New horizons in flow cytometry by cytomics and bioinformatics. A minireview.

New horizons in flow cytometry by cytomics and bioinformatics. A minireview.

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Article_Title: New horizons in flow cytometry by cytomics and bioinformatics. A minireview.
Authors: Daniela Bratosin, Manuela Sidoroff
Affiliation: 1 National Institute for Biological Science Research and Development, Bucharest, Romania
2 ”Vasile Goldis” Western University of Arad, Faculty of Biology, Arad, Romania
Abstract: Cytomics is the study of cell systems (cytomes) at a single cell level. It combines all the bioinformatic knowledge to attempt to understand the molecular architecture and functionality of the cell system (Cytome). Much of this is achieved by using molecular and microscopic techniques and flow cytometry that allow the various components of a cell to be visualised as they interact in vivo.
Keywords: flow cytometry, -omic, cytome, cytomic, bioinformatics, microscopy, human cytome project.
References: Bocsi J., Mittag A., Sack U., Gerstner AO., Barten MJ., Tarnok A., . Novel aspects of systems biology and clinical cytomics, Cytometry A, 69A,105–108, 2006
Bratosin D., Fagadar-Cosma E., Gheorghe A-M. , Rugina A., Ardelean A. ,Montreuil J., Marinescu Al. G., In vitro toxi and ecotoxicological assesment of porphyrine nanomaterials by flow cytometry
using nucleated erythrocytes, Carpathian Journal of Earth and Environmental Sciences, Vol. 6, nr. 2,
2011 (online first)
Chitty M., – Omes and -omics glossary. Available at: http://www.genomicglossaries.com/content/omes.
asp
Collins FS, Green ED, Guttmacher AE, Guyer MS., A vision for the future of genomics
research, Nature, 422, 835–847, 2003.
Coulton G., Are histochemistry and cytochemistry ‘Omics’?, J Mol Histol., 35(6), 603-613, 2004
Eils R., Athale C., Computational imaging in cell biology, Journal of Cell Biology, 161, 477–481, 2003.
Gerstnr AO, Mittag A, Laffers W, Dahnert I, Lenz D, Bootz F, Bocsi J, Tarnok A. Comparison of
immunophenotyping by slide based cytometryand by flow cytometry, J Immunol Methods, 311,130–138, 2006
Herrera, G., Diaz L., Martinez-Romero A., Gomes A., Villamón E., Callaghan R.C, O’Connor J-E,
Cytomics: a multiparametric, dynamic approach to cell research. Toxicol. In Vitro 21, 176–182, 2007
Hood L., Heath JR., Phelps M. E., Lin B., Systems biology and new technologies enable predictive and
preventative medicine. Science 306, 640–643, 2004 Jackson O., Lay Jr., Borgmann S., Liyanage R., Wilkins Ch. L., Problems with the ‘‘omics’’, Trends in Analytical Chemistry, 25, 11, 2006
Jain, K.K. Challenges of drug discovery for personalized medicine. Curr. Opin. Mol. Ther. 8, 487–492, 2006
Maddox, P.S., Moree, B., Canman, J.C., Salmon, E.D., Spinning disk confocal microscope system for rapid high-resolution, multimode, fluorescence speckle microscopy and green fluorescent protein imaging in living cells. Methods in Enzymology, 360, 597–617, 2003.
Mittag A., Lenz D., Gerstner AOH., Sack U., Steinbrecher M., Koksch M., Raffael A., Bocsi J., Tarnok A., Polychromatic eight color slide-based cytometry for the characterization of NK and NK-T subsets. Cytometry A ,65A,103–115, 2005
O’Connor J.E., Callaghan R.C., Escudero M., Herrera G., Martínez, A., Monteiro, M.C., Montolíu, H.,
The relevance of flow cytometry for biochemical analysis, IUBMB Life , 51, 231–239, 2001.
Peltri G., Bitterlich N., Increased diagnostic value of parameters by fuzzy logic-based multiparameter analysis, Cytometry, 53B,75–78, 2003
Perfetto SP., Chattopadhyay PK., Roederer M., Seventeen-colour flow cytometry: Unravelling the
immune system. Nat. Rev. Immunol. 4, 648–655, 2004..
Rosenwald A, Wright G, Chan WC, Connors JM, Campo E, Fisher RI,Gascoyne RD, Mu¨ller-Hermelink HK,
Smeland EB, Staudt LM. The use of molecular profiling to predict survival after chemotherapy for
diffuse large B-cell lymphoma. N Engl J Med 346, 1937–1947, 2002.
Rubart, M., Two-photon microscopy of cells and tissue, Circulation Research 95, 1154–1166, 2004.
Snow CD, Nguyen H, Pand VS, Gruebele M., Absolute comparison of simulated and experimental proteinfolding dynamics, Nature, 420,102–106, 2002
Tarnok A., New technologies for the human cytome project. J Biol Regul Homeost Agents, 18, 92–95,
2004
Tarnok A., Slide-based cytometry for cytomics- A minireview , CytometryA, 555-562, 2006.
Valet G, Hoeffkes HG., Data pattern analysis for the individualized pre-therapeutic identification of high risk diffuse large B-cell lymphoma (DLBCL) patients by cytomics. Cytometry, 59, 232-236, 2004
Valet G, Tarnok A., Potential and challenges of a human cytome project., J Biol Regul Homeost Agents, 18, 87–91, 2004
Valet G, Leary JF, Tarnok A., Cytomics—new technologies: towards a human cytome project. Cytometry 59A: 167–171, 2004
Valet G, Tarnok A. Cytomics in predictive medicine. Cytometry, 53B: 1–3, 2003
Valet G., Cytomics: An entry to biomedical cell systems biology, Cytometry A ,63A,67–68, 2005
Valet G. Predictive medicine by cytomics: Potential and challenges., J Biol Regul Homeost Agents, 16, 164-167, 2002
Valet, G., Cytomics: an entry to biomedical cell systems biology, Cytometry A, 63, 67–68, 2005
Weinstein JN, Scherf U, Lee JK, Nishizuka S, Ajay FG, Bussey K, Kim S, Smith LH, Tanabe L, Richman
S, Alexander J, Kouros-Mehr H, Maunakea A, Reinhold WC., The bioinformatics of microarray
gene expression profiling, Cytometry, 47, 46-49, 2002
Wenk MR., The emerging field of lipidomics, Nat Rev Drug Discov ., 4, 594-610, 2005
Werner T, Liebisch G, Grandl M, Schmitz G., Evaluation of a high-content screening fluorescence-based assay analyzing the pharmacological modulation of lipid homeostasis in human macrophages. Cytometry A 69A
Read_full_article: pdf/21-2011/21-s1-2011/SU21-s1-2011Bratosin1.pdf
Correspondence: Prof. Daniela BRATOSIN, National Institute for Biological Science Research and Development, Spl. Independentei nr 296, 060031 Bucharest, Romania, Tel/Fax: 40.21.2200881, e-mail: bratosind@yahoo.com

Read full article
Article Title: New horizons in flow cytometry by cytomics and bioinformatics. A minireview.
Authors: Daniela Bratosin, Manuela Sidoroff
Affiliation: 1 National Institute for Biological Science Research and Development, Bucharest, Romania
2 ”Vasile Goldis” Western University of Arad, Faculty of Biology, Arad, Romania
Abstract: Cytomics is the study of cell systems (cytomes) at a single cell level. It combines all the bioinformatic knowledge to attempt to understand the molecular architecture and functionality of the cell system (Cytome). Much of this is achieved by using molecular and microscopic techniques and flow cytometry that allow the various components of a cell to be visualised as they interact in vivo.
Keywords: flow cytometry, -omic, cytome, cytomic, bioinformatics, microscopy, human cytome project.
References: Bocsi J., Mittag A., Sack U., Gerstner AO., Barten MJ., Tarnok A., . Novel aspects of systems biology and clinical cytomics, Cytometry A, 69A,105–108, 2006
Bratosin D., Fagadar-Cosma E., Gheorghe A-M. , Rugina A., Ardelean A. ,Montreuil J., Marinescu Al. G., In vitro toxi and ecotoxicological assesment of porphyrine nanomaterials by flow cytometry
using nucleated erythrocytes, Carpathian Journal of Earth and Environmental Sciences, Vol. 6, nr. 2,
2011 (online first)
Chitty M., – Omes and -omics glossary. Available at: http://www.genomicglossaries.com/content/omes.
asp
Collins FS, Green ED, Guttmacher AE, Guyer MS., A vision for the future of genomics
research, Nature, 422, 835–847, 2003.
Coulton G., Are histochemistry and cytochemistry ‘Omics’?, J Mol Histol., 35(6), 603-613, 2004
Eils R., Athale C., Computational imaging in cell biology, Journal of Cell Biology, 161, 477–481, 2003.
Gerstnr AO, Mittag A, Laffers W, Dahnert I, Lenz D, Bootz F, Bocsi J, Tarnok A. Comparison of
immunophenotyping by slide based cytometryand by flow cytometry, J Immunol Methods, 311,130–138, 2006
Herrera, G., Diaz L., Martinez-Romero A., Gomes A., Villamón E., Callaghan R.C, O’Connor J-E,
Cytomics: a multiparametric, dynamic approach to cell research. Toxicol. In Vitro 21, 176–182, 2007
Hood L., Heath JR., Phelps M. E., Lin B., Systems biology and new technologies enable predictive and
preventative medicine. Science 306, 640–643, 2004 Jackson O., Lay Jr., Borgmann S., Liyanage R., Wilkins Ch. L., Problems with the ‘‘omics’’, Trends in Analytical Chemistry, 25, 11, 2006
Jain, K.K. Challenges of drug discovery for personalized medicine. Curr. Opin. Mol. Ther. 8, 487–492, 2006
Maddox, P.S., Moree, B., Canman, J.C., Salmon, E.D., Spinning disk confocal microscope system for rapid high-resolution, multimode, fluorescence speckle microscopy and green fluorescent protein imaging in living cells. Methods in Enzymology, 360, 597–617, 2003.
Mittag A., Lenz D., Gerstner AOH., Sack U., Steinbrecher M., Koksch M., Raffael A., Bocsi J., Tarnok A., Polychromatic eight color slide-based cytometry for the characterization of NK and NK-T subsets. Cytometry A ,65A,103–115, 2005
O’Connor J.E., Callaghan R.C., Escudero M., Herrera G., Martínez, A., Monteiro, M.C., Montolíu, H.,
The relevance of flow cytometry for biochemical analysis, IUBMB Life , 51, 231–239, 2001.
Peltri G., Bitterlich N., Increased diagnostic value of parameters by fuzzy logic-based multiparameter analysis, Cytometry, 53B,75–78, 2003
Perfetto SP., Chattopadhyay PK., Roederer M., Seventeen-colour flow cytometry: Unravelling the
immune system. Nat. Rev. Immunol. 4, 648–655, 2004..
Rosenwald A, Wright G, Chan WC, Connors JM, Campo E, Fisher RI,Gascoyne RD, Mu¨ller-Hermelink HK,
Smeland EB, Staudt LM. The use of molecular profiling to predict survival after chemotherapy for
diffuse large B-cell lymphoma. N Engl J Med 346, 1937–1947, 2002.
Rubart, M., Two-photon microscopy of cells and tissue, Circulation Research 95, 1154–1166, 2004.
Snow CD, Nguyen H, Pand VS, Gruebele M., Absolute comparison of simulated and experimental proteinfolding dynamics, Nature, 420,102–106, 2002
Tarnok A., New technologies for the human cytome project. J Biol Regul Homeost Agents, 18, 92–95,
2004
Tarnok A., Slide-based cytometry for cytomics- A minireview , CytometryA, 555-562, 2006.
Valet G, Hoeffkes HG., Data pattern analysis for the individualized pre-therapeutic identification of high risk diffuse large B-cell lymphoma (DLBCL) patients by cytomics. Cytometry, 59, 232-236, 2004
Valet G, Tarnok A., Potential and challenges of a human cytome project., J Biol Regul Homeost Agents, 18, 87–91, 2004
Valet G, Leary JF, Tarnok A., Cytomics—new technologies: towards a human cytome project. Cytometry 59A: 167–171, 2004
Valet G, Tarnok A. Cytomics in predictive medicine. Cytometry, 53B: 1–3, 2003
Valet G., Cytomics: An entry to biomedical cell systems biology, Cytometry A ,63A,67–68, 2005
Valet G. Predictive medicine by cytomics: Potential and challenges., J Biol Regul Homeost Agents, 16, 164-167, 2002
Valet, G., Cytomics: an entry to biomedical cell systems biology, Cytometry A, 63, 67–68, 2005
Weinstein JN, Scherf U, Lee JK, Nishizuka S, Ajay FG, Bussey K, Kim S, Smith LH, Tanabe L, Richman
S, Alexander J, Kouros-Mehr H, Maunakea A, Reinhold WC., The bioinformatics of microarray
gene expression profiling, Cytometry, 47, 46-49, 2002
Wenk MR., The emerging field of lipidomics, Nat Rev Drug Discov ., 4, 594-610, 2005
Werner T, Liebisch G, Grandl M, Schmitz G., Evaluation of a high-content screening fluorescence-based assay analyzing the pharmacological modulation of lipid homeostasis in human macrophages. Cytometry A 69A
*Correspondence: Prof. Daniela BRATOSIN, National Institute for Biological Science Research and Development, Spl. Independentei nr 296, 060031 Bucharest, Romania, Tel/Fax: 40.21.2200881, e-mail: bratosind@yahoo.com