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DNA Barcoding Complete Manuscript
Comment Prompt: Abstract Content
Please comment on how well the abstract provides a clear overview of the entire manuscript. The abstract should contain a very brief summary (1-3 sentences) of every component of the paper, including Introduction (background), Methods, Results and Conclusions. The hypothesis tested and the finals conclusions should be clear.
Rating Prompt: Abstract Content
Please provide a rating on how well the abstract provides a clear overview of the entire manuscript. The abstract should contain a very brief summary (1-3 sentences) of every component of the paper, including Introduction (background), Methods, Results and Conclusions. The hypothesis tested and the finals conclusions should be clear.
4 Excellent. All 4 sections are present and clearly, concisely explained. In one paragraph of not much more than 300 works, the reader understands the general idea of what experiment was performed and what the outcomes are.
3 Proficient. All 4 sections are present, but not all sections are clear. The abstract is well over or under 300 words.
2 Novice. One or more sections are not clearly addressed.
1 Not addressed. Two or more sections are missing.
Weight 1.0
Comment Prompt: Introduction: Background Information & Sources
Please comment on whether the background information provided in the introduction is accurate and relevant. There should be 3 primary, peer-reviewed literature references that help provide this background information. There can be additional sources and review articles that are used for clarification, but two of the sources must be primary, peer-reviewed and specifically discussed.
Rating Prompt: Introduction: Background Information & Sources
Please rate whether the background information provided in the introduction is accurate and relevant. There should be 3 primary, peer-reviewed literature references that help provide this background information. There can be additional sources and review articles that are used for clarification, but two of the sources must be primary, peer-reviewed and specifically discussed.
4 Excellent. 3 Primary sources are well discussed and the overall writing is clear and compelling, possibly with review articles used to introduce or clarify the topic.
3 Proficient. Background information is completely accurate. Primary literature references are relevant, adequately explained and indicate a reasonable literature search.
2 Novice. Background omits information or contains inaccuracies which detract from the major point of the paper. Background information is only partially relevant. Only one reference is primary and other references are reviews.
1 Not Addressed. Background information is missing or contains major inaccuracies. Primary literature references are absent or irrelevant.
Weight 3.0
Comment Prompt: Introduction: Context & Writing Quality
Please comment on how well the introduction demonstrates a clear understanding of the context or ‘big picture.’
Rating Prompt: Introduction: Context & Writing Quality
Please rate how well the introduction demonstrates a clear understanding of the context or ‘big picture.’
4 Proficient. The writer provides a clear sense of why this knowledge may be of interest to other researchers in the field. The writer describes the current gaps in our understanding of the field and explains how this research will help fill those gaps.
3 Intermediate. The writer provides one explanation of why others would find the topic interesting. The writer provides some relevant context for the research question(s).
2 Novice. The writer provides a generic or vague rationale for the importance of the question. The writer provides vague or generic references to the broader context of biology.
1 Not Addressed. The importance of the question is not addressed. How the question relates within the broader context of biology is not addressed.
Weight 1.0
Comment Prompt: Hypothesis
Please comment on the strengths and areas of improvement of the hypotheses. Is the hypothesis clearly stated and testable?
Rating Prompt: Hypothesis
Please rate the quality of the hypothesis.
4 Proficient. Hypotheses are novel, insightful, or actually have the potential to contribute useful new knowledge to the field.
3 Intermediate. Hypotheses indicate a level of understanding beyond the material directly provided to the student in the lab manual or coursework.
2 Novice. Hypotheses are plausible and appropriate though likely or clearly taken directly from course material.
1 Not Addressed. Hypotheses are trivial, obvious, incorrect, or completely off topic.
Weight 1.0
Comment Prompt: Methods: DNA Extraction, PCR, Purification and Electrophoresis (Partial Manuscript)
Please comment on the strengths and areas of improvement for the methods section which covers DNA Extraction, PCR, Purification and Electrophoresis. The methods should include everything needed to repeat these parts of the experiment, including, among others: sample description, PCR description (target gene, primers, cycles), and electrophoresis description (voltages, run times).
Rating Prompt: Methods: DNA Extraction, PCR, Purification and Electrophoresis (Partial Manuscript)
Please rate the methods section which covers DNA Extraction, PCR, Purification and Electrophoresis. The methods should include everything needed to repeat these parts of the experiment, including, among others: sample description, PCR description (target gene, primers, cycles), and electrophoresis description (voltages, run times).
4 Proficient. All information to repeat all experiments is included. Steps are clear.
3 Intermediate. Most information to repeat the experiments are included, with minor omissions
2 Novice. Most of the methods are there, but details are missing, such as target genes or electrophoresis voltages, so experiment cannot be replicated
1 Not addressed. Missing major parts of methodology, such as the entirely of PCR or electrophoresis
Weight 2.0
Comment Prompt: Methods: Sequencing and BLAST (Complete Manuscript)
Please comment on the strengths and areas of improvement for the methods section which covers Sequencing and BLAST. The methods should include everything needed to repeat these parts of the experiment, including, among others: search parameters used for BLAST.
Rating Prompt: Methods: Sequencing and BLAST (Complete Manuscript)
Please rate the methods section which covers Sequencing and BLAST. The methods should include everything needed to repeat these parts of the experiment, including, among others: search parameters used for BLAST.
4 Proficient. All information to repeat all experiments is included. Steps are clear.
3 Intermediate. Most information to repeat the experiments are included, with minor omissions
2 Novice. Most of the methods are there, but details are missing, such as target genes or electrophoresis voltages, so experiment cannot be replicated
1 Not addressed. Missing major parts of methodology, such as the entirety of sequencing or BLAST.
Weight: 2.0
Comment Prompt: Results: Electrophoresis Figure
Please comment on the strengths or areas of improvement for the Electrophoresis Figure. Is the figure appropriately cropped and electronically labeled? Are all lanes clearly labeled, including ladder, controls and test lane? Is it clear what primers are used? Is a figure legend included? Does the figure stand alone, with no need to refer back to the main text?
Rating Prompt: Results: Electrophoresis Figure
Please rate the quality of the Electrophoresis Figure. Is the figure appropriately cropped and electronically labeled? Are all lanes clearly labeled, including ladder, controls and test lane? Is it clear what primers are used? Is a figure legend included? Does the figure stand alone, with no need to refer back to the main text?
4 Proficient. Contains no mistakes. Uses a format which presents data clearly and allows insight into the data. Has informative, concise, and complete captions.
3 Intermediate. Contains minor mistakes that do not interfere with understanding. Includes captions that are at least somewhat useful.
2 Novice. Contains some errors in or omissions of labels, but the reader is able to derive relevant meaning from each figure. The presentation is technically correct but may have an inappropriate format. Captions are missing or inadequate.
1 Not Addressed. Labels are missing which prevent the reader from being able to derive any useful information from the figure. Captions are confusing or indecipherable.
Weight 2.0
Comment Prompt: Results: Text for PCR and Electrophoresis (Partial Manuscript)
Please comment on the strengths or areas of improvement for the text addressing the results of PCR and Electrophoresis. Does the text reference the electrophoresis figure and clearly walk through the data in the figure, with no interpretation of the results? Is the amplified gene and all controls included?
Rating Prompt: Results: Text for PCR and Electrophoresis (Partial Manuscript)
Please rate the text addressing the results of PCR and Electrophoresis. Does the text reference the electrophoresis figure and clearly walk through the data in the figure, with no interpretation of the results? Is the amplified gene and all controls included?
4 Proficient. All the data is included, including positive and negative control DNA. Is the data summarized in a logical format using appropriately labeled gel?
3 Intermediate. The data is comprehensive, accurate, and relevant with minor gaps.
2 Novice. At least one relevant data set is provided but some necessary data are missing or inaccurate.
1 Not Addressed. The data is too incomplete or haphazard to provide a reasonable basis for testing the hypothesis.
Weight 1.0
Comment Prompt: Results: Sequencing and BLAST (Complete Manuscript)
Please comment on the strengths or areas of improvement for the text addressing the results of Sequencing and BLAST. Does the text discuss the results of the sequencing, including reference to a figure of the electropherogram? Are BLAST parameters fully discussed, including e-value and BIT score?
Rating Prompt: Results: Sequencing and BLAST (Complete Manuscript)
Please rate the text addressing the results of Sequencing and BLAST. Does the text discuss the results of the sequencing, including reference to a figure of the electropherogram? Are BLAST parameters fully discussed, including e-value and BIT score?
4 Proficient. Electropherogram is referenced and included as a figure. BLAST parameter results are included, including both e-value and BIT score.
3 Intermediate. Both sequencing and BLAST results are included, but there are minor omissions from these sections
2 Novice. Both sequencing and BLAST are discussed, but some parameters are missing from both sections
1 Not addressed. Major omissions; sequencing or BLAST is missing.
Weight: 2.0
Comment Prompt: Discussion: Electrophoresis Controls
Please comment on the strengths and areas for improvement in the Discussion section, specifically the controls. Are all controls discussed and accurately interpreted? Controls will include positive control DNA and negative control DNA. Please be specific in your response.
Rating Prompt: Discussion: Electrophoresis Controls
Please rate the Discussion of the electrophoresis controls. Full discussion of the controls will include positive control DNA and negative control DNA.
4 Proficient. Controls consider all relevant factors and have methods of differentiating between multiple hypotheses. Replication is robust. Explanations of why these controls matter are thorough and clear.
3 Intermediate. Controls take most relevant factors into account. Replication is appropriate. Explanations are mostly accurate and reasonable as to why these controls matter to this experiment.
2 Novice. Controls consider one major relevant factor. Replication is modest with weak statistical power. Student explanations of controls are vague, inaccurate, or indicate only a rudimentary sense of the need for controls or replication.
1 Not Addressed. Controls and/or replication are non-existent or inappropriate. Student fails to mention controls and/or replication, or mentions them but the explanation is incomprehensible.
Weight: 1.0
Comment Prompt: Discussion: DNA Barcoding Sample Conclusions
Please comment on the strengths and areas for improvement in the Discussion section. Does the discussion provide a conclusion that is logically drawn from the data provided, including all controls? Does the paper clearly state what organism is or is not indicated by DNA Barcoding, with support from the controls, electropherogram and BLAST statistics? Please be specific in your response and provide suggestions for improvement where applicable.
Rating Prompt: Discussion: DNA Barcoding Sample Conclusions
Please rate the strength of the conclusions in the Discussion section. Does the discussion provide a conclusion that is logically drawn from the data provided, including all controls? Does the paper clearly state what organism is or is not indicated by DNA Barcoding, with support from the controls, electropherogram and BLAST statistics? Please be specific in your response and provide suggestions for improvement where applicable.
4 Proficient. Conclusions are completely justified by data. Connections between hypothesis, data, and conclusions are comprehensive and persuasive. Conclusions address and logically refute or explain any conflicting data. Synthesis of data in conclusion may generate new insights. All controls are discussed.
3 Intermediate. Conclusions are clearly and logically drawn from the data. A reasonable and clear chain of logic from hypothesis to data to conclusion is made. Conclusions attempt to discuss or explain conflicting or missing data.
2 Novice. Conclusions have some direct basis in the data but may contain some gaps in logic. Connections between hypothesis, data, and conclusions are present but weak. Conflicting or missing data are poorly addressed.
1 Not Addressed. Conclusions have little or no basis in data provided. Connections between hypothesis, data, and conclusions are non-existent, limited, vague, or otherwise insufficient. Conflicting data are not addressed.
Weight: 1.0
Comment Prompt: Discussion: Relevance of this Manuscript’s Findings to Other Research
Please comment on the strengths and areas for improvement in the Discussion section, in terms of how the author relates their findings to other findings in the related scientific field? How do these results compare to the results found by other scientists, such as scientists who are also using DNA Barcoding or genetically analyzing a similar species? The discussion must include two primary, peer reviewed studies which are loosely related to this study and briefly compare and contrast their findings to the author’s findings. May also include review papers, in addition to the two primary, peer-reviewed studies.
Rating Prompt: Discussion: Relevance of this Manuscript’s Findings to Other Research
Please rate the Discussion section, in terms of how the author relates to their findings to other findings in the related scientific field? How do these results compare to the results found by other scientists, such as scientists who are also using DNA Barcoding or genetically analyzing a similar species? The discussion must include two primary, peer reviewed studies which are loosely related to this study and briefly compare and contrast their findings to the author’s findings. May also include review papers, in addition to the two primary, peer-reviewed studies.
4 Proficient. Two relevant, primary, peer-reviewed papers are discussed and compared or contrasted with the current study. The writing is interesting and illuminates the significance of this work in relation to the work of others.
3 Intermediate. Two relevant, primary, peer-reviewed papers are discussed. The papers are contrasted to this study, but the connection between this study and the other study is not always clear or relevant.
2 Novice. One relevant, primary and peer-reviewed paper is compared to this study. Other review papers many be included, but were not primary.
1 Not addressed. No primary, peer-reviewed sources were included. Only review articles were included, or no sources were included at all.
Weight: 3.0
Comment Prompt: Discussion: Future Research
Please comment on the strengths and areas for improvement for how well the paper gives an indication of the significance of the research and its future directions.
Rating Prompt: Discussion: Future Research
Please rate how well the paper gives an indication of the significance of the research and its future directions.
4 Proficient. The writer clearly explains how this work fills our knowledge gaps and new questions or opportunities that are opened as a result of this work. Future directions are salient, plausible, and insightful.
3 Intermediate. The significance explained demonstrates only partial knowledge of the field. Future directions are useful, but indicate incomplete knowledge of the field (e.g. suggest research that has already been done or is improbable with current methodologies).
2 Novice. Mentions of significance are vague or inappropriate. Future directions are vague, implausible, trivial, or off topic.
1 Not Addressed. Significance of the project and future directions are not addressed.
Weight 1.0
Comment Prompt: Use of Primary Literature and Citations
Please comment on the strengths and areas for improvement in the discussion of and use of primary literature. Is there a relevant and reasonably complete discussion of how this research project relates to others’ work in the field? “Primary literature” is defined as peer reviewed, reports original data, the authors are the people who collected the data, and is published by a non-commercial publisher.
Rating Prompt: Use of Primary Literature and Citations
Please rate the use of primary literature.
4 Proficient. Primary literature references indicate an extensive literature search was performed. Primary literature references frame the question in the introduction and are used in the discussion to make the connections between the writer’s work and other research in the field clear. Primary literature references are properly and accurately cited.
3 Intermediate. Literature cited is predominantly primary literature. Primary literature references are used primarily to provide background information and context for conclusions. Primary literature references are properly and accurately cited.
2 Novice. Primary literature references are limited (only one or two primary references in the whole paper). References to the textbook, lab manual, or websites may occur. Citations are at least partially correctly formatted.
1 Not Addressed. Primary literature references are not included.
Weight 1.0
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