Food and Mouth Disease Virus

Animal Science 001
Fall 2019 - Assignment #2
Due Date and Time: 4:59:59PM on December 2nd, 2019, through CANVAS

The fever continues: Continuing to develop into the scientist you already are!
In Assignment #1 you had the opportunity to learn about African Swine Fever and the extent of its rapidly-evolving impact. It was also a chance to assess and reflect on where your writing skills are. The goal here is to introduce you to a scientific paper and to perform a dissection – of the paper, that is, while exposing you to another serious virus (only via a paper that is) – foot and mouth disease.

The scientific literature is where scientists share their findings and knowledge. This is often in the form of “journals” (or “journal publications”) that are periodically published as a collection of papers that go out in an issue (and/or volume) to scientists, libraries, etc. In the good old days (even now, but less so), the main destination was universities, Government labs, etc. because they were prepared only as hardbound copies. In the present day, they are shared digitally, and are more accessible to a wider audience range than ever before! This change alone has happened in only the past 25 years!

Please note: This original research paper (Ferreira et al) may seem hard/scary(!) to digest, given the average coursework background for students in ANS001. That’s OK and expected. There is a balance here. We are not expecting you to understand every little detail. But at the same time, the only way to ride a bull is to grab it by the horns!! (please don’t try that at home..). Therefore, do the best you can. Stumble through it – find out what you do know and what you don’t - and realize that by the end of your degree you will have the skills and confidence to read one of these from start to finish – how cool is that!!? You should expect to read the paper or its sections several times. Do not leave it till the last minute – it may end badly! In addition you may well have to do some additional searching to strengthen your understanding or interpretation of a certain topic, term, or research method. Reading a scientific paper is not like reading a novel – it takes quite a bit of work and dissection.

Here’s what you have to do:
Section A: Explain some “details” about the “original research” paper you have before you:
1. What “Journal” was it published in?
2. What page numbers did the article span?
3. In what year was it published?
4. Who were the authors?
5. What institution were the authors from? Were they all from the same place? Who was from where?
6. What was the volume of the Journal that this paper was published in?
7. What is the PMID number for this paper?
Section B: Getting into the paper itself:
8. First, seek to read and learn about foot and mouth disease. We want you to at least reference this following article we are pointing you to as the key source (PMID:31023873). Provide a concisely written paragraph (~250 words) on what you have learned. Be very very sure not to copy/paste or plagiarize!! You should cite this source at least once within your answer as an “in text” citation, just the way the authors did many times in their papers. The format of your in-text citation and its complete reference must match the exact “Journal of Animal Science” instructions to authors. This requires you to get all the parentheses, commas, order, etc correct (points deducted for mismatches). We want you to get used to appreciating that detail matters.
The “instructions to authors” can be found here: https://www(dot)asas(dot)org/ then by seeking out the Journal of Animal Science information and “instructions to authors” link within that page. (Check out the ASAS website as well while you are here!)

9. Now start diving into the paper by Ferreira et al. Did the authors specifically state their “objective” (if not phrased specifically that way, did they state what they were setting out to do?, which would be your interpretation of their objective?). Please briefly explain what you think their “objective” was.

10. Did the authors specifically state their “hypothesis” (If not phrased specifically that way, could you infer one?). As above, please briefly explain what you understand their hypothesis was – explaining at the level you would use to explain to friends or family over Thanksgiving dinner.

11. The authors conducted 2 experiments. To the best of your ability, we would like you to explain in your own words their “experimental design” for each experiment, separately. Your explanation should be pitched at the level of Thanksgiving dinner discussion. You should speak to how many subjects they used? What “treatments” did they apply? What were their subjects? How many subjects in any given group? What was their end point? What units of measure did they use? What form of data did they present when representing the individual data points as a combined measurement? This is your attempt to give an explanation back about what you interpreted. Your answers will be evaluated on evidence of interpretation and understanding. Please explain the 2 experiments in approximately 300 words, total.

12. We would like to know about the “materials and methods” they used to generate these data. There will be things (techniques, terminology) you don’t understand, but do your best to simply outline them. This should also be a “Thanksgiving dinner” type explanation. A couple of key points. Do not cut and paste strings of words or sentences (that would be plagiarism), but we understand you will have to represent some text and words “as is”. Also, be sure to look in more than one place of the Materials and Methods section, as there could be extra information across sections. Please explain these materials and methods in about 300 words. You must show a clear effort to avoid using the author’s words, where we will deduct points for signs of similarity or overlap.

13. In the results section the authors report a series of outcomes. First, for each experiment (Table 1 and Figs 1 and 2), describe the “measures” they made, and the “units” those measurements were made in. Then also describe the actual findings reported in Table 1 and Figures 1 and 2 (in Thanksgiving terminology, that is). Approximately 100-150 words.

14. In Table 1, there are terms called “P-value” and SEM. Using resources that you might find online, seek to understand and explain in your own words why they have used this type of terminology to describe their data in Table 1. Approximately 100 words. Your answer should be concise and written in a scientific tone.

15. In the discussion section, the authors take the chance to “explain and interpret” their findings. We would like you to interpret and explain the key elements of the discussion in your own words, to the best of your ability. What were the key outcomes and findings? Are they referring to their own findings? Are they referring to the work of others? Are they speculating? Are the suggesting where the work should go in the future? Approximately 200 words.

16. Lastly, you’ve had a chance to look over both the review paper (as above, PMID 31023873) and this “original research” paper. You may now consider yourself an expert…. or, you might be thinking “I can’t wait to continue my degree”!!
We would like you to summarize your thoughts on what you have just done in terms of gathering scientific information. Specifically, compare and contrast the 2 types of paper used here. Also, compare the level of science and information here to that you gathered in Assignment 1 – are they different? Which one(s) do you trust the most? How does your writing style compare to the writing style in these papers? Do you think that people from all backgrounds would be able to digest these sources of information? Do you foresee any potential for confusion or misinterpretation going from the scientific literature to the public press? (approximately 300 words).


Final Notes:
>Your submissions are due through Canvas by December 2nd 4.59 PM - no late submissions. Heavy penalties will be applied for late submissions.
>Just like Assignment 1, you should attach a cover “logo” to your submission with your name, student ID, lab section, and TA.
>Please cut and paste each question (1-16 above) into your answer sheet to provide a prompt below which you can enter your answer. This will help you check your responses match the question.
>Get help from as many sources as you can (writing assistance etc.). This is an important part of learning to write well. That means plan ahead. Also refer to any guidance you received from assignment 1. Please recognize that Assignment 1 was graded relatively “easily” and assignment 2 could be graded harder with less tolerance for writing deficiencies.
>Your TA will take the chance to review any questions you might have in lab next week. Please at least review the assignment and raise any questions.
> Do not leave this to the last minute. Anecdotal evidence from Assignment 1 would suggest that students who left it to the last minute tended to do poorly vs. those who submitted earlier.
> PS. How many “words or terms” did you see in this paper that have come up in ANS001 this quarter"
> PPS if there are any ambiguous details regarding this assignment please let your TA and Dr Ozzie know, there may be something that was overlooked or perhaps is confusing?