Kelly McDonell — HTGAA Spring 2026
Hey! I’m a second year undergraduate student at Carleton University in Ottawa, Ontario. I’m currently studying Health Sciences and I would love to learn more about bioengineering, specifically about how it can be worked into our built environment.
Contact info
Homework
Week 1:
1.Biofabrication in architecture; involves the use of living organisms in architecture and design for various purposes. This can include design purposes, fighting against climate change, etc. 2. Ethical considerations: incorporating new technology into new policies requires extensive studying to ensure safety and benefits for all. An important policy could include limiting certain organisms to certain regions, as there is a risk of introducing invasive or unwanted species in new areas. This might include regulations on certain biomaterials. 3. I) Globalisation has put an emphasis on sameness across different regions, cultures, countries, especially in terms of architecture and design. New buildings are finished quickly and often face criticism for cheap materials that do not suit the climate they are built for, leaving residents with the costs of the flaws. Biofabricated materials place emphasis on biological materials made from region specific organisms that are eco-friendly, design friendly, and cost friendly. II) Starts with science - researchers, academics, etc. that propose the materials. This must be reviewed by a government agency (Health Canada) to ensure safeness. Policies can be drafted at the municipal, provincial, and federal levels to ensure the products are used safely and properly. Government funded housing or developers with an interest in eco-friendly design would be responsible for purchasing and using (with the help of civil engineers, architects, city planners, etc.) the materials. Finally, homeowners could review the results. III) There are many risks with all building materials - it may be difficult to assess longevity or reliance of eco-friendly materials in buildings, especially in harsh climates. IV) The project may fail if costs exceed the normal building material expenditures. Unsuccessful advertising of the product or failure to promote the product may also cause the project to fail. 4. Table: Enhance biosecuirty: -preventing accidents (option1) -helping respond (option 2) Foster lab safety -preventing incident(option3) -helping respond(option1 Other considerations -minimising costs/burdens (option 1) -feasibility (option 1) -not impede research (option 2)) -promote constructuve applications (option 1) 5. I would prioritise the regulation of species used in different areas. Introducing potentially harmful species may do more harm than good and would destroy the reputation of the product and any actors involved should the environment suffer because of it. Additionally, as this project hopes to introduce a cheaper and better material onto the market there may need to be some form of protection for the company in its early stages or some form of appearance that would support other manufacturing companies.
Homework questions Prof. Jacobson:
- The error rate of polymerase is roughly 1:10^6 compared to a human genome of about 3.2Gbp. There are various methods of proofreading available in order to reduce the rate of mutations during DNA replication (other polymerases for example).
- Four nucleotides in DNA can arrange in 64 ways to produce three codon sequences (4^3=64) for an average protein length of 1036bp. The code is degenerative and many codons can code for the same protein, which may be why so many codes don’t work to code for a protein of interest. Dr. LeProust,
- Oligo synthesis can be done via the phosphonamidite DNA synthesis cycle for DNA.
- The yield of phosphonamidite DNA Synthesis cycle decreases rapidly as more bases are coupled. High error rates may also limit the length of the chain that is able to be produced.
- Similar to a 200nt strand, a 200obp (as opposed to base additions which the cycle is used for) would result in a very low yield due to its long length. The number of mutations would likely destroy the strand anyway. George Church
- The ten essential amino acids for all animals include: lysine, isoleucine, histidine, leucine, methionine, threonine, phenylalanine, tryptophan, arginine, and valine. “Lysine Contingency” refers to a theoretical experiment where the ability to make lysine was removed from dinosaurs in Jurassic Park so that they would be forced to eat lysine rich plants. However, essential amino acids are essential because they cannot be made by the animal. Instead, they must be taken in from the diet (lysine rich foods). It doesn’t really make much sense to ‘remove’ the lysine making ability from the dinosaurs as they wouldn’t have this ability anyway.
Homework Week 2:
PART I: Photos 1, 2
PART III UNIPROT
3.1 Haemoglobin (alpha subunit)
Protein sequence
MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
3.2
Nucleotide sequence
GTGCTGAGCCCGGCGGATAAAACCAACGTGAAAGCGGCGTGGGGCAAAGTGGGCGCGCATGCGGGCGAATATGGCGCGGAAGCGCTGGAACGCATGTTTCTGAGCTTTCCGACCACCAAAACCTATTTTCCGCATTTTGATCTGAGCCATGGCAGCGCGCAGGTGAAAGGCCATGGCAAAAAAGTGGCGGATGCGCTGACCAACGCGGTGGCGCATGTGGATGATATGCCGAACGCGCTGAGCGCGCTGAGCGATCTGCATGCGCATAAACTGCGCGTGGATCCGGTGAACTTTAAACTGCTGAGCCATTGCCTGCTGGTGACCCTGGCGGCGCATCTGCCGGCGGAATTTACCCCGGCGGTGCATGCGAGCCTGGATAAATTTCTGGCGAGCGTGAGCACCGTGCTGACCAGCAAATATCGC
3.3 Codon optimisation
atggtnytnwsnccngcngayaaracnaaygtnaargcngcntggggnaargtnggngcn caygcnggngartayggngcngargcnytngarmgnatgttyytnwsnttyccnacnacn aaracntayttyccncayttygayytnwsncayggnwsngcncargtnaarggncayggn aaraargtngcngaygcnytnacnaaygcngtngcncaygtngaygayatgccnaaygcn ytnwsngcnytnwsngayytncaygcncayaarytnmgngtngayccngtnaayttyaar ytnytnwsncaytgyytnytngtnacnytngcngcncayytnccngcngarttyacnccn gcngtncaygcnwsnytngayaarttyytngcnwsngtnwsnacngtnytnacnwsnaar taymgn
+PHOTO 3
3.4
As this protein is found in humans (human haemoglobin), the DNA sequence can be found in the human genome, which is then transcribed and translated in order to create the protein (cell dependent method). As this is an essential component in blood, many other organisms can produce it (or similar variations). For example, mice and other rodents would be capable of producing haemoglobin.
PART IV
PHOTOS 4, 5
PART V
5.1
- I think it would be really interesting to sequence any sort of viral DNA. Viruses can present a huge threat to human health as well as various other species, though they can also help us understand a lot of our own genome, as a lot of human DNA is thought to be remnants of past viral infections. Though viruses have relatively small genomes, they have many interesting characteristics (infectious agents/proteins/mutations) that would be worth sequencing.
- i) Given the size of the virus, I would use second generation (NGS) sequencing for viral DNA as it would probably work best for the less complex genome but still produce longer reads if a specific protein or mutation needed to be sequenced. ii)/iii) NGS sequencing involves extracted the DNA (or RNA) through purifying the nucleic acids (this is done usually through cell lysis); secondly, fragmentation and addition of adaptors is done to prepare the DNA/RNA for sequencing; the nucleic acids are sequenced using flow cells; finally, the results are obtained, and DNA can be compared/examined/etc. iv)NGS sequencing would allow a researcher to analyse certain mutations or alterations in a viral cell that may lead to new, infectious proteins or other agents that could be detrimental for human health or helpful in other areas based on the DNA/RNA analysed.
5.2
- Building off the last example, I think I woule like to continue with synthesizing viral proteins from DNA/RNA in order to watch for mutations and look at their effects in humans. This would probably involve screening the whole genome of a virus and maybe using differently mutated viruses to see how proteins might change. Although this project would analyse the whole genome, there would likely be a focus on particular genes if I were focusing on a health care aspect (looking at proteins such as reverse transcriptase in HIV, for example).
- It would be possible to use third- or second-generation sequencing as I would be looking for longer reads of DNA/RNA (the whole genome). I would consider using phosphonamidite solid phase synthesis in order to build oligonucleotides for the DNA/RNA strand though this might be difficult as it is limited to only a few hundred base pairs without high error. Microarray chips are another option though they are associated with higher costs and slightly less control over specific details.
5.3
- I would like to edit the genome of certain flora or fauna in order to combat their rising chance of death from climate change, invasive species, or other related issues. I think that species that are crucial for the biodiversity of a habit and that are failing to survive high heat, loss of habitat, acidification, etc. should have some form of intervention that can help with adaption. This would ensure that they are not lost and the role that they play is not lost as well.
- I think using gene editing tools such as CRISPR would likely benefit this goal the most. Using a cas9 and guide RNA molecule that has been designed for a specific sequence, specific parts of the DNA can be modified (insertions, deletions, etc.). CRISPR might be limited by errors such as recognition – if the intended target is not recognised then unwanted modifications may occur.