Transforming Growth Factor-Beta (TGF-beta) Signaling in Paravertebral Muscles in Juvenile and Adolescent Idiopathic Scoliosis

Most researchers agree that idiopathic scoliosis (IS) is a multifactorial disease influenced by complex genetic and environmental factors. The onset of the spinal deformity that determines the natural course of the disease, usually occurs in the juvenile or adolescent period. Transforming growth factors (TGF-s) and their receptors, TGFBRs, may be considered as candidate genes related to IS susceptibility and natural history. This study explores the transcriptional profile of TGF-s, TGFBRs, and TGF- responsive genes in the paravertebral muscles of patients with juvenile and adolescent idiopathic scoliosis (JIS and AIS, resp.). Muscle specimens were harvested intraoperatively and grouped according to the side of the curve and the age of scoliosis onset. The results of microarray and qRT-PCR analysis confirmed significantly higher transcript abundances of TGF-2, TGF-3, and TGFBR2 in samples from the curve concavity of AIS patients, suggesting a difference in TGF- signaling in the pathogenesis of juvenile and adolescent curves. Analysis of TGF- responsive genes in the transcriptomes of patients with AIS suggested overrepresentation of the genes localized in the extracellular region of curve concavity: LTBP3, LTBP4, ITGB4, and ITGB5. This finding suggests the extracellular region of paravertebral muscles as an interesting target for future molecular research into AIS pathogenesis

Epigenetic modification of genetic algorithm for outlier detection

The article presents a new operator in the genetic algorithm. The proposed operator mimics the epigenetic process of prion inheritance. For living organisms, epigenetic processes have a large impact on the differentiation of the population, hence the idea to imitate these processes in genetic algorithms. For the purposes of the experiments, a genetic algorithm to detect outliers was used. The proposed operator mimics the epigenetic process was added to the basic genetic algorithm and the impact of the operator on the effectiveness of the algorithm was assessed. The impact of the proposed modification on the efficiency of the genetic algorithm was tested on six data sets. The article also presents an experimental analysis of the proposed operator

Komputerowe wspomaganie gromadzenia i analizy danych z mikromacierzy oligonukleotydowych w badaniach ekspresji genów

A relatively new method o f biomedical data acquisition - microarray technology and an example o f computational capacity possibilities for filtering o f microarray data were described. The types o f microarrays used and subsequently microarray experiment steps were discussed. Such kind of experiments makes possible finding changes in gene expression in living cells effected by drugs and other xenobiotics to check the cell resistance or sensibility. Some terms necessary for understanding gene expression and its importance were explained. A proposal o f the data warehouse solution, developed with special attention for storage and the analysis o f microarray data was presented

Transforming Growth Factor-Beta (TGF- β

Most researchers agree that idiopathic scoliosis (IS) is a multifactorial disease influenced by complex genetic and environmental factors. The onset of the spinal deformity that determines the natural course of the disease, usually occurs in the juvenile or adolescent period. Transforming growth factors β (TGF-βs) and their receptors, TGFBRs, may be considered as candidate genes related to IS susceptibility and natural history. This study explores the transcriptional profile of TGF-βs, TGFBRs, and TGF-β responsive genes in the paravertebral muscles of patients with juvenile and adolescent idiopathic scoliosis (JIS and AIS, resp.). Muscle specimens were harvested intraoperatively and grouped according to the side of the curve and the age of scoliosis onset. The results of microarray and qRT-PCR analysis confirmed significantly higher transcript abundances of TGF-β2, TGF-β3, and TGFBR2 in samples from the curve concavity of AIS patients, suggesting a difference in TGF-β signaling in the pathogenesis of juvenile and adolescent curves. Analysis of TGF-β responsive genes in the transcriptomes of patients with AIS suggested overrepresentation of the genes localized in the extracellular region of curve concavity: LTBP3, LTBP4, ITGB4, and ITGB5. This finding suggests the extracellular region of paravertebral muscles as an interesting target for future molecular research into AIS pathogenesis

Familial or Sporadic Idiopathic Scoliosis - classification based on artificial neural network and GAPDH and ACTB transcription profile

Background: Importance of hereditary factors in the etiology of Idiopathic Scoliosis is widely accepted. In clinical practice some of the IS patients present with positive familial history of the deformity and some do not. Traditionally about 90% of patients have been considered as sporadic cases without familial recurrence. However the exact proportion of Familial and Sporadic Idiopathic Scoliosis is still unknown. Housekeeping genes encode proteins that are usually essential for the maintenance of basic cellular functions. ACTB and GAPDH are two housekeeping genes encoding respectively a cytoskeletal protein β-actin, and glyceraldehyde-3-phosphate dehydrogenase, an enzyme of glycolysis. Although their expression levels can fluctuate between different tissues and persons, human housekeeping genes seem to exhibit a preserved tissue-wide expression ranking order. It was hypothesized that expression ranking order of two representative housekeeping genes ACTB and GAPDH might be disturbed in the tissues of patients with Familial Idiopathic Scoliosis (with positive family history of idiopathic scoliosis) opposed to the patients with no family members affected (Sporadic Idiopathic Scoliosis). An artificial neural network (ANN) was developed that could serve to differentiate between familial and sporadic cases of idiopathic scoliosis based on the expression levels of ACTB and GAPDH in different tissues of scoliotic patients. The aim of the study was to investigate whether the expression levels of ACTB and GAPDH in different tissues of idiopathic scoliosis patients could be used as a source of data for specially developed artificial neural network in order to predict the positive family history of index patient. Results: The comparison of developed models showed, that the most satisfactory classification accuracy was achieved for ANN model with 18 nodes in the first hidden layer and 16 nodes in the second hidden layer. The classification accuracy for positive Idiopathic Scoliosis anamnesis only with the expression measurements of ACTB and GAPDH with the use of ANN based on 6-18-16-1 architecture was 8 of 9 (88%). Only in one case the prediction was ambiguous. Conclusions: Specially designed artificial neural network model proved possible association between expression level of ACTB, GAPDH and positive familial history of Idiopathic Scoliosis

The arrangement of Brachypodium distachyon chromosomes in interphase nuclei

The spatial organization of chromatin within the interphase nucleus and the interactions between chromosome territories (CTs) are essential for various biological processes, such as DNA replication, transcription, and repair. However, detailed data about the CT arrangement in monocotyledonous plants are scarce. In this study, chromosome painting was used to analyse the distribution and associations of individual chromosomes in the 3-D preserved nuclei of Brachypodium distachyon root cells in order to determine the factors that may have an impact on the homologous CT arrangement. It was shown that the frequency of CT association is linked to the steric constraints imposed by the limited space within the nucleus and may depend on chromosome size and morphology as well as on the nuclear shape. Furthermore, in order to assess whether the distribution of interphase chromosomes is random or is subject to certain patterns, a comparison between the experimental data and the results of a computer simulation (ChroTeMo), which was based on a fully probabilistic distribution of the CTs, was performed. This comparison revealed that homologous chromosome arm CTs associate more often than if they were randomly arranged inside the interphase nucleus

Multifunctional protein APPL2 contributes to survival of human glioma cells

Some endocytic proteins have recently been shown to play a role in tumorigenesis. In this study, we demonstrate that APPL2, an adapter protein with known endocytic functions, is upregulated in 40% cases of glioblastoma multiforme, the most common and aggressive cancer of the central nervous system. The silencing of APPL2 expression by small interfering RNAs (siRNAs) in glioma cells markedly reduces cell survival under conditions of low growth factor availability and enhances apoptosis (measured by executor caspase activity). Long‐term depletion of APPL2 by short hairpin RNAs (shRNAs), under regular growth factor availability, suppresses the cell transformation abilities, assessed by inhibited colony formation in soft agar and by reduced xenograft tumor growth in vivo. At the molecular level, the negative effect of APPL2 knockdown on cell survival is not due to the alterations in AKT or GSK3β activities which were reported to be modulated by APPL proteins. Instead, we attribute the reduced cell survival upon APPL2 depletion to the changes in gene expression, in particular to the upregulation of apoptosis‐related genes, such as UNC5B (a proapoptotic dependence receptor) and HRK (harakiri, an activator of apoptosis, which antagonizes anti‐apoptotic function of Bcl2). In support of this notion, the loss of glioma cell survival upon APPL2 knockdown can be rescued either by an excess of netrin‐1, the prosurvival ligand of UNC5B or by simultaneous silencing of HRK. Consistently, APPL2 overexpression reduces expression of HRK and caspase activation in cells treated with apoptosis inducers, resulting in the enhancement of cell viability. This prosurvival activity of APPL2 is independent of its endosomal localization. Cumulatively, our data indicate that a high level of APPL2 protein might enhance glioblastoma growth by maintaining low expression level of genes responsible for cell death induction

Novel visual analytics approach for chromosome territory analysis

This document presents a new and improved, more intuitive version of a novel method for visually representing the location of objects relative to each other in 3D. The motivation and inspiration for developing this new method came from the necessity for objective chromosome territory (CT) adjacency analysis. The earlier version, Distance Profile Chart (DPC), used octants for 3D orientation. This approach did not provide the best 3D space coverage since space was divided into just eight cones and was not intuitive with regard to orientation in 3D. However, the version presented in this article, called DPC12, allows users to achieve better space coverage during conification since space is now divided into twelve cones. DPC12 is faster than DPC and allows for a more precise determination of the location of objects in 3D. In this article a short introduction about the conification idea is presented. Then we explain how DPC12 is designed and created. After that, we show DPC12 on an instructional dataset to make it easier to understand and demonstrate how they appear and how to read them. Finally, using DPC12 we present an example of an adjacency analysis (AA) using the model of Chromosome Territories (CTs) distribution in the rice nucleus

Brachypodium distachyon - a model plant to study grass genome structure, dynamics and evolution

Plenary Session: Present status of cell, tissue and organ in vitro cultur

Transformujący czynnik wzrostu beta w raku podstawnokomórkowym, kolczystokomórkowym i rogowiaku kolczystokomórkowym

Introduction. Transforming Growth Factor β (TGFβ) activates signaling cascades which regulate cell proliferation, differentiation, apoptosis, inflammatory response and angiogenesis. In the early stages of malignant transformation this cytokine acts as an inhibitor of tumour growth. In the advanced stages of malignant transformation TGFβ acts as a promoter of metastasis. Changes in the expression of genes associated with TGFβactivity could provide a new strategy of molecularly targeted therapy.Aim. The aim of this study was to compare the mRNA profile of genes associated with TGFβ signaling pathways in non-melanoma skin pathologies biopsy specimens of bas-al cell carcinoma (BCC), squamous cell carcinoma (SCC) and keratoacanthoma (KA) in comparison to normal skin.Material and methods. Tissue samples of KA, SCC and BCC were obtained from the central part of tumours. Healthy skin margins comprised the control group. mRNA profile of genes coding TGFβ and proteins involved in TGFβ-induced signaling pathways was determined using oligonucleotide microarrays (Affymetrix).Results. Microarray analysis showed changes in profile of genes coding proteins in-volved in TGFβ-induced signaling pathways. In SCC TGFβ-1 (TGFB1) was upregulated, comparing to controls. Both in KA and SCC, the most statistically significant change re-ferred to TGFBR3 (Transforming Growth Factor beta Receptor III) mRNA.Conclusions. mRNA profile of genes coding proteins involved in TGFβ-induced signal-ization reveals strong molecular similarity of SCC and KA