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Wyświetlanie 1-15 z 18
Tytuł:
New face of the “RNA world”
Autorzy:
Tyczewska, Agata
Figlerowicz, Marek
Powiązania:
https://bibliotekanauki.pl/articles/703400.pdf
Data publikacji:
2009
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
non-coding RNA
small regulatory RNA
gene expression
RNA world
Opis:
For a very long time, RNA was considered just the medium by which information flows from DNA into the cell. The model proposed in the 1960s assumed that proteins are the main products and regulators of the gene expression process. In this context, the results of the Human Genome Project and the discoveries of RNA interference and small regulatory RNAs (srRNAs) came as a true surprise. The first ones demonstrated that less than 5% of the human genome encodes proteins. The second showed that RNA, especially 20-30 nt-long molecules should be placed among the most important factors controlling gene expression. srRNAs are capable of affecting the release and flow of genetic information in many different ways. They can induce changes in the genome structure, inhibit transcription, mediate mRNA degradation and repress translation. Interestingly, in different organisms, different pathways are used to regulate gene expression. It has recently been estimated that, in humans, the expression of 35-40% of genes is controlled by srRNA. As a result, RNA is currently believed to be a central molecule in many biological processes.
Źródło:
Nauka; 2009, 2
1231-8515
Pojawia się w:
Nauka
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
RNA interference and its role in the regulation of eucaryotic gene expression.
Autorzy:
Szweykowska-Kulińska, Zofia
Jarmołowski, Artur
Figlerowicz, Marek
Powiązania:
https://bibliotekanauki.pl/articles/1043669.pdf
Data publikacji:
2003
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
gene silencing
small RNAs
RNAi
PTGS
quelling
Opis:
Several years ago it was discovered that plant transformation with a transcribed sense transgene could shut down the expression of a homologous endogenous gene. Moreover, it was shown that the introduction into the cell of dsRNA (double-stranded RNA) containing nucleotide sequence complementary to an mRNA sequence causes selective degradation of the latter and thus silencing of a specific gene. This phenomenon, called RNA interference (RNAi) was demonstrated to be present in almost all eukaryotic organisms. RNAi is also capable of silencing transposons in germ line cells and fighting RNA virus infection. Enzymes involved in this process exhibit high homology across species. Some of these enzymes are involved in other cellular processes, for instance developmental timing, suggesting strong interconnections between RNAi and other metabolic pathways. RNAi is probably an ancient mechanism that evolved to protect eukaryotic cells against invasive forms of nucleic acids.
Źródło:
Acta Biochimica Polonica; 2003, 50, 1; 217-229
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Computational prediction of non-enzymatic RNA degradation patterns
Autorzy:
Rybarczyk, Agnieszka
Jackowiak, Paulina
Figlerowicz, Marek
Blazewicz, Jacek
Powiązania:
https://bibliotekanauki.pl/articles/1038733.pdf
Data publikacji:
2016
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
RNA degradation
non-enzymatic RNA hydrolysis
branch-and-cut algorithm
Opis:
Since the beginning of the 21st century, an increasing interest in the research of ribonucleic acids has been observed in response to a surprising discovery of the role that RNA molecules play in the biological systems. It was demonstrated that they do not only take part in the protein synthesis (mRNA, rRNA, tRNA) but also are involved in the regulation of gene expression. Several classes of small regulatory RNAs have been discovered (e.g. microRNA, small interfering RNA, piwiRNA). Most of them are excised from specific double-stranded RNA precursors by enzymes that belong to the RNaseIII family (Drosha, Dicer or Dicer-like proteins). More recently, it has been shown that small regulatory RNAs are also generated as stable intermediates of RNA degradation (the so called RNA fragments originating from tRNA, snRNA, snoRNA etc.). Unfortunately, the mechanisms underlying biogenesis of the RNA fragments remain unclear. It is thought that several factors may be involved in the formation of the RNA fragments. The most important are the specific RNases, RNA-protein interactions and RNA structure. In this work, we focus on the RNA primary and secondary structures as factors influencing the RNA stability and consequently the pattern of RNA fragmentation. Earlier, we identified the major structural factors affecting non-enzymatic RNA degradation. Now, based on these data, we developed a new branch-and-cut algorithm that is able to predict the products of large RNA molecules' hydrolysis in vitro. We also present the experimental data that verify the results generated using this algorithm.
Źródło:
Acta Biochimica Polonica; 2016, 63, 4; 745-751
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Nonenzymatic hydrolysis of oligoribonucleotides. V. The elements affecting the process of self-hydrolysis
Autorzy:
Bibiłło, Arkadiusz
Ziomek, Krzysztof
Figlerowicz, Marek
Kierzek, Ryszard
Powiązania:
https://bibliotekanauki.pl/articles/1044552.pdf
Data publikacji:
1999
Wydawca:
Polskie Towarzystwo Biochemiczne
Źródło:
Acta Biochimica Polonica; 1999, 46, 1; 145-153
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Mikromacierze DNA
DNA microarrays
Autorzy:
Kisiel, Agnieszka
Skąpska, Anna
Markiewicz, Wojciech
Figlerowicz, Marek
Powiązania:
https://bibliotekanauki.pl/articles/1199376.pdf
Data publikacji:
2004
Wydawca:
Polskie Towarzystwo Przyrodników im. Kopernika
Opis:
The breakthrough in DNA sequencing technology and completion of sequencing of first eucaryotic genomes raised the need for high-throughput methods of gene function analysis. To solve this problem the DNA microarray technology has been developed. It is based on traditional transcript profiling methods which use the hybridization ability of DNA and RNA to monitor gene expression. Due to miniaturisation and the use of fluorescent dyes DNA microarrays allow for simultaneous monitoring of the expression of tens of thousands genes. There are two main types of DNA microarrays: cDNA microarrays and oligonucleotide microarrays, also called DNA chips. In the former, several- hundred-nucleotide long cDNA probes are printed on a glass plate and hybridized to a fluorescently labeled target cDNA obtained from the tissue of interest. In the latter, type of microarrays, each gene is represented by several short oligonucleotides (about 30 nt), perfectly matching the target gene, and several oligomers with a single mismatch. Oligonucleotides are usually synthetised on a glass slide using the photolithographic technique and the slide is hybridized to fluorescently labeled target RNA. Analysis ofmicroarray data includes the comparison of gene expression in the experimental and control probes or the comparison of gene expression profiles obtained in several experiments, by different clustering methods. Medicine is one of the fields where DNA microarrays have already found practical application. At present they are especially useful in cancer research. DNA microarray analysis of tumor tissues allows to differentiate among various cancer types, to prognose the illness progress and plan the therapy. DNA microarrays are also an irreplaceable tool in a search for new drugs.
Źródło:
Kosmos; 2004, 53, 3-4; 295-303
0023-4249
Pojawia się w:
Kosmos
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Two types of non-homologous RNA recombination in brome mosaic virus
Autorzy:
Alejska, Magdalena
Malinowska, Nelli
Urbanowicz, Anna
Figlerowicz, Marek
Powiązania:
https://bibliotekanauki.pl/articles/1041326.pdf
Data publikacji:
2005
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
non-homologous RNA recombination
site-specific RNA recombination
heteroduplex-mediated RNA recombination
brome mosaic virus
Opis:
Non-homologous RNA recombination is a process enabling the exchange of genetic material between various (related or unrelated) RNA-based viruses. Despite extensive investigations its molecular mechanism remains unclear. Studies on genetic recombination in brome mosaic virus (BMV) have shown that local hybridization between genomic RNAs induces frequent non-homologous crossovers. A detailed analysis of recombinant structures suggested that local complementary regions might be involved in two types of non-homologous recombination in BMV: site-specific and heteroduplex-mediated. To verify the above hypothesis and better recognize the mechanism of the phenomenon studied we have tested how the putative types of recombination are affected by a specific mutation in the BMV polymerase gene or by changes in RNA structure. The experiments undertaken revealed substantial differences between site-specific and heteroduplex-mediated recombination, indicating that they occur according to different mechanisms. The former can be classified as homology-assisted, and the latter as homology-independent. In addition to local RNA/RNA hybridization, short regions of homology are required for site-specific crossovers to occur. They are most efficiently mediated if one homologous sequence is located at the beginning of and the second just before a double-stranded region. At present it is difficult to state what is the mechanism of heteroduplex-mediated recombination. Earlier it was postulated that strong RNA/RNA interaction enforces template switching by the viral replicase. There are, however, several observations questioning this model and indicating that some other factors, which are still unknown, may influence heteroduplex-mediated crossovers.
Źródło:
Acta Biochimica Polonica; 2005, 52, 4; 833-844
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Structural and functional characteristics of two novel members of pathogensis-related multigene family of class 10 from yellow lupine+
Autorzy:
Handschuh, Luiza
Femiak, Iwona
Kasperska, Alina
Figlerowicz, Marek
Sikorski, Michał
Powiązania:
https://bibliotekanauki.pl/articles/1040870.pdf
Data publikacji:
2007
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
pathogensis-related genes and proteins
gene silencing
salicylic acid
promoter analysis
yellow lupine
hydrogene peroxide
Opis:
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 organs, but their level of expression depends on the stage of development and is affected by wounding, oxidative stress and salicylic acid treatment. Silencing of the Llpr-10.2b gene in 4-week-old yellow lupine plants did not lead to any visible symptoms, which suggests that the function of the silenced gene is supplemented by its close homologues, still present in the studied plants.
Źródło:
Acta Biochimica Polonica; 2007, 54, 4; 783-796
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
AmiRNA Designer - new method of artificial miRNA design
Autorzy:
Mickiewicz, Agnieszka
Rybarczyk, Agnieszka
Sarzynska, Joanna
Figlerowicz, Marek
Blazewicz, Jacek
Powiązania:
https://bibliotekanauki.pl/articles/1038843.pdf
Data publikacji:
2016
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
artificial miRNA
RNAi
gene regulation
sequence specific
thermodynamic profiles
Opis:
MicroRNAs (miRNAs) are small non-coding RNAs that have been found in most of the eukaryotic organisms. They are involved in the regulation of gene expression at the post-transcriptional level in a sequence specific manner. MiRNAs are produced from their precursors by Dicer-dependent small RNA biogenesis pathway. Involvement of miRNAs in a wide range of biological processes makes them excellent candidates for studying gene function or for therapeutic applications. For this purpose, different RNA-based gene silencing techniques have been developed. Artificially transformed miRNAs (amiRNAs) targeting one or several genes of interest represent one of such techniques being a potential tool in functional genomics. Here, we present a new approach to amiRNA*design, implemented as AmiRNA Designer software. Our method is based on the thermodynamic analysis of the native miRNA/miRNA* and miRNA/target duplexes. In contrast to the available automated tools, our program allows the user to perform analysis of natural miRNAs for the organism of interest and to create customized constraints for the design stage. It also provides filtering of the amiRNA candidates for the potential off-targets. AmiRNA Designer is freely available at http://www.cs.put.poznan.pl/arybarczyk/AmiRNA/.
Źródło:
Acta Biochimica Polonica; 2016, 63, 1; 71-77
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Low recombination activity of R region located at both ends of the HIV-1 genome
Autorzy:
Urbanowicz, Anna
Kurzyńska-Kokorniak, Anna
Jankowska, Anna
Alejska, Magdalena
Figlerowicz, Marek
Powiązania:
https://bibliotekanauki.pl/articles/1039669.pdf
Data publikacji:
2012
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
copy-choice mechanism
template switching
homologous RNA recombination
strand transfer
R region
RNA virus
retrovirus
Opis:
Although two strand transfer events are indispensable for the synthesis of double-stranded DNA and establishing HIV-1 infection, the molecular basis of these phenomena is still unclear. The first obligatory template switching event occurs just at the beginning of the virus replication cycle and involves two copies of the 97-nucleotide long R region, located one each at the both ends of the HIV-1 genome (HIV-1 R). Thus, one can expect that the molecular mechanism of this process is similar to the mechanism of homologous recombination which operates in RNA viruses. To verify the above-mentioned hypothesis, we attempted to assess the recombination activity of HIV-1 R. To this end, we tested in vitro, how effectively it induces template switching by HIV-1 RT in comparison with another well-characterized sequence supporting frequent homologous crossovers in an unrelated virus (R region derived from Brome mosaic virus - BMV R). We also examined if the RNA sequences neighboring HIV-1 R influence its recombination activity. Finally, we tested if HIV-1 R could cause BMV polymerase complex to switch between RNA templates in vivo. Overall, our results have revealed a relatively low recombination activity of HIV-1 R as compared to BMV R. This observation suggests that different factors modulate the efficiency of the first obligatory strand transfer in HIV-1 and the homology-driven recombination in RNA viruses.
Źródło:
Acta Biochimica Polonica; 2012, 59, 4; 619-626
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
How RNA viruses exchange their genetic material.
Autorzy:
Alejska, Magdalena
Kurzyńska-Kokorniak, Anna
Broda, Magdalena
Kierzek, Ryszard
Figlerowicz, Marek
Powiązania:
https://bibliotekanauki.pl/articles/1044130.pdf
Data publikacji:
2001
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
RNA recombination
RNA structure
viral replicase
RNA viruses
retroviruses
Opis:
One of the most unusual features of RNA viruses is their enormous genetic variability. Among the different processes contributing to the continuous generation of new viral variants RNA recombination is of special importance. This process has been observed for human, animal, plant and bacterial viruses. The collected data reveal a great susceptibility of RNA viruses to recombination. They also indicate that genetic RNA recombination (especially the nonhomologous one) is a major factor responsible for the emergence of new viral strains or species. Although the formation and accumulation of viral recombinants was observed in numerous RNA viruses, the molecular basis of this phenomenon was studied in only a few viral species. Among them, brome mosaic virus (BMV), a model (+)RNA virus offers the best opportunities to investigate various aspects of genetic RNA recombination in vivo. Unlike any other, the BMV-based system enables homologous and nonhomologous recombination studies at both the protein and RNA levels. As a consequence, BMV is the virus for which the structural requirements for genetic RNA recombination have been most precisely established. Nevertheless, the previously proposed model of genetic recombination in BMV still had one weakness: it could not really explain the role of RNA structure in nonhomologous recombination. Recent discoveries concerning the latter problem give us a chance to fill this gap. That is why in this review we present and thoroughly discuss all results concerning nonhomologous recombination in BMV that have been obtained until now.
Źródło:
Acta Biochimica Polonica; 2001, 48, 2; 391-407
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Historia biologiczna populacji Homo sapiens zamieszkujących centralną i wschodnią części Europy
Biological history of Homo sapiens populations living in Central and Eastern Europe
Autorzy:
Marcinkowska-Swojak, Małgorzata
Stolarek, Ireneusz
Zeńczak, Michał
Handschuh, Luiza
Figlerowicz, Marek
Powiązania:
https://bibliotekanauki.pl/articles/2197849.pdf
Data publikacji:
2023-03-31
Wydawca:
Wydawnictwo Adam Marszałek
Tematy:
historia biologiczna
Homo sapiens
archeogenomika
sekwencjonowanie nowej generacji
kopalny DNA (aDNA)
haplogrupy mitochondrialnego DNA
haplogrupy chromosomu Y
biological history
archaeogenomics
next-generation sequencing
ancient DNA (aDNA)
mitochondrial DNA haplogroups
Y-chromosome haplogroups
Opis:
Archaeogenomis is a recently developed interdisciplinary research field that utilizes advanced molecular biology techniques, especially DNA sequencing, to study the history of biological species, including humans. Analyses of ancient genomes provide independent information about human ancestors and their migrations, allowing researchers to uncover history of mankind. Here, we present the fundamental principles of archaeogenomics and its application in the studies of biological history of the populations inhabiting central-east Europe.
Źródło:
Historia Slavorum Occidentis; 2023, 1(36); 143-165
2084-1213
Pojawia się w:
Historia Slavorum Occidentis
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Impact of DNA microarray data transformation on gene expression analysis - comparison of two normalization methods
Autorzy:
Schmidt, Marcin
Handschuh, Luiza
Zyprych, Joanna
Szabelska, Alicja
Olejnik-Schmidt, Agnieszka
Siatkowski, Idzi
Figlerowicz, Marek
Powiązania:
https://bibliotekanauki.pl/articles/1039855.pdf
Data publikacji:
2011
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
microarray
data normalization
enterocyte
transcriptome analysis
probiotic
adhesion
gene expression profiling
Opis:
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 results. In general, our results provide an additional piece of evidence that the normalization method can profoundly influence final results of DNA microarray-based analysis. The impact of the normalization method depends greatly on the algorithm employed. Consequently, the normalization procedure must be carefully considered and optimized for each individual data set.
Źródło:
Acta Biochimica Polonica; 2011, 58, 4; 573-580
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
RNA-Seq-based analysis of differential gene expression associated with hepatitis C virus infection in a cell culture
Autorzy:
Hojka-Osinska, Anna
Budzko, Lucyna
Zmienko, Agnieszka
Rybarczyk, Agnieszka
Maillard, Patrick
Budkowska, Agata
Figlerowicz, Marek
Jackowiak, Paulina
Powiązania:
https://bibliotekanauki.pl/articles/1038741.pdf
Data publikacji:
2016
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
RNA-Seq
HCV
transcriptome
Opis:
Hepatitis C virus (HCV) infection is one of the major causes of chronic liver diseases. Unfortunately, the mechanisms of HCV infection-induced liver injury and host-virus interactions are still not well recognized. To better understand these processes we determined the changes in the host gene expression that occur during HCV infection of Huh-7.5 cells. As a result, we identified genes that may contribute to the immune and metabolic cellular responses to infection. Pathway enrichment analysis indicated that HCV induced an increased expression of genes involved in mitogen-activated protein kinases signaling, adipocytokine signaling, cell cycle and nitrogen metabolism. In addition, the enrichment analyses of processes and molecular functions revealed that the up-regulated genes were mainly implicated in the negative regulation of phosphorylation. Construction of the pathway-gene-process network enabled exploration of a much more complex landscape of molecular interactions. Consequently, several essential processes altered by HCV infection were identified: negative regulation of cell cycle, response to endoplasmic reticulum stress, response to reactive oxygen species, toll-like receptor signaling and pattern recognition receptor signaling. The analyses of genes whose expression was decreased upon HCV infection showed that the latter were engaged in the metabolism of lipids and amino acids. Moreover, we observed disturbance in the cellular antiviral defense. Altogether, our results demonstrated that HCV infection elicits host response that includes a very wide range of cellular mechanisms. Our findings significantly broaden the understanding of complex processes that accompany HCV infection. Consequently, they may be used for developing new host-oriented therapeutic strategies.
Źródło:
Acta Biochimica Polonica; 2016, 63, 4; 789-798
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
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