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PubMed2001

KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice.

We produced transgenic rice calli, which constitutively express each of four KNOX family class 1 homeobox genes of rice, OSH1, OSH16, OSH15, and OSH71, and found that constitutive and ectopic expression of such genes inhibits normal regeneration from transformed calli, which showed continuous growth around their shoot-regenerating stages. Transgenic calli transferred onto regeneration medium began to display green spots, a sign of regeneration, but most of the transformants continued to propagate green spots at given stages. In the normal shoot-regeneration process of calli, expression of endogenous OSH1 was restricted in presumptive shoot-regenerating regions of calli and not observed in other areas. This restricted expression pattern should be required for further differentiation of the regenerating shoots. Thus our present results support the proposed function that KNOX family class 1 homeobox genes play a role in the formation and maintenance of the undetermined meristematic state of cells.

Cell Differentiation↗
PubMed1977

Calcium content and distribution as a function of growth and transformation in the mouse 3T3 cell.

Total Ca content and that fraction of Ca sensitive to removal by the chelator ethylene glycol-bis(beta-aminoethyl ether)N,N,N',N'-tetraacetate (EGTA) have been investigated in the mouse 3T3 cell as a function of growth stage, transformation with SV40 virus, and serum levels of the media. Cells were allowed to grow through several doublings in media containing (45)Ca. The cellular content of (45)Ca was used to access total cell Ca. That fraction of (45)Ca removed by EGTA was presumed to represent primarily surface-localized Ca. The data are expressed on a per cell volume basis to compensate for size differences as a function of growth stage and transformation. During exponential growth phase, the 3T3 cell contains 525pmol Ca/mul cell volume. Of this, approx. 457 pmol/mul is not removable by EGTA and, presumably, is cytoplasmically located. This value is in close agreement with previous studies on the HeLa cell (470 pmol Ca/mul cell water after the removal of the surface Ca). The low level of EGTA- removable Ca present in the 3T3 cell during early exponential growth (68 pmol Ca/mul cell volume) increases progressively with increasing cell density, and upon quiescence it is sevenfold greater. In contrast, SV40- transformed 3T3 cells growing exponentially possess total levels of Ca which are approximately two-thirds the levels of the normal 3T3 cell. However, their EGTA-sensitive Ca is not significantly different from that of exponentially growing, normal 3T3 cells. As the transformed cells continue to grow at high density, their total ca and their sensitivity to EGTA do not change, in contrast to the normal 3T3 cell. Thus, an increase in Ca associated with the cell surface appears to be correlated with growth inhibition. This has been investigated further by regulating growth of the normal and transformed cell with alterations in the serum level of the media. In 4 percent calf serum the normal cell is stopped from continued proliferation. Growth stoppage under these conditions is characterized by a nearly fourfold increase in EGTA-removable Ca, similar to the increase observed upon quiescence in depleted 10 percent serum. Similar treatment of the transformed cell does not reduce its growth rate, nor does it significantly alter Ca distribution. However, at 0.5 percent medium serum levels, the SV40 3T3 growth rate is substantially reduced and, under these conditions, EGTA-removable Ca increases twofold.

Blood↗
PubMed2006

Irreducible correlation functions of the S matrix in the coordinate representation: application in calculating Lorentzian half-widths and shifts.

By introducing the coordinate representation, the derivation of the perturbation expansion of the Liouville S matrix is formulated in terms of classically behaved autocorrelation functions. Because these functions are characterized by a pair of irreducible tensors, their number is limited to a few. They represent how the overlaps of the potential components change with a time displacement, and under normal conditions, their magnitudes decrease by several orders of magnitude when the displacement reaches several picoseconds. The correlation functions contain all dynamical information of the collision processes necessary in calculating half-widths and shifts and can be easily derived with high accuracy. Their well-behaved profiles, especially the rapid decrease of the magnitude, enables one to transform easily the dynamical information contained in them from the time domain to the frequency domain. More specifically, because these correlation functions are well time limited, their continuous Fourier transforms should be band limited. Then, the latter can be accurately replaced by discrete Fourier transforms and calculated with a standard fast Fourier transform method. Besides, one can easily calculate their Cauchy principal integrations and derive all functions necessary in calculating half-widths and shifts. A great advantage resulting from introducing the coordinate representation and choosing the correlation functions as the starting point is that one is able to calculate the half-widths and shifts with high accuracy, no matter how complicated the potential models are and no matter what kind of trajectories are chosen. In any case, the convergence of the calculated results is always guaranteed. As a result, with this new method, one can remove some uncertainties incorporated in the current width and shift studies. As a test, we present calculated Raman Q linewidths for the N2-N2 pair based on several trajectories, including the more accurate "exact" ones. Finally, by using this new method as a benchmark, we have carried out convergence checks for calculated values based on usual methods and have found that some results in the literature are not converged.

Journal Article↗
PubMed2000

Probabilistic Mental Models with Continuous Predictors.

Gigerenzer and his colleagues have sought to develop psychologically plausible models of human judgment. Their models are classified as ones of bounded rationality based on a principle of one-reason decision making. The models associated with the theory of Probabilistic Mental Models (PMM) have been developed for tasks in which all predictors are binary. This article extends PMM to the case of continuous predictors. The current model employs the limitation on the number of categories people use in making absolute judgments along a single perceptual dimension (7 +/- 2; Miller, 1956). The algorithm transforms each continuous predictor to be consistent with this limitation, then implements a step-down one-reason decision procedure similar to previous PMM models. Like previous PMM models, the 7 +/- 2 model predicts binary judgments as well as a multiple-regression model. However, the model does not successfully predict the probability judgments of individual participants, which is also true of all other models in the literature. Copyright 2000 Academic Press.

Journal Article↗
PubMed1978

Glioblastoma multiforme: morphology and biology.

Glioblastoma multiforme, representing about 50% of all gliomas, encompasses a group of intrinsic tumours of the brain in later years (age peak around 50 years), the morphological hallmarks of which are an ensemble of variations in tumour cell and tissue structure featuring its biological malignancy. Glioblastoma, while sometimes appearing as a distinct "primary" tumour type, is usually accepted as an extreme manifestation of anaplasia and dedifferentiation of glia, mostly astrocytic. The astrocytic nature of most glioblastomas has been confirmed by ultrastructural studies and progressive differentiation of tumours maintained in organotypic tissue culture. Reproducible experimental models are particularly induced by oncogenic RNA (oncorna) viruses. The cell kinetic parameters are similar to those of other solid malignant tumours except for a comparatively low growth fraction of glioblastoma. The frequent occurrence of giant cells as well as of regressive changes with necrosis and vascular responses are indirect (secondary) indicators of malignancy which coincide with histochemical (enzymatic anisochronia) and biochemical data (lower level of glia specific S100 protein than in differentiated gliomas). Vascular proliferation, a characteristic feature of glioblastoma, may occasionally progress to sarcomatous transformation with development of gliosarcomas (mixed glial-mesenchymal tumours). While dissemination of glioblastoma through the cerebrospinal pathways is not uncommon, extraneural distant metastatic spread is rare, and usually observed after craniotomy. The results of modern neuro-oncology support the pathogenetic view that glioblastoma results from neoplastic transformation of glial elements with continuing dedifferentiation. This transformation can be experimentally induced by various factors including oncogenic DNA (oncorna) viruses by using a reverse transcriptase, while there is indirect evidence for an oncorna-virus information in human glioblastoma. The significance of immunological factors in the pathogenesis of brain tumours and in the course of neoplastic transformation of glia is not yet understood, but both morphological and immunological data are in favour of a cell mediated immunological reaction against tumour-specific antibodies. Since immunological factors and changes in cytokinetics are apparently active after the transformed tumour cells proliferate, all available therapeutic methods, including radiation, chemotherapy, and immunotherapy of glioblastoma only influence the final stages of neoplastic development with clinical manifestation of the tumour. In spite of modern combination and multimodality therapy schemes the prognosis of glioblastoma is still poor.

Adult↗
PubMed1992

Localization of bovine papillomavirus type 1 E5 protein to transformed basal keratinocytes and permissive differentiated cells in fibropapilloma tissue.

We examined expression of the E5 transforming protein of bovine papillomavirus type 1 (BPV-1) in naturally and experimentally infected bovine cells. Bovine conjunctival fibroblasts transformed in vitro by experimental infection with purified BPV-1 virions expressed significantly higher amounts of the 7-kDa E5 protein than BPV-1-transformed murine C127 cells. Indirect immunofluourescence analysis revealed a cytoplasmic, predominantly juxtanuclear, localization of E5 protein in the in vitro virus-transformed bovine cells. In naturally infected bovine skin fibropapilloma tissue, two widely separated sites of E5 protein synthesis were identified within the epithelial layers. Transformed basal layer keratinocytes throughout the tumor tissue expressed cytoplasmic E5 protein at a low uniform level. In addition, abundant amounts of cytoplasmic E5 protein with a granular staining pattern were detected in highly differentiated keratinocytes in close association with sites of viral capsid protein synthesis. These observations imply roles for the viral E5 oncogene in the growth transformation of basal epidermal keratinocytes as well as in the differentiation-linked process of viral maturation. Detection of a papillomavirus protein in the basal cell population of warts lends support to the hypothesis that these cells are maintained in a transformed state by continuous expression of a viral transforming gene.

Amino Acid Sequence↗
PubMed1998

[Crackle detection and classification based on matched wavelet transform].

In this paper, we present a method for crackle detection which is based on 'matched' wavelet transform. We first modeled crackles as a mathematical function. Then we designed a matched mother wavelet based on this model. Applying a soft-threshold to the results of the continuous wavelet transform to suppress noise further, we obtained the optimal scale Crackles were detected based on the envelope of the signal at optimal scale, and could be classified based on energy distribution with scale. The theory, methods and experimental results are given in detail.

Algorithms↗
PubMed1991

Computer applications in diagnostic imaging.

This article has introduced the nature, generation, use, and future of digital imaging. As digital technology has transformed other aspects of our lives--has the reader tried to buy a conventional record album recently? almost all music store stock is now compact disks--it is sure to continue to transform medicine as well. Whether that transformation will be to our liking as physicians or a source of frustration and disappointment is dependent on understanding the issues involved.

Diagnostic Imaging↗
PubMed1991

Extracellular matrix and androgen receptor expression associated with spontaneous transformation of rat prostate fibroblasts.

Spontaneous transformation in continuous culture of the androgen-sensitive rat prostate fibroblast cell line, NbF-1, resulted in an aggressively tumorigenic nonmetastatic phenotype that coincided with few gross chromosome abnormalities. This study identified transformation-associated alterations in extracellular matrix and androgen receptor expression in the NbF-1 cell line. Substantial levels of procollagens I, III, and IV and fibronectin mRNAs were detected in nontumorigenic NbF-1 cells. Laminin B1 and B2 mRNAs were also detectable, but at lower levels. Expression of all six extracellular matrix mRNAs was nonuniformly lower in tumorigenic NbF-1 cells. This decrease in expression was greatest for alpha 2 procollagen IV mRNA, which was reduced 17-fold. Proteoglycans and glycosaminoglycans synthesized by the NbF-1 cultures were also characterized. The NbF-1 cell line expressed chondroitin sulfate proteoglycans predominantly, and expression was reduced 5- to 10-fold in tumorigenic cultures. In contrast to the extensive alterations in the extracellular matrix, measurement of high-affinity androgen binding and androgen receptor mRNA levels showed substantial expression of androgen receptors in both NbF-1 cultures. Cultures of early and late passage NbF-1 cells demonstrated a mitogenic response to dihydrotestosterone. These data indicate (a) that alterations in expression of extracellular matrix components may represent early markers for tumorigenic transformation in prostatic mesenchymal cells and (b) that these changes can occur without disrupting androgen receptor expression and androgen sensitivity.

Animals↗
PubMed1974

Observations on the type of infection by Epstein-Barr virus in peripheral lymphoid cells of patients with infectious mononucleosis.

Transformation to continuous cell lines has been studied in cultures of peripheral leuckocytes from infectious mononucleosis (IM) patients and in co-cultures of IM leukocytes and foetal cord blood leukocytes of opposite sex. The transformed cells in the co-cultures were of mixed origin with foetal cells usually predominating. Neutralizing antisera to EB virus markedly reduced or abolished the incidence of transformation in IM leukocyte cultures. This effect was not due to cytotoxicity and followed the pattern seen with cultures where transformation was known to depend on the inter-cellular transfer of infectious EB virus. The findings suggest that EB virus is harboured in peripheral lymphocytes of IM patients as a non-productive unexpressed infection which is activated to produce virus in vitro, the particles released then infecting neighbouring cells to give transformed lines. The differences between this mechanism and the one whereby lines arise in culture from malignant cells of Burkitt's lymphoma are considered, and their significance is discussed.

Blood↗
PubMed1993

Herpesvirus saimiri transformed human T cell lines: a permissive system for human immunodeficiency viruses.

Human peripheral blood T lymphocytes are readily transformed to continuous growth by Herpesvirus saimiri subgroup C strains. The immortalized cells express the phenotype of mature activated T cells and bear either CD4 or CD8 surface markers. Here we report that Herpesvirus saimiri transformed CD4+ cell lines are highly susceptible to infection with human immunodeficiency viruses types 1 and 2. The prototype viruses HIV-1IIIB and HIV-2ROD replicated rapidly and caused cell death within 14 days. These cell lines did also support growth of a poorly replicating HIV-2 strain (HIV-2NEP) and of primary clinical isolates. Thus H. saimiri transformed T cells represent a new system for HIV propagation and isolation, especially for HIV-2 strains with restricted cell tropism. These cells should be considered as an alternative approach in cases where conventional attempts fail.

Cell Line, Transformed↗
PubMed1990

The effect of T-DNA copy number, position and methylation on reporter gene expression in tobacco transformants.

Inter-transformant variability in the expression of introduced genes was studied in the R1 and R2 generations of 10 tobacco transformants, produced by Agrobacterium-mediated transformation. In replicated and physiologically equivalent material, tranformants showed considerable variability in the expression of the reporter gene uidA as shown by transcript levels and beta-glucuronidase (GUS) activity. However, homozygous R2 material could be investigated for seven of the transformants and among these, and in one line in which two inserts could segregate independently, this inter-transformant variability was reduced to simple bimodal expression. The two levels of expression for GUS activity in leaves were high or low (approximately 2.5 or 0.3 nmol cm-2 min-1 respectively), with no continuous variation. Transformants in the high group had single T-DNA insertions, while those in the low group had multiple T-DNA insertions, at the same or different loci. Within each group, although T-DNA was apparently integrated at different sites in the plant genome, there was no evidence of position effects. GUS activity levels of the transformants were very similar in the field and in environmentally controlled conditions under high or low light. Plants with multiple insertions and low expression also tended to have increased methylation of the integrated T-DNA.

Bacterial Proteins↗
PubMed2006

Visualization of synchronization of the uterine contraction signals: running cross-correlation and wavelet running cross-correlation methods.

In physiological research, we often study multivariate data sets, containing two or more simultaneously recorded time series. The aim of this paper is to present the cross-correlation and the wavelet cross-correlation methods to assess synchronization between contractions in different topographic regions of the uterus. From a medical point of view, it is important to identify time delays between contractions, which may be of potential diagnostic significance in various pathologies. The cross-correlation was computed in a moving window with a width corresponding to approximately two or three contractions. As a result, the running cross-correlation function was obtained. The propagation% parameter assessed from this function allows quantitative description of synchronization in bivariate time series. In general, the uterine contraction signals are very complicated. Wavelet transforms provide insight into the structure of the time series at various frequencies (scales). To show the changes of the propagation% parameter along scales, a wavelet running cross-correlation was used. At first, the continuous wavelet transforms as the uterine contraction signals were received and afterwards, a running cross-correlation analysis was conducted for each pair of transformed time series. The findings show that running functions are very useful in the analysis of uterine contractions.

Dysmenorrhea↗
PubMed1994

Fast wavelet transformation of EEG.

Wavelet transforms offer certain advantages over Fourier transform techniques for the analysis of EEG. Recent work has demonstrated the applicability of wavelets for both spike and seizure detection, but the computational demands have been excessive. We compare the quality of feature extraction of continuous wavelet transforms using standard numerical techniques, with more rapid algorithms utilizing both polynomial splines and multiresolution frameworks. We further contrast the difference between filtering with and without the use of surrogate data to model background noise, demonstrate the preservation of feature extraction with critical versus redundant sampling, and perform the analyses with wavelets of different shape. Comparison is made with windowed Fourier transforms, similarly filtered, at different data window lengths. We here report a dramatic reduction in computational time required to perform this analysis, without compromising the accuracy of feature extraction. It now appears technically feasible to filter and decompose EEG using wavelet transforms in real time with ordinary microprocessors.

Brain↗
PubMed2006

Improved Chou-Fasman method for protein secondary structure prediction.

BACKGROUND: Protein secondary structure prediction is a fundamental and important component in the analytical study of protein structure and functions. The prediction technique has been developed for several decades. The Chou-Fasman algorithm, one of the earliest methods, has been successfully applied to the prediction. However, this method has its limitations due to low accuracy, unreliable parameters, and over prediction. Thanks to the recent development in protein folding type-specific structure propensities and wavelet transformation, the shortcomings in Chou-Fasman method are able to be overcome. RESULTS: We improved Chou-Fasman method in three aspects. (a) Replace the nucleation regions with extreme values of coefficients calculated by the continuous wavelet transform. (b) Substitute the original secondary structure conformational parameters with folding type-specific secondary structure propensities. (c) Modify Chou-Fasman rules. The CB396 data set was tested by using improved Chou-Fasman method and three indices: Q3, Qpre, SOV were used to measure this method. We compared the indices with those obtained from the original Chou-Fasman method and other four popular methods. The results showed that our improved Chou-Fasman method performs better than the original one in all indices, about 10-18% improvement. It is also comparable to other currently popular methods considering all the indices. CONCLUSION: Our method has greatly improved Chou-Fasman method. It is able to predict protein secondary structure as good as current popular methods. By locating nucleation regions with refined wavelet transform technology and by calculating propensity factors with larger size data set, it is likely to get a better result.

Algorithms↗
PubMed1997

Transformation by v-Jun prevents cell cycle exit and promotes apoptosis in the absence of serum growth factors.

To gain insight into the mechanism of action of the v-Jun oncoprotein, we compared the growth and cell cycle behavior of normal and v-Jun-transformed fibroblasts. We show that v-Jun induces marked alterations in cell cycle regulation in both the presence and absence of serum growth factors. During asynchronous growth, v-Jun-transformed fibroblasts divide more rapidly than their normal counterparts, owing to a reduction in the length of the G1 phase of the cell cycle. When deprived of serum mitogens, normal fibroblasts exit the cycle and enter a reversible state of quiescence (G0). In contrast, v-Jun-transformed fibroblasts continue to cycle and maintain increased levels of retinoblastoma tumor suppressor protein phosphorylation and elevated expression of cell cycle-dependent markers such as cyclin A, cyclin-dependent protein kinase 2 (CDK2), and CDC2. v-Jun-transformed fibroblasts nevertheless remain wholly dependent on growth factors for cell multiplication, because cell cycle progression in the absence of serum is accompanied by high rates of apoptotic cell death. We conclude that v-Jun shares the capacity of the Myc, E1A, and E2F oncoproteins to promote both cell cycle progression and apoptosis under conditions of mitogen depletion.

Adenovirus E1A Proteins↗
PubMed1975

In vivo assembly of tight junctions in fetal rat liver.

Examination of glutaraldehyde-fixed, freeze-fractured livers from 14-15-day rat fetuses provided the basis for the following observations. Membrane particles align in otherwise poorly particulated areas of the presumptive pericanalicular plasma membrane (A face), frequently forming a discontinuous "honey-comb" network joining small particle islands. Even at this early stage, contiguous B-fracture faces contain furrows, rather than rows of pits, distinguishing the linear particle aggregates on the A face as developing tight junctions rather than gap junctions. Short segments of these linear arrays merge with smooth ridges clearly identifiable as segments of discontinuous tight junctions. With the continuing confluence of particulate and smooth ridge segments, mature tight junctions become fully appreciable. We conclude that tight junctions form de novo by the alignment and fusion of separate particles into beaded ridges which, in turn, become confluent and are transformed into continuous smooth ones. At 21 days of fetal life, most of the images of assembly have disappeared, and the liver reveals well-formed bile canaliculi sealed by mature tight junctions.

Animals↗