Biomedical subjects

Fariza Tahi

Publications and source records attributed to Fariza Tahi.

3 recordsLinked to original sources

PubMed2006

Modeling and simulation with Hybrid Functional Petri Nets of the role of interleukin-6 in human early haematopoiesis.

The regulation of human haematopoiesis is a complex biological system with numerous interdependent processes. In vivo Haematopoietic Stem Cells (HSCs) self-renew so as to maintain a constant pool of these cells. It would be very interesting to maintain these cells in vitro, in view of their therapeutical importance. Unfortunately, there is currently no known process to activate HSCs self-renewal in vitro. Since the difficulties related to in vitro experiments, modeling and simulating this process is indispensable. Moreover, the complexity of haematopoiesis makes it necessary to integrate various functionalities: both discrete and continuous models as well as consumption and production of resources. We thus focus on the use of Hybrid Functional Petri Nets, which offer a number of features and flexibility. We begin by modeling and simulating the role of a specific cytokine, interleukin-6, in the regulation of early haematopoiesis. Results obtained in silico lead to the disappearence of HSCs, which is in agreement with in vitro results.

Computational Biology↗

PubMed2002

Identification of genes involved in ceramide-dependent neuronal apoptosis using cDNA arrays.

BACKGROUND: Ceramide is important in many cell responses, such as proliferation, differentiation, growth arrest and apoptosis. Elevated ceramide levels have been shown to induce apoptosis in primary neuronal cultures and neuronally differentiated PC 12 cells. RESULTS: To investigate gene expression during ceramide-dependent apoptosis, we carried out a global study of gene expression in neuronally differentiated PC 12 cells treated with C2-ceramide using an array of 9,120 cDNA clones. Although the criteria adopted for differential hybridization were stringent, modulation of expression of 239 genes was identified during the effector phase of C2-ceramide-induced cell death. We have made an attempt at classifying these genes on the basis of their putative functions, first with respect to known effects of ceramide or ceramide-mediated transduction systems, and then with respect to regulation of cell growth and apoptosis. CONCLUSIONS: Our cell-culture model has enabled us to establish a profile of gene expression during the effector phase of ceramide-mediated cell death. Of the 239 genes that met the criteria for differential hybridization, 10 correspond to genes previously involved in C2-ceramide or TNF-alpha signaling pathways and 20 in neuronal disorders, oncogenesis or more broadly in the regulation of proliferation. The remaining 209 genes, with or without known functions, constitute a pool of genes potentially implicated in the regulation of neuronal cell death.

Animals↗

PubMed2002

Automatic RNA secondary structure prediction with a comparative approach.

This paper presents an algorithm, DCFold, that automatically predicts the common secondary structure of a set of aligned homologous RNA sequences. It is based on the comparative approach. Helices are searched in one of the sequences, called the 'target sequence', and compared to the helices in the other sequences, called the 'test sequences'. Our algorithm searches in the target sequence for palindromes that have a high probability to define helices that are conserved in the test sequences. This selection of significant palindromes is based on criteria that take into account their length and their mutation rate. A recursive search of helices, starting from these likely ones, is implemented using the 'divide and conquer' approach. Indeed, as pseudo-knots are not searched by DCFold, a selected palindrome (p, p') makes possible to divide the initial sequence into two sequences, the internal one and the one resulting from the concatenation of the two external ones. New palindromes can be searched independently in these subsequences. This algorithm was run on ribosomal RNA sequences and recovered very efficiently their common secondary structures.

Algorithms↗