Writing Assignment #1

            A primary research article is an article in which an author or authors presents original research based on an original experiment. These articles contain original scientific reports of new research findings. A primary research article must contain the following sections: introduction, methods, results, discussion, and references.

            A review article, also known as a secondary source, are articles which organize and critically analyze the research of others on a topic. These articles are based on primary research articles but can be easier to read then the primary source article.

            The scientific peer review process is an effort by scientists and other scholars to publish accurate information. The process works by a researcher submitting an article, and then that article is reviewed by another scholar in the same field to make sure the article is sound and accurate.

            Huntington’s Disease Mechanisms is the review article and Permanent Inactivation of Huntington’s Disease mutation is the primary article. Permanent Inactivation of Huntington’s Disease mutation is the primary article because it is a scientific report of research findings based on an original experiment. Huntington’s Disease Mechanisms is a review article because it summarizes research findings from multiple reports and experiments, and puts in an easy to read order for the layman.

Writing Assignment #2

            I am a marine biology major (naval leadership minor) here at Old Dominion University. As a marine biology major, I want to study marine arthropods, specifically decapods that are found in the polar waters of our planet. One of the main reasons I chose this focus on marine biology is because of where I grew up. I was raised in San Francisco, and while the waters there are cold, but aren’t artic cold, they are home to some marine arthropods that have adapted to the colder waters in the northern part of the state. One of these is the horseshoe crab, which I grew up with seeing their molts all year long on the beaches as well as fishing them up from the local waters.

            The citation I have listed a research article about how the CRP protein has evolved humans and compares it to that of invertebrates. The horseshoe crab makes a good candidate for this research because unlike most animals (to include humans) that only have one type of CRP protein, the horseshoe crab can have up to three types of CRP protein depending on the species. The CRP proteins in horseshoe crabs are also different than the CRP protein found in humans, which this article goes into the differences and how understanding the CRP proteins in invertebrates can be the keep to unlocking the evolution of the CRP protein in humans.

Pathak, A., Alock, A. Evolution of C-Reactive Protein. Fimmu; http://dx.doi.org/10.339/fimmu.2019.00943.

Writing Assignment #3

            The article that I chose goes over research into sequencing the genomes of specific shark species (mainly carpet sharks such as the whale and bamboo shark).  This research focuses on trying to sequence complete genomes of these sharks. Once sequenced, they then can compare the genomes to that of other vertebrates to try and figure out how genes may have evolved. Carpet sharks have the potential to contain genomes of early vertebrates as they have been around since the Early Jurassic. The carpet shark family itself has over 40 species of sharks, ranging from the tiny bamboo sharks to the largest living (whale) shark and can be found in all the tropical and temperate waters on the planet.

            This research mainly focuses on three members of the carpet shark family. These are the brown banded bamboo shark, whale shark, and cloudy catshark. These three carpet sharks are closely related to each other and are relatives on the Chondrichthyes family tree. The research focuses on the data pulled from the sequencing of the genomes of these three-shark family. That data is then taken and then compared to the sequenced genomes of bone fish (Osteichthyes)^₁.

References

1. Hara, Y. et al. Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates. Nature; https://doi.org/10.1038/s41559-018-0673-5 (2018)

Writing Assignment 4

The article that I chose from the Washington Post is about first man to receive a genetically modified heart from an animal. In this case it was from a pig, a mammal that shares a lot of similarities with humans. According to Shook, pigs have been used dating back to Ancient Greece to study humans without directly studying humans. Pigs have been used by the military to simulate live wounds and allow corpsman to get experience repairing live injuries, as well as dead pigs being used to ballistically simulate human flesh. I have not only heard this second hand from my hospital corpsman buddies, but this is also supported from a recent article written by Knodell. Through research and genetic modification, pigs have been not only modified for food supply purposes, but now have been modified to provide organs for humans.

Why do I think this article is accurate. Well first, there is a follow up article from the Washington Post in which the man that received this transplant unfortunately passed away. Second, as a Paramedic, I have seen the complications when it comes to not only harvesting human organs, but how difficult it is to get human organs and making sure those organs meet certain medical standards. This means that that the number of organs for donations are very rare, and the waitlists for these organs extensive.

However, as the article form the Washington Post states, the man who received the genetically modified pig heart didn’t even qualify to receive a human heart, even there was one available for him. Without a loophole for emergency surgery, this man wouldn’t have been able to receive a transplant in the first place.  The modification of the heart focused on removing three genes that would cause the human body to reject the organ.

References

Knodell, K. The Army is Spending Tens Of Thousands Of Dollars On Pigs In Hawaii. Civil Beat; https://www.civilbeat.org/2020/12/the-army-is-spending-tens-of-thousands-of-dollars-on-pigs-in-hawaii/#:~:text=The%20animals%20were%20anesthetized%20before,for%20a%20deployment%20to%20Iraq (2020).

Pietsch, B. In first surgery of its kind, Maryland man receives heart transplanted from genetically modified pig. The Washington Post; https://www.washingtonpost.com/science/2022/01/11/pig-heart-transplant-genetically-modified/ (January 11, 2022).

Shook, L. et al. Unraveling the swine genome: implications for human health. Annual Reviews; https://www.annualreviews.org/doi/10.1146/annurev-animal-022114-110815 (2015)

Writing Assignment 5

            I have spent my entire life on, in, or next to the water. I grew up in San Francisco, and the first skills my mother taught us was how to catch Dungeness crabs and fish for rainbow trout. I knew from an early age that I wanted to be a marine biologist, I just didn’t know it would be a straight road. That curvy road took me to war, and then dropped me into the world of Fire & EMS. However, that curvy road would give me the training and skills that make me the best candidate for the job.

            The Marine Corps core values of honor, courage, and commitment best describe my own values and how I am in any job. Honor means that I follow the rules, I am respectful to my fellow employees and/or clients, and that I hold myself responsible for my actions and like to paint the best image for myself. Courage means that I’m not afraid to step up to get the job done, or to admit when I don’t know something, to ask for help, or to admit when I have made a mistake, even it means me losing that position. Commitment means that I very dependable, I always show up early for any shift, I don’t mind staying late when needed, and I don’t mind doing any task if it means accomplishing the mission.

            Three skills that make me the best candidate for the job are that I am a crabber and a fisherman, an EMS provider, and I have experience operating different naval craft. In marine biology, we might have to study living organisms. To obtain these living organisms, the skills of a fisherman and crabber are needed to be able to bring the specimens out of the water and into the lab. Skills as an EMS provider are important because if anything happens, either in the lab or out in the field, I am well trained and experienced in stabilizing and treating any injury that happens to myself or my fellow teammates. Experience operating a wide arrange of vessels means that I am well acquainted with being out on the water, and I know my way around a vessel. I have also operated small, motorized vessels, and assisted in the operation of larger naval vessels. With my experience aboard military and civilian vessels means that I am useful on any type of research trip on the water.

            My listed values and my listed skills make me the best candidate for the job. Once I finish my bachelor’s in marine biology at Old Dominion University, I will be starting my master’s in marine science at Unity College. I don’t plan to stop there, and plan to go for my doctorate in marine biology and ecology. This, along with my lifelong passion for marine biology and my need to always be out on the water, whether its to fish, do research, or to just have fun, means that I will not only enjoy my work, but give the best effort that I have, as this is what I want to do for the rest of my life.

Genome Assignment

1. Chromosome 6
2. Approximately 1900 genes
3. Approximately 170 million base pairs, over 95% have been determined
4. IDDM1
5. This gene normally tells the immune system not to attack its own insulin or the pancreatic cells that produce insulin. However, in diabetes type 1, the gene doesn’t work properly and causes the body to attack and destroy any naturally produced insulin as well as the pancreatic cells that produce it.
6. Homo Sapiens CFTR promoter region (LOC111674463) on chromosome 7
7. Yes
8. The cystic fibrosis transmembrane conductance regulator (CFTR) protein is an anion channel expressed in the apical membrane of epithelia.
   1. Moran, O. The gating of the CFTR channel. Springer; https://link.springer.com/ article/10.1007/s00018-016-2390-z
9. Cystic Fibrosis
10. Chromosome 7
11. Pan Paniscus
12. Bonobo
13. No
14. Saimiri Boliviensis, Bolivian Squirrel Monkey
15. 1/119 (0%)
16. A gap in on e of the sequences means that one or more amino acid residues have been deleted from the sequence
17.  Mus musculus TAR DNA binding protein
18.  Ubiquilin 2
19.  FUS RNA binding protein
20.  Superoxide dismutase-1
21. Amyotrophic Lateral Sclerosis (ALS Disease), Lou Gehrig
22. NIH genetic sequence database, an annotated collection of all publicly available DNA sequences
23.  cDNA is a complementary strand of DNA that only contains coding sequences.
24.  Hemoglobin Subunit B (HBB)
25.  Spans of DNA sequence between the start and stop codons.
26.  Binds monomeric and dimeric human IgA of both subclasses with high specificity and affinity.
27.  Frame 1, because it was at the top of the list and had the most red highlighted open frames.
28.  Yes
29.  Line 781, there is an S in the third slot on the 2^nd sequence when there is a – in the 1^st sequence.
30.  Fibroblast growth factor receptor 3 – regulates bone growth by limiting the formation of bone from cartilage (ossification)
31.  Muenke Syndrome
32. I have learned that it takes a very dedicated person to read, identify, and study amino acids, genes, and how they interact. I am not ashamed to say that I am not that kind of person, and I have an appreciation for the people that study or

Genetics Topic Assignment

            For anyone that has gone crabbing, or if you have seen videos of people crabbing, it doesn’t seem like a dangerous job. As a season crabber myself, I know that crabbing is more than just baiting a net or trap, dropping it into the water, then coming back later to see if anything has wandered into the capture device. Fishing is rated by OSHA as the most dangerous job in the world (Invictus Law). Crabbing becomes more complicated when you target crabs that live in freezing cold water and at significant depths under the ocean. The king crab fishery alone has been going on for the last 70 years commercially (Alaska DF&G) and has had its share of injuries and deaths in the pursuit of what are known as crabs.

However, processing those crabs once they have been caught and delivered to the dock is not an easy job either. Once the crabs are caught, they are taken to processing centers and offloaded. It’s at these processing centers the crabs are inspected, frozen, and packaged up for shipment all around the world. The workers that operate these processing centers, usually aboard specialized processing ships, work in cramped, freezing cold positions for longer hours then most people’s 9-5 shifts. On top of workplace injuries and sickness due to being wet and cold for long hours, there is a new sickness going around these processing plants. This sickness is being referred to as “crab asthma” or “crab lung” and only seems to be popping up in areas that process not only king crab, but other deep water polar crab species such as snow crab and edible crab (Thomassen).

As a Paramedic, I found the fact that there is an illness that is only appearing under certain conditions very fascinating, and that I needed to learn more about this for my general knowledge in medicine. As a marine biology student, a crabber, and someone that just loves everything decapod I knew this was something that I was going to want to research more. My first question was, what was causing such an illness and how did they only link it to a few species such as king crabs? Well according to the CDC, asthma like symptoms developed by workers that handle crab and have no history of asthma isn’t a new occurrence. The CDC has been collecting data since March 13^th of 1981 on this illness. The symptoms have ranged from mild difficulty breathing, or dyspnea, to upper respiratory infections, to asthma-like wheezing and persistent cough that can disturb interrupt and shorten the sleep cycles of the patients. Since the start of the commercial crab fisheries, studies have shown between 4-36% of seafood workers have developed signs and symptoms related to the patient’s line of work (Kamath).

Now, with the advances in science and health research, one of the major proteins responsible for this illness is called Tropomyosin. On its own, tropomyosin is just a protein used by the muscles in the process of contraction. It is like troponin, the major protein used by heart in humans for contraction and an indicator of heart damage or death when found in the bloodstream. However, this protein isn’t designed to be used outside of the body, and when inhaled can cause a reaction in the respiratory system. This can start out with allergy like symptoms and with continued exposure, can lead to other respiratory diseases or even allergic reactions to the protein.

Genetic studies into the tropomyosin protein have found that different types of tropomyosin are configured differently based on the animal groups. The tropomyosin that causes the “crab asthma” is only found in crustaceans (Kamath). It was also discovered, according to Kamath, that the crustacean tropomyosin “shares a certain degree of amino acid homology of 75-83%sequence identity with house dust-mite and insect tropomyosin’s.” Certain insects, such as mites and cockroaches, have been linked to minor allergens as well. It was discovered a correlation with crustacean tropomyosin relations with people that had shellfish allergies.

To better understand the reaction of tropomyosin on the immune system, Kamath et al extracted the RNA responsible for creating the crustacean protein form and purified it to create recombinant tropomyosin. This recombinant protein was then used to create a purified antibody designed specifically to detect the aerosolized crustacean tropomyosin protein. The testing trials were successful. This means that the same procedures used for the experiment to detect airborne crustacean tropomyosin can be adapted and used to identify and track other airborne allergens. This in turn can lead to safer working conditions with faster identification of airborne particulates that can cause injury to food workers.

With the identification of the main airborne allergen that causes “crab asthma,” the creation of the synthetic tropomyosin, and studies into how crustacean tropomyosin affects the immune system, scientists can now use the antibodies created from the reaction to tropomyosin to work on a treatment, if not a cure for “crab asthma.” This wouldn’t be the first time a recombinant protein was used to improve human health. The horseshoe crab, an animal that is related to true crabs but resides on its own branch in the arthropod family, was studied genetically to improve the health of humanity. In a search for the way to detect endotoxins, especially in vaccines, it was discovered that the only living animal that naturally detects endotoxins was the horseshoe crab. The North American horseshoe crab has within its blue blood a type of cell called an amebocyte. This cell is responsible for the production of limulus amebocyte lysate, the only naturally occurring protein that can effectively detect endotoxins. I say this because there is a tachypleus amebocyte lysate (TAL) found in Asian horseshoe crabs that is less effective than the LAL protein.

Now, thanks to genetic research, the protein was successfully identified and extracted. Based on this naturally occurring protein, a synthetic version known as recombinant factor C was created to be used in lieu of the LAL protein (Bolden). Up until the creation of this synthetic version, to obtain a way to detect endotoxins meant that horseshoe crabs had to first be caught, then their blood had to be extracted, then the LAL protein had to be extracted from the blood. This was not only a tedious process, but studies showed that it played a role into the current decline of the North American horseshoe crab. Now with the creation of recombinant factor C, less and less horseshoe crabs need to be harvested to produce the means to detect endotoxins. Every vaccine that has ever been given in the United States has undergone the LAL test, which is all thanks to the genetic research into the LAL protein and the horseshoe crabs.

References

Alaska DF&G. Commercial Crab Fisheries. Alaska Department of Fish and Game; https://www.adfg.alaska.gov/index.cfm?adfg=CommercialByFisheryShellfish.crab#:~:text=The%20history%20of%20crab%20fisheries,developed%20in%20the%20Bering%20Sea.

Bolden, J., et al. Currently Available Recombinant Alternatives to Horseshoe Crab Blood Lysates: Are They Comparable for the Detection of Environmental Bacterial Endotoxins? A Review. NIH; https://pubmed.ncbi.nlm.nih.gov/32817324/ #:~:text=By%20use%20of%20a%20recombinantly,based%20on%20horseshoe%20crab%20blood.

Kamath, S., et al. Molecular and immunological approaches in quantifying the air-borne food allergen tropomyosin in crab processing facilities. Science Direct; https://www.sciencedirect.com/science/article/abs/pii/ S1438463914000327?via%3Dihub

Law, I. Top 10 Most Dangerous Jobs According to OSHA. Incitus Law; https://www.invictuslawpc.com/ most-dangerous-jobs-osha/

Mobidity and Mortatlity Weekly Report. Epidemiologic Notes and Reports Asthma-Like Illness among Crab-Processing Worker – Alaska. CDC; https://www.cdc.gov/mmwr/preview/ mmwrhtml/00000212.htm

Thomassen, M., Aasmoe, L., Bang, B., Braaten, T. Lung function and prevalence of respiratory symptoms in Norwegian crab processing workers. Taylor & Francis Online; https://www.tandfonline.com/doi/full/10.1080/22423982.2017.1313513

Thomassen, M., et al. Occupational Allergic Sensitization Among Workers Processing King Crab (Paralithodes camtschaticus) and Edible Crab (Cancer pagurus) in Norway and Identification of Novel Putative Allergenic Proteins. Falgy; https://www.frontiersin.org/articles/10.3389/falgy.2021.718824