CaInitially Posted: January 1, 2009
April 22, 2009
Copyright © 2009 Chester R. Cooper, Jr.

BIOL 6988: Seminar in Biological Sciences

Spring 2009 Semester
, CRN 20343
[Fall Semester Seminar Web Page]

Course Instructor:
Dr. Chet Cooper, Professor, Department of Biological Sciences

Friday, 1:00 PM - 1:50 PM

Location: Ward Beecher Science Hall, Room 4043
(Note: Some seminars will be presented at other locations than WBSH 4043.  Please check the course schedule for specific locations, especially presentations given by non-YSU faculty.)
fungus     butterfly     yest
Dr. Cooper's Office Hours:
(Ward Beecher Science Hall, Room 3016)

Monday, Wednesday, and Friday
8:00 AM - 10:00 AM
(subject to change/cancellation due to unforeseen circumstances)
Dr. Cooper's Contact Information:

Telephone/Voice Mail, 330.941.1361

NOTE! January 8, 2009: An addition to this syllabus may be forthcoming.  An e-portfolio project may be appended to student requirements.  Information regarding this possibility will be provided at a later date.

Quick Links to Weekly Seminars
(The names of seminar speakers are listed below the corresponding date/link.  Those names in orange letters are invited speakers.  Names in yellow letters are graduate students.  TBA, speaker to be announced.)

Jan. 16th Jan. 23rd Jan. 30th


Introduction Catterlin

Feb. 6th Feb. 13th Feb. 20th Feb. 27th

Gacura J. Mager Simmons P. Coschigano

Mar. 6th Mar. 13th Mar. 20th Mar. 27th


Pfeill G. Salama

Apr. 3rd
Apr. 10th
Apr. 17th
Apr. 24th
May 1st

Davidson/Nelson J. Yun Sood/Moparthi
K. Coschigano
N. Money

Seminar/Course Schedule
(subject to change/cancellation; please check back periodically for up-to-date schedule)

January 16th

Introduction to Course

Class Cancelled: University Closed Due To Severe Weather

January 23rd

Introduction to Course

January 30th

Graduate Student Presentation:  Mr. Richard Catterlin


Composition of Canyon-Slope Woodlands in Zoar Valley,
Western New York,
as Associated with Slope Orientation and Elevation

Topic-Related Article(s):
  • E. K. Pfeil et al.  2007.  Distribution, composition, and orientation of down deadwood in riparian old-growth woodlands of Zoar Valley Canyon, western New York State, USA. Forest Ecol Mgmt. 239: 159-168. [OhioLink]
  • T. P. Diggins and B. Kershner.  2005.  Canopy and understory conposition of old-growth riparian forest in Zoar Valley, New York, USA.  Nat Areas J 25: 219-227.  [PDF]

February 6th

Graduate Student Presentation:  Mr. Matt Gacura


The Impact of Nitrogen and Cyclodextrine on  the Bioremediation
of Mahoning River Sediment by Pleurotus ostreatus

Topic-Related Article(s):
  • D. Garon et al. 2004. Effects of fungal bioaugmentation and cyclodextrin amendment on  fluorene degradation in soil slurry. Biodegrad 15: 1-8. [OhioLink]
  • T. Eggen and P. Sveum. 1999. Decontamination of aged creosote polluted soil: the influence of  temperature, white rot fungus Pleurotus ostreatus, and pre-treatment. Internat Biodeter Biodegrad 43: 125-133. [OhioLink]

February 13th

Invited Speaker:  Dr. Jay Mager
Assistant Professor

Department of Biological & Allied Health Sciences
Ohio Northern University, Ada, Ohio

Location: Gallery Room, Kilcawley Center

Title: Lessons in Loon Music: Deciphering
the Language of the Common Loon

Ohio Northern University's

Web Page

Topic-Related Article(s):
  • J. N. Mager et al.  2007.  Male common loons, Gavia immer, communicate body territorial yodels. Animal Behav 73: 683–690.  [OhioLink]
  • C. Walcott et al.  2006.  Changing territories, changing tunes: male loons, Gavia immer, change their vocalizations when they change territories.  Animal Behav 71: 673–683.   [OhioLink]
  • J. N. Mager and C. Walcott   2007.  Structural and contextual characteristics of territorial “yodels” given by male common loons (Gavia immer) in Northern Wisconsin.  Pass Pigeon  69: 327-338.  [PDF]

February 20th

Invited Speaker:  Dr. Mark Simmons, Professor
Department of Integrative Medical Sciences, Northeastern Ohio Universities College of  Medicine and Pharmacy, Rootstown, Ohio

Location: Jones Room, Kilcawley Center

Title: Localization and function of the tachykinin
NK3  receptor: a therapeutic target for
schizophrenia and addiction

Dr. Simmon's
Web Page

Topic-Related Article(s):
  • M. A. Simmons et al.  2008.  Localization and function of NK3 subtype tachykinin receptors of layer V pyramidal neuorns of hte guinea-pig medial prefrontal cortex.  Neurosci 156: 987-994.  DOWNLOAD PDF

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February 27th

Invited Speaker:  Dr. Peter Coschigano
Associate Professor

Department of Biomedical Sciences, Ohio University College of Osteopathic Medicine, Athens, Ohio

NOTE!   Location: Bresnahan Rooms, Kilcawley Center

Title: Molecular genetic analysis of aromatic metabolism by the denitrifying bacterium T. aromatica strain T1

Dr. Coschigano's
Web Page

Topic-Related Article(s):
  • G. Fuchs.  2008.  Anaerobic metabolism of aromatic compounds.  Ann New York Acad Sci 1125: 82–99. [PDF]
  • R. Bhandare et al.  2006.  Site-directed mutagenesis of the Thauera aromatica strain T1 tutE tutFDGH gene cluster.  Biochem Biophys Res Comm 346: 992-998.  [OhioLink]
  • P. Coschigano and B. J. Bishop.  2004.  Role of benzylsuccinate in the induction of the tutE tutFDGH gene complex of T. aromatica strain T1.  FEMS Microbiol Lett 231:  261-266.  [OhioLink]

March 6th

Graduate Student Presentation:  Ms. Melissa Lydic

Title: The Ability of Mesenchymal Stem
Cells to Attach to Mesh Material Used in Hernia Repair

Topic-Related Article(s)
  • Y. Wu et al.  2007.  Bone marrow-derived stem cells in wound healing: a review.  Wound Rep Reg 15: S187-S26. [PDF Link]
  • G.-I. Im et al.  2001. Repair of cartilage defect in the rabbit with cultured mesenchymal stem cells from bone marrow. J Bone Joint Surg [Br] 83-B: 289-294.  [PDF Link]

Graduate Student Presentation:  Mr. Brandon Grant

Title: The role of MHR1p in the formation and resolution of mitochondrial
DNA replication structures in the yeast Saccharomyces cerevisiae

Topic-Related Article(s):
  • F. Ling et al.  2000.  A role for MHR1, a gene required for mitochondrial genetic recombination, in therepair of damage spontaneously introduced in yeast mtDNA.  Nucl Acids Res 28: 4956-4963.  [OhioLink]

March 13th

No Class - Spring Break

March 20th

Graduate Student Presentation:  Ms. Erin Pfeill

Title: Spatial and temporal-dependant shifts in grassland invasibility

Topic-Related Article(s):
  • I. J. Renne et al.  2006.  Shifts in grassland invasibility: effects of soil resources, disturbance, composition, and invader size.  Ecology 87: 2264-2277. [ESA Online Full Text] Note: A PDF document is also available from this web page.

March 27th

Invited Speaker:  Dr. Guy Salama, Professor
Department of Cell Biology and Physiology
University of Pittsburgh School of Medicine
Pittsburgh, Pennsylvania

NOTE!   Location: Room 3022 (Auditorium)
                                      Ward Beecher Science Hall

Title: The Role of Intracellular Calcium as a Determinant
of Arrhythmias in Long QT Syndrome

Dr. Salama's
Web Page

April 3rd

Graduate Student Presentation:  Ms. Jessica Davidson

Title: TBA

Topic-Related Article(s): Sent to Class via Email


Graduate Student Presentation:  Ms. Britta Nelson

Title: TBA

Topic-Related Article(s): Sent to Class via Email

April 10th

Invited Speaker:  Dr. June Yun
Assistant Professor

Department of Physiology and Pharmacology, Northeastern Ohio Universities College of  Medicine and Pharmacy, Rootstown, Ohio

NOTE!   Location: Gallery Room, Kilcawley Center

Title: Differential Effects of alpha1-Adrenergic
Receptor Stimulation

Dr. Yun's

Web Page

Topic-Related Article(s):

  • P.  Hein  and M.  C. Michel.  2007. Signal transduction and regulation: Are all alpha1-adrenergic receptor subtypes created equal? Biochemical Pharmacology 73: 1097-1106.  [OhioLink]<>
  • <>R.-P. Xiao et al.  2006.  Subtype-specific alpha1- and beta-adrenoceptor signaling in the heart.  Trends Pharmacol Sci  27: 330-337.  [OhioLink]

April 17th

Graduate Student Presentation:  Mr. Nittin Sood

Title: TBA

Topic-Related Article(s): Sent to Class via Email


Graduate Student Presentation:  Ms. Swarna Moparthi

Title:  TBA

Topic-Related Article(s):
  • <>C. Xu et al.  1996.  The chromosomal arsR gene of Escherichia coli encodes a trans-acting metalloregulatory protein.  J Biol Chem  271: 2427-2432.  [OhioLink]

  • <>J. Guzzo and M. S. Dubow.  2000.  A novel selenite- and tellurite-inducible gene in Escherichia coli.  Appl  Environ  Microbiol 66: 4972–4978. [PubMed]

April 24th

Invited Speaker:  Dr. Karen Coschigano
Assistant Professor

Department of Biomedical Sciences, Ohio University College of Osteopathic Medicine, Athens, Ohio

NOTE!   Location: Bresnahan Rooms, Kilcawley Center

Title: Diabetic Kidney Damage, Growth Hormon
 Signaling, and Inflammation


Dr. Coschigano's
Web Page

Topic-Related Article(s):
  • C. Mora and J. F. Navarro.  2006.  Inflammation and diabetic nephropathy. Curr Diabetes Rep 6: 463-468. [OhioLink]
  •  A. Flyvbjerga.  2006.  Inhibition and reversibility of renal changes: lessons from diabetic kidney disease.  Acta Pædiatrica Suppl 95: 83-92. [OhioLink]

May 1st

Invited Speaker:  Dr. Nicholas Money, Professor
Department of Botany, Miami University, Oxford, Ohio

Gallery Room, Kilcawley Center

Title: The Microscopic Circus: Fungal Movement
at 250,000 Frames Per Second

Dr. Money's
Web Page

Topic-Related Article(s):
  • Yafetto et al.  2008. The fastest flights in nature: high-speed spore discharge mechanisms among fungi.  PLoS ONE 3: e3237.  [Full Text Note: A PDF document is also available from this web page.
    Important Note: Videos associated with this study are available through links embedded in the Full Text web page holding this publication.

Some shameless advertising by Dr. Cooper on behalf of a colleague!

Students might be interested in reading one or more of Dr. Money's books.  The writing is uniquely humorous, easy to read, informative, and provides a fantastic window on the world of fungi!  All three books are available in Maag Library (links to library record/call numbers), through OhioLink as eBooks, or for purchase from the vendors noted below.


Mr. Bloomfield's Orchard:
The Mysterious World of Mushrooms, Molds, and Mycologists

Maag Library Record
OhioLink eBook

Oxford University Press
toxic fungi

Carpet Monsters and Killer Spores: A Natural History of Toxic Mold

Maag Library Record
OhioLink eBook

Oxford University Press

The Triumph of the Fungi:
A Rotten History

Maag Library Record
OhioLink eBook

Oxford University Press

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Primary Journal Articles for Student Review
  • T. C. Watkins et al.  2006.  Identification of skeletal muscle autoantigens by expression library screening using sera from autoimmune rippling muscle disease (ARMD) patients. J Cell Biochem 99: 79-87 [OhioLink]
  • E. K. Pfeil et al.  2007.  Distribution, composition, and orientation of down deadwood in riparian old-growth woodlands of Zoar Valley Canyon, western New York State, USA. Forest Ecol Mgmt. 239: 159-168 [OhioLink]
  • D. B. Murray et al.  2008.  Effects of nonselective endothelin-1 receptor antagonism on cardiac mast cell-mediated ventricular remodeling in rats.  Amer J Physiol Heart Circ Physiol 294: H1251-H1257. [PDFNote: This PDF document is very large (approx. 7 MB) and may take some time to download.  Alternatively, there is a copy of this journal article available in the Biology Office for your to read/copy.
  • I. J. Renne et al.  2006.  Shifts in grassland invasibility: effects of soil resources, disturbance, composition, and invader size.  Ecology 87: 2264-2277. [ESA Online Full Text] Note: A PDF document is also available from this web page.
  • Y. Wu et al.  2007.  Bone marrow-derived stem cells in wound healing: a review. Wound Rep Reg 15: S187-S26. [OhioLink]
  • X. J. Min and D. A. Hickey. 2007.  DNA barcodes provide a quick preview of mitochondrial genome Composition. PloS ONE 2: e325. [PloS Link]
  • X. J. Min and D. A. Hickey. 2007.  Assessing the effect of varying sequence length on DNA barcoding of fungi. Molec Ecol Notes 7: 365-373. [OhioLink]
  • M. T. Butcher and R. W. Blob.  2008.  Mechanics of limb bone loading during terrestrial locomotion in river cooter turtles (Pseudemys concinna).  J Exper Biol  211: 1187-1202 [PDF]
  •   M. T. Butcher et al.  2008.  In vivo strains in the femur of river cooter turtles (Pseudemys concinna) during terrestrial locomotion: tests of force-platform models of loading mechanicsJ Exper Biol  211: 2397-2407 [PDF]
  • C. Sims et al.  2008.  Sex, Age, and Regional Differences in L-Type Calcium Current Are Important Determinants of Arrhythmia Phenotype in Rabbit Hearts With Drug-Induced Long QT Type 2.  Circ Res 102: e86-e100.  [PDF]
  • M. A. Simmons et al.  2008.  Localizaton and function of NK3 receptors of layer V pyramidal neurons of the guinea pig prefrontal cortex.  (Accepted for publication in  the Journal of Neuroscience.)  [PDF]
  • C. B. Blackwood et al.  2007.  Molecular analysis of fungal communities and laccase genes in decomposing litter reveal differences among forest types but no impact of nitrogen deposition.  Environ Microbiol 9:1306-1316. [OhioLink]
  • C. Bar et al 2007.   Characterization of the proteins of bacterial strain isolated from contaminated site involved in heavy metal resistance — a proteomic approach. J Biotechnol 128: 444-451.  [OhioLink]
  • S. Thirach et al.  2008.  Molecular analysis of the Penicillium marneffei glyceraldehyde-3-phosphate dehydrogenase-encoding gene (gpdA) and differential expression of gpdA and the isocitrate lyase-encoding gene (acuD) upon internalization by murine macrophages.  J Med Microbiol 57: 1322-1328. [PDF]
  • J. M. Chandler et al.  2008. Protein profiling of the dimorphic, pathogenic fungus, Penicillium marneffei.  Proteome Sci 6:17. [BMC Full Text] Note: A PDF document is also available from this web page.

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Graduate Student Presentation Guidelines

Second year graduate students enrolled in this course are required to present a short seminar on their current or planned thesis research.  This presentation will not be counted towards the student's course grade.  However, students should use this opportunity as a learning experience.  As part of this experience, peer graduate students will provide constructive feedback using a presentation scoring rubric available via the button link provided below.   Student presentors should make themselves aware of the scoring criteria used in this rubric.

rubric button

Ideally, student presentations should be:
  • Organized: clear, logical sequence of information presentation that can be followed by audience;
  • Complete: Student demonstrates clear command of subject material; can answer all questions with explanations and elaboration; and
  • Professional: Slides strongly support topic without distracting; student uses clear speaking voice throughout and pronounces words properly; seldom refers to notes and maintains good eye contact.
Finally, students should be sure that their presentation is 15-20 minutes in length.   Also, students should be prepared to answer questions following their talk.

ysupete   ysu word mark

This course will expose students to a diverse range of research topics explored by departmental faculty and students, as well as individuals from other institutions.

Course Goals and Objectives

BIOL 6988 will help prepare students for professional careers and aid them in the selection of a research topic/mentor. As such, this couse is designed to help students strive towards the following specific goals:
  • learn the fundamental concepts underlying selected biological systems
  • recognize the importance of proper public dissemination of information
  • learn to write effectively about biology-related topics
Students who successfully complete BIOL 6988 will be provided the tools needed for continued learning in the area of their choice by achieving the following specific objectives:
  • learning scientific terminology
  • understand the real-world application of the scientific method
  • efficiently and effectively communicate scientific knowledge
  • understand the fundamentals of particular biological processes
  • select an area of concentration or a specific research project/mentor to complete their graduate degree

Available Resources

Electronic FilesAny electronic files of journal articles presented in this syllabus are made available soley for the personal educational use of students enrolled in this course.  Their use beyond this specific intent may violate applicable copyright restrictions.  When possible, links to pages where articles can be downloaded by the student alone are posted.

Writing Center.  This course will require students to write a number of summaries.  For those individuals desiring help in improving their writing skills, use of the YSU Writing Center is strongly recommended.*  Their services are free.  Appointments can be scheduled or walk-in visits are available both at the main site (Maag Library, Room 171) or at a satellite location in Stambaugh Stadium.  The Writing Center  can be contacted by telephone [
330.941.3055] or by email [].

NOTE: As of the posting of this syllabus, the Writing Center's web  page is outdated.   An alternative web page at is available for scheduling appointments online.

Computer/MediaThe YSU Tech Desk is available for students needing help with their personal computers or networking services at YSU (Phone: 330.941.1595  Email:  Also, students needing help or resources to address their multimedia and computing needs should contact the pertinent party in YSU's  Media and Academic Compuring (M&AC) department.

Disability Statement

In accord with the Americans with Disabilities Act, anyone requiring special adaptations or accommodations should privately inform Dr. Cooper as soon as possible. In accordance with University procedures, if you have a documented disability and require accommodations to obtain equal access in this course, please contact the Office of Disability Services (located at Wick House; telephone 330.941.1372) in the Center for Student Progress at the beginning of the semester or when given an assignment for which an accommodation is required. Students with disabilities must verify their eligibility through the Office of Disability Services.  Persons enrolled in this course and currently having a documented disability must notify Dr. Cooper of their needs no later than January 26, 2009.  Students with disabilities are reminded that in addition to certain rights and privileges covered by law and University policy, they also have obligations and responsibilities that must be met.  Students are strongly encouraged to review these rights and responsibilities as outlined on the Disability Services Office web page.


A student's grad for this course will be based upon the following items:
  • Attendance - Attendance of seminar is mandatory. This grade component comprises 110 points towards a students total score.  Excused absences are subject to Dr. Cooper's perogative.  For each unexcused absence, ten (10) points will be deducted from a student's score.
  • Participation - A total of 100 points have been allotted to this grade component.  The amount of points awarded to a student is at the Dr. Cooper's discretion.  

  • Students are expected to have read the material provided before each seminar and use it as the basis for interaction with the seminar speaker.
      Failure to ask pertinent questions or make suitable comments during the seminar will results in a deduction of points from the students total score. 

    In addition, graduate students who are required to provide feedback to graduate students (not faculty guests) presenting their work in a particular seminar session.  This feedback will be provided using a evaluation rubric available for downloading on this web page (see Graduate Student Presentation Guidelines).  Individuals enrolled in this course are responsible for bringing this form to class.  Dr. Cooper will not provide copies of this form.  Students will complete this form and submit it to Dr. Cooper immediately at the end of the class.  All comments will be essentially anonymous since only a Banner ID is required, not the name of the student submitting the evaluation.  The evaluations will be given to the student presentor as a form of constructive comment.  Evaluators should be honest and forthright in their scoring and written comments.  Students who do not submit an evaluation will have points deducted from their participation score.
    Seminar Summaries - students will submit summaries of any five (5) presentations that are presented this semester.  Each summary is worth 10 points and must be: i) no more than 250 words in length; ii) submitted no later than 5:00 PM on the Thursday after the presentation was made (e.g., a summary for a Friday, January 23rd seminar would be due by 5:00 PM on Thursday, January 29th);** iii)  a hard copy must be placed in Dr. Cooper's mailbox by the Thursday deadline after a seminar is presented; and iv) an electronic copy must be submitted by the stated deadline to (see below).  Late submissions will NOT be accepted.  Each summary will be graded mainly upon content and grammar/style.
            *NOTE: The exception is Summary #5 which is due             no later than Monday, May 4th. See below.
    In addition, each summary will be submitted to Dr. Cooper and according to the following schedule:

    Due Date
    Feb. 2nd
    Feb. 16th
    Mar. 16th
    Apr. 6th
    May 4th

    Each summary should briefly address the following questions:
    • What questions were addressed by this study?
    • How were these questions addressed? What specific approaches/methods were used?
    • What assumptions were made?  Were these reasonable and testable?
    • What were the major findings of the study?
    • What questions remain unanswered and how might these be sought?
    • What did you find particularly interesting about the presentation?
    • What improvements to the study or the presentation might you suggest? 
  • Primary Literature Summary - Students will read two primary journal articles and write a summary/critique of each.  One of these journal articles must come from among those listed in the syllabus section entitled "Primary Journal Arrticles for Student Review".  The second article may also come from this list or students may consider using the Maag Library resources (e.g., OhioLink) to search for a single PRIMARY journal article pertaining to a subject of interest. 

  • A hard copy of the first journal article review is due to Dr. Cooper by 5:00 PM on March 16th.  A hard copy of the second review is due to Dr. Cooper by 5:00 PM on May 4th.  If the student choses one article from outside the list provided, then a hard copy of the article must also be submitted to Dr. Cooper by the stated deadline.  By these same deadlines,
    electronic copies of the reviews must be submitted to (see below).  Late submissions will NOT be accepted.

    Each summary must be no more than 500 words and will be graded mainly upon content as well as grammar/style.  To better assist you in your summary, students are advised to consult
    A Short Guide to Writing About Biology, by J. A. Pechnik (5th ed., 2007).  Chapter 6 should be especially useful for the student.  This book is available at the Maag Library Circulation Desk.  Two links  to the library records are provided here for your convenience: Link1, Link2.  These assignments are worth 20 points each towards a student's total course score.
Grading Scale

A student's grade for this course will be based upon the following scale:
  • 180 – 200 points    Grade of A
  • 160 – 179 points    Grade of B
  • 140 –159 points     Grade of C
  • 120 – 139 points    Grade of D
  • 119 points or less  Grade of F
This scale is absolute, i.e., there is no curving!

Your final laboratory report for this course must be submitted electronically to, a web site that reviews all submissions for plagiarism.  To begin the process of electronic submission, students need to login to  To briefly summarize the process, students should point their web browser to  (Do not use the period [“.”] at the end of this address.).  Follow the process stated in the Turnitin Student User Guide to join my class, “BIOL 6988: Seminar in Biological Sciences (Spring 2009)”.  The class/account ID is 2548834 and the join/enrollment password is “biol6988” (“biol” is all in lower case; the password is case-sensitive).  Once you have established your account, you are now ready to submit copies of your written assignments.

Syllabus Acknowledgement

Students are required to submit a signed and completed Syllabus Acknowledgement Form to Dr. Cooper no later than 5:00 PM on January 23rd.  This form can be accessed as a PDF document through the button link below.  Failure to properly submit this form will cause Dr. Cooper to withhold the recording of any scores/grades for student(s) who do not comply with this requirement.


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at Youngstown State University

Total Number of Visits
January 1, 2009

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Copyright © 2009 Chester R. Cooper, Jr.