Robert Vidmar

PROFESSIONAL SUMMARY

My main research interests are method development for determination of protease cleavage sites and protease cleavage specificity, discovery of novel protease physiological substrates and implementation & development of bioinformatics tools for proteomics protease research. At the Department of Biochemistry, Molecular and structural biology I work at the Proteomics lab, where I cover all aspects of work from sample preparation to data analysis.

EXPERIENCE

Postdoctoral Researcher Jozef Stefan Institute

    • 2016 –

Assistant Researcher Jozef Stefan Institute

    • 2010 – 2016

Student Researcher Lek (Biopharmaceuticals Sandoz, Novartis)

    • 2008 – 2010 (with breaks)
EDUCATION

2010  – 2016

PHD Biochemistry, Jozef Stefan International Postgraduate School

Title: Proteomic characterization of legumain and its physiological substrates (mentor: prof. dr. Marko Fonović). Experimental work was performed at the Department of Biochemistry, Molecular and structural biology, Jozef Stefan Institute

2004  – 2010

University graduate in Biochemistry, B. Sc., Faculty of Chemistry and Chemical Biology, University of Ljubljana

Title: Peptide map development for identity testing of therapeutic protein (co-mentor: dr. Igor Štern, mentor: prof. dr. Lucija Zupančič-Kralj. Experimental work was performed at Lek (Biopharmaceuticals Sandoz, Novartis).

BIBLIOGRAPHY

I co-authored several research papers (PubMed, SICRIS), top 5 are listed:

Vidmar Robert, Vizovisek Matej; Turk Dušan; Turk Boris; Fonović Marko. Protease cleavage site fingerprinting by label-free in-gel degradomics reveals pH-dependent specificity switch of legumain. EMBO journal. 2017, vol. 36, no. 16, 2455-2465.

Vizovišek Matej; Vidmar Robert; Drag Marcin; Fonović Marko, Salvesen Guy Salvesen, Turk Boris. Protease Specificity: Towards In Vivo Imaging Applications and Biomarker Discovery. Trends Biochem Sci. 2018, vol. 10, 829-844.

Vidmar Robert; Vizovisek Matej; Turk Dušan; Turk Boris; Fonović Marko. Characterization of legumain degradome confirms narrow cleavage specificity. Acta chimica slovenica. 2019, vol. 66, no. 1, 50-57

Sobotič Barbara; Vizovisek Matej; Vidmar Robert; Van Damme Petra; Gocheva Vasilena; Joyce Johanna; Gevaert Kris; Turk Vito; Turk Boris; Fonović, Marko. Proteomic identification of cysteine cathepsin substrates shed from the surface of cancer cell. Molecular & Cellular Proteomics, 2015, vol. 14, no. 8, p. 2213-2228.

Vizovišek Matej; Vidmar Robert; Van Quickelberghe Emmy; Impens Francis; Andjelkovic Uroš; Sobotič Barbara; Stoka Veronika; Gevaert Kris; Turk Boris; Fonović Marko. Fast profiling of protease specificity reveals similar substrate specificities for cathepsins K, L and S. Proteomics, 2015, vol. 15, issue 14, p. 2479-2490.

Eva Žerovnik

PROFESSIONAL SUMMARY

My backgrounds are physical and structural chemistry, biochemistry and neuroscience, thus, multidisciplinary research. My carreer of the principle investigator is devoted to increase knowledge in the complementary fields of protein folding and protein mis-folding diseases (proteinopathies). We have studied oligomers, lower and higher of stefin B and their role in the process of amyloidogenesis. We have mutated the 5 prolines and discovered their important roles, both,  in protein folding and oligomerization, which can block amyloid formation. Especially, I am interested in the biophysical properties of amyloid fibrils and prefibrillar oligomers, including their interaction with cellular membranes and their optical properties. Recent aim is to visualise an “amyloid pore” by using the case of the intracellular myloidogenic protein – stefin B (cystatins B). We also study effects of antioxidants on cystatins aggregation.

I collaborate with leading labs, such as Medical School, Notthingham, Medical School, Newcastle upon Tyne, Biomolecular NMR, Sheffield, all UK., Dept. Physics, Drexel University USA, Brain and Mind Institute, Lausanne, CH and IRCCS Fatebenefratelli, Brescia, Italy.

CORE QUALIFICATIONS
    • Research title: univ.dipl.chem., MSc biochemistry, PhD science – chemistry
    • Academic title: full professor of Biochemistry, elected Nov 2017
    • Job title: scientific adviser at the “Jožef Stefan” institute, elected 4th Sep 2018
EXPERIENCE
CURRENT and PREVIOUS POSITIONS
    • Current: Institut Jožef Stefan, scientific adviser, elected 4th Sep 2018
    • From 2015 till July 2017: 10% at the Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CipKeBiP).
    • From Jan 1989 till Oct 2018: Institut Jožef Stefan, higher research assistant
    • 1986 – 1989 University of Newcastle upon Tyne, Medical School, Dept. Mol. Biology, research associate
    • 1981 – 1986 University of Ljubljana, dept physical chemistry, young assistant
MEMBERSHIPS OF SCIENTIFIC SOCIETIES

Biochemical Society U.K., American Chemical Society-ACS and several Slovenian societies: Biochemical, Chemical, Biophysical Society and Neuroscience Association – Sinapsa.   Member of the Board of Sinapsa from 2006 to 2007. From 2010 – 2018 member of ethical comitee of Sinapsa

EDITORIAL WORK, among others:
    • Amyloid. Žerovnik, Eva (editorial board member 2005-). Carnforth: Parthenon, 1994-. Abingdon: Taylor & Francis. ISSN 1350-6129.
    • Frontiers in behavioral neuroscience. Žerovnik, Eva (guest editor 2012-). Lausanne: Frontiers Research Foundation, 2007-. ISSN 1662-5153.
SUPERVISION OF GRADUATE STUDENTS AND POSTDOCTORAL FELLOWS

I have  supervised 8 post-graduate students for their PhD’s:  Manca Kenig, Sabina Rabzelj, Katja Škerget, Slavko Čeru, Mira Polajnar, Ajda Verčič-Taler at the University of Ljubljana and J.Stefan’s International postgraduate school (IPS), Ljubljana Slovenia, Aida Smajlović and Samra Hasanbasić from the University of Tuzla, Bosnia and Herzegovina. In addition, I am co-supervising a student of physics, Matjaž Žganec, who is finishing his PhD work on molecular dynamics simulations of stefins oligomers and Alma Jahić (finishing PhD) from the Uni. Tuzla. The former PhD students have all found employment, either at pharmaceutical industry or biotechnology laboratories; M.K. at University of Zurich and M.P. at Goethe University at Frankfurt a Main.

TEACHING ACTIVITIES

At J.Stefan’s International Postgraduate School (IPS) I teach two courses: “Stability, folding and aggregation of proteins” and “Mechanism and biological implications of protein aggregation”.  I also am appointed at Medical Faculty University of Ljubljana where I hold similar courses.

Lectures at foreign universities and summer schools (examples):

In vitro and cellular studies of a model amyloid protein : human stefin B : lecture presented at XIV School of Pure and Applied Biophysics on Molecular Mechanisms of Neurodegeneration, January 25-29, 2010, Venice, Italy. 2010.

Towards a general mechanism of amiloid-fibril formation : Case study of stefins: Presented at XV School of Pure and Applied Biophysics “Protein Stability and Pathways of Self-Assembly”,  January 24-28, 2011, Venice, Italy. 2011.

Stefin B case : structural and cellular studies of protein aggregation : putative new function : invited talk. Newcastle: Newcastle University, Campus for ageing & vitality, Oct. 27th,  2015.

Molecular bases of neurodegeneration : invited talk. Edinburgh: The University of Edinburgh, Centre for Intergrative Physiology, Oct. 29th,  2015.

EDUCATION
    • 1974 – 1978 BSc degree (diploma) in Chemistry, University of Ljubljana, Faculty of Chemistry
    • 1979 – 1982 MSc Biochemistry, University of Ljubljana, Medical Faculty
    • 1982 – 1987 PhD science (Chemistry) University of Ljubljana, Dept. Physical Chemistry
    • 1986 – 1989 Postdoctoral study: “A General Role of Molten Globule in Protein Folding”, University of Newcastle upon Tyne, UK, with prof. RH Pain, Medical School, Dept. Genetics and Molecular Biology
FELLOWSHIPS AND AWARDS
    • ARRS-MS_ERC_FS_JP-PP-2017 : 5 months grant to study at EPFL, prof. Hilal A Lashuel – as a host.
    • FEBS and TEMPUS 3 months fellowships in 1992 and 1994, respectively, to study NMR at the University of Sheffield, UK, with prof. Jon P. Waltho, Dept. Biomolecular NMR

 

Aleksandra Usenik

PROFESSIONAL SUMMARY

As a postdoctoral fellow in the Structural biology group lead by Prof. Dušan Turk I have been mainly involved in structural biology studies of recombinantly expressed cell wall proteins (CWPs) from Clostridioides difficile. The crystal structures of multi-domain Cwp8 and Cwp6 from C. difficile revealed the cell wall binding type 2 (CWB2) module (Usenik et al., 2017) that is shared among 29 CWPs of C. difficile 630 and represents one of the two evolutionary conserved surface layer (S-layer)-anchoring modules in Gram-positive bacteria. The aim of our studies is to gain structural insight into the CWPs to understand the functions of these proteins acting either alone or as a part of the surface (S-) layer assembly. Since no atomic resolution models of S-layers from pathogenic bacteria, such as C. difficile, have been determined so far, we hope our studies will significantly improve the knowledge in this field of research. I have also participated in structural and biochemical characterization of the system responsible for the export of CWPs and proteins involved in biosynthesis of the secondary polysaccharides that mediate anchoring of the CWPs to the cell wall.

CORE QUALIFICATIONS

molecular biology (molecular cloning and mutagenesis), protein expression, protein purification, protein crystallization, biochemical characterization of proteins

EXPERIENCE

2018 – NOW POSTDOCTORAL RESEARCHER/ RESEARCH ASSISTANT, Jožef Stefan Institute

2013-2018 PhD STUDENT/ASSISTANT with BA, Jožef Stefan Institute

Membership: Slovenian Biochemical Society

EDUCATION

2013-2018
Jožef Stefan International Postgraduate School

PhD; Structural and biochemical characterization of autolysins from Staphylococcus aureus Mu50

2008-2013
Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia

BA in Biochemistry; Preparation and use of recombinant aminopeptidase C from Lactococcus lactis ssp. cremoris to increase the crystallizability of proteins

Iztok Dolenc

PROFESSIONAL SUMMARY

My research interest is focused on the function of cysteine an aspartic cathepsins, as a part of endosomal/lysosomal proteases, by researching their regulation in normal and pathological processes.

CORE QUALIFICATIONS

Protein biochemistry, enzyme kinetics, molecular biology, cell biology.

EXPERIENCE

Since 1998 RESEARCH FELLOW, Jozef Stefan Institute

1995 – 1998 POST-DOC POSITION, Max-Planck Institute, Department for Molecular Structural Biology, Munich, Germany, Chair Professor Wolfgang Baumeister

1994 – 1995 POST-DOC POSITION, Jozef Stefan Institute, Department of Biochemistry and Molecular Biology, Ljubljana, Slovenia, Chair Professor Vito Turk

1991 – 1994 PHD STUDENT, Jozef Stefan Institute, Department of Biochemistry and Molecular Biology, Ljubljana, Slovenia, Chair Professor Vito Turk

1987 – 1991 M. SC. STUDENT, Jozef Stefan Institute, Department of Biochemistry and Molecular Biology, Ljubljana, Slovenia, Chair Professor Vito Turk

EDUCATION

1995-1998 Fellowship from Max-Planck Society

1994 Ph. D. in Chemistry – University of Ljubljana, Slovenia

1991 Sc. in Biochemistry – University of Ljubljana, Slovenia

1987 Diploma Engineer of Chemistry (B. Sc.) – University of Ljubljana, Slovenia

 

 

 

 

Georgy Mikhaylov

Education
2014, September PhD in Nanoscience and Nanotechnology. Jozef Stefan International Postgraduate School, Ljubljana, Slovenia
2007, June M.Sc. in Clinical Biochemistry. Faculty of Medical Biology, Siberian State Medical University, Tomsk, Russia (Graduated summa cum laude)
2001, January M.Sc. in Economy. Faculty of Business Administration, University of International Business, Almaty, Kazakhstan
Research and Professional Experience
2018-presence Researcher, Junior Team leader

Current research interests: in vivo Imaging, Metabolic Biochemistry, Protease Biology, Targeted Drug Delivery for Diagnostic and Therapeutic Applications.

2015-2018

Laboratory of Bioorganic Chemistry and Molecular Imaging, Federal School of Technology, Lausanne, Switzerland (EPFL).

Postdoctoral Researcher

Mentor: Tenure Track Assistant Professor Elena Goun (Dubikovskaya)

Achievements: New bioluminescent probes for monitoring of biological processes in real-time in a living system using biocompatible chemical reactions have been developed. Probes demonstrated excellent selectivity and a high potential for visualization of metabolic uptake of biological molecules (glucose, nicotinamide riboside) and detection of proteolytic activity in pathological conditions both in vitro and in vivo.

Research outputs: This work was presented at several international conferences and published in Nature Methods journal (IF 28.467).

2014–2015

Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia

Postdoctoral Researcher, Head of the Histology Laboratory

Mentor: Associate Professor Olga Vasiljeva

Achievements:

The study demonstrated that nanoparticle-based systems capable of disturbing extracellular tumor microenvieronment ion balance is a novel class of inorganic materials that exhibit a strong antitumor effect.

Research outputs: this work was published in NanoLetters journal (IF 12.080) and possible application of investigated nanomaterials was covered in the patent application.

2008-2014

Jozef Stefan International Postgraduate School, Ljubljana, Slovenia

PhD student, Research Assistant

Mentor: Associate Professor Olga Vasiljeva

Thesis: Development of a Novel Nano-Carriers for Targeted Drug Delivery and Diagnostics

Achievements: New delivery platforms for targeting the tumor and its microenvironment, based on ferrimagnetic nano-clusters (ferri-liposomes) and lipidated inhibitor of cysteine protease, cathepsin B, (LNC-NS-629), have been developed. Ferri-liposomes and LNC-NS-629 were shown to act as universal drug delivery systems, confirmed by the successful delivery of several chemically different types of cargo (therapeutic and diagnostic) to the tumor site.

Research outputs: This work was presented at several international conferences including two oral presentations at XI International Conference on Nanostructured Materials (Rhodes, Greece) and Gordon Research Conference (Barga, Italy). This work was published in Nature Nanothechnology Journal (IF 33.265), Angewandte Chemie International Edition Journal (IF 11.336). Development and possible applications of the developed targeting systems were covered in two patent applications.

2007-2008

Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia

Research Associate

Achievements: demonstrated the possible use of Fe3O4 nanoparticles as a MRI visible contrast agents for cancer diagnostics.

Research outputs: this work was presented at an international conference and one review publication.

2001-2007

Department of Human Morphology, Siberian State Medical University, Tomsk, Russia

Master student

Mentor: Professor Irina Sukhodolo

Thesis: An assessment of acute toxicity of Fe3O4 nanoparticles in rats.

Achievements: The possible adverse effects of Fe3O4 nanoparticles were evaluated in acute experiments on rats. The investigated nanoparticels were nontoxic in high doses demonstrating the possible use of them in targeted drug delivery systems.

Research outputs: this work resulted in one publication.

   
Publications
2019 Maric T1, Mikhaylov G1, Khidakivskyi P, Bazhin A, Sinisi R, Bonhoure N, Yevtodiyenko, Jones A, Muhunthan V, Abdelhady G, Shackelford D, Goun E. Biolumenescent-based imaging and quantification of glucose uptake in vivo. Nature Methods. 2019. 16(6):526-532. (impact factor 28.467).
2019 Bratos A, Kramer L, Mikhaylov G, Vasiljeva O, Turk B. Stefin A-functionalized liposomes as a system for cathepsin S and L-targeted drug delivery. Biochimie. 2019. pii: S0300-9084(19)30165-8.
2018 Lerner MI[1], Mikhaylov G1, Tsukanov AA1, Lozhkomoev AS, Gutmanas E, Gotman I, Bratovs A, Turk V, Turk B, Psakhye SG, Vasiljeva O. Crumpled Aluminum Hydroxide Nanostructures as a Microenvironment Dysregulation Agent for Cancer Treatment. Nano Letters 2018 18(9):5401-5410 (impact factor 12.080).
2014 Mikhaylov G, Klimpel D, Schaschke N, Mikac U, Vizovisek M, Fonovic M, Turk V, Turk B, Vasiljeva O. Selective targeting of tumor and stromal cells by a nanocarrier system displaying lipidated cathepsin B inhibitor. Angewandte Chemie International Editionl. 2014, 53(38):10077-81 (impact factor 11.336).
2014 Maher K, Jerič Kokelj B, Butinar M, Mikhaylov G, Manček-Keber M, Stoka V, Vasiljeva O, Turk B, Grigoryev SA, Kopitar-Jerala N. A role for stefin B (cystatin B) in inflammation and endotoxemia. Journal of Biological Chemistry. 2014, 289(46):31736-50.
2011 Mikhaylov G, Vasiljeva O. Promising approaches in using magnetic nanoparticles in oncology. Biological Chemistry. 2011, 392(11):955-60. Review.
2011 Mikhaylov G, Mikac U, Magaeva AA, Itin VI, Naiden EP, Psakhye I, Babes L, Reinheckel T, Peters C, Zeiser R, Bogyo M, Turk V, Psakhye SG, Turk B, Vasiljeva O. Ferri-liposomes as an MRI-visible drug-delivery system for targeting tumours and their microenvironment. Nature Nanotechnology. 2011, 6(9):594-602 (impact factor 33.265).
2008 Mikhaylov, G, Vasiljeva, O. Technology of the future: the use of magnetic nanoparticles in oncology. The Bulletin of Siberian Branch of Russian Academy of Medical Sciences. 2008, 131(3):17-22. Review.
2008 Milto, I, Mikhaylov, G, Ratkin, A, Magaeva, A. The influence of nanoparticles to morphology of internal organs of mice after intravenous administration of Fe3O4 nanoparticles. The Bulletin of Siberian Medicine. 2008, 1:32-36.
Patents
2018 Schaschke N, Vasiljeva O, Mikhaylov G, Turk B. Cathepsin-binding compound bound to a liposome and its diagnostic and therapeutic use. EP2723387B1. 2018. US (2); EP (2); WO (1).
2014 Vasiljeva O, Itin V, Psakhie S, Mikhaylov G, Mikac M, Turk B, Magaeva A, Naiden E, Terekhova O. Oxide ferrimagnetics with spinel structure nanoparticles and iron oxide nanoparticles, biocompatible aqueous colloidal systems comprising nanoparticles, ferriliposomes, and uses thereof. US20140186268A1. 2014. US (1); EP (1); WO (1).
2013 Psakhie S, Lerner M, Glazkova E, Bakina O, Vasiljeva O, Mikhaylov G, Turk B. Low-Dimensional Structures of Organic and/or Inorganic Substances and Use Thereof. US20160074325A1. 2013. US (1); DE (1); RU (1); WO (1).
2013 Psakhye S, Itin V, Magaeva A, Nayden E, Vasiljeva O, Mikhaylov G, Mikac M, Turk B. Contrast agent for t1 and/or t2 magnetic resonant scanning and method for preparing it. RU2471502C1. 2013. RU (1).

[1] The autors contributed equally to this work