Expectations

Course Goals and Objectives

BIOC 413 further advances record keeping and technical communication skills that were emphasized in BIOC 311: Experimental Biosciences. You will apply strategies in molecular biology to investigate gene expression and function in Arabidopsis, with an emphasis on experimental design, data analysis, and data interpretation. You will gain experience in preparation of a scientific poster. Overall goals and specific objectives for the course are outlined below.

Goal 1: Perform basic laboratory skills in an efficient manner to obtain reasonable results

Understanding the rationale behind procedures and asking questions that reflect a willingness to learn promote effective time management and successful completion of experiments. Our best students are always the ones who are engaged in the learning process. An engaged student

carries out common laboratory procedures efficiently and correctly
performs logical troubleshooting of laboratory procedures
adheres to instructions on laboratory safety, and recognizes hazardous situations and acts appropriately
uses and stores equipment properly
handles lab reagents and solutions sensibly
performs basic lab calculations to prepare solutions and samples for experiments
measures and reports uncertain quantities with appropriate precision
applies appropriate methods of analysis to raw data
converts raw data to a physically meaningful form with appropriate units

Goal 2: Understand the importance of effective communication and of detailed and accurate record keeping

Communication and record keeping are fundamental to the dissemination of science. A student who is an effective communicator

maintains a timely, comprehensive laboratory notebook with sufficient detail to repeat experiments, troubleshoot procedures, and analyze data
communicates effectively orally
writes effectively in appropriate style and depth
makes effective use of library and other information resources

Goal 3: Recognize the necessity of maturity and responsibility when working in a professional environment

In addition to working independently, on one's own initiative, each student is expected to work well with the other team members. A mature and responsible student

adequately prepares in advance for laboratory work
works independently but seeks help when appropriate
divides lab responsibilities with teammates to complete work in a timely manner
learns from mistakes as well as successes and is open to suggestions from teammates, TAs, or the instructor
recalls routine procedures without having to consult a teammate, TA, or instructor
takes the initiative to refresh past understanding of methods, procedures, explanations, and theory
shares specific observations and experiences with the rest of the team
when necessary, picks up responsibilities of other team members who are unable to carry them out

Goal 4: Recognize appropriate context

Paying attention to detail is important not only in performing experimental procedures but also in reporting the results to the scientific community and the general public. A meticulous and focused student

recognizes the relevance of data
relates laboratory work to the bigger picture
recognizes the applicability of scientific principles to real world situations
considers how seemingly minor oversights or mistakes can have serious consequences

Goal 5: Integrate and apply knowledge/experience to current and future work

On the path to become a self-reliant critical thinker, problem solver, and communicator, a student progresses through several proficiency levels. A highly proficient student recognizes when the current skill level is not adequate to handle a particularly complex problem, and EFFECTIVELY seeks resources to acquire the needed skill. A student's present level of achievement and success is a reflection of past experiences and opportunities that have been made available as well as self-confidence. A successful student

retains facts, methods, and principles learned in science and math courses and applies that information to another course, even in a different discipline
uses critical thinking in the laboratory by making observations, drawing conclusions, and acting upon those conclusions
recognizes whether results and conclusions "make sense"
figures out what "tools" to use when presented with a particular problem or task

Thus, I expect you not only to retain and use what you learned in other BIOC laboratory courses, but also to build on that foundation and achieve higher competencies. Here are some examples of how we are "raising the bar:"

The experimental procedures are often less demanding than those you performed in BIOC 311; HOWEVER, just because the experiments may be more "cookbook" does not mean the lab requires less effort. We place a greater emphasis on analysis, interpretation, and presentation of data; if you keep a "sloppy" notebook and slap a poster together at the last minute without really understanding "why" you did a procedure and "what" the results mean, you will be disappointed with your final grade.
The team lab notebook will be graded ONCE, after lab has ended; team members record their individual activities and observations and initial all entries. You are responsible for maintaining a research quality notebook that follows the guidelines we have given you.
We will use the BIOC 413 Notebook Checklist to grade your lab notebook.
We intend to use the overall quality of the laboratory notebook and your specific notebook entries to evaluate your individual effort.
You and your partner(s) will prepare a Scientific Poster that is 50% of your final grade; you do not submit a "rough draft" of the poster for instructor feedback before submitting the FINAL poster. The poster is a TEAM project, and each member will receive the SAME grade.
You must work as part of a TEAM as well as function INDEPENDENTLY.

Special note on our roles as your teachers: Our job is to guide your learning. Guidance means we help you find ways to get the answers. We encourage you to ask us questions during lecture and during the lab - sometimes we may not answer the question directly or give you all of the answer (and sometimes we may not know "the answer"). Our goal with this approach is to help you develop your ability to obtain and use information; simply giving you the information does not accomplish that goal.

Research Project Overview

Several techniques in molecular biology will be used to gain insight into the roles of specific genes in Arabidopsis thaliana:

You will isolate total RNA from Arabidopsis and use reverse transcripatase to generate cDNA
You will perform qPCR to measure level of gene expression in Arabidopsis
You will localize gene expression patterns by detection of beta-glucuronidase activity in transgenic plants.

This lab course requires greater independence than BIOC 311 and BIOC 313. You are expected to analyze, interpret, and present your work as a TEAM for the scientific poster. We assess your abilities to apply knowledge you've gained in other laboratory and lecture courses to the presentation and communication of a real research project. The poster is a TEAM project, and each member will receive the SAME grade. Therefore, EACH of you is responsible for the ENTIRE poster, not just the part(s) you worked on. Furthermore, you are expected to understand the rationale behind all of the experimental procedures and the meaning of the results. We will use the Poster Evaluation Form to score your poster.

Preparation

Requirements: PRE-requisite = BIOC 311: Advanced Experimental Biosciences
***You will need the following items for the FIRST day of lab:***
1. Lab notebook (ONE PER TEAM): Hayden-McNeil, Chemistry Top 100-set, ISBN 978-1-930882-00-9 OR Chemistry Top 50-set, ISBN 978-1-930882-50-5 (www.labnotebooks.net)
2. Extra Fine Sharpie
3. Ball Point Pen
This course is intended to allow you to apply your understanding of the material by participating in the design of the experiment. The procedures for experiments are not always "cookbook" and in some instances serve only as a guide to explain what is to be accomplished. You must understand the objectives of the experiments and the theory of the procedures to make rational decisions to meet the experimental goals.
You must come to lab prepared--this requires you to READ the experimental protocols on the course web site as well as additional background resources BEFORE coming to lab, not just print a copy and bring it with you. Bring only the information you need to perform the experiments. The procedures for each day are available from the Course Schedule page and supplemental materials are in Resources in OWL-Space; you will be given any additional information in the pre-lab lectures.
Interdisciplinary Web-based Teaching Laboratory Materials pages were developed so that you can continuously advance your skills as you progress throughout your undergraduate career, even as you take courses from different departments. We hope to eliminate inconsistencies, to reinforce universal truths, and to impress upon you the interdisciplinary nature of science and engineering.

Examples of reference materials (pdf format) include dimensions and units, graphing, and error analysis and significant figures.
SPECIAL NOTE: Digital image acquisition and processing tools make manipulation and idealization of raw images an easy task.
- A recent editorial in Nature, Not picture-perfect, addresses these concerns. The Nature family of journals has developed a guide for digital images, which will be incorporated into Guides for Authors.
  ***Please read the introductory and electrophorectic gels and blots sections in the Guide for digital images.***
- Also, read What's in a picture? The temptation of image manipulation published in The Journal of Cell Biology (JCB); additionally, see the JCB Instructions to Authors for image acquisition and manipulation.

Program Goals and Objectives

Despite the unique character of each discipline and corresponding academic department, we share a common set of teaching goals. Employers and admissions committees are looking for candidates who are critical thinkers, cooperative team players, and excellent problem solvers. Many of these attributes are developed in our laboratory courses in Natural Sciences and Engineering.
Five major learning objectives in the laboratory courses contribute to development of these attributes. Review the laboratory teaching/learning objectives and performance standards. These are the real goals of our program, which transcend all majors, departments, and individual courses, regardless of content.
Our Lab Proficiency Scale was developed to promote self-evaluation of competency in key areas: obtaining and analyzing data, communicating information and ideas, establishing context, integrating and applying knowledge, and maintaining productive work habits and relationships. We've developed surveys (Pre Lab Self Evaluation of Professional Laboratory Skills and Post Lab Self Evaluation of Professional Laboratory Skills) to help us improve our laboratory curriculum.
The undergraduate program is a series of steps. Keep in mind that a level of performance that would result in a B/B+ or sometimes even an A at the introductory level, does not (and should not) translate into a high grade at the advanced level. We forgive a lot of mistakes early on but you must recall the lessons learned from these mistakes when you conduct similar work at an advanced level. Additionally, the criteria we use to evaluate your performance in an advanced laboratory course are different from those we use in an introductory course.

Copyright, Acknowledgements, and Intended Use
Created by B. Beason (bbeason@rice.edu), Rice University, 16 June 2006
Updated 29 December 2011