A two-dimensional (2-D) correlation optimized warping (COW) algorithm has been developed to align 2-D gas chromatography coupled with time-of-flight mass spectrometry (GC×GC/TOF-MS) data By partitioning raw chromatographic profiles and warping the grid points simultaneously along the first and second dimensions on the basis of applying a one-dimensional COW algorithm to characteristic vectors, nongrid points can be interpolatively warped This 2-D algorithm was directly applied to total ion counts (TIC) chromatographic profiles of homogeneous chemical samples, ie, samples including mostly identical compounds For heterogeneous chemical samples, the 2-D algorithm is first applied to certain selected ion counts chromatographic profiles, and the resultant warping parameters are then used to warp the corresponding TIC chromatographic profiles The developed 2-D COW algorithm can also be applied to align other 2-D separation images, eg, LC×LC data, LC×GC data, GC×GC data, LC×CE data, and CE×CE data

/pdf/two-dimensional-correlation-optimized-warping-algorithm-for-4e78m1j2xc.pdf

Two-Dimensional Correlation Optimized Warping Algorithm for Aligning GC×GC−MS Data

Glucosinolates (GL) can inhibit, retard or reverse experimental multistage carcinogenesis. When brassica plant tissue is broken, GLs are hydrolyzed by the endogenous enzyme myrosinase (Myr), releasing many products including isothiocyanates (ITC). Synthetic ITCs like sulforaphane exert chemopreventive effects against chemically induced tumors in animals, modulating enzymes required for carcinogens' activation/detoxification and/or the induction of cell-cycle arrest and apoptosis in tumor cell lines. To investigate the chemopreventive potential of ITCs while reproducing the circumstances of dietary contact with sulforaphane, we studied proliferation, apoptosis induction and p53, bcl-2 and bax protein expression in Jurkat T-leukemia cells by sulforaphane, the ITC generated in situ in a quantitative manner by Myr starting from glucoraphanin (GRA). Jurkat cells were treated with different doses of GRA-Myr mixture. Effects on cell growth or survival were evaluated by counting trypan blue-excluding cells. Cell-cycle progression, apoptosis and expression of p53, bax and bcl-2 proteins were analyzed by flow cytometry. Results were analyzed by two-sided Fisher's exact test. Sulforaphane, but not GRA, caused G(2)/M-phase arrest (P = 0.028) and increase of apoptotic cell fraction (P < 0.0001) in a time- and dose-dependent manner. Necrosis was observed after prolonged exposure to elevated sulforaphane doses. Moreover, it markedly increased p53 and bax protein expression, and slightly affected bcl-2 expression. These findings indicate that sulforaphane but not the native GL GRA can exert both protective and toxic effects inhibiting leukemic cell growth. Sulforaphane therefore deserves study as a potential chemopreventive/chemotherapeutic antileukemic agent.

/pdf/growth-inhibition-cell-cycle-arrest-and-apoptosis-in-human-t-5ep9wgu0wt.pdf

Growth inhibition, cell-cycle arrest and apoptosis in human T-cell leukemia by the isothiocyanate sulforaphane

Different mutation profiles associated to P53 accumulation in colorectal cancer.

, and is frequently deleted in human tumors. We studied their mRNA expressions in 41 hematopoietic cell lines and in 137 patients with hematological malignancies; we used a quantitative reverse transcription-PCR assay. Normal peripheral bloods, bone marrow and lymph nodes expressed little or undetectable p16 INK4A and p14 ARF mRNAs, which were readily detected in 12 and 17 of 41 cell lines, respectively. Patients with hematological malignancies frequently lacked p16 INK4A

Expression of p16INK4A and p14ARF in hematological malignancies.

Human solid tumors develop multiple genetic abnormalities that accumulate progressively in individual cells during the course of tumor evolution. We sought to determine whether there are specific sequences of occurrence of these progressive evolutionary changes in human breast cancers by performing correlated cell-by-cell measurements of cell DNA content, p53 protein, Her-2/neu protein, and ras protein by multiparameter flow cytometry in 56 primary tumor samples obtained at surgery. In addition, p53 allelic loss and Her-2/neu gene amplification were determined by fluorescence in situ hybridization in cells from the same samples. We reasoned that if there is a specific order in which genetic changes occur, the same early changes would be found consistently in the cells with the fewest abnormalities. We reasoned further that late-developing abnormalities would not occur alone in individual cells but would almost always be found together with the early changes inherited by the same cells. By these criteria, abnormalities involving p53 generally occurred early in the course of development of invasive breast cancers, whereas ras protein overexpression was found to be a late-occurring phenomenon. Within individual tumors, cellular p53 overexpression was often observed alone in individual cells, whereas ras protein overexpression was rarely observed in the absence of p53 overexpression and/or Her-2/neu overexpression in the same cells. Furthermore, the intracellular level of each abnormally expressed protein was found to increase progressively as new abnormalities were acquired. Infiltrating ductal carcinomas exhibited characteristic phenotypic patterns in which p53 allelic loss and/or p53 protein overexpression, Her-2/neu amplification and/or overexpression, aneuploidy, and ras overexpression accumulated within individual cells. However, this pattern was not a prominent feature of lobular breast cancers. All six lobular breast cancers studied were diploid. p53 allelic loss and/or early p53 overexpression, and late ras cooverexpression in the same cells were less common in lobular breast cancers than in infiltrating ductal carcinomas. Although Her-21neu overexpression was a common finding in lobular breast cancers, Her-2/neu amplification was not observed in these tumors.

https://clincancerres.aacrjournals.org/content/clincanres/6/1/112.full.pdf

Correlations Among p53, Her-2/neu, and ras Overexpression and Aneuploidy by Multiparameter Flow Cytometry in Human Breast Cancer: Evidence for a Common Phenotypic Evolutionary Pattern in Infiltrating Ductal Carcinomas

Large genomic aberrations detected by SNP array are independent prognosticators of a shorter time to first treatment in chronic lymphocytic leukemia patients with normal FISH

We describe a rapid and simple flow cytometry technique for the detection and quantification of p53 in several human cell lines, including an adenocarcinoma cell line (SW 626) having a mutant (m) p53, and a pre-B leukemia cell line (NALM-6) having wild-type (wt) p53. By introducing a second antibody coupled to RPE-fluorescence, the discrimination between control and specific peaks was improved over that achieved with methods used previously. To quantify the content of p53 molecules in the cells, we used a series of beads with the capability to bind mouse monoclonal IgG antibodies. p53 cell content, expressed as antibody binding capacity (ABC), was directly quantified from logarithmic scattergrams; the results were reproducible in all cell lines tested. Flow cytometric results were compared with those of a standard immunocytochemistry method routinely used for the detection of p53 in cells, and found to be in correlation. Furthermore, cytometric data also reflect ELISA determinations. In summary, we showed for the first time that (i) p53 can be clearly detected by flow cytometry in various cell lines, (ii) p53 can be quantitated in terms of number of molecules per cell, and (iii) it can be easily monitored as a function of time after stimulation. Cytometry 31:180–186, 1998. © 1998 Wiley-Liss, Inc.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/%28SICI%291097-0320%2819980301%2931%3A3%3C180%3A%3AAID-CYTO5%3E3.0.CO%3B2-P

A novel flow cytometric method for the quantification of p53 gene expression.

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Large genomic aberrations detected by SNP array are independent prognosticators of a shorter time to first treatment in chronic lymphocytic leukemia patients with normal FISH

A novel flow cytometric method for the quantification of p53 gene expression.