Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2005-09-07
2010-10-12
Skowronek, Karlheinz R (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C382S133000
Reexamination Certificate
active
07813881
ABSTRACT:
The present invention provides a method useful for analysis of punctate distribution of supramolecular complexes that are compartmentalized in nuclear microenvironments. In preferred embodiments the method provides quantitative analysis of the assembly of regulatory machinery within the context of nuclear architecture and to provide a mechanistic link with biological control. In other embodiments, the invention provides a method of identifying a molecule by parameters of its subnuclear distribution, comprising the steps of quantifying organizational parameters of domains within subnuclear distributions of a molecule; performing factor analysis on the quantified organizational parameters; performing discriminant analysis on the quantified organizational parameters; comparing the results of the factor analysis and the results of the discriminant analysis to one or more standards, thereby identifying a molecule by parameters of its subnuclear distribution.
REFERENCES:
patent: 5048095 (1991-09-01), Bhanu et al.
patent: 2003/0023385 (2003-01-01), Lazaridis
patent: 2003/0027159 (2003-02-01), Ward et al.
patent: 2003/0139886 (2003-07-01), Bodzin et al.
Hazzouri et al (Molecular reproduction and development, vol. 55, p. 307-315, 2000).
Kahn et al (Cytometry, vol. 28, p. 269-279, 1997).
Armstrong (Journal of Neuroscience Methods, vol. 73, p. 141-147, 1997).
Theilmann et al. (J Cancer Res Clin Oncol, vol. 125, p. 193-208, 1999).
Traniello et al. (Oecologia, vol. 69, p. 413-419, 1986).
Weyn et al. (J. Pathol. 189: 581-589, 1999).
Jain et al. (IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 22, No. 1, Jan. 2000).
Stenoien, D.L. et al., Ligand-mediated assembly and real-time cellular dynamics of estrogen receptor alpha-coactivator complexes in living cells. Mol Cell Biol. Jul. 2001; 21 (13): 4404-4412.
Tanabe, H., et al., Non-random radial arrangements of interphase chromosome territories: evolutionary considerations and functional implications. Mutat Res. Jul. 25, 2002; 504 (1-2): 37-45.
Zhang, Y.W., et al., PEBP2alphaA/CBFA1 mutations in Japanese cleidocranial dysplasia patients. Gene. Feb. 22, 2000; 244 (1-2): 21-8.
Bolzer et al., “Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes”, PLoS Biology. 2005, 3 (5):0826-0842.
Bradbury, J. In This Issue: Intranuclear Informatics. Journal of Cell Science 117, 2102e (2004).
Young D.W. et al., “Quantitative signature for architectural organization of regulatory factors using intranuclear informatics”, J Cell Science. 2004(Pt 21):4889-96.
Aranda, A., et al., Nuclear Hormone Receptors and Gene Expression. Physiological Reviews. Jul. 2001; vol. 81, No. 2: 1269-1304.
Barseguian K, et al., Multiple subnuclear targeting signals of the leukemia-related AML1/ETO and ETO repressor proteins, Proc Natl Acad Sci U S A. Nov. 26, 2002; 99(24):15434-9. Epub Nov. 11, 2002.
Boland, MV, et al., Automated Recognition of Patterns Characteristic of Subcellular Structures in Fluorescence Microscopy Images. Cytometry 33: 366-375 (1998).
Bolivar, J., et al., The fragile-X-related gene FXR1 is a human autoantigen processed during apoptosis. J Biol Chem. Jul. 3, 1998; 273(27):17122-7.
Carrington, W.A. et al. Science 268, 1483-1487 (1995).
Chai, Z., et al., SET-related cell division autoantigen-1 (CDA1) arrests cell growth. J Biol Chem. Sep. 7, 2001;276 (36):33665-74. Epub Jun. 6, 2001.
Choi, J.-Y. et al. Subnuclear targeting of Runx/Cbfa/AML factors is essential for tissue-specific differentiation during embryonic development, Proc. Natl. Acad. Sci., USA 98, 8650-8655 (2001).
Dundr, M. & Misteli, T., Functional architecture in the cell nucleus, Biochem J 356, 297-310 (2001).
Dyck, J.A,, et al., Rapid diagnosis of acute promyelocytic leukemia by immunohistochemical localization of PML/ RAR-alpha protein, Blood. 1995 86(3):862-867.
Eils, R., et al., Quantitative Imaging of Pre-mRNA Splicing Factors in Living Cells. The American Society for Cell Biology. Feb. 2000; vol. 11: 413-418.
Guo et al., The nuclear matrix protein NMP-1 is the transcription factor YY1, Proc. Natl. Acad. Sci.USA 1995 92, 10526-10530.
Harrington, K.S. et al. Transcription factors RUNX1/AML1 and RUNX2/Cbfa1 dynamically associate with stationary subnuclear domains, J. Cell Sci. 115, 4167-4176 (2002).
Javed et al., Groucho/TLE/R-esp proteins associate with the nuclear matrix and repress RUNX (CBF(alpha)/AML/PEBP2(alpha)) dependent activation of tissue-specific gene transcription, J. Cell Sci. 2000 113, 2221-2231.
Karpuj, M.V., et al., Transglutaminase aggregates huntingtin into nonamyloidogenic polymers, and its enzymatic activity increases in Huntington's disease brain nuclei, Proc Natl Acad Sci U S A. Jun. 22, 1999;96(13):7388-7393.
Lemon, B. & Tjian, R., Orchestrated response: a symphony of transcription factors for gene control, Genes Dev. 14, 2551-2569 (2000).
Llopis, J., et al., Ligand-dependent interactions of coactivators steriod receptor coactivator-1 and peroxisome proliferator-activated receptor binding protein with nuclear hormone receptors can be imaged in live cells and are required for transcription. Proceedings of the National Academy of Sciences. Apr. 11, 2000; vol. 97, No. 8: 4363-4368.
Ma, H. et al., Spatial and temporal dynamics of DNA replication sites in mammalian cells, J. Cell Biol. 143, 1415-1425 (1998).
McNeil, S., et al., The t(8;21) chromosomal translocation in acute myelogenous leukemia modifies intranuclear targeting of the AML1/CBFalpha2 transcription factor, Proc Natl Acad Sci U S A. 1999;96(26):14882-7.
Mosgoeller, W., et al, Nuclear architecture and ultrastructural distribution of poly(ADP-ribosyl)transferase, a multifunctional enzyme. J Cell Sci. Feb. 1996;109 ( Pt 2):409-18.
Nielsen, J.A., et al., Nuclear organization in differentiating oligodendrocytes, J Cell Sci. 115, 4071-4079 (2002).
Noordmans, H.J., et al.,. Randomness of spatial distributions of two proteins in the cell nucleus involved in mRNA synthesis and their relationship, Cytometry 33, 297-309 (1998).
Pearce, D., et al., Determinants of subnuclear organization of mineralocorticoid receptor characterized through analysis of wild type and mutant receptors. The Journal of Biological Chemistry; vol. 277, No. 2: 1451-1456, 2002.
Price, R., et al., A splice variant of estrogen receptor β missing exon 3 displays altered subnuclear localization and capacity for transcriptional activation. The Endocrine Society. 2001; vol. 142, No. 5: 2039-2049.
Reyes et al., Components of the human SWI/SNF complex are enriched in active chromatin and are associated with the nuclear matrix, J. Cell Biol. 1997 137, 263-274.
Shiels, C. et al., PML bodies associate specifically with the MHC gene cluster in interphase nuclei, J Cell Sci. 114, 3705-3716 (2001).
Stein, G.S., et al., Cancer Res. 60, 2067-2076 (2000).
Stein, G.S. et al., Intranuclear trafficking of transcription factors: implications for biological control., J. Cell Sci. 113, 2527-2533 (2000).
Szentirmay, M., et al., Spatial organization of RNA polymerase II transcription in the nucleus. Oxford University Press, Nucleic Acids Research. 2000; vol. 28, No. 10: 2019-2025.
Tang, L. et al. Crystal structure of the nuclear matrix targeting signal of the transcription factor AML-1/PEBP2aB/CBFa2. J. Biol. Chem. 274, 33580-33586 (1999).
Westendorf, J.J. et al., Runx2 (Cbfa1, AML-3) interacts with histone deacetylase 6 and represses the p21(CIP1/ WAF1) promoter, Mol. Cell Biol. 22, 7982-7992 (2002).
Zaidi, S.K., et al., A specific targeting signal directs Runx2/Cbfa1 to subnuclear domains and contributes to transactivation of the osteocalcin gene., J. Cell Sci. 2001 114, 3093-3102.
Zaidi, S.K. et al. Integration of Runx and Smad regulatory signals at transcriptionally active subnuclear sites, Proc. Natl. Acad. Sci., USA 99, 8048-8053 (2002).
Zaidi, S.K. et al., Proc. Natl. Acad. Sci. USA 100, 14852-14855 (2003).
Zeng, C. et al., Identification of a nuclear matrix targeting signal in the leukemia and bone-related AML/CBF-alpha transcription factors, Proc. Natl. Acad. Sci.
Javed Amjad
Lian Jane B.
Stein Gary S.
Stein Janet L.
Van Wijnen Andre J.
Skowronek Karlheinz R
University of Massachusetts
Wolf Greenfield & Sacks P.C.
LandOfFree
Quantitative assessment of biological function based on the... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Quantitative assessment of biological function based on the..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Quantitative assessment of biological function based on the... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-4168986