Browsing by Subject "Protein bcl 2"

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Open Access
Implicit motif distribution based hybrid computational kernel for sequence classification
(Oxford University Press, 2005) Atalay, V.; Cetin Atalay, R.
Motivation: We designed a general computational kernel for classification problems that require specific motif extraction and search from sequences. Instead of searching for explicit motifs, our approach finds the distribution of implicit motifs and uses as a feature for classification. Implicit motif distribution approach may be used as modus operandi for bioinformatics problems that require specific motif extraction and search, which is otherwise computationally prohibitive. Results: A system named P2SL that infer protein subcellular targeting was developed through this computational kernel. Targeting-signal was modeled by the distribution of subsequence occurrences (implicit motifs) using self-organizing maps. The boundaries among the classes were then determined with a set of support vector machines. P2SL hybrid computational system achieved ∼81% of prediction accuracy rate over ER targeted, cytosolic, mitochondrial and nuclear protein localization classes. P2SL additionally offers the distribution potential of proteins among localization classes, which is particularly important for proteins, shuttle between nucleus and cytosol. © The Author 2004. Published by Oxford University Press. All rights reserved.
Open Access
The involvement of apoptotic regulators during in vitro decidualization
(Society of the European Journal of Endocrinology, 2003) Akcali, K. C.; Gibori, G.; Khan, S. A.
Objectives: The uterus responds to an implanting blastocyst by undergoing extensive tissue modification leading to decidualization. This modification includes differentiation and apoptosis of epithelial as well as stromal cell compartments. It is generally accepted that the decidual cell regression pattern is similar to the pattern of initial differentiation, suggesting that decidual cell death is the end point of timed differentiation. However, the molecular mechanisms controlling these events are not understood clearly. Therefore, we aimed to investigate the involvement of apoptotic factors using an in vitro cell culture system. Design: In order to assess the role of apoptotic factors during decidualization, we used a decidual cell line (GG-AD) that had been transformed with a temperature-sensitive SV-40 mutant. At the non-permissive temperature (39°C), these cells showed the characteristics of differentiated decidual cells. They dedifferentiated into stromal cells when the temperature was shifted back to 33°C. Methods: We performed Northern blot analysis for bax, bcl-XL and bcl-2 at both temperatures. The onset of apoptosis was examined by Annexin V staining. The expression of p53 protein was also determined by Western blot. Results: We found an increase in the expression of bax when GG-AD cells were grown at 39°C. We also showed apoptosis with Annexin V staining at 39°C. The p53 protein expression was also similar to that of the animal models, suggesting that the programmed cell death of the decidual cells occurred in a p53-independent manner. Conclusions: These data indicate that a parallelism exists between the increased expression of pro-apoptotic genes and decidual cell death, similar to animal models. Therefore, an in vitro model of GG-AD cells can be used to assess directly the relationship between apoptotic regulators and decidualization and could be used to study the mechanism of decidual cell regression.