Biology 18aIntroductory Biology

Laboratory Manual

Spring 2019

Department of BiologyBrandeis University, Waltham MA 02454

Professor Melissa Kosinski-Collins,Dr. Lindsay Mehrmanesh and Dr. Kene Piasta

Copyright 2019, MSKC

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Name____________________________________________________

TA ____________________________________________________

UTA ____________________________________________________

TA Office Hours ____________________________________________

Professor Melissa S. Kosinski-Collins SSC 016A

x63126

kosinski@brandeis.edu

Office Hours: 11:30-12:30 Tuesdays/Thursdays or by appointment

Please note: (1) Many labs during this class will be finished before the 5:30 pm time given to sections

by the registrar. The extra review time has been specifically built into the schedule such that you can complete the results and discussion questions with your partner

and your TAs before leaving lab.

(2) Many of the lab procedures involve coming into lab outside of the time designated by the registrar. By enrolling in this class, you are accepting the responsibility to

complete all experiments both in and out of class time.

(3) Almost every week of the semester involves performing multiple procedures and experiments during the regular lab period. You are responsible for completing pre and

post labs for all experiments listed on the course calendar.

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Course SyllabusCourse Objectives:

To teach you several basic biology concepts and how to apply that knowledge in an experimental setting.

To familiarize you with several common techniques, processes, and equipment used in modern genetics laboratories.

To teach you how to design your own experiment, test your own hypothesis, and to critically and objectively interpret your results.

To help you learn how to properly follow directions To teach you how to write a well-constructed scientific lab report.

You will find, as we progress through this year, each assignment, experiment, and assessment is designed with at least one, if not more, of these criteria in mind. Each one of these objectives is of equal importance, and will be evaluated and graded as such.

Learning Objectives:

By the end of this course students should be able to:

Perform basic laboratory techniques such as measuring liquids using pipettemen, setting up and performing PCR, running agarose gel electrophoresis, performing serial dilutions, and utilizing sterile technique.

Troubleshoot scientific experiments using the aforementioned techniques. Formulate reasonable conclusions when presented scientific data and design

rational hypotheses. Search for scientific articles using web-based search engines like PubMed. Write News and Views articles, posters and scientific lab reports.

The following is required of every student enrolled in Biology 18:

You must attend the lab section for which you are registered. In the case of a legitimate scheduling conflict, email Prof. Kosinski-Collins (kosinski@brandeis.edu) at least 24 hours in advance of the lab and you may be allowed to attend a different section.

Before coming to lab, you should read the lab and complete the pre-lab assignment. The pre-lab assignment and the previous lab’s post-lab (Results and Discussion questions) must be submitted to LATTE by 1:00 the day of your lab section. Late pre- and post- labs will not be accepted.

You must attend the weekly lab lecture. During these lectures we will review topics, introduce new concepts, go over important announcements, and summarize the week’s laboratory information. You are responsible for knowing and understanding this information and it will be included on exams.

Eye protection (goggles or eyeglasses) must be worn when necessary. Eyeglasses are sufficient for those students who wear them.

Cell phones and laptops are not permitted in the lab. Some labs require computers and you will be notified in advance when you should bring them.

If a staff member can see your cell phone in the lab, it will be confiscated to be cleaned and then held until the end of that laboratory.

You may not leave lab for any unauthorized reason during your scheduled lab section and you must stay until the day’s experiment is completed.

No shorts, open-toed shoes, open midriff shirts, hats, scarves, backpacks, bags, food, drink, gum or cell phones will be permitted in lab under any circumstances. Pants and

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skirts must be ankle-length and no skin can be visible at the ankle. Students violating these rules will be asked to leave and will be given a zero for the day’s performance points.

You are expected to complete all labs in their entirety. This may involve coming into lab outside of registrar-scheduled time. You are responsible for completing your work and you should plan your schedule accordingly. See the laboratory calendar for days that require extra time.

Some experiments span multiple weeks and we will be performing multiple experiments in one week. You are responsible for following the syllabus and completing all pre-labs, post-labs and assignments for that given week.

You are expected to check the Biol18 LATTE site regularly and often. This course is constantly evolving. Important announcements and syllabus updates will be posted on a semi-regular basis and you are responsible for this information.

The following concerns must be addressed to Dr. KC and not to your TA/UTA: exam re-grades, make-up lab sessions, and extensions on assignments. Questions regarding graded, written assignments must be addressed to graduate student TAs. Writing assignments will not be regraded for any reason.

Make-up exams will not be offered for any reason. The staff of Biol18 is here to help you learn and understand the material in any way

possible. Please remember, however, that all staff members have both personal and professional commitments beyond this course. All concerns and questions should be address during office hours or during appointments scheduled at least 72 hours in advance. Unannounced drop-ins and contacting staff member by means not provided by that individual (cell-phones, personal residences, etc.) is not appropriate.

Email is a reliable way to contact staff members. Please expect a 48 business-hour turn-around time on all email inquiries (longer over weekends) and plan accordingly.

Grading and Evaluation

Grades will be determined based upon the following:

1. Writing Assignments (25%)

This course is writing intensive. For this reason, different, varied writing assignments will be assigned throughout the semester. We will focus on four types of writing in this course including lab reports, news and views articles, and posters. All assignments are due both in hard copy and uploaded to LATTE by the beginning of lab of the specified week unless otherwise stated. Both the electronic and hard copy form must be received by your TA for the assignment to be considered on time. Late assignments are given a zero.

Learning how to write scientifically is a key component of this course. You will have two opportunities to write certain assignments. Your initial assignments will be graded and handed back in lab the following week. You must rewrite and resubmit your report with a copy of the graded initial submission. Your second draft will not be graded if the initial graded submission is not included. Late submissions of the initial report will not be accepted for any reason. If you fail to turn in either the first or second submission, a zero will

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be averaged into your grade for this assignment. Written assignments will not be re-graded for any reason.

A. Journal Club Feedback to Peers 2.5%

Uploaded to Latte the week of February 5th

B. Abstract for Grant Proposal

Initial to be turned in at the beginning of lab the week of March 5th 5%Final to be turned in at the beginning of lab the week of March 19th 5%

C. Science Communication written proposal 5%

D. Poster

Introduction, Materials and Methods, Results and Discussion for allowed experiments.

Draft Poster due at the beginning of lab the week of March 27th 2.5%Final Poster due at the beginning of lab the week of April 17th 5%

2. Exams (30%)

There will be two exams in lab lecture. Each quiz is worth 15% of your grade. Because exams are scheduled during regular class time, there is a no make-up policy for all exams in Bio18a.

Exam I: Tuesday, February 26, 2019Material covered: Lab and lectures: Labs 1, 2, 3a

Exam II: Tuesday, April 2, 2019Material covered: Lab and lectures: Labs 1, 2, 3, 4, 5

All exams will be electronically scanned before being returned.

Exam re-grades must be submitted in writing within 48 hours of exams being returned. These must be submitted in writing directly to Dr. Kosinski-Collins. All re-grade requests must be accompanied by a student signature. In all cases, your entire exam will be re-graded.

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3. Dissection Lab Assignment (5%)

During the Dissection and Histology Lab (6), you will be given a series of questions. This hands-on assignment must be submitted before leaving lab. You may work in groups of up to four for this assignment. Because of the nature of the assignment, no make-ups will be administered.

4. Oral Presentations (20%)

Learning how present scientific information to various audiences is a key component of this course. Several times during the semester, you will be asked design a presentation and present orally online, in lab or in class. Each presentation is worth 5% of your grade. No make-ups or extensions are granted on presentations. Presentations are not re-graded for any reason.

A. Journal Club Initial (uploaded link to Latte week of January 29th) 5%Final (uploaded link to Latte week of February 12th) 5%

B. Science CommunicationPresented in lab the week of March 26th 5%

C. PosterPresented in lab the week of April 9th 5%

5. Pre and Post Labs (10%)

A written “Purpose” and completed pre-lab questions must be submitted by the beginning of lab every week on LATTE. Your answers should reflect your best attempts at correctly and completely answering the questions provided. If all questions are attempted, you will receive full credit. (5%)

Completed results and discussion questions (post-lab) must be submitted by the beginning of lab for the prior week’s laboratory on LATTE. Your answers should reflect your best attempts at correctly and completely answering the questions provided. Collaborative discussion with your partner and/or course staff is encouraged. These submissions will be graded for completion and accuracy (5%).

On occasion, we will ask you to bring a portion of your prelab to lab in printed form.

Failure to complete the out-of-lab procedures as directed will result in loss of all pre- and post-lab points for the week.

6. Participation and Professionalism (5%)

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Participation and professionalism points will be determined from the following:

Paying attention to course staff

Participating in class-wide discussions and question sessions

Respecting the lab environment

Respecting the course staff including TAs, the professor and the lab technicians

Maintaining a respectful, professional tone in conversations, office hours, in the laboratory, and via email.

Cleaning up after yourself

Working/dressing/behaving in a safe and professional manner

Punctuality

Following directions safely and attentively Failure to complete the out-of-lab procedures as directed will result in loss

participation points for the week.

7. In Class Quizzes (5%)

Several times during the semester, we will have unannounced quizzes in lecture. These quizzes will cover lecture and lab material. No make-ups or extensions are offered for these quizzes.

Academic Integrity

Academic integrity is central to the mission of educational excellence at Brandeis University. Each student is expected to turn in work completed independently, except when assignments specifically authorize collaborative effort. It is acceptable to use the words or ideas of another person provided the source is properly acknowledged. You must use proper citations and quotation marks to indicate the source of any phrases, sentences, paragraphs or ideas found in published volumes, on the internet, or created by another student. Note that the use of full quotations is not acceptable. Violations of University policy on academic integrity, described in Section 4 of Rights and Responsibilities (on next page), may result in failure in the course or on the assignment, and could end in suspension from the University. If you are in doubt about the instructions for any assignment in this course, you must ask for clarification. Further, please notice that this course and the assignments contained within it are different from previous years. The use of written assignments from previous years as reference material is not allowed as expectations and rubrics change.

Any course materials including assignments, exams, podcasts, procedures, etc. are the sole property of the course professor in connection with Brandeis University and are to be used only by students enrolled in Biology18. Any unauthorized electronic or print distribution of this material is expressly prohibited.

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Disability

If you are a student with a documented disability on record at Brandeis University and wish to have a reasonable accommodation made for you in this class, please see Professor Kosinski-Collins immediately.

Experiential Learning Statement

This course is designated as an Experiential Learning course. This means you will have the opportunity to perform hands-on scientific experiments every week. Every laboratory activity requires your participation in inquiry-driven laboratory experiments. You will be asked to design components of procedure and problem-solve experiments as they progress. Working in a collaborative environment with your peers, you will develop assays for various biological systems and collect data based on your designs. Additionally, you will be asked to read and critically analyze primary literature relevant to your ongoing work. You will learn how to write, organize, and present your data and conclusions for a scientific audience. The experience and skills acquired in this class with respect to experimental design, data analysis, experimental trouble-shooting and scientific communication will be useful as you pursue careers in the biomedical research and the allied health professions.

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Course OutlineWeek Assignment Due Date of Lab Labs to be Performed

1 Jan. 15 Jan. 16 Jan. 17- Lab 1A: Drosophila Observation Actin-GAL4 x

UAS-PolyQ

2Jan. 22Brandeis Monday

Jan. 23 Jan. 24- No lecture or regularly scheduled lab.- Must come in for outside-of-lab-time procedure

Lab 1B

3Journal Club Initial (presented online) Jan. 29 Jan. 30 Jan. 14

- Lab 1C: Drosophila Actin-GAL4 x UAS-PolyQ (Scoring)

- Lab 2A: Yeast Lysine Mutants (Plating)

4Journal Club Critique (review online in Forum, upload to assignment)

Feb. 5 Feb. 6 Feb. 7- Lab 2B: Yeast Lysine Mutants (Crossing) - Lab 3A: Quantitative PCR (qPCR of plasmid

DNA)

5Journal Club Final (presented online) Feb. 12 Feb. 13 Feb. 14

- Lab 2C: Yeast Lysine Mutants (Analysis)- Lab 3B: Reverse Transcriptase Quantitative

PCR (Isolate RNA from PC12-HD-PolyQ cells)6 Break Feb. 19 Feb. 20 Feb. 21 Break

7 Feb. 26Exam I Feb. 27 Feb. 28

- Lab 3C: Reverse Transcriptase Quantitative PCR(Run and Analyze)

- Lab 3D: Pathway analysis

8Grant Abstract Initial(submitted online) Mar. 5 Mar. 6 Mar. 7

- Lab 5A: Drosophila Elav-GAL4 x UAS-PolyQ- Lab 4A: C. elegans- Oxidative stress response

(Pilot experiment)

9Proposal for Science Communication (in-class, submit online)

Mar. 12 Mar. 13 Mar. 14- Lab 4B: C. elegans- Oxidative stress response

(Final experiment)- Lab 5B: Drosophila Elav-GAL4 x UAS-PolyQ

10Grant Abstract Final(submitted online) Mar. 19 Mar. 20 Mar. 21

- Lab 5C: Drosophila Elav-GAL4 x UAS-PolyQ (Collection 1/Pilot experiment)

11Science Communication Presentation (in-class presentation)

Mar. 26 Mar. 27 Mar. 28- Lab 5D: Drosophila Elav-GAL4 x UAS-PolyQ

(Collection 2/Final experiment)

12Poster Initial(submitted online)

Apr. 2Exam II Apr. 3 Apr. 4

- Lab 6A: Brain Dissection and Histology In-class assignment

13Poster Presentation Final (summitted online, in-class presentation)

Apr. 9No

LectureApr. 10 Apr. 11 - Poster presentations

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Course CalendarMonday Tuesday Wednesday Thursday Friday

Week 1 Jan 14 Jan 15 Lab 1A

Jan 16Lab 1A

Jan 17Lab 1A

Jan 18

Week 2 Jan 21MLK day

Jan 22Brandeis Monday

T- transfer flies- procedure 1B

Jan 23W- transfer flies-

procedure 1B

Jan 24Th- transfer flies-

procedure 1B

Jan 25

Week 3JC Initial

Jan 28 Jan 29Labs 1C/2A

Jan 30Labs 1C/2A

Jan 31Labs 1C/2A

Feb 1T & W- count

coloniesWeek 4

JC CritiqueFeb 4

Th- count coloniesT- patch streak

Feb 5Labs 1C/3A

W- patch streak

Feb 6Labs 1C/3A

Th- patch streak

Feb 7Labs 1C/3A

Feb 8

Week 5JC Final

Feb 11 Feb 12Lab 2C/3B

Feb 13Lab 2C/3B

Feb 14Lab 2C/3B

Feb 15

Week 6 Feb 18 Feb 19 Feb 20 Feb 21 Feb 22

Week 7 Feb 25 Feb 26Labs 3C/3D

Exam 1

Feb 27Labs 3C/3D

Feb 28Labs 3C/3D

Mar 1

Week 8Grant Initial

Mar 4 Mar 5Labs 4A/5A

Mar 6Labs 4A/5A

Mar 7Labs 4A/5A

Mar 8

Week 9Sci. Comm.

Proposal

Mar 11 Mar 12Labs 4B/5B

Mar 13Labs 4B/5B

Mar 14Labs 4B/5B

Mar 15

Week 10Grant Final

Mar 18 Mar 19Lab 5C

Mar 20Lab 5C

Mar 21Lab 5C

Mar 22

Week 11Sci. Comm.Presentation

Mar 25 Mar 26Lab 5D

Mar 27Lab 5D

Mar 28Lab 5D

Mar 29

Week 12 Poster Initial

Apr 1 Apr 2Lab 6A Exam 2

Apr 3Lab 6A

Apr 4Lab 6A

Apr 5

Week 13Poster Pres. Poster final

Apr 8 Apr 9Poster

presentation

Apr 10Poster

presentation

Apr 11Poster

presentation

Apr 12

*Procedures requiring outside of registrar-allotted course time are indicated by your normal lab day Tuesday (T), Wednesday (W) or Thursday (Th) and are ALL 10:00 AM-12:15 PM.

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Writing a Purpose for Biology 18Background

A scientific purpose is a statement that tells the reader what organism you are studying, why you are studying it, how you are doing this study, and what you hope to find out in a brief, concise, and scientific manner. A purpose is the beginning of your experimental hypothesis statement.

Guidelines for writing a purpose

Use the appropriate tense

o When writing a pre-lab purpose, use the future tense. This is an experiment you will do.

o When writing an in-lab purpose, use the present tense. This is an experiment you are doing.

o When writing a post-lab purpose, use the past tense. This is an experiment you did.

Do not begin your purpose with the opening “The purpose of this experiment is….” The word “purpose” should not appear anywhere in your statement.

Your purpose should be written in complete sentences.

In general, purposes should not exceed 2 sentences and usually only require one sentence to be complete.

If you are performing an experiment on or with live organisms, your purpose should contain the scientific name of the organism in the correct format in italics with the Genus capitalized and the species in lower case (i.e. E. coli, Drosophila melanogaster, etc.)

Your purpose should contain a brief (two or three word) description of the method you are using. Are there any techniques that are integral to your experiment? If so, summarize them in the purpose.

Your purpose should contain a brief reason why you are performing this experiment. What do hope to find out? What is your ultimate goal?

Your purpose should not contain a laundry list of strains, experimental conditions, or steps. It should summarize these parameters with an underlying theme.

Your purpose should not describe the entire experimental procedure. It should summarize what is vital.

Your purpose should not contain learning or familiarization objectives.

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