Lab Report Writing Guidelines
by Dr. Justin Maresh, DePaul University

# General

In this laboratory course, your lab reports will follow the form and style of a formal scientific paper suitable for submission to a professional journal. A good paper is an organized description of hypotheses, methods, data, and conclusions designed to inform the reader while providing sufficient detail for the reader to critically evaluate the quality of the work Without a paper documenting a research effort, the work done is not truly science.1 Without peer review and criticism scientific knowledge has little authority. Without a detailed paper, peer review is not possible. Critical examination of a peer's work requires carefully presented data and independent replication. Detailed published methods, help others replicate the work. Detailed explanations for how results were interpreted, allow others to reach different conclusions that may have been overlooked by the authors. For scientific knowledge to exist, scientists must be able to write clearly, precisely, and include sufficient detail.

Before you begin writing, always read the assignment and the Grading Rubric to make sure that you are including everything that is required. Once you have finished your report, compare it to the Grading Rubric again. Completeness is the most important thing to remember when writing your reports. In this course, it is not uncommon to leave lab with poor the data cannot be interpreted. It is understood that an experiment may not work well when you are doing it for the first time. Because of this, the penalty for an "incorrect" result is minor. However, if all your figures are missing labels and your Discussion fails to state whether or not your effort achieved the purpose of the lab, your total score will drop a full letter grade!

Department of Chemistry and Biochemistry considers the ACS Style Guide 2 to be the ultimate authority for the details of report writing. The ebook in PDF format is available on the D2L course site and at http://j.mp/acsstyleDPU. All advice in this document is consistent with the guidelines in that book.

## Content of reports

Scientific papers are intentionally formulaic to facilitate the transfer of information to the reader. They consist of seven critical sections:  Abstract, Introduction, Experimental Procedures, Results, Discussion, Acknowledgements, and References. Within these sections, scientists have evolved reliable formulas to promote efficient communication. These are described in the corresponding sections of this document.

## General formatting for reports

• Always number the pages of manuscripts so that they can be easily reassembled in the correct order if they become detached, and so that the copy editor can refer to the locations of comments.
• To help conserve paper and maximize readability, use the defaults found in Microsoft Word 2007 or later:
• 1.0 inch margins on all sides
• a sans serif font (such as Calibri or Arial) at 11 or 12 point
• line spacing of 1.15.
• Describe all work done in the past using the past tense.
• You may use the present tense for any facts or conclusions that are generally true now and will be true in the future. However, if you are unsure of this distinction, it is safest to use the past tense throughout.

## Models of reports

In this course, you will be held to similar standards that scientists hold their colleagues when submitting a research report for publication. The basis for your writing style will be the norms of the published literature for the course topic. You are encouraged to use peruse articles from recent issues of the journal listed in the table below to get a feeling for the requirements and learn by example.

 Courses Topic Journal Notes CHE 13X General chemistry Journal of the American Chemical Society Consult your course specific writing guidelines before this guide as there may be minor differences. CHE 23X Organic chemistry Journal of Organic Chemistry CHE 34X Biochemistry Biochemistry

## References

1. Whitesides G.M. (2004) Whitesides' Group: Writing a Paper. Adv. Mater. 16(15):1375-1377. DOI: 10.1002/adma.200400767
2. Coghill A.M., Garson L.R.The ACS Style Guide: Effective Communication of Scientific Information. American Chemical Society: Washington DC, 2006. DOI: 10.1021/bk-2006-STYG
3. Whitesides G.M. (2004) Whitesides' Group: Writing a Paper. Adv. Mater. 16(15):1375-1377. DOI: 10.1002/adma.200400767
4. Kamat P., Schatz G.C. (2013) How to Make Your Next Paper Scientifically Effective". J. Phys. Chem. Lett. 4 (9): 1578–1581. DOI: 10.1021/jz4006916

# Writing an Abstract

An abstract should be a specific summary of the paper or report. An abstract should be written in such a way that any reader who is not familiar with the topic will be able to understand and appreciate the main points of the study.

## Content of an abstract

It should provide a brief summary of each of the main sections of the paper:

• First, state the principal objectives/purposes of the experiment (introduction),
• concisely describe the experimental and data analysis methods,
• mention key experimental conditions that were essential to the results,
• summarize the major results, and
• rationalize the results with the principal conclusions.

## Style of an abstract

• Because the abstract is evaluated by both the editors and general readers, extra effort should be taken to compose an effective and concise abstract.
• An abstract should be fewer than 250 words.
• Please write the abstract entirely in the past tense because it refers to work done.
• Note it was once the norm to write abstracts in present tense only. A few authors still publish in this style. Because the present tense abstract is acceptable in the publishing world, you will not lose points for writing in this style.
• An abstract must consist of text only. Never include figures or tables.
• Since the abstract will be published in searchable databases, footnotes or undefined abbreviations may not be used.
• Likewise, references to the literature must not be cited. If a reference must be cited (rare), complete publication data must be given in the abstract text, e.g. White, R. H. (1982) Biochemistry 21, 4271-4275.

# Writing an Introduction

The introduction section is the beginning of the body of your lab report. It is meant to provide an outline and purpose for the experiment that prepares the reader with the context to understand the experiments that will follow. This section should give the reader a detailed background on the "what" and "why" of the experiment, and put the experiment into a broader context. This context should be beyond this lab course and should not refer to the course itself, your instructors, or other students. Before writing your own introduction, you should review the examples below and try to find the parts described in a recent research paper from the journal Biochemistry.

## Content of an introduction

As with most parts of a scientific paper, the introduction is highly formulaic. Broadly it contains two parts: the background and description of the experiment. Although there is some variation, most Introductions include all the points listed below in the approximate order shown. The first three points are background and the final three points pertain to the experiment.

• First describe the broader context and importance of the work to the scientific community.
• Review the relevant current state of knowledge. Give the essential background that is not common knowledge to help the reader understand the paper.
• Present an unanswered question in the field that will be the novel contribution of your paper. For elementary student lab exercises, you may not be asking a totally novel question, nonetheless you should still explain the broader relevance of such experiments to your reader and/or state that you are attempting to replicate past observations.
• State the objective(s) in one of the last sentences/paragraphs of the Introduction.
• Conclude by following the objective with a description of the experiments that will be carried out.
• As needed, explain any specific background for the methods that is not common knowledge. Your assignment will specify when this is necessary in this course.

## Style of an introduction

• Cite references, such as the primary literature or a textbook, when stating any facts or information that you have not personally obtained in this work. See the Citations and References section of this document for more details.
• Nearly all of the Introduction is written in the present tense because it refers to facts that are currently true. You may find it easiest to stick to this tense throughout.
• Before presenting the current state of knowledge or your objective(s) you may find it relevant to describe specific data from recent relevant experiments. These data should be written in past tense because you are discussing something that was done at a specific time in the past.
• The introduction is the only place in scientific writing where personal pronouns ("we" or "I") are expected. The two limited uses are described below. Avoid the personal pronoun in all other sections of your report.
• When stating their objective(s), researchers nearly always use phrases like "In this work, we study..."; "Herein we report..."; "Here we present..."; "We report in this paper..."; etc. Please adopt this norm since the passive voice alterative is awkward and disappearing from modern published scientific literature.
• When presenting the current state of knowledge, researchers use "we" to refer to relevant work that their team has performed. If you wish to build on your past work in this course by developing a narrative of ongoing inquiry, you may do so. Remember to cite your past report(s) in the References.
• Everything we do in a lab setting has a broader context. Even though our experiments are designed to be teaching tools, it is unprofessional to write about them solely in that context. Avoid mentioning the "lab," "experiment," "instructor," or "students". From the reader's perspective, the organizational structure of research is team is not pertinent to the science.
• Example. Avoid a sentence like this. "This experiment was conducted in order for students to learn the technique of PAGE electrophoresis."
• We will assess your understanding of what you did in lab through your writing, not through tests. Therefore, when requested to explain theory, approach the task with the attitude that your report is your primary opportunity to demonstrate to your instructor what you understand.

## Analysis of a sample Introduction from Biochemistry

This Introduction is much longer and more detailed than anything we will expect from you. However, it illustrates the above principles. It opens with the broader context (understanding HIV-1 PR is important for the development of therapies for HIV) in present tense with cited references as superscript numbers. In this example, limited past tense is used to give context to a specific subject. Throughout this example, I will omit extraneous text with an ellipsis (...).

The human immunodeficiency virus type 1 protease (HIV-1 PR) mediates the processing of the Gag and Gag-Pol polyproteins into mature structural and functional proteins essential for assembly and maturation into infective progeny virus.1-4 The HIV-1 genome encodes a single copy of the 99-amino acid protease. PR is translated in the pol open-reading frame and catalyzes its own release at its termini (autoprocessing) from the Gag-Pol polyprotein via transient dimerization (Figure 1A).1-3 ... The active site of the mature PR dimer has been the subject of intervention strategies for almost 25 years since its discovery, and clinical protease inhibitors form a crucial part of combination antiretroviral therapy.5-6

Next the authors present a brief review of the current state of knowledge. Note that the authors generally use present tense passive voice, but switch to past tense first person to describe their team's specific results.

However, the short replication cycle (1.2 days7) of HIV-1, together with the error-prone reverse transcriptase, contributes to the rapidly evolving selection of mutations in PR leading to drug resistance. Major and accessory mutations involving 37 of the 99 PR residues contribute resistance to clinical protease inhibitors in current use by several mechanisms.8,9 We recently characterized an extreme multidrug resistant clinical isolate of PR... We proposed that mutations at or near these sites, which significantly limit autoproteolysis, can prolong the lifetime of mature PR20, thereby compensating for its reduced catalytic activity during the viral replication cycle.26

The authors finish the current state of knowledge summary with an unanswered question followed by more background related to that question.

However, to the best of our knowledge, molecular mechanisms of drug resistance pertaining to autoprocessing, a pivotal step in PR regulation, have not been thoroughly explored. We recently characterized an extreme multidrug resistant clinical isolate...

In the last paragraph, the objective is stated. It is easy to identify by the use of "Here we" in the last paragraph.

Here we address the effects of clustered drug resistance mutations on a comprehensive set of properties, for the first time, such as the dimer dissociation constant (K dimer), kinetic parameters (k cat/K m and K i), thermal stability in the absence and presence of protease inhibitor, Gag processing, autoproteolysis, and autoprocessing governing PR function.

Finally, the experiment that will be described is explained.

Initially, we substituted all PR20 clusters (or cassettes) into PR and its precursor mimetic and, conversely, all PR clusters into PR20 and its corresponding precursor and examined the effect of these mutations on the mature protease. Kinetic parameters of PR-mediated hydrolysis of synthetic substrates were compared with the rate and order of Gag processing. Subsequently...

## Analysis of a student sample Introduction

Read this complete sample Introduction written by a past student. Identify the (a) broader context, (b) current state of knowledge, (c) background of methods, (d) unanswered question, (e) objective of study, and (f) experiment. Mouse over each sentence to see if you are correct.

1 2+ and Zn 2+ at histidine residues positions 13 and 14. Such binding accelerates the rate of peptide aggregation and the formation of toxic fibrils and plaques.1

2+ binding site which includes 3 histidine residues. 2,3   Theoretical approaches have also been used to give information about the possible coordination intermediates between copper and Aβ peptide. 4

5 In ITC studies, ligand aliquots are injected into a sample of a macromolecule solution of known concentration to determine the heat released upon binding. This is measured indirectly by monitoring the power applied to the sample cell to keep the temperature difference between the sample cell and a reference cell constant. 6   Software has been developed that allows the determination of binding sites, ΔH values and equilibrium binding constants from the raw data generated from ITC experiments.

d) for the binding of Cu 2+ with Aβ is not known at physiological pH. d binding of Cu 2+ to the short Aβ peptide Aβ-(1-16) which contains the first 16 amino acid residues present in the complete peptide. 2+ binding but lacks the sequence critical for aggregation. Cu 2+ is only weakly soluble at physiological pH due to formation of a highly insoluble hydroxide species. 7 Thus, the binding affinity and thermodynamic parameters were measured at pH 5.5 and 6.0 in order to extrapolate thermodynamic parameters at a physiologically relevant pH.

# Writing an Experimental section

## Content of an Experimental section

• The journal accepts either "Material and Methods" or "Experimental" as synonyms for the title of this section.
• Materials and experimental details should be described in sufficient detail to enable others to repeat the experiments. See Appendix B for lists of minimum required details for common methods.
• UniProt Accession IDs and/or protein IDs (http://www.uniprot.org/) should be provided for all proteins that are purified and/or characterized.
• Always provide the composition of buffers and other solutions. If a solution is a commercial product with unknown composition, provide identifying product information.
• Names of products and manufacturers should be included only if alternate sources are deemed unsatisfactory.
• Provide the model and manufacturer for major analytical equipment.
• Provide the name, manufacturer, and version number of major software used to process data.

## Style of an Experimental section

• Divide this into separate sub-sections, each of which describes an experimental procedure performed.
• Always write methods in the past tense, passive voice.
• Do not rewrite the detailed procedures in your handout. Succinctly provide the minimum practical detail that the reader can reproduce your work.
• Simply provide the final concentrations of components in a system rather than a list of stock solutions and individual volumes. Only state the stock concentrations and volumes if different methods for arriving at the same final conditions will actually generate different results.
• Correct and preferred: "Reactions were performed at 25 °C in 50 mM Tris-HCl (pH 7.1) with 4.0 μM imiginin, 20 μg/ml imaginase, and either 0 or 150 mM MnCl2."
• Correct but unnecessary: "Reactions were performed at 25 °C in by mixing 500 μl of 100 mM Tris-HCl (pH 7.1), 10 μl of 400.0 μM imaginin, 100 μl of 200 μg/ml imaginase, and either 0 or 250 μl of 500 mM MnC2 to a final volume of 1000 μl using buffer to make up the difference."
• Incorrect: "Reactions were performed at 25 °C by mixing 500 μl of 100 mM Tris-HCl (pH 7.1), 10 μl of 400.0 μM imaginin, 100 μl of 200 μg/ml imaginase, and either 0 or 250 μl of 500 mM MnCl2." This example is ambiguous because it leaves-out the final volume. Please aoivd this common mistake.
• Whenever hazardous materials or dangerous procedures are utilized, the necessary precautions should be stated.
• Explain the procedures for data analysis. You must define any non-standard units (e.g. enzyme units) and provide the statistical basis of measurements (e.g. "values are the mean of three replicate measurements," "uncertainty is the standard deviation of values").
• Please use the Equation Editor in Word to draw equations. However, you may draw equations by hand. Center equations on their own line with an equation number in parentheses to the right. Italicize all variables in an equation and in the body of the report.
• In the Experimental section, you may use formulas for common inorganic reagents such as NaOH, HCl, H2SO4, MgSO4, etc., and for common organic solvents with very few carbons such as CH2Cl2 (dichloromethane) and CHCI3 (chloroform). Do not use formulas if they are not readily interpretable or if they take as much space as the name itself (e.g., use n-hexane, not CH3CH2CH2CH2CH2CH3).
• Uncertainty on values is not required the Experimental section because quantities are assumed to represent typical values with assumed uncertainty in the last digit.

Below is a student example of a well-written Experimental section:

# Writing a Results and Discussion section

You will write a combined Results and Discussion section. However, you should know the different functions of each part. The two parts do not need to be separated by headings.

Keep you audience in mind when you write. Ostensibly, your audience is a general reader of Biochemistry, however you should also explain what happened with enough detail that your instructor can see that you understand the phenomena at play.

## Figures, tables, and schemes

In general chemistry (CHE 13X) labs and papers in my liberal studies courses, place figures, tables, and schemes after the paragraph in which they are first mentioned.

In my CHE 2XX and 3XX labs, you may simply present figures, tables, and schemes together at the start of the Results and Discussion section. When you submit a manuscript to a journal, you are responsible for the content only, professional layout designers will integrate your text and graphics appropriately to make sure that each graphic is placed where it fits on the page after its first mention in your text. Lab reports in these courses have so many figures and tables that they often break up the text too often. We do not want you spending any time on layout design to deal with this issue. If you prefer to incorporate your figures, tables, and schemes into the report text you will not be penalized.

• Number figures, tables, and schemes consecutively in order of appearance in the text.
• Make sure that each image and its associated text is visually separate. It is good practice to separate each item with horizontal lines.
• See Appendix A: Data Presentation for details on the appearance of these.

## Text

A. Always begin the text of this section by restating the objective of the experiment and whether or not you successfully achieved that objective.

B. The discussion of each experiment conducted should follow this formula...

1. Briefly describe what was done
1. Present the results
• Describe what each of your figures and tables reveal (e.g. "Figure 1 reveals... "). Often the meaning of a piece of data is not obvious to someone who didn't perform the experiment. Guide your reader.
• Example: "Figure 1 plots the relationship between polarity and protease activity for the substrates."
• Do not list information from tables in sentence form. The whole point of a table is to visually organize information. Simply say describe the information in the table. Example: "Table 1 lists the enzyme inhibition activity and characterization data for the benzoxaxinones."
• Refer to each and every figure or table in your text or expect to lose points.
• See Appendix A: Data Presentation for details.
1. Comment on the quality of your results and explain whether quality limits the ability to make a conclusions from it.
• When commenting on quality of data, you should set some criteria for judgement and state whether or not your data meets that criteria.
• Quality is function of precision, accuracy, and the extent to which samples were omitted. Clearly state which of these parameters you are evaluating and your quality criteria.
• Precision. Always compare the relative standard deviation (RSD) rather than the absolute standard deviation. In biochemistry, <10% RSD is generally precise enough.
• Example: The value 4 ± 2 U has 50% error and 4.0 ± 0.3 U has 8% error. Although both values are the same, the high relative error for the former value indicates a poorer quality result.
• Accuracy. When available, compare the similarity of measured values to either known controls (e.g. positive and negtive controls). When these are not available, values still may be judged as potentially inaccurate if your trendline was imprecise.
• Typical criteria: For a series of measurements based on the same standard curve in biochemistry, an R2 > 0.98 generally suggests that the derived values are accurate, R2 < 0.94 generally suggests low accuracy, and R2 values in between suggest moderate accuracy. Ask your instructor or TA if you are unsure how to evaluate accuracy in a particular experiment.
• Omitted data. If you had to omit data because of significant outliers, this also suggests poor quality in the dataset.
• When fitting any model to data, it is assumed that each data point provides equally precise information about the deterministic part of the process and thus has the same relative standard deviation.4
• As a rule, only omit data points if you can justify that they are not equally precise as the primary data.
• You should invalidate data if you know that you made a specific mistake with a sample, explain what occured.
• You should invalidate data if they are measured values that fall outside your standard curve.
• Otherwise, apply a statistical test. Deleting trendline data simply to improve R2 is not a valid justification.
• You may omit data without a statistical test if it is data that you expect to deviate from a trend for technical reasons (e.g. the non-linear time points for initial rate kinetics).
• If you rejected any outlier data, you must present your omitted data along with the data you used and justify your reasons for omission.
• If you judge the results to be of poor quality,
• you are ethically required to state this to reader and explain how the results limit confidence in your conclusions
• and you must demonstrate your understanding of the concepts behind the lab by suggesting what went wrong.
• If you are unsure what went wrong, propose a testable hypothesis that would potentially uncover the reasons for your poor quality data.
• Direct the reader to important values or trends in the data.
• Describe general trends and highlight interesting values.
• Do not repeat a list of data from your tables, you created a table to avoid confusing lists of values in text.
• Do not state the trendline equations from your captions in your text unless you have a compelling reason to do so.
• If data are expected to follow a trend, be clear about this expectation and describe how closely the data follow it.
• Never fit a straight line to non-linear data.
• If you are not sure what to say, discuss highest and lowest values.
• If you claim that two values are different, make sure that their uncertainty ranges do not overlap. Statistically, the two values may be the same.
• Example: The values 55 ± 7 U and 65 ± 7 U are not statistically different.
• Demonstrate that you understand what happened.
• Example: Instead of saying "none of the lanes resembled one another", explain that "lane 1 showed X indicating Y happened when preparing the sample."
• When possible, relate your results to existing knowledge in the field.
• Compare your results to the most relevant values in the published literature.
• State what is different and similar about the conditions between the experiments.
• If the values differ significantly. provide a possible explanation.
• Always cite the source of your literature value.
• Interpret the data in terms of your objectives.

C. After discussing each experiment, summarize your discoveries.

D. Conclude by suggesting further work that should be performed.

1. A great scientist is not someone who knows the right answers, but someone who asks the right questions. Every scientific experiment creates more new questions than answers. These last sentences of your paper set the stage for the next scientific explorations.
2. If you did not completely accomplish your goals, identify what may have gone wrong, suggest a specific improvement, and explain why your improvement would reduce the effect of the problem you encountered.
3. If you see no need for improvement, briefly suggest a follow-up experiment that builds on the current work.

# Appendix A: Data Presentation

• Number figures, tables, schemes, and equations consecutively in order of appearance in the text.
• Equations should be presented on their own line and centered with an equation number to the right in parentheses. See Equations sub-section for more detail.
• Placement of figures, tables, and schemes.
• In general chemistry (CHE 13X) labs and papers in my liberal studies courses, place figures, tables, and schemes after the paragraph in which they are first mentioned.
• In my CHE 2XX and 3XX labs, you may simply present your figures, tables, and schemes together at the start of the Results and Discussion section. When you submit a manuscript to a journal, you are responsible for the content only, professional layout designers will integrate your text and graphics appropriately to make sure that each graphic is placed where it fits on the page after its first mention in your text. Lab reports in these courses have so many figures and tables that they often break up the text too often. We do not want you spending any time on layout design to deal with this issue. If you prefer to incorporate your figures, tables, and schemes into the report text you will not be penalized.
• Make sure that each image and its associated text is visually separate. It is good practice to separate each item with horizontal lines.
• Tip: In Microsoft Word, type three hyphens (---) then press Enter to create a horizontal line.
• Tip: In Google Docs, from the menu select Insert → Horizontal line.
##### Uncertainty
• All measured values in Results and Discussion must include an estimated uncertainty and units.
• Exact values do not require uncertainty, unless of course the quantity was measured by some estimating method.
• Example: "The gel had 12 lanes." The number 12 has no associated uncertainty.
• The standard deviation of replicate measurements will express the uncertainty for most values in this class.
• Tip: Use the =STDEV or STDEV.S function in Excel.
• When you have no replicate measurements, use your judgement to estimate the uncertainty based on the limits of your measuring method.
• Example: You measure the diameter of a quarter dollar coin with a millimeter ruler. You can see that the quarter is more than 24.0 and less than 25.0 mm, so you could estimate it as 24.5 ± 0.5 mm.
• If you have no basis for estimating uncertainty the convention in science is to assume that the uncertainty is ± 1 in the position of the last digit. Often in the literature authors omit uncertainty in their text when it is stated elsewhere. However, in this course you should demonstrate your understanding by always reporting the uncertainty in the Results and Discussion section.
• Example: You have no other information about the uncertainty of 2.50 g. Report it as 2.50 ± 0.01 g.
• For values derived from multiplication or division of two measurements, the percent uncertainty is the square root of the sum of the squares of the percent uncertainty of the measurements.
• Example: (862 ± 3 g)/(1.51 ± 0.02 mol) = 571 g/mol. The uncertainty is

The reported value is 571 ± 8 g/mol.
• Round your uncertainty to one significant digit.
• Your value may not have precision beyond your uncertainty.
• Example: Report 8.7 ± 0.5 μM, not 8.73 ± 0.48 μM.
##### Significant digits
• For measurments with uncertainty, the one significant digit of your uncertainty (see above) will typically limit the significant digits of your value.
• Example: Report 8.7 ± 0.5 μM, not 8.73 ± 0.48 μM.
• Guard digits are reported numbers beyond the significant digits that are provided to reduce rounding errors in numerical analysis. We suggest that you avoid them when reporting your values. Nonetheless, since they are accepted by professional journals, we will also accept guard digits. If you report guard digits you must clearly indicate your significant digits using one of the conventions below.
• Oldest conventions: Frequently guard digits are distinguished by underlining or subscripting all of them.
• Latest conventions: Recently, many textbooks and style guides recommend using either an overline or underline to represent the last significant digit. These styles look neater on the page. I recommend the undelining since it is a familiar and universal word processor feature (see MSWord tips for instructions on overlining).
• Examples: For each of these values 8.736 ± 0.487 μM, 8.736 ± 0.487 μM, and 8.736 ± 0.487 μM the tenths place is understood to be the last significant digit.
• It is common in publishing to report trendline equations with one or two guard digits because they are meant to be used for numerical analysis. For this reason, you may report up to five significant digits for trendline equations.
• Example: It is acceptable to report y = 23.495 x + 1.2948 as a trendline equation.
##### Units
• All values must include units unless the quantity is unitless by definition.
• Use a space between the numeral and the unit, except %, $, and ° (angular degrees). • Examples: 150 ml, 17%, 180°, 76 °C. • Absorbance is the common log of the intensity ratio and thus has no units for the same reasons that pH has no units. Some scientists erroneously report absorbance units as "a.u." (arbitrary units). This is not correct.1 • First-order and second-order rate constants (including steady-state values of kcat and kcat/KM for enzymes) should be reported in units of s-1 and M-1 s-1, respectively. • Equilibrium binding constants should be reported as dissociation constants (Kd) with units of concentration (M, mM, μM, etc.). • Steady-state enzyme activity (specific activity) should be optimally reported as kcat or, if there is uncertainty in the molar concentration of the catalyst, as a Vmax in amount of product formed per amount of protein per unit time (e.g μmol·min-1). • You must include units in the coefficients of trendline equations. (Note: At the start of Autumn Quarter 2019 CHE 341, units for coefficients were not required when the equation is presented in a figure caption. This rule will remain in place for the remainder of this quarter and this class specifically). ##### Figure format • Information conveyed in Figures and Schemes should be understandable without reference to the text. • Below every figure you should include a figure number (number consecutively) in bold text, a descriptive title (the image itself should not have a title), and a detailed caption. • Tip: An easy way to add a caption to a table or figure in Word is to right click it and select the "Add caption" action. This will add a caption to your figure that will stay grouped with it throughout the document and will prevent it from ending up on a separate page. • Either the figure or the caption should explain what is being plotted including the essential experimental conditions. See Appendix A for what details to include. • The only text on a graph should be the axes and data labels. Legends are discouraged, but permitted if they are clear and concise. • Important derived values and trend line equations should be presented in the caption, not on the graph itself. • Explain all symbols and abbreviations used in the illustrations. Simple symbols such as O, Δ, and ◊. The use of error bars on the data points is recommended. Example of a good figure: Figure 2. The initial rate of product formation as a function of imaginase concentration. Product formation was monitored by absorbance at 400 nm at 23 °C in 50 mM pH = 7.0 phosphate buffer. The trendline relationship is y = 5.03 (M·sec-1·mM-1imag) x + 0.0210 (M·sec-1) (R2 = 0.992). ##### Table format • Use tables only when the data cannot be presented clearly otherwise. • By convention, the table number and title are above the table. • By convention, the explanatory material (the detail that goes into a figure caption) is always a footnote to the title or headings designated by a lowercase letter. • Every table column should have a heading. • Clearly indicate the units of measure in the heading. • Data should be rounded to the nearest significant figure. • Give uncertainty estimates to all values, if appropriate. • If you choose not to use lines for table cells, the layout should be clear and easy to read. • It is good practice to separate your tables from the text with horizontal lines. • Tip: In Microsoft Word, type three hyphens (---) then press Enter to create a horizontal line. In Google Docs, from the menu select Insert → Horizontal line. Below is an example of a perfectly reported table taken from a random article in Biochemistry. Note that one guard digit is included on both the measurement and uncertainty. See above section on Uncertainty for more details. Table 2. Binding and Antiviral Activities of DV1 and DV1 Dimer a  Analogue CXCR4 binding (nM) b antiviral activity using infectious virus assays (μM) antiviral activity using single-cycle focal infectivity assays (μM) DV1 43.0 ± 5.0 12.1 ± 3.2 24.03 ± 0.10 DV1 dimer 3.02 ± 0.52 4.4 ± 3.1 10.12 ± 0.49 a. The binding and antiviral activities of DV1 and DV1 dimer are shown by their IC50 values. All data are shown as means ± the standard deviation from at least three independent experiments. b. 12G5 antibody competition binding assays were used to determine CXCR4 IC50 values. Stably transfected 293 cells were used in the binding experiments. The binding data were analyzed using PRISM (GraphPad Inc., San Diego, CA). ## References 1. Croarkin C, Tobias P, editors (2012) Engineering Statistics Handbook. National Institute of Standards and Technology, U.S. Department of Commerce: Washington DC, Section 4.1.4. https://www.itl.nist.gov/div898/handbook/pmd/section1/pmd14.htm (accessed Aug 18, 2018). # Appendix B: Minimum Details to Report for Common Methods The following are the critical details required to replicate common biochemical techniques. At minimum you must include these details in your methods and captions. • Agarose gel electrophoresis • Captions: percent agarose; staining methodology; identity of lanes; identity of important bands in reference ladder. • Methods: percent agarose; composition and pH of buffer used to make and run the gel; amount of sample loaded; type of reference ladder used; manufacturer of reference ladder; voltage per cm; time; staining procedure; visualization method (i.e. trans-illumination, epi-illumination ), wavelength of light. • Chromatography • Captions: method (e.g. column, thin layer); stationary phase (e.g. silica, Dowex 50WX4); composition of mobile phase; visualization procedure; identity of samples. • Methods: method (e.g. column, thin layer); identity (e.g. silica, Dowex 50WX4) and amount (e.g. height and diameter for column, dimensions for TLC plate) of stationary phase; composition of mobile phase; flow rate and gradients (for column); total time (for plate); visualization procedure. • Compositions of solutions • Methods: state composition solutions and buffers (e.g. 100 mM Tris buffer, pH 8.50 with 50 mM NaCl); you do not need to describe the recipes to make concentrated stocks and steps you carried-out to prepare the buffer. • Data analysis • Captions: if a figure has a trendline, give the equation of the trendline and the R2 value in the caption. • Methods: describe your methods of data analysis, important equations, and calculations used. Define non-standard units. If you analyzed and plotted your data using spreadsheet software, you must name the software package and manufacturer. • Enzyme reactions • Methods: provide the final composition and pH of buffer (not necessary to give detailed instructions for preparation), final concentrations of reactants, time, temperature. Alternatively, if you provide the various volumes of the reaction components, you must provide the concentration and composition of each and the final volume of the reaction. • Enzyme reactions with commercial kits • Methods: provide the volume and identity of buffer used (state manufacturer), volume of additives added (e.g. BSA, ATP; state concentration and manufacturer), volume of sample added (state concentration), total volume, time, temperature. • Enzyme kinetics data • Captions: follow requirements for Data analysis; identify the enzyme, substrate, buffer, and temperature. • Methods: follow requirements for Enzyme reactions, Spectrophotometric measurements, and Data analysis; define your activity units. • Polyacrylamide gel electrophoresis (PAGE) • Captions: percent of acrylamide in gel; staining methodology; identity of lanes; identity of important bands in reference ladder. • Methods: percent of acrylamide in gel; composition of the running buffer; approximate amount of sample loaded; type of ladder used including manufacturer; voltage; time; staining procedure with sufficient detail; imaging method (i.e. trans-illumination, epi-illumination ) including wavelength of light. • Protein assay (colorimetric methods) • Captions: plot the standard curve; identify the protein standard; give the equation of the trendline and the R2 value in the caption. • Methods: Identify the protein standard with concentration; state either the composition or product information for the reagent(s); the volume of reagents, standards, and samples; the development time and temperature, and requirements for "Spectrophotometric Measurements" and "Data analysis." • Spectrophotometric measurements • Model and manufacturer of spectrophotometer (our instruments are Thermo Spectronic 20, etc.); wavelength(s) measured; identity of the blank used as the zero reference; dilutions made on sample (if applicable). # Appendix C: Citations ## When to cite and reference • Any information that you did not determine in the study should be cited. • Use in-text citations anytime you cite a significant idea that is not your original work. • You must internally cross-reference all of your own figures and tables when discussing your results. ## What to cite Authoritative scientific knowledge resides in unchanging published peer reviewed documents that anyone can obtain. Therefore, • avoid references to webpages such as Wikipedia (can be changed any time), • lab handouts for this class (not published works), • blogs and educational web pages (not peer reviewed), • the Desire2Learn course site (no one outside of the course has access, you won't even have access in a few months). Instead, you should cite, • primary peer-reviewed literature, • scientific books including textbooks, • online databases (although these are occassionally updated when errors are found, the entries typically include a unique accession number to guide the reader to the information; also results from such databases may be a source of data in your paper). ## How to cite • Use either a superscripted number or a number in parentheses that refers to a specific numbered entry in your References section ## Bibliographic format Every journal has its own recommended bibliographic format. For this course, we will use the current format of the journal Biochemistry (n.b. this journal used a different format before 2004).  Article in a scientific journal Kuo HH, Mauk AJ (2012) Indole peroxygenase activity of indoleamine 2,3-dioxygenase. Proc Natl Acad Sci USA 109: 13966 - 13971. Article in a popular/ magazine Manning, R. (May 2004) Super Organics. Wired, pp 176-181. Article from an online journal (no DOI exists) Peacock-Lopez, E. (2007) Exact Solutions of the Quantum Double Square-Well Potential. Chem. Ed. [Online] 11: 383-393. http://chemeducator.org/bibs/0011006/11060380lb.htm (accessed Aug 23, 2007). Whole book, single author Chang, R. General Chemistry: The Essential Concepts, 3rd ed.; McGraw-Hill: Boston, 2003. Edited Book Gbalint-Kurti, G. G. (2004) Wavepacket Theory of Photodissociation and Reactive Scattering. In Advances in Chemical Physics; eds Rice, S. A. (Wiley: New York) Vol. 128, p 257. Article from a reference book Powder Metallurgy. In Kirk-Othmer Encyclopedia of Chemical Technology, 3rd ed., 1982 (Wiley, New York) Vol. 19, pp 28-62. Web page National Library of Medicine. Environmental Health and Toxicology: Specialized Information Services. http://sis.nlm.nih.gov/enviro.html (accessed Aug 23, 2008). ## Use Endnote to make citing easy Endnote is a database in which you can store citation data. It works as a plugin to Microsoft Office. With Endnote you can insert citations into the text of your documents that link to an automatically formatted your References section. You can change the style of your citations and references with a few clicks. If you use Endnote, you can be confident that your references will always be formatted to meet the requirements of your assignment without thinking about it. • Download the Endnote installer from the W:\software\Student folder at webdrive.depaul.edu. • Once installed, open Edit → Output Styles → Open Style Manager... and check the box next to Biochemistry. • In Microsoft Word, go to the Endnote tab and from the Output Styles dropdown menu select Biochemistry. From now on, every citation and reference you pull in from Endnote will be in the exact format this class! • For training in Endnote, I recommend the short course from LinkedIn Learning. • For access to the full course content, log-in using your free DePaul account by clicking Sign In and then enter your DePaul email (you may also have to click Sign in with your organization account). This will connect you to the DePaul Portal (which will require you entering your Campus Connect credentials). # Appendix D: Scientific Style ##### Active versus Passive Voice A sentence is said to be in active voice when the subject of the sentence is the doer of the action indicated by the verb. The subject of an active verb is doing the action of the verb. In passive voice, the subject is the receiver of the action indicated by the verb. • Use the passive voice when the doer of the action is unknown or not important or when you would prefer not to specify the doer of the action. • Procedures, results, and discussions of concepts should be written in the passive voice since the person doing the action is not important to the outcome. • The solution was shaken until the precipitate forms • Melting points and boiling points have been approximated. • Use the active voice when it is less wordy and more direct than the passive. • Use first person when it helps to keep your meaning clear and to express a purpose or a decision. • Avoid clauses such as "we believe", "we feel", and "we can see", as well as personal opinions. • Jones reported xyz, but I (or we) found .... • I (or we) present here a detailed study .... • Our recent work demonstrated .... • To determine the effects of structure on photophysics, I (or we) .... ##### Verb Tense Using the appropriate verb tense helps to orient the reader as to the nature of the information. • Use simple past tense to state what was done, either by others or by you. • The solutions were heated to boiling. • Jones reviewed the literature and gathered much of this information. • We found that relativistic effects enhance the bond strength. • The structures were determined by neutron diffraction methods. • Present tense is correct for statements of fact. • Absolute rate constants for a wide variety of reactions are available. • Hyperbranched compounds are macromolecular compounds that contain a branching point in each structural repeat unit. • Present and simple past tenses may both be correct for results, discussion, and conclusions, and present tense is correct for statements of fact. However, the use of present or simple past tense for results, discussion, and conclusions should be consistent within a paper. • The characteristics of the voltammetric wave indicate that electron transfer occurs spontaneously. • The absence of substitution was confirmed by preparative-scale electrolysis. • IR spectroscopy shows that nitrates are adsorbed and are not removed by washing with distilled water. ##### Language and tone • Do not refer to "the experiment," "the lab section," "the instructor," or other details about the course. The reader will assume that an experiment is being described. Administrative details about the course are irrelevant to the science reported (unless course design is the subject of the experiment). • Do not use lab slang in manuscripts or reports. • Example: You do not "mass" a substance. A mass balance weighs a substance, even though it is calibrated to output mass units. "Mass" is not recognized as a verb that means "to measure the mass of."1 By simply stating the mass, the reader understands that you measured it (e.g. "25.01 grams"). Although you may say it in person, stating the action of a measurement in writing is generally unnecessary. • Example: You do not "rotovap" a solution. This is also not a recognized verb outside of slang. Instead, state that "solvent was removed under reduced pressure." • In technical writing, it is inappropriate to call a scientific instrument a "machine." This word should only be used for devices that do work with mechanical energy. For example, instead of "NMR machine" or "mass spectroscopy machine", name the instrument as "NMR spectrometer" or "mass spectrometer" respectively. ##### Scientific style • There is a space between a quantity and its units; e.g., -78 °C, 7 mL, 5 h, 15 min. The only exceptions are$, %, and the degree sign when referring to an actual measured angle (e.g., α = 4.234°).
• With items other than units of time or measure, use words for cardinal numbers less than 10; use numerals for 10 and above.
• Never spell measured values. Thus, you should write "2 grams" not "two grams" or "a pH of 7.0" not "a pH of seven."
• Do not begin sentences with numerals, formulas, or abbreviations.
• It is permitted to begin a sentence with a number if it is part of a chemical name.
• Example: 1,3-Cyclohexadiene was the least reactive of the compounds in Table 2.
• When a sentence starts with a specific quantity, spell out the number as well as the unit of measure.
• Example: Fifteen milliliters of supernate was added to the reaction vessel.
• However, if possible, recast the sentence.
• Example: Acetone (25 mL) was added, and the mixture was centrifuged.
• Example: A 25 mL portion of acetone was added, and the mixture was centrifuged.
• Always hyphenate compound adjectives, such as a "10-mL portion" or a "freshly-distilled solvent."
• For decimal fractions less than unity, always give a leading zero; e.g., "0.5 mL," not ".5 mL."
• In specifying quantities in the Experimental section, do not omit "of." For example, "10 mL of buffer was added," not "10 mL buffer was added."
• You measure a spectrum "with" a spectrometer, not "on" a spectrometer. This applies to all spectra, i.e. NMR, infrared, optical rotations, etc.
• If you use abbreviation numbers to refer to chemical structures, the numbers are parenthesized if the number is used as an adjective and not parenthesized if the number is a noun; e.g., "amine 5 was distilled" and "the procedure gave 56% yield of 2-methylcyclohexanone (7)." In the first example "5" is the noun and "amine" is an adjective. In the second example "2-methylcyclohexanone" is a noun and "7" is an adjective. A simple test you can apply to see if the number should be parenthesized or not is to see whether you still have a valid sentence if the number is left out; the sentence will still work if an adjective is eliminated but not if a noun is eliminated.
• Italicize the genus and species of an organism (e.g. Agaricus bisporus) and use normal type for the genus only (e.g. Agaricus mushrooms).

• See Chapter 11 of the ACS Style Guide of more advice on numerical presentation.

## References

1. "mass, verb." The Oxford English Dictionary Online. 2019. https://www-oed-com.ezproxy.depaul.edu/view/Entry/114670?result=7 (accessed 5 Sept 2019).

# Appendix E: Pro Tips for Microsoft Word

##### Symbols in MS Word:
• Turn on Math AutoCorrect by going to File → Options → Proofing → AutoCorrect Options... → Math → Check both boxes. After doing this, you can create symbols in Word by simply typing the listed codes. Examples of some the most useful:
 Type this Becomes this +- ± >= ≥ \ne or \neq ≠ \mu μ \alpha α \degc ℃ \times × \bullet · \lrhar (left right harpoons) ⇌ x\bar (overline) x̅

• MS Word keyboard shortcuts. MacOS users should replace the Control key with the Command key (⌘).
 Shortcut Output Name Control+@ release, then press ° Degree symbol Control+@ release, then press A Å Ångstrom symbol MacOS only: Alt+* ° Degree symbol

• Greek letters:
• As shown above, you can activate Math AutoCorrect and get any Greek letter by typing a backslash and the name (e.g. \delta → δ, \Delta → Δ).
• MacOS has Greek letter shortcuts: Alt+n = μ; Alt+j = Δ; Alt+l = λ
• Windows: Make custom shortcuts to Greek letters. Insert Menu → Symbol (in the Symbols area) → More Symbols. In the pop-up window, select "Greek and Coptic" under "Subset." Highlight the symbol of interest, e.g. "μ." Then select "Shortcut Key." Now you can press any combination of keys (or even a series like the series for the "°" symbol above). For example, I like to use Control-Alt-m for "μ," Control-Alt-b for "β," etc.
##### Formatting in MS Word
• Superscript formatting: Control + Shift + =
• Subscript formatting: Control + =
• You can enter equations in MS Word with the Equation Editor. In Word 2007 and later, press Alt + = or select it under Insert Equation (in the Symbols area).
• Although, it is very intuitive to click on symbols, you can Equation Editor without touching your mouse! Visit equations.maresh.info for a list of Equation Editor keyboard shortcuts.
• An easy way to add a caption to a table or figure is to right click it and select the "Add caption" action. This will add a caption to your figure that will stay grouped with it throughout the document and will prevent it from ending up on a separate page.
##### Graphics
• If you wish to include screenshots in your document, such as data processing images, follow these instructions.
• Windows: simply press the "Print Screen" key. This will copy the current screen image to the system buffer. Next open an image editor such as MS Paint or Photoshop, create a new document, paste the image, and save.
• Mac OS: Simply press "Command+Shift+3" at the same time and a screen shot of your entire desktop will be saved to the desktop. To capture a portion of the screen, press "Command+Shift+4" at the same time, a cross-hair cursor will appear, click and drag to select the area you wish to capture. When you release the mouse button, the screen shot will be automatically saved on your desktop.