PH Jones, PhD *

CURRICULUM VITAE

Philip H. Jones, PhD

*** **** ******* **., **********, KY 40204

TELEPHONE: 605-***-**** EMAIL: acz9e3@r.postjobfree.com EMPLOYMENT: Advance Genomic Technology / University of Louisville 201 East Jefferson Street, Suite 303

Louisville, KY 40202

502-***-****

POSITION: Research Scientist

SUMMARY OF QUALIFICATIONS:

Research and academic experience in Microbiology, Molecular Biology, Virology, Genetics, Cell Biology, and Biochemistry in experimental design, execution, and analysis examining both viral pathogenesis and microRNA regulation of obesity-related gene utilizing various murine models. Has a proven track record with high impact publications as a first author as well as an excellent research collaborator demonstrated by several co-authorships. TECHNIQUES AND SKILLS:

Molecular Biology: Gene and recombinant DNA cloning, RT-qPCR, genomic PCR, gene array analyses, DNA, RNA, and Protein extractions, restriction digestion and ligation of vectors and plasmids, cDNA generation, DNA sequencing analysis, mammalian, ectoparasite, and bacterial DNA analyses, and the isolation and characterization of ectoparasite genetic (microsatellite) markers from Genomic DNA

Biochemistry: Gel electrophoresis, ELISA, immunodetection and western blot, immunoprecipitation, and chromatin immunoprecipitation, reporter promoter assays (luciferase, β- galactosidase, GFP reporter genes), antibody purification and validation, and protein quantification using Lowry and Bradford methods

Cell Biology: RNA inference (with siRNA, shRNA, and lentivirus), primary cell culture, live-animal imaging, flow cytometry, fluorescence-activated cell sorting (FACS), in vitro and in vivo infections using retroviruses, lentiviruses, and alphaviruses, mouse embryonic fibroblast (MEF) immortalizations, transfections and transductions of plasmids into cell lines and MEFs, stable cell line generation, interferon bioassays, leucocyte-killing assays, reverse transcriptase assays, differentiation of immune cells from mouse bone marrow, viral propagation from cell cultures and viral-induced tumors, Ficoll separation of lymphocytes from both human and mouse peripheral blood, viral titration and quantification by plaque assays, end point dilution assays (TCID50), cell viability, cell migration, cell adhesion, cell invasion, cell proliferation assays, xenograft assays, immunofluorescence, bright field, confocal, scanning, and election transmission microscopy, and thin layer chromatography analysis

Instrumentation: 7500 Fast RT-PCR system, Xenogen IVIS-200 live-animal imaging, Zeiss LCM 710 confocal microscope, Tecan microplate reader, Ultracentrifugation, FACSCaliber and PH Jones, PhD 2

FACSVerse cell sorters, Nanodrop spectrophotometer, Odyssey (LI-COR), ABI Genetic Analyzer, and Aligent Technologies’ 2100 Bioanalyzer

Computer Software: Microsoft Word, Excel, and Power Point, Adobe Photoshop, Adobe Illustrator, Endnote, SAS, GraphPad, MATLAB, FlowJo, Sequencing alignment analyses, Biostatistics, Genetic Parentage Estimations and Phylogenetic Analysis

Genetic Mice techniques and training: Mouse intraperitoneal, fat pad, footpad, and tail vein injections, retro-orbital, submandibular, and tail vein bleeding, cardiac puncture (terminal procedure), mouse euthanizing and anesthesia with CO2, adoptive transfer of syngeneic bone marrow-derived cells into mice, determining sex of mice, breeding knockout mice for two genes, and mouse breeding and handling

Additional skills and training: BSL2 containment environment, ectoparasite identification by species, Basic Biological laboratory safety training, PPE Awareness for Labs, bloodborne pathogens for Labs, and BSL3 security clearance

EDUCATION:

PhD, Biological Sciences, The University of South Dakota, Vermillion, SD, 2010

MS, Biological Sciences, Auburn University, Auburn, AL, 2004

AS, Laboratory Technology, Community College of Allegheny County, Pittsburgh, PA, 1997

BS, Biology, Temple University, Philadelphia, PA, 1994 TEACHING EXPERIENCE:

The University of South Dakota:

Graduate Teaching Assistant:

General Biology for Non-Majors, 2008

General Biology for Majors, 2006-07

Guest Lecturer: Causes and Consequences of Epidemics Title: The detection of a threshold prevalence of plague-positive fleas in plague epizootics on black-tailed prairie dog colonies, 2007

Auburn University:

Graduate Teaching Assistant:

Vertebrate Development, 2001-03

General Biology for Majors, 2003

General Biology for Non-Majors, 2002

Principles of Ecology, 2001

PROFESSIONAL EXPERIENCE:

2015-Present: Research Scientist, Advanced Genomic Technology/The University of Louisville, Louisville, KY:

PH Jones, PhD 3

Conducted laboratory experiments and tests examining microRNA effects on obesity using transgenic mouse models.

Developed several protocols for the purposes of inducing mouse stem cells to mature adipocytes.

Carried out RNA isolation and qPCR analyses on various mouse tissues demonstrating that specific microRNAs target obesity-associated genes.

Prepared mouse breeding and care protocols adhering to the University of Louisville’s Institutional Animal Care and Use Committee guidelines.

Conducted experiments using human plasma and sera samples.

Successfully cloned several microRNAs sequences into vectors for in vitro transfection experiments involving primary fibroblasts as well as commercial cell lines.

Trained and supervised several research assistants and technicians in various laboratory tasks including cell culturing, DNA and RNA extractions, molecular cloning and DNA sequencing, conducting PCR and RT-qPCR experiments.

2010-2015: Postdoctoral Research Scholar, University of Iowa, Department of Microbiology, Iowa City, IA:

Developed RNAi studies (siRNA and shRNA) to understand the impact of antiviral genes on viral infections.

Isolated and propagated viruses from cell cultures and oncolytic-induced breast tumors.

Conducted molecular studies and experiments into genetic expression and gene manipulation using recombinant DNA technology.

Purified and validated a polyclonal antibody using immuno-precipitation methods.

Conducted cell culture and in vivo studies with oncolytic retroviruses and an alphavirus

(Chikungunya virus) using RT-qPCR, FACS, Western blotting, ELISA, fluorescent, scanning, and electron microscopy.

Quantified viruses using plague assays and TCID50 analysis.

Isolated CD4+ T cell and CD11c Dendritic cell populations from mouse spleen cells and lymph nodes.

Trained undergraduate students, graduate students, and Postdocs in molecular biology, microbiology, genetic mice breeding and handling, and various other laboratory techniques.

Functioned as laboratory manager with duties that included purchasing lab supplies, lab equipment, managing and breeding genetic mice, maintaining all laboratory certifications, and determined that all laboratory practices complied with OSHA and USDA regulations. 2005-2010: Graduate Research Assistant, University of South Dakota, Department of Biology, Vermillion, SD:

Isolated and designed primers from ectoparasitic genomic (microsatellite) DNA to examine population genetic structure.

Isolated Yersinia pestis in exposed ectoparasites using PCR.

Collected and identified ectoparasites following CDC guidelines.

Generated and analyzed multiple, large-scaled mammalian, ectoparasite, and bacterial genetic databases.

Isolated and characterized different strains of Y. pestis using recombinant DNA cloning and DNA sequencing techniques.

Taught undergraduate courses in General Biology for Majors and Non-Majors.

Supervised several undergraduate conducting independent research. PH Jones, PhD 4

2001-2004: Graduate Research Assistant, Auburn University, Department of Biology, Auburn, AL:

Isolated DNA extractions and purifications from tissue samples and hair follicles of small mammals.

Characterize genetic structure of small mammals using PCR and biostatistics analyses.

Applied biostatistics to generate mathematical models theorizing reproductive success rate of small mammals.

Taught undergraduate lab courses in Vertebrate Development, Ecology, and General Biology. 2000-01: Laboratory Support Technician, Tallahassee Memorial Hospital, Tallahassee, FL:

Performed data entry into the Laboratory Information Systems used to report patient lab results.

Prepared blood, tissues and other bodily specimens for clinical testing. 1999: Laboratory Technician OPS, University of Florida, Pari-Mutuel Wagering Laboratory, Tallahassee, FL:

Performed thin-line chromatography to test for the presence of performance enhancing drugs in race horse and dog biological samples.

Reported suspected drugs determined to be present in biological samples tested.

Prepared solutions and autoclaving equipment necessary to conduct testing of biological samples. 1994-1995: Chemical Operation Specialist, United States Army, Ft. McClellan, AL:

Highest rank: Specialist, Honorable Discharge.

PEER-REVIEWED PUBLICATIONS:

Jones PH, Okeoma CM. 2015. Detection of Chikungunya virus (CHIKV) in urine of infected mice: a Potential Non-invasive Diagnostic Tool for CHIKV. Journal of Infectious Diseases & Therapy 3: 4.

Madison MN, Jones PH, Okeoma CM. 2015. Exosomes in human semen restrict HIV-1 transmission by primary vaginal cells and block intravaginal replication on LP-BM5 murine AIDS virus complex. Virology 482: 189-201.

Mahauad-Fernandez WD, Jones PH, Okeoma CM. 2014. Critical role for bone marrow stromal antigen 2 in acute Chikungunya virus infection. Journal of General Virology 95: 2450-61.

Jones PH, Mahauad-Fernandez WD, Madison NM, Okeoma CM. 2013. BST-2/tetherin is overexpressed in mammary gland and tumor tissues in MMTV-induced mammary cancer. Virology 444: 124-39.

Jones PH, Maric M, Madison MN, Maury W, Roller RJ, Okeoma CM. 2013. BST-2/Tetherin- mediated restriction of Chikungunya (CHIKV) VLP budding is counteracted by CHIKV non-structural protein 1 (nsP1). Virology 438: 37-49. Featured article for Virology Journal cover vol. 438, 30 March 2013.

Jones PH, Okeoma, CM. 2013. Phosphatidylinositol 3-kinase is involved in Toll-like receptor 4- mediated BST-2/tetherin regulation. Cellular Signaling 25: 2752-61.

Jones PH, Biggins DE, Eads DA, Eads SL, Britten HB. 2012. Deltamethrin flea-control preserves genetic variability of black-tailed prairie dogs during a plague outbreak. Conservation Genetics 13: 183-95.

Jones PH, Mehta HV, Maric M, Roller RJ, Okeoma CM. 2012. Bone marrow stromal cell antigen 2

(BST-2) restricts mouse mammary tumor virus (MMTV) replication in vivo. Retrovirology 9: 10.

Jones, PH, Mehta HV, Okeoma CM. 2012. A novel role for APOBEC: susceptibility to sexual transmission of murine acquired immunodeficiency virus (mAIDS) is aggravated in APOBEC deficient mice. Retrovirology 9: 50.

PH Jones, PhD 5

Jones PH, Van Zant JL, Dobson FS. 2012. Variation in reproductive success in male and female Columbian ground squirrels. Canadian Journal of Zoology 90: 736-43.

Mehta HV, Jones PH, Weiss JP, Okeoma CM. 2012. IFN-α and lipopolysaccharide upregulate APOBEC3 mRNA through different signaling pathways. Journal of Immunology 189: 4088-103.

Jones PH, Washburn LR, Britten HB. 2011. Gene flow in a Yersinia pestis vector, Oropsylla hirsuta, during a plague epizootic. Journal of Vector-Borne Diseases 48: 125-32.

Jones PH, Britten HB. 2010. The absence of concordant population genetic structure in the black- tailed prairie dog and the flea, Oropsylla hirsuta, with implications for the spread of Yersinia pestis. Molecular Ecology 19: 2038-49.

Jones PH, Wallace L, Britten HB. 2009. Isolation and characterization of 11 microsatellite loci from Oropsylla hirsuta, a vector of sylvatic plague. Molecular Ecology Resources 9: 1041-44. PEER-REVIEWED ABSTRACTS:

Jones PH, Britten HB, Hanson DA, Washburn LR. 2010. Monitoring Plague Epizootics in Black- tailed Prairie dog colonies with a sensitive PCR-based Protocol. Vector-Borne and Zoonotic Diseases 10: 96-96.

Jones PH, Wallace L, Britten HB. 2010. Landscape Genetic Concordance between the Black-tailed prairie dog and its associated flea, Oropsylla hirsuta. Vector-Borne and Zoonotic Diseases 10: 96- 96.

Jones PH. 1993. The staining of specific populations of cells found in the chick retina using Diamidino Yellow. The National McNair Journal 1: 20. ABSTRACTS PRESENTED AT SYMPOSIA AND SCIENTIFIC MEETINGS:

Okeoma CM, Jones PH, Maric M, Madison MN, Maury W, Roller RJ. 2013. Chikungunya virus

(CHIKV) non-structural protein 1 counteracts BST-2/tetherin-mediated restriction of CHIKV VLP budding American Society of Virology, 32nd annual meeting, The Pennsylvania State University, University Park, PA.

Jones PH, Mehta HV, Maric M, Roller RJ, Okeoma CM. 2012. Bone marrow stromal cell antigen 2

(BST-2) tethers mouse mammary tumor virus (MMTV) and restricts replication in vivo. American Society of Virology, 31st annual meeting, University of Wisconsin-Madison, Madison, WI.

Jones PH, Britten HB, Washburn L.R. 2009. The spatial and phylogenetic relationships among Yersinia pestis strains of black-tailed prairie dog colonies. American Society of Naturalists, Society for the Study of Evolution, and Society of Systematic Biologists annual meetings, University of Idaho, Moscow, ID.

Jones PH, Britten HB, Wallace L. 2008. Landscape genetic concordance between the black-tailed prairie dog and its associated flea, Oropsylla hirsuta. The symposium on the ecology of plague and its effects on wildlife, Ft. Collins, CO.

Jones PH. 2007. Workshop on plague ecology, Panelist, 56th Annual Wildlife Disease Association Conference, Estes Park, CO.

SELECTED ABSTRACTS FROM POSTER PRESENTATIONS (*undergraduate author):

Jones PH, Madison MN, Okeoma CM. 2013. Mouse mammary tumor virus (MMTV) modulates BST-2/tetherin expression and antiviral activity in a TLR4 dependent manner. Cold Spring Harbor Laboratory 38th annual meeting on retroviruses, Cold Spring Harbor, NY. PH Jones, PhD 6

Jones PH, Maric M, Madison MN, Maury W, Roller RJ, and Okeoma CM. 2013. BST-2/tetherin- mediated restriction of chikungunya (CHIKV) VLP budding is counteracted by CHIKV non-structural protein 1 (nsP1). The 7th Biennial All Iowa Virology Symposium, Ames, IA.

Mehta H, Jones PH, Okeoma CM. 2012. Mouse mammary tumor virus-induced modulation of APOBEC gene expression in vivo. American Society of Virology, 31st annual meeting, University of Wisconsin-Madison, Madison, WI.

Jones, PH, Mehta HV, Okeoma CM. 2012. A novel role for APOBEC: susceptibility to sexual transmission of murine acquired immunodeficiency virus (mAIDS) is aggravated in APOBEC deficient mice. Cold Spring Harbor Laboratory 37th annual meeting on retroviruses, Cold Spring Harbor, NY.

Gentles L*, Mehta HV, Jones PH, Maury W, Okeoma CM. 2012. Interaction of Chikungunya Virus with Toll-Like Receptor 4, University of Iowa 7th annual summer undergraduate research conference, Iowa City, IA.

Mehta HV, Jones PH, Weiss JP, Okeoma CM. 2012. IFNα and LPS up-regulate APOBEC3 (A3) mRNA through different signaling pathways. Cold Spring Harbor Laboratory 37th annual meeting on retroviruses, Cold Spring Harbor, NY.

Okoruwa E*, Mehta HV, Jones PH, Bedell K, Okeoma CM. 2011. Role of APOBEC3 (A3) in sexual transmission of retroviruses: mAIDS model. Iowa Biosciences Advantage, Iowa City, IA.

Filler J*, Jones PH, Bitten HB. 2009. Population genetic survey of a potential plague vector. Undergraduate forum, University of South Dakota, Vermillion, SD.

Jones PH, Wallace L, Britten HB. 2008. Population genetic structure of the black-tailed prairie dog flea, Oropsylla hirsuta, in north-central Montana with a panel of 13 microsatellite loci, The symposium on the ecology of plague and its effects on wildlife, Ft. Collins, CO.

Jones PH, Wallace L, Britten HB. 2008. Population genetic structure of the prairie dog flea, Oropsylla hirsuta. American Society of Naturalists, Society for the Study of Evolution, and Society of Systematic Biologists annual meetings, University of Minnesota, Minneapolis, MN. REVIEWER FOR SCIENTIFIC JOURNALS:

Proceedings of the South Dakota Academy of Sciences, 2010-2011

Journal of Human Virology & Retrovirology, Associate Editor, 2014-present COMMUNITY SERVICE:

Designed and assisted moderating an ecologically-themed science competition for the South Dakota Science Olympiad for elementary and middle-school aged students, 2008 STUDENT MENTORSHIPS:

Lauren Gentles, University of Iowa, NIH REU Program, 2012-13

Alexander Canfield, University of Iowa, undergraduate research, 2012-15

Wadie Mahauad-Fernandez and Abigail Berkebile, University of Iowa, Graduate Program rotational students, 2012.

Reneisha L. Stroter, University of Iowa, undergraduate research, 2012

Ebose Okoruma, University of Iowa, Biosciences Advantage Program, 201 PH Jones, PhD 7

Jenessa Filler, University of South Dakota, undergraduate research, 2009-10 GRANTS AND AWARDS:

Awarded NIH T32 Post-Doctoral Training grant in Parasitology, University of Iowa, 2013-14

Awarded NIH T32 Post-Doctoral Training grant in Immunology, University of Iowa, 2011-13

Awarded Graduate Research Grant, University of South Dakota, 2006

Alpha Theta Chi Collegiate Scholar, Auburn University, 2004

National Ronald E. McNair Post Baccalaureate Achievement Program Scholar, Temple University, 1993-94

AFFILIATIONS:

American Association for the Advancement of Science REFERENCES:

Available upon request

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