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Prediction of gene expression in human using rat in vivo gene expression in Japanese Toxicogenomics Project Hasselt University

Martin OTAVA, Ziv SHKEDY, Adetayo KASIM
The Japanese Toxicogenomics Project (TGP) provides large amount of data for the toxicology and safety framework. We focus on gene expression data of rat in vivo and human in vitro. We consider two different analyses for the TGP data. The first analysis is based on two-way analysis of variance model and the goal is to detect genes with significant doseresponse relationship in both humans and rats. The second analysis consists of a trend analysis ...

Steroids affect gene expression, ciliary activity, glucose uptake, progesterone receptor expression and immunoreactive steroidogenic protein expression in equine oviduct explants in vitro KU Leuven Research Institute for Agriculture, Fisheries and Food Ghent University

Hilde Nelis, Bartosz Wojciechowicz, Anita Franczak, Bart Leemans, Katharina D'Herde, Karen Goossens, Pieter Cornillie, Luc Peelman, Ann Van Soom, Katrien Smits, et al.
The oviduct undergoes dramatic functional and morphological changes throughout the oestrous cycle of the mare. To unravel the effects of steroids on the morphology, functionality and gene expression of the equine oviduct, an in vitro oviduct explant culture system was stimulated with physiological concentrations of progesterone and 17β-oestradiol. Four conditions were compared: unsupplemented preovulatory explants, preovulatory explants that ...

A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression Ghent University

Stewart TG Burgess, Edward J Marr, Kathryn Bartley, Francesca G Nunn, Rachel E Down, Robert J Weaver, Jessica C Prickett, Jackie Dunn, Stephane Rombauts, Thomas Van Leeuwen, et al.
Background: Psoroptic mange, caused by infestation with the ectoparasitic mite, Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry Worldwide. Control relies on injectable endectocides and organophosphate dips, but concerns over residues, environmental contamination, and the development of resistance threaten the sustainability of this approach, ...

Comparative gene expression analysis throughout the life cycle of Leishmania braziliensis: diversity of expression profiles among clinical isolates Institute of Tropical Medicine

V Adaui, D Castillo, M Zimic, A Gutiérrez, Saskia Decuypere, Manu Vanaerschot, S De Doncker, Katty Schnorbusch, Ilse Maes, Gert Van der Auwera, et al.
BACKGROUND: Most of the Leishmania genome is reported to be constitutively expressed during the life cycle of the parasite, with a few regulated genes. Inter-species comparative transcriptomics evidenced a low number of species-specific differences related to differentially distributed genes or the differential regulation of conserved genes. It is of uppermost importance to ensure that the observed differences are indeed species-specific and not ...

Real-time PCR expression profiling of genes encoding potential virulence factors in Candida albicans biofilms: identification of model-dependent and -independent gene expression KU Leuven

Heleen Nailis, Sona Kucharikova, Markéta Ricicová, Patrick Van Dijck, Dieter Deforce, Hans Nelis, Tom Coenye
BACKGROUND: Candida albicans infections are often associated with biofilm formation. Previous work demonstrated that the expression of HWP1 (hyphal wall protein) and of genes belonging to the ALS (agglutinin-like sequence), SAP (secreted aspartyl protease), PLB (phospholipase B) and LIP (lipase) gene families is associated with biofilm growth on mucosal surfaces. We investigated using real-time PCR whether genes encoding potential virulence ...

Differential expression of alpha B-crystallin and evidence of its role as a mediator of matrix gene expression in osteoarthritis Ghent University

Stijn Lambrecht, August Verbruggen, Dirk Elewaut, Dieter Deforce
Objective. Alpha B-crystallin belongs to the family of small heat-shock proteins (HSPs). The role of this protein family in chondrocytes is not well understood. The present study was undertaken to investigate expression levels of alpha B-crystallin in chondrocytes isolated from healthy subjects and patients with osteoarthritis (OA), and to explore the functional role of this potentially interesting protein in chondrocyte metabolism.Methods. ...

Extracting expression modules from perturbational gene expression compendia KU Leuven

Steven Maere, Patrick Van Dijck, Martin Kuiper
Background: Compendia of gene expression profiles under chemical and genetic perturbations constitute an invaluable resource from a systems biology perspective. However, the perturbational nature of such data imposes specific challenges on the computational methods used to analyze them. In particular, traditional clustering algorithms have difficulties in handling one of the prominent features of perturbational compendia, namely partial ...

Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families Ghent University

Amanda R De La Torre, Yao-Cheng Lin, Yves Van de Peer, Pär K Ingvarsson
The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (> 50,000 expressed genes) to study the relationship between gene expression, ...