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Viewing: BIOCHM 2484HW leecb : Macromolecular Techniques Laboratory - Honors/Writing Intensive

Last approved: Mon, 30 Jan 2017 18:21:26 GMT

Last edit: Mon, 30 Jan 2017 18:15:30 GMT

Proposal Type

Honors
Writing Intensive

Contact Information

leecb
Christopher
Lee
LeeCB@missouri.edu
573/884-6881
Agriculture Biochemistry
Are you submitting this proposal on behalf of an instructor?

Instructor for whom you are submitting proposal:
leecb
Christopher
Lee
LeeCB@missouri.edu
573/884-6881
Agriculture Biochemistry
Subject Area’s Department Chair/Director:
hazelbauerg
Gerald
Hazelbauer
HazelbauerG@missouri.edu
573/882-9825
Biochemistry

Term for Proposal

Fall 2017
 

Course Catalog Information

CAFNR
Biochemistry (BIOCHM)
Biochemistry
2484HW
3
 
30
Macromolecular Techniques Laboratory - Honors/Writing Intensive
The laboratory experiments include DNA isolation, DNA cloning, PCR, plasmid transformation, protein expression, affinity-tagged chromatography, SDS-polyacrylamide gel electrophoresis, enzyme isolation, enzyme assay, buffer preparation, and Michaelis-Menten kinetics. Graded on A-F basis only.
 
Lecture/Standard with Laboratory & Discussion
A-F Only
sophomore standing; Biochemistry majors only. Honors eligibility required.
 
 
 

Instructor Information

leecb
Christopher
Lee
LeeCB@missouri.edu
573/884-6881
Agriculture Biochemistry
(numbers only)
NTT Assistant Professor
117 Schweitzer Hall
 
 

The Campus Writing Program conducts a two-day faculty workshop to assist with the design and implementation of your writing intensive course. Once your course proposal has been approved by the Campus Writing Program, you will receive information on time, date and location of the workshop.
Indicate below if additional instructors are planned, but specific individuals have not yet been chosen. Check all that apply

Briefly describe the qualifications of the known graduate instructors, or planned qualifications if graduate instructors are still to be selected, bearing in mind that graduate students teaching honors courses should be advanced students with a record of excellent teaching.
 

Honors Course Information

Biochemistry 2484H is a 3-credit laboratory-based course, which includes one 50-minute lecture, a 3-hour lab, and an hour literature discussion each week. In this course, topics are examined on the theoretical level in lecture and then applied in the laboratory so that upon completion of the course, the students should be able to enter into a life sciences-based research laboratory and perform critical skills that researchers currently use to investigate their study topic.
This course covers the basics of protein chemistry and quantitation while developing an understanding of the instrumentation and its analytical limits used to perform studies. In this section of the lab, students are required to learn about applications of the Beer-Lambert law, and how to use it to quantify light-absorbing compounds in solution that are frequently analyzed in a biochemistry lab.
The next portion of the course teaches the students about the applications of recombinant DNA technology, the central dogma of molecular biology, and its uses in a research environment. The labs associated with this section use DNA manipulating enzymes to clone a gene into a protein expression plasmid, and utilizes current technologies to perform and purify the DNA after manipulations that are required for cloning.
We cover the basics of both Sanger-based and Next-Gen DNA sequencing to examine the clones the students made in the course, and then perform the computer-based sequence analysis that all researchers must become familiar with in order to perform the work that is done in modern research environments. We examine online public resources that are frequently used in examining how DNA sequences are analyzed to predict similarity to other genes and predict how DNA molecules can be translated into biological macromolecules that perform the work in living cells.
After the sequence analysis is performed, we use the clones created in the lab to express recombinant protein in a bacterial system (a common biochemical technique), and then we purify our recombinant protein away from the bacterial cells to produce a very pure protein sample with modern chromatography techniques.
After expressing the protein, we analyze it with common analytical methods by resolving them in a polyacrylamide gel system, and then transfer it to a membrane, which we probe with several antibodies to demonstrate the efficacy of our purification techniques. This is a critical technique that most biochemistry labs use in the analysis of their research.
Finally, we examine enzyme kinetics, and relate how enzymes and other proteins activities often play a role in disease. Through experimentation, we discover how kinetic information ascertained in a laboratory environment can be used for the design of drugs to treat specific diseases, as enzymes are often the specific targets of drugs designed by the pharmaceutical industries.
Another aspect of this course is the introduction of alternative careers that can be achieved with a degree in biochemistry other than medicine. Most of the biochemistry majors who come through our program enter the program with the goal of making it into medical school. As medical schools are extremely competitive, I introduce a variety of other interesting professions that students can pursue by bringing in outside speakers who work in a variety of fields associated with biotech and science to talk about their career paths and how they went from being biochemistry undergraduates to professional researchers in biotech industries, biotech patent lawyers, sales representatives, technicians for high-tech instruments used in research, government careers in science, and a large range of other options available to students with a biochemistry degree.
After completion of the laboratory experimentation, there is a discussion-based literature review. Students will be introduced to current scientific primary literature that utilizes the techniques that were explored in the experimentation to demonstrate how the tools that they use in the lab are applied in real research settings.
There are several specific aims of the literature review section of this course. The students are introduced to primary literature, and have to critically evaluate current work. Students will explore and gain a basic understanding of how research is presented to scientific audiences. The students are required to get into the data in the papers covered to explore the significance of how the information that the experiments that we learn in the lab lead to scientific discoveries; specifically to see what types of information can be ascertained from the experiments we perform and how that contributes to the overall body of work. The students have to critically evaluate figures and data presentation in the primary literature to develop a deeper understanding of the work performed. We will also explore brand new technologies that are just starting to be used in research environments, and how they fit into the big picture of life-sciences research. We will also explore developing fields of current research to demonstrate how the techniques that we use can lead to new types of analysis and applications, as the students in this section will most-likely end up being part of the generation that brings significant new ideas and applications of life-sciences research into fruition.
1
Answer the questions below as they would apply to one section. For all other sections, provide similar information in the Additional Sections Information box below.
 

 
 
 
Short essays
Final
Mid-term
Oral reports
Quizzes
Term papers
 
 
16
 
departmental advisor, Dr. Freyermuth
 

Writing Intensive Course Information

This Writing Intensive (WI) course is an honor college, sophomore-level Biochemistry Laboratory class with three meetings a week, one laboratory class (3 hrs), one lecture class (50 min), and one discussion section (50 min). During the laboratory section of the class, students will perform experiments with an emphasis on modern biochemical techniques. At the beginning of each week, an accompanying lecture provides relevant background information and outlines experiments to be performed during the week. At the end of each week, there is a discussion section that introduces the basic concepts of formal scientific writing, and introduces the students to current primary scientific literature on a plethora of topics that utilizes the laboratory skills and concepts we explore in the lab. The objectives of the WI aspect of this class are 1) to improve the overall written communication skills of students and 2) to introduce students to the discipline of formal scientific writing. Hopefully, students will gain experience in reporting on the results of experimentation in the laboratory environment and process data collected into meaningful results conveyed clearly and concisely in writing. Students will generate a total of 19 different writing assignments, and one 50 minute group oral presentation, the majority of which will be created outside of the classroom. There will be four distinct types of writing assignments: experimental laboratory reports, (semi-formal; total of 4 assignments, each four pages in length), a formal group term paper (formal literature review; 1 draft and 1 revised final paper, each 3 to 5 pages), peer-review of formal group term paper (semi-formal; 1 review, 1-2 pages), one lab notebook (informal; more than 50 pages), and 12 primary literature summaries (informal; 2 pages each). Writing assignments will coincide with the laboratory class, utilizing experimental data produced by students, or covering research topics explored during the weekly laboratory classes. All writing exercises will be graded by the instructor, based on detailed rubrics to ensure consistency of grading and to provide a high standard of feedback to the students. Students will be graded based on clarity and quality of writing, scientific content, data presentation and interpretation of results. Students will also be graded on whether answers to additional questions are coherent and argued in a logical manner. The lab notebooks will be collected in the middle and at the end of the semester and graded for clarity, completeness of experimental outline, data collection, and interpretation of results. Writing assignments will make up 69 percent of the students grade; the remaining 31 percent will be based on written exams, one laboratory practical exam, quizzes, and laboratory-based math assignments. Writing assignments will be evenly distributed throughout the semester in that all weeks of the class, students will compose and hand in some form of writing assignment. The experimental laboratory reports will be due two weeks after the completion of the labs the students will be reporting on to allow adequate time to process the data and interpret the results. The group term paper will be due six weeks into the semester, peer-reviewed the following week, and then edited over the next four weeks before the final paper is due. In addition, students are expected to maintain their informal laboratory notebook on a weekly basis before and during laboratory class periods. Finally, primary literature summaries are due on the day the papers are covered in the discussion section of the course. Teaching Experiences:Fall semester 2017 will be the fifth time I have taught this honors college class, and the third time I am using this assignment format. However, I will be teaching 5 sections of this course for the non-honors students, with the honors students dispersed throughout these sections with the distinction being the extra discussion lecture at the end of each week. The extra writing that the honors section has to do dictates the request for the WI designation. As most students in our department do not have any experience in scientific writing, I will dedicate a portion of each lecture in the honors discussion on how to write individual sections of a scientific paper. Generally, our students have an overall limited knowledge of using computer programs and web-based learning in the laboratory setting. Therefore, I will include additional assay questions that utilize internet-based computer analysis programs. These assay questions will be directly relevant to weekly experiments, in that they are essential for students to analyze and interpret their data. Thus, these assignments will not only deepen student's scientific knowledge on our laboratory topics but students will gain valuable scientific computer skills. In addition to the experimental laboratory reports, formal group term papers, and primary literature reviews, this WI class incorporates two additional types of writing assignments, the Lab notebook and peer-reviews. 1) Lab notebook (bound composition book) (mostly hand-written; more than 50 pages) One of the objectives of this informal writing assignment is to ensure that students come prepared to each lab class. To this end, students are required to write condensed but concise outlines of experimental procedures and to outline tables into this Notebook prior to arriving to each lab class. This assignment will enable students to identify possible problems or questions regarding experimental procedures in advance. Furthermore, this exercise highlights the role of laboratory notebooks as an essential scientific tool to ease data collection during the lab class period and to explore ideas or thoughts related to experiments. Students will also be introduced to the importance of keeping a comprehensible notebook because they are able to utilize their notebooks during their practical laboratory exam. Notebooks will be spot-checked periodically during class periods and collected at the middle and at the end of the semester. Notebooks will be graded by the instructor for clarity and completeness of experimental outline and data collection. 2) Peer review of draft version of the formal group term paper (one per semester). Length: one to two pages (1 1/2-spaced using standard fonts of 11 or 12 point with margins of 1 inch for the top and bottom; and 1 inch for the left and right margins). The objective of the group peer review is to teach students how to provide constructive criticism of a manuscript, and to work in a group environment. Furthermore, students will learn how to use the peer-review process to assimilate and improve on their own writing, data presentation and interpretation of their formal group term papers. Student groups will review a draft term paper of one of their colleague student groups based on peer-review guidelines provided with a copy of a draft term paper. The instructor will grade these assignments for clarity of the review and constructiveness of their criticism.
None
Face-to-face
Self paced?

11
16
Should this course be considered for funding?

Large Enrollment Courses:
 
 
 

Writing Intensive Assignments

Pages
Experimental laboratory reports (4)
Overview of all assignments

In this WI class, the main focus is on four types of writing assignments, namely experimental laboratory reports, the formal group term paper, primary literature reviews, and Power Point slides. Writing assignments are word-processed documents that are written in third-person narrative using complete sentences, proper English spelling and grammar, and correct use of scientific terminology. The use of scientific graphing programs for computer-generated graphs is encouraged. Hand-written calculations or graphs that are neatly written in ink, however, are also acceptable. For each assignment, students will be provided with specific rubrics outlining the specific exercise format and grading expectations for each report or paper. Students will be graded based on clarity and quality of writing, scientific content, data presentation and organization, and interpretation of results. Students will also be graded on whether answers to additional questions are coherent and argued in a logical manner. For Power Point slides, they are consulted with one on one for rethinking and revising that type of writing to reach audiences and fulfill the purpose of the presentation.

1. Experimental laboratory reports (total of 4 individual assignments, due two weeks after the completion of each lab module). The length of each assignment is 4 pages (4x4 =16). The objectives of the experimental laboratory reports are to introduce students to all of the major sections of a scientific paper, b) comprehend the experiments and background information on biochemical topics covered that week(s) in the experimental laboratory section of the class, c) understand how to present and analyze data from different types of experiments and subsequently interpret results using critical thinking and reasoning, and d) effectively express concepts and results clearly and concisely. Importantly, the general format of the experimental laboratory reports serves as model for scientific journal articles, thus preparing students for reading and understanding the components of the primary literature assigned in the course. All experimental laboratory reports will be graded by the instructor. All experimental laboratory reports will contain the following sections of a scientific article; a title, introduction, materials and methods, results, discussions, and references. All sections are written in scientific writing style and format. Each section of the reports will be relevant to the laboratory work performed that week, and will include answers to additional questions raised in the laboratory manual that are relevant to experiments meant to deepen the students understanding of the topic covered in that lab module, as well as the following information listed below: 1) The introduction to each report will contain a literature review performed by the students to discuss the history and relevance of each laboratory experiment, relevant background information as well as a clearly written objective for that lab module's topic. The introduction will also include a reference list in a format utilized by many scientific journals. 2) The materials and methods section includes the proper format utilized in scientific literature including the materials, potential sources of the materials including company catalog numbers, and a detailed protocol of the experimental procedure that was utilized in the lab module. 3) The results section includes experimental raw data collected throughout the lab period, graphs (reduced from raw data) and relevant calculations important to interpret results. Data and graphs will be presented in the appropriate tabular or graphical manner as requested in the lab modules. In addition, students describe their findings in written statements in one or two paragraphs. 4) The discussion (one each semester) includes interpretations and discussions of obtained results. If results diverge from expectation, students should include alternative explanations or hypotheses here. 5) The figures (one each semester) includes presentation of multiple forms of data in a visual representation often used in scientific literature. Students are expected to create professional quality images generated from data obtained during the experimental portion of the course.
Length of assignment:
16
Instructor
 
 
16

Formal Group Term Paper
Formal group term paper 3-6 pgs. (one draft term paper and one revised final term paper on selected research topic from a University of Missouri Columbia researcher). The main objective for the formal group term paper is to get students acquainted with finding information from primary scientific literature articles as a source of relevant information. Furthermore, students will learn how to write concisely and clearly, so that peers can understand their reasoning and can gain information presented on complex biochemical research that is being reported on. Students will be required to function in a group environment and learn how to coordinate, work, and write with others. They will be encouraged to use new software such as Google Docs, or the track changes features in Microsoft Word that allow for the online collaboration and composition of documents. For the formal group term paper, students will compose a draft version that is reviewed by the instructor and one of the other groups in the class (peer-review) to provide constructive criticism. Students will incorporate suggestions and corrections provided by instructor (and if applicable, by the peer group), thus improving the quality of the report. Students will then return the revised draft version as the final formal report that will be graded by the instructor. The formal group term paper will be composed in an essay consisting of the following sections: title, body of the paper, and a references section. More specifically: a) The title is a brief heading describing the weekly experimental topic. b) The body of the paper needs to address three major questions about the primary literature that is covered in the report. Students need to address the big picture problem that the research is trying to address (in essence, why is the research being funded by a federal funding source), they need to summarize the current state of the research field, and address the major professors, or their lab's contribution to the state of the research field. c) References are listed using standard methods for referencing (author, year, title, journal, volume, page number) in a consistent manner. References should be cited throughout the text.
Length of assignment:
4
Instructor/peers
10
Instructor
14

Primary literature reviews (12)
Primary literature reviews (twelve summaries covering primary literature assigned relevant to the topics covered in the course) Length of the reviews: 2 pages (x12=24) The objectives of the primary literature reviews are to get students acquainted with reading and comprehending scientific primary literature. Furthermore, students are required to extract specific protocol information out of the literature to learn new ways to perform and utilize the techniques presented in the laboratory portion of the course. Students will be required to think about how the techniques we used in the lab relate to how the technique is used in current primary literature to demonstrate understanding of the potential applications of the techniques. The primary literature reviews will be composed in an essay format in which the first half of the paper is dedicated to summarizing the work presented in the article chosen to review. The second part of these reviews will outline and highlight the technique that corresponds to the laboratory skills presented that week.
Length of assignment:
24
Instructor
 
 
24

Total pages for all assignments:
First drafts:
44.00
Revisions:
10.00
54.00
Regarding revision and individual writing assessment for groups, I have one major writing assignment that goes through the revision process, a group term paper 3-6 pages, but it goes through the peer review process as well as through a review from me followed by a meeting with the students to discuss the content of the work for revision. NOTE: For this group paper, which is part of the normal 2484 curriculum, the paper is peer reviewed in a group, and then I spend about 20 minutes with each group going over what needs to be improved, and what was done well. The students have to revise and edit their papers as a group. For the grading, I get as close to individual grading as realistically possible, since this is also an assignment that allows for students to learn "real world" group work. The final report is out of 100 points. I assign 80 of those points, and the students give each other the remaining 20 points so there is a mechanism to give full credit to those who participate in the group and to allow for a lesser grade for those that decided that the group work is not important. Also, and specifically for this 2484 Honors section of my course, I require all students to give a full 50-minute presentation on one of the primary literature papers covered in the class. This generally involves between 30 and 40 slides in PowerPoint. I assign students to prepare and give their presentation to me individually one week before presenting to the class, and then I spend about an hour going over what they presented well, what they need to work on, and specifically what they need to change in their slides for a better and more effective presentation. I also give tips to the students on how to bring their classmates into a discussion on the literature they are reading. My time spent with the students individually is about 2 hours for each student in the honors section, with about 12 slides of the presentation needing some form of revision. Out of 40 slides, students revise what can (conservatively) amount to 14-15 pages of writing. They reflect, rethink, and rewrite according to the principles of productive revising. To reiterate and clarify further: For this 50-minute presentation, the students have to revise and edit their presentation with peers as well as sit down with me to talk about their presentation prior to giving it to the class. I was not sure where to put this into the application or if it was relevant, but I think that this type of discussion between me and the group presenters is in the spirit of what constitutes writing intensive revision, as it is significant. The students will usually spend more than four hours making revisions to their presentation prior to giving them to the class. Spending that amount of time discussing and incorporating revision in a presentation relates closely to the "re-thinking" of a message related to audience and purpose in writing.

Writing Intensive Teaching

Instructor provided feedback
Oral presentation by student, followed by feedback
Peer review
 
Group work is assessed in one paper distributed to the entire non-honors sections as well. All members of each group are required to submit grades for their peers and themselves for 15% of the total grade. All group grades were averaged for each individual for the final total of 15% of the final grade.
The students are expected to collect, analyze and provide reasonable interpretations of their data. Considering that students of this class may be novice in performing experiments and data collection, collected data may vary between students. Because data interpretation is directly linked to collected results, final interpretation may differ from one student to another. Furthermore, it is not uncommon that data interpretation varies from one researcher to another. Thus, there is often more than one acceptable interpretation of an experiment, meaning that there is no correct or incorrect answer.
Writing assignments will be evenly distributed throughout the semester in that all weeks of the class, students will compose and hand in some form of writing assignment. The experimental laboratory reports will be due two weeks after the completion of the labs the students will be reporting on to allow adequate time to process the data and interpret the results. The group term paper will be due six weeks into the semester, peer-reviewed the following week, and then edited over the next four weeks before the final paper is due. In addition, students are expected to maintain their informal laboratory notebook on a weekly basis before and during laboratory class periods. Finally, primary literature summaries are due on the day the papers are covered in the discussion section of the course.
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0
 

Course Syllabus

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Administrative Information

Natural and Applied Sciences
 
 

Acknowledgement

I have read and reviewed the updated proposal

Additional Comments

The PLAs associated with this course will be junior or senior Biochemistry undergraduate students who have taken the course previously and earned at least a B. They will have a strong background in Biochemistry and, or Chemistry and will have expertise in the majority of the biochemical experimental procedures performed in this lab class. The PLAs are expected to pre-run all experiments and to make sure that all equipment and necessary reagents are available and set-up prior to each lab class period. In addition, the PLAs are expected to familiarize themselves with the experimental protocols and the theory behind the individual experiments, so that they will be able to answer relevant questions from the students. To gain valuable teaching experience, each PLA will be responsible for one lab section, in that the PLA will give one lecture and lead the accompanying lab experiments. The PLAs and the instructor will work closely together and will meet once or twice a week outside of the classroom for discussions regarding teaching the class and grading assignments. The instructor will make sure that any questions or problems will be addressed as soon as possible. To broaden the PLAs grading skills, the PLAs will assist with critiquing the lab notebooks for clarity and content before and during the laboratory periods. To ensure consistency in grading, the instructor will provide comprehensive rubrics outlining expectations in detail to the PLAs. The instructor and the PLAs will then discuss these rubrics and expectations prior to and if necessary, during grading assignments. Overall, the instructor will be responsible for overseeing the uniformity of grading on all writing assigned in the course.
Patricia Luckenotte (luckenottep) (Mon, 30 Jan 2017 18:15:30 GMT): I have added BIOCHM 2484HW, 01 with DIS 01AA and labs 01B-01G to the Fall 2017 Schedule of classes and cancelled the BIOCHM 2484H sections. The new sections of BIOCHM 2484HW are combined with the Non-Honors/WI sections of BIOCHM 2484.
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