Wyniki wyszukiwania - Biblioteka Nauki

1

Two novel aspects of the kinetics of gene expression including miRNAs

100%

Zhdanov V.

Open Physics

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2013

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tom 11

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nr 4

448-456

EN

In eukaryotic cells, many genes are transcribed into non-coding RNAs. Small RNAs or, more specifically, microRNAs (miRNAs) form an abundant sub-class of such RNAs. miRNAs are transcribed as long noncoding RNA and then generated via a processing pathway down to the 20–24-nucleotide length. The key ability of miRNAs is to associate with target mRNAs and to suppress their translation and/or facilitate degradation. Using the mean-field kinetic equations and Monte Carlo simulations, we analyze two aspects of this interplay. First, we describe the situation when the formation of mRNA or miRNA is periodically modulated by a transcription factor which itself is not perturbed by these species. Depending on the ratio between the mRNA and miRNA formation rates, the corresponding induced periodic kinetics are shown to be either nearly harmonic or shaped as anti-phase pulses. The second part of the work is related to recent experimental studies indicating that differentiation of stem cells often involves changes in gene transcription into miRNAs and/or the interference between miRNAs, mRNAs and proteins. In particular, the regulatory protein obtained via mRNA translation may suppress the miRNA formation, and the latter may suppress in turn the miRNA-mRNA association and degradation. The corresponding bistable kinetics are described in detail.

2

Non-coding RNAs and complex distributed genetic networks

100%

Zhdanov V.

Open Physics

|

2011

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tom 9

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nr 4

909-918

EN

In eukaryotic cells, the mRNA-protein interplay can be dramatically influenced by non-coding RNAs (ncRNAs). Although this new paradigm is now widely accepted, an understanding of the effect of ncRNAs on complex genetic networks is lacking. To clarify what may happen in this case, we propose a mean-field kinetic model describing the influence of ncRNA on a complex genetic network with a distributed architecture including mutual protein-mediated regulation of many genes transcribed into mRNAs. ncRNA is considered to associate with mRNAs and inhibit their translation and/or facilitate degradation. Our results are indicative of the richness of the kinetics under consideration. The main complex features are found to be bistability and oscillations. One could expect to find kinetic chaos as well. The latter feature has however not been observed in our calculations. In addition, we illustrate the difference in the regulation of distributed networks by mRNA and ncRNA.

3

Localized mRNA translation and protein association

100%

Zhdanov V.

Open Physics

|

2014

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tom 12

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nr 8

603-609

EN

Recent direct observations of localization of mRNAs and proteins both in prokaryotic and eukaryotic cells can be related to slowdown of diffusion of these species due to macromolecular crowding and their ability to aggregate and form immobile or slowly mobile complexes. Here, a generic kinetic model describing both these factors is presented and comprehensively analyzed. Although the model is non-linear, an accurate self-consistent analytical solution of the corresponding reaction-diffusion equation has been constructed, the types of localized protein distributions have been explicitly shown, and the predicted kinetic regimes of gene expression have been classified.

4

A generic 3D kinetic model of gene expression

100%

Zhdanov V.

Open Physics

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2012

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tom 10

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nr 2

533-537

EN

Recent experiments show that mRNAs and proteins can be localized both in prokaryotic and eukaryotic cells. To describe such situations, I present a 3D mean-field kinetic model aimed primarily at gene expression in prokaryotic cells, including the formation of mRNA, its translation into protein, and slow diffusion of these species. Under steady-state conditions, the mRNA and protein spatial distribution is described by simple exponential functions. The protein concentration near the gene transcribed into mRNA is shown to depend on the protein and mRNA diffusion coefficients and degradation rate constants.

5

Changes in DNA methylation in maize under herbicide stress conditions

86%

Tyczewska A. , Gracz J. , Szymkowiak J. , Twardowski T.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2015

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tom 96

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nr 1

6

Transkrypcja genów jako ciągły lub dyskretny proces produkcyjny

86%

Śmieja J.

Przegląd Elektrotechniczny

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2008

|

tom R. 84, nr 9

93-95

PL

W komórkach żywych organizmów zachodzi wiele procesów biochemicznych podlegających skomplikowanym mechanizmom regulacji. Jednym z nich jest proces produkcji cząsteczek mRNA, zachodzący w jądrze komórkowym. Z praktycznego punktu widzenia jest to proces dyskretny. W niektórych przypadkach może być on jednak opisywany modelami ciągłymi. W niniejszej pracy pokazane są warunki, w jakich zarówno opis dyskretny, jak i ciągły prowadzą do takich samych jakościowo wyników.

EN

Biochemical processes in living cells are controlled by complex regulatory systems. One of such processes is production of mRNA molecules during gene transcription, taking place in the nucleus. The nature of this production process is discrete but in some cases it can be described by means of continuous models. This work presents cases in which both discrete and continuous models lead to qualitatively equivalent results.

7

Mammalian DNA methyltransferases

86%

Siedlecki P. , Zielenkiewicz P.

Acta Biochimica Polonica

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2006

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tom 53

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nr 2

EN

DNA methylation is an epigenetic process affecting gene expression and chromatin organization. It can heritably silence or activate transcription of genes without any change in their nucleotide sequences, and for a long time was not recognized as an important regulatory mechanism. However, during the recent years it has been shown that improper methylation, especially hypermethylation of promoter regions, is observed in nearly all steps of tumorigenesis. Aberrant methylation is also the cause of several major pathologies including developmental disorders involving chromosome instabilities and mental retardation. A great progress has been made in our understanding of the enzymatic machinery involved in establishing and maintaining methylation patterns. This allowed for the development of new diagnostic tools and epigenetic treatment therapies. The new approaches hold a great potential; several inhibitors of DNA methyltransferases have already shown very promising therapeutic effects.

8

Signal transducer and activator of transcription STAT3 plays a major role in gp130-mediated acute phase protein gene activation

86%

May P. , Schniertshauer U. , Gerhartz C. , Horn F. , Heinrich P. C.

Acta Biochimica Polonica

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2003

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tom 50

|

nr 3

EN

Interleukin-6 is a potent inducer of acute-phase response gene transcription. The intracellular signal transduction mechanisms by which this and other biological effects of the cytokine are achieved include activation of the JAK-STAT signaling pathway. More specifically, activation of the signal transducers and activators of transcription STAT1, 3, and 5 in response to IL-6 has been described. We examined the relative potency of these three STAT factors for the activation of acute-phase gene promoters in HepG2 cells in a reporter gene-based assay, where specific STAT factors could be activated via recombinant receptor constructs bearing different STAT-recruiting modules. These experiments indicate that amongst the STAT factors known to be activated by IL-6 STAT3 is the most potent activator of acute-phase gene transcription.

9

Effect of some antidepressants on the low corticosterone concentration-induced gene transcription in LMCAT fibroblast cells

86%

Otczyk M. , Mulik K. , Budziszewska B. , Jaworska-Feil L. , Basta-Kaim A. , Kubera M. , Jagla G. , Nowak W. , Lason W.

Journal of Physiology and Pharmacology

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2008

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tom 59

|

nr 1

EN

The aim of the present study was to investigate effects of some classical and new antidepressants on functional activity of the glucocorticoid receceptor (GR) induced by low corticosterone concentration in mouse fibroblast cells stably transfected with mouse mammary tumor virus-chloramphenicol acetyltransferase plasmid (LMCAT cells). We found that the transcriptional activity of GR stimulated by 50 nM corticosterone was strongly attenuated by imipramine, desipramine, fluoxetine and tianeptine in a concentration-dependent way, whereas reboxetine had only a weak effect and venlafaxine was inactive. Further study revealed that the inhibitor of c-Jun N-terminal kinase - mitogen-activated protein kinase (JNK-MAPK), SP600125 (0.1 µM), reversed the imipramine-induced suppression of GR function, whereas the inhibitor of extracellular signal-regulated kinase (ERK)-MAPK, PD 98059 (15µM), potentiated the antidepressant action. No effect of selective inhibitors of p38-MAPK, phosphatidylinositol 3-kinase (PI3-K)/Akt, and glycogen synthase kinase (GSK-3) on the imipramine-induced inhibition of GR function was detected. These data indicate that the functional activity of GR evoked by low corticosterone concentration in LMCAT cells is efficiently inhibited by tricyclic antidepressants. Moreover, it was found that JNK- and ERK-MAPK were oppositely involved in the regulation of the imipramine-induced inhibition of the GR functional activity. Thus, the present study supports the notion that the interaction of antidepressants with GR may play a role in attenuating pathological hyperactivity of HPA axis in depression.

10

Identification of the DNA binding element of the human ZNF300 protein

72%

Qiu H. , Xue L. , Gao L. , Shao H. , Wang D. , Guo M. , Li W.

|

tom 13

|

nr 3

391-403

EN

The human ZNF300 gene is a member of the KRAB/C2H2 zinc finger gene family, the members of which are known to be involved in various developmental and pathological processes. Here, we show that the ZNF300 gene encodes a 68-kDa nuclear protein that binds DNA in a sequence-specific manner. The ZNF300 DNA binding site, C(t/a)GGGGG(c/g)G, was defined via a random oligonucleotide selection assay, and the DNA binding site was further confirmed by electrophoretic mobility shift assays. A potential ZNF300 binding site was found in the promoter region of the human IL-2Rβ gene. The results of electrophoretic mobility shift assays indicated that ZNF300 bound to the ZNF300 binding site in the IL-2Rβ promoter in vitro. Transient co-transfection assays showed that ZNF300 could activate the IL-2Rβ promoter, and that the activation was abrogated by the mutation of residues in the ZNF300 binding site. Identifying the DNA binding site and characterizing the transcriptional regulation property of ZNF300 would provide critical insights into its potential as a transcriptional regulator.

11

Variation in gene transcription and protein for key enzymes of carbohydrate metabolism in poplar xylem with respect to growth phase

72%

Alluvada J. , Fokar M. , Holaday A. S.

Acta Physiologiae Plantarum

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2014

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tom 36

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nr 09

EN

We compared gene expression levels for enzymes of carbohydrate metabolism in the twig xylem of two Populus species with the seasonal levels of starch and soluble sugars (sucrose, glucose, and fructose) and relative levels of the enzymes. Plants of Populus deltoides Bartr. ex Marsh and P. balsamifera L., 3–4 years old, were grown outside in Lubbock, TX, USA in 43 L pots. The xylem in the middle portion of the twigs was sampled during the dormant period (November–February), at bud break (for P. balsamifera), and during the growth flush (April–July). The gene expression for ADP-glucose pyrophosphorylase (AGPase), sucrose synthase (SuSy), and sucrose-phosphate synthase (SPS) generally coincided with the levels of the carbohydrates in whose metabolism these enzymes are involved. Gene expression for AGPase and its protein levels were high when the xylem starch content was high (growing period). However, P. balsamifera maintained high AGPase levels in dormant and growing twigs, unlike P. deltoides whose dormant twigs had low AGPase and low gene expression. Compared to growing twigs, gene expression for SuSy and SPS and their protein levels were higher in dormant twigs when soluble sugar content was higher. No down-regulation of these genes appears to occur when pools of the associated carbohydrates are high. Contrary to our expectation, the gene expression for bamylase was highest in growing twigs when starch content was high. High β-amylase gene expression in growing twigs may be involved in maintaining a sufficient level of soluble sugars for growth through possibly controlling the extent of starch accumulation.

12

The immunoreactivity of TGF-beta1 in non-alcoholic fatty liver disease

72%

Kempinski R. , Neubauer K. , Poniewierka E. , Kaczorowski M. , Halon A.

Folia Histochemica et Cytobiologica

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2019

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tom 57

|

nr 2

13

Molecular mechanisms underlying female sex determination - antagonism between female and male pathway

72%

Piprek R. P.

|

tom 57

|

nr 3-4

105-113

14

Cohesin Irr1/Scc3 is likely to influence transcription in Saccharomyces cerevisiae via interaction with Mediator complex

72%

Cena A. , Skoneczny M. , Chelstowska A. , Kowalec P. , Natorff R. , Kurlandzka A.

Acta Biochimica Polonica

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2013

|

tom 60

|

nr 2

EN

The evolutionarily conserved proteins forming sister chromatid cohesion complex are also involved in the regulation of gene transcription. The participation of SA2p (mammalian ortholog of yeast Irr1p, associated with the core of the complex) in the regulation of transcription is already described. Here we analyzed microarray profiles of gene expression of a Saccharomyces cerevisiae irr1-1/IRR1 heterozygous diploid strain. We report that expression of 33 genes is affected by the presence of the mutated Irr1-1p and identify those genes. This supports the suggested role of Irr1p in the regulation of transcription. We also indicate that Irr1p may interact with elements of transcriptional coactivator Mediator.

15

SSCP polymorphism within 5' region of bovine lactoglobulin [LGB] gene

72%

Kaminski S. , Zabolewicz T.

Journal of Applied Genetics

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1998

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tom 39

|

nr 1

EN

In the paper the detection of the SSCP polymorphism within the 5’ fragment of bovine beta-lactoglobulin (LGB) gene is described. The 5’ fragment of LGB gene (209 bp) was PCR-amplified and then subjected to electrophoresis allowing the detection of SSCP polymorphism. Among 124 animals (50 cows and 74 bulls) six SSCP patterns were identified and named Rl, R2, R3, R4, R5 and R6, which occured with the frequency of 0.32, 0.51, 0.09, 0.06, 0.01 and 0.01, respectively. The PCR-SSCP method is simple, fast, and relatively inexpensive. The SSCP polymorphism reported in the paper may be useful in looking for the associations between different SSCP patterns and LGB gene expression and milk properties.

16

Complete nucleotide sequence of the Campylobacter jejuni 72Dz asd gene

72%

Pawelec D. , Jagusztyn-Krynicka E.

Acta Microbiologica Polonica

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1996

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tom 45

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nr 3-4

17

Apoptosis in human polymorphonuclear leukocytes: searching for a genetic roadmap

72%

Kobayashi S. D. , Deleo F. R.

Archivum Immunologiae et Therapiae Experimentalis

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2003

|

tom 51

|

nr 1

18

Distribution of transcription factor binding sites along 5'-upstream sequences of genes: estimation of minimal promoters and upstream regulatory regions

72%

Malewski T. , Glazko G. , Sazanov A.

Biotechnologia

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2004

|

nr 3

19

Redox control of cellular function by thioredoxin; a new therapeutic direction in host defence

72%

Nishinaka Y. , Nakamura H. , Masutani H. , Yodoi J.

Archivum Immunologiae et Therapiae Experimentalis

|

2001

|

tom 49

|

nr 4

20

Analysis of polymorphisms in the mediator complex subunit 13-like (MED13L) gene in the context of immune function and development of experimental arthritis

58%

Sardar S. , Kanne K. , Andersson A.

Archivum Immunologiae et Therapiae Experimentalis

|

2018

|

tom 66

|

nr 5