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Biology · Studypool

problem based learning question

Post ID: 3071735

Overview

please note that my gene is AKT

A. Each student must turn-in a report through SafeAssign by February 29, 2024 at 11:59pm.

B. Problem-based Learning Questions:

Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are among the most ancient small RNAs in all domains of life and are generated by the cleavage of tRNAs. Emerging studies have begun to reveal the versatile roles of tsRNAs in fundamental biological processes, including gene silencing, ribosome biogenesis, and epigenetic inheritance, which when altered result in disease ranging from cardiac hypertrophy to cancer. Your assignment is going to be about selecting a gene of interest and preparing a comprehensive report about its biological role and function, its interacting partners, its regulatory miRNAs, as well as its regulatory tsRNAs.

  1. Select a gene of interest and provide a literature review about its role, function and regulation. (2 points)
  2. Using the NCBI nucleotide database, find its full-length cDNA (please include the FASTA nucleotide sequence of the full-length cDNA in appendix A at the end of your report). (1 point)
  3. Identify the open reading frame by highlighting in bold red text the start and stop codons on the FASTA cDNA sequence included in the appendix, and calculate the predicted molecular weight of the protein produced by the open reading frame. (1 point)
  4. Propose an experiment that can allow you to identify its interacting partner proteins (a summary scheme of your experiment can be included in appendix B after the FASTA cDNA nucleotide sequence), and include positive and negative controls in your experimental design. (1 point)
  5. Generate a restriction map of your cDNA, and propose a cloning strategy of your cDNA (including the open reading frame) into a eukaryotic expression vector (a summary scheme of your cloning strategy along with a circular map of the cloning vector should be included in appendix C). (1 point)
  6. You wish to investigate the biological function of your gene of interest in a cancer cell line, where you discover that expression of your gene of interest is dysregulated. You check its mRNA and protein expression and you are able to confirm that misexpression of your gene of interest stems from the fact that it is post-transcriptional. Therefore, you decide to determine if there are miRNAs and or tsRNAs involved in its regulation.

A. Using the miRNA search engine (https://mirbase.org/), provide the list of potential miRNAs involved in the regulation of your gene of interest (the miRNA list should be included in appendix D), and highlight in bold green text the binding sites of the strongest miRNA binding sites on the cDNA provided in appendix A. In addition, provide a short overview of what miRNA are (1/2 – 1 page). (1 point)

B. Using the tsRNA search engine (https://rna.sysu.edu.cn/tsRFun/), provide the list of potential tsRNA involved in the regulation of your gene of interest (the tsRNA list should be included in appendix E), and highlight in bold blue text their binding sites on the cDNA provided in appendix A. In addition, provide a short overview of what tsRNA are (1/2 – 1 page). (1 point)

7. In the conclusion of your report, assume that the gene you selected is dysregulated - Discuss the best possible experiment you can use to

correct expression of your gene of interest in a cancer cell line. (1 point)

The report should be no more than 8 pages long excluding references, which should include a total of 8-10 research articles. Websites are not considered references, and should not be included in the reference list.

C. Format of the report (7 pages without cover page, references and appendices):

Cover page: Include your name, QU ID number, Semester, Year, and the following text with answers to each question:

  1. Please indicate (check either yes or no) on the cover page of your report whether AI/ChatGPT has been used to generate any section of the report?

Yes: No:

  1. If yes, which section(s)? – please specify in the document the page(s) and line(s) numbers.

Introduction (3 pages): You should give background information about the role, function and regulation of your gene of interest. (2 points)

Strategy for addressing the PBLQs listed above 2-5 (4 pages): You should address the questions as specified above. (6 points)

Conclusion (1 page): You should provide your concluding remarks and propose how you can correct expression of your gene of interest. (1 point)

References: You need to follow the format described below.

Authors names – if less than 7 authors, you need to write all of the names – if more than 7 authors you can give the full name of the first author and then use et al. Next, you need to provide the year, followed by the title of the research article, followed by the name of the journal, the volume number and page numbers. Below are two examples you should use to write your references.

  1. Karkhanis, V., Y.-J. Hu, R.A. Baiocchi, A.N. Imbalzano, S. Sif. 2011. Versatility of PRMT5-induced methylation in growth control and development. Trends Biochemical Sciences 36:633-641.

Appendices A-E: Should include in the order shown bleow (1 point)

      1. Appendix A (cDNA sequence with highlighted relevant information as specified in the instructions).
      2. Appendix B (Summary scheme of experiment about interacting proteins).
      3. Appendix C (Summary scheme of cloning strategy along with a circular map of the cloning vector).
      4. Appendix D (List of miRNAs).
      5. Appendix E (List of tsRNAs).
  • The report should be written with Arial font size: 11, spacing: 1.5. No pictures are allowed in the report.
  • Please do not forget to number your references and to cite the references in your report.
  • Please make every effort to make the report your own, and limit copy and paste to no more than 20% matching score.
  • Any report found to have more than 20% matching score will receive point deductions as described below:

Matching score between 20% to 30%: 1 pt deduction

Matching score between 30% to 40%: 1.5 pts deduction

Matching score between 40 to 50%: 2.5 pts deduction

Matching score above 50%: Zero score

  • You should submit a soft copy of your report with you name, ID number, but without cover page, references or appendices thru SafeAssign before the deadline (02/29/2024 at 11:59PM), and you should also hand in a hard copy with cover page, references and appendices on the same day.
  • There will be no extension granted for the PBLQ assignment, and any delay will result in a 10% deduction of the final score for each day you are late in submitting the PBLQ assignment.
  • Only the hard copy should include the answers as to whether AI/ChatGPT has been used to generate the report.
  • All sections of the assignment should be collated – no loose assignments will be accepted