term paper

Term Paper Guideline

Draft Due: October 24, 2020

Term paper critique due; November 7, 2020

Final Report Due: November 20, 2020

Short literature review-maximum 3 pages

Please read the article by Duan (2019) and write a paper review. Please follow the guideline and the rubric below. I have uploaded a shorter version with marked paragraphs. (Duan2019_annot). Use this version to follow the guideline.

Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6872939/ Study Guide: General Background: This paper describes using phages to target gut bacteria which seems to cause liver disease. I have highlighted some questions in each section. Please include the answer to these questions in your review. Abstract: Summary

• This section summarizes its findings. Note how the first three sentences describe the background, and the third sentence starts talking about their results. An abstract should mostly contain the findings or results, not an introduction. Your abstract should follow this, and the introduction should not exceed more than 30 % of the abstract.

The main article-Paragraphs of each section is labeled as P1, P2…. Introduction A short introduction to the problem and the paper’s research direction. Cytolysin linked to increased mortality

P1: This section describes that they found a correlation between a bacteria species, E. faecalis, and alcoholic hepatitis. Figure 1a provides data for this. Since it is technically difficult to interpret, take their word for this section. (1) What is alcoholic hepatitis? Search the internet and describe it in 2~3 sentences. P2: Among the E. faecalis, the ones with an exotoxin, cytolysin, have a clinical effect. This is shown in Figures 1b and 1c. P3: Ignore this section P4: The authors built a phylogeny map based on the sequence. (2) Is the cytolysin a common trait among E. faecalis? Why or why not? Use Figure 1d to explain. P5: They found the total amount of E. faecalis is not different between the severe cases and milder cases. Cytolysin and ethanol-induced liver disease P1~3: The authors tested whether cytolysin induces liver damage in mice. P4: They wanted to test mice with cytolysin-positive and cytolysin-negative human fecal samples. Figure 2a~c shows the results. High ALT and hepatic triglyceride are indicators for liver damage. (3) Do you think cytolysin caused liver damage based on this data? Why or why not? Use the Fig 2a~c to explain. P5: Ignore this section. Bacteriophage treatment in liver disease P1-2: The authors used bacteriophage to kill the pathogenic E. faecalis. For this, they first isolated phages specifically kill the cytolysin E. faecalis, then given to mice infected with E. faecalis. Fig 3b-d shows the result. P3: the author did the same experiment using phage which targets non-cytolysin E. faecalis. The results show no effect. Fig. 4b-d shows the result. (4) Do you think the phage targeting the cytolysin E. faecalis reduces liver damage compared to the phage targeting the non-cytolytic bacteria? Why or why not? Use the figure 3b-d and 4b-d to explain Discussion: describes the summary and interpretation of their findings Maximum 3 pages- 1" margin on all side, typed

• Title page-not included in the 3-page limit • Abstract: Brief (<250 words) summary of the paper.

The rest of the content could be freestyle, but make sure to include the following content. Follow the guidelines provided.

• Begin with a summary of relevant background information and statement of the major question being addressed.

• A discussion of the experimental approaches- explaining the question/hypothesis, methodology, results, and interpretation of the data (1 page),

• a summary of the overall conclusions, including a discussion of whether hypotheses were supported or not. (1/2 page)

• A bibliography, not part of the 3-page limit, should be included. For the term paper, following the correct bibliography format is important. You can use any bibliography format typically found in a scientific journal. This includes "in-text" citation and detailed information in the "reference" section. Grading Rubric

Criteria Points

Abstract A concise summary of the paper: This is not an introduction. Do not put more than 30% of the background material in this section.

10

Background 25

Experimental Approaches Include the answers for questions asked above in red (1, 2, 3, 4)

30

Conclusion 15

Overall Organizations/Writing, Reference format 20