BIO 2133 Lecture Notes - Lecture 10: Sticky And Blunt Ends, Horse Length, Foxp2

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ceriseshark335

26 Nov 2015

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Topic 10: recombinant dna technology - transgenesis, knock-outs, and knock-ins. Foxp2 is a transcription factor involved in speech development. In humans, it helps in the development of the jaws, ears, etc. Know that the difference between the mouse and human protein for foxp2 is just 3 amino acids. Answer: d. putting the human version of foxp2 gene into a mouse might enable it to talk If we put in a mutated foxp2 gene, the mutation is that the speech would be affected: replacing the mutated human foxp2 gene with a mouse foxp2 gene is a way to cure speech disorders. The 2 proteins differ in only 3 amino acids. The 3 amino acids will probably not do the same things in the 2 different organisms. Mouse development occurs quicker than in humans and we can produce offspring within. The secondary oocyte is fertilized in the fallopian tubes.

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Discussion

Hi All - this week you will learn about DNA - the molecule of life! You may think that protein-coding genes are the most important, but results from the Human Genome Project revealed that only about 2% of our DNA codes for protein - so what about the rest of the "junk DNA" (or non-protein coding portion of the genome) - is it functionally important? Yes! Scientists are learning how "the non-protein-coding portion of the genome is of crucial functional importance: for normal development and physiology and for disease". I would like you to please choose a topic with regards to the non-protein coding portion of the genome (this will introduce you to gene regulation which we will cover in chapter 11) or you may also choose to write about a topic that describes a mutation in any protein that is involved in DNA replication, transcription, or translation (we did not talk about all of the enzymes involved in those processes). Please list your reputable source - this is worth 0.5 pt (even if you use one of my sources below) and tell me WHY you chose your topic (this is worth 1 pt.) please try to briefly explain your topic to the best of your knowledge - I don't expect you to write a lot of detail about your topic - it might be hard to understand (which you are welcome to comment on in your paragraph)!

Examples to choose from (but not limited to) include: noncoding RNAs (snRNAs, miRNAs, siRNAs, snoRNAs, piRNAs, lincRNAs) and RNA therapeutics:

LIST:

1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119351/ (Development of microRNA therapeutics is coming of age)

2. http://www.umassmed.edu/rti/ (RNA Therapeutics Institute)

3. http://www.genengnews.com/insight-and-intelligence/rna-based-therapeutics-and-vaccines/77900520/

4. http://genesdev.cshlp.org/content/26/21/2361.full (Biology of PIWI-Interacting RNAs: new insights into biogenesis and function inside and outside of germlines)

5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4265212/ (PIWI proteins and their interactors in piRNA biogenesis, germline development and gene expression)

6. http://www.news-medical.net/news/20121203/microRNAs-play-an-important-role-during-embryonic-development.aspx

7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578617/ (the role of microRNAs in cell fate determination)

8. http://news.berkeley.edu/2017/01/13/scientists-reprogram-embryonic-stem-cells-to-expand-their-potential/

9. http://www.the-scientist.com/?articles.view/articleNo/40871/title/The-Second-Coming-of-RNAi/

10. http://web.mit.edu/newsoffice/2013/cardiac-development-needs-more-than-protein-coding-genes-0124.html (long non-coding RNA molecules)

11. http://www.alzforum.org/news/research-news/new-role-micrornas-torpedoes-sink-neurons(microRNAs)

12. http://ghr.nlm.nih.gov/condition/rothmund-thomson-syndrome (mutation in human helicase gene)

13. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633371/ (mutation in mitochondrial helicase gene called TWINKLE)

14. http://sfari.org/news-and-opinion/news/2013/in-autism-related-disorders-rna-turns-out-to-be-key (RNA topoisomerase)

15. http://ghr.nlm.nih.gov/gene/TERC (dyskeratosis congenita - mutations in the TERC gene - the RNA component of telomerase)

16. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3853347/ (Top3beta is an RNA topoisomerase that works with Fragile X syndrome protein to promote synapse formation)

The following 3 articles discuss long non-coding RNAs - there are many examples in each article so you only need to talk about one example - not the whole article:

1. http://www.sciencedirect.com/science/article/pii/S2468054016300063 (mechanism of action and functional utility)

2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5084630/ (dysregulated expression in ovarian cancer)

3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736767/ (stem cells)

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Cystic Fibrosis (CF) is an autosomal recessive genetic disease that is characterized by the secretion of thick, abnormal mucous in the lungs. The mutated gene that leads these symptoms is the CF transmembrane conductance regulator (CFTR gene). The encoded protein is a chloride channel that moves chloride ions out of epithelial cells. In a homozygous individual, the lack of this chloride channel function in a mutant slows the flow of water into extracellular spaces. This lack of water export leads to the heavy mucus in the lungs of CF patients. Although children with CF would die in childhood, current treatments provide life expectancies into the 30âs.

CF is the most frequently inherited genetic disorder among American children. It affects 1 of every 2,500 children; 30,000 currently have the disease. Although its frequency is higher in European populations, it affects all human populations. Heterozygous carrier frequencies in the US are estimated to be 1 out of 29 Caucasians, 1 out of 46 Hispanics, 1 out of 61 African Americans and 1 out of 90 Asians. There are genetic screens for carriers of CF but they are not routinely performed despite this high frequency of carriers. At least all states in the US proscribe testing of newborns to identify children with CF early so that treatment can be started. Newborn tests for CF: http://www.cff.org/AboutCF/Testing/NewbornScreening/ScreeningforCF/ . If CF is such a common genetic disease, and such a simple Mendelian trait, why is genetic screening of parents not done more frequently? Is it just economic, a pain to do, or is it more complex such that the results of genetic testing are not just positive or negative?

Answer the following questions:
1. If two parents are heterozygous carriers of CF, show a pedigree with four children showing the incidence of carriers and afflicted children. If each unafflicted child (carrier or not) mates with another person, who has a 1 out of 30 chance of being a carrier of CF, what is the expected incidence CF disease in the third generation (frequency of CF in any one of grandchildren of the original couple)?

2. Pleiotropy of Cystic Fibrosis. Watch the two videos on the left at:

http://www.cftrscience.com/MOD-animation
or, if you can not view these, read the short NIH Genetics Home Reference for Cystic Fibrosis http://ghr.nlm.nih.gov/condition/cystic-fibrosis

Connect the description with one of the following videos, or related ones (there are many) you see:
video (10 minutes) of daily life of a child with Cystic Fibrosis http://www.youtube.com/watch?v=WUsuGKzdDg8
Lauraâs (20 year old) video diary of life with CF http://www.youtube.com/watch?v=Pgrf8qJXhpc&feature=related

In your own words, describe the range of CF phenotypes. List the other organs besides lungs that are affected and how does it affects those organs.

3.The DNA sequence of the CFTR gene is 170,000 base pairs in length and encodes the CFTR protein that is 1480 amino acids long. Open the accompanying text file (in Canvas/Files/Discussion folder) âCFTR gene DNA sequenceâ. You will see an alignment of the NIH human genome sequence of the CFTR gene â called âReferenceâ rather than âwild-typeâ- against a gene sequence containing a common mutation in CFTR. Look at the alignment and determine how the DNA sequence differs between them. What is the position number where they differ? How many and what nucleotides do they differ in? A â-â mark in one sequence in the alignment means that that base sequence is missing the corresponding bases in the other sequence. The sequence is a long one but the differences are in bolded bright red text. Matching sequence is marked with a | linking the two sequences. Look near the sequence AAATATCATC if you use FIND tool in Word.

In another file, you will an alignment of the reference translated into a protein sequence, compared to the mutant allele translated into protein sequence. The differences are again in red whereas the areas where the proteins match are in black. Look at the alignment. How do these two proteins differ? Again, find the position number and describe how they differ at that location. A â-â mark in the alignment means that amino acid is missing when compared to the other sequence.

4. Given that the CFTR gene can be analyzed for a mutation that causes CF, couples interested in being tested as carriers face several choices given the results.
What could be a consequence of a false positive result (couple is identified as carriers but they would not produce any children with symptoms)?

What could be a consequence of a false negative result (a test indicates the couple is not both carriers but they would produce some children with CF)?

5. The sensitivity of the test can vary with ethnic group. The following is a chart from the NCBI Genetic testing site. A sensitivity less than 100% would be likely to produce false negative results from an inability to determine that someone is carrier.

CF Carrier Test Sensitivity by Ethnic Group http://www.ncbi.nlm.nih.gov/projects/GeneTests/static/concepts/primer/ptscarr5.shtml
Ethnic Group ¹	Population Frequency of CF	Sensitivity of Carrier Detection ²
Caucasian	1 in 29	90%
Ashkenazi Jewish	1 in 29	97%
Native American	1 in 32	94%
Latino	1 in 46	57%
African-American	1 in 60	75%
Asian	1 in 90	30%

Why might different ethnic populations differ in the ability of the genetic test to identify carriers of CF?

PURPOSE: To examine the genetic, Biochemical, and Cell biological mechanisms of disease development.

In class we have focused on many of the fundamental principals and techniques of genetics and molecular biology. For this assignment I want you to see how these ideas are applied in studying genetic diseases. In addition, I want you to get insight into the experimental design and procedures that are used for expanding our understanding of genetics and how they are applied to studying and treating human genetic diseases.

The goal will be a final research paper that will be due by the last day of class (April 3, 2016). An outline of what is expected to be presented in the paper is listed below.

Paper Guidelines: Review of a Specific Disease

Components:

A. Clinical Features of the Disease

ï· Age of onset
ï· Male/ Female predominance
ï· Clinical symptoms and pathology ï· Population distribution

B. Genetics/ Transmission

ï· Spontaneous/ Inherited
ï· Inheritance distribution
ï· Identification/ isolation of gene/ loci ï· Mutation of gene

C. Molecular Pathology

ï· Effect of mutation on structure/ function of protein
ï· What/ how pathways are affected
ï· Effect on development/ function of cells, tissue, and organs ï· How gene(s) is related to clinical manifestations
ï· Animal models

Please note that all of the information may not be available or understood for your disease. I expect each of the sections to be addressed in the paper (A., B., & C.), however the subtopics (identified by bullet points) may not be understood. I would like the paper as complete as possible, however the final content will be determined by what is currently known about the disease.

You will accomplish this in three steps. A description of each step and the due date are presented below.

1) Choosing a disease.
Due Date: Sunday March 13, 2016

I want you to identify a human genetic disease and provide a very brief overview of the disease (Section A). I want you state how the disease is inherited (Autosomal dominant, Autosomal recessive,

etc) a brief description of the clinical features and the gene that is mutated (if known). This assignment should be no more than 2 pages and is worth 50 points towards your final grade.

2) Identify an experimental journal article. Due Date: Sunday March 20, 2016

I want you to identify a published research journal article that examines the genetic disease that you have chosen. The paper must have been published within the last two years. The paper must present experimental evidence that is relevant to your disease. I want you to submit the paper to me as well as write a one page summary of what was learned by the research study and how it applies to the understanding of the molecular pathology of the disease (Section C.). You can search for a journal article using the resources of the library. I would also like you to choose one experiment (figure) in the paper and describe what experimental techniques were used for that part of the study. This section should not exceed 1 page. This is worth 50 points towards your grade.

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BIO 2133 Lecture Notes - Lecture 10: Sticky And Blunt Ends, Horse Length, Foxp2

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