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1
Content available remote

mRNA Regulatory elements and bacterial virulence

100%
Pawlikowska-Warych M., Deptuła W.
Acta Biochimica Polonica
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2014
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vol. 61
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issue 1
63-65
EN
Pathogenic bacteria cause many diseases, some of which are fatal. For researchers, it is a challenge to understand bacterial mechanisms of pathogenicity, including their virulence pathways regulated by RNA. This work presents data on the mechanisms of regulation and expression of several virulence factors coded by RNA, namely 5' UTR fragments, riboswitches and small non-coding RNA (sRNA).
2

RNA World

100%
Szweykowska-Kulinska Z.
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issue 2
15-27
EN
Experimental data suggest that four billion years ago amino acids, purines and pyrimidines could be present in prebiotic soup. Non- enzymatic synthesis of peptides and RNA is possible. RNA can act as replicators and catalysts. Ribonucleic acids are very likely to be recognized as the molecules that gave rise to life. Riboorganisms used amino acids for the synthesis of purine and pyrimidine rings. They developed genetic code and translation. First proteins were used to create channels across phospholipid membranes and to stabilize ribozymes. Ribonucleoproteins containing catalytic RNA can be regarded as relicts from RNA World.
3

Regulatory ribonucleic acids

100%
Zywicki M., Szymanski M., Barciszewska M. Z., Barciszewski J.
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issue 2
28-53
EN
In recent years there was a growing number of reports of new non-protein-coding RNAs which are implicated in the regulation of many cellular processes. They differ in many respects from already known housekeeping RNA species involved in protein biosynthesis (tRNA, rRNA) and RNA maturation or modification (RNase P RNA, snRNAs, snoRNAs). Regulatory RNAs (riboregulators) are expressed only in certain cell types, at particular stages of organism development or cell differentiation or in response to biotic and abiotic stimuli. Their expression is usually accompanied by the alteration of patterns of the expression of other genes. The mechanisms employed by riboregulators can affect transcription, pre-mRNA processing and translation. In the post-genomic era, the noncoding regulatory RNAs emerge as key determinants of organismal complexity, providing efficient and highly specific means for integration of various cellular processes.
4
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Assessing the 5S ribosomal RNA heterogeneity in Arabidopsis thaliana using short RNA next generation sequencing data

100%
Szymanski M., Karlowski W.
Acta Biochimica Polonica
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2016
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vol. 63
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issue 4
841-844
EN
In eukaryotes, ribosomal 5S rRNAs are products of multigene families organized within clusters of tandemly repeated units. Accumulation of genomic data obtained from a variety of organisms demonstrated that the potential 5S rRNA coding sequences show a large number of variants, often incompatible with folding into a correct secondary structure. Here, we present results of an analysis of a large set of short RNA sequences generated by the next generation sequencing techniques, to address the problem of heterogeneity of the 5S rRNA transcripts in Arabidopsis and identification of potentially functional rRNA-derived fragments.
5
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StructAnalyzer - a tool for sequence versus structure similarity analysis

100%
Wiedemann J., Miłostan M.
Acta Biochimica Polonica
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2016
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vol. 63
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issue 4
753-757
EN
In the world of RNAs and proteins, similarities at the level of primary structures of two comparable molecules usually correspond to structural similarities at the tertiary level. In other words, measures of sequence and structure similarities are in general correlated - a high value of sequence similarity imposes a high value of structural similarity. However, important exceptions that stay in contrast to this general rule can be identified. It is possible to find similar structures with very different sequences, as well as similar sequences with very different structures. In this paper, we focus our attention on the latter case and propose a tool, called StructAnalyzer, supporting analysis of relations between the sequence and structure similarities. Recognition of tertiary structure diversity of molecules with very similar primary structures may be the key for better understanding of mechanisms influencing folding of RNAs or proteins, and as a result for better understanding of their function. StructAnalyzer allows exploration and visualization of structural diversity in relation to sequence similarity. We show how this tool can be used to screen RNA structures in Protein Data Bank (PDB) for sequences with structural variants.
6
Content available remote

Self-assembly of large RNA structures: learning from DNA nanotechnology

88%
Stewart J. M., Franco E.
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vol. 2
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issue 1
EN
Nucleic acid nanotechnology offers many methods to build self-assembled structures using RNA and DNA. These scaffolds are valuable in multiple applications, such as sensing, drug delivery and nanofabrication. Although RNA and DNA are similar molecules, they also have unique chemical and structural properties. RNA is generally less stable than DNA, but it folds into a variety of tertiary motifs that can be used to produce complex and functional nanostructures. Another advantage of using RNA over DNA is its ability to be encoded into genes and to be expressed in vivo. Here we review existing approaches for the self-assembly of RNA and DNA nanostructures and specifically methods to assemble large RNA structures. We describe de novo design approaches used in DNA nanotechnology that can be ported to RNA. Lastly, we discuss some of the challenges yet to be solved to build micron-scale, multi stranded RNA scaffolds.
7

RNA in biotechnology

75%
Figlerowicz M.
Biotechnologia
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2002
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issue 4
23-29
EN
The studies conducted during the last decade revealed that RNA molecules play much more different roles in the living world than it had been expected earlier. They can function in biological systems as: carriers of genetic information, enzymes, cofactors inducing or mediating biochemical reactions, inhibitors which deactivate enzymes or agents that regulate cellular processes. Consequently, several new RNA-based methods and techniques have been elaborated. They permit to identify RNA molecules that display some specific properties, selectively induce gene silencing or gene expression in bacterial, plant and animal cells. Generally, it is becoming increasingly apparent that RNA-based technologies should be considered one of the major factors influencing further development of modern biotechnology.
8
Content available remote

Heavy metals in the cell nucleus - role in pathogenesis

75%
Sas-Nowosielska H., Pawlas N.
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issue 1
7-13
EN
People are exposed to heavy metals both in an occupational and natural environment. The most pronounced effects of heavy metals result from their interaction with cellular genetic material packed in form of chromatin. Heavy metals influence chromatin, mimicking and substituting natural microelements in various processes taking place in the cell, or interacting chemically with nuclear components: nucleic acids, proteins and lipids. This paper is a review of current knowledge on the effects of heavy metals on chromatin, exerted at the level of various nuclear components.
9
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Wykrywanie obecności genomu rynowirusa w popłuczynach nosowych u chorych na astmę

51%
Hubalewska-Mazgaj M., Bochenek G., Pulka G., Sanak M.
Zeszyty Naukowe Towarzystwa Doktorantów Uniwersytetu Jagiellońskiego. Nauki Ścisłe
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2010
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issue 1
23-33
EN
Human rhinoviruses (HRV) are one of the nine genera belonging to a large family of Picornaviridae. They are responsible for the most cases of common cold, as well as one third to one half of upper respiratory tract (URT) infections. However, HRV are also associated with more severe illnesses, like acute otitis media, sinusitis and some lower respiratory tract diseases such as pneumonia, wheezing in children and exacerbations of asthma. Viral infections are associated with the majority of asthma exacerbations both in children (80-85%) and adults (75-80%), and about 60% of these are caused by HRV. However, the exact mechanism of HRV-induced exacerbations of the disease is not well understood, which makes it difficult to establish the effective treatment. There have already been many attempts to develop a sensitive and specific method of HRV detection in clinical samples. Some of them were based on virus cultures followed by acid lability test, whereas others implemented the reverse transcription-polymerase chain reaction (RT-PCR) and amplification of conserved sequences of the rhinoviral genome. As numerous of these sequences are common to both rhinoviruses and enteroviruses (EVs), further analyses were necessary, which made those methods laborious, time-consuming and too difficult to use in routine diagnostics. Steininger et al. established an RT-PCR-based sensitive and specific method of rhinovirus detection in clinical samples, which was tested to amplify 87 different tissue-culturegrown serotypes of HRV. The aim of this study was to evaluate a modified RT-PCR based method of HRV detection in clinical samples obtained from patients with asthma exacerbations. We collected 41 nasal lavages from patients with asthma exacerbations who received hospital treatment either following an admission or in an out-patient clinic. HRV was found in 22 cases (54%), which corresponded well with the published data.
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