Nematode (roundworm) age-1
Lab Part 1 Questions (/15)
1A. What is the name of the gene you are studying? (/1)
1B. What is the function of your gene (biochemical activity of the protein in the model organism? (/2)
1C. What mutant phenotypes occur in mutants of your gene? i.e. when the gene is non- functional or there is no protein product, what is the effect at the cellular and organismal level (if known). (/3)
1D. Is the gene pro- or anti-longevity? Provide the citation for one paper that describes this effect (access to this information is available if you selected “More Details” in the GenAge database). (/3)
1E. What is the scientific name for your model organism? (/1)
1F. What are some characteristics of this organism, including its lifespan? (/2)
1G. Why is it useful to study aging in this system? (/3)
Lab Part 2 Questions (/7.5)
2A. Which chromosome is your gene of interest encoded on? (/0.5)
2B. What is the base range of the gene (i.e. where exactly is it located? (/0.5)
2C. Which strand is your gene of interest encoded on? (/0.5)
2D. What is/are the gene name(s) and function(s) for the genes upstream and downstream of your gene? (/1)
2E. What is the total number of chromosomes for your model organism? (You may have to find this information from another source). (/0.5)
2F. Prepare figure 1 by taking a screen capture of your gene of interest as depicted in the Genome Context section (see example in figure 5). When preparing the figure caption, include enough relevant information for understanding the figure. (/3)
2G. The Bibliography section provides a list of research papers involving your gene of interest. Provide a citation (APA format) for the first paper listed in this section. Click HERE to for help with APA formatting (/1.5)
Lab Part 3 Questions (/13)
3A. List the protein sequence for your candidate gene plus the five other homologous protein sequences for each organism into a single text file in FASTA format (/6)
3B. We are asking you to conduct a BLAST-p search for this tutorial, but there is also an option to perform BLAST-n search. BLAST-n investigates DNA sequences (i.e. genes). What differences would you expect to see in terms of sequence conservation between DNA and protein sequences? (HINT: think about protein translation) (/2)
3C. Each BLAST result is given a series of scores: E-value, Score, and Percent Identity (%). Define each term (/1.5)
3D. Prepare Table I (/3), reporting the E-value, Score, and Percent Identity (%) for each of the five other homologous protein sequences. When preparing the table caption, include relevant information for understanding the table.
3E. Which homolog was most similar to your organism’s gene of interest? (/0.5)
Lab Part Part 4 Questions (/14)
4A. Are there regions of the protein sequences with strong alignment? Are there regions that seem quite different among the sequences? (/2)
- You may want to rerun alignments with fewer sequences, clustering those that are most similar in smaller searches.
- Note: You must include a minimum of 3 sequences for Clustal Omega to construct an alignment.
4B. After re-running the alignment with additional or fewer sequences, prepare a figure showing your final alignment. (/6)
4C. Are there gaps in alignment (i.e. where one or more sequences are not aligned with others)? Do these gaps seem to group by organism? In other words, are there sequences that seem to substantially diverge, either at the beginning or end of the sequence, that seem to be shared by organisms more closely related evolutionarily? (/3)
4D. Are there regions with substantial sequence identity (same exact amino acids), with sequence similarity (same TYPE of amino acid: acidic, neutral, etc.)? What might these blocks of similarity represent? (/3)
