Writing Exercise #10

Describe the process of peer review to someone who does not frequently read scientific articles. In your response, consider the pros and cons of peer review and how that might impact the credibility of the results that come from that scientific article.

The process of peer reviewing scientific articles.



Peer-reviewed articles provide a trusted form of scientific communication. Even if you are unfamiliar with the topic or the scientists who authored a particular study, you can trust peer-reviewed work to meet certain standards of scientific quality. We rely on scientific peer reviewed articles to reference for other papers so they must hold up to scrutiny.

Many fields outside of science use peer review to ensure quality. Philosophy journals, for example, make publication decisions based on the reviews of other philosophers, and the same is true of scholarly journals on topics as diverse as law, art, and ethics. There is essentially two types of peer review closed and open.

Closed peer review is a system where the identities of the reviewers are not disclosed in the journal or to authors, and the identities of authors may not be disclosed, during the review process, to the reviewers. Of course, the reviewers can identify the authors after publication. Closed review works in two ways: single-blind and double-blind. Single blind review works by revealing the names of authors to reviewers while withholding the names of reviewers from authors. In double-blind peer review—as described above—identities of authors and reviewers are mutually withheld.

Open peer review, in contrast, operates a more transparent approach to peer review. Identities of authors and reviewers are mutually disclosed and, furthermore, reviews are sometimes published alongside the published articles. This system is becoming increasingly popular and is often applied by open access journals.

Peer reviewing will help develop you as a writer. Just think about all the ideas another person could think of on the topic your writing about. More minds contributing to the same thing the better. I think peer reviewing helps the writer in ways they might not have thought of when first writing. The purpose of writing a paper is having somebody else read it and make sense of it. The best way to make it appealing to many people is having a few people in same field read it and agree that other people should read it to.

The pros  and cons of peer reviewing

There is no consensus on which of these peer review systems is best and it is agreed that both closed and open peer review have good points and bad; likewise single- versus double-blind peer review. The principle behind closed review is to minimize the bias of reviewers who may be influenced by the identity of the authors and to protect the reviewers from authors who may take exception to adverse reviews and rejections. The principle of only protecting reviewers operates in single-blind review. While it is always possible to protect the identity of reviewers during and after the review process, it is often possible for reviewers to identify authors by virtue of the work that is being reviewed.

Moreover, even when the author cannot be identified, reviewers may take exception to a line of work for reasons that are not concerned with the science or because the work competes with or refutes some of their own work. Therefore, the advantages of the system—minimizing bias and protecting identities—may be undermined by prejudice on behalf of reviewers.

As an ‘antidote’ to some of the issues raised by closed review, open review introduces transparency. By mutually revealing identities, the potential for bias by reviewers is attenuated by accountability to authors and readers. The advantages of this system may be outweighed by less-than-honest comments from reviewers who feel unable to be frank about the work.. On the other hand, the potential for unhelpful and inappropriate comments is reduced. Neither of the above systems of review-closed or open-is capable of completely obviating the problems they are designed to address.

The peer review process is extensive and complex. This is by design to make sure that the papers that make it to journals are held in high regard and hold validity across the board.

Photo retrieved from :

(n.d.). Retrieved May 26, 2017, from http://undsci.berkeley.edu/article/howscienceworks_16

Exercise #9

Human behaviors that contribute to decreased exposure to microbes.

We now know that microbial exposures could have positive health impacts later on in life. The hygiene hypothesis states that the lack of early childhood exposure to infectious agents microbes and parasites will suppress the natural development of the immune system.  The immune system can be broken down into sub categories the innate and the adaptive immune system. The hygiene hypothesis primary acts on the adaptive immune system. The adaptive immune response is antigen-specific and requires the recognition of specific “non-self” antigens during a process called antigen presentation. Antigen specificity allows for the generation of responses that are tailored to specific pathogens or pathogen-infected cells. The ability to mount these tailored responses is maintained in the body by “memory cells”. Should a pathogen infect the body more than once, these specific memory cells are used to quickly eliminate it. In other words if your not exposed to infectious agents then your adaptive immune system has less information to go off in immune response.

Potential risk factors could be:

  • Formula feeding instead of being exposed to microbes in breast milk
  • Infant being born through c-section and not exposed to vaginal microbes in delivery.
  • A kid that never plays outside (in dirt).
  • Parents that don’t get there kids vaccinated to be exposed to viruses that like virulence factors.
  • Antibiotic therapy not being used in the right way.
  • Over use of antimicrobial household products like (detergents, soaps, kitchen cleaners etc.)

The Human Microbiome: How It Works + a Diet for Gut Health

It is important to keep a biodiversity of microbes in and on your body. Certain behaviors can promote and depress the biodiversity of the micro biome.  The adaptive immune system needs to have infectious agents so it can adapt over time and prevent the later onsets of allergies and infection.

Writing Exercise #8 Free Write Brain Storm

Im am fascinated by the sheer number of microbes we coexist with. I was shocked to learn that the body houses specific microbes in certain parts of the body to utilize their metabolic processes or their use as a natural defense to other pathogens. In particular the mouth microbiota is something that interests me as a future dentist. I think that the interaction we have with the outside world ( our environment) and usually the first portal of entry being our mouth we don’t have more problems with dysbiosis and disease. Many people do have some sort of oral disease at any given point including cavities or gingivitis. Its amazing to me that this dysbiosis in the mouth doesn’t create more problems systemically. The more we study the relationship we have with microbes the better we can understand the mechanisms and use them to our advantage to maintain a healthy diversity of microbiota.

dysbiosis in the mouth

Dysbiosis in the mouth of a normal microbial diversity can have effects on a very macroscopic level. I don’t think many people outside of the scientific world understand the complexity of the interactions, including myself and I would like to research and write more about it. The topic of probiotics is sweeping the world and most people think of just ingesting probiotics to help with a healthy gut.  There is also talk of mouth rinses that have probiotics to maintain a healthy diversity of microbes in the mouth. Again this is one of the major entries into our body and if we don’t have good bacteria in our mouth protecting us from the bad we could experience disease that we would otherwise avoid.

I think the topic of oral microbiota would be very interesting for me to write about and I think I could take a lot away from it. The mouth is a perfect environment for many microorganisms to flourish in, good and bad. So how do we keep high levels of beneficial microbes  where they need to be. I think this focus is broad enough to use a lot of the information I have learned from this class and microbiology to write worth while paper. At the same time I think the focus on the mouth would intrigue me more then looking at the microbial community on the skin.

Factors That Influence the Colonization of Microbial Communities in New Borns

Microbial colonization of the infant occurs during a critical time window for immune and gastrointestinal development. Infant colonization sets the stage for the adult microbiome. The nature of infant environmental exposures, acting through the microbiome, affect the likelihood of developing childhood and adult diseases such as obesity, food allergy, and inflammatory bowel disease. Many bacterial sources for the infant derive from the maternal microbiota. Therefore, beneficial infant colonization is dependent upon maternal genetics, environmental exposures and diet before and during pregnancy as well as during breast feeding.

The mother not only gives the newborn everything for life but she also gives the newborn some of her microbiota through delivery, prebiotics, and breast milk.


The current fetus microbial model leads us to believe there are no bacteria present in the fetus (though they are surrounded by microbiota in the womb) and it’s not until childbirth that the first microbes are transferred to the baby through the birth canal during delivery. So according to what we know as of today, if that baby doesn’t come out of that birth canal, the baby does not get inoculated with healthy probiotic bacteria.

As of last month, a study dropped, proving that if a Cesarean-delivered newborn was swabbed with the mothers vaginal fluid, their gut, oral and skin bacterial communities were enriched with vaginal biome! So for all you parents out there who have the best intentions of delivering vaginally, but your life or the life of your unborn baby, or both, are at risk, there is a simple solution that is now officially backed by the science method (1).

Natural Prebiotics

The vernix caseosa, the waxy skin coating of a fetus, is shed into the amniotic fluid as the fetus approaches term. While still in utero, the near-term fetus swallows amniotic fluid containing pieces of vernix. While not digestible by human enzymes the vernix caseosa provides a good medium for bacteria to grow on. Once the infant begins to breastfeed, breast milk contains additional prebiotics. Colostrum contains especially high concentrations of human milk oligosaccharides (HMOs), which are indigestible by human enzymes alone. Their synthesis requires up to ten percent of the total energy expended to produce human milk. These oligosaccharides, like the vernix, promote growth of intestinal microbes (2).


Breast Milk

Breast milk contains both innate and adaptive immune components that inhibit pathogens from colonizing the infant gut. As part of the innate immune system, breast milk contains antibacterial peptides, such as lactoferrin and lysozyme. These antibacterial peptides provide broad spectrum bacteriostatic and bacteriocidal checks on microbial growth. Breast milk contains glycans that mimic cell surface adhesion molecules on the infant’s intestinal epithelium. These glycans act as decoy receptors to specific intestinal pathogens, providing a further level of protection for the infant.

Breast milk has long been known to contain bacterial DNA. Modern culture-independent techniques identified gut-associated obligate anaerobes in addition to facultative anaerobes in the breast milk as a source of diversity in the infant gut (3). Through these prebiotic and probiotic mechanisms, breast milk shapes the intestinal microbiome. Exclusively breast-fed infants have overall greater diversity of the microbiome when compared to exclusively formula-fed infants

  1. Bromberger, P., Lawrence, J. M., Braun, D., Saunders, B., Contreras, R., & Petitti, D. B. (2000). The influence of intrapartum antibiotics on the clinical spectrum of early-onset group B streptococcal infection in term infants. Pediatrics, 106(2), 244-250.
  2. Newburg DS, Walker WA. Protection of the neonate by the innate immune system of developing gut and of human milk. Pediatr Res. 2007;61(1):2–8.
  3. Jost T, Lacroix C, Braegger C. Assessment of bacterial diversity in breast milk using culture-dependent and culture-independent approaches. Brit J Nutr. 2013;110:1253–1262.

Writing assignment #6

Antibiotic personal philosophy

In my life I have only had to take antibiotics a hand full of times, once for a staff infection and another for when I had strep throat. Personally I have always been under the impression that if you can fight off the infection without antibiotics to do it that way. I remember the doctor telling me when I was younger that its a good thing that I haven’t had to take many antibiotics through out my life.

Antibiotics, also known as antimicrobial drugs, are drugs that fight infections caused by bacteria in both humans and animals. Antibiotics fight these infections either by killing the bacteria or making it difficult for the bacteria to grow and multiply. Antibiotics do not have any effect on viruses. Antibiotics are fundamental to modern medicine, essential for treating everything from routine skin infections to strep throat, and for protecting vulnerable patients receiving chemotherapy or being treated in intensive care units. This also poses the question of what type of infection should be treated with antibiotics.

Which infections are caused by viruses and should not be treated with antibiotics?

  • Colds
  • Flu
  • Most sore throats
  • Most coughs and bronchitis (“chest colds”)
  • Many sinus infections
  • Many ear infections

Antibiotics are necessary when infections are to fierce for the body to get rid of by itself. That being said when doctors do prescribe an antibiotic the full round should be taken to prevent antibiotic resistance. Although antibiotic resistance is not a new problem, its scope now constitutes a major threat to human health. According to the Centers for Disease Control and Prevention, at least 2 million Americans fall sick every year with antibiotic-resistant infections—and 23,000 die.

To avoid antibiotic resistant organisms from manifesting, a few precautions should be considered:

  • Ensure that antibiotics are only prescribed when necessary in human health care settings.
  • End the overuse of antibiotics in food animals.
  • Remove the regulatory economic and scientific obstacles that impede antibiotic discovery and development.
  • Dont save antibiotics for the next time you get sick.

Foods that Will Promote Gut Health

What choices do you make in terms of food/nutrition/product use and consumption that may have an impact on your microbial communities? 

There are approximately 10 times as many microorganisms within the gastro-intestinal (GI) tract of humans (approximately 100 trillion) as there are somatic cells within the body. While most of the microbes are bacteria, the gut can also harbor yeasts, single-cell eukaryotes, viruses and small parasitic worms.

So when it comes to influencing the microbial community in the stomach one should consider what foods might improve gut microbial health and what could hurt this microbial community. The microbial community plays a huge roll in immune health and has been linked with inflammatory bowel diseases, such as Crohn’s disease or ulcerative colitis, when the balance of gut microflora is out of whack .

This community, referred to by scientists as your “gut microbiota” or “gut microbiome,” can be composed of around 500 species which each supply their own benefits: Some of them break down your food and extract nutrients; others hunt for food pathogens; and others help protect you from colds and flus. In fact, they play such a critical role in our health that many experts have started to refer to the microbiome as its own organ.

When we consume too much junk food or sugary snacks this can have a negative effect on the gut microbiota. Our weight has been shown to correlate with types of bacteria in the gut. Studies have shown us that obese people have higher levels of bad bacteria from the phylum Firmicutes while lean people have higher levels of bacteria from the phylum Bacteroidetes (1).

Another aspect of a healthy gut is Inflammation and how to prevent chronic inflammation that could lead to inflammatory bowel disease. Your immune system attacks anything in your body that it recognizes as foreign—such as an invading microbe, plant pollen, or chemical. The process is called inflammation. Intermittent bouts of inflammation directed at truly threatening invaders protect your health. Many major diseases that plague us including cancer, heart disease, diabetes, arthritis, depression, and Alzheimer’s have been linked to chronic inflammation.One of the most powerful tools to combat inflammation comes not from the pharmacy, but from the grocery store. Choose the right foods, and you may be able to reduce your risk of illness. Consistently pick the wrong ones, and you could accelerate the inflammatory disease process.

Foods that inflame

Try to avoid or limit these foods as much as possible:

  • refined carbohydrates, such as white bread and pastries
  • French fries and other fried foods
  • soda and other sugar-sweetened beverages
  • red meat (burgers, steaks) and processed meat (hot dogs, sausage)
  • margarine, shortening, and lard

To reduce levels of inflammation, aim for an overall healthy diet. If you’re looking for an eating plan that closely follows the tenets of anti-inflammatory eating, consider the Mediterranean diet, which is high in fruits, vegetables, nuts, whole grains, fish, and healthy oils.


Figure from: Publications, Harvard Health. “Foods that fight inflammation.” Harvard Health. N.p., n.d. Web. 04 May 2017.


Boulangé CL, Neves AL, Chilloux J, Nicholson JK, Dumas M. 2016. Impact of the gut microbiota on inflammation, obesity, and metabolic disease. Genome Medicine. 8:42.

Publications, Harvard Health. “Foods that fight inflammation.” Harvard Health. N.p., n.d. Web. 04 May 2017.

Writing assignment #4

(1 )Lauri E. Markowitz Morbidity and Mortality weekly reportDivision of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention (proposed) . “Quadrivalent Human Papillomavirus”(2007) asserts that the epidemiology of HPV and associated diseases, describes the licensed HPV vaccine, and provides recommendations for its use for vaccination among females aged 9–26 years in the United States. (2) Markowitz provides evidence that clinical trials indicate that the vaccine is safe and immunogenic. Trials among females aged 16–26 years indicated the vaccine to be effective against HPV types 6-, 11-, 16-, and 18-related cervical, vaginal and vulvar cancer precursor and dysplastic lesions, and genital warts. HPV 16 and 18 are the cause of approximately 70% of cervical cancers. (3) The purpose of this report was to provide recommendations to immune practices.(4) Markowitz establishes a tone that is intended for medical professionals and then relatable to the patients and public at large.


How we influence our gut microbial community.

Bacteria in our gut

The gastrointestinal microbiota is one the most diverse and dense places of bacteria in the body. Gut flora is established by the age of 1-2 years old and from there on out you develop a relationship with those microorganisms.  The relationship between some gut flora and humans is not merely commensal (a non-harmful coexistence), but rather a mutualistic relationship. The composition of human gut flora changes over time, when the diet changes, and as overall health changes. The upper digestive tract has few microbe populations but the main place you will find bacteria in the gut is the colon. It contains a densely populated microbial ecosystem with up to 1012 cells per gram of intestinal content. (1 )

The positive 

Many studies have shown that microbial diversity in the gut is correlated to having a healthy colon.  The normal microbiota of the large intestine is extremely important in preventing the establishment of pathogenic organisms .(2) Some microbes out compete the pathogens and others have metabolic products that prevent pathogens from becoming established. In this way these microbes are essential for our immune health. Not only are they important for immune health but the gut microbes are also responsible for helping us with our metabolism. Without gut flora, the human body would be unable to utilize some of the undigested carbohydrates it consumes, because some types of gut flora have enzymes that human cells lack for breaking down certain polysaccharides.

The negative 

When there is an imbalance of the normal microbe community by either a lack of diversity or lack of numbers, the epithelial layer the colon becomes susceptible to pathogen exposure. Enough exposure over a long period of time can result in chronic disease. Crohn’s disease is chronic inflammation of the lower intestine. Current thinking is that microorganisms are taking advantage of their host’s weakened mucosal layer and inability to clear bacteria from the intestinal walls, which are both symptoms of Crohn’s (3). Different strains found in tissue and different outcomes to antibiotics therapy and resistance suggest Crohn’s Disease is not one disease, but a variety of diseases related to different pathogens.

Behaviors for a healthy gut

A nutritional diet will help the health of your gut. Eating for a healthy gastrointestinal tract try adding this to your diet:

  • Eat plenty of fiber; think fruit, vegetables, and whole grains.
  • Eat three to five servings of fish each week.
  • Choose lean cuts of meat and remove the skin from poultry.
  • Stay well hydrated — water is best.
  • Avoid high-fat, processed, and fried foods.
  • Don’t overeat at any one sitting; stick to smaller, more frequent meals throughout the day.

Obesity and stress also play an important role in maintaining homeostasis within the gut. A healthy weight is correlated to less bowel problems. Regular exercise can contribute to a healthy weight and can lower stress levels. Exercise also helps with constipation and staying regular with bowel movements. The use of probiotics (microorganisms that are believed to provide health benefits when consumed) are recommended. Putting more “good” bacteria in the stomach can push out the “bad” bacteria.

Behaviors that put you at risk

Smoking and drinking are potentially harmful to the gut. Smoking can cause damage to just about any one of your major organ systems including your gut.  Protect your digestive tract by quitting smoking and avoiding secondhand smoke, since tobacco exposure has been linked to many conditions including heartburn, indigestion , esophageal cancer, pancreatic cancer, and colon cancer. Relying on vending machine fare, junk foods, and fast foods instead of fresh fruits, vegetables, and whole grains gets many of us into trouble.


Eating healthy, maintain a healthy weight, limiting stress, and reducing behaviors that put you at risk will give you a better probability of maintaining a healthy gut. The composition of human gut flora changes over time, when the diet changes, and as overall health changes. A microbial community in the gut that is more complex and diverse promotes a healthy gut.

  1. Guarner, F; Malagelada, J(2003). “Gut flora in health and disease”. The Lancet361 (9356): 512–9.
  2. Willey JM, Sherwood L, Woolverton CJ. 2014. Prescott’s Microbiology. Mcgraw-Hill EducationNew York, NY.
  3. Sartor, R Balfour (2006). “Mechanisms of Disease: Pathogenesis of Crohn’s disease and ulcerative colitis”. Nature Clinical Practice Gastroenterology & Hepatology3 (7): 390–407.

Writing assignment #2

As a healthcare professional, a colleague asks your opinion as to which HPV strains should be covered in a new treatment.

Cancer is a term which still strikes fear in the hearts and minds of most people diagnosed with it and even those who aren’t, but I don’t think anyone with cervical cancer would align themselves with groups fighting lung cancer, pancreatic cancer or colon cancer. While the commonality which exists because they are also a form of cancer there is a significant difference. That difference is the fact that cervical cancer, unlike the other cancers mentioned, is the result of a virus – human papillomavirus (HPV).

As a medical professional I would recommend a round of vaccines that cover strains of HPVs 16, 18, 31 and 45 first because these strains are known to account for up to 80% of cervical cancer(1.) This would be the most cost effective strains to cover given that one vaccine can’t cover all the strains of HPV.  The other strains of cancer causing HPV arnt as high risk as these first few so as a medical professional I would only recommend the round of vaccines that cover HPVs 16, 18, 31 and 45 if looking at just cost. If cost wasn’t a issue I would recommend HPV vaccine for all the strains across the board just to be safe.

Low risk HPV’s usually are not carcinogenic but can cause genital warts. For example, HPV types 6 and 11 cause 90% of all genital warts. HPV types 6 and 11 also cause recurrent respiratory papillomatosis, a disease in which benign tumors grow in the air passages leading from the nose and mouth into the lungs.(2.) HPV infections are the most common sexual transmitted infection in the U.S.  Centers for Disease Control estimates that more than 90% and 80%, respectively, of sexually active men and women will be infected with at least one type of HPV at some point in their lives. This is a scary number because around half of all these infections are high risk HPV’s that are known to be carcinogenic.

As a medical professional I would recommend that if you have access to get these vaccines you do so. This is to ensure that you have a lower risk of getting cancer associated with HPV if you are ever exposed which most likely you will be at some point in our life.

(1.)  Sarid R, Gao S-J. 2011. Viruses and Human Cancer: From Detection to Causality. Cancer Lett 218–227.

(2.) Human Papillomavirus (HPV) Vaccines. National Cancer Institute.