Joe Daniele, Ph.D.

Post-doctoral Fellow



I received my Bachelor’s degree in Biology from the Massachusetts Institute of Technology (MIT) and my Ph.D. in Biochemistry from Harvard University in Cambridge, MA. In my doctoral work, I employed a wide range of techniques to study how the morphogen Hedgehog (Hh), which is implicated in stem cell maintenance and neoplastic disease (cancer), is released from Drosophila photoreceptor neurons (Biology Open 2017a,b). This work provided a new, important, and accessible target for human cancer treatment and drug development.

In my post-doc, I developed tools to characterize the organelle basis of aging and disease. With Prof. Edgar Arriaga (U. Minnesota) I developed high-throughput methods to measure mitochondrial bioenergetics and morphology at the organelle and organismal level. Through flow cytometric analysis, I developed a technique to characterize mitochondrial subpopulations from crude isolates (Anal Chem 2016, Dev Cell 2017, Curr Prot Cyt 2018). With Prof. Anu Suomalainen-Wartiovaara (U. Helsinki) I have applied this method to the characterization of mitochondrial subpopulations in patient-derived heteroplasmic cells. This new method has revealed a mitochondrial subpopulation which correlates with disease prognosis. Further, the ability to track these mitochondria has provided molecular insight into therapeutic targets.

With an interest in performing whole-organismal measures of health, I developed a software and data visualization platform for large particle flow cytometer data to enable high-throughput characterization of (1) mitochondrial bioenergetics and morphology and (2) lipid quantity and distribution (Sci Reports 2017). This platform has dramatically increased the quality of screening data and enabled (1) the identification of early prognostic biomarkers for longevity, and (2) a comprehensive characterization of endoplasmic reticulum stress-induced longevity. These new tools offer the complement of high-throughput screening (of organismal models of human disease and aging) and high-content characterization of potentially pathogenic organelles.


Current Collaborations

Dr. Edgar Arriaga, Department of Chemistry, University of Minnesota

Dr. Anu Wartiovaara, Program for Molecular Neurology, University of Helsinki

Union Biometrica, Inc. 



Technique Development

Daniele JR, Heydari K, Dillin A.  Mitochondrial Subtype Identification and Characterization.  Curr Protoc Cytome.  2018 July.

Daniele, J.R., Esping, D.J., Garcia, G., Parsons, L.S., Arriaga, E.A., Dillin, A. High-Throughput Characterization of Region-Specific Mitochondrial Function and Morphology.Scientific Reports 2017 Jul 27;7(1):6749. (andPresented at the Bay Area Meeting on Organelle Biology, BAMOB, Berkeley, CA 06/06/2017 and the International Flow Cytometry Conference, CYTO 2017, Boston, MA 06/14/2017) [PDF]

Daniele J.R., Heydari, K., Arriaga, E.A., Dillin, A. Identification and characterization of mitochondrial subtypes in C. elegans via analysis of individual mitochondria by flow cytometry. Analytical Chemistry 2016, May 23. (and Presented at the International CE Topics Conference, Madison, WI 7/23/16). [PDF]

Zhang X*, Roeffaers MBJ*, Basu S*, Daniele JR, Fu D, Freudiger CW, Holtom GR, Xie XS. Label-free Live Cell Imaging of Nucleic Acids using Stimulated Raman Scattering (SRS) Microscopy. ChemPhysChem. 2012 Feb 24. (* authors contributed equally) [PDF]


Biochemistry/ Cell and Developmental Biology / Neuroscience 

Nguyen, T.B., Louie, S.M., Daniele, J.R., Tran, Q., Dillin, A., Zoncu, R.,, Nomura, D.K., Olzmann, J.A, DGAT1-dependent lipid droplet biogenesis protects mitochondrial function during starvation-induced autophagy. Dev Cell. 2017 Jul 10;42(1):9-21.e5. [PDF]

Daniele J.R., Chu T.Y., Kunes S. A Novel Proteolytic Event Controls Hedgehog Intracellular Sorting and Distribution to Receptive Fields. Biology Open 2017 May 15;6(5):540-550. doi: 10.1242/bio.024083. [PDF]

Daniele, J.R.*, Baqri, R.M.*, Kunes, S. Analysis of Axonal Trafficking via a Novel Live Imaging Technique Reveals Distinct Hedgehog Transport Kinetics. Biology Open 2017 May 15;6(5):714-721. doi: 10.1242/bio.024075. *co-first author* [PDF]

Hu Y.C., Nicholls P.K., Soh Y.Q., Daniele J.R., Junker J.P., van Oudenaarden A., Page D.C.Licensing of primordial germ cells for gametogenesis depends on genital ridge signaling. PLoS Genet. 2015 Mar 4;11(3):e1005019. [PDF] * Built upon my MIT thesis *

Jones K.M., Lloret J., Daniele J.R., Walker G.C. Characterization of type IV secretion system mutants of Sinorhizobium meliloti strain 1021. J Bacteriol. 2007 Mar;189(5):2133-8. [PDF]


Brain and Cognitive Science

Daniele, J.R. The ‘Rhythmic Fingerprint’: An extension of the nPVI to quantify rhythmic influence. Empirical Musicology Review 2017 11 (2), 243-260. [PDF]

Daniele J.R. A tool for the quantitative anthropology of music: Use of the nPVI equation to analyze rhythmic variability within long-term historical patterns in music.Empirical Musicology Review 2017 11 (2), 228-233and Presented at the International Cognition and Perception Conference ICMPC14 in San Francisco, CA, July 9th, 2016) [PDF]

Daniele J.R. & Patel, A.D. Stability and change in rhythmic patterning across a composer’s lifetime: a study of four famous composers using the nPVI equation. Music Perception Dec. 2015, Vol. 33 No. 2, pp. 255-265. [PDF]

Daniele J.R. & Patel, A.D. An empirical study of historical patterns in musical rhythm: Analysis of German & Italian classical music using the nPVI equation. Music Perception Sept. 2013, Vol 31, Issue 1, pp. 10–18, ISSN 0730-7829.- featured in a corpus issue on “Empirical Musicology Methods” [PDF]

Daniele, J.R. & Patel, A.D. The interplay of linguistic and historical influences on musical rhythm in different cultures. In: Proc. of the 8th Intl. Conference on Music Perception and Cognition, Evanston, IL, 2004. S.D. Lipscomb et al. (Eds.),pp. 759-762. Adelaide: Causal Productions. [PDF]

Patel, A.D. & Daniele, J.R. Stress-timed vs. syllable-timed music? A comment on Huron and Ollen. Music Perception, 2003 21:273-276.  [PDF]

Patel A.D. & Daniele J.R. An empirical comparison of rhythm in language and music. Cognition. 2003 Feb;87(1):B35-45. (and Presented at ICMPC7, Sydney, Australia 7/18/02) [PDF]