META-analysis of microarray data to assess gender biased differential gene expression in hepatic tissue

Hepatocellular carcinoma (HCC) is the second deadliest cancer globally, and with an estimated 782,000 new cases in 2012, it is the fifth most common cancer in men and ninth in women. HCC is of particular concern in Egypt because of the high prevalence of Hepatitis C Virus (HCV). Due to its poor prognosis, HCC is the leading cause of cancer-related deaths in Egypt. A gender disparity is observed in liver cancer cases, with higher prevalence in men by three to five fold. This sex bias is even more pronounced in mouse models of HCC, which was found to be sex hormone-dependent. Some studies have attempted to elucidate the molecular mechanisms of this disparity; but with inconclusive and sometimes contradicting outcomes, they remain largely unresolved. Understanding the natural protective mechanisms in females would allow for the development of preventative and therapeutic strategies for patients at risk for HCC or already inflicted with the disease. In this study, we applied a meta-analysis approach on already available microarray data from human normal liver tissues to identify differentially expressed genes between males and females. Microarray datasets were downloaded from the Gene Expression Omnibus database, Robust Multiarray Average pre-processed and analyzed for differential expression. The combination of 2 distinct datasets and analysis using a p-value cut-off of 0.05 and fold change cut-off of 2 revealed male up-regulated genes including RPS4Y1, EIF1AY, CYorf15B, UTY, DDX3Y and USP9Y. Female up-regulated genes included XIST, PNPLA4 and PZP. Our results confirm gender-specific differential expression patterns found in other tissues and call for further investigation using a larger sample size and more sensitive approaches such as RNA-Sequencing and, targeted protein-level studies

Analysis of Gene Expression Microarray Time Series Data

Regulatory interactions among genes and gene products are dynamic processes, and hence, modeling these processes is essential. In recent years, research efforts in the field of microarray data analysis have been constantly increasing due to the rapid growth of microarray technology, and due to the growing interest in the understanding of complex diseases. It is of vital importance to identify and characterize changes in gene expression over time. Since genes work in a cascade of networks, reconstruction of gene regulatory networks is a crucial process for a thorough understanding of the underlying biological interactions. Analysis of large scale microarray data is a challenging problem, where most of the microarray time series have only five to ten time points and the conventional time analysis techniques are not applicable. The present study focuses on two important aspects of the microarray data analysis. The first part is concerned with the identification of the differentially expressed genes, whereas the second part with the reconstruction of the gene regulatory networks. New computational methods for time course microarray data that assist in analyzing and modeling the dynamics of the gene regulations are developed in this study. The main challenges in the identification of differently expressed genes arise due to the availability of a very small number of replicated samples (usually two or three samples) in the face of a huge number of genes (thousands of genes). Further, most of the previous works, in this area have focused on static gene expressions, with only a limited number on methods for selecting the genes that exhibit changes with time. In the first part of this study, a general statistical method for detecting changes in microarray expression over time within a single or multiple biological groups is presented. The method is based on repeated measures (RM) ANOVA, in which, unlike the classical F-statistic, statistical significance is determined by taking into account the time dependency of the microarray data. A correction factor for this RM F-statistic that leads to higher sensitivity as well as a high specificity is introduced. The two approaches for calculating the p-values that exist in the literature, that is, those resampling techniques of gene-wise p-values and pooled p-values, are investigated. It is shown that the pooled p-values method compared to the method of the gene-wise p-values is more powerful and computationally less expensive, and hence it is applied along with the correction factor introduced to various synthetic data sets and a real data set. The results from the synthetic data sets show that the proposed technique outperforms the state-of-the-art methods, whereas those from using the real data set are found to be consistent with the existing knowledge concerning the presence of the genes. As for the reconstruction of gene regulatory networks, challenges, such as the relatively large number of genes compared to the small number of time points, result in an underdetermined problem. Additional constraints and information are needed to be able to capture the gene regulatory dynamics. Since gene regulatory interactions involve underlying biological processes, such as transcription and translation that take place at different time points, the consideration of different delays is a very crucial, yet a demanding problem. In the second part of this study, an approach based on pair-wise correlations and lasso that take into account the different time delays between various genes, is presented to infer gene regulatory networks. The proposed method is applied to both synthetic and real data sets. The results from the synthetic data show that the proposed approach outperforms the existing methods, and the results from the real data are found to be more consistent with the existing knowledge concerning the possible gene interactions. The study on the identification of differentially expressed genes and the reconstruction of the gene regulatory networks, undertaken in this thesis, can be regarded to be directed towards a better understanding of the cellular dynamics

Déterminants moléculaires de la scoliose idiopathique de l'adolescent

La scoliose est la déformation de la colonne vertébrale la plus répandue. Elle atteint 3 à 4% de la population pédiatrique et dans 85% des cas, aucune cause n’a été identifiée. Ces cas sont appelés idiopathiques et les symptômes apparaissent durant la puberté; d’où le terme de ‘scoliose idiopathique de l’adolescent (SIA). Cette pathologie atteint le plus souvent les jeunes filles, en nombre et en sévérité. Ces dernières années, plusieurs hypothèses ont été proposées afin d’élucider l’étiologie de cette pathologie. Celles-ci ont mis de l’avant différents facteurs génétiques, biochimiques, mécaniques, neurologiques, musculaires ou hormonaux. Plusieurs études ont rapporté des formes familiales de scoliose, soutenant la thèse d’une prédisposition génétique. Nous avons démontré que les patients souffrant de SIA présentent un défaut de signalisation cellulaire médiée par les protéines Gi et un taux élevé d’ostéopontine (OPN) circulante. En utilisant une approche de type ‘gène candidat’, nous avons montré que la protéine tyrosine phosphatase μ (PTPμ) régule l’activité du complexe d’intégrines α5/β1 (récepteur de l’OPN) via la protéine kinase PIPKIγ. Dans ce but, nous avons utilisé des cultures primaires d’ostéoblastes issues de biopsies de patients et de cas traumatiques comme sujets contrôles. Les biopsies osseuses de patients ont été obtenues lors de l’intervention chirurgicale à partir des vertèbres T3 à L4, selon les différentes procédures. Les biopsies issues de cas traumatiques proviennent d’autres types d’os (tibia, crête iliaque, fémur). Les profils d’expression du gène PTPRM (codant pour la protéine PTPμ) ont été étudiés par PCR quantitative (qPCR). Les taux de protéines PTPμ ont été analysés par immunoprécipitation suivi d’un western blot. Pour évaluer le rôle de cette protéine, nous avons bénéficié d’un modèle murin. Machida et al. ont démontré qu’il existe un taux plus élevé de scoliose parmi les souris C57Bl/6 bipèdes obtenues suite à l’amputation des membres supérieurs, sous anesthésie, cinq semaines après la naissance. Nous avons utilisé des cultures primaires d’ostéoblastes issues de la colonne ii vertébrale de souris C57Bl/6 bipèdes, délétées du gène PTPRM (souris dites ‘KO’), afin d’évaluer le niveau de signalisation cellulaire spécifique des protéines Gi par un test fonctionnel: la technique de spectroscopie cellulaire di-électrique (SCD). Selon nos données, 85% des souris bipédales ‘KO’ pour le géne PTPRM développent une scoliose (modérée à sévère) contre 55% des souris contrôles C57Bl6 bipèdes. De plus, les niveaux de PTPμ exprimée par les ostéoblastes de 34 patients SIA se trouvent diminués par comparaison à 17 sujets contrôles. Nos études de souris bipèdes ont montré que l’inactivation du gène PTPRM augmente l’incidence et la sévérité de la scoliose, sans pour autant affecter les taux circulant d’OPN ou l’expression de ses récepteurs. Par ailleurs, dans ce même contexte, nous avons remarqué une augmentation de l’interaction entre l’OPN et l’intégrine β1 en l’absence du gène PTPRM. Les cellules issues de ces souris bipèdes KO montrent une réduction dans leurs niveaux de signalisation cellulaire médiée par les protéines Gi après stimulation par l’OPN. Cette diminution est en grande partie récupérée après traitement des cellules par un siRNA spécifique de la protéine PIPK1γ, substrat de PTPμ qui favorise la fixation de ligands aux intégrines. Ces études apportent les premières indications que la perte d’expression de PTPμ est impliquée dans le développement de la SIA, en amplifiant probablement l’effet inhibiteur de l’OPN sur la signalisation cellulaire médiée par les protéines Gi. Ces études permettent une meilleure compréhension de l’étiologie de la SIA. Elles pourraient avoir une contribution importante dans le développement futur de méthodes diagnostique et thérapeuthique dans le but d'arrete l’apparition et l’évolution de la maladie chez les enfants atteints.Adolescent idiopathic scoliosis (AIS) is the most common form of scoliosis that affects 3-4% of the global pediatric population. In more than 85% of cases, no specific cause can be identified. Such cases are called idiopathic and occur mostly during adolescence. AIS affects mainly females in number and severity. Over the past years, many hypotheses were proposed to explain the etiology of AIS, including genetic, biochemical, mechanics, neurological, muscular and hormonal factors. Several studies have reported a high incidence of scoliosis in some families, which argues for a genetic cause of this disease. We demonstrated that AIS patients have a Gi protein signaling defect and exhibit high levels of circulating Osteopontin (OPN). The goal of this thesis is to identify the mechanisms regulating OPN signaling activity in AIS patients. We have used a candidate gene driven approach and discovered that protein tyrosine phosphatase μ (PTP μ) regulates α5β1 integrin (a known OPN receptor) through phosphate kinase type 1 gamma (PIPK1γ). To achieve our goal, we have used primary osteoblast cell cultures derived from AIS patients and biopsies from control subjects. Bone specimens were obtained intraoperatively from vertebras (varying from T3 to L4 according to the surgical procedure performed) while with trauma cases used as non-scoliotic controls, bone specimens were obtained from other anatomical sites (tibia, femur or iliac crest). Expression profiles of the RPTPM gene (encoding for PTPμ) were studied by qPCR. On the other hand, PTPμ protein levels were determined by immunoprecipitation followed by western blot. To evaluate the role of this protein in AIS etiopathogenesis, we took advantage of an animal model exhibiting a higher scoliosis incidence when maintained in a bipedal state. [1], [2] Bipedal surgeries were performed on C57Bl/6 mice after weaning (5-weeks after birth) by amputation of the forelimbs and tail under anesthesia as reported by Oyama et al. (2006). [1] We used the same approach with PTPμ knockout mice and primary osteoblast culture were derived from the spine of these mice to assess Gi protein signaling through a functional assay termed Cellular Dielectric Spectroscopy (CDS). Bipedal PTPμ knockout mice develop scoliosis more often (85%) in number and severity, than control C57Bl/6 bipedal mice (55%). Interestingly, functional analysis of osteoblasts derived from PTPμ KO mice by CDS method showed a flaw in the transmission of Gi protein coupled receptor signaling similar to a specific AIS patient subgroup. Furthermore, the clinical relevance of PTPμ was strengthened by the fact that a decrease in the gene expression level of PTPμ was observed in 34 AIS patients when compared to 17 control subjects. Such a decrease was also confirmed at the protein level. We demonstrated that genetic deletion of PTPμ enhances the incidence and severity of scoliosis without affecting plasma levels of OPN or the expression of its receptors. In contrast, increased interaction of OPN with β1 integrin was noticed in cells depleted of PTPμ. Furthermore, reduction of Gi- protein coupled receptor GiPCR signaling by OPN was also enhanced in these cells, while their response to GiPCR stimulation was improved with siRNA of phosphatidylinositol-phosphate kinase type 1 gamma (PIPK1γ), a PTPμ substrate that favours ligand binding to integrins. These studies provide the first indication that the loss of PTPμ influences the nature of idiopathic scoliosis, possibly by amplifying the inhibitory effect of OPN on GiPCR signaling. This study allows a better understanding of AIS etiology and could have an impact for the future development of innovative diagnostic methods and eventual pharmacological approaches in order to prevent AIS and stop its progression in affected children

IMMUNOMODULATORY ROLE OF HONEY AND PROPOLIS ON CARBON TETRACHLORIDE (CCl4) INJECTED RATS

Objective: To evaluate the role of some inflammatory cytokines in hepatic injury induced by carbon tetrachloride (CCl4). Also, the effects of honey bee and propolis extract to modulate the role of these cytokines.Methods: Fifty female Wister rats were divided into five groups, 10 per each group. After 6 w of all treatments, rats were sacrificed, whole blood and serum were collected to determine the number of white blood cells (WBCs), percentage of granulocytes, percentage of lymphocytes and the level of some cytokines such as gamma interferon(INF-γ), tumor necrosis factor(TNF-α) and interleukin-2(IL-2).Results: CCl4 administration resulted in significant increase in the number of WBCs and percentage of granulocytes (P<0.05 and P<0.01 respectively). After treatment with honey and propolis, the number of WBCs was decreased significantly in the case of propolis treatment (P<0.05) compared with CCl4 group. The levels of TNF-α and INF-γ cytokines were significantly decreased (P<0.05) after treatment with honey or propolis compared with CCl4 group. However, there is no significant change in the level of IL-2 after treatment of CCl4 administered rats with honey or propolis.Conclusion: The present study suggested that honey and propolis can improve the immune disorders induced by CCl4 in rats by modulating the levels of inflammatory cytokines, TNF-α, and IFN-γ.Â

Behavior of Square RC Short Columns with New Arrangement of Ties Subjected to Axial Load: Experimental and Numerical Studies

Reinforced concrete columns consume large quantities of ties, especially inner cross-ties in columns with large dimensions. In some cases, nesting of the pillars occurs as a result of the presence of cross-ties. The main objective of this paper is to develop new methods for transverse reinforcement in RC columns and investigate their effect on the behavior of the columns. The proposed V-ties as transverse reinforcement replacing the ordinary and cross-ties details are economically feasible. They facilitate shorter construction periods and decrease materials and labor costs. For this purpose, experimental and numerical studies are carried out. In the experimental program, nine reinforced concrete columns with identical concrete dimensions and longitudinal reinforcing bars were prepared and tested under concentric axial load with different tie configurations. The main parameters were the tie configurations and the length (lv) of V-tie legs. As part of the numerical study, the finite element model using the ABAQUS software program obtained good agreement with the experimental results of specimens. A numerical parametric study was carried out to study the influence of concrete compressive strength and longitudinal reinforcement ratio on the behavior of RC columns with the considered tie configurations. Based on the experimental and numerical results, it was found that using V-tie techniques instead of traditional ties could increase the axial load capacity of columns, restrain early local buckling of the longitudinal reinforcing bars and improve the concrete core confinement of reinforced concrete columns

The legality of 'war' in Al-Shari'a Al-Islamiya (the Islamic Law) and contemporary international law

This thesis is a comparative study in Al-Shari'a Al-Islamiya (The Islamic Law) and contemporary international law on the subject of the legality of `lq War. It must be pointed out at the outset that the term `lq War is not the precise term to apply to the subject of this thesis, and we often put this term between quotation marks. Other terms have been used in the United Nations Charter; and the meaning of Jihad in Al-Shari'a Al-Islamiya is not compatible with the term `lq war in international law. This thesis is divided into a Prologue, four Parts preceded by an Introductory Part and followed by an Epilogue. The Prologue deals with generalities relating to the topic presented as a necessary background for the Introductory Part. The Introductory Part entitled `lq Al-Shari'a Al-Islamiya And International Law is divided into Six Chapters. The main purpose of this Part is to explain the distinction between the principles of international law in Al-Shari'a Al-Islamiya and public international law, including the different sources and the basis of the obligatory nature of the two systems of law. Part I entitled `lq War and Legality aims to distinguish between certain conceptions in Al-Shari'a Al-Islamiya and public international law. It is divided into Five Chapters dealing with Jihad and legality in Al-Shari'a; and `lq War and legality in international law. Part II entitled `lq The Limitations Of The Legality Of War is divided into three Chapters. The First Chapters deals with the limitations of Jihad in Al-Shari'a Al-Islamiya, and explains, inter alia, the nature of relations between the Islamic State and non-Islamic States; and the legality of certain aspects of the use of force in Al-Shari'a. The Second Chapter deals with the limitations of the legality of `lq War in international law. In this Chapter, we traced the evolution of international law under the League of Nations and the United Nations, and the legality of certain aspects of the use of force in international law. The Third Chapter covers the study of the consequences of the unlawful use of force in Al-Shari'a Al-Islamiya and international law. Part III is entitled `lq The Legality Of `lq War Within The Framework Of Regional Organization. This Part is subdivided into Two Chapters. The First Chapter deals with Universalism and Regionalism in Al-Shari'a Al-Islamiya and international law. A new division of regional organizations is suggested in the Second Chapter to cope with the subject of this thesis. Thus, we divide regional organizations into three categories, regional organizations of Muslim Member States; regional Organizations of Muslim and non-Muslim Member States; and regional Organizations of non-Muslim Member States. Part IV entitled `lq The Judicial Approach To The Legality Of War is divided into Two Chapters. The First Chapter deals with the judicial approach to Muslim States. Thus, we studied the different projects to establish an Arab Court of Justice and an Islamic Court of Justice. In the Second Chapter, we studied the evolution in punishment of war crimes before the First World War, and after the First and Second World Wars. The Epilogue deals with the Conclusions of this comparative study

An efficient technique for out-of-band power reduction for the eliminated CP-STC-shaped system for 5G requirements

The most dominant needs for the recent wireless mobile applications are higher bandwidth (BW) efficiency, higher energy efficiency higher quality of services (QOS). The main technique in 4G systems is OFDM but it suffers from some limitations such as large peak to average power ratio (PAPR), higher Out-of-Band (OOB) power radiation, and wasting bandwidth efficiency due to cyclic prefix (CP) extension. In his paper, these OFDM limitations will be reduced with low computational complexity compared to filter bank multicarriers (FBMC). The proposed scheme is based on symbol time compression (STC) for OFDM system. The proposed STC-Shaped system is achieved via interleaver-spreader and symbol shaper in the transmitter side in addition to equalization and combining processes in the receiver side. Comparative study between the proposed system and the conventional OFDM in case of additive white Gaussian noise (AWGN) and COST 207 typical multipath fading channel will be presented. The numerical results show that the proposed STC-Shaped scheme reduces OOB significantly. The proposed scheme improves BER in multipath Rayleigh fading although it is without CP. Thus, the proposed system is more robust against inter symbol interference (ISI) compared to conventional OFDM system. Also, the numerical results show that the PAPR of the proposed system is decreased significantly and also, it is derived theoretically. Also, the proposed scheme overcomes CP extension, and hence increases the bandwidth (BW) efficiency. Finally, the computational complexity for the proposed scheme is derived and it has very low complexity compared to FBMC. The system performance measurments has been fulfilled using cumulative distribution function (CDF), power spectral density (PSD) and bit error rate (BER)

DNA repair synthesis and histone deposition partner during homologous recombination

Chromatin remodeling is critical for the regulation of the DNA damage response. We highlight findings from our recent study showing that the deposition of the histone variant H3.3 by the alpha-thalassemia mental retardation X-linked protein (ATRX) and the death domain associated protein (DAXX) chromatin remodeling complex regulates DNA repair synthesis during homologous recombination

ATRX and RECQ5 define distinct homologous recombination subpathways

Homologous recombination (HR) is an important DNA double-strand break (DSB) repair pathway that copies sequence information lost at the break site from an undamaged homologous template. This involves the formation of a recombination structure that is processed to restore the original sequence but also harbors the potential for crossover (CO) formation between the participating molecules. Synthesis-dependent strand annealing (SDSA) is an HR subpathway that prevents CO formation and is thought to predominate in mammalian cells. The chromatin remodeler ATRX promotes an alternative HR subpathway that has the potential to form COs. Here, we show that ATRX-dependent HR outcompetes RECQ5-dependent SDSA for the repair of most two-ended DSBs in human cells and leads to the frequent formation of COs, assessed by measuring sister chromatid exchanges (SCEs). We provide evidence that subpathway choice is dependent on interaction of both ATRX and RECQ5 with proliferating cell nuclear antigen. We also show that the subpathway usage varies among different cancer cell lines and compare it to untransformed cells. We further observe HR intermediates arising as ionizing radiation (IR)-induced ultra-fine bridges only in cells expressing ATRX and lacking MUS81 and GEN1. Consistently, damage-induced MUS81 recruitment is only observed in ATRX-expressing cells. Cells lacking BLM show similar MUS81 recruitment and IR-induced SCE formation as control cells. Collectively, these results suggest that the ATRX pathway involves the formation of HR intermediates whose processing is entirely dependent on MUS81 and GEN1 and independent of BLM. We propose that the predominant ATRX-dependent HR subpathway forms joint molecules distinct from classical Holliday junctions