1. Thanks for volunteering for our study. Your chart says you have problems eating, facial weakness and overall poor muscle tone. Looks like your mother had the same symptoms. Your diagnosis is nemaline myopathy. I am sad to tell you that no known treatment exists, but my researchers and I are working hard to find a treatment. You can find information on this genetic disorder in a website called OMIM. http://www.OMIM.org which says you might have a mutation in your Actin alpha 1 gene. We won’t experiment on you! It is much faster, kinder and less expensive to use a plant model. Thanks for your help, Doctor!

2. Lesson 1: Using bioinformatics to find human disease-related genes in plants After Part A you will demonstrate your ability to: Use the bioinformatics NCBI Gene and BLASTn tools to search for a human gene of interest in plants. Evaluate the significance of your search results.

3. What I want to know is??? Find and analyze gene and protein data to answer my question. Which biological processes are involved? What do I know about those biological processes? Which genes or proteins are involved in the biological processes? My new or revised question ???

4. http://www.bbc.co.uk/progra mmes/p00lx6cl http://www.bbc.co.uk/progra mmes/p00lx6cl https://www.youtube.com/w atch?v=eDA8rmUP5ZM https://www.youtube.com/w atch?v=eDA8rmUP5ZM My starting question ??? http://aboutlifting.com/music-helps-plants- grow-and-will-help-muscles-grow/

5. Which biological processes are closely involved? photosynthesis reproduction growth development death energy use movement response to environment defense

6. Your textbook, open access textbooks, videos and databases can be helpful.. https://www.boundless.com/biology/

7. A general search engine will give you too many hits for the question below!

8. 108 results Even a broad scientific database may provide too many unrelated hits! Why are there SO MANY results?

9. “BIG DATA” Biologists are increasingly able to quickly generate enormous amounts of data but their data analysis may take weeks or even years. https://en.wikipedia.org/wiki/List_of_RNAs

10. What scientific approach finds better information? Bioinformatics is an interdisciplinary approach which uses computational, mathematical, and engineering methods to analyze and make discoveries from enormous data sets.

11. A few examples of how bioinformatics is used…. UseQuestions addressed: Basic researchHow is DNA organized in chromosomes? Are genes related to other genes? Given sequence data, how do we find a gene? How are genes expressed in response to the environment? BiomedicineWill this drug work on this patient? Can we cure genetic diseases? Which genetic variations are associated with heart disease? Which pathogen proteins are best for vaccine development? MicrobiologyCan microbes remove pollution? Can microbes decrease the impact of climate change? Where did a disease originate? AgricultureCan drought resistant plants be identified, bred or engineered? Can insect resistant plants improve food supplies? Can more healthful food sources be developed? UseQuestions addressed: Basic researchHow is DNA organized in chromosomes? Are genes related to other genes? Given sequence data, how do we find a gene? How are genes expressed in response to the environment? BiomedicineWill this drug work on this patient? Can we cure genetic diseases? Which genetic variations are associated with heart disease? Which pathogen proteins are best for vaccine development? MicrobiologyCan microbes remove pollution? Can microbes decrease the impact of climate change? Where did a disease originate? AgricultureCan drought resistant plants be identified, bred or engineered? Can insect resistant plants improve food supplies? Can more healthful food sources be developed?

12. Scientists use bioinformatics portals that support their particular research.

13. To address the problem of BIG DATA, scientists can share data and analysis with other scientists. This speeds analysis and adds expertise. Scientists can share their data in research- specific portals. These research-specific portals usually have customized bioinformatics tools.

14. National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/gene Araport https://www.araport.org/ An example of increasingly more specific research-centered portals

15. How can I search on the NCBI portal to find names of human muscle genes? Use http://www.ncbi.nlm.nih.gov/ and enter information shown, use the pull- down menu to select Gene. (Note: Other genome browsers will also let your search for genes and proteins of interest.)http://www.ncbi.nlm.nih.gov/

16. Would a similar plant gene have a similar function?

17. Actin subunits self-assemble to form filaments which have a role in cell structure. Check the “Inner Life of the Cell” video. https://www.youtube.com/watch?v=FzcTgrxMzZk https://www.youtube.com/watch?v=FzcTgrxMzZk https://www.youtube.com /watch?v=VVgXDW_8O4U is a video showing polymerization of G-actin, a protein similar to Alpha Actin.

18. Click on FASTA to obtain the human ACTA1 gene sequence. If it is reasonable that plants might have a gene similar to human ACTA1, you will need to find the ACTA1 gene sequence.

19. Copy, then paste the ACTA1 gene sequence to a new Word document or clipboard—we will use this to look for an Arabidopsis thaliana version of this gene. Save the Word document as “human ACTA1 DNA sequence”.

20. Which plant should I use to find a a plant version of human ACTA1 actin alpha 1 gene? https://www.youtube.com /watch?v=foHiKrlY9Qc https://www.youtube.com /watch?v=foHiKrlY9Qc explains why scientists use a model plant.

21. I want to search for a version of the human ACTA1 gene in Arabidopsis thaliana. What bioinformatics tool could I use?

23. BLAST Types BLASTn compares 2 or more DNA sequences BLASTp compares 2 or more protein sequences BLASTX reads a DNA sequence in the 6 possible reading frames then compares it to a protein sequence database tBLASTX compares 2 or more DNA sequence translated in 6 reading frames

25. http://www.ncbi.nlm.nih.gov / There are several ways to access NCBI BLAST. Start at the URL and page, then select BLAST. http://blast.ncbi.nlm.nih.gov/Blast.cgi Or just go to the BLAST page URL below. Select nucleotide blast If I have a known DNA sequence, how can I use BLASTn to look for an unknown similar sequence?

26. Click on FASTA to obtain the human ACTA1 gene sequence. You found a human gene to compare…

27. And you’ve already copied and pasted the ACTA1 gene sequence to a Word document or clipboard—we will use this to look for an Arabidopsis thaliana version of this gene.

28. Steps to use Blastn Paste in your copied ACTA1 sequence Enter the name of the organism in which we are looking for the same gene (Arabidopsis thaliana) Select the program –use “Somewhat similar sequences” for the broadest search #4 push blast button Check “show results” in a new window, then click on BLAST

29. The BLAST report will usually provide many alignments. How do you pick the alignment most similar to the human gene?

30. What is an alignment? What might it mean if two or more genes align? What values tell us that the alignment is meaningful?

31. What information is provided in an NCBI BLASTn report? Each “track” represents a sequence that the BLASTn tool discovered in the database that is similar to your input sequence. The colored sections in each track are blocks of DNA which align with varying similarity (score), shown by the colored bar above. The black lines connecting the colored blocks are poorly aligned sequences (less than 40% alignment). By moving the mouse over a block, you can see the definition and score for that sequence result (also called “hit”). By clicking on a colored box, you will jump to the actual DNA alignment farther down the page.

32. What BLAST information tells you whether genes are aligned by chance or by similarity? Go to https://www.youtube.com/watc h?v=mvjHYMgJDTQ https://www.youtube.com/watc h?v=mvjHYMgJDTQ For an NCBI webinar on BLAST. Watch and answer questions 11- 12 (through about 8:30 into the video).

33. http://homepages.ulb.ac.be/~dgonze/TEACHING/stat_scor es.pdf http://ocw.mit.edu/courses/ biology/7-91j-foundations- of-computational-and- systems-biology-spring- 2014/video- lectures/lecture-2-local- alignment-blast-and- statistics/ is a video explaining alignment scores. Watch starting at 31:55 until about 45 min.

34. http://homepages.ulb.ac.be/~dgonze/TEACHING/sta t_scores.pdf

35. http://homepages.ulb.ac.be/~dgonze/TEACHI NG/stat_scores.pdf

36. http://homepages.ulb.ac.be/~dgonze/TEACHI NG/stat_scores.pdf

37. Results are arranged from smallest E-value to lowest. Compare the E- value, Query cover and % identity for the checked “hits”. Which GENE is most similar to the human ACTA1 sequence query? Click on the accession number for more information about a sequence.

38. “Alignments” provides details about nucleotide locations, matches, gaps or mismatches. Access more info about the sequence by clicking on t e sequence ID

39. We used the BLASTn report to find that the Arabidopsis thaliana gene, ACT7, had the maximum similarity with the human ACT7 gene. Click on Graphics to see information about the gene, its coding sequences and the resulting mRNA.

40. Summarize steps used to find a version of the human ACTA1 gene in Arabidopsis thaliana. Tell what information you used to assess whether the discovered version was a meaningful find.

41. Mouse over the colored tracks to identify them and compare them.

42. 1.Pick one human gene which you think is highly conserved between plants and animals. 2.Follow the procedure you just learned to see if a similar Arabidopsis version exists. 3.Record your info on the scorecard. 4.Repeat for a gene that you predict is unique to humans.

43. What information so far indicates whether or not plants have animal muscle genes? What additional information might you need to be more certain whether or not plants have animal muscle genes?

44. Gene Discovery Scorecard Human Gene Name Human Gene ID Human Gene Function Arabid opsis Gene Name Arabid opsis Gene ID Arabidopsis Gene Function Out-come evidence : Score, E-value, Similar Function, Predic- tion? Actin alpha 1 ACTA1Cytoskele tal structure ACT7Actin 7Cytoskeletal structure E value was 1e-80, not random, both have similar functions…. Yes