Lactase Evolution Problem Space. Mark Bergland Karen Klyczek Chi-Cheng Lin Arline Toro C. Dinitra White
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1 Lactase Evolution Problem Space Mark Bergland Karen Klyczek Chi-Cheng Lin Arline Toro C. Dinitra White
2 Preface to the case study: This case is divided into three parts in order address three main concepts: Part I: Inheritable traits Part II: The use of a Single Nucleotide Polymorphism data set to explore evolution of genes in humans using Case-it! Part III: The use of rich data sets to expand the exploration of genetic evolution
3 Revenge of The Dairy Products An Investigation of Lactose Intolerance
4 Part I. The Baker Family Condition
5 Anita Baker Anita Baker is a Junior biology major at the Outer Banks College in North Carolina. She noticed that many of her family members, including her older sibling, suffer from a painful stomach condition that only occurs after drinking milk, eating cheese or consuming products that contain dairy. However she does not have this problem. In her family, the illness is known as the family condition and Anita believes the condition may be inherited.
6 Anita Baker Anita is preparing to take a course in Genetics this fall and has many questions including the following: Why do I have my mother s hair but my fathers eyes? Why don t I suffer from the family condition? If I have children, will they suffer from the family condition?
7 Dr. Smith s s Genetics Class On the first day of class, Anita decides to talk to Dr. Smith, her genetics professor, about the illness that persist in her family. After listening to Anita describe the symptoms, Dr. Smith recommends that she develop a family tree detailing the various symptoms described by each member of the family for her semester project.
8 Anita s s Work Over the next two months Anita interviews her two grandmothers, grandfather on her father s side of the family, aunts, uncles, and several cousins. Take a look at the family tree that Anita presented to her Genetics class
9 Anita s s Family Tree Edna *Edward Joe Lila *Sam Sue *Rob *James Dorothy Diane Charlie Kyle Linda Anita *JoAnne Kevin Tim Kevin, Jr Key: * = Mild Family Condition, = Severe Problems
10 Questions: What can you say about Anita s family and the family condition? Based on the family tree do you think the family condition is inherited? Explain your answer. How could you determine for sure whether the family condition is inherited?
11 Part II. The next step Is genetics involved in the family condition?
12 More on the family condition After Anita presented her family tree, Dr. Smith decided to show the class a scientific article that would likely explain Anita s family condition. The title of the article was Lactase Persistence
13 SNPs associated with diseases and other biological processes:
14 SNPs associated with lactase persistance
15 The class studied the articles in groups and Anita s group made the following conclusions: The lactase protein is responsible for allowing our bodies to break down lactose, the major carbohydrate in milk. The lactase protein is encoded by the lactase gene (LCT). In the absence of lactase, stomach cramps, diarrhea, and flatulence usually occurs. Single nucleotide changes (also called single nucleotide polymorphisms, SNPs) in a neighboring gene called MCM6 appear to be linked to people becoming lactose intolerant. SNPs located in the MCM6 neighboring gene may cause expression of the lactase protein to decrease.
16 Anita s s Class Assignment: To follow up the in-class assignment, Dr. Smith asked her class to do the following: Examine a set of data containing LCT and MCM6 nucleotide sequences from humans to determine whether there is a link between sequence differences and lactose intolerance. DATA
17 Modifications to Case It Software Add microarray simulation genotyping expression Import/export data for analysis using Excel/ESTEEM and other tools Connect directly to bioinformatics tools for further exploration BLAST Alignments Tree building Gene function, pathways Other
18 SNP probes
19 Output from Case It microarray simulation DNA from lactase non-persistant donor
20 Output from Case It microarray simulation DNA from lactase-persistant donor
21 Analysis of SNP microarray data, exported from Case It software, in Excel
22 Tools for analyzing and visualizing SNP data dchip SNPTools
23 Part III. The final step Exploring lactase evolution Anita s s question: Is lactase only produced by humans?
24 Anita s s final project For extra credit, Anita chose to explore the evolution of the LCT gene and the MCM6 gene. (see Lactase evolution file)
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