Jennifer Roecklein-Canfield Simmons College

From GEP Wiki
Jump to: navigation, search

Genomics at Simmons College

Course Overview

New for Fall 2013:


HONOR Learning Community:  Your Microbes and You

This course will be an introduction to open source bioinformatics tools used to examine the Human Microbiome.  Students will also be introduced to computer programing, (Python for Bioinformatisists).  As a learning community, the course will include material from general biology, microbiology, math and computer science.  The course description:


How do we untangle it all?  How do scientists - working in teams - generate data and make sense of it?  In this course you will work with a biochemist and a computer scientist to discover how the microbes living in your own body change the way your own genes act.  How do the wee beasties living inside us actually play an important role in our own health?  We will use biology, math and computer science to answer these excellent questions.

Implementation

Materials from GEP are used in two core Biochemistry courses, CHEM345 Biochemistry and CHEM347 Advanced Topics in Biochemistry and will be used in Fall 2013 in a new Freshman Learning Community:  Your Microbes and You.

Syllabus for CHEM347:

=== Chem. 347 Advanced Topics in Biochemistry                         Spring 2012<o:p></o:p>

 

 

Microbes, Microbes Everywhere!<o:p></o:p>

 

Instructors:  Jennifer Roecklein-Canfield, S438<o:p></o:p>

                           jennifer.canfield@simmons.edu<o:p></o:p>

                  Stephanie Walker<o:p></o:p>

                           stephanie.walker@simmons.edu<o:p></o:p>

 

Recommended Text for Background:  Biochemistry, 5th Ed., by Lubert Stryer (or any college level biochemistry text book)<o:p></o:p>

<o:p> </o:p>

Course Overview:<o:p></o:p>

<o:p> </o:p>

This course is a research-integrated course emphasizing modern biochemical techniques and functional application of advanced biochemistry topics. We will integrate advanced topics in biochemistry, molecular biology, microbiology, and cell biology and apply them to the systematic exploration of microbial organisms.<o:p></o:p>

<o:p> </o:p>

 We will introduce the field of bioinformatics using computer-based tools to explore the Human Microbiome and to develop biological questions utilizing the data contained therein.  We will be participating in ongoing research projects involving: 1. the Genetics Education Partnership  and gene annotation of species of the Drosophila fruit fly and 2. analysis of putative interactions between gamma herpesviridae, Epstein-Barr virus and Kaposi Sarcoma Virus, and their human host.<o:p></o:p>

<o:p> </o:p>

Student Learning Goals:<o:p></o:p>

-identify and define structural features of the genome<o:p></o:p>

-explain the relationship between the genome, the proteome, and the interactome of an organism<o:p></o:p>

-recognize and interpret evolutionary relatedness and function of proteins<o:p></o:p>

-apply current laboratory techniques in protein dynamics to study the functional relevance of protein-protein interactions between gamma herpesviridae and the host<o:p></o:p>

-use the Human Microbiome database to analyze biological questions about microbes in the body<o:p></o:p>

-design, implement, and analyze experiments to address those biological questions<o:p></o:p>

-present experimental results both orally as a research talk and written as a manuscript for publication<o:p></o:p>

<o:p> </o:p>

 

 

 

 

 

 

Tentative Course Outline: <o:p></o:p>

<o:p> </o:p>

Week 1-5                                Bioinformatics and Genomics on HMB<o:p></o:p>

                                                Research on gamma-herpesviruses: EBV<o:p></o:p>

                                                and KSHV<o:p></o:p>

<o:p> </o:p>

Week 5-6                                Design of Experimental Process for analysis of the <o:p></o:p>

                                                HMB biological relevance and analysis of viral <o:p></o:p>

                                                interference of apoptosis<o:p></o:p>

<o:p> </o:p>

Week 6-7                                Preparation of protocols, constructs, and solutions<o:p></o:p>

                                                for expression assays for viral proteins<o:p></o:p>

 

                                                Analysis of biological hypotheses using the <o:p></o:p>

                                                Human Microbiome database <o:p></o:p>

<o:p> </o:p>

Week 8-9                                Implementation of Experimental Designs<o:p></o:p>

<o:p> </o:p>

Week 11-10                            Final experiments and analysis of data<o:p></o:p>

<o:p> </o:p>

Week 12                                  Presentations<o:p></o:p>

<o:p> </o:p>

<o:p> </o:p>

<o:p> </o:p>

This class will include a weekly lab meeting, time and place will be determined by students and instructors schedules. This meeting is mandatory attendance!<o:p></o:p>

<o:p> </o:p>

Students will work in lab groups of 2 (maybe 3), determined by the instructor.<o:p></o:p>

<o:p> </o:p>

Emphasis will be on independent student performance of protocols (which will be provided or researched).  There is no lab manual!  Students will determine the course of experiments and will troubleshoot when things go wrong.<o:p></o:p>

 

 

Grades for the course will be based on:<o:p></o:p>

<o:p> </o:p>

Research Progress Reports                                         10pts each                   <o:p></o:p>

Literature analysis                                                       10pts each                   <o:p></o:p>

Weekly lab quizzes                                                     10pts each<o:p></o:p>

Genomics Assignments                                               100pts total                  <o:p></o:p>

Laboratory Notebook/Journal                                     100pts<o:p></o:p>

Formal Journal Club Presentation                               100pts <o:p></o:p>

Final Data presentation (Written and oral)                  200pts             <o:p></o:p>

<o:p> </o:p>

Final grade in this course is NOT based on completing all possible experiments, but rather on student's motivation, participation, and dedication.  <o:p></o:p>

This course incorporates the following Chemistry Department Student Competencies:<o:p></o:p>

<o:p> </o:p>

mso-yfti-tbllook:191;mso-padding-alt:0in 5.4pt 0in 5.4pt;mso-border-insideh: .5pt solid black;mso-border-insidev:.5pt solid black"

width="17%" valign="top" style="width:17.04%;border:solid black 1.0pt;
 mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt" | 

(C)ore<o:p></o:p>

(F)oundation<o:p></o:p>

(I)n-Depth<o:p></o:p>

width="14%" valign="top" style="width:14.88%;border:solid black 1.0pt;
 border-left:none;mso-border-left-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

Course<o:p></o:p>

width="10%" valign="top" style="width:10.26%;border:solid black 1.0pt;
 border-left:none;mso-border-left-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

Area*<o:p></o:p>

width="57%" colspan="12" valign="top" style="width:57.8%;border:solid black 1.0pt;
 border-left:none;mso-border-left-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

Student Competencies<o:p></o:p>

width="17%" valign="top" style="width:17.04%;border:solid black 1.0pt;
 border-top:none;mso-border-top-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

 

width="14%" valign="top" style="width:14.88%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

 

width="10%" valign="top" style="width:10.26%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

 

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

1<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

2<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

3<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

4<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

5<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

6<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

7<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

8<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

9<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

10<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

11<o:p></o:p>

width="4%" valign="top" style="width:4.8%;border-top:none;border-left:none;
 border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;mso-border-top-alt:

solid black .5pt;mso-border-left-alt:solid black .5pt;mso-border-alt:solid black .5pt; padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

12<o:p></o:p>

width="17%" valign="top" style="width:17.04%;border:solid black 1.0pt;
 border-top:none;mso-border-top-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

I<o:p></o:p>

width="14%" valign="top" style="width:14.88%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

CHEM347<o:p></o:p>

width="10%" valign="top" style="width:10.26%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

B<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

x<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

 

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

x<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

x<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

x<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

x<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

x<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

x<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

x<o:p></o:p>

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

 

width="4%" valign="top" style="width:4.82%;border-top:none;border-left:
 none;border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;

mso-border-top-alt:solid black .5pt;mso-border-left-alt:solid black .5pt; mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

 

width="4%" valign="top" style="width:4.8%;border-top:none;border-left:none;
 border-bottom:solid black 1.0pt;border-right:solid black 1.0pt;mso-border-top-alt:

solid black .5pt;mso-border-left-alt:solid black .5pt;mso-border-alt:solid black .5pt; padding:0in 5.4pt 0in 5.4pt;height:13.6pt" |

x<o:p></o:p>

<o:p> </o:p>

mso-yfti-tbllook:191;mso-padding-alt:0in 5.4pt 0in 5.4pt;mso-border-insideh: .5pt solid black;mso-border-insidev:.5pt solid black"

width="443" valign="top" style="width:6.15in;border:solid black 1.0pt;
 mso-border-alt:solid black .5pt;padding:0in 5.4pt 0in 5.4pt" | 

2012 Student Competencies<o:p></o:p>

width="443" valign="top" style="width:6.15in;border:solid black 1.0pt;
 border-top:none;mso-border-top-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

Knowledge-Based <o:p></o:p>

All our graduates will be able to:<o:p></o:p>

width="443" valign="top" style="width:6.15in;border:solid black 1.0pt;
 border-top:none;mso-border-top-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

1.    

 Master a broad set

of chemical knowledge concerning the fundamentals in the basic areas of the discipline (organic, inorganic, analytical, physical, and biological chemistry).<o:p></o:p>

width="443" valign="top" style="width:6.15in;border:solid black 1.0pt;
 border-top:none;mso-border-top-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

2.    

 Solve

quantitative and qualitative problems competently by identifying the essential parts of a problem and formulating a strategy for solving the problem.  Rationally estimate the solution to a problem, apply appropriate techniques to arrive at a solution, test the correctness of the solution, and interpret the results.<o:p></o:p>

width="443" valign="top" style="width:6.15in;border:solid black 1.0pt;
 border-top:none;mso-border-top-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

Performance/Skills-Based <o:p></o:p>

All our graduates will demonstrate the

 ability to:<o:p></o:p>
width="443" valign="top" style="width:6.15in;border:solid black 1.0pt;
 border-top:none;mso-border-top-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

3.     Design chemical experiments, properly carry

 out the experiments, be able to troubleshoot

experiments, appropriately record and interpret the results, and recognize what constitutes “reasonable” data.<o:p></o:p>

width="443" valign="top" style="width:6.15in;border:solid black 1.0pt;
 border-top:none;mso-border-top-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

4.     Use standard laboratory equipment, modern

 instrumentation, and classical techniques to carry out experiments. <o:p></o:p>
width="443" valign="top" style="width:6.15in;border:solid black 1.0pt;
 border-top:none;mso-border-top-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

5.     Follow proper procedures and regulations for

 safe handling and use of chemicals. <o:p></o:p>
width="443" valign="top" style="width:6.15in;border:solid black 1.0pt;
 border-top:none;mso-border-top-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

6.    

 Communicate the

concepts and results of laboratory experiments through effective writing and oral communication skills. <o:p></o:p>

width="443" valign="top" style="width:6.15in;border:solid black 1.0pt;
 border-top:none;mso-border-top-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

7.    

 Use computers in

data acquisition and processing and use available software as a tool for data analysis.<o:p></o:p>

width="443" valign="top" style="width:6.15in;border:solid black 1.0pt;
 border-top:none;mso-border-top-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

8.    

 Employ modern

library search tools to locate and retrieve scientific information about a topic, chemical, chemical technique, or an issue related to chemistry.<o:p></o:p>

width="443" valign="top" style="width:6.15in;border:solid black 1.0pt;
 border-top:none;mso-border-top-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

Professional<o:p></o:p>

All graduates will:<o:p></o:p>

width="443" valign="top" style="width:6.15in;border:solid black 1.0pt;
 border-top:none;mso-border-top-alt:solid black .5pt;mso-border-alt:solid black .5pt;

padding:0in 5.4pt 0in 5.4pt" |

9.    

 Maintain the integrity of data and

demonstrate ethical and professional standards, in accordance with the American Chemical Society guidelines for professional conduct.<o:p></o:p>

10.  

 Act in a highly

ethical and professional capacity as a scientist in the articulation, evaluation, and employment of methods and chemicals that are benign for human health and the environment, which include but are not limited to the 12 Principles of Green Chemistry, the 12 Principles of Green Engineering, and the Principles of Global Sustainability as set forth by the Report of the Brundtland Commission, Our Common Future, in 1987.<o:p></o:p>

11.  

 Successfully pursue

personal career objectives following graduation. These may include an advanced education in professional or graduate school, a scientific career in government or industry, a career in teaching, or a related career.  <o:p></o:p>

12.  

 Function successfully as part of a

team, exhibit good citizenship in group interactions, and be an active contributor to group projects.<o:p></o:p>

<o:p> </o:p> ===