Chromosome Maps

1.  WHAT CHROMOSOME DID YOU CHOOSE?

Chromosome 12

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

1600 genes and 130 million base pairs

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

PAH gene.

5.  STATE THE FUNCTION OF THE GENE YOU LISTED IN #42

The gene for phenylalanine hydroxylase (PAH) converts phenylalanine to tyrosine.

Introduction to Nucleotide BLAST

6.  WHAT IS THE SECOND SEQUENCE DESCRIPTION MATCH FOR YOUR QUERY SEQUENCE?  

Homo sapiens CFTR (CFTR) gene, partial cds

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

It functions as a chloride channel, controlling ions and water secretion and absorption in epithelial tissues.

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

Cystic fibrosis

9.  ON WHAT CHROMOSOME IS THE GENE LOCATED? 

Chromosome 7

10.  Return to the original nucleotide sequence alignment descriptions.  CHOOSE A SPECIES (STATE THE SCIENTIFIC NAME) OTHER THAN HOMO SAPIENS THAT ALSO HAS A 100% IDENTITY (Per. Ident) FOR THIS SEQUENCE? 

Pongo abelii

11.  WHAT IS THE COMMON NAME FOR THIS SPECIES?

Sumatran orangutan

12.  DOES IT SURPRISE YOU THAT THIS SPECIES ALSO HAS A 100% SIMILARITY IN IDENTITY?  WHY OR WHY NOT?

It does not as orangutans are also primates and share common ancestry with homo sapiens.

13. 

a.  WHAT IS THE GENUS AND SPECIES WITH THIS NUCLEOTIDE SEQUENCE? 

Sapajus apella

b.  WHAT IS THE COMMON NAME? 

Tufted capuchin

c.  ARE THERE ANY GAPS BETWEEN THE TWO SEQUENCES (THE ONE YOU ORIGINALLY SUBMITTED AND ONE THAT HAS LESS THAN 100% QUERY COVER)? 

Yes, the original has 0/120 and the other has 1/119.

14.  WHAT IS A GAP IN SEQUENCE ALIGNMENTS? 

Gaps in sequence alignments are used to account for mutations that occur from insertions or deletion in the sequence.

FOR EACH, STATE WHAT THE GENE IS (#15-18).  (Again, give the description of the gene or gene product, not the nucleotide sequence.)

15.  NM_145556

Mus musculus TAR DNA binding protein

16.  NM_013444
Homo sapiens ubiquilin 2 

17.  NM_001010850

Homo sapiens FUS RNA binding protein

18.  KJ174530

Homo sapiens superoxide dismutase-1 (SOD-1) gene

19.  WHAT DISEASE IS ASSOCIATED WITH MUTATIONS OF THE GENES REFERENCED IN #15-#18?  WHAT IS A “COMMON NAME” OF THE DISEASE? 

Amyotrophic lateral sclerosis (ALS), commonly called Lou Gehrig’s disease

20. WHAT IS GENBANK? 

GenBank is a database from the NIH which is a collection of all DNA sequences that are publicly available.

Introduction to Protein BLAST

21.  First, answer this question:  WHAT IS cDNA?\

cDNA is complementary DNA that was reverse transcribed from RNA.

22.  WHAT IS THE SEQUENCE MATCH?

Beta-globin

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

Yes

24.  IF YOU SAW DIFFERENCES, WHAT WERE THEY?

There is one gap where the query sequence is missing an ‘R’ where the subject has one. There is another where the query is missing an ‘S’ where the subject has one

25.  ARE THERE ANY GAPS IN THE SEQUENCE ALIGNMENT?

Yes, 1/806

26.  WHAT GENE ENCODES FOR THE POLYPEPTIDE YOU WERE ANALYZING?

Fibroblast growth factor receptor 3

27.  WHAT IS THE FUNCTION OF THIS PROTEIN? 

Interacts with fibroblast growth factors and influences mitogenesis and differentiation. It binds with the fibroblast growth hormone and plays a role in bone development and maintenance.

28.  WHAT HUMAN DISEASE IS CAUSED BY A MUTATION IN THIS GENE? 

Craniosynostosis and skeletal dysplasia.

29.  WHAT IS THE CONNECTION AMONG THE FOLLOWING:  NIH, NLM, NCBI, and HHS? 

The National Library of Medicine (NLM) and The National Center for Biotechnology Information (NCBI) are both a part of and overseen by the National Institutes of Health (NIH). The NIH falls under the U.S Department of Health and Human Services (HHS) and is overseen by them.

30.  WHAT WAS ONE POSITIVE THING AND ONE NEGATIVE THING YOU ENCOUNTERED WHILE DOING THIS ASSIGNMENT?

One positive I encountered while doing this assignment was getting to explore the genomic sequencing databases and learn a lot about all of the information available on the websites provided. One negative thing I encountered was navigating the information that went over my head in order to actually find what I was looking for.

1. When lactose is absent, the lacl produces a repressor which binds to the DNA of the operator, preventing gene expression.

2. When lactose is present, it acts as an inducer and binds to the repressor. Therefore, the repressor cannot bind to the operator. RNA polymerase now has access to the promoter and initiates the transcription of the three lactose-utilization genes.

3. When glucose is absent, CAP (activator) is active due to high levels of cAMP is present.

4. When glucose is absent, but lactose is present, cAMP levels are high therefore CAP is active and bound to the DNA of the promoter. CAP allows RNA Polymerase to bind to the promoter. The lac repressor is inactive and strong transcription can occur.

5. The lac operon is regulated during the transcriptional stage of gene expression.

            In an NBC News article titled” A quick test could protect against fatal chemo overdose, yet few doctors use it,” Arthur Allen tells the story of a 70-year-old woman who tragically died after an overdose of a chemotherapy drug. The drug she was prescribed is a pill called capecitabine which is chemically similar to the intravenous chemotherapy drug known as 5-FU or fluorouracil. While these drugs are used commonly in cancer treatment, those who are deficient in an enzyme that metabolizes the drugs can experience a slew of unpleasant symptoms or, in Carol Rosen’s case, die.

In his article, Allen states that the reason patients die from chemotherapy drugs is because the drugs stay in the body for hours instead of being quickly metabolized. In a review titled” Testing for Dihydropyrimidine Dehydrogenase Deficiency to Individualize 5-Fluorouracil Therapy,” the authors go into more detail about the way that the molecular mechanisms work for an overdose to happen. Genetic factors are a big contributor to the risk of developing severe toxicity to 5-FU. This was confirmed by researchers through advanced pedigree analyses (Diasio & Offer, 2022). The enzyme necessary for metabolizing the drugs is dihydropyrimidine dehydrogenase (DPD) and two deleterious variants were identified in the gene that encodes DPD. The genes segregate independently and have an autosomal codominant inheritance pattern (Diasio & Offer, 2022). Since then, many other variants have been identified after more clinical testing. In individuals with DPD deficiency, it causes the catabolic pathway to shift toward anabolism, potentially causing severe toxicity. However, not all of those with the deficiency will be at severe risk if they use the topical forms of the chemotherapy drugs. Arthur Allen did a good job of simplifying the way that the overdose is caused, but Diasio and Offer went more into depth about what happens at a cellular level. 

Due to the correlation between DPD deficiency and 5-FU toxicity, it is important to give doctors ways to identify DPD deficiency so that adjustments to the dosage of the medication can be made. There are both phenotypic tests and genotype-based tests that can be performed to test for DPD deficiency. Genotypic tests have higher accuracy and have been used frequently in European countries (Diasio & Offer, 2022). After her mother’s death, Carol Rosen’s daughter urged the hospital to implement genetic testing before prescribing fluoropyrimidine. The hospital quickly adopted a system to test patients and around 50 patients were detected with the deficiency within 10 months (Allen, 2024). Multiple different tests can be used; some check for eleven potentially dangerous variants, whereas others only screen for eight or four. An important factor in these genetic tests is that they are not one size fits all and different tests may be necessary for different ancestries. Most of the clinical studies have been conducted in Europe but different variants of the enzyme deficiency have been found in African American individuals that did not appear in European patients (Diasio & Offer, 2022). A man named Dr. Anil Kapoor died as a result of fluoropyrimidine poisoning. Kapoor was tested for four variants of the deleterious gene, but he carried a variant of the gene associated with South Asian descent that is not covered in the European-based genetic tests (Allen, 2024). While tests that screen for hundreds of variants are out there, they can be expensive, and getting results back can take longer. Some doctors have pushed back on mandatory testing, stating that the results can be unclear and lead to undertreatment of patients. Fluorouracil is not the only drug that has been prescribed to people who lack the enzyme to properly metabolize it. An anti-blood clotting medication called clopidogrel was marketed as safe for Native Hawaiians while more than 50% of them lack an important enzyme that processes clopidogrel.

References

Allen, A. (2022, March 27). A quick test could protect against fatal chemo overdose, yet few doctors use it. NBCNews.com. https://www.nbcnews.com/health/cancer/quick-test-protect-fatal-chemo-overdose-yet-cancer-doctors-use-rcna144664

Diasio, B. Offer, S. Testing for Dihydropyrimidine Dehydrogenase Deficiency to Individualize 5-Fluorouracil Therapy. MDPI; https://www.mdpi.com/2072-6694/14/13/3207 (2022).

 

            In the article titled,” Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing,” researchers aim to improve the diagnosis of rare genetic diseases by using transcriptome sequencing. By focusing on the patterns of gene activity, the researchers were able to diagnose previously unsolved cases. This type of sequencing can improve diagnostic rates by 7.5% to 36% depending on the tissue sampled and the patient’s condition. Rather than looking for specific genetic changes upfront, the methods used here searched for unusual patterns in gene activity that could point to underlying genetic issues. As a result, they were able to diagnose 12% of their cases overall, and 17% when excluding cases that were already answered by standard genetic testing. This approach looks specifically at how genes are being used to understand what may be going wrong at the genetic level. This method is distinct from typical genetic testing, which begins with looking at individual genetic abnormalities and attempts to match them with observed traits or phenotypes. Instead by focusing on gene activity patters, transcriptome sequencing can uncover issues that may be missed by standard testing. Such as noncoding genetic agents or small variations in DNA.

            In this study, the researchers used RNA sequencing as the first step in their process. They analyzed the gene activity patterns in patients’ blood and skin cells to guide their genetic analysis. While other studies have used this approach, this is the first study to apply this method to a wide range of conditions in patients. By analyzing the gene activity in both whole blood and fibroblast cells, which are commonly used in clinical research, they found that fibroblast cells in particular were more informative for a variety of conditions, especially those involving the nervous system. This is because they showed more consistent gene expression than whole blood, making them better for detecting relevant differences in gene expression. The researchers were also able to highlight the limitations of standard genetic testing such as exome sequencing and chromosomal microarray analysis. These tests have the potential to miss important genetic changes, particularly in the noncoding regions of DNA or when the changes are very small. The transcriptome-directed approach, which combines RNA sequencing with genetic analysis, proved to be more effective in finding these missed variations.

            Several cases proved to be very important. Including one in which RNA sequencing identified a genetic variant missed by other testing, leading to the diagnoses of Renpenning syndrome. In another case, RNA sequencing showed a deletion in CLTC gene, causing intellectual disability. In other cases, KANSL1 and NSD2 gene abnormalities were detected through RNA sequencing, leading to the diagnosis of Koolen-de Vries syndrome and NSD2-associated intellectual disability syndrome, respectively.

            In conclusion, this study shows thar analyzing gene activity patterns is effective in diagnosis rare Mendelian diseases that standard genetic testing may overlook. By focusing on how genes are being used, specifically in fibroblast cells, researchers can uncover genetic issues that traditional tests overlook. This approach could significantly improve the diagnostic rates for patients with challenging conditions. What was unique about this study is the diverse group of patients with various symptoms and age ranges. The researchers believe that integrating RNA sequencing into standard genetic testing will help diagnoses more patients, especially those who cannot be diagnoses through exome sequencing or chromosomal microarray analysis.

References

Murdock, D. et al. Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing. The Journal of Clinical Investigation; https://doi.org/10.1172/JCI141500 (2021).

Yu, L., Bostrom, C., Frazenburg, S. Bayer, T., Dagan, T., Reusch, T. Somatic genetic drift and multilevel selection in a clonal seagrass. Nat Ecol Evol; doi: 10.1038/s41559-020-1196-4 (2020).

            A primary article is a body of work that has original findings or analysis that is conducted by the authors of the article. Typically, primary articles go through the peer review process in which they undergo evaluation before publication to ensure their validity (“Primary vs. Secondary,” 2021). Primary articles typically follow a structured format. This includes sections such as methodology, results, discussion, and references (“Primary vs. Secondary,” 2021). They also typically include some form of data or another form of evidence to back their research findings.

            A review article is distinct from a primary article. It is a comprehensive analysis of existing research or literature (Balon, 2022). Review articles will usually cover a broad range of studies and findings to provide a holistic view of the subject matter. Rather than just restating what the existing research says, review articles identify the strengths and weaknesses of the studies (Balon, 2022). They may also examine conflicting evidence or inconsistencies within the literature. Overall, review articles help academics remain up to date on the latest developments in a particular field (Balon, 2022).

            The peer review process for articles is a system in place to attempt to put out accurate information (“Peer Review,” 2022). A researcher will submit their work and then it will be reviewed by experts in their field to ensure the information is reliable and accurate. There are a few things that the reviewers are specifically looking for. A few of these things are a fully described methodology, no obvious errors, and that the research describes supports the conclusions made by the researcher (“Peer Review,” 2022). While the peer review process is important to ensuring accuracy, the system is not fool proof and there is a chance for a bad article to make it through the process.

            The article titled Rapid and Sensitive Detection of SARS-CoV-2 Using Clustered Regularly Interspaced Short Palindromic Repeats is a primary article. The reason I came to that conclusion is because in the abstract section the authors state their previous experimental research findings and lay out the experiments they did for this particular study. The article titled Development of clustered regularly interspaced short palindromic repeats/CRISPR-associated technology for potential clinical applications is a review article. It is explicitly stated in the abstract that their study is a review of the recently reported application platforms.

References

Balon, Richard. “What Is a Review Article and What Are Its Purpose, Attributes, and Goal(s).” Karger Publishers, S. Karger AG, 2 May 2022, karger.com/pps/article/91/3/152/826565/What-Is-a-Review-Article-and-What-Are-Its-Purpose.

“Libguides: Tutorial: Scholarly Literature Types: Peer Review.” Peer Review – Tutorial: Scholarly Literature Types – LibGuides at Cornell University, 16 June 2021, guides.library.cornell.edu/c.php?g=293669&p=2004554.

“Libguides: Tutorial: Scholarly Literature Types: Primary vs. Secondary Articles.” Primary vs. Secondary Articles – Tutorial: Scholarly Literature Types – LibGuides at Cornell University, 16 June 2021, guides.library.cornell.edu/c.php?g=293669&p=2004549.

Something about me that some people find surprising because of where I’ve ended up is that I hated my biology class in High school. I didn’t even like doing the dissections, it was just smelly and boring for me at the time. Everything really changed when I took my introductory biology class in community college. I became completely enthralled with everything biology-related like how cells work and how plants and animals adapt to their environments. By the time I was in General Biology II, I was outside all of the time identifying different plants and their respective phyla. The teacher who taught me General Biology I and II loved to talk during class about different biomedical advancements and relate them back to the topics we were learning at the time. This is what really sparked my interest in biomedical science.

The more science classes I’ve taken, the more I’ve been reassured that I choose the best major for myself as I am constantly looking forward to learning more in my courses. For example, I am in a genetics class this semester and am so fascinated by how one small mutation in the genetic sequence can lead to devastating diseases. I am also incredibly interested in the immune system and how so many microscopic parts are constantly working together to keep us healthy. Biomedical science interests me particularly because of the way it is constantly changing, and research is always providing us with new and useful information. Like the development of Casgevy, a gene therapy to help people with sickle cell disease. Or the creation of the lifesaving drug, Narcan, which reverses the effects of opioid overdoses.

I also recognize the importance of the other sciences that link with biology such as chemistry and mathematics. I have found that General Chemistry I and II have been crucial for me to learn the molecular aspect of biology. Especially when learning about biological processes in which chemical reactions take place and can decide the outcome of that process. The main example of this that I can think of is the topic of cellular metabolism and the oxidation and reduction occurring in the Krebs Cycle. I also found my mathematics course, Calculus for Life Sciences, incredibly useful. Not only because it taught me the higher-level math needed for advanced science courses but also because it gave me some perspective on how Calculus can be used to solve for things like bacteria growth or the potential spread of disease.

            When I’m not in class or doing homework, most of my time is spent at my part-time jobs. I currently work as a nanny for two children as well as at a print shop near my school’s campus. I find working to be very fulfilling and while it can be hard to balance working, going to class, and getting my homework done, I always manage to make it work. When I do have time off, I love to spend time outdoors or go on trips. This past summer I took a day trip to Washington D.C to visit the Smithsonian National Museum of Natural History and it was so amazing to see all of the preserved specimens and replicas they had on display.

            My unexpected journey in biology has been a remarkable transformation. I feel as though biomedical science is the most fast-moving and transformative field of biology right now. The best part about it is a lot of the research coming out in this area is actively helping people and saving lives. This is the reason I am seeking a graduate degree in biomedical science with the intention of conducting research in the future. I am particularly interested in pharmaceutical research. One thing that I know for sure is that I do have the passion and enthusiasm to succeed in my graduate studies. I hope that it will be a stimulating and exciting opportunity for me to deepen my knowledge of not only biological science but also professional and personal skills I can take with me in my future career.