Papers by Luiza Handschuh
BioMed Research International, 2015
Molecular Genetics and Genomics, 2015
Heat shock inhibits NF-κB signaling, yet the knowledge about its influence on the regulation of N... more Heat shock inhibits NF-κB signaling, yet the knowledge about its influence on the regulation of NF-κB-dependent genes is limited. Using genomic approaches, i.e., expression microarrays and ChIP-Seq, we aimed to establish a global picture for heat shock-mediated impact on the expression of genes regulated by TNFα cytokine. We found that 193 genes changed expression in human U-2 osteosarcoma cells stimulated with cytokine (including 77 genes with the κB motif in the proximal promoters). A large overlap between sets of genes modulated by cytokine or by heat shock was revealed (86 genes were similarly affected by both stimuli). Binding sites for heat shock-induced HSF1 were detected in regulatory regions of 1/3 of these genes. Furthermore, pre-treatment with heat shock affected the expression of 2/3 of cytokine-modulated genes. In the largest subset of co-affected genes, heat shock suppressed the cytokine-mediated activation (antagonistic effect, 83 genes), which genes were associated with the canonical functions of NF-κB signaling. However, subsets of co-activated and co-repressed genes were also revealed. Importantly, pre-treatment with heat shock resulted in the suppression of NF-κB binding in the promoters of the cytokine-upregulated genes, either antagonized or co-activated by both stimuli. In conclusion, we confirmed that heat shock inhibited activation of genes involved in the classical cytokine-mediated functions of NF-κB. On the other hand, genes involved in transcription regulation were over-represented in the subset of genes upregulated by both stimuli. This suggests the replacement of NF-κB-mediated regulation by heat shock-mediated regulation in the latter subset of genes, which may contribute to the robust response of cells to both stress conditions.
PloS one, 2014
Small non-coding RNAs (sncRNAs) are indispensable for proper germ cell development, emphasizing t... more Small non-coding RNAs (sncRNAs) are indispensable for proper germ cell development, emphasizing the need for greater elucidation of the mechanisms of germline development and regulation of this process by sncRNAs. We used deep sequencing to characterize three families of small non-coding RNAs (piRNAs, miRNAs, and tRFs) present in Sus scrofa gonads and focused on the small RNA fraction present in both male and female gonads. Although similar numbers of reads were obtained from both types of gonads, the number of unique RNA sequences in the ovaries was several times lower. Of the sequences detected in the testes, 2.6% of piRNAs, 9% of miRNAs, and 10% of tRFs were also present in the ovaries. Notably, the majority of the shared piRNAs mapped to ribosomal RNAs and were derived from clustered loci. In addition, the most abundant miRNAs present in the ovaries and testes are conserved and are involved in many biological processes such as the regulation of homeobox genes, the control of cel...
Acta biochimica Polonica, 2011
Two-color DNA microarrays are commonly used for the analysis of global gene expression. They prov... more Two-color DNA microarrays are commonly used for the analysis of global gene expression. They provide information on relative abundance of thousands of mRNAs. However, the generated data need to be normalized to minimize systematic variations so that biologically significant differences can be more easily identified. A large number of normalization procedures have been proposed and many softwares for microarray data analysis are available. Here, we have applied two normalization methods (median and loess) from two packages of microarray data analysis softwares. They were examined using a sample data set. We found that the number of genes identified as differentially expressed varied significantly depending on the method applied. The obtained results, i.e. lists of differentially expressed genes, were consistent only when we used median normalization methods. Loess normalization implemented in the two software packages provided less coherent and for some probes even contradictory resu...
Acta biochimica Polonica, 2007
PR-10 proteins (pathogensis-related), ubiquitous within the plant kingdom, are usually encoded by... more PR-10 proteins (pathogensis-related), ubiquitous within the plant kingdom, are usually encoded by multigene families. To date we have identified 10 homologous pr-10 genes in a yellow lupine cDNA library. Here, the structure and expression of two newly identified yellow lupine pr-10 genes (LlYpr10-2b and LlYpr10-2f) are presented. Many potential regulatory sites were found in both gene promoters including common ones as well as those unique for each gene. However, promoter deletion analysis in transgenic tobacco plants revealed similar patterns of reporter gene (gus) expression. Shortened fragments of both gene promoters studied caused high GUS activity in leaves (along vascular bundles), stamen stigma, anthers and pollen grains. When conjugated with longer LlYpr-10.2 promoter fragments, GUS was additionally present in petal edges. Only a long fragment of the LlYpr10-2b gene promoter caused GUS expression in the stem. In yellow lupine the pr-10.2 genes are present in all studied orga...
Remote Instrumentation and Virtual Laboratories, 2010
Nowadays, there is no science domain that does not use specialized software, on-line tools, and c... more Nowadays, there is no science domain that does not use specialized software, on-line tools, and computational resources. Genomics is a new branch of science that developed rapidly in the last decade. As the genome research is very complex it must be supported by professional informatics. In a microarray field the following steps cannot be performed without computational work: design of probes, quantitative analysis of hybridization results, post processing, and finally data storage and management. Here, the general aspects of Virtual Laboratory systems are presented, together with perspectives of their implementation in genomics in order to automate and facilitate this area of research.
The International Journal of Biochemistry & Cell Biology, 2014
Computational Methods in Science and Technology, 2010
... Clustering with the pvclust package is used for assessing the uncertainty in the hierarchical... more ... Clustering with the pvclust package is used for assessing the uncertainty in the hierarchical cluster analysis. ... What is important, pvclust provides two types of p-values: AU (Approximately Unbiased) p-value and BP (Bootstrap Probability) value. ...
Computational Methods in Science and Technology, 2009
International Journal of Molecular Medicine, 2013
Journal of Proteomics, 2012
Acta Crystallographica Section D Biological Crystallography, 2005
Pathogenesis-related (PR) proteins of class 10 are abundant in higher plants. Some of these prote... more Pathogenesis-related (PR) proteins of class 10 are abundant in higher plants. Some of these proteins are induced under stress conditions as part of the plant defence mechanism. Other homologues are developmentally regulated and their expression varies in different plant organs. The PR-10 proteins are encoded by multigene families, have a weight of about 17 kDa and are found in the cytosol. In yellow lupin, nine different homologues have been identified and divided into two subclasses, LlPR-10.1 and LlPR-10.2. Within each subclass the sequence identity is about 75-91%, while across the subclasses it is only 59-60%. Here, the crystal structure of a yellow lupin PR-10 protein from the second subclass, LlPR-10.2A, is presented. The structure was solved by molecular replacement and refined to R = 0.205 using 1.9 A resolution data. The general fold of LlPR-10.2A resembles that of the other PR-10 proteins and consists of a long C-terminal alpha-helix surrounded by a seven-stranded antiparallel beta-sheet, with two shorter alpha-helices located between strands beta1 and beta2. The most variable part of the structure, the C-terminal helix, is strongly kinked towards the beta-sheet core in both LlPR-10.2A molecules present in the asymmetric unit. This unexpected feature reduces the size of the hydrophobic cavity observed in other PR-10 proteins that is reported to be the ligand-binding site. As in other PR-10 structures, a surface loop located near the entrance to the cavity shows very high structural conservation and stability despite the high glycine content in its sequence.
Acta Crystallographica Section A Foundations of Crystallography, 2006
The phylogenetic relationships between Tc1 transposable elements have previously been reported fo... more The phylogenetic relationships between Tc1 transposable elements have previously been reported for the genomes of some fish species. However, research in this field has been hindered by the low number of fish genome sequences available in databases. The application of a DNA microarray as a universal tool for Tc1 transposon sequence analysis in fish genomes is described here. A prototype oligonucleotide microarray was constructed and used to compare samples of genomic DNA isolated from selected fish species. These results, combined with earlier reported molecular analysis of Tc1 showed the usefulness of DNA microarray in the screening of transposon sequences.
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Papers by Luiza Handschuh