Work History

Work History
Jul 2012 - Present

Associate Attorney

Aquilla Patents & Marks, PLLC

Patent prosecution and litigation, Trademark litigation, Theft of Trade Secrets litigation

Sep 2011 - May 2013

Associate Professor (Adjunct)

Franklin Pierce University
  • Teaching:IC112 and IC113 Integrated Science, hybrid course (live and online components)
Nov 2011 - Jan 2013

Academic Consultant, Online Curriculum Development (Law and Science)

The Saylor Foundation
  • Currently designing:LAW205 Intellectual Property
  • Courses designed:BIO306 Botany;
  • Assisted with designing of course:BIO102 Introduction to Evolutionary Biology and Ecology
  • Courses reviewed:BIO301 Cell Biology; BIO304 Human Physiology
Jul 2010 - Jul 2011

Associate Professor (Adjunct)

NHTI
  • Courses taught:BI195 Anatomy and Physiology I with lab, BI196 Anatomy and Physiology II with lab
  • Courses designed and taught:LNC102 Risk Management Studies hybrid live/online, LNC105 Legal and Healthcare Ethics hybrid live/online
Jul 2010 - Jul 2011

Associate Professor (Adjunct)

Manchester Community College
  • Courses taught:BIOL110 Anatomy and Physiology I with lab, BIOL120 Anatomy and Physiology II with lab
Mar 2009 - Mar 2010

Associate Professor (Adjunct)

Hesser College
  • Courses taught:HUMN101 Conflict Resolution (three times), NSCI100 Anatomy and Physiology I (fivetimes), NSCI200 Anatomy and Physiology II (four times), GNED201 Critical Thinking Workshop (once), MDAS280 Medical Ethics and Law (twice), NSCI115 Biology of the Human Body (once), NSCI352 Human Biology (once), BADM240 Introduction to Business Law (once)
  • Additional:Course Level Assessments
May 2008 - Mar 2009

Research Associate

Dartmouth College
  • Project:Investigating the role of transcriptional co-activators and chromatin remodeling in steroid hormone-regulated gene expression in breast cancer cells.
  • Responsibilities:Responsible for designing, implementing and managing multiple research projects.Reviewing grant proposals and manuscript submissions.Training and supervising of technical and research staff.Representation of laboratory at scientific research conferences.
  • Methodologies:Chromatin Immunoprecipitation (“ChIP”) assays, multiplex real time PCR, large scale protein purification for mass spectrophotometric analysis of post-translational modifications, site-directed mutagenesis and over-expression, and siRNA inhibition of expression, of said proteins in human breast cancer cells.
Sep 2007 - Dec 2007

Legal Intern

Fletcher Allen Health Care
  • Project:Performed a comprehensive analysis of Fletcher Allen Healthcare-affiliated hospitals and academic medical centers for compliance with Federal Medicare/Medicaid laws, rules and regulations (Stark, Anti-kickback, Anti-Fraud, etc…).Also assisted Offices of General Counsel, Risk Management and Institutional Review Board (oversees clinical trials) with a wide variety of legal projects.Accompanied representatives on lobbying visits at Vermont State House hearings on State Healthcare legislation reform.
  • Responsibilites:Oral and memoranda-based legal analysis provided under severe time constraints.These analyses and recommendations were relied upon by legal counsel.
  • Methodologies:Extensive legal research of state and federal case law, statutes, rules and regulations.Extensive legal analyses and memo writing.
Aug 2002 - Aug 2003

Senior Scientist

Atherogenics, Inc.
  • Project:Validated small molecule therapeutics for arteriosclerosis, asthma, COPD, and other inflammatory diseases.
  • Responsibilities:Established Research Division of Cellular and Molecular Immunology.Trained and assisted other researchers in methods of Molecular Immunology.Set up Florescent Activated Cell Sorter (FACS) facility.Implemented and managed multiple research projects.Reviewed grant proposals and manuscript submissions.Represented company at scientific research conferences.Assisted in compliance with FDA clinical trial rules and regulations.
  • Methodologies:Attended several FACS training courses at Becton-Dickenson FACS facility and learned to use the BD FACS VantageSE high-speed sorter, BD FACS Calibur flow analyzer, and BD FACScan flow analyzers, using multiple software platforms, including FloJo, CellQuest, ModFit, and Cytometric Bead Assay.Established purified primary mast cell and T helper cell cultures for use in drug validation.
Jan 2001 - May 2002

Scientist

EpiGenesis Pharmaceuticals, Inc.
  • Project:Validated aerosol-delivered antisense therapeutics for asthma, COPD, and other pulmonary diseases.
  • Responsibilities:Implemented and managed multiple research projects.Trained others in methods of Molecular Immunology including basic FACS use.Reviewed grant proposals and manuscript submissions.Assisted in compliance with FDA clinical trial rules and regulations.Established blood born pathogen training course.
  • Methodologies:Designed and implemented complex combinatorial primary human cell culture models of pulmonary disease states using B cells, antigen-specific T helper cells, mast cells, macrophages, pulmonary smooth muscle cells, and endothelial cells.Constructed several phagemid cDNA libraries from rabbit, mouse and cynomologous monkey tissues.Cloned antisense target genes.Assisted with cynomologous monkey surgery and tissue collection.
Aug 1996 - Jan 2001

Postdoctoral Fellow, Dept of Microbiology

Columbia University
  • Project:Discovered and studied novel genes involved in primary macrophage differentiation, activation and microbial pathogenesis.
  • Responsibilities:Implemented and managed multiple research projects.Wrote several grant proposals.Reviewed others’ grant proposals and manuscript submissions.Attendance and presentation at several scientific conferences.
  • Methodologies:Cloned cDNAs using the PCR-based technique, Representational Difference Analysis (“RDA”).Established primary macrophage, monocyte, granulocyte and neutrophil cultures using human hematopoietic stem cells.Retroviral infection of human stem cells, using multiple variations of the Phoenix retrovirus system.Designed (using molecular modeling software) and successfully used antisense-hammerhead ribozymes to knock-down endogenous gene expression.Extensive cDNA cloning and subcloning.Muliplex RNase protection assays for gene expression.Construction of inducible EBV episomal plasmid expression system.Established and employed several microbial pathogenic cell models including HIV, Legionella pneumophila, Mycobacterium tuberculosis, Staphylococcus aureus, and Entamoeba histolytica (amoebic dysentery).Extensive use of FACS including cell cycle analysis by BrdU and propidium iodide, phagocytosis of fluorescent beads, and expression/cell sorting of cDNA-IRES-GFP/YFP positive infected cells.Affymatrix microarray and bioinformatic analyses.Also briefly worked on v-abl infection of mouse bone marrow-derived B cell cultures (“Whitlock-Witte” cultures).Independently initiated collaborations with multiple labs at Columbia, Albert Einstein, Sloan-Kettering, and Princeton.
Jun 1995 - Jul 1996

Postdoctoral Fellow, Dept of Mol.Cell Biology

University of California, Berkeley
  • Project:Discovered and studied novel genes involved in negative and positive selection of thymocytes in transgenic mice.
  • Responsibilities:Implemented and managed multiple research projects.Wrote several grant proposals.Reviewed others’ grant proposals and manuscript submissions.
  • Methodologies:Created thymus cDNA libraries from transgenic antigen-specific mouse models of positive and negative T cell selection.Employed multiple apoptosis and proliferation assays to validate genes;TUNEL, BrdU, propidium idodide, Caspase C, and Annexin V.
Aug 1990 - Jun 1995

Graduate Student, Dept of Genetics

Harvard University
  • Project:Studied the transcriptional regulation of cytokine genes in primary T helper 1 and T helper 2 cell clones.Helped to identify c-Maf as the master regulatory factor for T helper 2 fate commitment.
  • Responsibilities:Implemented and managed multiple research projects.Reviewed grant proposals and manuscript submissions.Attendance and presentation at several scientific conferences.
  • Methodologies:Establishment and transfection of primary mouse T helper 1 and T helper 2 cell clones.Mutational analysis of Interleukin 2 (IL-2), Interleukin 4 (IL-4), and MHC class II promoters and transient transfection reporter assays.Identification and analysis of transcription factors.DNase I and in vivo footprinting.Creation of hybridomas and antibody purification.Cell proliferation assays.Cell fusion studies.ELISA assays.Immunoprecipitations, co-immunoprecipitations, and Western analyses.In vivo metabolic protein labeling and phospho-amino acid analysis.Transgenic mice studies.Quantitative RT-PCR.Gel Shift assays.
  • Projects during two years of lab rotations:
    • Yeast genetics in the lab of Fred Winston, Ph.D.Complementation analysis of the transcription factors TFIID and SPT3.Reverse genetics/mutational analysis.
    • Role of the transcription factor, MyoD, in muscle cell differentiation and embryogenesis in the lab of Andrew Lassar, Ph.D.
    • Genes expressed during E. coli stationary phase in the lab of Roberto Kolter, Ph.D.
Nov 1994 - Apr 1995

Traveling Scholar/Visiting Researcher

Tularik, Inc.
  • Project:Isolated and characterized cytokine promoter DNA-binding proteins as part of Harvard graduate thesis work (see below).
  • Responsibilities:Implemented and managed multiple research projects.
  • Methodologies:Large scale (10-20 liter) primary cell cultures.Large scale protein isolation, fractionation, purification and identification (by micro-peptide sequencing).
Feb 1988 - Jul 1990

Research Technologist, Dept of Genetics

University of Washington
  • Project:Transcriptional regulation of Immunoglobulin genes in human B cells.
  • Responsibilities:Carried out several research projects.Trained graduate students.Managed daily lab operations.
  • Methodologies:PCR.DNA sequencing. Northern (RNA) and Southern (DNA) analyses.Creation and complementation analysis of mutated human B cell lines (“reverse genetics”).Isolation and analysis of primary B cells.Also briefly worked on molecular biology of Plasmodium falciparum (malaria) and Leishmania sp.

Education

Education
Aug 2005 - May 2008

J.D.

Vermont Law
Jun 2006 - Aug 2006

Certificates

Franklin Pierce Law Center

Certificates:Intellectual Property Summer Institute, Advanced Licensing Institute

Coursework:  Patent Law, Introduction to Patent Prosecution, Advanced Licensing

Aug 1990 - Jun 1995

Ph.D.

Harvard University

Ph.D. Thesis:  "Regulation of the Interleukin 2 and Interleukin 4 genes in Murine T Helper 1 and T Helper 2 Cell Clones"

Aug 1982 - Dec 1987

B.A.

University of California, Berkeley

Skills

Skills

Patents

Experience in Patent Prosecution.  I am a USPTO-registered Patent Agent.

Law

Experience in Health and Patent Law.

Higher Education

Three years experience designing and teaching both online and live courses in a variety of subjects (Law, Science, Liberal Arts).

Science

Eighteen years experience in research on molecular and cellular immunology.

John W. Rooney - Awards

Academic Excellence Award, Vermont Law School, 2008

Dean’s List, Vermont Law School, 2008

NIH Arteriosclerosis training grant (T32-HL07343), 2000-2001

Postdoctoral Fellowship Award, Cancer Research Institute, New York, NY, 1996-1999

Traveling Scholar Research Award, Tularik, Inc., South San Francisco, CA, 1994-1995

National Research Service Award, 1992-1995

John W. Rooney - Publications

Postel, E. H., Berberich, S. J., Rooney, J. W., and Kaetzel, D. M. (2000).  Human NM23/Nucleoside Diphosphate Kinase regulates gene expression through DNA binding to nuclease-hypersensitive transcriptional elements.  J. Bioenergetics and Biomembranes 32(3): 277-284.

Rooney, J. W., Postel, E. H., and Calame, K. L.  (1999).  Proc. 3rd Intern. Congr. Genet. Biochem. Physiol. Nm23/Nucleoside Diphosphate Kinase.  University of Bordeaux2, France, 20-22.  September 1999, Absh. P15.

Ho, I.-C., Kim, John H.-I., Rooney, J. W., Spiegelman, B. M., and Glimcher, L. H.(1998). A potential role for the nuclear factor of activated T cells family of transcriptional regulatory proteins in adipogenesis. Proc. Natl. Acad. Sci. USA 95, 15537-15541.

Ho, I.-C., Hodge, M. R., Rooney, J. W., and Glimcher, L. H. (1996). The proto-oncogene c-maf is responsible for tissue-specific expression of interleukin-4. Cell 85, 973-983.

Rooney, J. W.  (1995).  Regulation of the Interleukin-2 and Interleukin-4 genes in T helper 1 and T helper 2 cell clones.  Doctoral Thesis, Harvard, Dept of Genetics.

Rooney, J. W., Sun, Y.-L., Glimcher, L. H., and Hoey, T. (1995). Novel NF-AT sites that mediate activation of the IL-2 promoter in response to T cell receptor stimulation. Mol. Cell. Biol. 15, 6299-6310.

Rooney, J. W., Hoey, T., and Glimcher, L. H. (1995). Coordinate and cooperative roles for NF-AT and AP-1 in the regulation of the murine IL-4 gene.  Immunity 2, 473-483.

Rooney, J. W., Hodge, M. R., and Glimcher, L. H. (1995). The proximal promoter of the IL-4 gene is composed of multiple essential regulatory sites which bind at least two distinct factors. J. Immunol. 154, 6397-6405.

Rooney, J. W., Hodge, M. R., McCaffrey, P. G., Rao, A., and Glimcher, L. H. (1994). A common factor regulates both Th1 and Th2 specific cytokine  gene expression. EMBO J. 13, 625-633.

Reimold, A. M., Kara, C. J., Rooney, J. W., and Glimcher, L. H. (1993). Transforming Growth Factor Beta-1 Repression of the HLA-DRalpha gene is mediated by conserved proximal promoter elements. J. Immunol. 151, 4173-4182

Eisenmann, D. M., Arndt, K. M., Ricupero, S. L., Rooney, J. W., and Winston, F. (1992). SPT3 interacts with TFIID to allow normal transcription in Saccharomyces cerevisiae. Genes & Dev. 6, 1319-1331

Miller, C. L., Feldhaus, A. L., Rooney, J. W., Rhodes, L. D., Sibley, C. H., and Singh, H. (1991). Regulation and a possible stage-specific function of Oct-2 during pre-B-cell differentiation. Mol. Cell. Biol. 11, 4885-4894.

Rooney, J. W., DuBois, P., and Sibley, C. H. (1991). Cross-linking of surface IgM activates NF-kappa B in B lymphocyte. Eur. J. Immunol. 21, 2993-2998.

Bomstzyk, K., Rooney, J. W., Twasaki, T., Rachie, N. A., Dower, S. K., and Sibley, C. H. (1991). Evidence that interleukin-1 and phorbol esters activate NF-kappa B by different pathways: role of protein kinase C. Cell Regulation 2, 329-335.

Bomsztyk, K., Toivola, B., Emery, D. W., Rooney, J. W., Dower, S. K., Rachie, N. A., and Sibley, C. H. (1990). Role of cAMP in interleukin-1-induced kappa light chain gene expression in murine B cell line. J. Biol. Chem. 265, 9413-9417.

Rooney, J. W., Emery, D. W., and Sibley, C. H. (1990). 1.3E2, a variant of the B lymphoma 70Z/3, defective in activation of NF-kappa B and OTF-2.  Immunogenetics 31, 73-78.

Rooney, J. W., Emery, D. W., and Sibley, C. H. (1990). Slow response variant of the B lymphoma 70Z/3 defective in activation in LPS activation of NF-kappaB. Immunogenetics 31, 65-72.

Emery, D. W., Rooney, J. W., and Sibley, C. H. (1989). A gamma interferon-unresponsive variant of cell line, 70Z/3, IFN-4, can be partially rescued by phorbol myristate acetate. Mol. Cell. Biol. 9, 5231-5233.

John W. Rooney - Links

Summary

Attorney John W. Rooney, Ph.D. is admitted to the Massachusetts State Bar and the U.S. District Court, District of Massachusetts, and is registered with the U.S. Patent and Trademark Office as a U.S. Patent Attorney. He holds degrees from University of California, Berkeley (B.A., Molecular Biology) and Harvard University (Ph.D., Genetics). Prior to becoming an attorney, Dr. Rooney worked as a drug development scientist for multiple biotech and pharmaceutical companies. While in law school he interned at Fletcher Allen Health Care, Burlington, Vermont, under the Offices of Integrity and Compliance, Risk Management, and General Counsel. His practice now focuses on Patent, Trademark, and Theft of Trade Secrets litigation in Federal Court. He is with Aquilla Patents & Marks, PLLC. He is also an Adjunct Professor at multiple local colleges teaching courses in both science and law.

He currently lives near the Boston area.

Objective

Attorney John W. Rooney, Ph.D. is admitted to the Massachusetts State Bar and the U.S. District Court, District of Massachusetts, and is registered with the U.S. Patent and Trademark Office as a U.S. Patent Attorney. He holds degrees from University of California, Berkeley (B.A., Molecular Biology) and Harvard University (Ph.D., Genetics). Prior to becoming an attorney, Dr. Rooney worked as a drug development scientist for multiple biotech and pharmaceutical companies. While in law school he interned at Fletcher Allen Health Care, Burlington, Vermont, under the Offices of Integrity and Compliance, Risk Management, and General Counsel. His practice now focuses on Patent, Trademark, and Theft of Trade Secrets litigation in Federal Court. He is also an Adjunct Professor at multiple local colleges teaching courses in both science and law.

He is looking for an IP Associate position in the Boston area.

Memberships

Member, Massachusetts Bar Association (MBA)

Member, Boston Patent Law Association (BPLA)

Member, American Intellectual Property Law Association (AIPLA)

Registered Patent Attorney, United States Patent and Trademark Office (USPTO)

Certifications

Certifications
Apr 2012 - Present

Registered Patent Attorney

USPTO
Dec 2012 - Present

Member, Bar

State of Massachusetts
Jan 2013 - Present

Member, Bar

U.S. District Court, District of MA