Research and Writing Conventions of Molecular Cellular Developmental Biology

Authors: Brianna Yanover & Brooklynn Newberry

The University of Colorado’s Molecular, Cellular, and Developmental Biology (MCDB) department concentrates on the structure of various organisms at the molecular level, preparing students for careers in a variety of health, medicine, and research related fields. Among the faculty in this department is Kenneth Krauter. Kenneth Krauter is a professor and the associate chair of MCDB. Krauter started his higher education with a bachelor’s degree in Biochemistry but eventually found his way to Cell Biology during his Ph.D program and later Molecular Cell Biology during his postdoctoral research. After arriving to CU Boulder, his research shifted from his work on the Human Genome Project, which is an international research project to determine the entire DNA complex in humans, to a broader study of genetics. Focusing on the human DNA, Krauter touches on topics in behavioral genetics (which is the study of the nature or origin of an individual’s behaviour) and the human microbiome (which focuses on all of the microorganisms that live in the human body). His most common research interests include environmental exposures and its effect on DNA within the human mouth and gut. This research helps create a better understanding of the relationship between human development and disease. Through the work of Kenneth Krauter, we are able to determine both the conventions of research and writing expected in the field of Molecular, Cellular, and Developmental Biology. Krauter’s work demonstrates research conventions including studying unexplored areas of research, using various scientific techniques, and using quantifiable data. With his writing, we are able to see the conventions of the use of a discussion, annotations on figures, and specific word choice that appeals to any biology major.

In the publication “The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Control: An Exploratory Study” Krauter, along with his co-authors, investigates the gut microbiome in a sample of PTSD affected individuals from South Africa. Their overall objective was to determine whether there would be differences in microbial diversity or microbial community structure, which essentially means they are looking at the range of different microorganisms such as bacteria and archaea present on an affected individuals gut (Pg. 2). PTSD was diagnosed based on the CAPS-5 scale (Pg. 5). Using a DNA extraction kit, DNA was extracted from 18 individuals with PTSD and 12 trauma-exposed control participants (Pg. 5). Their DNA was sequenced to determine the microbial community structure. This data was used to analyze alpha and beta diversity, which are measures to assess the diversity within or between samples, and to look at random forest analysis, which is simply a method used for classification (Pg. 2). While there were no differences in the alpha or beta diversity measures between the PTSD individuals and the control groups, three phyla were identified to distinguish PTSD (Pg. 2). Phyla refers to a group of classes with similar distinctive characteristics. The decreased relative abundances of these three phyla play an important role in

immunoregulation capabilities, thus inspiring future studies to evaluate the association between these phyla and PTSD (Pg. 2).

Krauter published a research article in August, 2017 called “Genetic influences on the human oral microbiome”. This research focused on the human DNA within the mouth of twins. He wanted to test the microorganisms in our mouth to see if their populations are affected based on their environment or if they are influenced by our DNA. Krauter hypothesized that human DNA influences these microbial populations and that our environment around us has less of an impact (Pg. 2). In order to test his hypothesis, Krauter used 752 identical twin pairs from the Colorado Twin Registry (Pg. 5). He used identical twins due to their matching DNA structure (Pg. 6). Samples were extracted from their mouths over a 2-7 year period (Pg. 7). He found that there are several heritable features in the oral microbiome and that heritability is consistent in twins even when their environment or cohabitation changes (Pg. 14). In addition, Krauter identified the exact place in the human DNA that influences the human oral microbiome (Pg. 3). Due to his discovery, scientists now have a better understanding of the microorganisms that live within us. This study is important for its ability to lift boundaries to further explore the DNA and microbiome that live within us.

Another study Krauter published, “Genome-wide association study of behavioral disinhibition in a selected adolescent sample”, takes a deeper look into behavioral disinhibition (which refers to the patterns of abnormal or impulsive behavior) to discover the specific place in the human DNA that is responsible for it. In this research article, Krauter directs his focus to adolescents to possibly discover why some individuals have antisocial behavior or substance misuse. In order to get results, Krauter sampled 1,901 adolescents that were selected from substance abuse treatment centers, special schools and the criminal justice system (Pg. 3). All participants had an average age of 16.5 and 28.9% were reported female (Pg. 3). In order to determine the specific location that is responsible for behavioral disinhibition in the human DNA, Krauter uses a genome-wide association study (GWAS) (Pg. 4). This is a research method that is used in order to locate diseases in DNA. This method involves using a large number of participants with the same disability to scan their genome (Pg. 4). While using this method, scientists look for similar markers in all individuals that may be able to determine a location in the DNA that is causing their specific disability. In his research, Krauter determines that there is no significant data that can locate behavioral disinhibition (Pg. 6). He does, however, identify seven genes that are associated with behavioral disinhibition. Krauter states that in order to find the location in the human DNA that is responsible for behavioral disinhibition in adolescents, he will need to replicate his study with a larger number of participants in order to receive more accurate results (Pg. 6).

MCDB publications use numerous conventions of research in order to solidify their work. The first convention to note is that many MCDB hypotheses strive to fill in gaps in the field’s knowledge. Unexplored or poorly understood questions drive the focus of the study. In “The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Control: An Exploratory

Study”, an objective is written in the abstract, stating that the purpose of this research is to identify potential differences in microbial community structure because, “the association between the gut microbiota and PTSD is unknown” (Krauter et al 2016, pg 2). In the next publication, “Genetic influences on the human oral microbiome”, the abstract states that, “The influence of human genes on the composition and stability of the oral microbiome is still poorly understood” (Krauter et al 2017, pg 1). Lastly, the abstract of “Genome-wide association study of behavioral disinhibition in a selected adolescent sample” states “no GWAS has specifically examined the overall BD construct” (Krauter et al 2015, pg 1). This convention of research is important to the MCDB field because it ensures that the field is constantly trying to fill in the gaps of its published literature to solidify its relevancy and ensure that the field reaches to all levels of its broad subject matter.

The second convention of research in MCDB includes the use of various known scientific techniques. This field is filled with both scientific and exploratory research however, the underlying methods typically remain constant. In both of the 2017 publications, the researchers extracted DNA from a given sample and sequenced this DNA, ultimately allowing researchers to look at the exact order of DNA bases. In the first publication, the specific DNA extraction and isolation kit, PSP® Spin Stool DNA Plus Kit, is explicitly stated (Krauter et al 2016, pg 5). In the second publication, the DNA isolation process had been, “previously described” and referenced to an article so that one could find the procedure in a different publication (Krauter et al 2017, pg 2). Additionally, in both these publications, the use of MiSeq sequence determination is used to sequence the extracted DNA. These are just a few of the scientific techniques involved in each study. Using these techniques allows for each experiment to be replicated or even critiqued. In the MCDB field, it is important to have a systematic way of obtaining results so this data can be argued as being valid.

With the use of scientific techniques described above, the field of MCDB highlights the important research convention of quantifiable data. Most of the data obtained through each study has a numerical value associated with it. The importance of this type of data is that researchers can use it to statistically analyze to further make general conclusions. For example, in the PTSD study, P and T values are used to show the differences in alpha diversity, which assesses diversity within a sample (Krauter et al 2016, pg 7). The oral microbiome study also used P values, this time to rank traits based on heritability (Krauter et al 2017, pg 9). Additionally, both of these studies used percentages to quantify phyla abundances (Krauter et al 2016, pg 7 & Krauter et al 2017, pg 5). Quantifiable data is an important research convention in MCDB because it allows studies to be compared quickly to both replicated or competing studies.

Throughout publications in the MCDB department, there seems to be a common trend within the writing conventions. Specific conventions are used for this major in order to make strong arguments and help the reader make connections that enable researchers to push ideas and make discoveries. The first convention of writing that was noticed throughout the published literature in MCDB is the continuous use of a discussion section. The discussion section allows

readers to understand the significance of the research and think about how the results of the research creates a new understanding of the problem. The section dives into the importance of the results and makes an argument to support the overall conclusion of the publication. This section is also good for explaining how previous studies can help determine the end result of the study. In both the publications “Genetic influences on the human oral microbiome” and “Genome-Wide Association Study of Behavioral Disinhibition in a Selected Adolescent Sample.” the authors use a discussion section to expand their thinking. This section is particularly useful for MCDB majors because it allows readers to make connections and develop their own research questions that could progress our general knowledge on the subject. For example, Krauter says “However, the current sample is likely underpowered to detect realistic effect sizes of individual SNPs”(Krauter et al, 2015, pg. 3). This example shows how Krauter uses the discussion section to explain how his end results could lead into a new research project by suggesting that his sample is likely underpowered and that a new sample taken would get a more clear result. In another publication, we see that Krauter suggests “twin studies are particularly powerful in differentiating between them” (Krauter et al, 2017, pg. 3). This example also shows us that the author is suggesting twin studies to be a powerful way of collecting genetic data. This causes the reader to think about other research projects that could be done by using twin studies.

Another convention of writing that is seen throughout MCDB, is the use of specific word choice that relates to the overall major. By writing this specific vocabulary in these publications, the author is under the assumption that the audience has a higher level scientific background and knowledge in order to understand each key word or phrase. For example, Krauter discusses how “The family Carnobacteriacea was excluded from the GWAS analyses since it was highly correlated with the genus Granulicatella” ( Kraurter et al, 2017, pg.4). In this example, Kraurter chooses vocabulary such as; Carnobacteriaccea, GWAS analyses, genus, and Granulicatella. He does not explain what any of these terms mean because it is under the assumption that the audience already has an understanding of these terms. In another publication, Kraurter says “However, one issue with searching for specific genetic influences on many continuous phenotypes, such as BD, is that the most severe, clinically significant levels are relatively rare in the general population” (Kraurter et al, 2015, pg.1). Here, he uses terminology such as; genetic influence, continuous phenotypes, BD, and clinically significant.

Lastly, in the MCDB department, scholars with published literature tend to write brief annotations underneath images or figures in order to clarify precisely what the image is showing. This provides the reader with an in-depth understanding of what the figure is explaining and what each value or image means in terms of the overall result of the research. For example, Kraurter annotates an image by saying “Plot of −log 10( p ) from the CADD GWAS, arranged by chromosomal location. The top (dashed) horizontal line indicates genome-wide significance at p =5×10− 8 ; the lower (solid) line marks p =5×10− 5 ” (Kraurter et al, 2015, pg.4). In this example, Kraurter explains exactly what the figure is showing and explains what certain markings are

indicating. By writing this, readers are able to have a better understanding of what the research is observing. In another publication, Krauter explains “Violin plots of the Principal Coordinate 3 of Unweighted UniFrac for each genotype within each ancestry population” (Kraurter et al, 2017, pg.4). In this example, Kraurter explains the specific type of plot he used and describes to the reader what they are viewing.

Works Cited

Demmitt, B.A., Corley, R.P., Huibregtse, B.M. et al. Genetic influences on the human oral microbiome. BMC Genomics 18, 659 (2017).

Derringer, Jaime et al. “Genome-Wide Association Study of Behavioral Disinhibition in a Selected Adolescent Sample.” Behavior genetics vol. 45,4 (2015): 375-81. doi:10.1007/s10519-015-9705-y

Hemmings, Sian M J et al. “The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study.” Psychosomatic medicine vol. 79,8 (2017): 936-946. doi:10.1097/PSY.0000000000000512

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