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A list of our published work can also be found at PubMed:

bioRxiv | March 2023

Chaiamarit T, Verhelle A, Chassefeyre R, Shukla N, Novak SW, Andrade LR, Manor U, Encalada SE. 2023. Mutant prion protein endoggresomes are hubs for local axonal organelle-cytoskeletal remodeling. bioRxiv doi:

Bio-Protocol | April 2023


Chaiamarit T., Wu Y., Verhelle A., Encalada S.E. 2023. Fluorescence assays for real-time tracking of cell surface protein internalization and endosomal sorting in axons of primary mouse hippocampal neurons. Bio-Protocol 13(07): e4651. DOI: 10.21769/BioProtoc.4651.

bioRxiv | September 2022


Yoon L., Botham R.C., Verhelle A., Sanz-Martinez P., Xu J.,  Cole C.M., Tan E.P., Chou C.C., Cuoco C.A., Massey L.A., Labra S., Elia L.P., Ta A., Ardejani M.S., Lee K., Kline G.M., Xiao Q., Cano-Franco S., Lyang N.J., Hou W.C., Yu A., Fox S., Ko Y., Wulkop-Gil C., Ibrahim L.H., Jiang S., Meneses A., Nelson L.T., Peng H., Lipton S.A., Bollong M.J., Hansen M., Morimoto R.I., Petrassi H.M., Wiseman R.L., Powers E.T., Finkbeiner S., Garza D., Finley D., Prado M.A., Dikic I., Frydman J.*, Johnson K.A.*, Silva M.C.*, Haggarty S.J.*, Stolz A.*, Encalada S.E.*, Kelly J.W.* 2022. mTOR inhibitor-independent autophagy activator ameliorates tauopathy and prionopathy neurodegeneration phenotypes. bioRxivSept 30.

* Co-corresponding authors.

Science Advances | December 2021


Chassefeyre R., Chaiamarit T., Verhelle A., Novak S.W., Andrade L.R., Leitao A.D.G., Manor U., Encalada S.E. 2021Endosomal Sorting Drives the Formation of Mutant Prion Protein Endoggresomes. Cover article, Sci. Adv. Dec 22; 7(52), DOI: 10.1126/sciadv.abg3693.

bioRxiv version at:


         Comment on Faculty Opinions:







Autophagy | October 2021


Nieto-Torres J.L., Encalada S.E., Hansen M. 2021. LC3B phosphorylation: autophagosome's ticket for a ride toward the cell nucleus. Autophagy. Oct;17(10):3266-3268. 

doi: 10.1080/15548627.2021.1961073. Epub 2021 Aug 23.

Current Biology | August 2021


Nieto-Torres J.L., Shanahan S-L., Chassefeyre R., Chaiamarit T., Zaretski S., Landeras-Bueno S., Verhelle A., Encalada S.E.*, Hansen M.* 2021LC3 phosphorylation regulates FYCO1 binding and directional transport of autophagosomes. Current Biology. Aug 9;31(15):3440-3449.e7. doi: 10.1016/j.cub.2021.05.052 PubMed PMID: 34146484; NIHMSID:NIHMS1717570.

* Co-corresponding authors.

bioRxiv version at:

Viruses | July 2021


Race B., Williams K., Baune C., Striebel J.F., Encalada S.E., Chesebro B. 2021Deletion of Kif5c does not alter prion disease tempo or spread in mouse brain. Viruses. Jul;13(7), 1391.

Human Molecular Genetics | May 2019

Butler V.J., Salazar D.A., Soriano-Castell D., Alves-Ferreira M., Dennissen F.J.A., Vohra M., Oses-Prieto J.A., Li K.H., Wang A.L., Jing B., Li B., Groisman A., Gutierrez E., Mooney S., Burlingame A.L., Ashrafi K., Mandelkow E-M., Encalada S.E., Kao A.W. 2019Tau/MAPT disease-associated variant A152T alters tau function and toxicity via impaired retrograde axonal transport. Human Molecular Genetics. May 1;28(9):1498-1514. PMID: 30590647. PMCID: PMC6489414 

PNAS | July 2018

Madhivanan K., Greiner E.R., Alves-Ferreira M., Soriano-Castell D., Rouzbeh N., Aguirre C.A., Paulsson J.F., Chapman J., Jian X., Ooi F.K., Lemos C., Dillin A., Prahlad V., Kelly J.W., Encalada S.E. 2018Cellular Clearance of Circulating Transthyretin Decreases Cell Non-Autonomous Proteotoxicity in Caenorhabditis elegans.  Proc Natl Acad Sci U S A. Jul 30;115(33) E7710-E7719. doi: 10.1073/pnas.1801117115. PMID:30061394. PMCID: PMC6099907.

          Cited in EurekAlert!:             

Traffic | October 2016

Neumann S., Chassefeyre R., Campbell G.E., Encalada S.E. 2017. KymoAnalyzer: a software tool for the quantitative analysis of intracellular transport in neurons. TrafficJan;18(1):71-88. doi: 10.1111/tra.12456. Epub 2016 Dec 11. PMCID: PMC5473519.

Click here to download the KymoAnalyzer software!

eLife | December 2015

Rangaraju S., Solis G.M., Thompson R.C., Gomez-Amaro R.L., Kurian L., Encalada S.E., Niculescu III A.B., Salomon D.R., Petrascheck M. 2015Suppression of transcriptional drift extends C. elegans lifespan by postponing the onset of mortality. eLife. Dec 1;4:e08833. doi: 10.7554/eLife.08833. PMCID: PMC4720515.  

Nature Reviews Drug Discovery | September 2015

Eisele Y.S., Monteiro C., Fearns C., Encalada S.E., Wiseman R.L., Powers E.T., Kelly J.W. 2015Targeting protein aggregation for the treatment of degenerative diseases. Nat Rev Drug Discov. Nov;14(11):759-80. doi: 10.1038/nrd4593.  PMCID: PMC4628595


J Am Chem Soc | June 2015

Baranczak A., Liu Y., Connelly S., Han Du W-E., Greiner E.R., Genereux J.C., Wiseman R.L., Eisele Y.S., Bradbury N.C., Dong J., Noodleman L., Sharpless K.B., Wilson I.A., Encalada S.E.*, Kelly J.W.* 2015A fluorogenic aryl fluorosulfate for intraorganellar transthyretin imaging in living cells and in Caenorhabditis elegans. J Am Chem Soc. Jun 17;137(23):7404-14. doi: 10.1021/jacs.5b03042. Epub 2015 Jun 8. PMCID: PMC4472559

*Co-corresponding Authors



JoVE | October 2014

Neumann S., Campbell G.E., Szpankowski L., Goldstein L.S.B., Encalada S.E.* 2014Characterizing the composition of molecular motors on moving axonal cargo using “Cargo Mapping” analysis. J Vis Exp. Oct 30;(92):e52029. doi: 10.3791/52029 PMCID: PMC4353387.

*Corresponding Author

      Click here to see JoVE Video!

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Annual Review of Biophysics | May 2014

Encalada S.E.*, & Goldstein L.S.B.* 2014. Biophysical challenges to axonal transport: motor-cargo deficiencies and neurodegeneration. Annu Rev Biophys141-69. PMID: 24702007. PMID: 24702007.

*Co-Corresponding authors

J Cell Sci | April 2014


Otero M.G., Alloatti M., Cromberg L.E., Almenar-Queralt A., Encalada S.E., Pozo Devoto V.M., Bruno L., Goldstein L.S.B., Falzone T.L. 2014Fast axonal transport of the proteasome complex depends on membrane interaction and molecular motor function. J Cell Sci. Apr 1;127(Pt 7):1537-49. doi: 10.1242/jcs.140780. PMID: 24522182. 


PNAS | May 2012

Szpankowski L., Encalada S.E., Goldstein L.S.B. 2012Subpixel colocalization reveals amyloid precursor protein-dependent kinesin-1 and dynein association with axonal vesicles. Proc Natl Acad Sci U S A. 2012May 29;109(22):8582-7. doi: 10.1073/pnas.1120510109. PMID: 22582169. PMCID: PMC3365224. 

          Cited in Faculty of 1000:
          Stevens, D:


Cell | February 2011

Encalada S.E.*, Szpankowski L., Xia C.H., Goldstein L.S.B.* 2011Stable kinesin and dynein assemblies drive the axonal transport of mammalian prion protein vesicles. CellFeb 18;144(4):551-65. PMID: 21335237. PMCID: PMC3576050. 

*Co-Corresponding authors


          Cited in Faculty of 1000:
              Sheng Z:
              Kuta A, Fisher E:
          Cited in Alzheimer Research Forum:

     Featured in:


Encalada S.E., Goldstein L.S.B. 2009Axonal Transport of the Prion Protein and Prion Neuroinvasion. The New Encyclopedia of Neuroscience (Larry Squire, ed.). Elsevier, Oxford, UK, pp. 1071-1075.



Encalada S.E., Moya K.L., Lehmann S., Zahn R. 2007The role of the prion protein in the molecular basis for synaptic plasticity and nervous system development. J Mol Neurosci. 34(1):9-15. Epub 2007 Jun 14. doi: 10.1007/s12031-007-0011-x. PMID: 18157653. 

[PubMed Link]



Encalada S.E., Willis J., Lyczak R., Bowerman B. 2005A spindle checkpoint functions during mitosis in the early Caenorhabditis elegans embryo. Mol Biol Cell.  Mar;16(3):1056-70. Epub 2004 Dec 22. (cover). doi: 10.1091/mbc.e04-08-0712. PMID: 15616189. PMCID: PMC551473. 

[PubMed Link]



Gomes J.E., Encalada S.E., Swan K.A., Shelton C.A., Carter J.C., Bowerman B. 2001The maternal gene spn-4 encodes a predicted RRM protein required for mitotic spindle orientation and cell fate patterning in early Caenorhabditis elegans embryos. Development128(21):4301-14. PMID: 11684665.

[PubMed Link]



Encalada S.E., Martin P.R., Phillips J.B., Lyczak R., Hamill D.R., Swan K.A., Bowerman B. 2000DNA replication defects delay cell division and disrupt cell polarity in early Caenorhabditis elegans embryos.  Developmental Biology. Dec 15;228(2):225-38. doi: 10.1006/dbio.2000.9965. PMID: 11112326. 

[PubMed Link]


Fernando P., Pfrender M.E., Encalada S.E., Lande R. 2000Mitochondrial DNA variation, phylogeography and population structure of the Asian elephant. Heredity (Edinb). Mar;84 ( Pt 3):362-72. doi: 10.1046/j.1365-2540.2000.00674.x. PMID: 10762406. 

[PubMed Link]


Encalada S.E., Zurita J.C., Bowen B.W. 1999Genetic consequences of coastal development:  the sea turtle rookeries at X’cacel Mexico. Marine Turtle Newsletter. 83:8-10.



Bolten A.B., Bjorndal K.A., Martins H.R., Dellinger T., Biscoito M.J., Encalada S.E., Bowen B.W. 1998Transatlantic developmental migrations of loggerhead sea turtles demonstrated by mtDNA sequence analysis.  Ecological Applications. 8:1-7.



Encalada S.E., Bjorndal K.A., Bolten A.B., Zurita J.C., Schroeder B., Possardt, E., Sears C.J., Bowen B.W. 1998. Population structure of loggerhead turtle (Caretta caretta) nesting colonies in the Atlantic and Mediterranean as inferred from mitochondrial DNA control region sequences. Marine Biology1130:567-575.



Lahanas P.N., Bjorndal K.A,. Bolten A.B., Encalada S.E., Miyamoto M.M., Valverde R.A., Bowen B.W. 1998. Genetic composition of a green turtle (Chelonia mydas) feeding ground population:  evidence for multiple origins.  Marine Biology 130:345-352.



Rankin-Baransky K., Williams C.J., Bowen B.W., Encalada S.E., Spotila J.R. 1998Origin of loggerhead sea turtles in the western north Atlantic as determined by mtDNA analysis. In: Proceedings of the Seventeenth Annual Sea Turtle Symposium. (Epperly, S. P., and Braun, J. Compilers), U.S. Dep.  Commer.  NOAA Tech Memo. NMFS-SEFSC-415. 294 pp.; 1998, p. 79. doi: 10.2307/1565903



Encalada S.E., Lahanas P.N., Bjorndal K.A., Bolten A.B., Miyamoto M.M., Bowen B.W. 1996Phylogeography and population structure of the green turtle (Chelonia mydas) in the Atlantic Ocean and Mediterranean Sea:  a mitochondrial DNA control region assessment. Molecular EcologyAug;5(4):473-83. PMID: 8794558.

[PubMed Link]



Encalada S.E. 1996. Conservation genetics of Atlantic green turtles:  cases of imminent rookery extinctions.  In:  Proceedings of the First Sea Turtle Genetics Symposium (Bowen, B. W., and W. N. Witzell, eds). NOAA Technical Memorandum NMFS-SEFSC-396, pp33-40.



Abreu-Grobois F.A., Bass A.L., Dutton P.H., Encalada S.E. 1996PCR-RFLP analysis of sea turtle populations in the era of DNA sequencing:  is it still useful? In:  Proceedings of the First Sea Turtle Genetics Symposium (Bowen, B. W., and W. N. Witzell, eds).  NOAA Technical Memorandum NMFS-SEFSC-396, pp55-67.

Encalada S.E., Eckert S.A., Bowen B.W. 1994Forensic applications of mitochondrial DNA markers:  origin of a confiscated green turtle. Marine Turtle Newsletter 66:1-3. [Link]



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