CaInitially Posted: August 24, 2009
November 9, 2009
Copyright © 2009-2010 Chester R. Cooper, Jr.

BIOL 6988: Seminar in Biological Sciences

Fall 2009 Semester
, CRN 40060
[Spring Semester Seminar Web Page]

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

Friday, 12:00 PM - 12:50 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

Quick Links to Weekly Seminars

Aug. 28th


Sept. 4th
Sept. 11th
Sept. 18th Sept. 25th

Introcution to
Library Resources
Asch Butcher, Renne

Oct. 2nd Oct. 9th
Oct. 16th Oct. 23rd Oct. 30th

Chuey, Sims
Diggins Dr. Naeli Vardanyan Fagan Johnston

Nov. 6th
Nov. 13th Nov. 20th Nov. 27th Dec. 4th

Usis, Cooper

Leipheimer, Walker


Dr. Cooper's Office Location:

Ward Beecher Science Hall, Room 3016

(PLEASE NOTE: Dr. Cooper's office is located in a secured wing of the building.  You will need to use the telephone on the wall to the left of the secured glass doors to dial his extension [x1361] and he will come and escort you to his office.  DO NOT ask others to let you in the secured area without an escort!)

Dr. Cooper's Contact Information:

Telephone/Voice Mail, 330.941.1361

Dr. Cooper's Office Hours:
(subject to change/cancellation due to unforeseen circumstances)

Mondays and Fridays (8/24/09 through 12/04/09)
9:00 AM - 10:30 AM
[Please Note: No office hours will be held on the following Fridays: 9/11, 10/9, 11/6, and 11/13]

(8/26/09 through 12/02/09)
10:00 AM - 12:00 PM
[Please Note: No office hours will be held on the following Wednesdays: 9/2 and 10/7]

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

August 28th

Introduction to Course

September 4th

Introduction to Maag Library Resources

All students should report to the instruction room on the fourth floor of Maag Library.  There, Ms. Cynthia Harrison, Science Librarian Liason, will provide a short hands-on workshop on available literature search rescources available to YSU students.  Attendance is mandatory!

September 11th

Facutly Presentor:   Dr. David Asch, Associate Professor

Topic-Related Article:
  • Arnett, D. R., et al.  2009.  Catabolite repression directly affects transcription of the qa-y gene of Neurospora crassa.  Fungal Genet Biol 46: 377-380.  [OhioLink]

September 18th

Facutly Presentor:   Dr. Michael Butcher, Assistant Professor

Topic-Related Articles:
  • Blob, R. W. and A. A. Biewener.  1999.  In vivo locomotor strain in the hindlimb bones of Alligator mississippiensis and Iguana iguana: implications for the evolution of limb bone safety factor and non-sprawling limb posture.  J Exp Biol 202: 1023-1046. [PDFNote: A PDF document can be downloadedfrom this web page.  Look for the appropriate citation.

  • Butcher, M. T., 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 mechanics.  J Exp Biol  211: 2397-2407.  [FullTextNote: A PDF document is also available from this web page.

Facutly Presentor:   Dr. Ian Renne, Assistant Professor

Topic-Related Article:
  • Renne, I. M., et al.  2006. Shifts in grassland invasibility: effects of soil resources, disturbance, compostion, and invader size.  Ecology 87: 2264-2277.    [FullText/PDF]

September 25th

Facutly Presentor:   Dr. Jonathon Caguiat, Assistant Professor

Topic-Related Article(s):
  • Holmes, A., et al.  2009.  Comparison of two multimetal resistant bacterial strains: Enterobacter sp. YSU and Stenotrophomonas maltophilia ORO2.  Curr Microbiol (in press) [OhioLink]
  • Jasenec, A., et al.  2009.  Proteomic profiling of L-cysteine induced selenite resistance in Enterobacter sp. YSU. Proteome Sci  7: 30 [FullText/PDF]
  • Müller S., et al.   1997 The path of unspecific incorporation of selenium in Escherichia coli. Arch Microbiol 168: 421-427. [OhioLink]
  • Bébien, M., et al.   2002 Involvement of superoxide dismutases in the response of Escherichia coli to selenium oxides.  J Bacteriol 184: 1556–1564. [PDF]

October 2nd

Facutly Presentor:   Dr. Carl Chuey, Professor

Topic-Related Article(s):

PLEASE NOTE: Dr. Atwood is a recent YSU biology graduate who studied under Dr. Chuey.
  • J. J. Atwood and B. A. Allen.  2009.  A synopsis of the Orthotrichum strangulatum complex (Orthotrichaceae).  The Bryologist 112: 208-220.  [OhioLink]
  • J. J. Atwood.  2009.  A taxonomic revision of Schlotheimia subg. Stegotheca (Orthotrichaceae).  The Bryologist 112: 290-300.  [OhioLink]
  • J. J. Atwood.  2009.  New records of mosses from Pennsylvania.  Evansia 26: 7-9.  Note: This document is not available electronicallly.  Students may retrieve the orginal from Dr. Cooper and make a photocopy for their own use.

Facutly Presentor:   Dr. Carl Sims, Assistant Professor

Topic-Related Article:
  • 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.  [FullText] Note: A PDF document is also available from this web page.

October 9th

Facutly Presentor:  Dr. Thomas Diggins, Associate Professor

Topic-Related Article(s):
  • Diggins, T.  P.and Newman, A. M.  2009.  Environmental and spatial influences on benthic community composition in wooded headwater streams in Zoar Valley, New York, USA.  Hydrobiologia  630: 313 - 326  [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]

October 16th

Special Guest Presentor:   Dr. Nazeli Vardanyan

NOTE!!!   Location of Presentation:  
Bresnahan Rooms I and II
Kilcawley Center

Title: Armenian Environmental Situation: Problems and Ways of Solution

Brief Biography:   Dr. Vardanyan is the Director of “Armenian Forests” [web link], an non-government organization whose main activities are forestation, reforestation and forest protection in Armenia.  She supervises projects on 740 hectares  of reforestation in Armenia, and she has also been coordinator of a working group on drafting of a forest  policy for Armenia. She is also president of “GOY”, an environmental/legal organization whose main activities are environmental education, environmental rights protection, lobbying, public participation in decision-making and access to justice on environmental issues.  She is a licensed attorney in the Republic of Armenia. She is a member of both the Chamber of Advocates of the Republic of Armenia and of the International Bar Association. As an international expert on environmental law, Dr. Vardanyan has testified at numerous international conferences and participated in drafting several international environmental conventions, e.g. the Convention on the Rights of the Child, the Aarhus Convention, and other agreements. She is a lecturer at the Russian-Armenian University in the capital, Yerevan, and coordinator of the Human Rights and Sustainable Development Working Group of the Northern Alliance for Sustainable Development.

October 23rd

Facutly Presentor:   Dr. Diana Fagan, Associate Professor

Topic-Related Articles:
  • Brinchmann, J. E.  2008.  Expanding autologous multipotent mesenchymal bone marrow stromal cells.  J Neurol Sci 265: 127–130.  [OhioLink]

  • Hone, R. and C. Keane.  1974.  A clinical study of infections caused by methicillin-resistant Staphylococcus aureusInfect 2: 213 - 217.  [OhioLink]

October 30th

Facutly Presentor:   Dr. Carl Johnston, Associate Professor

Topic-Related Article(s):
  • Bamforth, S. M. and I. Singleton, Ian.  2005.  Bioremediation of polycyclic aromatic hydrocarbons: current knowledge and future directions.  J Chem Technol Biotechnol 80: 723 - 736.  [OhioLink]

November 6th

Facutly Presentor:   Dr. John Usis, Professor

Topic:  Experimental Design


Facutly Presentor:   Dr. Chet Cooper, Professor

Title: Morphogenesis in Penicillium marneffei

Topic-Related Articles:
  • Cooper, C. R., Jr., and N. Vanittanakom.  2008.  Insights into the pathogenicity of Penicillium marneffei.  Future Microbiol 3: 43-55.  [PDF]
  • J. M. Chandler et al.  2008. Protein profiling of the dimorphic, pathogenic fungus, Penicillium marneffei.  Proteome Sci 6:17. [BioMedCentralt]


Facutly Presentor:   Dr. Johanna Krontiris-Litowitz, Professor

Topic-Related Article:
  • Mukherjee, D. and S Sen.  1990.  Collagen phenotypes during development and regression of myocardial hypertrophy in spontaneously hypertensive rats. Circulation Research 67: 1474-1480.  [PDF]

November 13th

Facutly Presentor:   Dr. Robert Leipheimer, Professor


Topic-Related Article(s):


Facutly Presentor:   Dr. Gary Walker, Professor

Topic-Related Article(s):

  • Walker, G. R.,  et al.  1999.  Identification of autoantibodies associated with rippling muscles and myasthenia gravis that recognize skeletal muscle proteins: possible relationship of antigens and stretch-activated ion channels.  Biochemical and Biophysical Research Communications264: 430-435.  [OhioLink]
  • Watkins, T. C.,  et al.  2006.  Identification of skeletal muscle autoantigens by expression library screening using sera from autoimmune rippling muscle disease (ARMD) patients.   Journal of Cellular Biochemistry 99: 79 - 87.  [OhioLink]
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November 20th

Facutly Presentor:   Dr. Heather Lorimer, Associate Professor

Topic-Related Article(s):
  • Lecrenier, N. and Foury, F.  2000.  New features of mitochondrial DNA replication system in yeast and man.  Gene 246: 37-48.  [OhioLink]
  • Ling, F.  et al.  2007.  DNA recombination-initiation plays a role in the extremely biased inheritance of yeast [rho–] mitochondrial DNA that contains the replication origin ori5.  Molecular and Cellular Biology 27: 1133-1145.  [ASM Journals]

November 27th

Thanksgiving Holiday - NO CLASS

December 4th

Facutly Presentor:   Dr. Xiangjia Min, Assistant Professor

Title:  Secretome Prediction in Eukaryotes

Topic-Related Articles:
  • Klee, E. W. and L. B. Ellis.  2005 . Evaluating eukaryotic secreted protein prediction.  BMC Bioinformatics 6: 256. [BioMedCentral]
  • Tsang,  A., et. al.  2009.  Analytical and computational approaches to define the Aspergillus niger secretome.  Fungal Genet Biol 46 (Suppl 1): S153-S160.  [OhioLink]

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ysupete   ysu word mark

Quick Links to
Syllabus Sections
(The above links were corrected on 9/18/09)

Course Description

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.  The Writing Center  can be contacted by telephone [
330.941.3055] or by email [].

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 (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 September 11, 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 130 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 70 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. 
    Journal Article Summaries - Students will submit a summariy of any single article provided by a faculty member for background reading.  Students must submit ten (10) summaries, each from a different presentor.  Each summary is worth 15 points and must be: i) no more than 200 words in length, and ii) submitted to (see below) no later than 11:59 AM on the day of the corresponding faculty member's presentation.  Late submissions will not be accpeted!!!!!

    IMPORTANT NOTICE!  Be sure to place your summary in the appropriate folder in the course page.  The correct folder is the one named for the faculty member whose journal article you have summarized.  Placing your summary in the incorrect folder will be considered as not having turned in the assignment!!!!

    Each summary will be graded mainly upon content and grammar/style.
    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? 
Grading Scale

A student's grade for this course will be based upon the following scale:
  • 315 - 350 points    Grade of A
  • 280 - 314 points    Grade of B
  • 245 - 279 points     Grade of C
  • 210 - 244 points    Grade of D
  • 209 points or less  Grade of F
This scale is absolute, i.e., there is no curving!

Your journal article summaries 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 (Fall 2009)”.  The class/account ID is 2820283 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.

IMPORTANT NOTICE!  Be sure to place your summary in the appropriate folder in the course page.  The correct folder is the one named for the faculty member whose journal article you have summarized.  Placing your summary in the incorrect folder will be considered as not having turned in the assignment!!!!

Syllabus Acknowledgement

Students are required to submit a signed and completed Syllabus Acknowledgement Form to Dr. Cooper no later than 5:00 PM on September 11, 2009.  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
August 24, 2009

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Copyright © 2009 Chester R. Cooper, Jr.