Tuesday, April 30, 2013

End of Project Reflection

It is hard to believe that this semester is coming to a close-- and that we have already wrapped up our grid computing service learning project!  The summary statistics document that our group ran the grid computing software for a total of 6 hours and during this time, we provided valuable RAM and processing power to the research of 'Project Say NO Schistosoma'.  



 The goal of 'Project Say NO Schistosoma' is to research various medications and the genome of the schistosoma parasitic worm in order to improve treatment for the disease as it affects some 240 million people worldwide.  This specific grid is the 20th grid aimed at humanitarian research launched by the World Community Grid project.  Below is the most up-to-date statistics of this grid and it's pretty amazing to see how much effort has been poured in to researching new treatments for the schistosoma parasite!



Although our personal contribution to this effort is miniscule in comparison to the larger scheme of the project-- we believe that every access to the grid helps, as each computer adds a little bit to help achieve an extraordinary effort in a manageable way.  We encourage the continued support of this grid project and plan to continue to run this program in hopes that our individual contribution will continue to add to the research that will one day make schistosoma a rare & easily managed condition, rather than a disease plaguing millions of individuals in third-world countries across the globe!

Friday, April 19, 2013

Questions regarding our posted article:

Question 1 - multipart:
a.)  Which species of Schistosoma have been sequenced?
b.)  For each species, list the number of haploid chromosomes, the genome size, GC content, number of genes, and number of proteins.
c.) Are the answers for each of these species similar? Why? Why study these three species?

Answer 1
Schistosoma mansoni 

  1. # of haploid chromosomes:  8
  2. Genome size: 258.72
  3. GC content: 35%
  4. Number of genes: 11,332 
  5. Number of proteins: 8,293 
Schistosoma japonicum
  1. # of haploid chromosomes: 8
  2. Genome size: 369.09
  3. GC content: 34.1%
  4. Number of genes: N/A 
  5. Number of proteins: N/A
Schistosoma heamatobium
  1. #of haploid chromosomes:  N/A
  2. Genome size: N/A
  3. GC content: N/A
  4. Number of genes: N/A
  5. Number of proteins: N/A 

The genmone size of Mansoni and japonicum are different by over a hundred Mb's. However, their GC content is almost identical. They also both have 8 haploid chromosomes. These characteristics are similar because they are closely related organisms. They may have differences because they may have undergone evolutionary changes in order to better infect their hosts. They may also be different because they live in different environments.

Question 2:

What type of markers were used to establish linkage groups in this study?  Why is it important, in an evolutionary sense, to identify linkage groups?

Answer:
In this study, eight types of markers that were consistent with chromosome numbers were used to establish the linkage groups of Schistosomes.  Linkage groups were identified and anchored to the chromosomes using fluorescent in situ hybridization (FISH).  By identifying the linkage groups, higher female recombination, confirmed ZW inheritance patterns, identified recombination hotpots and regions of segregation distortion were identified. 

Identifying linkage groups is very important in an evolutionary sense because it highlights the incidence of traits being inherited together.  Thus, traits that are selected for in future generations are often linked to other traits that may be also inherited, with or without beneficial contribution of fitness.  As far as the study, linkage has proved very helpful in establishing the genome map


Question 3:
Visit http://schistoDB.org On the right, click on “Browse S. mansoni v5.0 Chromosome 6.  Click on a colored part of the high-level map of chromosome 6.  What gene is it?  What does it code for?

Answer:
 It is a protein-coding gene and it’s systematic name is Smp_095880, which codes for a hypothetical protein.


Question 4:
Why is it important to study protein folding/misfolding in schistosomes? (refer to p. 157 of your paper for guidance)

Answer:
It is important to study protein folding/ misfolding in schistosomes because it may be a key in preventing the successful reproduction and regeneration of schistosomes both within the human body and within that of a host’s body.  When proteins are translated from mRNA to produce an amino acid chain, the protein remains non-functional until it is properly folded into the standard double helix form of DNA.  By studying the base pair positioning and being able to influence the order of amino acid base pairs, researchers may be able to prevent the proper folding (or misfolding) of proteins, thus affecting the fitness of schistosomes by causing mutations and non-functional genes.



Monday, March 25, 2013

Light Reading

Recent advances in Schistosoma genomics
Here's a little light reading for everyone over Easter Break! Recent advances in Schistosoma genomics explores the use of genomics to help provide a control tool for Schistosoma, as well as the biological insight that can be provided by epigenetic research.
Enjoy the article, and the break!

Friday, February 15, 2013

Schistosomiasis Interview With An Expert  


The next step in our service learning project was to conduct an interview with an expert on the subject of Schistosoma.  We chose to interview the parasitology teacher at Rockhurst University, Mary Haskins. The interview happened in the science faculty offices at Rockhurst University.  We sent Dr. Haskins an initial email to get a time set up to interview with us and she was more than willing to meet with us.  We chose to interview her because she teaches parasitology here at Rockhurst and would have the best understanding of the parasitic disease we are learning about, Schistosoma.  

We went in with several questions prepared for Dr. Haskins, these included: 

1. Why are you interested in parasitology?
2. Have you interacted with Schistosoma patients or the parasite itself?
3. In what ways could evolution have impacted the distribution of Schistosoma?
 4. Is a spreading of this parasite very likely or a major worry?
5. Currently, what is the main treatment for this parasite?
6. How important is the search for a cure for Schistosoma?
7. What do you know about grid computing and its’ impact on this search?

Q1: Why are you interested in parasitology?
A1: The diversity of what you see with parasitology and the impact this type of study has on others around.  Parasites are a global issue and are not just limited to one reason, there is a large range of parasites to look at.  There is also never a dull story, they are very interesting and sometimes gross.  

Q2: Have you interacted with Schistosoma patients or the parasite itself?
A2: No, I've never directly worked with it, only researched/learned about it in text books.  It has to have certain conditions for it to be passed on.  It is contracted from ingesting water that is contaminated by fecal matter or urine.  Since most places in America have sanitary water conditions it is much more rare for us to see cases of it.  If conditions are managed correctly the exposure is limited.  

Q3: In what ways could evolution have impacted the distribution of Schistosoma?
A3: There is a geographic distribution of the disease due to the three different types of species that infect the population.  There are three different kinds of Schistosoma and they are identified by the shape of their spine.     This spine is used to burrow out of the capillary system into either the bladder or the intestines, depending on the type of spine.  The type of species is dependent on where the person is located.  

Dr. Haskins then showed us this picture of the distribution of the disease throughout the world. 

Q4: Is spreading the parasite very likely or a major worry?
A4:  In cultures where the water supply isn't correctly monitored yes, however here in America there isn't a place where it is likely to infect people.  

Q5: Currently, what is the main treatment for this parasite?
A5:  An antibiotic most likely is used, but they change the drug used to treat it so often, due to resistance and   more efficient drugs coming onto the market.  

Q6: How important is the search for the cure for Schistosoma?
A6:  Every year there is a convention held just about this illness, so based on the amount of people attending and working for a cause pretty important.  There is not a known cure yet, just treatment methods.  Usually once people notice it is a problem they are too far gone to fully get rid of the worms.  

Q7: What do you know about grid computing and its impact on this search?
A7: I'm not exactly sure what they are doing with the grid computing at this time. I'm sure something to help prevent or treat the disease.  


Q8: How has Schistosoma evolved since its occurrence?
A8: I'm not up to date about the evolution, but I can imagine that the parasite has become resistant to certain types of medications used to treat it.  

Q9: Is it likely to change/increase in geographic distribution?
A9: There has been a lot of progress made to manage/control and minimize exposure to the disease.  Including educating cultures on the importance of maintaining clean water supplies.  

Q10:  Do you think there will be a cure or just preventative measures taken against this disease?
A10:  If the cycle can be broken then there can be a cure.  The first goal is to gain control over the fecal/urine waste in the water supply.  If this can be done the problem will be eliminated because the parasite won't be prevalent without that factor.  

We also learned during the interview that some cultures in Africa actually encourage the continuation of this disease because when the parasites burrow out of the capillaries and into the bladder they cause blood to enter the urine.  However there have to be a lot of parasites for this to be noticeable and usually occurs during the time of puberty.  In a few African cultures bloody urine is the sign of manhood and they don't consider it a problem until it's too far gone to treat.  
The Schistosoma parasite also is one of the only parasites that has a separate male and female gender and these two organisms mate for life once in the blood stream.  This way the can continually lay eggs and keep the cycle in the human body going.  

Our interview with Dr. Haskins was a very insightful conversation and helped to deepen our understanding of the disease we are working to help prevent.  She really helped to define exactly what happens while this illness runs its course and explained to us why things happen the way they do with this illness.    

Friday, January 25, 2013

Introduction to Schistosomiasis & 'Project Say NO to Schistosoma'

    As part of a Service Learning project through Rockhurst University's Evolution lecture, led by Dr. Mindy Walker, we have been assigned to not only join a Grid Computing effort but to also record our progress as we learn about the disease that our Grid Computing efforts are researching. 

     Grid computing, or the mass networking of computers driven to process together a single application, is a truly novel concept.  The advantage of grid computing is that instead of utilizing one computer, those who utilize grid computing have unlimited hard drive space, memory, and processing power.  In essence, grid computing allows many computers to tackle an extraordinary effort in a manageable way.

     The Grid that we have joined as part of our individual service learning is focused on researching Schistosomiasis medications and is called 'Project Say NO Schistosoma' (http://www.schistosomaonline.com.br/)
Schistosomiasis is a parasitic disease caused by an infestation of  larval parasitic worms of the helminth species known as blood flukes or schistosomes. Snails in freshwater sources serve as the carrier to the worm, which is contracted by humans through the skin.  Often those who contract this parasite live in tropical or sub-tropical third-world countries, such as countries in Africa or lower Asia, and have no access to clean, potable water.  Thus, they are easily exposed to schistosomiasis when unclean water carrying the microscopic larvae comes in contact with exposed skin abrasions.

     Once infected, the larvae matures and the worms live parasitically inside the host's body, with different species concentrating on different organs.  The most common organ affected is the urogenital system and the associated veins.  According to the World Health Organization, schistosomiasis affects 240 million people worldwide (http://www.who.int/schistosomiasis/en/). 
The map below illustrates the most affected areas.

http://wwwnc.cdc.gov/travel/yellowbook/2012/chapter-3-infectious-diseases-related-to-travel/schistosomiasis.htm

     The symptoms of infection can escalate to fatal conditions, however they most often consist of abdominal pain and swelling due to enlarged liver and spleen (as the organs are overrun with larvae and adult schistosomes).  Symptoms also include diarrhea, fever, fatigue, and has even been linked to a increase in the incidence of bladder cancer (http://relief.unboundmedicine.com/relief/ub/view/cdc-yellow-book/204110/all/Schistosomiasis).

Schistosomiasis can be treated with oral drugs, although there is no current vaccine.
A child with schistosomiasis (http://www.ivmproject.net/about/index.cfm?fuseaction=static&label=schistosomiasis)



Adult schistosomes (http://www.e-cleansing.com/wp-content/uploads/2009/12/schistosoma-schistosoma-japonicum.jpg)