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UCSDwinter‘20microbiology laboratoryWelcome to microbiology laboratory. Herewe’ll be using Techniques in microbialphysiology, microbial genomics, microbialevolution, and microbial ecology toexplore the role of microbes in health,industry, and the environment. Inquiry-based experiments will cover thefundamentals of both working with livemicroscopic organisms at the bench andbioinformatically analyzing their genomesat the computer.lecture, york 3010, t&H 9:30-10:50lab, tata 2101&2102, T&H, 11-2:50INSTRUCTOR Dr. KATHERINE PETRIEkpetrie@ucsd.eduOFFICE: MUIR BIO 2202OFFICE HOURS: M 9:30-10:30IAsdaniel tylerdatyler@ucsd.eduJacob Robertsonjmrobert@ucsd.eduDid you know UCSD HASCORE SKILLS for allstudents To MASTER?Here are some of them.What this course will enable you to do:LEARNING OUTCOMES aka LO’sBy the END OF THE COURSE YOU’LL BE ABLE TO:1. appreciate the structure, physiology, and diversity of microorganisms.GOALS FORBIO Majorsunderstandbiotic and physical interactions2. appreciate interactions of microbes with otherorganisms.3. Appreciate interactions of microbes with theirenvironment.4. Detect and interpret evidence of microbial evolution.7. plan an experiment from a general outline ofresearch objectives.8. analyze and interpret experimental data to drawaccurate and statistically sound conclusions.9. Communicate scientific research - its justification, methods, and findings - effectively.10. Recognize unknowns in microbiology11. Value the relevance of microbiology todayunderstand evolutionand diversityuse contemporarybiological researchtechniques and quantitativeapproaches to analyzeresults5. isolate, identify, grow, and quantitate microorganisms.6. execute laboratory tasks using aseptic technique.GOALS FORALL STUDENTSQuantitativeReasoningCritical ThinkingConstructreasonablehypothesesto explainbiologicalphenomenaWritten & OralCommunicationInformation LiteracyRecognize theinteractionsbetweenbiology andsociety

UCSDwintermicrobiology laboratoryHow WILL YOUdemonstrate thatyou accomplishedthe 11 Lo’s?‘20Assessments and basis for final grade:AssessmentweightIn-Lecture CLICKER QUESTIONS10 %packback participation10%notebook checks6%practical2%effective paraphrasing homework2%microbial zoo5%Microbes & health lab reports20 %microbes & industry lab report10 %microbes & Environment Presentation5%For reportguidelines & rubrics,stay tuned totriton Ed!midterm exam10 %final exam20 %No bell curve:you won’t becompetingagainsteach other!.GRADING 7360-70 60A AAB BBC 1.0)(0)Materials needed to succeed:A Clicker:via Canvas.for lecture, you are required to have and bring an i clicker That is registeredlab Manual:physical copy, available from the bookstore ( 28), ISBN: 9781533901750Packback access code:we’ll be using this AI-moderated forum to dive deeper intothe topics we cover in class. You’ll need to purchase an access code, ( 28), available fromthe bookstore website (Look up BIMM 121 under ‘textbooks’).PPE:a lab coat that you only use for this class that extends to your knees, safetyglasses (regular prescription glasses aren’t sufficient).lab notebook:bound style, with carbonsCanvas: Grades, and other course information will be posted on Canvas, so make sureyou can access it via coursefinder.ucsd.edu.something to take notes with During Lecture:research shows that pen & paper note-taking is best.Lectures will be podcast, but

UCSDmicrobiology laboratorywinter‘20How to succeed in this class:DAILY Clicker Questions (10% of grade):Lectures will start with a BRIEF clicker ‘quiz’ on the basic details for the upcoming lab. Ifyou‘ve read the lab manual pages for the next lab session, you should be able to answerthese questions. After that, there will be Clicker questions throughout the lecturethat Will challenge you to apply what you’ve just leanred. For this second type, You willusually have the opportunity to collaborate with your neighbors.Every day you will have the opportunity to earn:2 participation points (Submit answer to 75% of ALL questions for 2 Pts, else Get 0/2)3 Performance Points (Get 1 pt for every Correctly answered question)There are usually more than 3 clicker questions per class, so even if you get somewrong you may still get full points.if you miss lecture.Packback (10% of grade)If You miss Lecture, or if your clicker ishaving technical difficulties, you may Notmake up the questions. However we’ll dropyour lowest 4 clicker days.This ai-moderated discussion forum is a keylearning tool for the class. It is driven byyour curiosity and will help you make connections between what we learn in classand the real world.If you miss the midterm, your final will beworth a bigger % of your grade to compensate. If you miss the final, You may be eligible for an incomplete.Use these drops wisely: It’s better tosave them for the unexpected.if you miss lab.you must let dr. Petrie, Your IA, & your groupknow ahead of time. you will still be responsible for what you missed. in the case of repeated absences, you may be asked to provide documentation. absences due to scheduling conflicts (other coursework, vacations, Lizzoconcerts, etc) will not be excused and Eachwill result in a penalty (1 % off overall grade).Every week, you are required to:make 2 posts, at least 1 ofwhich must be a responseto earn credit, your posts must meet certain guidelines. Packback will assign a curiosity score to each post based on itsdepth, credibility, and presentation. consistently High curiosity scores are an opportunity to earn extra credit. You can miss 2packback weeks.If Health orfamily emergenciesmake you miss too much,seeDr. Petrie to discussThe possibility of annotebook checks (6% of grade)“Incomplete”. Per UCSDthere will be weekly In-Lab checks of your lab notebook. thePolicy, Your grade mustguidelines for how to keep your notebooks are in the lab manual.Be in good standingOne thing that will help you ensure you get full credit is toto be eligible.answer all questions Listed in the manual

UCSDmicrobiology laboratoryInclusivity:‘20Academic integrity:Everyone will come to this course withdifferent backgrounds, knowledge, andperspectives. We want to create aclassroom culture that respects andrevels in this human diversity. If youhave any concerns related to inclusivity or feel your identities (Race, Gender,sexuality, religion, ability, etc) are notbeing honored, please let us know!Accommodations can be made for students with a letter from the OSd.For more information on campus & community resources, check canvas.Regraderequests:winterAn Inclusive environment is one whereeveryone has an equal opportunity tosucceed. Academic dishonesty (Including, but not limited to: Cheating, plagiarizing, answering with someone else’sclicker) fractures The playing field, bygiving some students an unfair advantage. Assignments will be monitored viaTurn-it-in, and students found to havecommitted academic dishonesty will bereferred to the UCSD academic integrityOffice and may receive a failing gradefor the course.WE All make Mistakes. If you think your Homework, worksheet, report,or Exam was Graded in Error, submit a request by email to Dr. Petriewithin 7 days of receiving your grade. include a written description ofthe error, Including which question you are concerned about and whyyou think the grade is mistaken. No in-person requests will be considered. The regrade option is to safeguard you from genuine mistakes ingrading; there is no guarantee you score will go up.We’re working to improve your educational experience:Did you knowthat you canbe part of aResearch studyin this class?No! Not Like that! Instead, duringThis class, I’ll be working to figureout the Most Effective teachingmethods for your learning. ThisMeans you might do surveys andprovide feedback. For more information, please read the opt-out formhanded out in class or on canvas .

fallCourseschedule(Tentative):Microbiology laboratory‘19microbes andmicrobes and health microbes and industry the environmentweek 2.week 1.UCSDT LECT. (1/7): intro to courseT lab. (1/7): Lab 1H lect. (1/9): cultures, colonies,& microscopyPlease remember that your work inlecture (clickers) will be graded, sobe sure to show up!H lab. (1/9): Lab 2T LECT. (1/14): biofilms & dilutions 1g HWparaphrasindue 1/14!T lab. (1/14): LAb 3H LecT. (1/16): cell appearance &dilutions 2H lab. (1/16): LAb 4g HWparaphrasine 1/21!udsnoisivretHe lab practical is a graded observation of your lab skills. makesure you get in lots of practiceby sharing the work with yourpartner in weeks 1 &2. while you’rewaiting your turn, you can work onyour microbial zoo.week 3.T lect. (1/21): microbial genomesT lab. (1/21): Lab 5H lect. (1/23): Illumina sequencingH lab. (1/23): lab 6, lab practical/23practical! 1

winterCourseschedule(Tentative):Microbiology laboratory‘20microbes andmicrobes and health microbes and industry the environmentweek 6.week 5.week 4.UCSDT LECT. (1/28): (more) illumina sequencingT lab. (1/28): Lab 7H lect. (1/30): midterm!!!!!midterm1/30!H lab. (1/30): lab 81 duetrapbalmbiofilPM95:114/2TueT LECT. (2/4): fermentation &differential id 1T lab. (2/4): Lab 9H lect. (2/6): PCRH lab. (2/6): lab 10T lect. (2/11): discuss DNAlibrary poolT lect. (2/11): natural crisprT lab. (2/11): pool &submit illumina sequencing (planned)T lab. (2/11): lab 11H lect. (2/13): Known crisperloci in L.A.B., differential id 2H lab. (2/13): lab 12see classwebsite forlab reportguidlines.!

UCSDMicrobiology laboratoryweek 7.microbes and healthoomicrobial z:59 pm1181/2eudue TCourse schedule (Tentative): winter‘20microbes andmicrobes and industry the environmentT LECT. (2/18): sanger sequencingT lab. (2/18): lab 13H lab. (2/20): lab 14week 9.week 8.T lect. (2/25): photosynthesisand tolerance to changeT lab. (2/25): lab 15T lab. (2/25): lab 15H lect. (2/27): BLAST, CRISPRsand the microbiomeH lab. (2/27): lab 16H lab. (2/27): lab 16T lect. (3/3): Analyzing Illuminasequence dataT lab. (3/3): lab 17H lect. (3/5): final reviewH lab. (3/5): lab 18T lab. (3/3): lab 17duetroperbalyogurt9 PMfri 3/6 11:5H lab. (3/5): lab 18

winterCourseschedule(Tentative):Microbiology laboratory‘20microbes andmicrobes and health microbes and industry the environmentweek 10.UCSDT lect. (3/10): Presentations!!T lab. (3/10): Lab 19H lect. (3/12): final!!H lect. (3/12): final!!H lab. (3/12): Lab 20Final!2 duetrapbalmbiofil9 PM5:1171/3sTueFinal!that’s duringfinals week.!H lect. (3/12): final!!Final!