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High-throughput sequencing identification of novel and conserved miRNAs in the Brassica oleracea leaves.
Get PDFConclusively, for the first time, the large set of miRNAs was identified in mature cabbage leaves. Potential targets designation for these miRNAs may suggest their essential role in many plants primary biological processes. Presented study not only supplements the knowledge about B. oleracea miRNAs, but additionally it may be used in other research concerning the improvement of the cabbage cultivation
Polarne ekosystemy lądowe w kontekście zmian klimatycznych
Get PDFRapid climate changes observed during the last
decades, which are especially visible in the polar
regions, both directly and indirectly influence terrestrial
ecosystems. Glacier retreat causes emerging
of new areas that are later colonized in the process
of primary succession. Species composition of tundra
communities is changing and expansion of alien
species is being observed. Due to long-term research
programs, it is possible to detect and follow trends
and rate of the ongoing changes. The article presents
results of original research carried out by Polish
teams in the Arctic and in the Antarctic, which
document the main directions of recent changes in
tundra vegetation
Transforming growth factor β1 protein and mRNA levels in inflammatory bowel diseases: towards solving the contradictions by longitudinal assessment of the protein and mRNA amounts
Get PDFPreviously published studies on levels of the transforming growth factor-β1 (TGF-β1) protein and mRNA of the corresponding gene in patients suffering from inflammatory bowel diseases (IBD) gave varying results, leading to contradictory conclusions. To solve the contradictions, we aimed to assess longitudinally TGF-β1 protein and mRNA levels at different stages of the disease in children suffering from IBD. The study group consisted of 19 pediatric patients with IBD at the age between 3.5 and 18.4 years. The control group consisted of 42 children aged between 2.0 and 18.0 years. The plasma TGF-β1 concentration was measured with ELISA. mRNA levels of the TGF-β1 gene isolated from samples of the intestinal tissue were assessed by reverse transcription and real-time PCR. Levels of TGF-β1 protein in plasma and corresponding mRNA in intestinal tissue were significantly higher in IBD patients than in controls. TGF-β1 and corresponding transcripts were also more abundant in plasma and intestinal tissue, respectively, in patients at the active stage of the disease than during remission. In every single IBD patient, plasma TGF-β1 level and mRNA level in intestinal tissue was higher at the active stage of the disease than during remission. Levels of TGF-β1 and corresponding mRNA are elevated during the active stage of IBD but not during the remission. Longitudinal assessment of this cytokine in a single patient may help to monitor the clinical course of IBD
Eukaryotic translation initiation is controlled by cooperativity effects within ternary complexes of 4E-BP1, eIF4E, and the mRNA 50 cap
Get PDFInitiation is the rate-limiting step during mRNA 50 cap-dependent translation, and thus a target of a
strict control in the eukaryotic cell. It is shown here by analytical ultracentrifugation and fluorescence
spectroscopy that the affinity of the human translation inhibitor, eIF4E-binding protein
(4E-BP1), to the translation initiation factor 4E is significantly higher when eIF4E is bound to the
cap. The 4E-BP1 binding stabilizes the active eIF4E conformation and, on the other hand, can facilitate
dissociation of eIF4E from the cap. These findings reveal the particular allosteric effects forming
a thermodynamic cycle for the cooperative regulation of the translation initiation inhibition
Halogen bonding at the ATP binding site of protein kinases: preferred geometry and topology of ligand binding.
Get PDFHalogenated ligands have been widely developed as potent, and frequently selective, inhibitors of protein kinases (PK). Herein, all structures of protein kinases complexed with a halogenated ligand, identified in the PDB, were analyzed in the context of eventual contribution of halogen bonding to protein-ligand interactions. Global inspection shows that two carbonyl groups of residues located in the hinge region are the most abundant halogen bond acceptors. In contrast to solution data, well-defined water molecules, located at sites conserved across most PK structures, are also involved in halogen bonding. Analysis of cumulative distributions of halogen-acceptor distances shows that structures displaying short contacts involving a halogen atom are overpopulated, contributing together to clearly defined maxima of 2.82, 2.91 and 2.94Å for chlorine, bromine and iodine, respectively. The angular preference of a halogen bond favors ideal topology (180°, 120°) for iodine. For bromine the distribution is much more dispersed, and no such preference was found for chlorine. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012)
Electrochemical Detection of Avian Influenza Virus Genotype Using Amino-ssDNA Probe Modified Gold Electrodes
No full textA DNA biosensor for the detection of specific oligonucleotide sequences of Avian Influenza Virus type H5N1 has been proposed. The NH2-ssDNA probe was deposited onto a gold electrode surface to form an amide bond between
the carboxyl group of thioacid and the amino group from ssDNA probe. The signals generated as a result of
hybridization were registered in square wave voltammetry and electrochemical impedance spectroscopy in the presence
of [Fe(CN)6]3�/4� as a redox marker. The genosensor is capable to determine 20-mer and 180-bp (PCR products)
oligonucleotides complementary sequences with detection limit in the fM range. The genosensor displays good
selectivity and sensitivity. The 20-mer as well as 180-bp oligonucleotides without a complementary sequence generate
very low signal
Ternary Complex Formation and Competition Quench Fluorescence of ZnAF Family Zinc Sensors
Get PDFOur current understanding of the intracellular thermodynamics and kinetics of Zn(II) ions is largely based
on the application of fluorescent sensor molecules, used to study and visualize the concentration,
distribution and transport of Zn(II) ions in real time. Such agents are designed for high selectivity for zinc
in respect to other biological metal ions. However, the issue of their sensitivity to physiological levels of
10 low molecular weight Zn(II) ligands (LMWLs) has not been addressed. We followed the effects of eight
such compounds on the fluorescence of ZnAF-1 and ZnAF-2F, two representatives of ZnAF family of
fluorescein-based zinc sensors containing the N,N-bis(2-pyridylmethyl)ethylenediamine chelating unit.
Fluorescence titrations of equimolar Zn(II)/ZnAF-1 and Zn(II)/ZnAF-2F solutions with acetate,
phosphate, citrate, glycine, glutamic acid, histidine, ATP and GSH demonstrated strong fluorescence
15 quenching. These results are interpreted in terms of an interplay of the formation of the [ZnAF-Zn(II)-
LMWL] ternary complexes and the competition for Zn(II) between ZnAF and LMWLs. UV-vis
spectroscopic titrations revealed the existence of supramolecular interactions between the fluorescein
moiety of ZnAF-1 and ATP and His, which, however, did not contribute to fluorescence quenching.
Therefore, the obtained results show that the ZnAF sensors, other currently used zinc sensors containing
20 the N,N-bis(2-pyridylmethyl)ethylenediamine unit, and, in general, all sensors that do not saturate the
Zn(II) coordination sphere, may co-report cellular metabolites and Zn(II) ions, leading to
misrepresentations of the concentrations and fluxes of biological zinc
Oligomerization interface of RAGE receptor revealed by MS-monitored hydrogen deuterium exchange.
No full textActivation of the receptor for advanced glycation end products (RAGE) leads to a chronic proinflammatory signal, affecting patients with a variety of diseases. Potentially beneficial modification of RAGE activity requires understanding the signal transduction mechanism at the molecular level. The ligand binding domain is structurally uncoupled from the cytoplasmic domain, suggesting receptor oligomerization is a requirement for receptor activation. In this study, we used hydrogen-deuterium exchange and mass spectrometry to map structural differences between the monomeric and oligomeric forms of RAGE. Our results indicated the presence of a region shielded from exchange in the oligomeric form of RAGE and led to the identification of a new oligomerization interface localized at the linker region between domains C1 and C2. Based on this finding, a model of a RAGE dimer and higher oligomeric state was constructed
Sequence determination and analysis of three plasmids of Pseudomonas sp. GLE121, a psychrophile isolated from surface ice of Ecology Glacier (Antarctica)
No full textPseudomonas sp. GLE121 (a psychrophilic Antarctic strain) carries three plasmids: pGLE121P1 (6899 bp), pGLE121P2 (8330 bp) and pGLE121P3 (39,583 bp). Plasmids pGLE121P1 and pGLE121P2 show significant sequence similarity to members of the IncP-9 and IncP-7 incompatibility groups, respectively, while the largest replicon, pGLE121P3, is highly related to plasmid pNCPPB880-40 of Pseudomonas syringae pathovar tomato NCPPB880. All three plasmids have a narrow host range, limited to members of the genus Pseudomonas. Plasmid pGLE121P3 encodes a conjugal transfer system, while pGLE121P1 carries only a putative MOB module, conserved in many mobilizable plasmids. Plasmid pGLE121P3 contains an additional load of genetic information, including a pair of genes with homology to the rulAB operon, responsible for ultraviolet radiation (UVR) tolerance. Given the increasing UV exposure in Antarctic regions, the expression of these genes is likely to be an important adaptive response
The quantum casimir effect may be a universal force organizing the bilayer structure of the cell membrane.
Get PDFA mathematic-physical model of the interaction between cell membrane bilayer leaflets is proposed based on the Casimir effect in dielectrics. This model explains why the layers of a lipid membrane gently slide one past another rather than penetrate each other. The presented model reveals the dependence of variations in the free energy of the system on the membrane thickness. This function is characterized by the two close minima corresponding to the different levels of interdigitation of the lipids from neighbor layers. The energy barrier of the compressing transition between the predicted minima is estimated to be 5.7 kT/lipid, and the return energy is estimated to be 3.1 kT/lipid. The proposed model enables estimation of the value of the membrane elastic thickness modulus of compressibility, which is 1.7 × 10(9) N/m(2), and the value of the interlayer friction coefficient, which is 1.9 × 10(8) Ns/m(3)