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D. Mark Eckley Summary: Ph.D. Trained Biologist with 13 of Years Of

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D. Mark Eckley Summary: Ph.D. Trained Biologist with 13 of Years Of D. Mark Eckley Summary: Ph.D. trained biologist with 13 of years of experience planning cell biology experiments and implementing computational analysis and data/image processing. Contributed molecular biology, biochemistry and cell imaging data to published studies focusing on the interplay of DNA replication, chromosome structure and the aging process. Successfully led teams, worked on multiple projects simultaneously and collaborated with internal and external investigators. Proficient using microscopes, liquid handlers and all computer platforms. Oriented and trained professional staff on use of Deltavision 3D image reconstruction system. Education: Ph.D. Cell Biology The Johns Hopkins School of Medicine, BCMB department May 1998 M.A. Immunology University of California, Santa Barbara, Neuroscience Research Institute B.A. Chemistry University of Colorado, Boulder, Chemistry department Skills and Expertise: Computational Analysis: Command line implementation of Fiji, WND-CHARM for image feature calculation Microarray Data Normalization, Z score calculation for group to group comparisons, PCA OpenCV image calculation package (Keras, Tensorflow for deep learning) NGS data using Biopython Molecular biology: Recombinant DNA, gene cloning and expression. CRISPR gene knockout and knockin to produce intentional genetic alterations (IGA) DNA sequencing, PCR and qPCR for IGA validation. RNA seq, microarray hybridizations. ELISA, Western blot, in-gel proteolysis. Cell Biology: Ex vivo culture of immortalized and primary Stem Cells. Optimized cytokine mixture for stroma-free B-cell cultures. Flow cytometry (Beckman-Coulter CytoFlex, Becton-Dickinson Canto II). Virus generation: lentivirus and retrovirus, viral transduction to produce cell lines. Microscopy: Confocal and light microscopy, 3D reconstruction and structured illumination. Microtubule gliding and vesicle motility assays Microinjection of cultured cells and germline to produce IGA (nematodes). Protein biochemistry: Native and recombinant protein purification FPLC, ion exchange chromatography Sucrose gradient and size exclusion chromatography Work Experience: National Institute on Aging, Intramural Research Program (NIA-IRP) Jan 2005 - Present Research Contractor, Epigenetics & Stem Cell Section, Translational Gerontology Branch Sep 2017- present Study reprogramming process as Hematopoietic stem cells (HSC) age to identify pathways to limit DNA damage and increase ability to differentiate into lymphoid rather than myeloid cells. ● Isolate stem cells, culture in vitro without stromal layer. Develop ex vivo culture conditions for B and T cell proliferation. ● Work in a team of 2 post-baccalaureate fellows, 3 post-doctoral fellows, and PI. ● Plan and implement molecular biology techniques, follow experimental design and microscopy sample preparations and analysis using Comet Assay. Research Contractor, Image Informatics & Computational Biology Unit, LGG Jan 2005- Sep 2017 Use image informatics and machine learning to discover basic processes underlying aging. ● Orient and train professional staff including summer students, post-baccalaureate students and postdoctoral fellows. ● Recommend methods and develop methods and procedures to meet the experimental objectives within the IICBU lab. Grow mouse ESC under adipogenic and osteogenic conditions ● Recommend and develop methods for quantitative processing and interpretation of multiplex immunofluorescent images with lymphoma classification (chronic lymphocytic leukemia (CLL), follicular lymphoma (FL) and mantle cell lymphoma (MCL). ● Analyze and interpret data and prepare summaries of findings in final form for publication in reports. Presented paper at scientific meeting (2008) and published in scientific journals. ● Maintain light microscopy facility including conventional light microscopes, confocal and structured illumination microscopes and Deltavision 3D restoration system (deconvolution and precise Z stack positioning). ● Calibrate instruments, coordinate annual preventative maintenance and assist in managing service contracts. ● Assisted with budget by recommending end of year purchases. The Johns Hopkins School of Medicine Sep 1991-Dec 2004 Postdoctoral Scientist, Institute of Genetic Medicine Jan 2003- Dec 2004 Identify DNA replication factors involved in sister chromatid cohesion. ● Performed successful synthetic lethal interaction screen by mating haploid single gene mutants to generate diploid double knockout strains. Assessed GFP-lac Repressor foci number with high resolution imaging. ● Collaborated internally to make screens high throughput with Tecan and Biomek liquid handlers. ● Analyze and interpret data and prepare summaries of findings in final form for publication Postdoctoral Fellow, Johns Hopkins University, Biology department Jun 1998- Dec 2003 Biophysical characterization of dynactin complex to discover 3 previously unknown proteins, Arp11, p27 (dctn-6) and p25 (dctn-5). Developed a functional assay, Arp1 cable disruption, to identify Drosophila Arp11. ● Collaborated internally to assess effect of microinjected plasmids on centrosome duplication in cell lines. Validated expression with Western blots and immunofluorescence. ● Collaborated externally to study Nuclear Envelope breakdown in cultured cells. Graduate Student, The Johns Hopkins School of Medicine, BCMB program Sep 1991- May 1998 Determined roles for chromosome passenger proteins in cytokinetic furrow positioning. ● Identified and characterized exon/intron structure of human INCENP genomic locus. Awards and Honors: Distinguished Achievement Award, Kelly Government Services (Feb 2015, Feb 2013, Oct 2008) Certification: Pyimagesearch Gurus Computer Vision Course (November 2017) Selected Publications (includes 5 first author *): https://scholar.google.com/citations?user=yQzM0wMAAAAJ&hl=en *Eckley DM, Coletta CE, Orlov NV, Wilson MA, Bastian P, Lehrmann E, Zhang Y, Becker KG, Goldberg IG. Transcriptome States Reflect Imaging of Aging States. J Gerontol A Biol Sci Med Sci. 2017 Dec 5. doi: 10.1093/gerona/glx236. *Eckley, D Mark; Rahimi, Salim; Mantilla, Sandra; Orlov, Nikita V; Coletta, Christopher E; Wilson, Mark A; Iser, Wendy B; Delaney, John D; Zhang, Yongqing; Wood, William; Molecular characterization of the transition to mid-life in Caenorhabditis elegans Age (2013) v:35(3)pp.689-703 Orlov, Nikita V; Weeraratna, Ashani T; Delaney, John D; Eckley, D. Mark; Shamir, Lior; Goldberg, Ilya G; Automatic detection of melanoma progression by histological analysis of secondary sites Cytometry Part A (2012) v:81(5)pp.364-373 Kazanis, Ilias; Lathia, Justin D; Vadakkan, Tegy J; Raborn, Eric; Wan, Ruiqian; Mughal, Mohamed R; Eckley, D Mark; Sasaki, Takako; Patton, Bruce; Mattson, Mark P; Quiescence and activation of stem and precursor cell populations in the subependymal zone of the mammalian brain are associated with distinct cellular and extracellular matrix signals Journal of Neuroscience (2010) v:30(29)pp.9771-9781 Orlov, Nikita; Shamir, Lior; Macura, Tomasz; Johnston, Josiah; Eckley, D Mark; Goldberg, Ilya G; WND-CHARM: Multi-purpose image classification using compound image transforms Pattern recognition letters (2008) v:29(11)pp.1684-1693 Warren, Cheryl D; Eckley, D Mark; Lee, Marina S; Hanna, Joseph S; Peyser, Brian; Irizarry, Rafael; Spencer, Forrest A; S-phase checkpoint genes safeguard high-fidelity sister chromatid cohesion Molecular biology of the cell (2004) v:15(4)pp.1724-1735 *Eckley, D Mark; Schroer, Trina A; Interactions between the evolutionarily conserved, actin-related protein, Arp11, actin, and Arp1 Molecular biology of the cell (2003) v:14(7)pp.2645-2654 Salina, Davide; Bodoor, Khaldon; Eckley, D Mark; Schroer, Trina A; Rattner, JB; Burke, Brian; Cytoplasmic dynein as a facilitator of nuclear envelope breakdown Cell (2002) v:108(1)pp.97-107 *Eckley, D Mark; Gill, Steven R; Melkonian, Karin A; Bingham, James B; Heuser, John E; Schroer, Trina A; Analysis of dynactin subcomplexes reveals a novel actin-related protein associated with the arp1 minifilament pointed end The Journal of cell biology (1999) v:147(2)pp.307-320 *Eckley, D Mark; Ainsztein, Alexandra M; Mackay, Alastair M; Goldberg, Ilya G; Earnshaw, William C; Chromosomal proteins and cytokinesis: patterns of cleavage furrow formation and inner centromere protein positioning in mitotic heterokaryons and mid-anaphase cells The Journal of cell biology (1997) v:136(6)pp.1169-1183 .
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