Understand how to assess gene chromosome maps, BLAST for both nucleotide and protein analysis, and ExPASy to translate cDNA.

1.  WHAT CHROMOSOME DID YOU CHOOSE?

Chromosome 6

2 & 3.  STATE THE NUMBER OF GENES AND BASE PAIRS ON THE CHROMOSOME YOU CHOSE.

~1900 genes

~170 base pairs

4.  LIST ONE GENE THAT IS LOCATED ON THIS CHROMOSOME.    

EPM2A

5.  STATE THE NORMAL FUNCTION OF THE GENE YOU LISTED IN #4. 

Making the protein laforin that is critical for neuron survival

6.  STATE THE POSSIBLE DISEASE(S) RELATED TO THIS GENE.  (This should be possible by clicking on the gene you stated in #4.)

Epilepsy

7.  WHAT IS GENBANK?

The NIH genetic sequence database containing all publicly available DNA sequences

8.  WHAT IS THE TOP SEQUENCE DESCRIPTION MATCH FOR YOUR QUERY SEQUENCE?  DO NOT CHOOSE THE PREDICTED SEQUENCE.  For this answer, you should give the description listed. 

Homo sapiens CF transmembrane conductance regulator (CFTR), RefSeqGene (LRG_663) on chromosome 7

9.  WHAT DOES THE ENCODED PROTEIN DO IN THE BODY? 

The encoded protein functions as a chloride channel, making it unique among members of this protein family, and controls ion and water secretion and absorption in epithelial tissues.

10.  FOR WHAT DISEASE IS A MUTATED FORM OF THIS GENE RESPONSIBLE? 

Mutations in this gene cause cystic fibrosis, the most common lethal genetic disorder in populations of Northern European descent.

11.  ON WHAT CHROMOSOME IS THE GENE LOCATED? 

Chromosome 7

12.  Scroll to the first described sequence that does not have 100% Query Cover. WHAT ORGANISM IS THE SOURCE OF THIS DNA?

Olive baboon

13.  HOW MANY GAPS OCCUR BETWEEN THE TWO SEQUENCES (THE ONE YOU SUBMITTED AND THE FIRST ONE THAT HAS < 100% QUERY COVER)? 

2/198

14.  WHAT IS A GAP IN SEQUENCE ALIGNMENTS?

When one or more amino acid residues have been deleted from the sequence  (1.)

15.  STATE WHAT THE FOLLOWING GENE IS:  NC_045512.2

Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome

16.  SCROLL DOWN THE LIST BELOW THIS SEQUENCE.  THERE ARE MANY SEQUENCES THAT LOOK SIMILAR.  CAN YOU DETECT WHAT IS DIFFERENT ABOUT THE OTHER SEQUENCES?

The only difference I see is the accession numbers and the query coverage percentage.

17.  WHAT IS cDNA?

Complementary DNA

18.  USING THE SAME PROGRAM YOU USED IN THE INTRODUCTION TO BLAST ABOVE, WHAT IS THE SEQUENCE MATCH?

Human beta hemoglobin

19.  HOW MANY 5’ TO 3’ FRAMES DID YOU OBTAIN? 

3

20.  BASED UPON THE LENGTH OF THE POLYPEPTIDE, WHICH FRAME(S) IS (ARE) MOST LIKELY THE CORRECT ONE?

Frame 3, ICF-HNCVH-QPQTDTMVHLTPEEKSAVTALWGKVNVDEVGGEALG

21.  DO YOU SEE ANY DIFFERENCES BETWEEN THE TWO AMINO ACID SEQUENCES? 

There is a difference at 380 and 783

22.  WHY WOULD DIFFERENCES BE IMPORTANT AND POSSIBLY CLINICALLY USEFUL?

Differences in amino acids in these sequences could mean a difference in proteins and mutations or even species.

23.  WHAT IS THE PROTEIN THAT YOU WERE ANALYZING?

Fibroblast growth factor receptor that is in both humans and chimpanzees

24-25.  REFLECT ON ONE THING YOU ALREADY KNEW, AND ONE THING THAT YOU LEARNED FROM DOING THIS ASSIGNMENT.

Something I already knew was how severe a malignant mutation can be in a single chromosome. Something I did not realize was truly how close humans and various ape/monkey species are. I knew we were close, but just never thought about how close.

1.  Sequence alignment: scores, gaps and gap penalties. https://proteinstructures.com/Sequence/Sequence/sequence-alignment.html

Draw and describe the regulation of the Lac Operon in the following situations.

With lactose absent, the repressor binds to the operator and blocks the RNA polymerase from binding to the promoter and prevents transcription.

When lactose is present, the lactose binds to the repressor, releasing it from the operator. The RNA polymerase is able to bind to the promoter and allow transcription to begin.

The catabolic activator protein (CAP) binds to the CAP site before the promoter. Cyclic AMP (cAMP) binds to the CAP to signal low glucose levels, or “hunger.” When glucose is absent, the cAMP levels are high and keeps the CAP active.

In the absence of glucose, the CAP site will be active. When lactose is present while glucose is absent, the active CAP allows the RNA polymerase to attach to the promoter and for the repressor to release from the operator to allow transcription. This regulation affects the transcription and translation phases and controls whether the lac Z, Y, and A genes will be expressed. This is a key function for glycolysis since glucose and lactose can
both be used as an energy source.

Write a Personal Statement.

Over the course of my time at Old Dominion University, I have had a lot of second thoughts about what I would like to do after getting my bachelor’s degree. I started out as a physics major because I fell in love with astronomy at Tidewater Community College. I planned to become an astrophysicist and transfer out of state to pursue a doctoral degree. While at ODU, I also planned to get a minor in computer science to aid me in the future.  Unfortunately, at least right now, that is not the path for me.  I could not hold my own in the coursework, so I decided to change majors.

            Biology and chemistry were other fields I enjoyed in STEM and played into my interests, so I decided biology would be a better fit for me in the long run. There are many fields I could get into with a bachelor’s in biology that I am interested in doing, such as dermatology, creating makeup, pharmacology, and genetic testing. All of these come from different obstacles I’ve dealt with in my life. Of course, the creation of makeup is a more frivolous endeavor, being a makeup artist, but pairing that with dermatology would allow me to find new formulas in cosmetics and skincare, and possibly start my own line of products.

             Pharmacology and genetic testing would also pair together as well as I’ve been fighting to find medications that work for me and I know others are equally tired of trial and error with medications. Dealing with chronic depression, anxiety, insomnia, ADHD, and chronic pain has been a large obstacle for me to overcome, especially in the last few years. I want to be able to not only help my own diagnostics and treatments but for others who can’t seem to find balance or relief. Being tested for which medications I can metabolize and which genes play a factor in pain tolerance has been a big help, but there’s still more information waiting to be found. I would genuinely love to help be a part of this type of research and development to make the tests more accurate and more accessible to people.

            Even though these are some great fields to enter, I still don’t have a plan. Granted, these areas of interest would benefit me and my own struggle, but is that something I really want to do? Do I want to pursue a graduate’s degree, or do I want to stick with the degree I already have? What do I want to do with my life?

            The answer is: I don’t know. I’ve never had a plan for my life; no dreams to chase, no goals to work towards. My teenage self screams through my subconscious to make a career in the music industry, whether it be production, management, music therapy, music journalism, or even an event photographer. I haven’t grown out of these fantasies of being lost in the world that shaped my life. With the threat Covid-19 places on the music industry, finding creative solutions to live events for musicians who rely on touring would be paramount.

            What I want to do with my life, my career, and my education is still in the wind. I don’t find that it’s necessarily a bad thing, it just means I have many open doors in front of me. I can move up the chain and enter a graduate program or I can start a second degree. I can even take what I have and run with it until I make a decision. I can settle. Being an older student has taught me that timeframes aren’t important. They don’t define my success in school nor in life. I still have time to decide what I really want to do and not pressure myself into a career that won’t give me a sense of accomplishment or purpose. Whatever choice I make, I’ll have ODU to turn to.

Write a summary of a genetics related coronavirus article from a popular news source.

“Does Covid-19 Risk Depend On Blood Type? More Research Points To Yes”

            Forbes Magazine posted an article on their website describing recent findings between COVID-19 and genetics. The first are studies posted in Blood Advances[2,5] which suggests people with type O blood are less likely to test positive for COVID-19 and less likely to have severe symptoms. The Danish study[2] noted people with type O blood were 13% less likely to test positive and people with blood types A and AB are associated with increased risk of severe symptoms. The study compared data from 473,000 tests for COVID-19 from a 2.2 million person control group. Having such an ethnically homogenous country makes for a great control group when health care is public and data is accessible to the researchers. Blood types will vary considerably due to different ethnic groups and countries, and a control population can be hard to maintain. They found that patients with blood type A or AB were more likely to require ventilation and kidney dialysis and had longer stays in intensive care units.

Genetic testing company 23andMe[1] released data on a study with more than 750,000 people and found that people with type O blood were between 9 to 18% less likely to test positive. 23andMe has access to 12 million already sequenced people with a large test pool consenting to take part in the study. They’ve found that a gene on chromosome 3 has a specific variant that coincides with blood type. A study in Spain and Italy[4] found that those with type A blood were at increased risk for respiratory failure and type O had a “protective effect.[3]” with 35% lower risk. The study also found that many of the cases had a similar variant on the gene that codes for blood type. Studies done by Harvard Medical School[6] and Columbia Presbyterian Hospital in New York did not find an independently associated link between blood type, although they did find that people with blood type B and AB were more likely to test positive for the virus. They also found symptomatic people with blood type O were less likely to test positive.  

Though the findings are still being discussed, these studies have brought in new data about the nature of the virus and it infects cells. The link between blood type and the possibility of testing positive for COVID-19 still needs to be studied to use this information in a meaningful way. While correlation does not equal causation, the data is consistent over the span of these studies mentioned in the article. However, as stated, “[..] ABO blood typing still shouldn’t be considered predictive in patients who get Covid-19.”

Works Cited

1. 23andMe finds evidence that blood type plays a role in COVID-19. 23andMe Blog. Published June 8, 2020. Accessed October 27, 2020. https://blog.23andme.com/23andme-research/blood-type-and-covid-19/

2. Barnkob MB, Pottegård A, Støvring H, et al. Reduced prevalence of SARS-CoV-2 infection in ABO blood group O. Blood Adv. 2020;4(20):4990-4993. doi:10.1182/bloodadvances.2020002657

3. Gajewski M. Does covid-19 risk depend on blood type? More research points to yes. Forbes. Accessed October 27, 2020. https://www.forbes.com/sites/mishagajewski/2020/10/14/does-covid-19-risk-depend-on-blood-type-more-research-says-yes/

4. Group TSC-19 G. Genomewide association study of severe covid-19 with respiratory failure. New England Journal of Medicine. Published online June 17, 2020. doi:10.1056/NEJMoa2020283

5. Hoiland, RL. Fergusson, NA. Mitra, AR. Griesdale, DEG. Devine, DV. Stukas, S. Cooper, J. Thiara, S. Foster, D. Chen, LYC. Lee, AYY. Conway, E. Wellington, CL. Sekhon, MS. The association of ABO blood group with indices of disease severity and multiorgan dysfunction in COVID-19. Blood Adv. 2020;4(20):4981-4989. doi:10.1182/bloodadvances.2020002623

6. Latz CA, DeCarlo C, Boitano L, et al. Blood type and outcomes in patients with COVID-19. Ann Hematol. 2020;99(9):2113-2118. doi:10.1007/s00277-020-04169-1