Alexa Sawa

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Molecular and Cell Biology

Course Overview

This is is our Molecular and Cell Biology course for students planning to transfer as science majors. There are typically 28 students per lab section, and labs are 1 day a week for three hours.

Implementation 

GEP materials were used in the last six weeks of the lab curriculum. Students spent three weeks learning how to annotate and another three weeks annotating their independent projects individually or in groups of 2-3.

Lessons Learned and Future Plans

Annotation projects were first done in the Fall of 2016. The first time through only one group of three students submitted their annotation report before the semester was over, I convinced another 4 groups to finish on their own time in January 2017. So 13/35 students competed their annotation projects. In the Spring of 2017, I made a few changes that improved the completion rate. First, I recruited two tutors from my Fall 2016 class to help my Spring 2017 students. Our Academic Skills Center paid the tutors to attend laboratory class and hold office hours outside of class. Second I gave students the option of either submitting the Project Report or writing a paper on their unfinished annotation project for a grade. The unfounded fear of having to write a paper motived all but two students (one group) to finish their annotations. So far 18/22 students have had projects submitted back two the GEP (I am waiting on minor revisions by two more groups).

Syllabus

Academic Objective:

This course presents a survey of basic biological principles with a strong emphasis on biochemistry, cell biology and genetics. Topics include: biological organization, bio-molecular and cell structure and function, cellular respiration, photosynthesis, DNA replication, protein synthesis, Mendelian genetics, mitosis, meiosis, and embryology. This course is primarily designed for students pursuing careers in science, medicine, dentistry, veterinary medicine and other health fields requiring a strong foundation in biology. Together BI-005 and BI-006, Biology of Organisms, provide students with the basic biology core curriculum for transfer.

Prerequisites:

BI004 or high school biology

ENG 001A or concurrent enrollment

CH 001A or concurrent enrollment

Instructor:

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Alexa Sawa, PhD

Phone: (760) 776-7276

Email: asawa@collegeofthedesert.edu

Course Material:

  • Required text: Campbell Biology, 10th edition by Reece et. al.
  • Required online homework access: Pearson Mastering Biology http://www.pearsonmylabandmastering.com/northamerica/masteringbiology/
  • Course ID: MBSAWA49698
  • Required laboratory manual: Investigating Biology Laboratory Manual (7th/e), Menlo Park Benjamin/Cummings custom edition for College of the Desert.

Student Learning Outcomes: Upon successful completion of this course students will be able to:

  • Apply the scientific process
  • Develop laboratory techniques (such as light microscopy, recording experimental data, and an understanding of the principles of laboratory safety).
  • Demonstrate and ability to read, understand, and critically review scientific papers.
  • Recognize the relationship between structure and function at all levels: molecular, cellular, and organismal.
  • Explain major cellular processes in eukaryotes and prokaryotes, the two major classifications of cells.
  • Describe the relationship between genetics and evolutionary theory.

Online Homework:

  • Before each lecture exam there will be a 20 point homework assignment due on the Pearson Mastering Biology website.
  • Homework assignments are due at the beginning of class on the lecture day before the exam.
  • These assignments are longer activities, and can’t always be done on a mobile device. Working on them as we cover the material in class is highly encouraged.

Exams:

  • There are 4 lecture exams and 1 laboratory exams administered throughout the semester. Lecture exams will focus on material presented in lecture. Laboratory exams will focus on material presented in lab.
  • Students enrolled in DSPS must provide me with the appropriate paperwork. DSPS students must take the exams on the same day and at the same time as the rest of the class whenever possible. You must ask for accommodations from DSPS at least one week in advance of an exam. You are personally responsible for working with DSPS to determine the extent of your allowable accommodations.
  • Exams must be taken at the times scheduled. If dire circumstances dictate that you need to take the exam at an alternate time, you must notify me before the exam is scheduled. Missed exams must be taken within two days (48 hours) of the original exam and will not necessarily be the same format as the original exam. There will be no points given for unexcused missed exams

Attendance:

  • Attendance in lecture is very important, but not mandatory. If you must miss a lecture, it is your responsibility to ensure that you catch up with all class material before the next exam. Attendance in laboratory class is mandatory. Laboratory quizzes and activates cannot be made up. Missing a lab day guarantees you will lose points.
  • It is your responsibility to drop the class if you stop attending. Students who remain enrolled beyond the withdrawal deadline must receive an evaluative letter grade in the class. A “W” cannot be assigned to any student enrolled after this date.

Genomics Education Partnership (GEP) Research Project

In lab this semester we have to opportunity to perform original research in the field of genomics. This will be done in collaboration with the Genomics Education Research Partnership operated out of Washingtion University in Saint Louis (https://gep.wustl.edu/). Students will collaborate it groups of 3 to annotate a region of the Drosophila (fruit fly) genome. If you complete the project, and stay in touch with me, your name and work will be published in a scientific journal. As part of this project students are required to fill out an online survey and quiz before and after we do our research. The online assessments are not part of your grade, but do help the GEP determine its effectiveness.

Electronic Devices:

Cell phones, electronic dictionaries, and other electronic devices are not allowed during lecture or labs exams. TURN OFF OR MUTE CELL PHONES AT ALL TIMES.

Please contact me if you need to make audio recordings of lecture or lab. Video recordings of lecture or lab are not permitted.

Grading:

One grade, combining both your lecture and lab scores, will be assigned based on a percentage of total possible points. Grades are rounded to the nearest 10th place. For instance, a final score of 79.89 rounds to 79.9, a C.

A = 90.0 to 100%

B = 80.0 to 89.9%

C = 70.0 to 79.9%

D = 60.0 to 69.9%

F = below 60%

Distribution of Points:

Unit                                         Each               Total

Lecture Exams (3)                      200                  600

Final Lecture Exam (1)               300                  300

Lecture Activities (18)                   5                    90

Online Homework (4)                  20                     80

Lab Exam (1)                            100                  100

Lab Quizzes (9)                          10                    90

Lab Manual Work (1)                   50                    50

GEP Worksheets (2)                   30                    60

Lab Reports (3)                           50                  150

Total points available                                      1520                                                               

 

Lecture Schedule

The following is the schedule of lecture topics and exam days. We will attempt to adhere to this schedule. Any changes to this schedule will be announced in lecture.

 

Week

Date

Topic

Chapter

1

1/31

Introduction/A T5our of the Cell

1/6

2/2

A Tour of the Cell/Biological Molecules

6/5

2

2/7

Biological Molecules

5

2/9

The Cell Cycle

12

3

2/14

Meiosis

13

2/16

Conclude and Review HW Due

 

4

2/21

Exam 1

1, 5, 6, 12, 13

2/23

Membrane Structure and Function

7

5

2/28

An Introduction to Metabolism

8

3/2

Cellular Respiration and Fermentation

9

6

3/7

Cellular Respiration and Fermentation

9

3/9

Photosynthesis

10

7

3/14

Cell communication

11

3/16

Conclude and Review HW Due

 

8

3/21

Exam 2

7-11

3/23

Mendel and the Gene Idea

14

9

3/28

Chromosomal Basis of Inheritance

15

3/30

Molecular Basis of Inheritance

16

10

4/4

Molecular Basis of Inheritance

16

4/6

Gene Expression: From Gene to Protein

17

Spring Break

11

4/18

Gene Expression: From Gene to Protein

17

4/20

Conclude and Review HW Due

 

12

4/25

Exam 3

 

4/27

Regulation of Gene Expression

18

13

5/2

Regulation of Gene Expression

18

5/4

Viruses

19

14

5/9

Genomes and their Evolution

21

5/11

Bacteria and Archaea

27

15

5/16

Animal Development

47

5/18

Conclude and Review HW Due

 

16

5/23

Final Exam 2:00 pm

18,19, 21, 27, 47 and Cumulative

Laboratory Schedule

 

Week

Date

Topic(s)

Lab Manual

Ch./page

1

2/3

Lab Safety

Scientific Investigation

Microscopes and Cells

 

1/1

2/29

2

2/10

Mitosis

Animal Development

7/151

19/497

3

2/17

Holiday No Lab

 

4

2/24

Molecular Biology: set up

8/181

5

3/3

Molecular Biology: analysis

8/181

6

3/10

Fermentation

Lab Report 1 Due

4/107

7

3/17

Photosynthesis

5/131

8

3/24

Meiosis

Lab Report 2 Due

Handout

9

3/31

Lab Exam (Lab Manuals Due)

 

10

4/7

GEP Introduction

Studying Eukaryotic Genes Using a Genome Browser and BLAST

Handout

Spring Break

11

4/21

GEP: Annotation Walkthrough

Handout

12

4/28

GEP: Annotation Walkthrough

 

13

5/5

Gene annotation

Handout

14

5/12

Gene annotation

Handout

15

5/19

Gene annotation

Lab Report 3 Due

Handout

Undergraduate Research Experience

Course Overview

This course was originally designed to give our undergraduates a taste of research in any science discipline. I co-opted it for GEP annotation research for the first time in Spring 2017.

Implementation

There were ten students in the class; five had annotated previously as part of a larger course and five were new to annotation. Student completed a minimum of two annotation projects, one working in pairs and a second one working independently. Students were required to design and present posters based on their first annotation project, and write a research paper on their second. We also spent time on non-GEP related material in the form of journal clubs.

Lessons Learned and Future Plans

Nine students completed the course with one having to take a medical incomplete. To date, 14 projects have been submitted back to the GEP. Student feedback was positive, and they are quite proficient at annotating. Each of them chose a moderately difficult project the second time around. This is also a great pool of student to draw tutors from when implementing the GEP in the larger course. In the future I am going to require students two speak out loud about their projects on a regular basis. This time around most were not confident speaking up to the entire group either about their project or journal articles we were reading.

Syllabus

Academic Objective:

This semester we will participate in a nation-wide undergraduate research project in collaboration with the Genomics Education Partnership sponsored by Washington University in St. Louis. Students will use bioinformatics techniques and programs to annotate a region of newly sequenced Drosophila DNA, based on homology to D. melanogaster. Students are expected to complete their annotation projects as well as communicate their findings in written lab reports and oral presentations. Additional topics covered include information retrieval, computer skills applied to laboratory research, time management and organizational skills, application of modern research methods, experimental design, data collection and analysis, and presentation skills (written and oral). This course is intended for students pursuing a STEM degree and who have completed a minimum of 35 college level units.

Prerequisites:

BI005 or BI006

 'Instructor':

Alexa Sawa, PhD

Office: Science 2

Phone: (760) 776-7276

Email: asawa@collegeofthedesert.edu

Course Material:

Students must be able to save data each day onto a USB drive, their own personal laptop, or a cloud data storage service.

Your textbook from BI005/BI006, Campbell Biology, can serve as a useful reference.

Student Learning Outcomes Upon successful completion of this course students will be able to:

  1. Demonstrate the use of modern research methods.
  2. Utilize skills relating to the process of conducting scientific research and applying the scientific method.
  3. Apply the basics of experimental design, data collection, data analysis and hypothesis testing.
  4. Analyze current research published in the scientific literature.
  5. Summarize ideas, scientific knowledge and experimental outcomes through written and oral communication.
  6. Apply time management and study skills to successfully complete a research project during the semester.

'Attendance':

Attendance is mandatory. Missing more than 3 classes will drop your grade one letter grade. If you miss more than 5 classes I will drop you from the class.

Genomics Education Partnership (GEP) Research Project

In lab this semester we have to opportunity to perform original research in the field of genomics. This will be done in collaboration with the Genomics Education Research Partnership operated out of Washington University in Saint Louis (https://gep.wustl.edu/). Students will annotate a region of the Drosophila (fruit fly) genome. If you complete the project, and stay in touch with me, your name and work will be published in a scientific journal. As part of this project students are required to fill out an online survey and quiz before and after we do our research. The online assessments are not part of your grade, but do help the GEP determine its effectiveness.

 Grading:

Your final grade in the course will be assigned based on a percentage of total possible points. As indicated below grades are rounded to the nearest tenths place. For instance, a final score of 79.86% rounds to 79.9%, a C.

A = 90.0 - 100%

B = 80.0 - 89.9%

C = 70.0 - 79.9%

D = 60.0 - 69.9%

F = below 60%

'Distribution of Points':

Unit                                         Each               Total

Quizzes (3)                                10                    30

Notebook sheets (6)                    20                  120

Research Poster (1)                    50                    50

Research Presentation (1)           50                   50

Research Paper (1)                     50                   50

Research paper review (1)           10                    10

Journal club participation (5)          5                    25

Journal club presentation (1)        25                    25

GEP submission (2)                    20                    40

Total points available                                        400                                                                  

Schedule

We will attempt to adhere to this schedule. Any changes to this schedule will be announced in class and on Canvas.

Week

Date

Lecture Topic

Lab Activity

1

1/30

Course introduction

Pre-survey/quiz

2/1

Comparative Genomics

Reading: Hardison Comparative Genomics

Using BLAST to compare DNA/Protein sequences (due 2/6)

2

2/6

Comparative Genomics

Using BLAST to find orthologues (due 2/8)

2/8

Quiz 1(BLAST)

Eukaryotic Gene Structure

Using a genome browser to analyze the structure of a eukaryotic gene (due 2/15)

3

2/13

Eukaryotic Gene Structure

Using a genome browser to analyze the structure of a eukaryotic gene

2/15

Quiz 2 (Eukaryotic Gene Structure)

Annotation Strategy

Reading: Annotation Instruction Sheet

Practice annotation (due 3/1)

4

2/20

Holiday No Class

2/22

Annotation Strategy

Practice annotation

5

2/27

Using Evidence Tracks

Practice annotation

3/1

Annotation workflow

Claim annotation projects: Independent research pt. 1: find the genes (due 3/13)

6

3/6

Quiz 3 (Annotation)

Independent research pt. 1: find the genes

3/8

Independent research: find the genes

Independent research pt. 1: find the genes

7

3/13

Flybase and literature searches

Independent research pt 2: annotate 1 gene with at least 2 exons (due 3/20)

3/15

Journal Club

Independent research pt 2: annotate 1 gene with at least 2 exons

8

3/20

Finish annotating contigs

Finish annotating contigs

3/22

Finish annotating contigs

Finish annotating contigs

9

3/27

Finish annotating contigs

Finish annotating contigs

3/29

Journal Club

Finish annotating contigs

10

4/3

Annotation posters due

Annotation presentations

Annotation presentations

4/5

Annotation presentations

Annotation presentations

Spring Break

11

4/17

Regulation of Transcription

First GEP Submission DUE

Claim second annotation project or transcription start site project

4/19

Journal club

Independent research

12

4/24

Scientific writing

Independent research

4/26

Independent research

Independent research

13

5/1

Independent research

Independent research

5/3

Journal club

Independent research

14

5/8

Drafts of final research paper due

Independent research

5/10

Independent research

Independent research

15

5/15

Independent research

Independent research

5/17

Journal Club

Post- Survey and Quiz

16

5/22

4:00 pm Final Research Paper Due

Second GEP Submission DUE