Education & Training
1998 Ph.D. Biochemistry University of Minnesota, Minneapolis, MN
1992 B.S. Biochemistry University of Nebraska, Lincoln, NE
2014-present Instructor: bash shell, python, R, version control.
Workshops taught at: Cornell University, University of Toronto.
2013-present Course developer and instructor, Introduction to
Cellular and Molecular Biology lecture & lab
2013-present Course developer and Instructor, Medical Genetics,
Physician Assistant Didactic Phase
2011-2012 Course developer and instructor, Freshman Biology Seminar
2010 Course developer, Techniques in Molecular Medicine
2010 Co-Instructor and course developer, Natural Science
Perspectives: Humans and Nature, a thematic non-majors course
integrated with Theology and Nature
2009 Co-Instructor and course developer, Topics in Bioinorganic
2008-present Instructor and course developer, Systems Biology
2006-present Instructor and course director, Genetics lecture & lab
2006-present Instructor, Biochemistry lecture and lab
2006-present Instructor, Biochemical Techniques
2006-present Instructor, Biological Research I
2006,2008 Instructor, Junior Biology Seminar
2006 Instructor and course developer, Contemporary Biology
2006 Instructor, Human Genetics (non-majors)
2006 Adjunct instructor and course developer, From SNPs to Gene
Chips: Introduction to Bioinformatics
Cedar Crest College
2005 Invited lecturer, Advanced Bioinformatics
2005 Invited lecturer, Teacher Leadership Institute
Washington University in St. Louis
2002 Invited lecturer, Introduction to Molecular Biology
University of Minnesota
1994 Teaching Assistant, Protein Structure and Function
1993 Teaching Assistant, Biochemistry (Medical)
2014-present Program Director, Biochemistry and Molecular Biology
2013-present Faculty mentor, Freeport High School SMART (Students
Modeling A Research Topic) team
2013-2014 Chair, Academic and Professional Affairs Committee, King’s
2012-2013 Chair-elect, Academic and Professional Affairs Committee,
2011-present Co-advisor, Health Professions, King’s College
2008-present Faculty Advisor, Pre-Health Club, King’s College
2009-2011 Division A representative, Faculty Council, King’s College
2006 Biology Career Panel, Tri-Beta/Biology Club, Cedar Crest College
2006 Judge, Protein Structure Trial Event, New Jersey Science Olympiad
2003-2004 National meeting committee, National Postdoc Association
2003-2004 Implementation committee, Washington University Postdoctoral
2003-2004 Steering committee, Washington University Postdoc Society
2002-2004 Steering committee, Young Scientist Program, Washington
2002-2004 Web site administrator, Young Scientist Program, Washington
2001-2003 Supervisor, Undergraduate research, Washington University
2003 High school student tutor, Young Scientist Program, Washington
1994-1998 Chemistry Day – Boys Scouts and Girls Scouts, University of
1997 Treasurer, Beta Chapter, Alpha Chi Sigma, University of Minnesota
1996 Aide-de-camp, Alpha Chi Sigma National Meeting, Minneapolis, MN
1994 Graduate Student:Faculty Liaison, University of Minnesota
Using biochemistry, molecular biology and genetics, my lab wants to
understand mechanisms of fungal evolution utilizing a variety of
laboratory and computation techniques. Specifically, we are interested
in trace metal detection and the evolution of virulence pathways of
fungi in relation to mammalian or plant hosts.
2006-present Assistant/Associate Professor of Biology, King’s
Research advisor, sophomore through senior research
students. Biochemical and genetic characterization of copper sensing
and transport in the pathogenic fungus Cryptococcus neoformans.
Molecular genetic screening of local fungal populations. Whole genome
and transcriptome analysis of clinical and environmental strains of
2004-2006 Biochemical Information Specialist, Research Collaboratory
for Structural Bioinformatics – Protein Data Bank.
implemented a high throughput computational strategy to standardize
the chemical information content of the PDB ligand database using a
combination of commercially available libraries and open source tools.
Helen Berman, Director.
2002-2004 Research associate, Washington University in St. Louis.
Characterization of copper sensing and transport in the pathogenic
fungus Cryptococcus neoformans. Purification, characterization and
crystallization of nucleotide sugar processing enzymes from the same
organism. Tamara Doering, principal investigator.
2001-2002 Postdoctoral research associate, Washington University in
Purified and crystallized protein complexes associated
with H. pylori pathogenicity islands, Gabriel Waksman, principal
1998-2001 Postdoctoral fellow, Washington University in St. Louis.
Using NMR spectroscopy, measured the dynamics of intestinal fatty acid
binding protein mutants found in the human population, David Cistola,
1992-1998 Ph.D. Thesis, University of Minnesota.
Kinetic Characterization of the Binding Cavity of Adipocyte Lipid
Binding Protein,” Leonard Banaszak, advisor
1992 Summer research intern, Bristol-Myers Squibb.
efficacy of various bovine vaccines.
1990-1992 Undergraduate research, University of Nebraska.
Construction of plasmids to over express the E. coli proteins dnaJ
and dnaK, under the guidance of Paul Blum.
1989-1990 Undergraduate research, University of Nebraska.
Screening A. thaliana cDNA libraries for myosin related genes, under
the guidance of David Marks.
1987, 1988 Summer research intern, Eppley Institute for Research in
Restriction mapping the upstream region of human cytochrome
P450-IAI, Ronald Hines, principal investigator.
Grants and Fellowships
2012 Northeastern Pennsylvania Technology Institute’s Undergraduate
Training Grant Program
2011 Professor Thomas V. Tobin Science Faculty Research Fund
2009 Departmental Civic Engagement Grant, The Shoval Center for
Community Engagement and Learning
2009 Service-Learning Curriculum Development Grant, The Shoval Center
for Community Engagement and Learning
2009 American Society for Microbiology Undergraduate Research
Fellowship (S. Ellis)
2009 American Society for Microbiology Student Travel Grant Award,
109th General Meeting (S. Ellis)
2007 Pennsylvania Academy of Science Undergraduate Research Grant. (S.
Honors and Awards
1998 NIH Individual National Research Service Award (F32)
1994 NIH Training Grant in Molecular Biophysics
1992 Graduate School Fellowship, University of Minnesota
1991 Milton E. Mohr Scholarship in Biotechnology, University of Nebraska
Active Professional Memberships
2006-present American Society for Microbiology
2005-present Pennsylvania Academy of Science
2013 “Engaging Students in Their Space to Increase Motivation: Expanding
Small College Lessons to a Large University” University of Nebraska,
2013 “Virulence of the Fungus Cryptococcus neoformans” Doane College
2010 “Virulence and Gene Expression in the Fungus Cryptococcus
neoformans,” Cedar Crest College
2010 “Effects of Copper on Virulence and Gene Expression in the Fungus
Cryptococcus neoformans,” Western Connecticut State University
2007 “Copper Regulation in C. neoformans,” College of Wooster
McClelland EE, Hobbs LM, Rivera J, Casadevall A, Potts WK, Smith JM,
Ory JJ. The Role of Host Gender in the Pathogenesis of Cryptococcus
neoformans Infections. PLoS ONE, 2013 8(5): e63632.
Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S,
Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL,
Markley JL, Nakamura H, Newman R, Shimizu Y, Swaminathan J, Velankar S,
Ory J, Ulrich EL, Vranken W, Westbrook J, Yamashita R, Yang H, Young
J, Yousufuddin M, Berman HM. Remediation of the protein data bank
archive. Nucleic Acids Res. 2008 Jan;36(Database issue):D426-33.
Burkhardt K, Schneider B, Ory J. A Biocurator Perspective:
Annotation at the Research Collaboratory for Structural Bioinformatics
Protein Data Bank. PLoS Comput Biol, 2006 2(10): e99
Ory JJ, Griffith CL, Doering TL. An efficiently regulated promoter
system for Cryptococcus neoformans utilizing the CTR4 promoter.
Yeast, 2004 Aug;21(11):919-926.
Terradot L, Durnell N, Li M, Li D, Ory J, Labigne A, Legrain P,
Colland F, Waksman G. Biochemical characterization of protein complexes
from the Helicobacter pylori protein interaction map: strategies for
complex formation and evidence for novel interactions within type IV
secretion systems. Mol Cell Proteomics. 2004 Aug;3(8):809-819.
Bar-Peled M, Griffith CL, Ory JJ, Doering TL. Purification and
kinetic characterization of UDP-glucose dehydrogenase from Cryptococcus
neoformans. Biochem. J., 2004 Jul 1;381(Pt 1):131-6.
Ory, J. Scientists & Society: Two body problem. Nature. 2004 Jun
Bose I, Reese AJ, Ory JJ, Janbon G, Doering TL. A yeast under cover:
The capsule of Cryptococcus neoformans. Eukaryotic Cell 2003
Ory JJ, Banaszak LJ. Studies of the ligand binding reaction of
adipocyte lipid binding protein using the fluorescent probe
1-anilinonaphthalene-8-sulfonate. Biophys. J. 1999 Aug;77(2):1107-16.
Thompson J, Ory J, Reese-Wagoner A, Banaszak L. The liver fatty acid
binding protein — comparison of cavity properties of intracellular
lipid-binding proteins. Mol. Cell, Biochem. 1999 Feb;192(1-2):9-16.
Ory JJ, Mazhary A, Kuang H, Davies RR, Distefano MD, Banaszak LJ.
Structural characterization of two synthetic catalysts based on
adipocyte lipid-binding protein. Protein Eng. 1998 Apr;11(4):253-61.
Ory J, Kane CD, Simpson MA, Banaszak LJ, Bernlohr DA. Biochemical
and crystallographic analyses of a portal mutant of the adipocyte
lipid-binding protein. J. Biol. Chem. 1997 Apr 11;272(15):9793-801.
Blum P, Ory J, Bauernfeind J, Krska J. Physiological consequences of
DnaK and DnaJ overproduction in Escherichia coli. J. Bacteriol. 1992
<span style=”font-variant:small-caps;”Conference papers</span
Kosak Z, McClelland EE and Ory JJ. Exploring Microarray Data from
Cryptococcus neoformans to Identify Novel Cryptococcal Meningitis
Virulence Indicators. 90^th^ Annual Meeting of the Pennsylvania Academy
of Science. Selinsgrove, PA.
Manes C and Ory JJ. Exploring the role of CUF1 in phagocytosis of
C. neoformans var neoformans. April 2013. 89^th^ Annual Meeting of the
Pennsylvania Academy of Science. Bradford, PA.
McClelland EE, Hobbs LM, Bisson GP, Smith JM and Ory JJ. The Role of
Host Gender in the Pathogenesis of Cryptococcus neoformans Infections.
May 2012. 112^th^ General Meeting of the American Society For
Microbiology. San Francisco, CA.
Ory JJ, Phillips K, Kliman RM and McClelland EE. Genetic Determinants of
Virulence in the Fungal Pathogen Cryptococcus neoformans. April 2012.
88^th^ Annual Meeting of the Pennsylvania Academy of Science. Allentown,
Ellis SE, Attanasio NA, Sapienza SA, Kish AJ and Ory JJ. Analysis of
Copper Homeostasis Pathways in Cryptococcus neoformans via Microarray
and Bioinformatic Characterization of a cuf1- Strain. May 2011. Eighth
International Conference on Cryptococcus and Cryptococcosis. Charleston,
De Palma R and Ory JJ. The Effect of Modified Copper-Sensing
Elements in the Regulated CTR4 Promoter System of Cryptococcus
neoformans. April 2011. 87^th^ Annual Meeting of the Pennsylvania
Academy of Science. Altoona, PA.
Trenge S, Manes C and Ory JJ. The Role of the Copper Sensing
Transcription Factor Cuf1p on Macrophage Phagocytosis and Killing by
Cryptococcus neoformans. April 2011. 87^th^ Annual Meeting of the
Pennsylvania Academy of Science. Altoona, PA.
Kish A and Ory JJ. Microarray Analysis of Clinical Isolates of C.
neoformans from Patients in Botswana. April 2011. 87^th^ Annual Meeting
of the Pennsylvania Academy of Science. Altoona, PA.
Grundowski J, Miller J, and Ory JJ. The Role of CNLAC1 and CNLAC2 in
Azurre B Reactive Activity in Cryptococcus neoformans. April 2011.
87^th^ Annual Meeting of the Pennsylvania Academy of Science. Altoona,
Ellis SE, Doering TL and Ory JJ. Microarray analysis of a Δcuf1
strain of Cryptococcus neoformans suggests Cuf1p is involved in both
repressor and enhancer activities. May 2010. 110^th^ General Meeting of
the American Society For Microbiology. San Diego, CA.
Miller JB and Ory JJ. Characterization and Isolation of Azure B
Reactive Compounds from the Fungal Pathogen Cryptococcus neoformans.
May 2010. 110^th^ General Meeting of the American Society For
Microbiology. San Diego, CA.
Attanasio N and Ory J. Effects of Copper on the Expression of the
CTR4 and CUF1 Genes in Different Strains of C. neoformans. April
2010. 86^th^ Annual Meeting of the Pennsylvania Academy of Science. Camp
Capozzeli R and Ory J. Cloning and Expression of the Copper
Sensitive Transcription Factor Cuf1p from Cryptococus neoformans.
April 2010. 86^th^ Annual Meeting of the Pennsylvania Academy of
Science. Camp Hill, PA
Ellis SE, Doering TL, Ory JJ. Effect of copper concentration on
growth morphology and genome wide expression in the fungal pathogen
Cryptococcus neoformans var. neoformans. May 2009. 109^th^ General
Meeting of the American Society For Microbiology. Philadelphia, PA.
Ory J. An Undergraduate Systems Biology Course Designed Around
Saccharomyces Metabolism. May 2008. American Society for Microbiology
Conference for Undergraduate Educators. Beverly, MA.
Ellis S, Kujat B, Portonova D, Portonova M, Ory J. Effects of Copper
on the Growth Morphology of the Fungal Pathogen Cryptococcus
neoformans. April 2008. 84th Annual Meeting of the Pennsylvania Academy
of Science. Camp Hill, PA.
Yousufuddin M, Dimitropoulos D, Feng Z, Ory J, Sun H, Westbrook J,
Henrick K, Berman H. Revised chemical component dictionary for the
Worldwide Protein Data Bank. August 2007. 234th National Meeting &
Exposition of the American Chemical Society. Boston, MA.
Ory JJ, Brown RH, Brent MR, Doering TL. Searching for copper
regulated genes in C. neoformans using TWINSCAN. August 2003. 3^rd^
International Cryptococcus neoformans Genome Conference. Vancouver,
Ory JJ, Griffith CL, Doering TL. Inducible promoter design in
Cryptococcus neoformans. May 2003. The 15^th^ Congress of the
International Society for Human and Animal Mycology. San Antonio, TX.
Ory JJ, Griffith CL, Doering TL. Structure and Functional Analysis
of UDP-sugar enzymes in Cryptococcus neoformans. October 2002. 9^th^
Annual Midwest Microbial Pathogenesis Conference. Indianapolis, IN.
Ory JJ, Monsey JD, Cistola DP. A Genetic Polymorphism in Human
Intestinal Fatty Acid Binding Protein Affects Ligand Release. October
2001. The 15^th^ Annual Gibbs Conference on Biothermodynamics.
Ory JJ, Monsey JD, Cistola DP. Characterization of Millisecond
Dynamics of Human Intestinal Fatty Acid Binding Protein. January 2001.
Keystone Symposium on Frontiers of NMR in Molecular Biology. Big Sky,
Distefano MD, Kuang H, Qi D, Haring D, Ory JJ, Banaszak LJ.
Semisynthetic Approaches for the Design of Protein with Catalytic
Activity Using Fatty Acid Binding Protein as a Scaffold. 16th American
Peptide Symposium. July 1999. Minneapolis, MN.
Ory JJ, Banaszak LJ. Role of the Portal Region of Adipocyte Lipid
Binding Protein in Ligand Binding and Kinetics. July 1998. American
Crystallographic Association Annual Meeting, Washington DC.
Distefano MD, Qi D, Kuang H, Mazhary A, Ory JJ, Banaszak LJ. Design
of Artificial Enzymes Using Protein Cavities as scaffolds. The 216th
American Chemical Society (ACS) National Meeting. August 1998. Boston,
Senior Research Projects:
“Isolating and determining diversity of Endophytic species within
Elymus Virginicus” – George Hadeed (2013)
“Longitudinal Study of Castor Canadensis in a Leatherleaf-sedge
Wetland Habitat” – Laura Barna (2013)
“The Effects of Copper Starvation on Growth Phenotypes of Cryptococcus
neoformans” – Morgan Coslett (2013)
“Cryptococcus neoformans: Altered CuSE and Fungus Virulence” – Paul
“The Phenotypic Effects of Oxidative Stress on Cryptococcus
neoformans.” – Amanda Goetz (2013)
“Exploring the role of CUF1 in phagocytosis of C. neoformans var
neoformans.” – Chelsea Manes (2013)
“Phylogenetic Analysis of Major Virulence Genes in Cryptococcus
neoformans substrains.” – Garrett Harvey (2013)
“Comparison of Urease Activity in Strains of Cryptococcus neoformans.”
– Samantha Fisher (2013)
“Metal Tolerance of Environmental Strains of C. neoformans” – Matthew
“The effect of iron concentration on the CTR4 promoter system of
Cryptococcus neoformans strain H99D.” – Harry Pockevich (2012)
“Bioinformatic inquiry into the upstream regions of potential Cuf1p
binding sites” – Salvador Sapienza (2011)
“The Effect of Modified Copper-Sensing Elements in the Regulated CTR4
Promoter System of Cryptococcus neoformans.” – Ryna De Palma (2011)
“The Role of the Copper Sensing Transcription Factor Cuf1p on Macrophage
Phagocytosis and Killing by Cryptococcus neoformans.” – Shelby Trenge
“Microarray Analysis of Clinical Isolates of C. neoformans from
Patients in Botswana.” – Alex Kish (2011)
“The Role of CNLAC1 and CNLAC2 in Azurre B Reactive Activity in
Cryptococcus neoformans.” – Janel Grundowski (2011)
“Microarray analysis of a Δcuf1 strain of Cryptococcus neoformans
suggests Cuf1p is involved in both repressor and enhancer activities” –
Shannon Ellis (2010)
“Characterization and Isolation of Azure B Reactive Compounds from the
Fungal Pathogen Cryptococcus neoformans” – Johnna Miller (2010)
“Analysis of Fatty Acid Composition of Cryptoccus neoformans” – Mike
“Pilot Study: Microsatellite Analysis of Genetic Variation of Invasive
Rusty Crayfish (Orconectes rusticus) in the Susquehanna River” – Jamie
Rafter (Dr. Brian Mangan, co-advisor, 2010)
“Cloning and Expression of the Copper Sensitive Transcription Factor
Cuf1p from Cryptococus neoformans” – Regina Capozzeli (2010)
“Effects of Copper on the Expression of the CTR4 and CUF1 Genes in
Different Strains of C. neoformans” – Nick Attanasio (2010)
“Effects of Copper and Iron Levels on the Viability of Cryptococcus
neoformans Strains Varying in Virulence” – Tanya Giuliani (2009)
“Microbial Diversity in Susquehanna River Soil Samples” – Rose Vencak
“Detection of Molecular Pathways of Copper in C. neoformans Using RNA
Interference” – Christina Boutros (2008)
“Effect of Copper on Total Protein Composition in Cryptococcus
neoformans” – Katelyn Knick (2008)
“Protective Capabilities of Mannitol in C. neoformans” – Brittany
“The Effects of Iron and Copper on the Growth of Cryptococcus
neoformans” – David Portonova (2008)
“Competition of Local Fungal Species Grown Using Different Sugar
Mediums” – Ashley Starry (Dr. David Glick, co-advisor, 2008)
“Fungal Species within Local Soil” – Jayme Doyle (2007)
“Effects of differing copper concentrations on the delta-cuf1 mutant of
Cryptococcus neoformans” – Mike Portonova (2007)