BISC209 lab notebook guide:labnotebookguide.doc

MICROBIOLOGY 209 Laboratory Notebook Guidelines

Keeping clear thorough records is a vital part of any laboratory process. Careful attention to organization and details will have a positive impact on your laboratory experience.

Keeping a notebook increases your ability to organize your thoughts and follow the development of your understanding over the semester. Recording comments, ideas, and thoughts about what you understand or do not understand as you assimilate the steps in a protocol or examine the results of the tests performed will make writing about your research finding much less difficult.

Purchase a notebook with a stitched binding such as the black and white marbled “composition” books available in the Wellesley bookstore.

• 1. If your notebook does not have pre-numbered pages, immediately number each page by hand in the top right corner (preferably).
• 2. Leave the first 2-4 pages of your notebook empty so you can add a Table of Contents as you work.
• 3. Label the front cover of the notebook: Microbiology 209 lab notebook, your full name, and the year and semester.
• 4. Label the INSIDE cover with your name, mailing address, and email.

In order to keep track of the various components of your research this term, divide your notebook into sections. Leave plenty of blank pages between each section and consider adding tabs to make finding the sections easy.

Suggested Sections:

• 1. Culture-Independent Analysis
• • •Community phylogenetic relationship analysis by rRNA sequencing
•
• 2. Community Culture-Dependent Analyses
• • Functional soil community profiling
• 3. Culture-Dependent Isolates Analysis
• • Culturable Isolation procedures
• • Culturable Isolates - tests

The Culture-Independent Analysis will involve our class identification of a sample of soil community bacteria by rRNA gene identification and our work to establish phylogenetic relationships among the bacteria identified.

The Community Culture-Dependent Analysis will examine functional soil community profiling (looking for evidence to show how a total soil community co-operates to share resources and to meet its members metabolic needs and function in an eco-system).

The Culture-Dependent Isolates Analysis will provide experience with traditional microbiology culture techniques to isolate microbes to pure culture. Your goal is to enrich, select, and grow in pure culture a few individual bacterial representatives from among the community. We will also perform several traditional microbiological tests on our cultured isolates to examine their physical composition and metabolic abilities as representatives of the community from which they were selected.

Guidelines

• • Never, under any circumstances, remove pages from your notebook.
• • Always record entries legibly, neatly and in permanent ink.
• • Enter the date each time you make a new entry in each section of your notebook. Use AM/PM designations for all time entries.
• • Leave plenty of room in each section to write about the work that you do in lab under each of the approaches.
• • Do not erase errors or changes to a protocol. Just draw a single thin line through any erroneous entry and enter the correction. Include records of all mistakes, problems with procedures, and lapses in data collection as this is often useful to help fully explain "odd" results at the end of your experiment.
• • Identify field locations by including a general sketch or image of where the field site is situated. • For each protocol you will find it useful to include concepts, questions, comments, notes, results, references and other information in a systematic and orderly manner in the appropriate section.
• • It is acceptable to make your entries brief. Always, however, include enough details for someone else to successfully follow your thinking or find the reference you cite. Including details such as the thermal cycler program and the base sequence of primers used in pcr amplification here will aid your understanding of a protocol as well as save you time later.
• • Don't forget to give the context of each protocol you describe: both large and small goal(s) should be clear and identify where the protocol fits in the scope of the project. You will find it very useful to record the logic behind your ideas (stated, in your own words or with reference to other published research that you read as you were preparing for lab).
• • If you have received suggestions (from your instructors or colleagues) through email, you may paste the relevant passages into your notebook or reference those suggestions in notes.
• • It is useful to assign experiments, cultures, techniques, or tests a short version of a name and then use that short version each time you make a related entry. If it will be difficult later or for another reader to understand that notation, make a glossary of those acronyms in the back of the notebook.
• • While you are making flow charts of protocols, calculate final concentration of key ingredients in reactions. Make sure that the recipe and ingredients for all stock reagents are also included and clearly differentiated from effective concentration.
• • As you record your observations, specify the purpose for each entry. For example, in daily entries during isolation of bacteria on selective media, you might record: "checked for colony formation; no visible growth yet.")
• • Make lots of notes about the results of each experiment: did you achieve the goal? How do you know? What do any control reactions tell you that's important in interpreting the data? Never just call something a "control". What does it control exactly? How and why does a control result allow you to have more confidence in the test reactions? Again it is acceptable to make your entries brief as long as you include enough details for someone else to successfully follow your ideas and the work you have recorded.
• • Document key details of experimental results by attaching photographs (or print-outs of digital photographs). Cameras are provided in the lab.
• • Whenever water is used, specify de-ionized, distilled, tap, cold, hot, sterile, RNA-free, etc.
• • Record purchased reagent details. Details include product information (vendor, brand, product number, chemical structure, purity grade, lot number, date of mixing/production, expiration date, etc.). Take the time to jot down Manufacturer name, Kit name, Product Number and Lot number of proprietary reagents. You may cite a standardized procedure (e.g., DNA isolation from soil as per Power® Soil DNA Isolation Kit by Mo Bio Laboratories Manufacturer Information at [ http://www.mobio.com/]. (Don’t forget to include full citation details in your notebook to save time when you begin writing your paper).
• • Also write down the ingredients (for example in the "Master Mix" of a PCR reaction) and calculate effective concentration of key components in solutions and be sure to include the units so you won't have to do all of those calculations at paper writing time. Annotate all calculations so that all numbers, concentrations, etc. are fully explained and would be interpretable by another researcher.
• • Record field, greenhouse, laboratory, and growth chamber conditions such as temperature (in Celsius), humidity, light levels, light/day cycle (hours of each, and when night starts), etc. Note that conditions sometimes change, so record these parameters often if variation is likely to affect your results.
• • Label any figures you choose to include in your notebook.
• • You can supplement your entries with supporting material (e.g., test-result printouts and other documentation). But you must permanently affix the material onto a page in its proper chronological location.
• • Record names of people providing assistance with data collection, techniques, statistical advice. Write this information down immediately so that you remember to include it in your future "acknowledgements" sections.
• • If you happen to record some data directly onto datasheets (e.g., Excel spreadsheets that exist on computers or within ring binders), include dated entries for all such occasions: "entered data onto heat.xls spreadsheet." Ideally, construct your spreadsheets so that you can paste them into your notebook, perhaps right after your experimental details are explained: you could "mark" this page with a flag so that you can easily add data to these pages.
• • When you include datasheets, photographs, graphs, product labels, etc., use glue to cleanly and permanently attach all edges. Do not use staples (they poke through to the other side) and do not use tape (it becomes brittle and yellow)

Modified from:
Swarthmore College: Advice on keeping a laboratory notebook: http://www.swarthmore.edu/NatSci/cpurrin1/notebookadvice.htm

Links to Labs

Lab 1
Lab 2
Lab 3
Lab 4
Lab 5
Lab 6
Lab 7
Lab 8
Lab 9
Lab 10
Lab11
Lab 12