Sunday, May 4, 2014

Statistics & Reflection

Statistics

Our group’s POEM@Home (Protein Optimization with Energy Methods) grid completed 7248 total units of work throughout the duration of this semester. We noticed that the program began working on a new project about every 3 hours.

This grid was utilized to:
  • predict the biologically active structure of proteins
  • understand the signal-processing mechanisms when the proteins interact with one another
  • understand diseases related to protein malfunction or aggregation
  • develop new drugs on the basis of the three-dimensional structure of biologically important proteins
  • simulate miscellaneous nanoscale systems, which are of importance for current biological or physical research

Reflection
Our group was extremely grateful to be involved in this service learning project throughout this class. Dr. Walker introduced us to a new side of service. Most students in the past have believed that service is only beneficial if done in the community, but it was interesting to learn that a project of this nature was just a beneficial. Additionally, meeting with a medical professional allowed us to connect our class learning to real world experiences through the informative stories Mrs. Liebergen  shared. We are very fortunate to have learned much more about the specifics of this disease and to make essential connections from this grid project to professionals in this field.
By simply downloading and running a program in the background on a computer can help to solve medical mysteries. We hope that in the future, this blog will help others to learn the benefits of grid computing. If more people were willing to help in this way, the opportunities to learn more about protein encoding are endless. By making a slight contribution to the worldwide grid computing effort, scientists are one step closer to learning how to make more effective drugs to combat cystic fibrosis.

Sunday, April 6, 2014

Cystic Fibrosis Questions

These questions address the J. R. Soc. Interface article entitled “Evaluating candidate agents of selective pressure for cystic fibrosis” by Poolman and Galvani, 2007. Be sure to explain your answers.

1. Is cystic fibrosis a qualitative or quantitative trait?
The introduction asserts that about 2% of the population are carriers of the CF allele. Using H-W, tell me the frequency of the mutant alleles in the population (q), as well as the frequency of the wild type allele (p).
  • Cystic fibrosis is a qualitative trait, meaning that trait or allele is either present or absent. In the case of cystic fibrosis, the recessive allele must be present for a person to have the disease.
  • 2%=0.02 are carriers of CF allele
  • q2 = 0.02
            √0.02 = 0.14142
1-0.14142 = 0.85858 = p
q frequency (mutant allele) = 0.14142
p frequency (wild type allele) = 0.85858
  • Check: p2 + 2pq + q2 = 1
(0.85858)2 + 2(0.85858)(0.14142) + (0.14142)2 = 1
0.73716 + 0.24284 + 0.02 = 1
1 = 1

2. What evidence do the authors have that tuberculosis was sufficient to act as a selective agent for CF heterozygotes?
  • “The correct selective agent must be plausible according to three lines of evidence: molecular, clinical; and historical-geographical” (Poolman and Galvani 2006).
  • 1. “Resistance to tuberculosis in CF patients was recently postulated to arise from diminished activity of the enzyme arylsulphatase B” (Tobacman 2003).
“Thus, dysfunction of arylsulphatase activity in CF is postulated to protect against tuberculosis by depriving the bacteria of a necessary nutrient” (Tobacman 2003).
  • 2. Clinical evidence: “There is also clinical evidence of an association between CF and resistance to tuberculosis. A lower tuberculosis mortality rate has been observed among heterozygotes versus controls” (Crawfurd 1972).
  • 3. The low incidence of tuberculosis in CF patients has been noted by a number of investigators (Poolman and Galvani 2006)
  • “Thus, tuberculosis is supported by both molecular and clinical evidence” (Poolman and Galvani 2006)
  • 4. As the researchers model relates CF to tuberculosis, “it predicts that the incidence of CF will fall in regions of the world where tuberculosis is well controlled at a rate of approximately 0.1% per year” (Poolman and Galvani 2006).

3. If, in a population like that of early 17th-century Europe, heterosis were acting on the CF alleles, what might you expect to happen to these alleles over the long term? In a region with no selective pressure conferred by tuberculosis, what would happen to the recessive CF alleles? (Think fitness tables...)
  • Heterosis is the tendency of heterozygotes to show qualities superior those of both parents. This is also known as heterozygote superiority (Freeman and Herron 2014).
  • If heterosis were acting on CF alleles, it would be expected that both the CF alleles and wild-type alleles would eventually reach an equilibrium.
  • If there is no selective pressure conferred by tuberculosis, it is assumed that selection is still acting on the CF alleles. In that case, the recessive CF allele will go towards extinction (but not reach it). In addition, the wild-type dominant allele will go towards and eventually reach fixation.

4. Could founder effect have generated the levels of CF we see today? Why or why not?
  • The founder effect is a sampling error in the origin of a small population due to sampling error, only a small fraction of genetic variation in the parent population will be present in the small number of individuals in the founder population (Freeman and Herron 2014). "The founder effect has been proposed to explain the high incidence of CF" (Klinger 1983).
  • In this study, the founder effect was modeled as a putative [assuming to have existed] bottleneck population consisting solely of heterozygotes (Poolman and Galvani 2007). "In such a population, CF incidence begins at 1 in 4 births and decays below the observed European incidence in 1800 years" (Poolman and Galvani 2007). Therefore, their model demonstrates that a founder effect could not have proceded the current existing levels of cystic fibrosis, as there has been no such dramatic bottleneck for the entire European population within the past 1800 years.

5. Note: for mathematical modeling of the population, the authors used Freeman and Herron (2004) as their source. What significance does this source have to you?
  • This source is our current evolution textbook. We are utilizing the fifth edition in class, but the researchers of this paper used an edition published in 2004 by the same authors.


Works Cited
Crawfurd, M.A., 1972 A genetic study, including evidence for heterosis, of cystic fibrosis of the pancreas. In 168th Meeting of the Genetical Society of Great Britain, pp. 126. University of Leeds.

Freeman, S. & Herron, J. C., 2004 Evolutionary analysis. Upper Saddle River, NJ: Pearson Prentice Hall.

Freeman, S. & Herron, J. C., 2014 Evolutionary analysis. 5th ed. Upper Saddle River, NJ: Pearson Prentice Hall.

Klinger, K. W. 1983, Cystic fibrosis in the Ohio Amish: gene frequency and founder effect. Hum. Genet. 65, 94-98. (doi:10.1007/s004390050407)

Poolman, E. M., & Galvani, A. P., 2007. Evaluating candidate agents of selective pressure for cystic fibrosis. Journal of The Royal Society Interface, 4(12), 91-98.

Tobacman, J.K., 2003. Does deficiency of arylsulfatase B have a role in cystic fibrosis? Chest 123, 2130-2139. (doi:10.1378/chest.123.6.2130)

Friday, February 14, 2014

Questions Answered

       On a chilly Kansas City afternoon, we embarked on an adventure to KU Medical Center. We met with Adrienne Liebergen, ARNP. As a nurse practitioner who has specialized in cystic fibrosis for the past 37 years, she was the ideal person to answer our plethora of questions about this disease. As we began our conversation and got to know her, we were curious as to how she began her career in this field. After having a child, she sought a part-time nurse practitioner position. As history would have it, the cystic fibrosis department was hiring. She even admitted that she was only vaguely familiar with the disease at the time and had to seek additional information from the library prior to beginning. After working in the field for 30+ years, she is "married to it", but each day presents new challenges which keeps her coming back for more. She explained, "It's different everyday...different problems come up everyday...laws change...Medicaid changes..."

       As we began the interview portion, Mrs. Liebergen clarified the details of cystic fibrosis. She explained that cystic fibrosis is a genetically caused progressive disease. It is a recessive disease, which requires the cystic fibrosis genes from both parents. Infants are commonly diagnosed with the disease just after birth. A newborn screen is blood testing that is done within 24 hours of birth and tests for 30+ diseases and conditions. As of 2009, the state of Kansas requires that cystic fibrosis is one of the diseases that newborns are screened for. If there are any abnormalities, the parents and their newborn are referred to a specialist. This is where Mrs. Liebergen comes into the process. To test for cystic fibrosis in particular, a sweat test is performed. It is a noninvasive test in which electrodes are placed on the arm to stimulate the sweat glands. This process measures chloride concentration in the sweat. If a patient has cystic fibrosis, the concentration of chloride will be elevated. A test with a measurement over 60 indicates a positive test. This simple process allows parents to know the results within about 30 minutes and before leaving her office.

       When asked about additional symptoms of cystic fibrosis, she responded that there are multiple common and evident signs of this disease. Pneumonia at a young age (under 6 months), asthma, bronchitis, poor weight gain, salty skin, and greasy, poorly formed stools are all symptoms. If a pancreas is blocked by mucus, then the digestive enzymes cannot reach the intestines. This leads to greasy stools.

       Mrs. Liebergen stated that she sees 4-6 patients per week with cystic fibrosis on a repeating basis. It is recommended by the Cystic Fibrosis Foundation that patients have a checkup with a specialist quarterly after being diagnosed. It is essential to ensure that patients, especially young children, are at an adequate height and weight for their age. Although the disease can be crippling, growth stunts are preventable. A unique aspect regarding treatment of this disease is the work of an entire care team. On her team in particular, there are physicians, a nurse practitioner, a clinic nurse, a respiratory therapist, a psychologist, a dietitian, and a social worker. They are all present on clinic days while seeing patients and all play a vital role in caring for each patient who is battling this disease.

       When asked to elaborate on influential stories that have resonated with her, she recalled a story of one patient in particular who has a severe case of CF. Despite recommendations from her care team of when to take medications and how to perform at-home treatments, the patient has failed to follow through. This has led to multiple hospital visits, and eventually a chest tube was temporarily put in due to a partial lung collapse. Although this story is a tragic one, it is an influential reminder of how essential it is for patients to incorporate at-home treatments into their daily routines. There are various at-home therapies such as vests that the patient wears for a set period of time. These vests emit a high frequency chest wall oscillation which sloughs off excess mucus from airways. It allows the patient to cough up (via a "huff cough") and expel the excess, making it easier to breathe.

       Although there is no current cure for cystic fibrosis, science is coming close. Mrs. Liebergen elaborated on various drugs that are in the research phase. To learn more about research development, visit the "Drug Development Pipeline" link at http://www.cff.org/research/DrugDevelopmentPipeline/. Most of the drugs that have been approved by the FDA already are used to prolong life after diagnosis, but Kalydeco is different. This drug is the first one that targets the gene mutation (G551D mutation) that causes the disease. There are also inhalational drugs that are effective at reaching the airways quickly and easily. Patients with cystic fibrosis have more treatment options than ever before, but the medications do come with a price. Mrs. Liebergen admitted that a 30 day supply of some medications can be as expensive as $5000. Factoring in the price of an at-home airway clearance vest can be upwards of $15000-$20000. Although insurance does help, battling this disease does become a significant expense.

       We are so thankful to have had the pleasure of learning more about this disease from Mrs. Liebergen. She gave informative insight that eluded a more personable element through her firsthand experiences. Her extensive knowledge helped to clarify the misconceptions of cystic fibrosis. Although the fight against cystic fibrosis is stressful and expensive, there is hope. Medical breakthroughs are happening everyday. Our group is so grateful to have had this opportunity to have had the chance to sit down and speak with Mrs. Liebergen and know that there is special care for patients with cystic fibrosis at KU Medical Center.

       Interviewing Mrs. Liebergen was very interesting and enjoyable. She gave incredible insight to this devastating disease, which helped us have a better understanding of cystic fibrosis. She explained not only the medical side of cystic fibrosis, but also the personal and mental aspect of the disease. It was personally shocking for us to learn that there is such a large number of cystic fibrosis cases, and they're all different from one another. It was really eye-opening to learn about the extensive lifetime care that one has to follow if diagnosed with this disease. It is not something that you can take multiple medications, for and it is not something relatively inexpensive. You have to be dedicated to your health at all times, and it's very sad and almost disturbing to realize how much the disease can consume you. Every decision that you make has to be based on your condition. Apart from the ongoing care and lifestyle changes, there are also emotional issues that you must face. This is a problem that is often overlooked a lot by people. Living with cystic fibrosis can cause fear, anxiety, depression, stress and much more. This condition is not physically draining but also emotionally draining. Through this interview, we were able to understand the struggles one faces with cystic fibrosis--at least as much as a third party can understand. Mrs. Liebergen was truly knowledgeable about cystic fibrosis, and she showed us how she is in fact "married" to this disease. This interview gave us a new outlook on cystic fibrosis, and we truly appreciate Mrs. Liebergen for making time for us to talk to her.

"For to be poised against fatality, to meet adverse conditions gracefully, is more than simple endurance; it is an act of aggression, a positive triumph." - Thomas Mann

Friday, January 24, 2014

Description of Project

Why Grid Computing?

       Grid computing is a revolutionary technology in which millions of individual computer devices are linked to a huge global supercomputer. These devices include desktops, laptops, game systems, and even mobile phones. This technological network has a much quicker processing time as compared to a normal personal computer we think of today. Because data can be processed simultaneously, research time is drastically shortened, which is more cost-effective. Grid technology works via volunteers downloading and installing a program on their computer. Our group began the use of this technology by downloading our own computing grid, which is discussed in more detail below.
       The personal computer will perform computations of data that it receives from the World Community Grid’s server then send the results back. Since scientists do not have to individually calculate the data, the grid computations speed up the rate of research. This critical information is vital to current research projects, leads to more accurate diagnosis of diseases, and quicker analysis of medical images.
To learn more about grid computing, visit the following links: http://www.gridcafe.org/EN/who-can-use-grid-computing.html
http://www.worldcommunitygrid.org/index.jsp


Grid Computing And Cystic Fibrosis

Our group is using a grid in particular entitled POEM@Home. Protein Optimization with Energy Methods is utilized to:
  • predict the biologically active structure of proteins
  • understand the signal-processing mechanisms when the proteins interact with one another
  • understand diseases related to protein malfunction or aggregation
  • develop new drugs on the basis of the three-dimensional structure of biologically important proteins
  • simulate miscellaneous nanoscale systems, which are of importance for current biological or physical research
This grid's ultimate goal is to solve scientific mysteries pertaining to the biological encoding of proteins with unknown structures.
To participate in this grid computing project as well, visit: http://boinc.fzk.de/poem/index.php


Cystic Fibrosis Background

       To determine the reasoning behind becoming a volunteer in the grid computing project, we look to a disease in particular: cystic fibrosis. Cystic fibrosis is a genetically inherited disease which is characterized by a buildup of thick, sticky mucus within the organ systems. Mucus is a slippery, watery substance which keeps the lining of organs and airways moist and prevents desiccation. This disease disrupts the salt balance within the body. Too little salt and water within the body causes the normally thin layer of mucus to become thick and sticky. This environment is ideal for excessive bacterial growth. The thick mucus is difficult to cough up, which clogs the airways and leads to frequent and serious lung infections. These infections, such as pneumonia and bronchitis, cause chronic coughing, wheezing, and inflammation. With time, the infections result in permanent lung damage due to the formation of scar tissue (fibrosis) and cysts in the lungs.
Normal airway vs airway with CF
http://discovermagazine.com/2013/september/14-doorway-to-a-cure
       In addition to lung issues, many people with cystic fibrosis also experience digestive problems. Babies affected often have an intestinal blockage, referred to as meconium ileus. Blockage of the pancreas also occurs via blockage of the pancreatic ducts. This reduces the production of insulin and prevents enzymes from reaching the intestines to aid in digestion. For those with cystic fibrosis, there is a greater likelihood for diabetes and osteoporosis.
       The cause of cystic fibrosis is from a gene mutation of the cystic fibrosis transmembrane conductance regulator (CFTR). The CFTR gene encodes a protein that affects multiple bodily organ systems. This protein functions to produce mucus, sweat, saliva, tears, and digestive enzymes. CFTR transports chloride ions into and out of tissues via protein channels. The transport of these ions help to regulate water flow into and out of tissues, which is necessary for the production of thin mucus. Normal humans contain two copies of the CFTR gene. Cystic fibrosis is an autosomal recessive disease, which can only be expressed if both parents are carriers. If a child inherits two mutated copies of a defective CFTR gene, cystic fibrosis results. On the other hand, if an individual only inherits one defective copy of the gene, he or she still express enough normal copies of the gene to lead a normal life.
       This uprising disease has about 1,000 new cases diagnosed each year, with about 70% of patients diagnosed by the age of two. The predicted age of survival with this disease is until early 40s. With current education and research, scientists are seeking a cure for cystic fibrosis. With our grid application, POEM@Home seeks to understand protein mutations in relation to cystic fibrosis.
To learn more about cystic fibrosis, visit the following links: http://www.cff.org/AboutCF/
http://embryo.asu.edu/pages/cystic-fibrosis-transmembrane-conductance-regulator-cftr-gene
http://ghr.nlm.nih.gov/condition/cystic-fibrosis
http://www.medicalnewstoday.com/articles/147960.php