Areas of Expertise
Teaching Responsibilities: General Biology 1, Principles of Biology, Genetics, Molecular Cell Biology, Molecular Genetics
Research Interests: Molecular, Cellular and Genetic Mechanisms of Skeletal Muscle Atrophy
B.S. (Genetics) University of California, Davis (1997)
Ph.D. (Molecular Cancer Biology) Duke University (2004)
Postdoctoral Fellow: University of California, Davis (2004-2010): Mentors: Dr. David Furlow and Dr. Sue Bodine
My research interests are concerned with the molecular mechanisms of aging and in particular on a phenomenon called sarcopenia. Sacropenia is the gradual deterioration of skeletal muscle that accompanies the aging process and is a serious medical condition facing millions of elderly people. The sarcopenic muscle shows signs of atrophy as well as a reduced capacity to regenerate following damage. Muscle loss or atrophy occurs as the result of a number of different conditions including disuse, cachexia, inflammation, exposure to corticosteroids and aging. A number of studies aimed at identifying differentially expressed genes in atrophy and aging models have found a number of interesting genes, including the E3 Ubiquitin Ligase, MuRF1, which is expressed predominantly in skeletal muscle and is up-regulated in virtually all atrophy models. In addition to MuRF1, HDAC4, a class II Histone Deacetylase, is rapidly and significantly up-regulated only under neuromuscular damage-induced skeletal muscle atrophy. Furthermore, a targeted disruption of the MuRF1 gene in mice leads to a resistance in muscle wasting under atrophic conditions. These observations, among others, have led to the hypothesis that these genes may play a pivotal role in regulating a suite of other genes important in general skeletal muscle physiology, including the processes of sarcopenia and cellular stress handling. With this hypothesis in mind, my research is focused on understanding the molecular and genetic controls of longevity and the role that cellular stress may play in aging. In particular, I am interested in determining if an “aging signature” of skeletal muscle may exist and how this process may progress. Several projects will be undertaken in the lab, including: 1) identifying and analyzing genes that are differentially expressed in young and old muscle, 2) determining how these differently expressed genes may be regulated and if cellular stresses play a role in these changes, and 3) studying the epigenetic events (such as chromatin remodeling and DNA methylation) that may result from cellular stresses and ultimately contribute to long-term and irreversible changes in the heritable material. My lab will be using the mouse as a model organism, as well as cell culture and an array of molecular biological techniques to address the topics mentioned above and outlined below.
Project 1: Gene expression analysis of skeletal muscle from aged animals.
This project will involve performing a microarray analysis of aged skeletal muscle tissue. We will collect tissues from animals and perform an array comparing gene expression profiles in 6, 12, 18, and 24 month old mice. The hope is that we will identify an aging specific signature of gene expression in older animals compared to younger animals. Genes that show a differential expression profile will be further analyzed using cell culture and well established gene expression techniques, such as transfections and reporter assays. A long-term goal of this project will be to study animals with targeted disruption of the most promising gene(s) identified from the array that also show potential to be important aging effectors.
Project 2: Analysis of the role of cellular stresses, including Reactive Oxygen Species (ROS), in aged tissue using skeletal muscle as a model organ.
In addition to gene expression analysis of aged skeletal muscle tissue, the lab will also undertake a project to analyze the more specific role of ROS and other cellular stresses in the aging process. Preliminary evidence, from microarray data generated from MuRF1 null and wild-type mice following denervation, suggests that loss of muscle innervation leads to changes in expression of a collection of genes that play an important role in regulating ROS levels in the cell. Based on these observations, we will conduct research into the role of ROS in the aging process and determine if environmental and heritable differences may impact this role. It is known that as muscle ages, it shows a reduction in the number of neuromuscular junctions resulting in a decrease in innervation of the muscle. Based on preliminary results from the microarray mentioned above, it is reasonable to hypothesize that a reduction in innervation might lead to an increase in ROS, resulting in an increase in cellular stress and ultimately macromolecular, cellular and tissue damage. We will strive to employee a combinatorial approach to studying ROS by using biochemical techniques, tissue culture and animal models. In tissue culture, ROS stress can be mimicked by addition of hydrogen peroxide to cells, which will then be analyzed by determining transcriptional (via qPCR or Northern Blot analysis) and translational (via Western Blot analysis) responses of known ROS regulated genes. Identified transcriptional changes in expression of ROS responsive genes will then be further analyzed by use of reporter gene techniques in cell culture. A more long range goal of this research will be to use the SOD1 null mice, which have increased oxidative stress, and monitor both gene expression and epigenetic events induced by ROS as the animals age. This would be done by performing microarray and ChIP-CHIP or ChIP-Seq techniques to analyze changes in gene expression, DNA methylation and/or histone acetylation in SOD1 null mice compared to wild type, age-matched litter mates.
Project 3: Analysis of chromatin remodeling in aged skeletal muscle tissue.
This project will focus on the global epigenetic changes that appear to occur naturally in aged individuals. In particular, the fact that HDAC4, a class II histone deacetylase, shows increased expression in skeletal muscle of aged rodents and humans suggests that remodeling of the chromatin structure might be one important factor that results in loss of plasticity of this tissue in older individuals. Furthermore, previous studies have shown that HDAC4 expression increases significantly during denervation and is accompanied by a rapid translocation to the nucleus. In light of these findings, it is not unreasonable to speculate that in aged muscle, in which innervation is reduced and HDAC4 levels are increased, HDAC4 may play a role in global chromatin remodeling and alterations in gene expression. Therefore, I am particularly interested in identifying regulatory regions of genes that are either bound by HDAC4 and/or have undergone significant changes in histone acetylation in aged muscle when compared to tissue from younger animals. This work will again entail the use of several advanced molecular techniques including ChIP-CHIP or ChIP-Seq analysis of skeletal muscle tissue in hopes of identifying global changes in DNA that occur during the aging process. This powerful and relatively new technique would allow us to analyze samples from aged rodents and potentially identify regulatory regions that might be important in the progression of aging. A long term objective of this project will be to eventually analyze identified regions of the genome using cell culture, advanced molecular techniques and animal models in hopes of elucidating the importance of these regions in the aging process.
- Outstanding Faculty Scholarship Award Nominee, 2019-2020
- Outstanding Faculty Service Award Nominee, 2019-2020
- Outstanding Undergraduate Teaching Award (2018-2019)
- Outstanding Faculty Service Award Nominee, 2018-2019
- Outstanding Graduate Teaching Award Nominee, (2018-2019)
- Research Mentor of the Year Award Nominee, 2018-2019
- Outstanding Undergraduate Teaching Award Nominee, 2017-2018
- Outstanding Graduate Teaching Award Nominee, 2017-2018
- Research Mentor of the Year Award Nominee, 2017-2018
- Research Mentor of the Year Award Nominee, 2016-2017
- Distinguished Professor Award Nominee, 2015-2016
- Outstanding Graduate Teaching Award Nominee, 2014-2015
- Outstanding Undergraduate Teaching Award Nominee, 2014-2015
- Outstanding Faculty Engaged Scholarship Award Nominee, 2013-2014
- Outstanding Faculty Service Award Nominee, 2013-2014
- Outstanding Faculty Scholarship Award Nominee, 2013-2014
- Distinguished Professor Award Nominee, 2013-2014
- Outstanding Undergraduate Teaching Award (2012-2013)
- Distinguished Professor Award Nominee, 2012-2013
- Distinguished Professor Award Nominee, 2010-2011
- American Physiological Society (APS) - Member (2011 - present)
- American Society of Biochemistry and Molecular Biology (ASBMB) - Member (2011 - present)
- American Society for Cell Biology (ASCB) - Member (2011 - present)
- Society of Integrative and Comparative Biology (SICB) - Member (2012 - present)
- Council on Undergraduate Research (CUR - Member (2018 - present)
- National Association of Advisors for the Health Professions (NAAHP) - Member (2016 - present)
Grants and Contracts Awarded
- UNF Transformational Learning Opportunity Grant, 2020-2021 ($18,000)
- UNF Transformational Learning Opportunity Grant, 2019-2020 ($23,000)
- UNF Transformational Learning Opportunity Grant, 2018-2019 ($23,000)
- UNF Academic Affairs Faculty Development Scholarship Grant, 2018-2019 ($7500)
- Research Enhancement Plan Grant, 2018-2019 ($1500)
- UNF Transformational Learning Opportunity Grant, 2017-2018 ($20,000)
- UNF Transformational Learning Opportunity Grant, 2016-2017 ($20,500)
- UNF Foundation Board Grant, 2015-2016 ($14,112)
- UNF Transformational Learning Opportunity Grant, 2015-2016 ($24,500)
- UNF Academic Affairs Faculty Development Grant, 2015 ($7500)
- COAS Experiential Learning Grant, 2015 ($1000 from COAS and $500 from Biology Department)
- COAS-ORSP Research Enhancement Award, 2014 ($3000 and paid course release)
- UNF Transformational Learning Opportunity Grant, 2014 - 2015 ($21,000)
- UNF Transformational Learning Opportunity Grant, 2013 - 2014 ($24,500)
- UNF Transformational Learning Opportunity Grant, 2012 - 2013 ($8500)
- UNF Academic Affairs Faculty Development Grant, 2012 ($7500)
- COAS Dean's Leadership Council Fellowship Award, 2012 ($4000 and paid course release)
- UNF Transformational Learning Opportunity Grant, 2011 - 2012 ($20,000)
- UNF Academic Affairs Faculty Development Grant. 2011 ($7500)
- Ruth L. Kirschstein National Research Service Award (NRSA) Postdoctoral Fellowship from the National Institutes of Health, 2005 - 2008 Grant Number: 5F32 AR052611-03 (~$116,340)
- Department of Defense Breast Cancer Research Predoctoral Fellowship, 2001 - 2003, (~$45,000)
Publications & Presentations
Google Scholar Citation Statistics Summary (as of July 2020):
- Total number of citations = 1576
- h-index = 12
- i10-index = 12
Research Gate Profile: https://www.researchgate.net/profile/David_Waddell
*: denotes UNF undergraduate student co-author, **: denotes UNF graduate student co-author
Peer Reviewed Publications:
Hughes, D.C., Baehr, L.M., Driscoll, J.R.*, Lynch, S.A.**, Waddell, D.S.^, and Bodine, S.C.^ Identification and Characterization of Fbxl22, a Novel Skeletal Muscle Atrophy-Promoting E3 Ubiquitin Ligase. American Journal of Physiology - Cell Physiology. 2020 Aug 12. Epub ahead of print. doi.org/10.1152/ajpcell.00253.2020 ^Co-corresponding authors. Call for Papers: Muscle Wasting: Cellular and Molecular Mechanisms.
Cooper, L.M.**, West, R.C.*, Hayes, C.S.**, and Waddell, D.S. Dual Specificity Phosphatase 29 is Induced During Neurogenic Skeletal Muscle Atrophy and Attenuates Glucocorticoid Receptor Activity in Muscle Cell Culture. American Journal of Physiology - Cell Physiology. 2020 Aug 1; 319(2): C441-454. doi.org/10.1152/ajpcell.00200.2020 Call for Papers: Muscle Wasting: Cellular and Molecular Mechanisms.
Cooper, L.M.** and Waddell, D.S. A Tale of Two DUSP27s - Proposed Resolution for the Naming of Distinct Dual Specificity Phosphatases. American Journal of Physiology - Cell Physiology. 2020 Jul 1; 319(1):C148-C150. doi.org/10.1152/ajpcell.00201.2020
Cooper, L.M.**, Hanson, A.*, Kavanagh, J.A.*, and Waddell, D.S. Fam83d Modulates MAP Kinase and AKT Signaling and is Induced During Neurogenic Skeletal Muscle Atrophy. Cellular Signalling. Volume 70, 2020. doi.org/10.1016/j.cellsig.2020.109576
Labuzan, S.A.#,**, Lynch, S.A.#,**, Cooper, L.M.**, and Waddell, D.S. Inhibition of Protein Phosphatase Methylesterease 1 Dysregulates MAP Kinase Signaling and Attenuates Muscle Cell Differentiation. Gene. Volume 739, 2020. doi.org/10.1016/j.gene.2020.144515 #These authors contributed equally to this work.
Lynch, S.A.**, McLeod, M.A.*, Orsech, H.C.*, Cirelli, A.M.*, and Waddell, D.S. Zinc Finger Protein 593 is Upregulated During Skeletal Muscle Atrophy and Modulates Muscle Cell Differentiation. Experimental Cell Research. 383(2) 2019. doi.org/10.1016/j.yexcr.2019.111563
Hayes, C.S.**, Labuzan, S.A.**, Menke, J.A.*, Haddock, A.N.**, and Waddell, D.S. Ttc39c is Upregulated During Skeletal Muscle Atrophy and Modulates ERK1/2 MAP Kinase and Hedgehog Signaling. Journal of Cellular Physiology. 234(12) 2019: 23807-23824. doi.org/10.1002/jcp.28950
Haddock, A.N.#**, Labuzan, S.A.#**, Haynes, A.E.*, Hayes, C.S.**, Kakareka, K.M.** and Waddell, D.S. Dual-specificity Phosphatase 4 (Dusp4) is Upregulated During Skeletal Muscle Atrophy and Modulates Extracellular Signal-Regulated Kinase (ERK) Activity. American Journal of Physiology - Cell Physiology. 2019 Apr 1; 316(4):C567-C581. #These authors contributed equally to this work. APSselect Award. doi.org/10.1152/ajpcell.00234.2018
Waddell, D.S., Duffin, P.J.*, Haddock, A.N.**, Triplett, V.E.*, Saredy, J.J.**, Eldredge, J.T.* and Kakareka, K.M.* Isolation, Expression Analysis and Characterization of NEFA Interacting Nuclear Protein 30 and RING Finger and SPRY Domain Containing 1 in Skeletal Muscle. Gene. 576(1) 2016: 319-332. doi.org/10.1016/j.gene.2015.10.046
Furlow, J.D., Watson, M.L., Waddell, D.S., Neff, E.S., Baehr, L.M., Ross, A.P. and Bodine, S.C. Altered Gene Expression Patterns in Muscle Ring Finger 1 Null Mice During Denervation and Dexamethasone Induced Muscle Atrophy. Physiological Genomics. 45(13) 2013: 1168-85. doi.org/10.1152/physiolgenomics.00022.2013
Loucks K., Waddell, D.S., and Ross, C. Lipopolysaccharides Elicit an Oxidative Burst as a Component of the Innate Immune System in the Seagrass Thalassia testudinum. Plant Physiol Biochem. 70 2013: 295-303.
Gomes, A.V., Waddell, D.S., Siu, R., Stein, M., Dewey, S., Furlow, J.D., and Bodine, S.C. Upregulation of Proteasome Activity in Muscle RING Finger 1-null Mice Following Denvervation. FASEB J. 26(7) 2012: 2986-99. doi.org/10.1096/fj.12-204495
Waddell, D.S., Baehr, L.M., van den Brandt, J., Johnsen, S.A., Reichardt, H.M., Furlow, J.D. and Bodine, S.C. The Glucocorticoid Receptor and FoxO1 Synergistically Activate the Skeletal Muscle Atrophy Associated MuRF1 Gene. Am J Physiol Endocrinol Metab. 295(4) 2008: 785-797. doi.org/10.1152/ajpendo.00646.2007
Guo, X., Waddell, D.S.*, Wang, W., Liberati, N.T., Yong, S., Liu, X. and Wang, X-F. Ligand-dependent ubiquitination of Smad3 is regulated by casein kinase 1 gamma 2, an inhibitor of TGF-b signaling.Oncogene 27(58) 2008: 7235-47. *Co-First Author.
Guo, X., Ramirez, A., Waddell, D.S., Liu, X., and Wang, X-F. Axin and GSK3-β control Smad3 protein stability and modulate TGF-β signaling. Genes and Development 22(1) 2008: 106-120.
Cohen, T.J., Waddell, D.S., Barrientos, T., Lu, Z., Feng, G., Cox, G.A., Bodine, S.C. and Yao, T-P. The Histone Deacetylase HDAC4 Connects Neural Activity to Muscle Transcriptional Reprogramming. J. Biol. Chem. 282(46) 2007: 33752-33759.
Weidner, W.J., Waddell, D.S. and Furlow, J.D. Measurement of the filtration coefficient (Kfc) in the lung of Gallus domesticus and the effects of increased microvascular permeability. J. Comp. Physiol. [B]. 176(6) 2006: 567-74.
Waddell, D.S., Liberati, N.T., Guo, X., Frederick, J.P. and Wang, X-F. A Functional Role for Casein Kinase Iε in the TGF-β Signaling Pathway. J. Biol. Chem. 279(28) 2004: 29236-29246.
Frederick, J.P., Liberati, N.T., Waddell, D.S., Shi, Y. and Wang, X-F. TGF-β Mediated Transcriptional Repression of c-myc is Dependent on Direct Binding of Smad3 to a Novel Repressive Smad Binding Element. Mol. Cell. Biol. 24(6) 2004: 2546-59.
Shen, X., Li, J., Hu, P. P-C., Waddell, D.S., Zhang, J. and Wang, X-F. The Activity of Guanine Exchange Factor Net1 is Essential for TGF-b Mediated Stress Fiber Formation. J. Biol. Chem. 276(18) 2001: 15362-15368.
Weidner, W.J., Waddell, D.S. and Sillman, A.J. Low Levels of Cadmium Chloride Alter the Immunoprecipitation of Corneal Cadherin-Complex Proteins. Archives of Toxicology. Arch. Toxicol. 74(10) 2000: 578-581.
Kim, A.E., Dintaman, J.M., Waddell, D.S. and Silverman, J.A. Saquinavir, an HIV Protease Inhibitor, is Transported by p-Glycoprotein. J Pharmacol Exp Ther. 286(3) 1998: 1349-1445.