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Table of Contents

Acknowledgements

Course Operation and Rules

A. Course OverviewB. Course OperationC. PurposeD. Learning ObjectivesE. Specific Course ResourcesF. RulesG. General Expectations

Project 1Preparation of Competent E. coli

Project 2 -Research Project

Purpose

Timeline

o Week Io Week IIo Week IIIo Week IV and Vo Week VIo Week VII through XIo Week XIIo Completing the Project

Materials and Equipment

Schedules, Performance and Marks

Schedule

Performance and MarksLab EtiquetteEffort and Etiquette

ParticipationLab Notebook

Reflective Weekly JournalProject ReportsTheory ExamsGrading Rubrics

Weekly Summaries Competent Cell Preparation Individual Project Proposal Team Project Proposal Team Oral Presentation

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Draft Paper Lab Notebooks Video Presentation Question from Team Presentations

Appendix A - Basic Methods

I. Efficient Organization

II. Aseptic Work

A. Preparation for Aseptic WorkB. FlamingC. Aseptic Transfer by an InoculatorD. Aseptic Transfer by Pipette

III.Mixing Samples

IV.Pipettes and Pipetting

A. Classes of PipettesB. Sizes of PipettesC. Types of Pipettes and Pipetting AidsD. Pipetting Procedures

V. Plating and Enumeration

A. Streak Plating for IsolatesB. Enumeration

C. Replica Plating for Multiple Tests

Appendix B - Laboratory Safety

A. Laboratory HazardsB. WHMISC. National Fire Protection Association Diamond CodesD. GlovesE. Laboratory TechniquesF. Personal PracticesG. Chemical DisinfectantsH. Disposal Procedures

I. Radiation Safety and Working Rules

Appendix CUnits, Graphs, and Calculations

A. Units and PrefixesB. GraphsC. Reliability of ResultsD. Growth CalculationE. Dilutions and Dilution Schemes

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F. Sample Problems with Dilution and Growth Calculations

Appendix D - Technical Theory

I. Centrifugation

A. General InformationB. Types of Centrifuges

II. Electrophoresis

III.Enzyme Assays

IV. Growth Media

V. Buffers

VI. Ion Probe Measurement

A. pH ProbesB. Other Probes

VII.Nomenclature

A. Strain NamesB. Genetic Nomenclature

VIII. Protein Isolation

A. Protein Release from the Cell

B. Stabilization of Released Enzyme ActivityC. Isolation of the Released Enzyme ActivityD. Protein Measurement

IX. Radioactivity

A. General InformationB. Nomenclature of Radioactive MoleculesC. Properties of Some IsotopesD. Measuring RadioactivityE. Incorporation Properties

X. Spectrophotometry

A. General InformationB. Problems and Compromises in Spectrophotometer Design

Appendix ETeams and Teamwork

A. TeamsB. Choosing Teams

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Appendix FRecords and Reports

A. Project ReportsB. Format Requirements for Project Reports

C. Participation ReportsD. Lab NotebookE. Oral Presentations

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Microbiology 421

Manual for ExperimentalMicrobiology

Compiled by:

W.D. RameyD.C. Oliver

(2015)

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Acknowledgements

This lab manual for MICB 421 has been developed by using an assortment of information and ideasconcerning the aims, objectives and results of former MICB 321, MICB 421 and MICB 421 classes. The

manual is intended to be used in conjunction with the MICB 421 Connect website at

https://connect.ubc.ca/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2F

execute%2Flauncher%3Ftype%3DCourse%26id%3D_27433_1%26url%3D

Nick Cheng wrote many of the directions for operating the equipment and took most of the digital imagesthat are used throughout the website and the manual. Nick Cheng, Chris Gin, Kevin Lin, Kyla Omilusik,Lando Robillo, Kristen Schurek, Jennifer Sibley, Gaye Sweet, and Alice Wang helped to locate, developand test content for the experiments as well as experimental protocols, assays and proofreading. KarenSmith compiled details and content for the section on laboratory safety and disposal of hazardousmaterials in Appendix B. Kristen Schurek compiled the detailed section on the formatting reports inAppendix F.

Department of Microbiology and ImmunologyUniversity of British ColumbiaJanuary 2016 William Ramey / David Oliver

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Course Operation and Rules

A. Course Overview

Traditional lab courses tend to present students with experimental recipes and supplies, and

then ask students to follow the recipes, look at the results and write a report. This approach

allows each student to have the same learning experience but it limits the range of availableexperiments. In addition, even though instructors expect students to understand the work

before attempting an experiment the traditional lab approach allows some students to get

through the work by following the directions rather than understanding the purpose of thework. In this course teams of students are expected to design experiments and protocols to

test their approach to provided categories of observations rather than just following a

supplied recipe. In some cases the explanations might require a simple modification of aprevious experiment, in other cases the teams might need to invent an entirely new

experimental protocol. In either case, once the experiment has been acceptably designed,

your team will be expected to prepare the supplies, set up equipment, carry out the

experiment, analyze the results and prepare a formal journal style report that describes theexperimental purpose, the methods, the results and the conclusions. The course instructors

will review this report. The report will then be returned to the team to correct any

significant observed problems in style, logic or fact before it is published to the "UBC

eJournal of Experimental Microbiology and Immunology" (JEMI) where it will be availableon-line. Teams may repeat a previous experiment to ensure that the results were correct but

will still be expected to produce and test an original experiment based on the resulting

observations and explanations. The experiments will have some constraints imposed bytime, equipment and costs.

This approach is intended to provide a more complete and realistic research experience. We

also hope that it will be more interesting for you because you will be contributing

knowledge and skills to solve real scientific questions instead of working on recipes chosenby the instructor.

B.Course Operation

The class will operate as teams of three or four students.

The majority of the course is concerned with designing and carrying out a research project

but each Tuesday there will be a scheduled class meeting. During that part of the class wewill discuss/review different aspects of project design and advanced molecular and

microbiology. Towards the end of term we will also talk about the final report and the

characteristics of the final report. The actual content of these classes will depend on generalneeds for the different projects in the class. Individual weekly meetings will be scheduledduring the lab periods on Tuesday and Thursday afternoons to discuss details of their

projects with each team. By the start of the weekly meeting each team member should have

an idea of the work that the team is intending to complete in the following week and howthe team will do that work.

An original copy of the team records must be maintained in a bound lab book whenever theteam is working in the laboratory. This book must include all important laboratory details

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such as the working hypotheses, ideas, data, explanations of observations, and conclusions

as well as significant discarded ideas, relevant references, equipment names and models,

chemical sources and catalogue numbers. The first page of the book must be reserved for anindex that is updated each week. Each page in the book must be numbered and dated as it is

used so that the important pages can be identified in the index.

The final report must be a formal journal article written in the style of the Experimental Journalof Microbiology and Immunology. This style is adapted from the style used in the American

Society for Microbiology journals such as J.Bacteriol and J.Immunol. Approximate examples

can be seen in recent volumes of the Journal of Experimental Microbiology and Immunology(JEMI) at:

https://www.jemi.microbiology.ubc.ca

Keep in mind that the ASM style of citing references changed in January 2011. Please use the

current ASM style:

http://jb.asm.org/site/misc/ifora.xhtml

C.Purpose

The purpose of the course is to carry out a research project involving aspects of molecularbiology and microbiology in order to:

1. demonstrate your ability to apply your skills in this area of science2. expand your background in this area of research3. learn additional molecular biology skills

D.Learning Objectives

1. To develop your ability to define a research problem.

2. To develop your ability to adapt your knowledge and background to develop protocolsto experimentally solve scientific problems.

3. To develop your ability to locate information and background for designing anexperimental protocol.

4. To further your understanding of some of the constraints of an experimental protocol ortestable question as well as recognition of the common elements in research protocols.

5. To further your ability to quantitatively analyze data and formulate logical and testablemechanistic models that account for the observations.

6. To reinforce your ability to maintain scientific records and communicate scientificresults.

7. To further your ability to prepare and present written scientific reports.

8. To further your ability to organize and complete technical projects with finite resourcesand time.

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9. To further your ability to work in scientific teams.

E.Specific Course Resources

Most of the course material is described in the lab manual. Some resources, inventories and

assignments for the course are located at the MICB 421 Connect site. There will also beprinted copies of the equipment operation, strain inventories and chemical inventories inroom 104 and 110 and 114 Wesbrook. Some of the files in the website can be downloadedand searched.

F.Rules

1. The major part of your lab work each week should be planned to fit your scheduledclass time. However, some work will need to be done at other times to allow yourprojects to proceed in a timely manner. If you are working outside the scheduled classtime the available lab hours are 9:00 AM to 5:00 PM. Plan to work within thosetimes.

2. There should be two people present when you are working in the lab. One of thepeople must be the instructor or the teaching assistants if you are starting any workinvolving heat, gas, compressed air or hazardous chemicals. If you are countingcolonies or weighing safe ingredients to prepare media or supplies you do not needsupervision but it might be helpful to have supervision in case questions arise as youproceed with the work. Work that requires long periods of supervision should beconfined to the scheduled lab times.

3. You must be certified before you use any hazardous or expensive or fragile equipment.Certification means that the operation of the equipment has been demonstrated to youby the MICB 421 instructor or teaching assistant. Please have the person thattrained you initial your lab training record. If there is doubt about the operation of anyof this equipment, it is important to clarify your uncertainty before you use theequipment.

4. You must be aware of the hazards of any work that you attempt. As part of thatawareness you must consult the MSDS site for every chemical that you attempt to useand copy down or print out any significant risks and the corresponding first aidtreatments.

5. You must understand the intent of each step in every protocol that you attempt to usebecause you will make the work safer for everyone in the lab if you understand theintent of each step in each experiment.

6. Each team must maintain complete experimental records in a single notebook that will

be submitted to the course at the end of the term. You may keep individual recordbooks but the team record book must be kept up-to-date each week and available atany time the team is working in the lab.

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G. General Expectations

We expect you to remember all the general features of basic, safe aseptic work that you

have encountered in other classes. These expectations include:

1. Disinfect the top of your desk with Westosan at the beginning and the end of each labday to minimize the chance of spreading contaminants around. Wash your hands withdisinfectant soap before leaving the lab.

2. Do not eat or drink in the laboratory.

3. Do not take cultures out of the laboratory without permission.

4. Inform the instructors if you spill a culture, and then disinfect the area. Use the brushat the discard cart to sweep up any broken glass or hazardous chemicals and discardthem to the designated waste containers.

5. Inform the instructors about any accidents such as cuts, burns or abrasions, even ifthey seem slight.

6. Wear a protective lab coat when working in the laboratory and secure your hair so thatit will not swish into any open flames or chemicals involved in your experiment.Wear gloves and eye protection when the hazards warrant the use of gloves and eyeprotection.

7. Use the lockers outside room 110, 104, and room 5 to store backpacks and otherequipment and materials that are not needed in the lab room. Lockers can be signedout by providing a deposit that will be returned when the locker key or lock arereturned

8. Drain tubes containing toxic or corrosive chemicals to the appropriate discards thenrinse the tubes with cold water before they are discarded.

9. Cultures and other solutions that are contaminated with microbes should be discardedin closed flasks or tubes so they can be autoclaved before they are dumped out.Adequate closure is achieved by covering the top of a flask with a cotton bung or alayer of aluminum foil when the flasks are discarded to the trays in the lab room.

10. Discard standard calibrated pipettes into the tall discard jars at the bench. Discarddisinfected Pasteur pipettes into glass waste.

11. Keep your work space tidy and organized so it is safe and aseptic.12. Put away your supplies between lab days and return communal chemicals and

other supplies to the appropriate storage places.

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Project 1Preparation of Competent Esher ichia col i

Purpose:

The intent of this project is to provide an opportunity for your team to begin workingindependently in the laboratory setting. Your teams goal is to prepare aliquots of competentE.coliand to determine the transformation efficiency of your preparation. You have course weeks2, 3, 4 and 5 to plan, execute and document this task. You will need to source protocols, planyour experimental steps, and prepare the requisite reagents such as growth media, chemicalsolutions, and sterile equipment and glassware. You should include appropriate controls todemonstrate that your experiment worked as expected. You should also think about replicates

when performing transformations in order to be able to report transformation efficiency withstatistical support. You may choose any (non-pathogenic) E. coli strain available in the MICB421 Ramey strain collection (e.g HB101, DH5, BL21, B). It is recommended that you thinkahead to Project 2 in order to produce competent E. colithat may be useful to your team later inthe course (Note: competent cells stored in cryoprotectant can be stable for years at -80C).Similarly, you may select any plasmid available in our collection to test transformation efficiency,however, it may be prudent to choose something relevant to your subsequent research in Project 2.

Instructions:

Your team is responsible for planning, execution, and documentation of your experiment. Labnotebook guidelines in Appendix F should be followed. The Instructor and TAs will be available

throughout the scheduled lab period to provide guidance, technical demonstrations (e.g makingmedia and pouring plates), and training on equipment such as the centrifuge, shakers, andautoclave. We can also introduce you to reference manuals and online sources of protocols.

The sections of the course manual describing proper aseptic technique, bench organization,pipetting, and safety should be carefully reviewed before beginning your work.

When determining transformation efficiency, perform an experiment that allows you to graph (1)plasmid concentration versus transformation efficiency, and (2) plasmid concentration vs totaltransformants. How do you predict these plots will compare?

Assessment:

Document Project 1 as experiments in your teams lab notebook. Relevant pages of your teamslab notebook can be submitted to MICB 421 Connect as a word document or as a scanned PDF ofthe lab notebook pages (scanning can be done using the photocopier). The deadline forProject 1submission is 11:59PM on Feb 5

th 2016. The submitted notebook pages will be assessed for

formatting and scientific rigor. The results themselves will not specicially be graded, ratherqualities of the report will be evaluated. We will look for an effective title, a well written andreferenced Introduction section, a complete Materials and Methods section, a Results sectioncontaining appropriate observations and interpretations, well presented data with appropriate

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statistical backing and noted limitations, objective Conclusion(s), and a feasible Future Directionssection.

Project 2 - Research Project

Purpose:

The intent is to reinforce your understanding of the constraints of the scientific process bydeveloping explanations of a supplied scientific observation, designing an experiment to test aproposed explanation, preparing your supplies, identifying required equipment, doing yourexperiments and communicating your results as an article for a scientific journal. The specificexperimental objectives will depend on the observation that your team chooses to explain and themanner in which your team chooses to test the explanation.

References

Barker, K. 1998. "Chapter 4, How to setup an experiment", At the Bench, a laboratory navigator,p 69-87 Cold Spring Harbour Laboratory Press, New York, New York.

Barker, K. 1998. "Chapter 5, Laboratory notebooks", At the Bench, a laboratory navigator, p 89-99 Cold Spring Harbour Laboratory Press, New York, New York.

Instructions:

1. The project will be done by teams consisting of three or four students.

2. The general requirement is to review previous course projects to identify a research question,then to devise protocols to address your approach to the observations or problems, prepare thesupplies, carry out the tests and analyse the results. A list of the titles and a list of generalreferences are included after the materials and methods section in this project outline.

3. The proposed project may not be an exact duplicate of any other posted experiment but youmay repeat an experiment in the Journal of Experimental Microbiology and Immunology(JEMI) in order to confirm the results before proceeding with your own experiment. You maydevelop and use a modification of a published experiment if the modification provides a bettersolution or better insight into the problem and your explanation.

4. The number of teams choosing a particular approach or methodology might be restricted.Each proposal must be different. If two teams suggest the same proposal and same general

approach then the first proposal received will be permitted to proceed and the second teamwill need to develop an alternative proposal (unless the second team provides evidence thatthe first team pirated their proposal). However, proposals that assess similar ideas bysignificantly different approaches or methods are still acceptable.

5. Each team is encouraged to develop the details of their proposed project. However, if youhave a good idea but are unsure how to develop the idea into a testable explanation or developa suitable protocol you should discuss the idea with the instructor or the teaching assistant tosee if they have worthwhile advice. Similarly, if you are having trouble choosing anexperiment or you think that you have a suitable experiment but are uncertain whether

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particular protocols could be attempted with the available equipment or supplies then youshould discuss those concerns with the instructors or teaching assistants to get their advice.The teaching lab is not equipped to deal with pathogens or eukaryote tissue cultures .

6. Teams proposing projects involving a lot of samples or sampling should do a pretest with afew samples to ensure that the strain(s) have the correct phenotypes, the results are falling in

the expected assay ranges and that the methods will work and give reproducible results.

7. The results will be presented as a research article suitable for publication in JEMI. Any majorproblems or technical errors in the submitted report will need to be corrected before themanuscript is accepted for publication. The article must be accepted for publication before themark for the project is added to your grade.

8. The instructor or the teaching assistant must approve proposals before you start significanttechnical preparation. Some basic preparation of media or buffers or glassware can be done inadvance. Ask if you are in doubt about what could be done in advance.

9. The lab will normally be open between 9:00 AM and 5:00 PM to allow you to work on theproject outside the scheduled lab periods if that work is necessary or helpful. However, we

expect some of the work to be scheduled for your registered lab period when assistance will beavailable. Your teams lab book may be checkedeach week by the instructor or the teachingassistant during your registered lab period. If you work in the lab outside your registered classthere must be at least one other person present if the work involves any potentially hazardousprocedures or equipment.

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10.Week I.

i. Each student must individuallypropose a project based on an observation orsuggested follow up experiment described in a JEMI paper that they would like toinvestigate and prepare (1) a flow chart and (2) a brief report of approximately 300500 words that explains their choice. One electronic copy of these individual

reports must be submitted to the MICB 421 Connect assignment drop box by11:59 PM on the due date (See schedule). When you submit the report use yourinitials, surname, day and alphanumeric as the name for the file. For example,JohnSmithTuesA. Other copies must be distributed to your team mates by the startof the lab session for your team.

Here is a link to JEMI:

https://www.jemi.microbiology.ubc.ca

You can also review the titles of papers submitted by MICB 447 students last term. These areposted on MICB 421 Connect. If approved by the authors, the Instructor will send you draftmanuscripts from MICB 447 2015 upon request as these papers are still under revision.

ii. Begin by preparing a 1 page flow chart on your proposal. A model flow chart as wellas a templated in Powerpoint format is available on MICB 421 Connect. Theflowchart must be uploaded to Connect by 11:59pm on Sunday January 10

th2016.

iii. Your report should be a maximum size of 1 page in single spaced TNR size 10 font.The written individual proposal must be uploaded to Connect by 11:59pm on FridayJanuary 15

th2016. The written proposal must include specific labeled sections for:

- Identification: your name and your lab day at the top right corner of the page.- Source of the observation: the category of the project and a reference to the

specific observation or problem. These are typically JEMI articles, althoughother scientific papers may be permitted with permission from the Instructor.This reference should be formatted as per ASM 2013 style.

- Background: the background necessary to understand / explain therelationship between the problem and the proposed explanation. (This sectionis not expected to be a full review of the topic but it needs enough detail for thereviewer to understand the logic for your subsequent explanation(s) andproposed experiment. In most cases this would take approximately 300 or 400words)

- Observation: a brief description of the observation / problem.- Explanation / Hypothesis: a preliminary potential explanation(s) / hypothesis

that might account for the observation that you will work on.- Experimental question(s): state the actual scientific question that will test the

explanation. Include an explanation of how answering the question would

assess the validity of the explanation.- Approach: the general experimental approach for testing your explanation.(What methods or combinations of feasible methods would be the key way ofgetting data to test your explanation? What would the results from thatapproach show if the explanation was correct or incorrect?)

- Feasibility: the feasibility and outcomes of the proposed approach. (What arethe main technical difficulties? What are the main details that need to beworked out to know whether it would work? What are the limitations imposedon the analysis by these methods?)

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Each student should think about additional project details and requirements and why they wanted

to work on their particular proposal. This additional level of detail is not expected in the

individual proposal but the information might be helpful when the team chooses the topic for theproject they will develop for the rest of the term.

11.Week II.

i. By Week II you should have selected teammates and been assigned a lab day and bay.

ii. Please register your team for a 15 minute team meeting on the door to room 138.Register your team with the TA and be prepared to discuss your flowchart. Only 3minutes will be allotted to each team members presentation so please be prepared.The Instructor and TA may provide guidance and ask a few questions forclarification. Using this feedback, prepare your written proposal.

12.Week III

iii. To choose a project, compare and discuss the merits of the potential projects proposedby the different team members. Consider the pros and cons of different projects, thegeneral interest of the team and alternative explanations that might account for theobservation.

iv. If your team is sure about the intended project then one choice is sufficient. If theteam is less certain it is better to choose two. For each of these projects the teamshould identify the major specific information or general background relevant tounderstanding the observations or the preliminary explanations. When the membersdraw up this list they should consider what they already know about the topic andhow well they recall details. They should also consider whether their knowledge issuperficial or detailed, whether the knowledge is dated or current et cetera. Forexample:

a. What is known about the process that formed the original experiment? Wouldknowing more about that process be beneficial? Is it known whether relatedprocesses would work? Is anything known about those processes?

b. Are there known mechanisms involved in the molecular genetics for any of thecomponents involved in the project. Would a more detailed understanding ofthese mechanisms give more insight into potential explanations and processes?Et cetera.

v. Each team member should take responsibility for researching / checking some of thevarious sets of information that are necessary or helpful for choosing one project andrefining the preliminary hypothesis that is going to be presented at the scheduledmeeting with the TA and the instructor on Week III.

vi. The team should also consider whether anyone already has a source for some of thebackground. The web can sometimes provide some ideas and details but the qualityof information is inconsistent. More reliable sources can be found by doing librarysearches for journal articles and compendiums of research facts and methods. Thelibraries provide workshops on the use of electronic indexes for finding relevantjournal articles and searching for relevant key words. Some indexes that might beuseful include:

- Biosis

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- Medline- PubMed- Web of Science- NCBI Resources- PubMed

There are more sites at

Google Scholarcan also be helpful but is less complete than the dedicated researchindexes. In addition, by accessing articles through the UBC library, you go throughthe library subscriptions so more prepaid journal access is available for you.

vii. At this stage you can still consider other projects if the initial choices seem lesssuitable when you consider the details.

viii. After considering the additional information reported by each team member, the teamshould decide which problem and which hypothesis or approach will be investigated.This will be your team project for the rest of the term . When that choice is madeeach person on the team should consider the known facts and logic that support theproposed explanation. Each person should also bear in mind that the eventual

evaluation of the project will consider:

a. Whether the experiment is testing an explanation/model of the observations orat least setting up the potential to test an explanation/model rather thandabbling with experimental variables.

b. Whether the proposal is practical. Can it be done within the constraints oftime, expertise and available equipment and supplies?

c. Whether the experiment is worth doing. Some experiments are exciting andinteresting. Some experiments are bland but the results are important to furtherunderstanding. Some experiments are not worth doing because the answers areeither obvious or insignificant. For some experiments the distinctions are mostobvious in retrospect.

ix. During the scheduled meeting with the TA and / or the instructor during the lab classthe team should be able to:a. State the observation they intend to investigateb. Give preliminary explanation(s) of the problem and present testable modelsc. Explain what information was sought and discovered by each team member and

how it applies to the potential projects.d. Discuss the general feasibility of your project with the instructors.

x. Consider any major additional details that the team will need to look up or work outin order to finish refining and designing the experiment. Examples of these details

could include relevant strains, chemical requirements, potential hazards, necessaryassays, potential equipment, recipes, scheduling et cetera.

xi. Assign particular team members specific duties to sort out by the following class.

13.Weeks IV and V

During the scheduled meeting with the TA and / or the instructor during the lab class theteam should be able to:

a. State the problem that has been approved in principle by the instructors

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b. Provide the potential explanation(s) of the problemc. Explain the evidence or logic for the explanationd. State the experimental question that will be specifically addressed and how that

question relates to the original hypothesis or explanation concerning theoriginal observation.

e. Explain the experimental approach for testing the stated question and the

probable outcomes if the hypothesis is true and the probable outcomes if thehypothesis is false.f. Summarize any outstanding issues or changes to the original questions posed in

the preceding week that that need to be addressed.g. Explain your progress over the preceding week.

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14.Week VI

i. By 11:59 PM on the Friday February 12th 2016 the team must submit a detailedwritten proposal. In 2500to5000 words the report must provide:

- Identification: the team alpha-numeric and the names of the team members

- Overview Chart: a chart that shows how the tests and work fit together as anoverview of the project.- Title: a relevant working title for your experiment (It might change by the

final report).- Introduction and Background: sufficient background to understand the

explanation of the observation, the chosen approach to testing the question andthe outcomes.

- Observation and Explanation: the experimental observation and theproposed explanation that the project is addressing.

- Experimental Aims: the experimental question(s) that you are aiming toanswer that will test your explanation / hypothesis of the observation. Includethe potential outcomes if the explanation is correct or incorrect.

- Protocol: description of the project that explains what will be doneand how

the tests fit together. It would include details of sampling, number of samples,timing of sampling, types of assays for the different types of proposedmeasurements, controls, growth requirements. It is recommended that his bearranged in a table.

- Methods: description of how the assays and tests will be done. It wouldinclude recipes or step by step explanations and details to makemeasurements, grow the cultures, and actually assay the samples. Includequantities and control conditions et cetera. It must be detailed enough toallow the team to make the supplies in appropriate quantities.

- Supplies and Equipment: provides quantities, and condition of thechemicals, equipment and strains. Any required chemicals or kits or strainsthat are not available in the inventories for the class must be clearly identified.

- Weekly Time Frame: the detailed schedule of the project work that will bedone by the team each week in order to finish the project on time. Some workcan be overlapped to allow testing of unfamiliar procedures, testing of strains,taking preliminary measurements to assess response ranges et cetera beforethe final experiment is attempted. A Gantt chart may be useful.

- Potential Pitfalls: potential problems that might arise to put the work behindschedule.

- Known Hazards: any significant unusualhazards associated with the workand your means of controlling those hazards so the work is safe.

ii. This report should be submitted on the MICB 421 Connect assignment drop box.There should only be one submission for each team.

iii. The report will be graded for completeness, relevance and readability for each of theexpected sections.

iv. Submit a separate list of required strains, kits or chemicalsthat are not in the classinventories directly to the instructor by e-mail. Include sources, quantities andcosts for each item. Strains that are not available locally can take weeks to arrive sothey need to be requested early in the process. The list should have Required Strainsfor MICB 421 or Required Chemicals for MICB 421in the subject heading.

v. During the scheduled meeting with the TA and / or the instructor during the lab classfor Week V the team should be able to explain the timeframe, the required amounts of

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supplies and equipment, the strains and the sources of strains that will be needed forthe project.

vi. The team can start to prepare basic supplies that will be needed for the project.

Weeks VII-through XI.

i. Over this time the team must finish preparing the required supplies (if they are notalready available). Carry out the experiment. Examine the results. Then use theobservations from your first experiment to re-design or refine the first experiment toimprove or confirm the initial results. Sometimes the second experiment should usethe same general approach with a better sampling strategy, additional controls ordifferent input. Sometimes the second experiment should use a different approach tothe initial hypothesis. In either version of the second experiment the intent is to refineyour understanding of the initial observation and your proposed explanation of thatobservation. In all cases the second experiment must continue to test the idea or anexplanation of the problem or observation made in the first round of testing.

ii. Starting on Week VIII, prior to the scheduled meeting with the TA and / or theinstructor during the lab class the team should submit a Weekly Summary atMICB421 Connect by 11:59pm on Sunday.

Weekly Summaries should include:

a. The team name and submission date.b. Project title (once defined).c. A summary of the weeks activities as bullet points.

max 1/2 page in single spaced TNR size 10 font. Each point should concisely explain:

experimental reference numbers from your lab notebook the rationale for work performed results, key observations, conclusions any decisions made and major changes to project any technical challenges and difficulties any remaining work with respect to timeline

15.Weeks XI-XIII.

During the scheduled lecture time, each team will present a summary of their project,including background, results, analysis, conclusions and future directions.

Presentations may be delivered by one or more members of the team. Presentationsshould be no longer than 12 minutes maximum (points will be deducted forpresentations exceeding 12 minutes in length). The audience is expected to composequestions for each presentation. Each team should choose one question to submit tothe presenting team via Connect. Each presenting team can choose to respond to 3questions submitted by their peers via video. Responses will be posted on Connect.

All team members must attend the lab during their normal scheduled class time toclean upsupplies and work places unless the cleanup was done the week earlier.

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Completing the project

i. By 11:59pm on the April 15th 2016 each team must submit a formal journal articlethat documents their hypothesis, their experiment, their results and their conclusions.The article must be written in the style prescribed in Appendix F of the lab manual. Ifthis article is started in the last week of class it could be a large amount of work.

However, much of the effort can be dispersed if the team coordinator assigns tasksthat initiate the article by early - to- mid-November. For example, even though thefinal draft might require revisions to include the final results it is possible to make adraft version of the introduction as well as the materials and methods section. It isalso possible to prepare preliminary graphs and tables that portray the preliminaryresults from the first round of the experiment before doing the second round. It is alsopossible to develop a written list of the major thoughts and provisional conclusionssuggested by that data. Even though the final tables and figures need to be embeddedat the end of the word document as pictures pasted into text boxes the preliminarytables and figures can be prepared in Excel (or an analogous spread sheet program)and saved so they are easy to update and use when the final experiments arecompleted.

ii. The final report is expected to include at least four journal article references asidefrom JEMI articles that are relevant to the explanation of the ideas being tested. Tomeet this requirement, it would be useful to continue the library searches and developa provisional reference list well before the article is due. An early search might behelpful for interpreting the observations from the first experiment and designing thesecond experiment.

iii. Streaked plates of all relevant bacterial strains, clones, constructs and plasmidsused in your project must be prepared and submitted to the instructor so thestrains can be preserved and accessible for any future students that wish tocontinue your project.

18. The submitted draft reports will be reviewed in the order that they are received and thereviewers comments will be returned to the team that submitted the report within a few days.The team must complete any required revisions and corrections then resubmit the report inelectronic form before the end of April.

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Materials and Equipment:

- Lists of inventories of the available equipment, strains and chemicals are available in theresources section at MICB 421 Connect. There are bound paper copies of this information inroom 104 and 114 Wesbrook.

- Major equipment that could be available include:

:- a variety of centrifuges for microcentrifugation, high-speed centrifugation and ultracentrifugation. Some of this

equipment has restricted access but it can be used as long as you have suitable instruction in the use.

:- a variety of spectrophotometers. Some machines like the Spectronic 20 are suitable for working with larger volumes

and are well suited for following growth, measuring the results of chemical assays and enzymatic assays but lack the

capacity to measure ultraviolet light. Others work well in the ultraviolet light. These spectrophotometers generally have

a maximum volume of approximately one millilitre but special cuvettes are available to measure 100 microlitre volumes.

Another one has a carousel that can be programmed to rotate in order to automatically read the absorbance of samples in

successive cuvettes. Some of the instruments that read at ultraviolet wavelengths can be set to scan multiple

wavelengths of light and give a reading at the specified wavelengths. Some of the spectrophotometers can be linked to

the SpecX data acquisition program to automatically collect digitized data that can be imported into spreadsheet

programs. The SpecX program can also be adapted to give automatic readings of temperature and ion-probe

measurements:- a variety of electrophoresis equipment. There are gel systems for working with protein gels and nucleic acids. The

nucleic acid systems are mostly for submerged agarose gels. The agarose gel systems are available in a range of sizes.

The bigger boxes can hold more samples than the smaller boxes and the samples can be run further to improve the

resolution between bands. However, the smaller boxes run a lot faster and use less agarose so they are much better for

tests that involve fewer samples with well-resolved bands. There is also a Western Blottingapparatus and a special

pulse-field gel apparatus that is used to electrophorese and isolate large molecules such as whole genomes,

chromosomes and viruses.

:- a variety of incubators,air-shakers, tube rotators and waterbaths to grow cultures. Some incubators are stationary

and are suitable for static incubations of flasks and plates. Some move to allow agitation or aeration of flasks or tubes or

other containers. Some work at ambient temperature. Some have thermostats to work above room temperature. Some

of the waterbaths can be hooked to cooling systems to work below ambient temperature. Some work can also be done in

cold rooms to lower the ambient temperature.

:- ovensfor higher temperature incubations.

:- digital cameras, an Alpha Imager(geldoc) system and a scanner to create electronic files that store data and images.

The digital cameras can be used in freestanding mode or stabilized in box stands or hooked to some microscopes.

:- a fluorimeter that measures fluorescence. It is analogous to a spectrophotometer but measures the intensity of light

created by the sample rather than transmitted light. It can be more sensitive than spectrophotometry and has wide

application for a variety of chemical and enzymatic assays.

:- a spectrofluorimeter that is analogous to the fluorimeter but allows a broader range and combination of excitation and

emission wavelengths.

:- a luminometerto measure light emitted by luminescent assays.

:- small capacity bead beaters, large capacity bead mills, grinders, a sonicator and other equipment for breaking cells.

:- an electroporator to shock and transform cells.

:- a gas chromatograph(GC) for separating and measuring volatile molecules such as acetic acid, butyric acid and other

metabolic wastes. It can also be used to measure some types of storage products.:- a variety of gas tanksand pressure regulatorsto adjust and control the atmosphere in cultures and reactions.

:- a variety of ion-probesfor measuring pH, oxygen, ammonium and re-dox.

:- a scintillation counter for quantifying tritium and carbon-14 isotopes. There is also an x-ray developer system for

working with autoradiographs.

:- two hybridization ovensfor working with nucleic acid hybridizations or protein blots.

:- an ultraviolet light chamberfor mutagenesis and binding molecules to specific activated membranes.

:- polymerase chain reaction machines(PCR).

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General References that might be Useful to find Project Background

1. Books

Molecular Cloning: A Laboratory Manual,Green and Sambrook 2014.

At the Bench ; a Laboratory Navigator, Barker K.. 1998. A guide to many basic laboratory research skills andfunctions.

Difco & BBL Manual , Manual of Microbiological Culture Media , Zimbro MJ, Power DA., (eds.). 2003. Amanual discussing the history, properties and uses of the Difco and BBL media that are commonly used in microbiological work.

Molecular Cloning, 2nded., Sambrook J, Fritsch EF, Maniatis T. 1989. A manual molecular biological techniques.

Molecular Biology of Bacteriophage T4, Karam, J.D. and J.W. Drake (eds.) (1994) Reference text concerning T4properties

Principles and Techniques of Practical Biochemistry, 5thed., Wilson K. Walker J. 1999. Theory and application ofbiochemical techniques.

Short Protocols in Molecular Biology, 4thed., Ausubel FM et al. 1999. A manual of molecular biological techniques.

2. Catalogues

Bio-Rad Life Science Research ProductsInformation on molecular biology reagents and methods

Fisher Biotech CollectionInformation on molecular biology reagents and methodsInvitrogenInformation on molecular biology reagents and methods

New England BiolabsInformation on molecular biology reagents and methods

Promega (Fisher Scientific)Information on molecular biology reagents and methods

Roche Molecular BiochemicalsInformation on molecular biology reagents and methods

Sigma CatalogueInformation on chemicals

3. Websites

UBC Libraryathttp://www.library.ubc.ca

Search for journal articles related to topics by using

Biosis

MedlinePubMed

Web of Science.

These are good places to find journal articles in the topics and to search whether published authors have

published more recent studies.

Google Scholarat http://scholar.google.ca/schhp?sourceid=navclient&ie=UTF-8

Search for research articles and scholarly books

Googleatwww.google.com

General information search site

EcoCyc andMetaCycathttp://ecocyc.organdhttp://metacyc.org

Information on metabolic pathways and enzymes in hundreds of different organisms including Escherichia coli

andBacillus subtilus.

Coli Genetic Stock Centerat http://cgsc.biology.yale.edu/Data base and source for mutant strains ofEscherichia coli including the single gene knockout strains in the Keio

Collection.

Hancock Laboratory Methodsathttp://cmdr.ubc.ca/bobh/methodsall.html

Extensive collection of common assays for molecular and cellular work.

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Data Presentation and Analysis:

1. The final report for this project must be written as a journal article in a modified form of thegeneral style used by the American Society for Microbiology for 2013. Examples of this styleinclude the Journal of Bacteriology, the Journal of Immunology, the Journal of ClinicalMicrobiology and the Journal of Virology. Detailed instructions for preparing and submitting

the article are available in the "instructions for authors" for the UBC Journal of Microbiologyand Immunology (JEMI) at the MICB 421 Connect site and Appendix F of this lab manual

2. When the initial draft of the report has been submitted and reviewed by the editors it will bereturned to the authors for any required corrections or revisions. The mark for the project willnot be applied to the grade until the corrected article has been returned to the editors andaccepted for publication in JEMI. All accepted articles will be published and available forother students in other classes to read and study.

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Schedules, Performance, Marks

Schedule

The course has two projects (Project 1 or P1 and Project 2 or P2), a lab notebook, an optional

journal, several written reports, an oral presentation, a video communication assignment, several

mandatory scheduled meetings, a WHMIS assignment, an in-class final exam. You will need to

work concurrently on some assignments. Material may be submitted in advance of the due date.

Schedule Overview

Week Date Lecture Lab Phase Assessment Due Date

1 48 Jan 1/2 P2 Individual

Proposal

Project 2 Individual Proposal - Flowchart 10-Jan-16

2 1115 Jan 3/4 Project 2 Individual Proposal - Written 15-Jan-16

3 1722 Jan 5 P2 Team

Proposal / P1

Project

WHMIS and Lab Introduction Quiz 14-Jan-16

4 2529 Jan 6 Refworks Assignment 29-Jan-16

5 15 Feb 7 Project 1 Report 5-Feb-16

6 812 Feb 8

P2 Research

Project 2 Team Proposal 12-Feb-16

7 1519 Feb RW

8 22- 26 Feb none

9 29 Feb4 Mar 9

10 711 Mar 10

11 1418 Mar Exam In class Final Exam 15-Mar-16

12 2125 Mar 11/12 Guest lecture 22-Mar-16

13 28 Mar1 Apr 12/13P2 - Writing

Presentations and Questions (#1/2) 29/31-Mar 16

14 48 Apr 14/15 Presentations and Questions (#3/4) 5/7Apr-16

UBC Exam Period (note: there is no exam

during this period for MICB 421)Draft Paper 15-Apr-16

P2 Revisions Revised Paper, Lab Notebook 30-Apr-16

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Week Lecture Date Activities for Week

Lecture (8am Tues and Thurs,

WESB201) Team Meetings* Lab

1 1/2 48 Jan Tues and Thurs Class none Lab Tours

2 3/4 1115 Jan Tues and Thurs*** Classes Team Meeting

Project 1 and Lab

Demos

3 5 1722 Jan Only Tues Class Team Meeting Project 1

4 6 2529 Jan Only Tues Class Team Meeting Project 1

5 7 15 Feb Only Tues Class Team Meeting Project 1

6 8 812 Feb Only Tues Class Team Meeting Prep - Project 2

7 RW 1519 Feb No lecture Team Meeting Project 2

8 none 22- 26 Feb No lecture Team Meeting** Project 2

9 9 29 Feb4 Mar Only Tues Class Team Meeting** Project 2

10 10 711 Mar Only Tues Class Team Meeting** Project 2

11 Exam 1418 Mar In Class Final Exam on Tues Team Meeting** Project 2

12 11/12 2125 Mar Tues and Thurs ClassTeam Meeting** Project 2

13 12/13 28 Mar1 Apr Tues and Thurs Class Pres. Team Meeting** Project 2

14 14/15 48 Apr Tues and Thurs Class Pres. Team Meeting Project 2

* Team meetings may be optional on some weeks depending on lab actvity. Visit MICB 421Connect for updates on a week to week basis.

** Weekly Summaries begin on Week 8 and end on Week 13

*** WHMIS and Introductory Lab Quiz In Class

RW = UBC reading week

Detailed Schedule

Week 1 (Jan 4)Select a problem and research background about the problem and themethods normally used to work with the problem. Submit flowchart via Connect. Attend labtour. Recruit team members.

Week 2 (Jan 11)Register your team. Have team photo taken. Sign up for a team meetingwhere we will discuss set-up and execution of Project 1. Each person must submit a 1-pagewritten proposal of the project that they would like to pursue to the drop box at MICB 421Connect by 11:59 pm. Reference can be added on a separate page.

Week 3As a team, choose a lead project. Begin to refine your experimental problem, set

objectives, start to develop an experimental plan, check sources of additional information,consider specific resource requirements (are the types of supplies and equipmentavailable?), safety constraints.

Weeks 3, 4, 5Execute Project 1 in the laboratory and compile report for submission on 5Feb 2016 at MICB 421 Connect by 11:59 pm. As a team, refine and draft Project 2proposal.

Weeks 5 - 6 - Start to prepare general supplies that will be needed to do the project.Common supplies may be shared. Request any chemicals or supplies that will likely beneeded but are not available in the class inventory.

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Week 6 - submit the formal written proposal to the drop box at MICB 421 Connect by11:59 pm.

Weeks 7 and 8 - begin Project 2 experiments.

Weeks 7 -13continue experimental work. Each week discuss progress of the results,observations and problems at the weekly team meeting. Report progress / problems /changes to proposals. Bring a printed copy of the results and experimental proposals to

each meeting. Week 11 and 12. Begin writing the introduction, methods and references for the final report.

(Some of these details could be started sooner by writing them out as you encounter them inthe project). Be able to provide an outline of the available results and general outline of thediscussion at the weekly meeting. Clean up lab, stabilize useful cultures and supplies, anddiscard other materials.

Week 11 -13deliver oral presentation of the project. Submit video assignmentby 1-week post-presentation.

Week 14meet with Instructor and TA to discuss plans for research article. Submit draft manuscript for review and grading on 15 Apr 2016 at MICB 421 Connect by

11:59 pm. It will be reviewed, graded and available to be emailed to you by D22 Apr to dofinal revisions.

30 Apr 2016submit the final corrected manuscript(as an electronic copy) and the labrecord bookfor final grading. If you are away from UBC on a work term makearrangements before you leave to submit the record book.

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Checklist for MICB 421

Training, Safety, and Library Assignments

WHMIS and Lab Quiz (15 Jan 2016)

RefWorks Set-up (29 Jan 2016)

Project 1

Notebook (5 Feb 2016)

Project 2

Individual Proposal Flowchart (10 Jan 2016)

Individual Proposal Written (15 Jan 2016)

Team Proposal (12 Feb 2016)

Draft Paper Submission (15 Apr 2015)

Revised Paper and Lab notebookSubmission (30 Apr 2016)

Weekly Summary #1 (28 Feb 2016)

Weekly Summary #2 (6 Mar 2016)

Weekly Summary #3 (13 Mar 2016)

Weekly Summary #4 (20 Mar 2016)

Weekly Summary #5 (27 Mar 2016)

Weekly Summary #6 (3 Apr 2016)

Team Oral Project Presentation

Questions Presenation Set #1

Questions Presenation Set #2

Questions Presenation Set #3

Questions Presenation Set #4

Video Responsedue 1-week post-presentation

Exams

In Class Final Exam (15 Mar 2016)

Optional

Reflective Journal (submitted Week 3 through Week 13)

Bonus Seminar Summary #1

Bonus Seminar Summary #2

Bonus Seminar Summary #3

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Performance and Marks

Grading Scheme

Weight (%)

Activity Due Date Scheme 1 Scheme 2 Scheme 3 Scheme 4

P1 Notebook 5 Feb 2016 10 10 10 10

P2 Individual projectproposal

8 Feb 2016 (flowchart)and 15 Feb 2016 (written)

5 5 5 5

P2 Final team projectproposal 12 Feb 2016 15 15 15 15

P2 OralPresentations

29, 31 March and 5, 7 or April 2016 15 15 15 15

P2 Draft paper 15 April 2016 20 25 30 35

P2 Revised paper* 30 April 2016 2.5 2.5 2.5 2.5

WHMIS/Lab Quiz**and RefWorksAssignment

29 Jan 2016 2.5 2.5 2.5 2.5

In class final exam 15 Mar 2016 20 20 10 10

Weekly summary

Two weekly summaries will be chosen atrandom and marked during the term (2.5%per submission); 0.5% will be deducted for

missed submissions

5 5 5 5

Optional ReflectiveJournal (via Connect)

Submitted each week throughout the term. 5 NA 5 NA

Optional SeminarBonus

Up to 1.5% of your course grade can beearned by attending up to 3 seminars at

UBC. See below for details.Up to 1.5 Up to 1.5 Up to 1.5 Up to 1.5

There will be a 20% penalty for late submissions of the reports unless permission for a latesubmission has already been arranged.

Notes:

1. The potential grade for each student will be individually assessed in each of the grading

schemes. The student will be given the higher grade from the different schemes. The

patterns should be read vertically. The total in each vertical column is 100%. Entries

with NA indicate that the category is not applicable for that pattern.

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2. * There is no grade for the draft report or the lab notebook until an adequate final

electronic report and the lab notebook are submitted.

3. * The lab notebook must be submitted to get the grade.

4. If the contribution to the project by some team members is less than 9/10

th

of theexpected average participation for the team then the project marks for the students

with weak participation will be prorated in proportion to the apparent contribution

to the project.

5. Significant breeches of etiquette or inadequate preparation that affect the safety or

convenience of other students will be penalized by subtracting a penalty mark from the

final grade of the offending student.

6. ** A minimum mark of 80% is required on the WHMIS assignment in order to begin

working in the lab.

Effort and Etiquette

Other research courses such as directed studies expect approximately 20 hours of labwork per week. The weekly workload for your team should be similar. Some weeks itmight be higher.

Your lab work affects other people in the department that either share the sameequipment, clean equipment, prepare media or instruct. There are seven rules that youwill be expected to follow in order to minimize problems with other people.

1. Clean up balances, centrifuges, and spectrophotometers each time you use them.

2. Clean up your working area including the sinks and balances before leaving the lab.Put the capped tubes that need to be autoclaved and the uncapped tubes inseparate discard racks in room 112. Remove tape labels and felt pen labels fromflasks and beakers. Use cold water to rinse out all flasks and tubes that containeddangerous chemicals before you put the flasks on the discard cart for washing.

3. Place working equipment back in the storage areas when you finish.

4. Tell the instructors about malfunctioning equipment so that it can be repaired.

5. Tell the instructor if any particular bottles of chemicals are running low so that the

chemicals can be ordered before there is a shortage.

6. Discard your cultures from the incubator and the refrigerator when the lab work iscompleted.

7. Prepare your own project supplies unless you have made formal arrangements toborrow supplies from another team. Respect other students spaces and supplies.

Participation

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1. Students are expected to show enthusiasm for their projects and commitment to doingthe best possible job. This commitment includes demonstrating concern for otherteam members as well as their individual part of the projects.

2. On average over the term, each member in the team is expected to participate in theplanning, lab work, analysis and writing phases of all the projects.

3. Participation will be assessed by using the weekly summary, the draft report and thefinal, peer comments with regard to the participation, and observed effectiveparticipation in the class work throughout the term. Refer to Appendix O for gradingrubric.

4. The average weekly amount of work for each team member over the term is expectedto be 5 or 6 hours per week. Some weeks might be shorter than the average if otherweeks are longer as long as the overall participation balances out every two or threeweeks.

5. Individual students can meet with the instructors if they feel that there is a problem in

the way the workload or effort is distributed. If a member of the team is consistentlynot participating in the assignments or blocking participation of others then the othermembers of the team should discuss the problem with the instructors.

Laboratory Notebook

The lab notebook must be brought to each lab to keep it up to date and be a record of allraw experimental details. It is your responsibility to ensure that it is maintainedthroughout the term. The TAs and Instructor may check lab notebooks from time totime throughout the term to provide feedback and to assess progress. Refer tolabnotebook formatting guidelines.

Reflective Weekly Journal (via Connect)

This option expects you to keep track of the various aspects of your learning process asthe course progresses. To keep track of these processes you will be required to write ashort weekly statement of 250 to 500 words that describes the different parts that youfind difficult or time consuming or frustrating or rewarding or appealing in the projects. Inorder for the journal to work it must be done each week. Journal submission must bemade each week before the deadline of 11:59 PM Sunday evening on MICB 421Connect.

Project Proposals and Papers

The requirements for the reports are described in Appendix F of this course manual andthe JEMI link in The UBC Connect eLearning site for MICB 421. Data will not bespecifically graded in the reports. About 40% of the points will be determined by thequality of presentation details such as the suitability of units, adequate labeling ofgraphs, correct arithmetic processing, suitable rounding of values and generalreadability. Another 40% will depend on how you analyze, correlate and explain youractual observations and the potential meaning of your results rather than whether you

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discover the actual expected answers for the experiments. The last 20% will bedetermined by the quality and appropriateness of the concluding statement, the follow-up experiment and the referencing.

Each report must be submitted by the due date and time. Reports submitted latewill be penalized by 10% per day overtime. Reports will not be accepted once the

material is covered in class or any submitted reports are returned to the class. Missingreports will be marked as zero when the final grade is calculated. Each marked reportwill be returned with written comments and suggestions on how to improve futurereports. If you feel that the mark is less than you expected and you do not understandthe comments in the report, please discuss your concerns about the mark with theinstructor.

Project Presentation, Questions, and Video Responses

The goal of the project presentations is to give each time an opportunity to share theirresearch with their peers. We recognize that projects will be underway and that data willrepresent a work-in-progress. Teams should follow the presentation guidelines described

in lecture. Conclusions should be derived from the presented evidence only (i.e. avoidspeculation or extrapolation). During each presentation, each audience member shouldthink of / compose 1 or 2 questions. These questions can be asked at the end of thepresentation or can be discussed after class with your team. Each team must submit 1question for every other team via Connect by 5pm the day after the presentation. Teamswill review the submitted questions and choose 3 to respond to via video. Video responseshould be uploaded within 1-week of your presentation. The scores from each rubric willbe tallied to determine your teams grade for the assignment. Each component of thisactivity will be marked against a rubric. In addition to contributing to your course mark, thisassignment may have long term value to you as evidence of your ability to communicate, ahighly valuable skill in any field.

Seminar Bonus Option

UBC is a fantastic place for research! As such, in the spirit of a research-driven coursesuch as MICB 421, bonus marks can be earned for attending seminars. For each seminaryou attend upload a short summary paragraph (3-5 sentences) and you will earn 0.5%toward your course grade. You can earn a maximum of 1.5% for attending a total of 3different seminars. Uploaded submissions will be visible to the class via an open blog onConnect.

Theory Exam

Exam questions could include:

- any concepts presented or encountered in the lectures.- application of any general type of calculation encountered in lab work such as

growth rate, growth yield, unit conversions, dilutions and data transformations- principles for establishing or designing experiments.- the theory covered in Appendix C, D and E of the lab manual.- the safety concepts and hazards discussed in Appendix B of the lab manual such

as the WHMIS symbols, aerosols and containment.

Some questions might require calculators. Graph paper will be provided with the exam ifit might be useful or necessary to answer particular questions.

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Grading Rubrics

The following pages have rubrics for the various reports that will be submitted over theterm. The points in the rubrics reflect the relative weighting of each consideration in thegrade for that report rather than the final calculated grade.

Weekly Summaries and Activity Chart

Competent Cell PreparationProject 1

Lab NotebooksProjects 1 and 2

Individual Project ProposalProject 2

Team Project ProposalProject 2

Draft PaperProject 2

Team Oral PresentationProject 2

QuestionsProject 2

Video ResponseProject 2

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Grading Rubric for the Weekly Summaries (Total of 22 Points)

Proposal detail

Clearly meets

expectations.

Few, if any

problems

Acceptable

but definite

weaknesses

Does not meet

expectations.

Significant

weaknesses

Criteria

Identification 1 Notapplicable

0

Identifies your submission with

team alphanumeric and

individual names

Working Title 1Not

applicable0 Current working title for project

Major Progress 4 2 0

Explains the goal and what has

been accomplished; provide

experimental reference numbers

from lab notebook

Major Difficulties 4 2 0

Explains any major difficulties

that have slowed progress or led

to changes in approach

Major Changes 4 2 0Explains any major changes and

the purpose for the changes.

Remaining Work 4 2 0

Description of the remaining

work and the week by week

staging of the remaining work.

Overall 4 2 0

Demonstrates care and critical

understanding throughoutreport. Has been checked to

eliminate most spelling,

grammar and syntax problems.

Clearly and concisely presented.

Complete. Readily understood.

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Grading Rubric for Project 1 Preparation of Competent Cells (Total of 42 Points) (1 bonus point)

Proposal detail

Clearly

meets

expectations.

Few, if any

problems

Acceptable

but definite

weaknesses

Does not

meet

expectations.

Significant

weaknesses

Criteria

Identification 1Not

applicable0

Lab notebook is labelled withteam name and names ofindividual team members.

Report formatting 12 6 0

Formatting guidelinesdescribed in Appendix F arefollowed. Refer to markingrubric on Lab Notebooking.

Title 2 1 0Experiment is given adescriptive title.

Purpose 4 2 0

States the goal of the projectand the context of the workwith respect to previous and

future work.

Materials and

Methods4 2 0

All materials and methods aredocumented. Relevant

literature is referenced.

Results 4 2 0

All observations are recorded.

Data is presented as stand-alone tables or figures and is

also clearly described in the

text. Intepretations of data arestated. In general, results are

written in past tense.

Figures and Tables 4 2 0Formatted as per ASM 2013guidelines for papersubmission. Appendix F.

Conclusions 4 2 0Bullet point summary of mainfindings and points of interest.

Future Directions 4 2 0

Comment on the potential

outcomes and technicalproblems that need to beaddressed.

Overall impression 4 2 0

Demonstrates care and criticalunderstanding throughout the

report. Correct language,tenses, and terms. Correct and

appropriate citations.

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Grading Rubric for Lab Notebooks (total 12 points)

Expected DetailClearly meets

expectations.

Does not meet

expectations.Criteria

Title 2 0

Suitable and relevant

to experiment.

Sufficient detail tobe unique and

complete with

regard to the

objectives.

Experiment

Code1 0 Present and accurate.

Page Numbers

Correct2 0 Present and accurate.

All Sections

Complete2 0

Purpose, Methods,

Results, Discussion

and Conclusion

documented.

Table of

Contents1 0

Present and up todate.

References 2 0

References made

throughout when

appropriate.Experiment codes or

literature citations.

Date1 0 Present and accurate

on every page.

Witness 1 0Signed and datedwith a week of

initial entry.

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Grading Rubric for the Individual Project Proposal (Total of 31 Points)

Proposal detail

Clearly

meets

expectations.

Few, if any

problems

Acceptable

but definite

weaknesses

Does not

meet

expectations.

Significant

weaknesses

Criteria

Identification 1Not

applicable0

Identifies your submission with

your name

Source of observation /

problem2 1 0

Source of observation/problem is

mentioned and cited in

appropriate ASM style

Background 4 2 0

Clearly written background to

understand / explain the

relationship of the explanation to

the problem and the approach.

Observation / problem 2 1 0Clearly written description of the

selected observation or problem

Explanation / hypothesis 4 2 0

Clearly articulated explanation of

the cause of the observation /

problem that you will work on.

Experimental Aims 4 2 0

Clearly stated experimental

question(s) that will test the

explanation / hypothesis. Includes

a brief explanation of how

knowing the answer to the

question testing the hypothesis.

Approach 2 1 0

Clearly written description of the

general technical approach you

would use to test the experimental

question. Mention the specific

type of methods (PCR,

mutagenesis et cetera).

Feasibility / potential

outcomes4 2 0

Comment on the potential

outcomes and technical problems

that need to be addressed.

Flow Chart 6 3 0

Flow chart sections are clearly

communicated. Research plan islogical.

Overall impression 2 1 0

Demonstrates care and critical

understanding throughout the

report. Correct language, tenses,

and terms. Correct and

appropriate citations.

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Grading Rubric for the Detailed Team Project Proposal (Total of 46 Points)

Expected Detail

Clearly

meets

expectations.

Few, if any

problems

Acceptable

but definite

weaknesses

Does not

meet

expectations.

Significant

weaknesses

Criteria

Proposed Title 2 1 0

Suitable and relevant to proposal.Sufficient detail to be unique and

complete with regard to theobjectives.

Introduction and

Background4 2 0

Clearly written. Addressesdetails needed to understand the

explanation, approach andoutcomes for your proposal.

Observation and

Explanation2 1 0

Clearly articulated explanationfor the observation. Suitablerelevance. Builds on an idea

instead of dabbling with amethod.

Experimental

Aims2 1 0

Clearly written question (or partof a question) that will test theexplanation. Relates toexplanation and providesoutcome.

Overview Chart

(Concept Map)4 2 0

Brief overview that shows adiagrammatic relationship of the

tests within the context of theexperimental question.

Protocol6 3 0

Explains what will be done. Anoverview of the work and how

the methods fit together toaddress the objectives

Methods 4 2 0

Explains how the parts / testswill be done. Choice of suitablemethods for the protocol andobjective. Can be referenced butshould give operational details.

Supplies and

Equipment4 2 0

List of supplies and chemicalsneeded. Include quantities and

details of preparation ofsolutions such as solvationconditions for your actual

experiment.

Weekly Time

Frame for

Completing the

Work

4 2 0

Week by week staging of the

work. Allow time to test/workwith unfamiliar procedures or

equipment, testing strains,determining preliminary valuesto assess ranges before

attempting the main experiment.

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Potential Pitfalls 2 1 0

Description of the main obstacles

or difficulty that might beencountered in the protocol.

Known Hazards 2 1 0

Identifies unusualandsignificanthazards (if any).Marginal if reasonable unusual

problems missed. Inadequate ifdeadly problems are missed.

Distinguishes routine, minorrisks from real hazards.

References 2 1 0

At least four backgroundreferences supporting the

proposed explanation and

protocol. Proper ASM style.

Participation

Report2 0 0

Includes a meaningful sectiondescribing how each teammember contributed to the work

and the report.

Overall 6 3 0

Demonstrates care and criticalunderstanding throughout the

proposal. Has been checked toeliminate most spelling,

grammar and syntax problems.Clearly and concisely presented.

Complete. Readily understood.

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Grading Rubric for the Draft Paper (Total of 100 Points)

Report detail Consideration Clearly meets

expectations.

Few, if any

problems

Acceptable

but definite

weaknesses

Does not meet

expectations.

Significant

weaknesses

Criteria

Title Clear and Accurate 2 1 0 Concisely conveys intent andoutcome of project

Relevant 2 1 0 Relates to the study purpose

Abstract Clear and accurate.

Appropriate format

2 1 0 Easy to read. Consistent with

article. Includes purpose, main

observations and main

conclusion. No abbreviations

or references

Relevant details 2 1 0

Introduction Clear and accurate 2 1 0 Easy to follow. Focused on the

purpose of project. Proper

coverage of background for the

analysis and the discussion.

Does not include parts thatshould be in Methods

Relevant details.

Appropriate content.

4 2 0

Appropriate depth 4 2 0

Materials

and Methods

Complete and accurate 2 1 0 Mentions relevant details. Uses

paragraph form. Uses citations

where appropriate. Provides

enough detail to follow

approach.

Appropriate format and

content. Suitable

abbreviations

2 1 0

Results Consistent and

accurate processing

6 3 0 Consistent interpretation

between uses. No processing

errors

Appropriate format.

Details are clear and

accurate

12 6 0 Tables and figures processed

with expected details. Suitable

expressed comparablesignificance.

Appropriate

interpretation of the

results

8 4 0 Interpretation of trends and

observations is reasonable

Appropriate

observations

4 2 0 Has recognized the major

relevant observations

Appropriate comments 6 3 0 Integrated ideas and wrote

about the ideas rather than

simple descriptions

Discussion Clear and accurate 4 2 0 Statements are consistent with

the results, help to understand

the results and relate the results

to the purpose. Statements

show insight. Makes use of

supporting knowledge. Covers

all major observations

Relevant 4 2 0

Reasonable depth of

analysis

4 2 0

Conclusion Accurate deductive

statement

4 2 0 Deductive statement proved

by the results rather than

explanations

Addresses the

experimental question

4 2 0 Conclusion addresses the

experimental question

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Future

Directionss

Relevant and feasible 6 3 0 Addresses a significant

problem or explanation raised

in the discussion. Relevant to

original purpose.

Outcomes 2 1 0

References Additional, appropriate

and relevant

2 1 0 Four additional references that

provide depth to discussion.

Helpful. RelevantASM format, accurate

and appropriate

citation

4 2 0 Cited by number in the

manuscript. Correct ASM

style in listing.

Participation

Report

Explain how each

author contributed to

the project and the

report.

2 0 0

Includes a meaningful section

describing how each teammember contributed to thework and the report.

Overall Overall impression 6 3 0 Demonstrates care and critical

understanding throughout the

report. Correct language,

tenses, and terms. Good

insight into results.

Lab

Citizenry

Weekly lab work

assessed by TAs and

Instructor.

+5 0 -5 Demostrates safe, courteous,

and organized work habits in

the lab.

Draft papers will be reviewed upon submission for formatting. Papers that do notneed formatting expectations will be returned to the authors for revision prior tomarking. A formatting checklist will be posted to Connect later in the term. Papersthat do not meet minimum formatting requirements will penalized 5% of the finalgrade for each round of revision required.

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Grading Rubric for the Oral Presentation (Total of 34 Points)

Presentation detail

Clearly meets

expectations. Few, if

any problems

Acceptable

but definite

weaknesses

Does not meet

expectations.

Significant

weaknesses

Criteria

Title 2 1 0 Effective title. Title is supported bydata presented.

Introduction 2 1 0

Effectively explains: research

question, significance, observation,

hypothesis, and experimental aims.

Experimental concepts 2 1 0Effectively explains experimental

question and key concepts.

Data presentation and

interpretation2 1 0

Effectively explains experimental

set-up (including figures and tables),

observations, and interpretations.

Conclusions and Future

Direction4 2 0

Conclusions are supported by

presented data. Future directions are

logical, feasible, extensions of

conclusions.

Acknowledgements 2 1 0Recognize team members,

collaborators, contributors, funding.

Visual aids 2 1 0

Appropriate use of presentation

technology (e.g. Powerpoint).

Slides are well designed and easily

interpreted.

Formatting 6 3 0

All Figures and Tables are formatted

as per ASM style guidelines. All

figures show markers and are

labeled clearly.

Delivery 2 1 0

Speaker(s) sets a reasonable pace,

displays enthusiasm and confidence

(e.g. makes eye contact), and

modulates tone for emphasis.

Timing 2 1 0

Presentation meets time constraint of

maximum ___ minutes. (Time will

depend on number of teams in class)

Question and Answer

Period (not included in

___ minute presentation)

2 1 0

Presenters effectively addressquestions from audience. e.g.

openly considers perspectives,

provide logical, direct responses.

Overall 6 3 0

Overall quality of presentation.

Logical flow. Attention to details

such as figure formatting, font size,

and references.

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Grading Rubric for Questions from Team Presentations (1 point per team)

Team ____________________

Criteria: Full marks will be given for constructive questions that help to improve or promote further thinking

about the project. Questions may be scientific or technical in nature. Question may address specific aspectsof the material presented or inquire about possible future directions or alternate models. Questions must be

respectful and should demonstrate some appreciation for the presentation (e.g. Thank-you for a very clear

presentation. I really like your experimental system where. Have you considered var iable X and Y and how

these parameters might impact your i nterpretation of the resul ts?)

Team

Clearly meets

expectations.

Few, if any

problems

Acceptable

but some

weaknesses

Does not meet

expectations.

Significant

weaknesses

Comments

1 0.5 0

1 0.5 0

1 0.5 0

1 0.5 0

1 0.5 0

1 0.5 0

1 0.5 0

1 0.5 0

1 0.5 0

1 0.5 0

1 0.5 0

1 0.5 0

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Grading Rubric for Video Response (Total of 33 Points)

Proposal detail

Clearly meets

expectations.

Few, if any

problems

Acceptable

but some

weaknesses

Does not meet

expectations.

Significant

weaknesses

Criteria

Title and

Credits/References2 1 0

Includes a descriptive

presentation title at the

beginning. Closes with team

names and relevant references.

Summary of Project 4 2 0

Video opens with a brief (1-3

minute) summary of the project

outlining key background info,

the research question,

hypothesis, and approach.

Originality /

Creativity4 2 0

Demonstrates some original

thought or presentation style.

Quality of Answers 9 4.5 0

Answers address the stated

question. Evidence is presented

clearly. Assumptions and

limitations are acknowledged.

Each questions will be scored

out of 3 points.

Delivery 4 2 0

Video is well paced; vocal tone

is enthusiastic or modulated to

engage viewer / listener.

Appropriate level of

detail 4 2 0

Video explains concepts at a

level that suits the targetaudience.

Timing 2Not

applicable.0

Video presentation meets

maximum 15 minute time

constraint.

Overall Impression 4 2 0

Video presentation demonstrates

care and critical understanding.

Clearly and concisely presented.

Complete. Readily understood.

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Appendix A - Basic Methods

I. Efficient Organization

1. Arrange your working space so that you can work safely, accurately andefficiently.

2. Start the organization by facing the workbench and imagining a line thatdivides the surface into a left and right side. Things that are to be used orheld by the left hand should be placed on the left side of the line and viceversa for the right side.

3. Things that are used infrequently should be placed further back from theimaginary centerline than other things that are used more frequently.

4. You should be able to use the equipment (vortex, pipettes, Bunsenburner, tubes et cetera) without having to walk around. In a well-organized bench you should generally be able to reach and use theequipment while standing in one place.

5. In aseptic work organize the material and equipment with the Bunsenburner at the imaginary centerline, about 20-to-30 centimeters from thefront of the bench.

6. Ensure that hoses and electrical cords do not dangle over the edge of thebench where they could inadvertently be hooked while working. Becareful that the flame from the Bunsen burner is not burning either theBunsen burner tubing, electrical cords or the over-head counters.

7. Keep your notebook and flow charts to one side of the workspace, or onthe shelf above the bench or in a drawer out of the way. They should notbe in the center of your work space where they get in the way andbecome contaminated with spilled chemicals or bacteria

8. The organization is dynamic and should change as different stages of thework proceed. For example, when you are diluting and plating bacteriafor viable plate counts