Jan Pawel Jastrzebski | University of Warmia and Mazury in Olsztyn (original) (raw)
Papers by Jan Pawel Jastrzebski
P0 protein is found exclusively in peripheral nervous system, it comprises more than 50% of the t... more P0 protein is found exclusively in peripheral nervous system, it comprises more than 50% of the total myelin proteins. P0 is a Nlinked and glycosylated at a single site, Asparagine 93. There are at least 8 different glycans contributing to this ‘‘posttranslational’’ modification. The overall structure of (peptide chain) P0 is known, but little is known about 3D structure of linked glycan components. In this work we are presenting structural gallery of P0 glycans. In summary MWof naked P0 peptide (for example for bovine) is about 24.5 kDa, when there is included sorting peptide, the MW is 27.5 kDa. The MW of P0 glycans varies 2,000–3,000 Da. The virtual 3D model of P0 protein with attached glycans is presented. The possible location of the single glycosylation site relative to the myelin lipid bilayer is emphasized. Acknowledgements: This study was supported by the grant from the Swedish Research Council 2008-0086 (to JS and JT), and by the JSPS Program for Research in Japan – short and long term (JS).
International Journal of Biological Macromolecules, 2019
Lipopolysaccharide (LPS) is a bacterial endotoxin which can participate in the induction of infla... more Lipopolysaccharide (LPS) is a bacterial endotoxin which can participate in the induction of inflammatory responses. LPS may also play a significant role in some neurodegenerative, oncological and metabolic disorders. The aim of the current study was to determine the effect of a subclinical low single dose of LPS from Salmonella Enteritidis administrated in vivo on the transcriptome of porcine adrenal cortex cells, especially gene expression levels, long non-coding RNA (lncRNA) profiles, alternative splicing events and RNA editing sites using RNA-seq technology. The subclinical dose of LPS changed the expression of 354 genes, 27 lncRNA loci and other unclassified RNAs. An analysis of alternative splicing events revealed 104 genes with differentially expressed splice junction sites, and the single nucleotide variant calling approach supported the identification of 376 canonical RNA editing candidates and 7249 allele-specific expression variants. The obtained results suggest that the RIG-I-like receptor signaling pathway, may play a more important role than the Toll-like signaling pathway after the administration of a subclinical dose of LPS. Single subclinical dose of LPS can affect the expression profiles of genes coding peptide hormones, steroidogenic enzymes and transcriptional factors, and modulate the endocrine functions of the gland.
PLOS ONE
The European beaver (Castor fiber L.) is an important free-living rodent that inhabits Eurasian t... more The European beaver (Castor fiber L.) is an important free-living rodent that inhabits Eurasian temperate forests. Beavers are often referred to as ecosystem engineers because they create or change existing habitats, enhance biodiversity and prepare the environment for diverse plant and animal species. Beavers are protected in most European Union countries, but their genomic background remains unknown. In this study, gene expression patterns in beaver testes and the variations in genetic expression in breeding and non-breeding seasons were determined by high-throughput transcriptome sequencing. Paired-end sequencing in the Illumina HiSeq 2000 sequencer produced a total of 373.06 million of high-quality reads. De novo assembly of contigs yielded 130,741 unigenes with an average length of 1,369.3 nt, N50 value of 1,734, and average GC content of 46.51%. A comprehensive analysis of the testicular transcriptome revealed more than 26,000 highly expressed unigenes which exhibited the highest homology with Rattus norvegicus and Ictidomys tridecemlineatus genomes. More than 8,000 highly expressed genes were found to be involved in fundamental biological processes, cellular components or molecular pathways. The study also revealed 42 genes whose regulation differed between breeding and non-breeding seasons. During the non-breeding period, the expression of 37 genes was up-regulated, and the expression of 5 genes was down-regulated relative to the breeding season. The identified genes encode molecules which are involved in signaling transduction, DNA repair, stress responses, inflammatory processes, metabolism and steroidogenesis. Our results pave the way for further research into season-dependent variations in beaver testes.
Chemosphere
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a toxic man-made chemical compound contaminating th... more 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a toxic man-made chemical compound contaminating the environment. An exposure of living organisms to TCDD may result in numerous disorders, including reproductive pathologies. The aim of the current study was to examine the effects of TCDD on the transcriptome of porcine granulosa cell line AVG-16. By employing next-generation sequencing (NGS) we aimed to identify genes potentially involved in the mechanism of TCDD action and toxicity in porcine granulosa cells. The AVG-16 cells were treated with TCDD (100 nM) for 3, 12 or 24 h, and afterwards total cellular RNA was isolated and sequenced. In TCDD-treated cells we identified 141 differentially expressed genes (DEGs; p < 0.05 and log2 fold change ≥1.0). The DEGs were assigned to GO term, covering biological processes, molecular functions and cellular components. Due to the large number of genes with altered expression, in the current study we analyzed only the genes involved in follicular growth, development and functioning. The obtained results showed that TCDD may affect ovarian follicle fate by influencing granulosa cell cycle, proliferation and DNA repair. The demonstrated over-time changes in the quantity and quality of genes being affected by TCDD treatment showed that the effects of TCDD on granulosa cells changed dramatically between 3-, 12- and 24-h of cell culture. This finding indicate that timing of gene expression measurement is critical for drawing correct conclusions on detailed relationships between the TCDD-affected genes and resulting intracellular processes. These conclusions have to be confirmed and extended by research involving proteomic and functional studies.
Chemosphere, 2017
Polychlorinated dibenzo-p-dioxins (PCDDs) are widespread by-products of human industrial activity... more Polychlorinated dibenzo-p-dioxins (PCDDs) are widespread by-products of human industrial activity. They accumulate in tissues of animals and humans, exerting numerous adverse effects on different systems. In living organisms, dioxins are metabolized by enzymes of the cytochrome P450 family, including CYP1A1. Particular dioxin congeners differ in their toxicity level and ability to undergo biodegradation. Since the molecular mechanisms underlying dioxin susceptibility or resistance to biodegradation are unknown, in the present study the molecular interactions between five selected dioxins and porcine CYP1A1 protein were investigated. It was found that the ability of a dioxin to undergo CYP1A1-mediated degradation is associated mainly with the number and position of chlorine atoms in the dioxin molecule. Among all examined congeners, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) demonstrated the highest affinity to CYP1A1 and, at the same time, the greatest distance to the active site of the enzyme. Interestingly, in contrast to other dioxins, the binding of the TCDD molecule to the porcine CYP1A1 active site resulted in a rapid and continuous closure of substrate channels. All the information may help to explain the extended half-life of TCDD in living organisms as well as its high toxicity.
Prace Komisji Geografii Przemyslu Polskiego Towarzystwa Geograficznego, 2012
ABSTRACT Modern biotechnology is widely regarded as information technology, a new wave of knowled... more ABSTRACT Modern biotechnology is widely regarded as information technology, a new wave of knowledge-based economy. It is one of the key technologies of the 20th century, with potentially a versatile range of applications, such as healthcare, agriculture and industrial processes. Simultaneously, biotechnology and pharmacy are the strongest fields in the currently funded basic research which contributes to progress in other sciences.According to the European Parliament’s report “Life sciences and biotechnology – A Strategy for Europe”, it is taken for granted that modern biotechnology offers unique opportunities of satisfying many human needs. Biotechnology could thus serve the European Union as a great contribution to the achievement of its policy objectives of economic growth and job creation, public health, environmental protection and sustainable development.In the following years, life sciences and biotechnology industry could potentially become the major areas of science, industry and employment and could improve the quality of life through innovative medical applications, upgrading of industrial bases of Europe, and better environment.This article aims at presenting regional differences in the development of biotechnology in Europe. Delimitation of regions will take place both on the basis of academic achievement in the field and the location of the biotechnology industry in Europe. An attempt will also be made to link the development of biotechnology with other markers of socio-economic regions of Europe.
Journal of Molecular Graphics and Modelling, 2016
The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that can be activa... more The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that can be activated by structurally diverse synthetic and natural chemicals, including toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). In the present study, homology models of the porcine AhR-ligand binding domain (LBD) and the porcine aryl hydrocarbon receptor nuclear translocator-ligand binding domain (ARNT-LBD) were created on the basis of structures of closely related respective proteins i.e., human Hif-2α and ARNT. Molecular docking of TCDD to the porcine AhR-LBD model revealed high binding affinity (-8.8kcal/mol) between TCDD and the receptor. Moreover, formation of the TCDD/AhR-LBD complex was confirmed experimentally with the use of electrophoretic mobility shift assay (EMSA). It was found that TCDD (10nM, 2h of incubation) not only bound to the AhR in the porcine granulosa cells but also activated the receptor. The current study provides a framework for examining the key events involved in the ligand-dependent activation of the AhR.
Page 1. Chapter / Structural and functional differences between KATP channel subunits Kir6.1 and ... more Page 1. Chapter / Structural and functional differences between KATP channel subunits Kir6.1 and Kir6.2 isolated from rabbit heart Carol Ann Remme, Ronald H. Lekanne Deprez, Marieke W. Veldkamp, Arthur AM Wilde, Antoon FM Moorman Page 2. Chapter / Introduction ...
Gene expression analysis as key to understanding the functioning oforganisms – comparison of high... more Gene expression analysis as key to understanding the functioning oforganisms – comparison of high-throughput methods Development of molecular research in the last decade allowedbetter understanding of disease etiology and also made disease treatment more efficient. Results of the Human Genome Project, have shown that identification and localization of human genes are not sufficient for the purpose of understanding of human body biological machinery. For these purposes, gene expression analysis, which shows the true role of genes in metabolic pathways, seems to be necessary. Development of functional genomics facilitatedanalysis of the whole set of genes simultaneously and complexed genome analysis was named high-throughput methods. Microarrays was one of the first developed methods.The popularity of Next- Generation RNA Sequencing has highly increased among scientific community with a development of this technology. The aim of this research is comparison of both technologies with re...
Nowadays biotechnology industry is "the next big issue" after the boom in the IT sector... more Nowadays biotechnology industry is "the next big issue" after the boom in the IT sector. It is claimed that “life code” (the famous A, G, T and C bases of the DNA) will have the same importance for the next generation as the digital code (1’s and 0’s) has now for us. Biotechnology is characterised by innovation, wide application range and progress generation in other branches of basic sciences. According to financial analysts, investment in biotechnology sector is currently most profitable. Therefore, biotechnology acquires majority of investment offers from venture capital (together with software and IT sectors). Hence, biotechnology seems to be the most important indicator of innovation development.In Europe the beginnings of biotechnology sector development date back to the end of 70s ofthe 20th century and are associated with the appearance of a great number of small and medium-sized enterprises related to research and scientific institutions. Therefore, biotechnology ...
P0 protein is found exclusively in peripheral nervous system, it comprises more than 50% of the t... more P0 protein is found exclusively in peripheral nervous system, it comprises more than 50% of the total myelin proteins. P0 is a Nlinked and glycosylated at a single site, Asparagine 93. There are at least 8 different glycans contributing to this ‘‘posttranslational’’ modification. The overall structure of (peptide chain) P0 is known, but little is known about 3D structure of linked glycan components. In this work we are presenting structural gallery of P0 glycans. In summary MWof naked P0 peptide (for example for bovine) is about 24.5 kDa, when there is included sorting peptide, the MW is 27.5 kDa. The MW of P0 glycans varies 2,000–3,000 Da. The virtual 3D model of P0 protein with attached glycans is presented. The possible location of the single glycosylation site relative to the myelin lipid bilayer is emphasized. Acknowledgements: This study was supported by the grant from the Swedish Research Council 2008-0086 (to JS and JT), and by the JSPS Program for Research in Japan – short and long term (JS).
International Journal of Biological Macromolecules, 2019
Lipopolysaccharide (LPS) is a bacterial endotoxin which can participate in the induction of infla... more Lipopolysaccharide (LPS) is a bacterial endotoxin which can participate in the induction of inflammatory responses. LPS may also play a significant role in some neurodegenerative, oncological and metabolic disorders. The aim of the current study was to determine the effect of a subclinical low single dose of LPS from Salmonella Enteritidis administrated in vivo on the transcriptome of porcine adrenal cortex cells, especially gene expression levels, long non-coding RNA (lncRNA) profiles, alternative splicing events and RNA editing sites using RNA-seq technology. The subclinical dose of LPS changed the expression of 354 genes, 27 lncRNA loci and other unclassified RNAs. An analysis of alternative splicing events revealed 104 genes with differentially expressed splice junction sites, and the single nucleotide variant calling approach supported the identification of 376 canonical RNA editing candidates and 7249 allele-specific expression variants. The obtained results suggest that the RIG-I-like receptor signaling pathway, may play a more important role than the Toll-like signaling pathway after the administration of a subclinical dose of LPS. Single subclinical dose of LPS can affect the expression profiles of genes coding peptide hormones, steroidogenic enzymes and transcriptional factors, and modulate the endocrine functions of the gland.
PLOS ONE
The European beaver (Castor fiber L.) is an important free-living rodent that inhabits Eurasian t... more The European beaver (Castor fiber L.) is an important free-living rodent that inhabits Eurasian temperate forests. Beavers are often referred to as ecosystem engineers because they create or change existing habitats, enhance biodiversity and prepare the environment for diverse plant and animal species. Beavers are protected in most European Union countries, but their genomic background remains unknown. In this study, gene expression patterns in beaver testes and the variations in genetic expression in breeding and non-breeding seasons were determined by high-throughput transcriptome sequencing. Paired-end sequencing in the Illumina HiSeq 2000 sequencer produced a total of 373.06 million of high-quality reads. De novo assembly of contigs yielded 130,741 unigenes with an average length of 1,369.3 nt, N50 value of 1,734, and average GC content of 46.51%. A comprehensive analysis of the testicular transcriptome revealed more than 26,000 highly expressed unigenes which exhibited the highest homology with Rattus norvegicus and Ictidomys tridecemlineatus genomes. More than 8,000 highly expressed genes were found to be involved in fundamental biological processes, cellular components or molecular pathways. The study also revealed 42 genes whose regulation differed between breeding and non-breeding seasons. During the non-breeding period, the expression of 37 genes was up-regulated, and the expression of 5 genes was down-regulated relative to the breeding season. The identified genes encode molecules which are involved in signaling transduction, DNA repair, stress responses, inflammatory processes, metabolism and steroidogenesis. Our results pave the way for further research into season-dependent variations in beaver testes.
Chemosphere
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a toxic man-made chemical compound contaminating th... more 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a toxic man-made chemical compound contaminating the environment. An exposure of living organisms to TCDD may result in numerous disorders, including reproductive pathologies. The aim of the current study was to examine the effects of TCDD on the transcriptome of porcine granulosa cell line AVG-16. By employing next-generation sequencing (NGS) we aimed to identify genes potentially involved in the mechanism of TCDD action and toxicity in porcine granulosa cells. The AVG-16 cells were treated with TCDD (100 nM) for 3, 12 or 24 h, and afterwards total cellular RNA was isolated and sequenced. In TCDD-treated cells we identified 141 differentially expressed genes (DEGs; p < 0.05 and log2 fold change ≥1.0). The DEGs were assigned to GO term, covering biological processes, molecular functions and cellular components. Due to the large number of genes with altered expression, in the current study we analyzed only the genes involved in follicular growth, development and functioning. The obtained results showed that TCDD may affect ovarian follicle fate by influencing granulosa cell cycle, proliferation and DNA repair. The demonstrated over-time changes in the quantity and quality of genes being affected by TCDD treatment showed that the effects of TCDD on granulosa cells changed dramatically between 3-, 12- and 24-h of cell culture. This finding indicate that timing of gene expression measurement is critical for drawing correct conclusions on detailed relationships between the TCDD-affected genes and resulting intracellular processes. These conclusions have to be confirmed and extended by research involving proteomic and functional studies.
Chemosphere, 2017
Polychlorinated dibenzo-p-dioxins (PCDDs) are widespread by-products of human industrial activity... more Polychlorinated dibenzo-p-dioxins (PCDDs) are widespread by-products of human industrial activity. They accumulate in tissues of animals and humans, exerting numerous adverse effects on different systems. In living organisms, dioxins are metabolized by enzymes of the cytochrome P450 family, including CYP1A1. Particular dioxin congeners differ in their toxicity level and ability to undergo biodegradation. Since the molecular mechanisms underlying dioxin susceptibility or resistance to biodegradation are unknown, in the present study the molecular interactions between five selected dioxins and porcine CYP1A1 protein were investigated. It was found that the ability of a dioxin to undergo CYP1A1-mediated degradation is associated mainly with the number and position of chlorine atoms in the dioxin molecule. Among all examined congeners, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) demonstrated the highest affinity to CYP1A1 and, at the same time, the greatest distance to the active site of the enzyme. Interestingly, in contrast to other dioxins, the binding of the TCDD molecule to the porcine CYP1A1 active site resulted in a rapid and continuous closure of substrate channels. All the information may help to explain the extended half-life of TCDD in living organisms as well as its high toxicity.
Prace Komisji Geografii Przemyslu Polskiego Towarzystwa Geograficznego, 2012
ABSTRACT Modern biotechnology is widely regarded as information technology, a new wave of knowled... more ABSTRACT Modern biotechnology is widely regarded as information technology, a new wave of knowledge-based economy. It is one of the key technologies of the 20th century, with potentially a versatile range of applications, such as healthcare, agriculture and industrial processes. Simultaneously, biotechnology and pharmacy are the strongest fields in the currently funded basic research which contributes to progress in other sciences.According to the European Parliament’s report “Life sciences and biotechnology – A Strategy for Europe”, it is taken for granted that modern biotechnology offers unique opportunities of satisfying many human needs. Biotechnology could thus serve the European Union as a great contribution to the achievement of its policy objectives of economic growth and job creation, public health, environmental protection and sustainable development.In the following years, life sciences and biotechnology industry could potentially become the major areas of science, industry and employment and could improve the quality of life through innovative medical applications, upgrading of industrial bases of Europe, and better environment.This article aims at presenting regional differences in the development of biotechnology in Europe. Delimitation of regions will take place both on the basis of academic achievement in the field and the location of the biotechnology industry in Europe. An attempt will also be made to link the development of biotechnology with other markers of socio-economic regions of Europe.
Journal of Molecular Graphics and Modelling, 2016
The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that can be activa... more The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that can be activated by structurally diverse synthetic and natural chemicals, including toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). In the present study, homology models of the porcine AhR-ligand binding domain (LBD) and the porcine aryl hydrocarbon receptor nuclear translocator-ligand binding domain (ARNT-LBD) were created on the basis of structures of closely related respective proteins i.e., human Hif-2α and ARNT. Molecular docking of TCDD to the porcine AhR-LBD model revealed high binding affinity (-8.8kcal/mol) between TCDD and the receptor. Moreover, formation of the TCDD/AhR-LBD complex was confirmed experimentally with the use of electrophoretic mobility shift assay (EMSA). It was found that TCDD (10nM, 2h of incubation) not only bound to the AhR in the porcine granulosa cells but also activated the receptor. The current study provides a framework for examining the key events involved in the ligand-dependent activation of the AhR.
Page 1. Chapter / Structural and functional differences between KATP channel subunits Kir6.1 and ... more Page 1. Chapter / Structural and functional differences between KATP channel subunits Kir6.1 and Kir6.2 isolated from rabbit heart Carol Ann Remme, Ronald H. Lekanne Deprez, Marieke W. Veldkamp, Arthur AM Wilde, Antoon FM Moorman Page 2. Chapter / Introduction ...
Gene expression analysis as key to understanding the functioning oforganisms – comparison of high... more Gene expression analysis as key to understanding the functioning oforganisms – comparison of high-throughput methods Development of molecular research in the last decade allowedbetter understanding of disease etiology and also made disease treatment more efficient. Results of the Human Genome Project, have shown that identification and localization of human genes are not sufficient for the purpose of understanding of human body biological machinery. For these purposes, gene expression analysis, which shows the true role of genes in metabolic pathways, seems to be necessary. Development of functional genomics facilitatedanalysis of the whole set of genes simultaneously and complexed genome analysis was named high-throughput methods. Microarrays was one of the first developed methods.The popularity of Next- Generation RNA Sequencing has highly increased among scientific community with a development of this technology. The aim of this research is comparison of both technologies with re...
Nowadays biotechnology industry is "the next big issue" after the boom in the IT sector... more Nowadays biotechnology industry is "the next big issue" after the boom in the IT sector. It is claimed that “life code” (the famous A, G, T and C bases of the DNA) will have the same importance for the next generation as the digital code (1’s and 0’s) has now for us. Biotechnology is characterised by innovation, wide application range and progress generation in other branches of basic sciences. According to financial analysts, investment in biotechnology sector is currently most profitable. Therefore, biotechnology acquires majority of investment offers from venture capital (together with software and IT sectors). Hence, biotechnology seems to be the most important indicator of innovation development.In Europe the beginnings of biotechnology sector development date back to the end of 70s ofthe 20th century and are associated with the appearance of a great number of small and medium-sized enterprises related to research and scientific institutions. Therefore, biotechnology ...