Research Divisions

Subcellular Architecture

Group LeaderLocation and ContactMembersHistory of the GroupLines of ResearchNotable PublicationsProjectsPhD ThesesNews
Dr José Jesús Fernández

José Jesús Fernández is a CSIC Research Scientist affiliated to CINN (Centro de Investigación en Nanomateriales y Nanotecnología) who joined ISPA in 2020. He obtained his PhD in Information Technology from the Universidad de Granada in 1997 and was a Tenured Lecturer at the Universidad de Almería until 2009. He spent five years (2002-2006) as a visiting scientist at the prestigious Laboratory of Molecular Biology in Cambridge (UK), an institute with more than ten Nobel prizes, working with Dr RA Crowther (one of the pioneers of tomographic reconstruction methods) and Dr R. Henderson (Nobel Laureate in Chemistry 2017). From 2009 to 2013, he was an Associate Researcher at the Agencia Nacional de Evaluación y Prospectiva (National Agency for Assessment and Prospective Studies), Ministerio de Ciencia e Innovación, where he led the Image Processing and High Performance Computing lines of research within the Information Technology division (INF).

His scientific career has focused primarily on structure determination through nanotomography and image processing techniques, his work straddling methodological development and resolution of the structural problem in molecular biology, cell biology and biomedicine. His scientific contributions are situated within the fields of new computational methods for tomographic data processing and the structural characterisation of important biological and biomedical specimens. Working at the forefront of research in nanotomography, he regularly collaborates with the leading international groups in this field. He has produced more than 100 international scientific publications and his H-index is over 30. Some of his computational developments have been widely cited and have played an important role in a number of scientific achievements published in Cell, Nature and Science.

His work has been recognised with several awards and accreditations: the Best Academic Results and Outstanding PhD awards of the Universidad de Granada; the Research Award of Andalusia 2004, and ANECA (Spanish National Agency for Quality Assessment and Accreditation) accreditation for a University Professorship in 2008.


Avenida Hospital Universitario s/n
33011 Oviedo, Spain.

Name Organisation Activity Euraxess classification
Fernández Fernández, María del Rosario CSIC Research R2
Fernández Rodríguez, José Jesús CSIC Research R4
Martínez Sánchez, Antonio Universidad de Oviedo Research R3
Sola Alarcón, Pablo CSIC Research No classification

Our group has a long history of conducting structural studies using nanotomography and image processing. We develop computational methods for tomographic data processing and analysis and use them for the 3D structural characterisation of important biological and biomedical specimens, such as microtubule organising centres (MTOCs).

The group´s main line of work dates back to 2010, when our newest member joined, neurobiologist Dr M.R. Fernández-Fernández. Her incorporation enabled us to establish an innovative new line of research, involving the in situ analysis of subcellular architecture and the characterisation of alterations in neurodegenerative processes, using Huntingdon’s Disease (HD) as a model. Our working hypothesis is that identifying structural alterations in the subcellular architecture can provide information about the pathogenic bases of diseases, enable therapeutic targets to be identified and serve as a biomarker for disease progression and the effect of potential treatments.

Within this line of work, we have developed protocols for the extraction and optimal preservation of brain tissue and peripheral tissue (muscle) through cryofixation techniques that keep the tissue extremely close to its native state. We use cutting-edge nanotomography techniques and advanced 3D image processing methods as key tools for obtaining quantitative 3D information and objectively interpreting the alterations in pathological conditions.

During this period, we have secured national, international and individual funding at a range of levels and have performed multidisciplinary training that is commensurate with the nature of our research.

Current and Future Priorities
Upon joining ISPA, our priority is to expand our work to include the analysis of HD patient biopsies, which is the natural next step in our research, making the most of the opportunity ISPA offers us to interact directly with clinical groups. This will facilitate analysis of the subcellular architecture of peripheral tissue biopsies, which are more accessible and may be obtained in a minimally invasive manner, so as to monitor biomarkers of disease progression and, ideally, the effect of therapies. Additionally, studying brain tissue samples from post-mortem subjects, typically as a reflection of the most advanced stages of the disease, will also be of enormous interest for our research. Interaction with clinical groups will enable us to expand our lines of work in the near-future, to include research into other neurodegenerative diseases and other pathological conditions that are suitable for study through our experimental approach.

The incorporation of the group and its technical knowledge in image processing into ISPA may also serve to provide additional support to the various bioimaging platforms within the institute. Our collaboration with the ISPA groups that use these platforms may stimulate the development of new image processing and analysis methods.

  • Analysis of subcellular architecture using nanotomography and image processing
  • Analysis of Microtubule Organising Centres using cryo-electron tomography
  • Development of 2D and 3D image-processing methods
  • High-performance computing
Analysis of subcellular architecture using nanotomography and image processing
  • J.J. Fernández, T.E. Torres, E. Martín-Solana, G.F. Goya, M.R. Fernández-Fernández. (2020) PolishEM: image enhancement in FIB-SEM. Bioinformatics 36:3947-3948.
  • I. Fernandez de Castro, R. Tenorio, P. Ortega-Gonzalez, J.J. Knowlton, P.F. Zamora, C. H. Lee, J.J. Fernández, T.S. Dermody, C. Risco. (2020) A modified lysosomal organelle mediates nonlytic egress of reovirus. J Cell Biol 219: e201910131.
  • J.J. Fernández, S. Li, D.A. Agard (2019) Consideration of sample motion in cryo-tomography based on alignment residual interpolation. J Struct Biol 205:1-6.
  • S. Li, J.J. Fernández, W. Marshall, D.A. Agard (2019). Electron Cryo-Tomography Provides Insight into Procentriole Architecture and Assembly Mechanism. eLife 8:e43434.
  • J.J. Fernández, S. Li, T.A.M. Bharat, D.A. Agard. (2018) Cryo-tomography tilt-series alignment with consideration of the beam-induced sample motion. J Struct Biol 202:200-209.
  • J.J. Moreno, A. Martinez-Sanchez, J.A. Martinez, E.M. Garzon, J.J. Fernández. (2018) TomoEED: Fast Edge-Enhancing Denoising of Tomographic Volumes. Bioinformatics 34:3776-3778.
  • M.R. Fernandez-Fernandez, D. Ruiz-Garcia, E. Martin-Solana, F.J. Chichon, J.L. Carrascosa, J.J. Fernández (2017) 3D electron tomography of brain tissue unveils distinct Golgi structures that sequester cytoplasmic contents in neurons. J Cell Sci 130:83-89.
  • I.H. Hernández, J. Torres-Peraza, M. Santos-Galindo, E. Ramos-Morón, M.R. Fernández-Fernández, M.J. Pérez-Álvarez, A. Miranda-Vizuete, J.J. Lucas. (2017) The neuroprotective transcription factor ATF5 is decreased and sequestered into polyglutamine inclusions in Huntington’s disease. Acta Neuropathologica 134:839-850.
  • I. Fernandez de Castro, J.J. Fernández, D. Barajas, P.D. Nagy, C. Risco. (2017) Three-dimensional imaging of the intracellular assembly of a functional viral RNA replicase complex. J Cell Sci 130:260-268.
  • M. Bernabe-Rubio, G. Andres, J. Casares-Arias, J. Fernandez-Barrera, L. Rangel, N. Reglero-Real, D.C. Gershlick, J.J. Fernández, J. Millán, I. Correas, D.G. Miguez, M.A. Alonso. (2016) Novel role for the midbody in primary ciliogenesis by polarized epithelial cells. J Cell Biol 214:259-273.
  • E. Vazquez-Fernandez, M.R. Vos, P. Afanasyev, L. Cebey, A.M. Sevillano, E. Vidal, I. Rosa, L. Renault, A. Ramos, P.J. Peters, J.J. Fernández, M. van Heel, H.S. Young, J.R. Requena, H. Wille. (2016) The structural architecture of an infectious mammalian prion using electron cryomicroscopy. PLoS Pathogens 12: e1005835.
  • J.J. Fernández, U. Laugks, M. Schaffer, F.J.B. Bauerlein, W. Baumeister, V. Lucic (2016) Removing contamination-induced reconstruction artefacts from cryo electron tomograms. Biophysical J 110:850–859.
  • J. Arnold, J. Mahamid, V. Lucic, A. de Marco, J.J. Fernández, T. Laugks, T. Mayer, A.A. Hyman, W. Baumeister, J.M. Plitzko (2016) Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy. Biophysical J 110:860-869.
  • J.I. Agulleiro, J.J. Fernández (2015) Tomo3D 2.0 – Exploitation of Advanced Vector eXtensions (AVX) for 3D reconstruction. J Struct Biol 189:147-152.
  • J. Kollman, C. Greenberg, S. Li, M. Moritz, A. Zelter, K. Fong, J.J. Fernández, A. Sali, J. Kilmartin, T. Davis, D.A. Agard (2015) Ring closure activates yeast gamma-TuRC for species-specific microtubule nucleation. Nature Struct Mol Biol 22:132–137.

Identification of alterations in the subcellular architecture of peripheral tissues in Huntingdon’s Disease

PI JJ Fernández
Funding Body MINECO
Reference No SAF2017-84565-R
Date 2018-2020
Budget €133,100

Grant for hiring a Youth Guarantee laboratory technician

PI JJ Fernández
Funding Body C omunidad Autónoma de Madrid (Autonomous Community of Madrid)
Reference No PEJ-2019-TL/BMD-14354
Date 2020-2022
Budget €38,000

Visualisation of neuronal polysomal architecture and its alterations in Huntingdon’s Disease

PI JJ Fernández
Funding Body Fundación Ramón Areces
Reference No CIVP18A3892
Date 2017-2020
Budget €109,599

Analysis of neuronal subcellular architecture by FIB-SEM

PI JJ Fernández
Funding Body CORBEL (Coordinated Research Infrastructures Building Enduring Life-science Services)
Reference No Project ID 2301
Date 2017-2020
Access to European biomedical research infrastructure

Quantification of the percentage of hypusine in the elF5 alpha translation factor and its relationship to the development and progression of the neurodegenerative disorder, Huntingdon’s Disease

PI M. Menéndez
Funding Body ProteoRed-ISCIII (Carlos III Networked Proteomics Platform)
Proof of Concept Projects
Date 2019-2020
Budget €5,000

Severo Ochoa and the genetic code: deciphering encrypted messages

PI M. R. Fernández
Funding Body Fundación General del CSIC (FGCSIC)
Programa Cuenta la Ciencia (Share the Science Programme)
Date 2020
Budget €3,000

Electron tomography: computation and application in Neurobiology

PI JJ Fernández
Funding Body MINECO
Reference No TIN2012-37483-C03-02
Date 2013-2015
Budget €14,812

Computational techniques based on Differential Geometry for Segmentation in Electron Tomography

PhD Student: Antonio Martínez-Sánchez
Supervisors: José Jesús Fernandez and Inmaculada Garcia
Universidad de Almería (2013)
European Honours

Biophysical characterization of a chaperone complex involved in macroautophagy

PhD Student: Marcos Gragera Cabezudo
Supervisors: María del Rosario Fernández and José María Valpuesta
Universidad Autónoma de Madrid (2020)