Our group has had the grid computing program running on two different computers. This has allowed us to do more work on the grid. We started off with "Help Fight Childhood Cancer" as our main grid, but about a month into the project it went from having an active status to having a status of intermitent meaning that it had very few items being sent to computers. Once it went to intermitent status Courtney changed her main grid to "Help Conquer Cancer" so that we would still be working on a cancer grid.
Here are the stats from Linda's computer:
11 results returned with a ranking of 502,029
8,271 points with a ranking of 483,423
Here are the stats from Courtney's computer:
206 restults returned with a ranking of 255,068
123,352 points with a ranking of 216,631
We know that these stats may not mean much other than just numbers to some people, but they do show that there is work being done on trying to combat cancer as well as other world problems. Being that the grid computing program sometimes sends work from other grids not all of the data that is gathered is for cancer. There are grids doing research Malaria, Leishmaniasis, Schistosoma, AIDS, clean enercy, and human proteome folding.
This project has allowed us to learn about evolution and how it can affect cancer. The project has also made us think about evolution in new ways.
Tuesday, April 30, 2013
Friday, April 19, 2013
Q and A for our research article
In our previous blog post we found an article and provided a link to the article. After the submission of the article our teacher (Dr. Walker) has given us a series of questions that she would like us to answer based on the article and our topic. Below is the series of questions with our answers.
1. This is a multi-part question. To answer it, you will need to go to www.ncbi.nlm.nih.gov and follow these instructions. From the drop-down search menu, choose "Nucleotide." Type cebpa in the box to the right and hit "search." Click on the Sus scrofa cebpa gene (third entry). On the right side of the page, click "Run BLAST." On the next page, click the BLAST button at the bottom (and wait...)
a. Scroll down your results page. Name ten other taxa (scientific and common names) that share some sequence identity with this Sus gene.
Canis (lupus) familiaris à Dog
Tursiops truncates à Bottlenose dolphin
Odobenus rosmarus à Walrus
Orcinus orca à Killer whales
Oryctolagus cuniculus à Rabbit
Pan troglodytes à Chimpanzee
Homo sapiens à Human
b. What is Sus scrofa? In an evolutionary sense, why study gene regulation in this animal?
Sus scrofa is wild boar.
c. What does wild type cebpa do in these animals? Why is it conserved across so many disparate species?
The wild type effects remission duration and overall survival.
2. According to the paper, what does the mutated cebpa allele indicate in human patients?
Patients with CEBPA mutations had higher hemoglobin levels, lower platlet counts, and higher peripheral blood (PB) blast counts. Also they were less likely to have lymphadenopathy or extramedullary leukemia. Other significant differences were not present regarding other clinical features between patients with mutated and unmutated CEBPA regions.
3. At what age are symptoms of adult AML typically evident in humans? Is this disease subject to natural selection? Why or why not?
The symptoms of adult AML are usually evident around 65 years of age. Fewer than 10% of people with AML are children. The CEBPA mutation is subject to natural selection becasue it has favorable outcomes in AML patients and can increase their lifespan and prognosis. This is only evident in patients who plan on having children and they would pass this mutation on. Becasue most of the symptoms of adult AML occur in older men and women, this mutation and disease are mainly evident in later age after many have already had children. Natual selection would work on AML if the symptoms were present with adults of reproductive age and having children. Selection would act against AML and those individuals with the disease would not survive to reproduce, unless they had the CEBPA mutation. The CEBPA mutation would be selected for because it increases the longevity and prognosis of a person with AML.
4. What does AML have to do with MDS?
AML (Acute Myeloid Leukemia) is the progression of MDS (pre-leukemia). So most people who suffer from MDS will unfortunately progress into AML. The comparisson is like HIV to AIDS, so most people whom have HIV will eventually transition into AIDS.
1. This is a multi-part question. To answer it, you will need to go to www.ncbi.nlm.nih.gov and follow these instructions. From the drop-down search menu, choose "Nucleotide." Type cebpa in the box to the right and hit "search." Click on the Sus scrofa cebpa gene (third entry). On the right side of the page, click "Run BLAST." On the next page, click the BLAST button at the bottom (and wait...)
a. Scroll down your results page. Name ten other taxa (scientific and common names) that share some sequence identity with this Sus gene.
Canis (lupus) familiaris à Dog
Tursiops truncates à Bottlenose dolphin
Odobenus rosmarus à Walrus
Orcinus orca à Killer whales
Oryctolagus cuniculus à Rabbit
Pan troglodytes à Chimpanzee
Homo sapiens à Human
Papio anubis à Olive baboon
Pongo abelii à Sumatran orangutan
Callithrix jacchus
à
common marmoset
Otolemur garnettii
à(northern)
greater galago à
thick-tailed bushbabies
Bos Taurus àBovine
à
cattle
Trichechus manatus
latirostris à
Florida manatee
b. What is Sus scrofa? In an evolutionary sense, why study gene regulation in this animal?
Sus scrofa is wild boar.
c. What does wild type cebpa do in these animals? Why is it conserved across so many disparate species?
The wild type effects remission duration and overall survival.
2. According to the paper, what does the mutated cebpa allele indicate in human patients?
Patients with CEBPA mutations had higher hemoglobin levels, lower platlet counts, and higher peripheral blood (PB) blast counts. Also they were less likely to have lymphadenopathy or extramedullary leukemia. Other significant differences were not present regarding other clinical features between patients with mutated and unmutated CEBPA regions.
3. At what age are symptoms of adult AML typically evident in humans? Is this disease subject to natural selection? Why or why not?
The symptoms of adult AML are usually evident around 65 years of age. Fewer than 10% of people with AML are children. The CEBPA mutation is subject to natural selection becasue it has favorable outcomes in AML patients and can increase their lifespan and prognosis. This is only evident in patients who plan on having children and they would pass this mutation on. Becasue most of the symptoms of adult AML occur in older men and women, this mutation and disease are mainly evident in later age after many have already had children. Natual selection would work on AML if the symptoms were present with adults of reproductive age and having children. Selection would act against AML and those individuals with the disease would not survive to reproduce, unless they had the CEBPA mutation. The CEBPA mutation would be selected for because it increases the longevity and prognosis of a person with AML.
4. What does AML have to do with MDS?
AML (Acute Myeloid Leukemia) is the progression of MDS (pre-leukemia). So most people who suffer from MDS will unfortunately progress into AML. The comparisson is like HIV to AIDS, so most people whom have HIV will eventually transition into AIDS.
Friday, April 5, 2013
Research
For this assignment we had to find a research article that links our topic and evolution. Our group found an article that links myeloid leukemia and evolution.
Citation for our article.
Citation for our article.
Fröhling, Stefan, Richard F. Schlenk, Ina Stolze, Jörg
Bihlmayr, Axel Benner, Sylvia Kreitmeier, Karen Tobis, Hartmut Döhner, and
Konstanze Döhner. "CEBPA Mutations in Younger Adults With Acute
Myeloid Leukemia and Normal Cytogenetics: Prognostic Relevance and Analysis of
Cooperating Mutations." Journal of Clinical Oncology 22.4 (2004):
624-33.
Link: http://jco.ascopubs.org/content/22/4/624.full.pdf+html
Thursday, February 28, 2013
Reflection on Interview
The interview was very interesting and insightful due to the many challenges that a donor must overcome. It is hard enough to have a sister who has cancer, but to also be the donor is very daunting. From how he described the methods of the transplants and side effects, it seemed both physically and mentally challenging to go through the process. The interviewee mentioned that he had no problem volunteering for the task and would do anything to help his sister even though an allogenic stem cell transplant is a lot to handle.
The reason why we chose this project is because two of our group members personally know people who have this disorder. What makes MDS an important project is that the only known cure is an allogenic stem cell transplant. The most difficult part about the transplant is finding a donor. If there are not family members who match the person with MDS, it can be very hard to find an outside donor would match on all levels. Hopefully through grid computing, an answer can be found to help patients who have no donor matches. Another important reason to research MDS is that it is very rare in people under the age of 50. Christine and Emily are the two group members who know people under the age of 25 with this pre-leukemia. This is especially rare and there are no known causes for this to occur in healthy, young adults. MDS relates to evolution because there is a mutation in the bone marrow of people with this disease. This mutation is not useful and is detrimental to a person’s health. Because there are no know causes for MDS in young adults, doctors must look to evolution to try and understand how this cancer has developed to effect younger people who have never had cancer before.
~Christine Schatz
The reason why we chose this project is because two of our group members personally know people who have this disorder. What makes MDS an important project is that the only known cure is an allogenic stem cell transplant. The most difficult part about the transplant is finding a donor. If there are not family members who match the person with MDS, it can be very hard to find an outside donor would match on all levels. Hopefully through grid computing, an answer can be found to help patients who have no donor matches. Another important reason to research MDS is that it is very rare in people under the age of 50. Christine and Emily are the two group members who know people under the age of 25 with this pre-leukemia. This is especially rare and there are no known causes for this to occur in healthy, young adults. MDS relates to evolution because there is a mutation in the bone marrow of people with this disease. This mutation is not useful and is detrimental to a person’s health. Because there are no know causes for MDS in young adults, doctors must look to evolution to try and understand how this cancer has developed to effect younger people who have never had cancer before.
~Christine Schatz
Sunday, February 17, 2013
Interview
As part of our project we needed to interview an expert on our topic. We interviewed Christine's boyfriend (TJ) who is the donor for his sister who has MDS.
The treatments that you used/are using consist of what, or what are they? (Did you have to take different methods than the normal route since people who usually receive this are of an older age)
- Allogenic stem cell transplant.
- In allogenic stem cell transplant the stem cells do not come from the patient, but from a donor whose tissue type closely matches the patient. The donor is often a family member, usually a brother or sister.
- The donor receives a series of growth factor G-CSF shots to increase the stem cell production in their bone marrow.
- Usually the donor receives one shot a day for five days, but due to my age and body mass, they increased it to a double dosage.
- The donor is hooked up to dialysis-type machine on sixth day, in which the blood runs through a centrifuge and separates the stem cells, and returns the rest of the blood to the body.
How does the treatment affect you differerntly since you are younger than the average age of the person that gets this type of cancer? Or did it matter really your age?
- Because of the dosage size of the growth factor, I was at a higher risk for side effects. Abour the third day I started having flu-like aching symptoms and couldn't sleep. This lasted for three days.
How has MDS affected you/your family?
- My mother and sister and niece had to live in St. Louis for the entire 6 months of treatment. My father worked in Independence and was traveling between there, home and St. Louis. I had to house sit for them the entire summer. It was very difficult on us and our relationships.
What all did you/your family go through in the process of finding a cure for your sister?
- I gave blood to the Barnes Jewish Hospital in St. Louis for lab work and I was a 5/5 match to donate so there was no need to look for donors elsewhere.
- My mother and sister had to constantly drive to St. Louis for doctor's appointment
How long did it take for the doctors to diagnose the cancer since it is such a rare form?
- 1-2 months
The treatments that you used/are using consist of what, or what are they? (Did you have to take different methods than the normal route since people who usually receive this are of an older age)
- Allogenic stem cell transplant.
- In allogenic stem cell transplant the stem cells do not come from the patient, but from a donor whose tissue type closely matches the patient. The donor is often a family member, usually a brother or sister.
- The donor receives a series of growth factor G-CSF shots to increase the stem cell production in their bone marrow.
- Usually the donor receives one shot a day for five days, but due to my age and body mass, they increased it to a double dosage.
- The donor is hooked up to dialysis-type machine on sixth day, in which the blood runs through a centrifuge and separates the stem cells, and returns the rest of the blood to the body.
How does the treatment affect you differerntly since you are younger than the average age of the person that gets this type of cancer? Or did it matter really your age?
- Because of the dosage size of the growth factor, I was at a higher risk for side effects. Abour the third day I started having flu-like aching symptoms and couldn't sleep. This lasted for three days.
How has MDS affected you/your family?
- My mother and sister and niece had to live in St. Louis for the entire 6 months of treatment. My father worked in Independence and was traveling between there, home and St. Louis. I had to house sit for them the entire summer. It was very difficult on us and our relationships.
What all did you/your family go through in the process of finding a cure for your sister?
- I gave blood to the Barnes Jewish Hospital in St. Louis for lab work and I was a 5/5 match to donate so there was no need to look for donors elsewhere.
- My mother and sister had to constantly drive to St. Louis for doctor's appointment
How long did it take for the doctors to diagnose the cancer since it is such a rare form?
- 1-2 months
Friday, January 25, 2013
Introduction to MDS
For evolution class we have formed a group to do a grid computing project. The project entails the writing of a blog, signing onto a grid to help participate in grid computing research, and an interview with an expert in the field of our topic. Our group members are Linda Nwachukwu, Christine Schatz, Courtney Waters, and Emily Hinsley. Our topic is Myelodysplastic syndrome (MDS) which is a preleukemia.
Grid computing is a large system of netweorked computers whose processing power is used to solve difficult and time-consuming problems (dictionary.com). Grid computing uses many computers to work on a single project. By using many computers at once multiple processing cycles can be done at once. It allows for access to large amounts of data. In a grid computing community thousands of people can share their computer's processing cycles to work towards finding a solution to a problem. Grid computing uses the computer resources from multiple locations to reach a common goal.
Myelodysplastic syndrome (MDS) is a blood and bone marrow disorder where stem cells do not mature normally. The disorder causes an increase of immature cells and abnormally developed cells with a decrease of healthy mature cells. Because of a low level of healthy cells the person is more likely to be anemic and may have neutropenia (abnormally low levels of white blood cells) and thrombocytopenia (abnormal drop in platlets).
http://www.cancer.net/cancer-types/myelodysplastic-syndromes-mds
If any step in the process of making of the different blood cells is not done or is done incorrectly the number of a given type of cell can decline and lead to an anemia or blood disorder/disease. The figure below shows the normal process of blood stem cell to red blood cell, platelet, or white blood cell.
http://www.cancer.gov/cancertopics/pdq/treatment/myelodysplastic/Patient/page1
We have chosen to use a childhood cancer grid.
Grid computing is a large system of netweorked computers whose processing power is used to solve difficult and time-consuming problems (dictionary.com). Grid computing uses many computers to work on a single project. By using many computers at once multiple processing cycles can be done at once. It allows for access to large amounts of data. In a grid computing community thousands of people can share their computer's processing cycles to work towards finding a solution to a problem. Grid computing uses the computer resources from multiple locations to reach a common goal.
Myelodysplastic syndrome (MDS) is a blood and bone marrow disorder where stem cells do not mature normally. The disorder causes an increase of immature cells and abnormally developed cells with a decrease of healthy mature cells. Because of a low level of healthy cells the person is more likely to be anemic and may have neutropenia (abnormally low levels of white blood cells) and thrombocytopenia (abnormal drop in platlets).
http://www.cancer.net/cancer-types/myelodysplastic-syndromes-mds
If any step in the process of making of the different blood cells is not done or is done incorrectly the number of a given type of cell can decline and lead to an anemia or blood disorder/disease. The figure below shows the normal process of blood stem cell to red blood cell, platelet, or white blood cell.
http://www.cancer.gov/cancertopics/pdq/treatment/myelodysplastic/Patient/page1
We have chosen to use a childhood cancer grid.
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