three bacterial morphology types: coccus, rod, and spirillum  YSU logo  conidiophores of Talaromyces marneffei, a pathogenic fungus

© 2020 Chester R. Cooper, Jr.


BIOL 3702H Syllabus and Laboratory Schedule

(September 5, 2021)

BIOL 3702H Laboratory Syllabus

Course Purpose

This honors laboratory section, designated BIOL 3702H, was established to provide an enriched educational experience for students enrolled in BIOL 3702H than is provided in the more traditional laboratory component (BIOL 3702L).  BIOL 3702H is a limited- and selective-enrollment laboratory requiring students participate in time- and effort-intensive activities.  Active participants shall gain an extraordinary learning experience through the exposure to “real life” microbiological applications. 

BIOL 3702H is targeted towards those students wishing to pursue (or consider) a research-oriented career in the microbiological sciences or a related field.  BIOL 3702H is not intended for those students whose sole career aim is the practice of medicine or related health profession.  The latter type of students would be better served by the traditional laboratory section, BIOL 3702L.  Student participants in BIOL 3702H are selected by Dr. Cooper for enrollment prior to the start of the semester through an application process.  Only Dr. Cooper’s approval suffices for  student enrollment in this course.

Course Design

BIOL 3702H substitutes for the traditional section of BIOL 3702L.  All activities would fulfill the same learning objectives/outcomes as BIOL 3702L as well as extend them to meet the stated nature of an honors course (  By comparison, instead of a focus on a various laboratory activities, the BIOL 3702H experience centers on the application of various microbiological skills to study fecal bacteria from selected water sources. 

General Overview of Course Content

In brief, students enrolled in BIOL 3702H shall be trained in the essential foundational techniques in the manipulation of microbes (  This training would replicate that received by students in BIOL 3702L, albeit over a shorter time frame.  Subsequently, students enrolled in BIOL 3702H would work in groups throughout the remainder of the semester to i) develop a hypothesis regarding fecal contamination of selected water samples; ii) over an established time course, regularly collect these water samples; iii) employ standard microbiological methods to assess the level of fecal contamination in these samples; iv) use biochemical and molecular methods to identify and characterize selected types of fecal bacteria with regard to their potential pathogenicity (disease-causing ability), v) critically analyze the study results with regard to the original experimental hypothesis, and vi) present the experimental findings in writing and in a public forum.  Collectively, these activities represent an expansion as well as the “real-time” application of the fundamental technical and critical skills learned by students enrolled in BIOL 3702L (a non-honors section).

Laboratory Learning Objectives

The laboratory experiences in BIOL 3702H were developed in accord with the recommended curriculum guidelines established by the American Society for Microbiology (  

Throughout the semester in BIOL 3702H, students will be taught to:

  • Utilize aseptic techniques in the safe handling of microbes and to avoid culture contamination;
  • Properly and appropriately employ scientific equipment and methods;
  • Isolate pure cultures using selective media and the streak-plate method;
  • Identify cell morphology and arrangement by microscopy and simple staining;
  • Differentiate bacterial species using specific staining techniques (e.g., Gram stain);
  • Determine physiological differences among bacteria using biochemical assays;
  • Enumerate microbes by serial dilution and viable plate counts;
  • Assess the effects of physical and chemical agents on microbial growth;
  • Evaluate microbial susceptibility and resistance to antibiotics;
  • Isolate and identify fecal bacteria in water using the membrane filter technique;
  • Participate in scientific research and take on significant responsibility for their education in the topic area.

·       Apply current technological approaches in pursuit of microbiological inquiry;

  • Understand important facts, concepts, and the investigative procedures of a microbiology laboratory;

·       Identify higher-level microbiological concepts requiring critical analyses of methodology and results;

·       Develop better, more accurate written and oral communication skills; and

  • Communicate scientific concepts, experimental results, and analytical arguments clearly and concisely to peers and to the public.

Laboratory Learning Outcomes

Knowledge and skill competencies in BIOL 3702H shall be evaluated through written reports, technical demonstrations, online exercises, a final project report, and a public presentation of the research results.  In addition, a student’s collegiality, leadership, and professional demeanor shall be observed subjectively. 

A student who successfully completes BIOL 3702H shall demonstrate the following microbiological technical skills:

·      Practice safe microbiology, using appropriate protective and emergency procedures;

·      Demonstrate correct techniques for the isolation, subculture, and maintenance of microorganisms;

·      Prepare properly-stained specimens for examination using bright-field microscopy;

·      Perform pure culture and selective techniques to enrich for and isolate microorganisms;

·      Employ appropriate methods to identify microorganisms (e.g., media-, biochemical-, molecular- and serologically-based);

·      Estimate the number of microorganisms in a sample using, for example, viable plate counts and spectrophotometric methods; and

·      Effectively and safely operate microbiological and molecular biological equipment to derive data for subsequent critical analysis.

A student who successfully completes BIOL 3702H shall demonstrate the following critical thinking and communication skills:

·      Synthesize a defined hypothesis

·      Apply scientific principles to design effective experimental protocols and controls testing the formulated hypothesis;

·      Collect and organize experimental data generated using traditional and modern technologies;

·      Document and report on experimental protocols, results, and conclusions.

·      Apply the process of science to analyze and interpret results from a variety of microbiological methods;

·      Use quantitative reasoning and graphing skills to solve problems in microbiology;

·      Postulate the impact of the study’s findings upon the field and the community;

·      Articulate findings to mentors and research peers as well as the general public; and

·      Actively develop collegial and effective working relationships with peers.

Laboratory Section

BIOL 3702H students will be granted access to Dr. Cooper’s secured laboratory (Ward Beecher Science Hall, Room 3124) for purposes of conducting their experimental work.  All student activities will take place in this location and in the adjacent conference room. 


The laboratory complex, in which Dr. Cooper’s research laboratory is located, is a secured area.  Persons wishing to enter the area must have an access code.  Students enrolled in BIOL 3702H shall be given access codes for both the laboratory complex/Dr. Cooper’s laboratory and Ward Beecher Science Hall.  The latter is for those times when students need to return to the laboratory after the building is closed.

Students must never i) give their access code to anyone or ii) allow non-authorized persons to enter the laboratory complex.  Violations of this directive shall be considered violations of The Code of Conduct and subject the student to expulsion from BIOL 3702H.

Based upon the collective schedules of the participants, a common time for all students to meet weekly with Dr. Cooper will be established.  This time will be used to make and review assignments as well as to discuss results and any difficulties encountered.

Because the fluid nature of studying a “real-time” biological system cannot be constrained to a particular time frame, no standard meeting time for laboratory work shall be established.  Moreover, additional hours of student participation shall be required, possibly at times outside “normal work hours”.  Dr. Cooper will make specific provisions for being present for instructional/advising activities.

Course Materials

Laboratory Manual.  There is no required laboratory manual for BIOL 3702H, although portions of a FREE on-line laboratory manual for students enrolled in BIOL 3702L will be used for some laboratory experiences.  The online BIOL 3702L manual can be viewed at the following URL:

Please refer to this site often.  It contains a number of downloadable laboratory exercises, supporting videos, documents, etc., that shall make this an outstanding laboratory experience.  Any corrections, suggestions, etc., are welcome.  Please send any items to Dr. Cooper via email at

CONNECT Subscription: This required lecture subscription of this learning management platform shall also be used in BIOL 3702H primarily to post documents in the “Files” section.

Protocols/Background Materials.  All protocols and background reading materials, shall be provided by Dr. Cooper.  Many of these shall be made available as downloadable documents.

Weekly Laboratory Reports.  A Weekly Research Progress Report is required (available through the highlighted link).  This report must be submitted each Monday by noon during the semester and shall briefly summarize a student’s progress for the prior week.

Group Notebook.  A research notebook shall be provided to each working group.  Guidelines on how to keep/manage the notebook shall be provided by Dr. Cooper.  The notebook shall be subject to periodic review by Dr. Cooper and must be submitted to him at the end of the course.

Other Required Materials.  The items listed below are also required.

·      Laboratory coat/smock.  This item does not have to be an “official” lab coat.  It can be any garment (e.g., old sweatshirt) that shall protect an individual from common laboratory hazards (e.g., stains, spills, etc.) and which can be disposed.

·      Protective eyewear.  The University’s safety program requires that safety glasses be worn when working in a laboratory (  Regular glasses will not suffice as a substitute.  Neither will the “side shields” for normal eyewear qualify as sufficient eye protection.  Students must obtain approved protective eyewear to be worn at in the laboratory.

Lab Fee.  There is a fee for BIOL 3702H which helps defray the costs of materials.  The fee is included in a student’s semester charges billed by the University.


Attendance Expectations.  Attendance of laboratory meetings of the entire class is absolutely required.  Exceptions are detailed in the “Excused Absence” Policy section of the Lecture Syllabus.  NOTE: Vacations are not defined as an excused absence even if plans were made prior to enrolling in BIOL 3702H/3702H!

Tardiness for Laboratory.  Tardiness is not excusable except for extenuating circumstances.  What is deemed excusable is entirely at Dr. Cooper’s discretion.  Chronic tardiness is not acceptable. 

Group Activities.  As a member of a research team, a student is expected to keep a commitment to actively participate in taking responsibility for their share of the work.  Chronic absence/tardiness or shirking of responsibilities will figure prominently in a student’s overall score for BIOL 3702H. 

Laboratory Decorum

At all times, students are expected to exhibit appropriate behavior.  Such behavior is delimited by University policy (see The Code for one of many resources in this regard).

Proper decorum in the laboratory shall include, but is not be limited to, the following:

·      Appropriate dress is REQUIRED.  Students are expected to wear clothing that would be appropriate for working in a professional laboratory environment.

·      Following all safety rules is REQUIRED.

·      Disturbing (e.g., moving, using, destroying, etc.) the materials of others is PROHIBITED.  If done intentionally, this is grounds for removal from the course and possible other charges.

·      The use of electronic items (e.g., cell phones) is absolutely PROHIBITED.

·      Collegiality and acting in a considerate manner are EXPECTED.  Students are expected to interact with one another in accord with the “Golden Rule” – that is, the principle of treating others as one would wish to be treated.

Laboratory Schedule

This schedule presents all the activities that shall be attempted this semester.  Due to unforeseen circumstances, this schedule and its associated documents may be amended at any time during the semester to meet the course objectives or difficulties encountered with materials.

At the beginning go the semester, some activities shall be performed by individual students, whereas the remainder of the semester shall involve group work.  Dr. Cooper will assign individuals to different groups.  When working in groups, each individual is expected to be actively engaged in the laboratory activity being performed and to participate in a collegial manner.  Dr. Cooper will subjectively evaluate an individual’s in-group behavior which becomes part of Laboratory Etiquette/Citizenship score (see below).

Open Laboratory Sessions

BIOL 3702H students shall be required to regularly return to the laboratory to continue experimental work.  As such, students will be working semi-independently, i.e., there may not be direct supervision by Dr. Cooper, although he will make specific provisions for being present for instructional/advising activities.  If Dr. Cooper is not present in the laboratory, students must exercise caution at all times and follow all safety rules (see Laboratory Safety Rules below). 

Safety Note: If an incident occurs during an open laboratory period and Dr. Cooper is not present, report it immediately to the Biology Office (330.941.3601; Ward Beecher Science Hall, Room 4037).  In extreme cases during normal business hours, contact Mr. Tim Styranek (330.599.9095; or the Office of Environmental and Occupational Health and Safety (330-941-3700;  After hours, contact the YSU Police by dialing 911 on any campus phone.

Laboratory Grade Components

Like the traditional laboratory section, BIOL 3702H is worth 20% of the overall BIOL 3702H course grade.  The grade components for BIOL 3702H are listed below.  The collective score of these components shall be normalized (i.e., proportionally converted) to represent 20% of the overall BIOL 3702H course grade.

A student’s mastery of BIOL 3702H will be evaluated using the following components:

·      Laboratory Safety: 10%

Students shall be expected to actively follow all safety rules and procedures throughout the semester.  Dr. Cooper will note any deficiencies in this area on an individual’s weekly report (see below). 

Early in the semester, a student must pass a safety quiz with a score of at least 80% before being permitted to participate in the laboratory.  In addition, students must successfully complete an online safety course (  The registration details of this course will be provided by Dr. Cooper.

·      Attendance/Effort: 25%

A student’s active participation and presence in the laboratory shall be monitored by several means, including attendance of class meetings and weekly reports (see below).  It is expected that students put forth more than a minimal effort to accomplish the goals of their assigned project.  It is anticipated that a student shall commit to actively participating in the laboratory for a minimum of 10 hours per week.  Dr. Cooper will note any deficiencies in this area on an individual’s weekly report (see below).

·      Weekly Reports/Group Notebook: 25%

Students shall be required to submit individual reports on a weekly basis regarding their activities for the week, results obtained, areas needing attention, and a brief synopsis of next steps.  Dr. Cooper will note any deficiencies on this report and return it to the student.

In addition, groups working together on a particular project shall maintain an up-to-date and detailed laboratory notebook.  The notebook is subject to periodic inspection by Dr. Cooper.

·      Laboratory Etiquette/Citizenship: 10%

Students shall work collaboratively and collegially with all persons in the laboratory, abide by all safety considerations, perform their respective share of routine laboratory tasks, and maintain an orderly and clean laboratory environment.  Dr. Cooper will note any deficiencies in this area on an individual’s weekly report (see above).

·      Semester Report: 25%

A group of students assigned to a particular project shall prepare a scientific report that details the group’s methods, results, and conclusions.  The specific parameters for the preparation and grading of this report shall be provided by Dr. Cooper. 

·      Public Presentation:

Normally, a group of students assigned to a particular project shall present their work in a public forum (e.g., biology seminar, QUEST, etc.).  Depending upon the type of presentation, this may require with a PowerPoint or poster presentation that details the group’s methods, results, and conclusions.  The specific type of presentation and the parameters for its preparation and grading shall be provided by Dr. Cooper.  However, for the Fall 2021 semester, this requirement shall not be implemented.

Laboratory Grading Scale

There is no actual letter grade given with BIOL 3702H.  On a student’s transcript, the letters ‘NG’ (meaning No Grade) shall appear.  Do not take this as a negative; this means the laboratory is an integral part of the overall grade for the parent course, in this case BIOL 3702H.

As per the overall course grading policy detailed in the Lecture Syllabus, the following policy for BIOL 3702L is also in force for BIOL 3702H:

·      Students who earn the equivalent of a “C” grade in the laboratory section of this course shall not be eligible for a final course grade of “A”.

·      Students who earn the equivalent of a “D” grade in the laboratory section of this course shall not be eligible for a final course grade of “B” or better.

·      Students who earn the equivalent of an “F” grade in the laboratory section of this course shall not be eligible for a final course grade of “C” or better.

Therefore, the “letter grade” for BIOL 3702H shall be determined as follows:

·      Students shall receive a grade of “A” by achieving an assessment score of 90% or better.

·      Students shall receive a grade of “B” by achieving an assessment score of 80% to 89%.

·      Students shall receive a grade of “C” by achieving an assessment score of 70% to 79%.

·      Students shall receive a grade of “D” by achieving an assessment score of 60% to 69%.

·      Students shall receive a grade of “F” by achieving an assessment score of less than 69%.

Potential Health Risks

The possibility of acquiring an infection from BIOL 3702H activities is extremely low.  Yet, that does not mean the risk of infection is non-existent.  Infections could occur under non-standard and/or inappropriate practices as well as to persons having particular underlying health conditions.  Also, some exercises will expose students to unknown environmental isolates, which must be handled with care.  Moreover, though the risk of physical injury is low, careless behavior by students can lead to cuts and burns, thereby possibly serving as sites for infection.

It is incumbent upon all students to follow all safety precautions (see Laboratory Safety Rules below).  The risk of infection or injury rises when these precautions are not followed – not just to the particular student not following safety rules, but also that student’s peers in the laboratory.

SPECIAL NOTE TO STUDENTS WITH KNOWN HEALTH CONDITIONS: If a student has a documented health condition that may make that person susceptible to infection (e.g., immune dysfunction, pregnancy, etc.), please PRIVATELY contact Dr. Cooper so that arrangements may be made to limit exposure to particular microbes.

Laboratory Safety Rules

General Information.  The BIOL 3702L web page details important safety rules and waste disposal guidelines that must be followed by all BIOL 3702H students (  Read these rules carefully.  They will be reviewed at the first laboratory meeting and students must successfully pass the quiz that will be administered covering these rules.  In addition, students enrolled in BIOL 3702H will be provided a tour of the laboratory and informed of the various safety procedures.  Information from this tour shall also be included on the safety quiz.

Laboratory Waiver.  After having read and understood the Laboratory Safety Rules, please read the Liability Waiver available via CONNECT.  Failure to submit this waiver shall prohibit a student’s participation in any laboratory activities. 

Laboratory Materials.  No one, regardless of enrollment in BIOL 3702H, may EVER remove ANY materials from the laboratory without the EXPLICIT permission of Dr. Cooper.  Doing so shall be the basis for disciplinary action.

BIOL 3702H Laboratory Schedule

Weekly Report

The Weekly Research Progress Report is a fillable PDF.  Students need to submit a completed report each Monday no later than 12:00 PM (noon).  The form should be downloaded and the various areas filled using Adobe Acrobat.  The student should then save the file using the following format for the title: “Last Name”-3702H-report-numerical date”.  For example, a weekly report submitted on August 1st by Dr. Cooper should have the title Cooper-3702H-report-080120.  The student should then send this file to Dr. Cooper via email being sure to use the Subject Line of BIOL 3702H Lab Report.




Week of Aug. 30

No Activity This Week

Week of Sep. 6

General Lab Personnel Meeting

Week of Sep. 13

Introduction to BIOL 3702H

Microbiology Safety Rules

The Bright-Field Microscope: Its Proper Use and Care

Week of Sep. 20

Safety Quiz (via CONNECT)

Microscopy Proficiency - Skills Test I

Basic Culture Technique: Aseptic Transfer

Preparation of media (Protocol To Be Distributed)

Week of Sep. 27

Streak Plate Proficiency - Skills Test II

Differential Staining – The Gram Stain

Overview of semester project (Protocol To Be Distributed)

Week of Oct. 4

Gram Stain Unknown - Skills Test III

Collect and process waste water sample (Sample 1)

Membrane Filter Isolation of Enterococcus (Protocol To Be Distributed)

Week of Oct. 11

Biochemical characterization of fecal bacteria from Sample 1

Hydrolysis of Esculin and L-Pyroglutamic Acid-b-Naphthylamide

Temperature and Salt Tolerance

Week of Oct. 18

Molecular characterization of fecal bacteria from Sample 1

PCR Characterization of Enterococcus (Protocol To Be Distributed)

Week of Oct. 25

Continue characterization of Sample 1 isolates

Week of Nov. 1

Collect and process waste water sample (Sample 2)

Week of Nov. 8

Collect and process waste water sample (Sample 2)

Week of Nov.15

Continue characterization of Sample 2 isolates

Begin to prepare semester report (Instructions To Be Distributed)

Week of Nov.22

Continue characterization of Sample 2 isolates

Continue to prepare semester report

Week of Nov. 29

Continue laboratory work (if needed)

Continue to prepare semester report

Week of Dec. 6

Submit semester report


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Youngstown State University does not discriminate on the basis of race, color, national origin, sex, sexual orientation, gender identity and/or expression, disability, age, religion or veteran/military status in its programs or activities. Please visit the EIT Home Page for contact information for persons designated to handle questions about this policy.

It is possible that portions of this web page are not wholly in accord with the American with Disabilities Act.  If this is the case, a student currently enrolled in this course should contact Dr. Cooper (; 330.941.1361) and compliant material shall be provided as soon as practical.

© 2021 Chester R. Cooper, Jr.