BIO130 Library Information Resources Assignment

BIO130 Library Information Resources Assignment

Objectives
• To examine the peer review process and understand how this applies to scholarly journal articles • To be able to distinguish between peer-reviewed primary research papers and review papers • To learn how to use on-line library resources to locate a review paper and primary research paper on a topic of interest • To begin to learn about the parts of a primary research paper and how scientists read the primary literature.
Tasks • Read the following notes and Appendix. • View the following movies/tutorials on Blackboard in the Library Assignment Tab: o Sources of Information o Web of Science o PubMed These movies/tutorials were created in partnership with the Gerstein Library. There is also a link to the BIO120 Library Guide in case you have forgotten how to determine if your chosen papers are peer-reviewed or need some help avoiding plagiarism. • Complete the library information resources assignment and hand it in to your TA at the beginning of Lab 4. Overview In this assignment you will locate 2 science articles using online search resources: one peer-reviewed primary research article and one peer-reviewed review article. You will need to fill in and print the table on pages 4-5 of this document. You will also need to print a few pages from each of your articles to hand in to your TA. Carefully follow the instructions on the next few pages. Your TA will go over his/her expectations during Labs 2-3.
Topic choice Your TA has chosen the topic for your lab group. Please refer to the table on the next page to find your topic:
BIO130 Library Information Resources Assignment 2
Library Assignment 2017 *Topics can be determined by TA name or lab section and group. This list is not in alphabetical or numerical order. Topic TA Lab Section and Group Evolution of prokaryote and eukaryote organisms Sonhita P0201C/P0202C Cell fate specification during early development Adam, and Nathan P5101C/P5102C, and P0601B/P0602B DNA damage or repair and its relationship to cancer Parama and Hayley P0101E/P0102E and P0301E/P0302E
Histone modifications Linda P0501C/P0502C
Protein structure Ree and Yunyun P0101B/P0102B and P0401A/P0402A
Protein folding Michael P0401C/P0402C
RNA Processing Patrick P5101B/P5102B Advances in genome sequencing for disease treatment Priyank, Shalabh and Jarlath P5201B/P5202B, P0301A/P0302A and P0401B/P0402B Control of gene expression Medha, Varshinie, Van, and Kevin P0101D/P0102D, P5101A/P5102A, P0301B/P0302B, AND P0501D/P0502D Chromatin structure, function, or regulation Farah P0101A/P0102A Taq polymerase and DNA amplification Armand, June, and Joey P0301C/P0302C, P5401A/P5402A, and P0401E/P0402E Proteomics Sebastian P0201D/P0601C Protein post-translational modifications Kenana, Abdiwahab and Derek P0101C/P0102C/P0202A, P5401B/P5402B, AND P0501B/P0502B Transcriptome- wide RNA sequencing Cassandra P0401D/P0402D Regulation of homologous recombination Ehsan and Matthew P0201A/P5301A/P5302A and P0301D/P0302D
Regulation of Eukaryotic cell death
Maryna, Syed, Justin, Lisza, Stuart, and Lidia
P5201A/P5202A. P0201B/P0202B, P5301B/P5302B, P5401C/P5402C/P0501E/P0502E, P0501A/P0502A, and P0601A/P0602A
BIO130 Library Information Resources Assignment 3
Instructions 1. Find a peer-reviewed review article that addresses your topic. Refer to the tutorial and animations in our Library Assignment tab on Blackboard for guidance. Also read Appendix 1 at the end of this document. 2. Download the review article and print the first page of the article. Make sure it includes the title, authors and the beginning of the text of the article—some journals include a cover page without this information—please do not print this page. 3. Find a peer-reviewed primary research article that addresses your topic. Again, refer to the animations and tutorial on our Library Assignment site for guidance. Note: Your primary research article must cover the same topic as your review article. 4. Search for and download your primary research article, and print the first page of the article. Make sure it includes the title, authors, abstract and the beginning of the introduction. Again, some journals include a cover page without this information—please do not print this page. 5. Fill in the table on the following page. a. Use the CSE style for your citations. Refer to the BIO120 Library Guide: Citing Sources—scroll down to “Citation Format in the Literature Cited” section to see how to do this. b. Note that you will need to view the “Sources of Information” tutorial as well as read Appendix 1 to complete the table. c. Print pages as indicated in the table for each of your journal articles. Where required, be sure to clearly circle and label the required components on the pages you print. 6. Attach the printed and labeled pages of your journal articles to the back of the completed table and hand in to your TA at the beginning of Lab 4.
BIO130 Library Information Resources Assignment 4
BIO130 Library Assignment Worksheet Please attach this to the front of your printed journal pages Name:______________________________________________ TA and Lab Section: ___________________________________
Review Article Primary Research Article Citation: Use the CSE style to cite your peer-reviewed review and primary research articles (4 marks: 1 mark for each appropriate article and 1 mark for each accurate citation).
Print the first page of each article.

a) Compare and contrast the features of each chosen article by listing 3 points specific to each article showing why they are “primary” or “review”. (6 marks) b) Print out a page from each article that contains at least one of these features. Circle and label this feature. (4 marks).
Note that circling the word “review” will not earn a mark.

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BIO130 Library Information Resources Assignment 5
Review Article Primary Research Article When determining which experiments to conduct, the authors of a primary research article must first determine their research question. a) What is the research question for your primary research article? (2 marks)
b) What other research questions could the authors have addressed? (2 marks)

BIO130 Library Information Resources Assignment 6
A primary research article presents a collection of experimental data which will usually support or contradict the authors’ hypothesis and will answer or partly answer their research question. (Hint: You can find this information in the abstract and introduction).
a) For your primary research article, did the results support or contradict the authors’ research question/hypothesis? (1 mark)
b) Explain (3 marks)

Bibliography/References Cited: Compare your two articles in terms of the quantity and types of references (primary vs. review) cited in each. (2 marks)

If you do not remember from BIO120H how to use the library resources or how to determine whether your journal article is peer- reviewed, please see the library guide created for BIO120H at http://guides.library.utoronto.ca/bio120
Modified from an earlier document created for BIO241 (Dr. Melody Neumann, Dr. David Dansereau and Heather Cunningham).
BIO130 Library Information Resources Assignment 1
Appendix—Reading and Distinguishing Between Primary Research and Review Articles Reading Scientific Papers
Biology is a collective enterprise; the growth of our understanding depends on the work and insight of many individuals and on the exchange of data and ideas. Ultimately, biologists must be effective writers because no experiment can contribute to the existing scientific knowledge unless it has been described so others working in the same field can access this information. With so much information out there, to be a successful biology student, and perhaps later an effective research scientist, you will need to develop competent writing skills as well as information-literacy skills. In other words, you need to know how to locate the scholarly work of others, how to critically evaluate these sources, and how to incorporate this information effectively into your own writing.
For this course, you will be required to find and do some reading of original scientific papers for your Library Assignment. The guidelines in this section are intended to help you distinguish between different types of scientific papers. Another goal of the Library Assignment is to learn about the parts of a primary research paper. Understanding the key components of primary research papers will help you to read them more easily. Furthermore, reading scientific papers will help you write better papers in the future, and writing your own papers will help you read other scientific papers with deeper understanding.
Learn to distinguish primary and secondary sources
Primary sources are reports of original findings and ideas usually found in peer-reviewed research papers in scholarly journals directed at a specialized scientific audience. There are thousands and thousands of journals. Some (e.g., Nature, Science, Proceedings of the National Academy of Science (PNAS)) report findings across many disciplines, while others focus on more specialized areas (e.g., Plant Cell Biology). One of your tasks as a student is to become familiar with the key journals in the area you are studying; for this course the area is molecular and cell biology.
In addition to research papers in peer-reviewed journals, other primary sources include conference papers and technical reports of government or private agencies. However, refereed journals are a safer source for credible information as the articles have been reviewed and scrutinized by peers before being published.
Secondary sources are more general works that are based on primary sources. Some types of secondary sources such as review articles are also written for a specialized knowledgeable audience. Other types of secondary sources are intended for readers with little specific knowledge of the area including magazines such as American Scientist, Scientific American or The New Scientist. These secondary sources are a good place to start if you want an overview of the area without a lot of unexplained jargon.
BIO130 Library Information Resources Assignment 2
Primary Research Article
Ultimately you will need to read the original (primary) source, but this information assumes a thorough understanding of the background information and is therefore a difficult place to start. Primary articles are written by research scientists to inform the larger scientific community, primarily their specialized peers, of their findings; therefore, the authors assume readers are knowledgeable in the area. Research articles tend to have a very narrow focus. To appreciate the context and relevance of a particular research paper, you may find it easier to read reviews and other secondary sources first.
Review Article
A primary research article differs significantly from a review article. A review article summarizes and synthesizes and more importantly evaluates the concepts and/or results from several research articles on a related topic; thus authors of review articles compare, contrast, and interpret work of others. Authors of review articles are themselves experts in the field and bring to the topic an integrated perspective. Original or new data are not introduced in a review, but knowledge of the area is assumed. Authors of review articles are often invited by journal editors to review a topic; other authors write unsolicited reviews.
However, many review articles are not easy to read at first either. Before reading the review you will need to familiarize yourself with the terms and general concepts in other secondary sources such as a textbook or course lecture notes.
Where do you find review articles? Some journals publish review articles exclusively: Trends in Biochemistry/Genetics/Biotechnology/Microbiology or Current Opinion in Chemical Biology. Many journals have a mixture of primary research and review articles (e.g. Science and Nature).
How do you recognize a review article and distinguish it from primary research? The format of a review article is different from a primary research paper as the review does not present original experimental results. Abstracts may or may not be included, the Materials and Methods section is usually omitted, and tables and graphs are rare except for summarizing comparative data. Often review articles have “Review” or “Minireview” near the title. A review paper typically has a Title, Author(s), Abstract (or Summary), and then the Discussion is the main part of the paper with an extensive list of references at the end.
Components of a primary research paper
Now that you have been introduced to the differences between primary and secondary sources, we will now go into greater detail about the components of a primary research paper.
Primary papers in most scientific journals strictly adhere to a traditional format with Title, Author(s), Abstract (sometimes called Summary), Introduction, Materials and Methods, Results, Discussion, and References. Although some journals (e.g., Science) do not explicitly print the section headings, the content usually follows in that order.
BIO130 Library Information Resources Assignment 3
The context of a paper is set up in the Introduction and elaborated in the Discussion section. The Introduction is a good place to start when reading a paper, especially in areas less familiar to you, as this section frames the scientific question that the paper addresses. The Abstract is a concise description of what was done and the outcome, often given very tersely, and is more difficult to follow than the Introduction.
The Materials and Methods section will contain a description of each technique used by the authors, generally separated by headers. The methods and materials are described in enough detail that someone skilled in the field could repeat the experiments. Therefore, detailed descriptions are not necessary and often the authors reference other papers for details on the techniques used. A growing number of journals provide the Materials and Methods at the end of the article.
The Results section is where the authors will describe the outcomes of their experiments. A scientist will approach a primary paper in his/her own field very critically, paying particular attention to the Results section. The Results are usually presented as a series of tables, graphs, or photographs and a scientist will critically read this section to determine whether the author’s interpretation of the data is correct. In future courses, you will also learn to look at the data carefully, to evaluate the data independently of the author’s own interpretation. A primary research paper typically has one critical figure summarizing the most significant data related to the experimental question – try to pick this figure/table when examining your chosen primary research paper. Usually the rest of the data are provided to reinforce/supplement this key finding.
The Discussion contains the interpretation of the results and explains how the findings relate to those of others.
Table 1 on the next page summarizes the features of a primary research paper and how these are used by a) an expert reading the paper in depth and b) someone from outside the field reading the paper (students fit most often into this second category).
BIO130 Library Information Resources Assignment 4
Table 1. The Primary Research Paper: summary of components and their purpose(s) Function a) In depth reading by expert in the field b) Reading by someone outside the area
Title
Tells what the paper is about.
Authors
Who did the work and who assumes responsibility for it.
Can follow work in a particular lab.
Get to know key names in the field and institutions doing specific types of research.
Abstract
Summarizes the results and sometimes the interpretations
Important-most salient facts in one place.
Not as important as the Intro.
Introduction
Sets the framework of the paper: why is it important or interesting?
Not that important-the more informed can put the paper in context.
Very/most important part of the paper.
Materials and Methods
Details the materials used and experimental methods
Worth detailed analysis to see exactly what was done–also place to look for weakness in approach.
Usually obscure for someone not in the field– important when methods are not standard or if paper is unbelievable.
Results
Reports what the authors actually found.
The most important section of the paper: “just the facts”
Important to see if the data support the stated hypothesis or alternative views or raise additional questions.
Discussion
Two sets of issues: 1) the adequacy of the experiments themselves. 2) the relationship of the results to other work in the field.
Not so important because the reader can and should evaluate the data and place in context.
The best insight into the author’s context, revealing the level of confidence in the conclusions.
Bibliography
List of papers relevant to experiments or conclusions
Where to find details of methods and context.
Source of additional information.
Adapted from: Tobin, A.J. and Morel, R.E. 1996 Asking About Cells. Harcourt, Brace and Company. p. 26-27. Printed with permission, Universal Access Copyright.

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