Thursday, May 2, 2013

Statistics



    • Seen in the pictures below here are the statistics from the World Community Grid over the past semester.


    • Total Run Time: 4 days, 6 hours, 14 minutes, and 44 seconds
    • Points Generated: 9,743
    • Points Generated Ranking: #447,034
    • Results Returned: 9
    • Results Returned Ranking: #513,276
    • Projects Worked On: Say No to Schistosoma, Drug Search for Leishmaniasis, The Clean Energy Project- Phase 2, Human Proteome Folding- Phase 2, and FightAIDS@Home


Statistics from World Community Grid




Additional Statistics from World Community Grid 




Although our contribution was minimal, the overall effects of the World Community Grid throughout the years it has been in existence has allowed a vast amount of aid to research. No matter how little the contribution may be, there is no task too small. The World Community Grid will continue to be installed on the computer to allow completion of projects, and give us piece of mind that even when our computer is not being used by us, it may be helping find a cure. 

Wednesday, April 17, 2013

Follow Up Questions Based on Exon Skipping Article



 Questions – Muscular Dystrophy

These questions are based on the Journal of Clinical Investigation article entitled “Exon Skipping during Splicing of Dystrophin mRNA Precursor due to an Intraexon Deletion in the Dystrophin Gene of Duchenne Muscular Dystrophy Kobe” by Matsuo et al. (1991). The link to this article is in the previous blog post.

     Questions 1-3 need an outside resource to answer.  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 dystrophin in the box to the right and hit “Search”. Click on the Rattus beta-spectrin gene (tenth entry). On the right side of the page, click “Run BLAST.” On the next page, click the BLAST button at the bottom (and wait…).
 
Scroll down the results page... What other taxa (scientific and common names) share some sequence identity with this Rattus gene? 
     Mus musculus (common mouse), Cricetulus griseus (Chinese hamster), Cavea porcellus (guinea pig), Oryctolagus cuniculus (domestice rabbit), Homo sapien (human)


What is Rattus? In an evolutionary sense, why study the dystrophin/spectrin genes in this animal?

      Rattus is the part of the scientific name for the brown rat, its full name being Rattus norvegicus. It is a species that is often used to study genetic principles and human disease. They are used for a variety of reasons. First, they are a practical species to use. They are relatively inexpensive and breed quickly. There are few ethical dilemmas to overcome when working with this species. More specifically, they are used to study the dystrophin and spectrin genes in this animal because due to the evolutionary history shared by both humans and Rattus norvegicus. A simple BLAST of the Rattus beta-spectrin gene shows how similar the two species are, at least at certain gene levels. For example, the beta spectrin III gene in Homo sapiens (humans) has a 95% query coverage, meaning that 95% of that particular human gene lines up with the Rattus beta-spectrin gene. Additionally, the BLAST shows that this human spectrin gene has an 87% maximum identity value, which means that there is an 87% similarity between the Rattus gene and the human gene over the length of the coverage area.


What does wild type dystrophin do in these animals? Why is it conserved across so many disparate species? 

      The dystrophin protein provides a structural link between the muscle cytoskeleton and extracellular matrix to maintain muscle integrity. Also, new studies show that dystrophin may also act as the scaffolding for several signaling molecules, but these pathways remain unknown. This gene is conserved across many different species, which shows major shared history. The dystrophin gene developed far back in the evolutionary path. There has been evolutionary pressure to not change the gene because its encoded product is so important to many species. It has been conserved across many species because any change to the sequence can cause dramatic phenotypic diseases.
 What does the mutated dystrophin allele cause in humans? According to the paper, what does this mutation involve?

A mutated dystrophin allele in humans has the ability to cause Duchenne muscular dystrophy (DMD). A fatal defect in the dystrophin allele may cause this life threating disease. The dystrophin allele contains over 2,500 kilobases, and is encoded by a 14 kilobase RNA transcript. This 14 kilobase RNA transcript is managed by 70+ exons.  The mutation occurs when exon 18 is directly joined to exon 20; therefore, exon 19 is missing. Exon 19 has a 52 base pair deletion. Exon 19 is skipped when the dystrophin mRNA is processed which therefore creates an abnormally spliced mRNA.

At what age are symptoms of MD typically evident in humans? Is MD subject to natural selection? Why or why not?

MD is typically evident in humans when the child begins walking. Therefore, in the case study from the article it states the Japanese boy was around the age of five when he was diagnosed. Since MD has to do with the genetics of a human, a 52 base pair deletion, most likely it cannot be subject to natural selection. Most often, the mutation does not allow the patient to reach reproductive age and therefore they are not able to pass their genes onto the next generation. Which would lessen the chance of MD rising in the population, but since mutations never fully leave a population if they are recessive alleles, the mutation will never go extinct, there will always be women carrying the recessive allele or a random mutation of the embryo.
Why might it be important to look at folding/misfolding in these proteins, even though we know the inheritance pattern of MD?

Since we already know that MD is an X-linked recessive inherited disease, it is also important to look at the folding and misfolding of these proteins. It is important to look at the misfoldings because it may give scientists multiple insights. One of these insights is to other disease and how they compare to the misfoldings of MD. Another insight that may be important is by looking at these proteins it may help reduce the factors of environmental protein misfolding. The last insight that misfoldings can produce is if a scientist knows how the protein folding wrong, then they may be able to come to the conclusion of how to unfold or fix the misfolded protein and therefore find a cure.

Monday, March 25, 2013

MD Research

There is no cure for MD, but there are studies that experiment to find a reason as to why MD occurs, which has the potential to lead to a cure. Here is a little bit of light reading about exon skipping during splicing of the dystrophin mRNA precursor due to an intraexon deletion in the dystrophin gene. This research looks at how a mutation, deletion, can influence the splicing of the dystrophin mRNA which can lead to MD. Still interested? Click on the link and read the journal article!

enjoy...

Exon Skipping During Splicing

Sunday, February 17, 2013

Welcome to Holland

Every Day is a Blessing

On Friday, Brigid and I interviewed Dr. Catherine Thompson, PhD, MS, PT of the Physical Therapy school here at Rockhurst. We were not sure what to expect when we met with Dr. Thompson, and in fact neither of us had even been in the part of Van Ackeren where Dr. Thompson's office was located. It is safe to say we left with a truly unforgettable experience.

Dr. Thompson is the type of person you could speak with for hours about anything. She has been a physical therapist for upwards of 35 years and has extensive experience not only domestically, but in many foreign countries as well. She has treated numerous patients with muscular dystrophy (MD), especially children and young adults suffering from Duschennes MD. I do not exaggerate when I say that Dr. Thompson transformed our outlook on the research project. 

We began by explaining the idea of grid-computing. She was not familiar with the concept, but she was very helpful in explaining different ideas of research, therapy, and treatment for people suffering from MD. She was well aware that there is no cure for MD, but she was very well-versed in therapeutic alternatives. For example, she told us about an organization that sells equipment, such as electric wheel chairs, for a fraction of what the equipment actually costs, but makes you promise to return the equipment after your child passes. She said it can be likened to a library, where you can check out the equipment and return it. Children with Duschennes can live in to their twenties, but, according to Dr. Thompson, usually develop respiratory infections and other curable illnesses that end up as the cause of death, because the young adult is unable to cough. Coughing is the usual mechanism for getting out bacterial fluids, but people living with MD do not have enough muscle strength to expel said fluids. 

She had an striking amount of compassion, which is the main thing I will never forget about the interview. She truly hurt for the kids who grow up being ridiculed for being clumsy--for kids who are yelled at by their fathers because they are not any good at sports. She recalled a time when she was working with a child in Kyrgyzstan who had been diagnosed with MD, and seeing the pain in not only the child, but the father as well. She reminded us that not all countries in the world have "Disability Acts" that require buildings to have elevators and ramps, and that this family would have an extremely trying time dealing with this disease. Dr. Thompson teaches with the same compassion. Part of her curriculum involves showing her students the poem, "Welcome to Holland", and allowing the students to make worksheets that are designed to address treatment methods, both physical and mental for both child and parent.

With tears in her eyes, Dr. Thompson talked about a poem, entitled "Welcome to Holland". This poem is posted in our blog. It really summarizes our new outlook to the research project. Prior to the interview, I will not deny that the research project was somewhat intangible for myself, as I could not see the fruits of our contribution. This poem brought the project back to a very personal level for both Brigid and I. From a parent's viewpoint, it describes the excitement of anticipating the birth of a child. It then moves to talk about how having a child born with a disability is not what the parent had planned, but how this child is still a beautiful gift with unthinkable potential.

Dr. Thompson gave incredible insight to a devastating disease. She allowed Brigid and I to personally see the affects both physically and mentally on the patient and the family. After leaving the interview, we both now know why research for a cure is a very important aspect of muscular dystrophy, because a cure gives hope in our every day. Until the cure is found, people need to see Holland how it truly is… a blessing.

Thursday, January 24, 2013

Description of project


        Through the idea of grid-computing, research in countless areas has been expedited due to the contributions of millions of personal computer processors. Grid-computing has allowed millions of people around the world to volunteer without having to leave their couches. The purpose of our specific service learning project is to contribute a personal computer’s idle resources towards the research of muscular dystrophy. Our project will run through the World Community Grid, a project started by IBM to “tackle projects that benefit humanity.” According to IBM, they have pledged to “work with only public and not-for-profit organizations, and to place all results in the public domain available to the research community.” Just one of multiple projects, the “Help Cure Muscular Dystrophy” project has focused its research potential towards understanding disorders that hinder muscle function through muscle pathology as well as nerve pathology. Specifically, the world community grid project will be “helping in the fight against neuromuscular disease by stimulating protein to protein interactions for known protein structures including those that are mutated in these diseases.”

                    In order to better understand the project, it will be important to introduce muscular dystrophy. The term muscular dystrophy is actually in fact a set of over 200 disorders “that impair muscle function functioning either directly through muscle pathology or indirectly through nerve pathology” (World Community Grid). Muscular dystrophy is a genetic disorder that weakens the muscles that allow the body to move. The people that have this disorder are missing genes that permit them to produce proteins to allow for healthy muscle function. Muscular dystrophy is genetic. Therefore, people are born with the disease. It is not necessarily right at birth; some people even develop the symptoms into adulthood.  Most commonly though, as a person with muscular dystrophy’s life progresses the muscle continuously deteriorates, therefore they lose the ability to do common things that some people take for granted such as walking, sitting up, even feeding themselves on their own (Kids Health). Seven common types of muscular dystrophy are known by the public by specific names instead of all 200 of them. 
Picture #1: Main Areas of Muscle Weakness in Different Types of Dystrophy
The seven are Duchenne muscular dystrophy (DMD), Becker muscular dystrophy (BMD), Emery-Dreifuss muscular dystrophy (EDMD), Limb-girdle muscular dystrophy (LGMD), Facioscapulohumeral muscular dystrophy (FSMD), Myotonic muscular dystrophy (MMD), and Congenital muscular dystrophy (CMD) (Kids Health).  Duchenne muscular dystrophy is the one that is most commonly associated with “muscular dystrophy”. Briefly, DMD “is caused by a problem with the gene that makes a protein called dystriphin” (Kids Health). This protein allows for cells in muscles to keep their shape and strength. Becker muscular dystrophy, BMD, is similar to DMD but the symptoms start later in life. Emery-Dreifuss muscular dystrophy (EDMD), is seen in teens and mostly in boys and affects shoulders, upper arms, and shins. Limb-girdle muscular dystrophy (LGMD),  progresses slowly and is equal in boys and girls. Facioscapulohumeral muscular dystrophy (FSMD),  usually begins during the teenage years and it affects the muscles in the face, shoulders, and sometimes in the lower legs. People with this type may have issues raising their arms. Myotonic muscular dystrophy (MMD), is where the muscles have a problem relaxing. Congenital muscular dystrophy (CMD), is the type that shows up in babies (Kids Health). The life expectancy of a person with muscular dystrophy is relative to the severity of the disease.
Picture #2: DMD Skeletal Muscle Cells



                      There are so many different versions of muscular dystrophy, not one has a cure, and that is why this community grid is a great help for the future of finding a cure. The MDA, Muscular Dystrophy Association, is helping fund scientific research for a cure. There are many other funding projects such as a telethon hosted by Jerry Lewis during Labor Day weekend. Time, research, and patience will eventually lead to a cure.