Figuring Out the Genes of Peanut Allergies

            Food allergies have been rapidly growing all over the world, with about two to ten percent of children being affected in the United States. This growth in food allergies has become a major health problem due to the fact that they can potentially be life threatening, as well as their impact in the medical and economic fields. The three most common food allergies in the United States are peanut, egg, and milk.  Peanut allergies are considered to be one of the most fatal food allergies that are often life-long.

            A research team at the Johns Hopkins Bloomberg School of Public Health began researching the idea that genes could factor into food allergies. The team has discovered a region in the human genome that is associated with children’s peanut allergies in the United States. DNA samples of 1, 315 children and then 1,444 of their biological parents were collected. Most of the children being tested had some type of food allergy. The team scanned about 1 million different gene markers throughout the entire human genome to try and find which genes if any contribute to food allergies. The team discovered that on chromosome six, which is the region that has genes like HLA-DQ and HLA-DR, is linked to peanut allergies. This region of HLA-DQ and HLA-DR accounted for 20% of all of the peanut allergies in this study.

Not everyone that had these mutations developed a peanut allergy, which confused the team. They then theorized that epigenetic changes could also be a factor. An epigenetic change is when a methyl group attaches to the DNA, which causes the gene expression to be altered but not the underlying code. So they concluded that the level of DNA methylation determines if the peanut allergy will develop in people with the susceptibility. These levels can be altered by environmental factors such as in-utero or the first couple years of life. If these factors could be identified this could lead to being able to discover treatment or prevention plans.

Reference

http://www.jhsph.edu/news/news-releases/2015/do-genes-play-a-role-in-peanut-allergies-new-study-suggests-yes.html

Cancer Causing Fluke Worms

I first learned of fluke worms from my favorite TV show The X-Files, but they painted fluke worms in a different way than they really are. So I decided to do a little research into what they actually are. In this blog I’m going to talk about the liver fluke parasite that causes bile duct cancer.

            The liver fluke, or Opisthorchis viverini, is a tremadodes that infect humans who eat raw or undercooked fish that are contaminated with the fluke mostly in Asia. Once in the human body the fluke lodges itself in the liver’s bile duct and it feeds and matures. It is not completely known how they cause cancer, but the accepted theory is that the fluke secretes a protein that mimics granulin, which is the human growth hormone. When this worm infects someone their bodies are continuously exposed to these mimicking granulin protein and the host cells multiply uncontrollably. This rapid growth leads to tumor growth.

            Research is being done on these flukes by using a genome assembly tool called OPERA-LG to study the life of the fluke while it is inside the bile duct. This research has lead to the largest parasitic worm genome studied. In furthering their research the team hopes to find the cause and hopefully the cure for the bile duct cancer these flukes cause.

Reference:

http://phys.org/news/2014-09-genetic-code-cancer-causing-liver-fluke.html

Music Used to Identify Proteins

            Music for me is something that plays a huge role in my life. I’m always listening, playing, or singing some kind of music. So when I saw this new study it definitely peaked my interest. Structures of proteins can now be studied in a completely new and different way, by listening to music. This technique is theorized to more easily help scientists identify anomalies in proteins.

            By using a process called sonification, the data about the proteins can be turned into musical sounds and melodies. This approach is being used to ask three questions: what can protein data sound like? Are there any analytical benefits to this? In this data can specific elements or anomalies be heard? This technique can be used to help recognize fold structures of proteins by each protein sequence having a melodic shape. The amino acid sequences correlate to musical notes, with their properties being reflected by sound qualities.

            38 people were selected for the test to decide how well the sonification of the three proteins; 1ny9, 1r75, and 1div.pdb, were perceived in relation to data sources. From the 38 people, most of them were students, with 21 of them having more than one year of musical training, 17 having up to or more than one year of protein study, and 10 with no training in either. The subjects were giving four answer choices to choose from in their comparison of the sonifications to visual components: A) similar, B) not similar, C) sometimes similar, D) mostly similar. There were a total of six experiments, with the first two used to establish both positive (similar) and negative (not similar) controls. The results from the experiments showed that a good majority of the subjects were able to discern the correlations between the data related images and sounds. The study is hoping to expand to a more complete fold identification system to identify 3D folds of different proteins. Sonification is also being done on DNA sequences and gene expressions.

Reference:

http://www.heliyon.com/article/e00175

DNA Analysis of Cats Shows Domestic History

            The first full genome of a cat did not appear until 2007, but in 2014 a higher quality map of an Abyssinian cat named Cinnamon was published. And now since the price for DNA analysis has dropped, further study into a cat’s genome could then be done. An evolutionary geneticist from the Institut Jacques Monod in Paris named Eva-Maria Geigl presented her research on the mitochondrial DNA of 209 domestic cats that were found at 30 different archeological sites in Europe, Africa, and the Middle East. To give you an idea the history of cats span all the way from the dawn of agriculture to the 18^th century.

            There were found to be two waves in which the spread of cats occurred. The first was in the eastern Mediterranean and Turkey when agriculture first appeared. It is theorized that there were wild cats that would run off the rodents that tried to eat the farmers’ crop. So the farmers wanted them to stick around to help them out, which eventually lead to domestic breeds. The second wave was found by looking at the mitochondrial DNA lineage from Egypt, showing that the cats began appearing in Bulgaria, Turkey, and sub-Saharan Africa between the times of the fourth century B.C. and the fourth century A.D. The researchers theorize that the cats were kept on ships to help with rodents, and were spread at port cities. This came from the fact that the team found a cat in North Germany that dated back between 700 and 1000 A.D. that had Egyptian mitochondrial DNA.

            It has been believed for years that cats became domesticated in Egypt about 4000 years ago. But based on findings that cat bones had been discovered buried in a 9,500 year old human burial in Cyprus along with Geigl’s findings shows that cats have had a history with humans for a lot longer than first thought. Geigl also discovered by looking at the nuclear DNA of some of the samples that in the Middle Ages the mutation for tabby cats appeared, and that further study could lead to more information. As a cat lover and owner of many cats, I found this article to be very interesting and informative. I had no idea that cats had this kind of history.

http://www.smithsonianmag.com/smart-news/dna-study-details-spread-cats-around-world-180960573/?no-ist

Is Someone Really Allergic to Penicillin?

            It is being said by the CDC that people who thought they were allergic to penicillin might not actually be. In the US about 10% of patients state that they have an allergy to penicillin, where in actuality less than 1% of the population has a true allergy to the drug. First lets talk about what actually causes a person to have an allergy. A penicillin allergy is actually caused by IgE-mediated reactions to the reactive ingredients in penicillin called antigen determinants. IgE-mediated stands for immunoglobulin E-mediated.  When a person is allergic to penicillin their immune system reacts to the drug as if it is a harmful viral or bacterial infection. When the allergy develops the person’s immune system is then sensitive to penicillin.

            So how could the people who thought they were allergic to penicillin not actually be allergic? One way is that when the person was initially diagnosed as being allergic to penicillin they actually just had similar symptoms as the actual allergy. Or that someone who was allergic simply lost their allergy over time. About 80% of people who had a true penicillin allergy lose their sensitivity to the drug about 10 years after the reaction. So why is this important? This is important because it can reduce the unnecessary use of broad-spectrum antibiotics that people who are allergic to penicillin use. For the people who have thought they were allergic to penicillin they can take a penicillin skin test as well as an oral penicillin-class challenge to test if they are allergic. If both of these are negative then a penicillin allergy can be ruled out.

References

http://www.medscape.com/viewarticle/868552

http://www.mayoclinic.org/diseases-conditions/penicillin-allergy/basics/causes/con-20024205