Categories
Uncategorized

Writing Exercise #13

Can experiments detect differences that matter?

This question asked by readers of scientific literature is important because it seeks to ensure the results used to make a conclusion are valid. In the field of microbiology, for example, this can be seen when trying to understand functional differences between closely related genes versus sequences.

Does the study show causation or correlation?

This question is important to ask because while there may be correlation, it can be difficult to prove causation. One example which I have been always told, is that ice cream consumption is correlated with pool drownings. While these are correlated, it is clear that eating ice cream does not cause you to drown. Instead, there is a confounding variable of warmer weather; when it is sunny outside, there is both increased ice cream consumption and frequency of pool usage, and thus increased incidence of drowning. This can be applied to scientific literature because correlation almost always insists some type of causation, but the direct cause can be hidden or covered in the variables studied.

What is the mechanism?

This question asks readers to understand the conclusions on a deeper level before interpreting and analyzing the claims made by the scientific literature. Thus, understanding the mechanisms can help to determine if the study shows causation or correlation.

How much do experiments reflect reality?

This question serves to address the differences between the research in scientific literature and real life. For example, many studies cannot exactly replicate human microbiome, and use animal models or human cells. Thus, the results may not exactly translate to human health mechanisms. A general example which is common, is comparing the virulence factors of some bacteria is varying effectiveness in in-vivo and in-vitro studies.

Could anything else explain the results?

This question further explores the idea of correlation versus causation. Thus, it seeks to find other plausible confounding variables which influence the results found.

Categories
Uncategorized

Writing Exercise #12

Microbial communities are hypothesized to influence mental health states via the gut-brains axis. The gut, which also known as the “second brain” is linked through several nerves and neurons to the brain. Thus cytokine production in response to microbes, as well as precursors for neurotransmitter produced to microbes, can then travel to and influence the brain. An example of this, is a study in which depressed mice whose vagus nerve was severed (removing the link between the gut and the brain), the symptoms of depression were no longer alleviated with probiotic use.

The brain and mental health states have also been found to, in turn, influence gut health. This is through the gut-brain axis, once again, and neurotransmitters, hormones, and steroids produced by the brain can influence the gut. One example is how catecholamines and norepinephrine during stress can travel to the gut and cause dysbiosis; there is an overall decrease in motility and nutrient absorption.

Thus overall, these relationships can influence health and disease because there are never ending lists and ways to promote mental health, which can then promote gut health and limit the risks of diseases associated with gut dysbiosis. On the other side, taking care of gut health can encourage a healthy mental state. Thus they can both promote health and disease by influencing on another.

Categories
Uncategorized

Writing Exercise #11

Being a peer-reviewer was an interesting process. As I critiqued other’s writing, I felt like I was in the process of writing the paper, collecting and verifying sources myself. I enjoyed the anonymity of the peer review, as in other writing classes which were not, I felt obliged to soften my critiques at the expense of the writer’s feelings. One thing I learned which I can apply to revising my own final essay would be to take the time to read my paper out loud to see how well the ideas flow together. I think having a fresh set of eyes reviewing helped to catch mistakes in other’s drafts, and thus I also will apply this to editing my own paper. I will start to revise and edit my paper early, so that I can have ample time in between my revisions to look at it with a new pair of eyes. Furthermore, while addressing the peer-review questions provided for a classmate’s drafts were not questions I kept in mind while writing my paper. Thus, I now have a more clear rubric when finishing my final draft of my Final Essay.

Categories
Uncategorized

Writing Exercise #10

The process of a peer review is an important step for scientific articles as it validates the credibility of the research being cited, as well as the information being provided. This process helps the author to understand and analyze where information may be misconstrued, misunderstood, or misinterpreted by its audience before the final publication. Thus, the peer-reviewer must be someone with the same or a higher-level of expertise than that of the author. This peer-review process should also be done by more than one reviewer to increase validity.

There are many pros to peer-reviewing which include valuable feedback from reviewers. It can be difficult to self-review and edit your own paper because rereading your own paper makes it difficult to catch errors or mistakes. Thus, peer reviewing provides a fresh set of eyes to catch these. This also helps authors to make sure they have the most up to date research.

However, the peer review process can have some disadvantages, as well. For example, this increases the time required to publish articles due to extended time reviewing and editing after review. In smaller fields of work with less experts, it can be hard to also have a variety of peers to review and validate work. Finally, reviewers who share the same opinions of the authors can make it difficult to see through biased opinions which may need more evidence for its audience.

Categories
Uncategorized

Writing Exercise #9

Changes in human activity which decrease our exposure to microbes:

Increased hand washing: Many hand soaps today are anti-bacterial and remove microbes from our hands and thus our overall exposure

Urbanization of towns: The movement away from farm-lifestyles and into cities decreased our exposure to farm animals and the microbes they carry.

Modern toilets and sewage: Fecal matter contains many microbes and our toilets and sewage have improved, reducing the risk of exposure to it and thus microbes.

Cleaning supplies: Household cleaning supplies are now used to kill bacteria on many different surfaces.

More time indoors: the outdoors, especially the dirt, is filled with many, many microbes.

Mode of Delivery for birth: Cesarean sections do not introduce newborns to the bacteria in the vaginal canal like in more traditional vaginal deliveries.

Antibiotic use: The point of these are to kill bacteria and other life without being specific to the kind, and reducing the total number that live in us.

Limited exposure to others: Growing up with siblings or hanging out with other children increase our exposure to others, and thus having a limited exposure to others does the opposite.

Categories
Uncategorized

Writing Exercise #8

This term all of the papers we have read have been very interesting because they correlate to chronic diseases which were before thought to not relate to bacteria or other microbes. I think it would be interesting to see what kinds of diets affect the microbiome and how they do; for example, veganism, vegetarianism or even fad diets such as keto or intermittent fasting. It would also be interesting to learn more about the relationship between the microbiome and vaccines, as this is a very controversial topic. I have throughly enjoyed reading a lot about the microbiome and obesity, and what other factors increase the risk. I also liked learning about pre-,pro- and syn-biotics. I would like to learn more about which specific pre-pro- and syn-biotics have an overall benefit for health.

Fad diets such as keto promotes the consumption of high protein and high fat diets, while lowering the overall consumption of carbohydrates. I would imagine that this has a negative health effect on the gut microbiome as many fruits are excluded from the diet, which can be a great source of probiotics. Furthermore, high-fat diets are often diets which mice are fed when conducting studies on obese mice. I would like to know also how other diets such as intermittent fasting affect the gut because this encourages people to eat within a 8-hour time period everyday or to fast for 24-hours once or twice a week. The diet is not limited to certain foods so this could vary greatly among participants but I am not sure how the fasting periods affect the gut.

I might begin to prepare for my final paper by looking for articles about a specific diet and how it affects the microbiome. I can then organize the papers by diet or later decide if I would like to focus on just one. Once I have a clear argument to make, I can start an outline to make a roadmap for my paper.

Categories
Uncategorized

Writing Exercise #7

There are many factors that can influence the colonization of an infant’s microbial community:

Bacteria in amniotic fluid: Before the infant is even born, bacteria can enter in the amniotic fluid, but currently it is still up for debate if there is a placental microbiome.

Antibiotic exposure: Antibiotics, just as for adults, disrupt the growth of microbial communities and thus cause dysbiosis. This can be caused by either the mother or the infant taking them.

Delivery and feeding modality: Infants who are born vaginally are exposed to the bacteria in the vaginal canal and varies significantly from those born from cesarean section. Some doctors recommend swabbing the vaginal canal and painting the cesarean-born infant with the bacteria it would have been in contact with if delivered vaginally. Furthermore, feeding by breastmilk or formula also varies the exposure to bacteria which colonize the infant.

Smoking: Smoking is known to reduce adult microbiota and mothers who smoke are also risking their infant’s as well. Studies have found that this can cause dysbiosis for the children later on in life, increasing the risk for obesity.

Categories
Uncategorized

Writing Exercise #6

In regards to antibiotics, I previously took them without any regard. Every time that I had previously been prescribed antibiotics, it was from a PA at an urgent care clinic and not my primary physician. I had never thought to discuss the effects. However, since I have read more articles about the impact of our microbial communities on our health, I have changed my perspective on this. I have now decided that I would rather take other routes to improve my microbial health in response to infections or to let my immune system deal by itself. I do not have an autoimmune disease and have never been hospitalized due to an infection, therefore I would rather suffer through the consequences unless I presumed that doing otherwise could cause life-threatening infections. Before I attended Oregon State, I lived in a community in which treatment from physicians, such as vaccines or antibiotics were considered “sinful”, and soon after I decided to neglect these rules after and took them without consideration. I wish I knew the impacts of these before I took them.

Categories
Uncategorized

Writing Exercise #5

Growing up, I never thought much about my nutrition; as I grew up in a low-class society and had little choice in what I ate. Furthermore, organized group sports were not an option for me to participate in. However, since enrolling into college, I have used med education and resources to help me become more active and in control of my health. Before I knew of the benefits for my microbial communities, I decided to engage in some sort of physical activity at least an hour a day. Furthermore, I recently decided to invest into a vegan lifestyle. This diet and activity promote by being dense in foods which are considered probiotics and increase the activity of the bacteria in our gut, as well as increase in anti-inflammatory cytokines (https://www.healthline.com/health-news/exercise-improves-your-gut-bacteria#1). One activity which negatively impacts my microbial health is not getting enough sleep. I am constantly up late and waking up early, which disrupts the rhythm of the gut and increases the risk of obesity and other gut-related diseases.

Categories
Uncategorized

Writing Exercise #4

Wen Gao and Hong Cheng from the Department of Gastroenterology in Peking University First Hospital, Beijing, China explicate in their primary research article “The Evolution of Helicobacter pylori Antibiotics Resistance Over 10 Years in Beijing, China” (2010) that the percentage of antibiotic resistance strains of H. pylori is increasing and eradication regimes should reflect the local epidemiologic status of the bacterium. Gao and Cheng collected and cultured samples from patients over the course of 10 years from untreated and previously treated individuals and found that along with the increase in antibiotic treatment, so did antibiotic resistant H. pylori strains. The research served to identify the trends in H. pylori strains alongside common treatments in order to find proper eradication of the human pathogen. Researchers Gao and Cheng intend to reach out to other researchers in the gastroenterology or microbiology field, as well as physicians treating patients with H. pylori infections.