Genetics Lab Notebook (ELN 7)
Instructions
- Lab notebooks are completed digitally using the Crowdmark platform. You will submit your lab notebook before the end of the lab time.
- The amount of work expected for these lab notebooks is reflective of the time available! Labs run for 3 hours – we have therefore designed the lab activities and the lab notebook prompts in such a way that they will be able to be completed within the 3 hour window of provided time.
- It is strongly advised that you read the lab outline BEFORE the lab starts to ensure you will be prepared to manage your time effectively and complete all protocols during the lab.
- This lab notebook will be completed as PAIRS
- This lab notebook (and completion of the lab) is pass/fail
- Assignment Deadlines
- Policies on Submitting Work, Absences and Missed Work
- Specifications guidelines for Electronic Lab Notebooks
Pre-lab
- What is the purpose of today’s lab activity?
Lab Part 1 Questions
Reminder: Provide a web link for any acquired information instead of citation and reference list. This is to save you time in completing the ELN.
1A. What is the name of the gene you are studying?
1B. What is the function of your gene (biochemical activity of the protein in the model organism?) Be sure to cite a resource you used to answer this question.
1C. Is the gene pro-longevity or anti-longevity? Provide the citation for one paper that describes this effect.
1D. What is the typical lifespan of this organism? Why is it useful to study aging in this system?
Lab Part 2 Questions
2A. Which chromosome is your gene of interest encoded on?
2B. What is the base range of the gene (i.e., where exactly is it located)?
2C. Which strand is your gene of interest encoded on?
2D. What is/are the gene name(s) for the genes upstream and downstream of your gene? Be sure to indicate which is upstream and which is downstream.
2E. What is the total number of chromosomes for your model organism (you may have to find this information from another source)?
2F. Take a screen capture of your gene of interest as depicted in the Genomic Context section (see example in figure 4) and upload it to Crowdmark.
Lab Part 3 Questions
3A. List the protein sequence for your candidate gene plus the four other homologous protein sequences for each organism in FASTA format. Upload this to Crowdmark as a PDF.
3B. We are asking you to conduct a BLASTp search for this tutorial, but there is also an option to perform BLASTn search. BLASTn 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.
3C. Which homolog was most similar to your organism’s gene of interest?
Lab Part Part 4 Questions
4A. Take a screen capture of your final alignment. If the alignment spans more than one screen/page, capture a region of the alignment that shows the most overlap between all of the sequences you provided.
Note: You must include a minimum of 3 sequences for Clustal Omega to construct an alignment. Things to consider when constructing your alignment:
- Are there regions of the protein sequences with strong alignment? Are there regions that seem quite different among the sequences?
- You may want to rerun alignments with fewer sequences, clustering those that are most similar in smaller searches.
4B. 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?
4C. 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? Hint: this was discussed in lecture.