Dr. Sc. Marko Haramija. (Biokemija, Molekularna medicina, Masena spektroskopija, Biomedicinske znanosti)

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1 Dr. Sc. Marko Haramija (Biokemija, Molekularna medicina, Masena spektroskopija, Biomedicinske znanosti) Obrazovanje OŠ Čavle OŠ Nikola Tesla Gimnazija Andrije Mohorovičića Prirodoslovno-matematički fakultet, Zagreb, Dipl. inž. Kemije, smjer Biokemija Diplomski rad: "Pročišćavanje seryl-trna sintetaze kukuruza dobivene heterolognom ekspresijom u bakteriji Escherichia coli mentor: prof. Ivana Weygand-Đurašević, Institut Ruđer Bošković Sveučilište u Muensteru, NJemačka, znanstveni suradnik, Bioanalitička masena spektrometrija Institut za medicinsku fiziku i biofiziku Medical College of Georgia, Georgia, SAD, 2002 Exchange student visitor, Institute for Molecular Medicine and Genetics Uspostavljanje Mass Spectrometry Core Facility od Jasne Peter-Katalinić Medical College of Georgia, Georgia, SAD, Ph.D. iz Biomedicinskih znanosti, smjer Molekularna medicina Doktorski rad: Influence of DNA Ends on Structure and Function of the DNA-dependent Protein Kinase Major Advisor: William Dynan, Prof., Institute for Molecular Medicine and Genetics Medical College of Georgia, Georgia, SAD, 2007 Postdok -Popravak dvolančanih lomova u DNK pomoću Non-Homologous End-Joining mehanizma

2 Cjeloživotno obrazovanje ASMS Short Courses: FTMS: Principles and Applications, ASMS, May 26-27, 2001 Practical LC/MS, ASMS, June 1-2, 2002, 2002 FEBS Advanced Courses: FEBS Advanced Course: Ligand-binding Theory and Practice, Nove Hrady, Češka republika, 2016 FEBS Advanced Course: Glycoconjugates, Versatile structuresintriguing functions, Lovran-Opatija, Hrvatska, 1999 Diplome: AB Applied Biosystems: Qstar with omaldi Option Training Class, Foster City, CA, SAD, 2002 Ciphergen: Ciphergen ProteinChip Technology Basic Course, CA, SAD, 2002 Ostalo obrazovanje: 1st Summer School in Mass Spectrometry in Biotechnology & Medicine, Dubrovnik, Hrvatska, th International Summer School on Biophysics, Rovinj, Hrvatska, 2000 State-of-the-art vještine i iskustvo iz Masene spektroskopije Administrator: AB Sciex MALDI/ESI Q-TOF, QStar Pulsar i Micromass MALDI TOF, TofSpec 2E Ciphergen SELDI TOF, ProteinChip Operator: AB Sciex MALDI/ESI Q-TOF, QStar Pulsar i Micromass ESI Q-TOF, Q-Tof Micromass MALDI TOF, TofSpec 2E Ciphergen SELDI TOF, ProteinChip AB Sciex MALDI TOF, Voyager

3 Iskustvo: Razvijanje MS metoda: razvoj nanoesi Q-TOF Affinity mass spectrometry metoda za analizu nekovalentnih kompleksa proteina i ugljikohidrata razvoj pripreme uzoraka za MALDI MS razvoj bioinformatičkih metoda za analizu glikomskih MS podataka Analiziranje MS rezultata: Afinitetna masena spektrometrija Glikomika Proteomika Optimizacija instrumentalnih parametara: na nivou administratora na nivou operatora Optimizacija pripreme uzoraka za MALDI MS QA za AB Sciex MALDI/ESI Q-TOF, QStar Pulsar i QA za Micromass MALDI TOF, TofSpec 2E Obrazovanje postdoktoranada i ostalih gostujućih znanstvenika Radovi 1. Haramija M., Peter-Katalinić J.: Quantitative Characterization of Galectin-3-C Affinity Mass Spectrometry Measurements: Comprehensive Data Analysis, Obstacles, Shortcuts and Robustness, Rapid Communications in Mass Spectrometry, 31, , 2017, /rcm Haramija M., Tyldesley-Worster R.: Analysis of matrix-assisted laser desorption/ionization quadrupole time-of-flight collision-induced dissociation spectra of simple precursor ions and isobaric oligosaccharide ion mixtures based on product ion intensities and pattern recognition, Rapid Communications in Mass Spectrometry, 31, , 2017, doi: /rcm Haramija M., Peter-Katalinić J.: Preliminary mass spectrometry characterization studies of galectin-3 samples, prior to carbohydrate-binding studies using Affinity mass spectrometry, Rapid Communications in Mass Spectrometry, 31, , 2017, doi: /rcm.7775

4 4. Haramija M., Peter-Katalinić J.: Negative ion MALDI-TOF MS, ISD and PSD of neutral underivatized oligosaccharides without anionic dopant strategies, using 2,5-DHAP as a matrix", Journal of Mass Spectrometry, 51, , 2016, doi: /jms Haramija M., Tyldesley-Worster R, Pohlentz G, Peter-Katalinić J, "MALDI Q-TOF CID MS for Diagnostic Ion Screening of Human Milk Oligosaccharide Samples", International Journal of Molecular Sciences, 15, , 2014, doi: /ijms Haramija M., Dynan WS: Terminal DNA structure and ATP influence binding parameters of the DNA-dependent protein kinase at an early step prior to DNA synapsis, Nucleic Acids Research, 34, , 2006, doi: /nar/gkj504 Ostali radovi 7. Lee KJ, Haramija M., Udayakumar D, Bladen CL, Dynan WS: "Identification of DNA-PKcs phosphorylation sites in XRCC4 and effects of mutations at these sites on DNA end joining in a cellfree system", DNA Repair, 3, , 2004, doi: /j.dnarep Hanisch FG, Haramija M., Peter-Katalinić J: "Glycoprotein Identification and Localization of O- Glycosylation Sites by Mass Spectrometric Analysis of Deglycosylated/Alkylaminylated Peptide Fragments", Analytical Biochemistry, 290, 47-59, 2001, doi: /abio Područja znanstvenog djelovanja State-of-the-art temeljna znanstvena istraživanja iz: Biokemije - 8 radova Masene spektroskopije - 7 radova Glikobiokemije - 5 radova Nanobiokemije - 1 rad Interdisciplinarna istraživanja - 6 radova Molekularne medicine - 7 radova

5 Glikomike - 3 rada Proteomike posttranslacijskih modifikacija - 3 rada State-of-the-art temeljna znanstvena istraživanja nekovalentnih kompleksa proteina: Protein ugljikohidrat - 2 rada Protein DNK - 1 rad Protein protein - 1 rad State-of-the-art temeljna znanstvena istraživanja iz Masene spektroskopije: MALDI MS - 5 radova nanoesi MS - 3 rada Q-TOF MS - 6 radova TOF MS - 3 rada MS/MS sequencing - 6 radova Affinity Mass Spectrometry - 2 rada Glikomika - 3 rada Proteomika PTM-a - 3 rada State-of-the-art temeljna znanstvena istraživanja proteina: ljudski galektin-3 (lektin) - 2 rada ljudska DNA-PKcs (proteinska kinaza, protein u popravku DNK) - 2 rada ljudski Ku (protein u popravku DNK) - 1 rad ljudski XRCC4 (protein u popravku DNK) - 1 rad ljudski glikoforin A (glikoprotein) - 1 rad State-of-the-art interdisciplinarna znanstvena istraživanja u glikomici: oligosaharidi ljudskog mlijeka - 2 rada razvoj MALDI MS metoda u glikomici - 1 rad razvoj bioinformatičkih metoda za analizu MS podataka u glikomici - 1 rad

6 Proteomika posttranslacijskih modifikacija: Glikoproteomika - 2 rada Fosfoproteomika - 1 rad Knjige 1. Haramija M.: "Introduction to Mass Spectrometry of Biomolecules: Theory and Principles", Nova Science Publishers, Inc., Editor:, ISBN: , 2016, New York, USA, ISBN-10: Haramija M.: "Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects", Nova Science Publishers, Inc., Editor: ISBN: , 2016, New York, USA, ISBN- 10: X Poglavlja u knjigama 1. Haramija M. (2016): Introduction to mass spectrometers. In: Introduction to Mass Spectrometry of Biomolecules: Theory and Principles, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 2. Haramija M. (2016): Basic terms in analysis of mass spectra. In: Introduction to Mass Spectrometry of Biomolecules: Theory and Principles, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 3. Haramija M. (2016): Overview of basic classes of biomolecules. In: Introduction to Mass 4. Haramija M. (2016): MS/MS Structural Analysis Basic Principles. In: Introduction to Mass 5. Haramija M. (2016): MS/MS structural analysis of biomolecules. In: Introduction to Mass 6. Haramija M. (2016): Mass spectrometry data acquisition techniques In: Introduction to Mass

7 7. Haramija M. (2016): Advanced MS/MS data acquisition techniques. In: Introduction to Mass 8. Haramija M. (2016): Basic calculation problems related to analyses of MS spectra. In: Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 9. Haramija M. (2016): MS/MS analysis of peptides. In: Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 10. Haramija M. (2016): MS/MS analysis of oligosaccharides and glycoconjugates. In: Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 11. Haramija M. (2016): MS/MA analysis of lipids and polyphenols. In: Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 12. Haramija M. (2016): Overview of selected modern MS instruments. In: Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 13. Haramija M. (2016): Sample preparation for MS analyses and related accessories. In: Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 14. Haramija M.: Advances and challenges in structural analysis of milk biomolecules using modern mass spectrometry techniques, In: Bernhardt LV, editor. Advances in Medicine and Biology, Vol 94. New York: Nova Science Publishers, Inc.; p Haramija M., Peter-Katalinić J, "Advances and challenges in structural analysis of human milk oligosaccharides using modern mass spectrometry", In: Bernhardt LV, editor. Advances in Medicine and Biology, Vol 86. New York: Nova Science Publishers, Inc.; p Sudjelovanje na većim kongresima th ASMS Conference on Mass Spectrometry and Allied Topics, Long Beach, CA, USA, th ASMS Conference on Mass Spectrometry and Allied Topics, Chicago, IL, USA, th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, FL, USA, XVI th International Symposium on Glycoconjugates, The Hague, Netherlands, XXIII rd International Symposium on Glycoconjugates, Split, Croatia, 2015

8 Pozvana predavanja 1. Haramija M., Svensson I., Leffler H. and Peter-Katalinić J: "Interactions of Intact Human Galectin-3 and its C-terminal Fragment with Oligosaccharides: an Electrospray Ionization Mass Spectrometry Study", (Galectins Session), XVIth International Symposium on Glycoconjugates, The Hague, Netherlands, Haramija M., Willets M, Tyldesley R, Brown J and Peter-Katalinić J: "Fragmentation of native and peracetylated oligosaccharides in PSD MALDI-TOF and CID MALDI-Q-TOF MS", MODpm (Carbohydrate Sequencing session), 49th ASMS Conference on Mass Spectrometry and Allied Topics, Chicago, IL, USA, 2001 Prezentacije - posteri 1. Marko Haramija, Ulf Nilsson, Hakon Leffler, Jasna Peter-Katalinić: Applicability of ESI MS for screening of galectin-3c affinity data for carbohydrates, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, Marko Haramija, Ulf Nilsson, Hakon Leffler, Jasna Peter-Katalinić: Applicability of tandem MS experiments for study of galectin carbohydrate non-covalent complexes, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, Marko Haramija, Jasna Peter-Katalinić: Fragmentation patterns of oligosaccharides in MALDI MS based on ion mode selection and the nature of precursor ion, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, Marko Haramija: Novel bioinformatic tools needed for high-throughput data analysis and visualization of oligosaccharide MS/MS spectra, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, Marko Haramija, Franz-Georg Hanisch, Jasna Peter-Katalinić: Applicability of MALDI MS for mapping and sequencing of oligosaccharides and glycoconjugates, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, Marko Haramija, Nenad Ocelić, Jasna Peter-Katalinić: Bioinformatics-assisted survey of branching patterns in complex oligosaccharide mixtures, 50 th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, FL, SAD, Marko Haramija, Koenig, Simone; Peter-Katalinić, Jasna: Applicability of MALDI-PSD in Negative Mode for Analysis of Oligosaccharides, N-Glycans and O-Glycosylated Amino Acids, 48 th ASMS Conference on Mass Spectrometry and Allied Topics, Long Beach, SAD, 2000

9 8. Haramija M., Svensson I., Leffler H. and Peter-Katalinić J: "Interactions of Intact Human Galectin-3 and its C-terminal Fragment with Oligosaccharides: an Electrospray Ionization Mass Spectrometry Study", (Galectins Session), XVIth International Symposium on Glycoconjugates, The Hague, Netherlands, 2001