to fight malaria is for the well-being of those living in affected areas, she sees this example as a way to make the disease hit a little bit closer to home for Americans.
When asked about prevention methods, Dr. Haskins responded with multiple medications such as methylquin, doxycyclin, chloroquine, and quinine. Methylquin and doxycyclin are medications being used today as anti-malaria medications. Dr. Haskins went on to explain that quinine was the first medication used but the parasite soon became resistant. Physicians then moved on to chloroquine until that too started to fail due to malaria resistance. She now thinks that more anti-malarial drugs are on the market because not only does it decrease the chance of all malaria becoming resistant to all the different types of drugs but now there is a money making market for malaria medication. There are side effects to the medications though which turn some people away from them. Especially with methylquin, a major side effect is very horrible, very vivid nightmares. Another problem is that doctors do not feel the need to tell their patients that this is a very common side effect. If a patient is unaware that his or her dreams may become very gruesome and vivid, and they are in a different country, it might scare them enough to stop taking the medication. She also explained other forms of prevention that did not include medication. This were some behavioral things such as wearing certain colors that mosquitos are not attracted to, not being outside during certain hours of the day, wearing long pants and long sleeves, sleeping in a netted area, and always wearing repellant. As far as repellants went, she said DEET products were the best. She also said DDT works really well but it is illegal in America because it killed a big part of our eagle population, but we still support the use of it in other countries, and possibly even continue to sell it to other countries.

We then started to ask Dr. Haskins about malaria in America and how long it has affected the American population and how we got rid of it here. She told us that when we started to settle in America, malaria was a big problem. But once we got a little more civilized and started to take care of things like standing water and started to spray towns, we were able to break the mosquitos cycle. She remembers not too long ago, in the early 80s, a truck coming through a town and fogging up communities spraying for mosquitos. When asked if she thought there were any side effects to that treatment, she seemed pretty certain there was but doesn't know if anyone has made a connection to them yet. We then started to talk about all the regulations and laws for medications these days and she thinks that going around spraying towns would be met with a lot of resistant today. She thinks it would depend on the community though. If the community is well educated and an active community, she thinks it would be met with resistance. But if the community was a poor community just working to put food on the table, she thinks that they would not have the time or energy to fight against it.

Dr. Haskins then went on to explain how even in third world countries, their government is still bright enough to know the dangers and risks of malaria and are very proactive in trying to get rid of it. They simply do not have the funding though. So that is where world health organizations and foundations such as the Bill Gates Foundation come into play with supporting funding for getting malaria medication and modes of prevention into these communities. The Bill Gates Foundation has pour millions of dollars into malaria research and prevention and once stated he wished to eradicate malaria by the year 2015 (or something very close). Obviously, that date is not going to be reached but there are huge strides being made. Dr. Haskins was not aware of the malaria research being performed by computer-gridding but she was very excited to hear that some 1.3 million people were on the grid and she said it sounds promising.

It was a great honor to be able to speak with Dr. Haskins on the topic of malaria. She was very knowledgeable of the topic and was very willing to share it with us. She is very passionate not only about malaria but all parasites in general and we suggest, if you get the chance, to sit down and talk to her about them.