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Search results for: PROTEIN GENE EXPRESSION
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Agri Gene
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Plant Gene
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Human Gene
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Gene: X
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TRNA-Leu (UUR) gene haplotypes observed in canine mammary gland tumours and its deleterious effect assessment according to the comparative analysis with TRNL1 human gene
Open Research DataThe aetiology and pathogenesis of many canine tumours are likely to be similar to cancers found in humans. This study aimed to present a plausible link between changes in tRNA-Leu (UUR) gene and the carcinogenesis process in dogs with mammary gland tumours. The whole mitochondrial DNA (mtDNA) isolated from blood and tumour tissues of 13 dogs with malig-nant...
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Taurine as a water structure breaker and protein stabilizer
PublicationThe enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as “structure breaking” solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between...
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Architectural expression in designing museums as places of remembrance
PublicationMuseums commemorating tragic historic events require the application of particular means of architectural expression. Both the form of the building, the interior design, lighting and materials and its surroundings became a part of the exhibition. In this article the narrative role of architectural components is discussed based on three museums located in different cultural and geographical areas. These are: the Nanjing Massacre...
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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule
PublicationThe influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described....
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Protein thermal stabilization in aqueous solutions of osmolytes
PublicationProteins’ thermal stabilization is a significant problem in various biomedical, biotechnological, and technological applications. We investigated thermal stability of hen egg white lysozyme in aqueous solutions of the following stabilizing osmolytes: Glycine (GLY), N-methylglycine (NMG), N,N-dimethylglycine (DMG), N,N,N-trimethylglycine (TMG), and trimethyl-N-oxide (TMAO). Results of CD-UV spectroscopic investigation were compared...
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Emotion Recognition - the need for a complete analysis of the phenomenon of expression formation
PublicationThis article shows how complex emotions are. This has been proven by the analysis of the changes that occur on the face. The authors present the problem of image analysis for the purpose of identifying emotions. In addition, they point out the importance of recording the phenomenon of the development of emotions on the human face with the use of high-speed cameras, which allows the detection of micro expression. The work that was...
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The investigation of the effects of counterions in protein dynamics simulations
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PROTEIN SCIENCE
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Phenotypic consequences of LYS4 gene disruption in Candida albicans
PublicationA BLAST search of the Candida Genome Database with the Saccharomyces cerevisiae LYS4 sequence known to encode homoaconitase (HA) revealed ORFs 19.3846 and 19.11327. Both alleles of the LYS4 gene were sequentially disrupted in Candida albicans BWP17 cells using PCR-based methodology. The null lys4Δ mutant exhibited lysine auxotrophy in minimal medium but was able to grow in the presence of L-Lys and α-aminoadipate, an intermediate...
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MP3vec: A Reusable Machine-Constructed Feature Representation for Protein Sequences
Publication—Machine Learning (ML) methods have been used with varying degrees of success on protein prediction tasks, with two inherent limitations. First, prediction performance often depends upon the features extracted from the proteins. Second, experimental data may be insufficient to construct reliable ML models. Here we introduce MP3vec, a transferable representation for protein sequences that is designed to be used specifically for sequence-to-sequence...
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MutL protein as a constituent of vsp, ner and mmr repair systems
PublicationMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mis- match repair system (MMR). However, there is growing evidence that MMR system is not the only field of action for these pro- teins. Moreover, the participation in MMR does not even have to be their primary function. There are some reports indicat- ing involvement of MutL in BER, NER and VSP (very short patch repair)....
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Modified Peptide Molecules As Potential Modulators of Shelterin Protein Functions; TRF1
PublicationIn this work, we present studies on relatively new and still not well-explored potential anticancer targets which are shelterin proteins, in particular the TRF1 protein can be blocked by in silico designed "peptidomimetic" molecules. TRF1 interacts directly with the TIN2 protein, and this protein-protein interaction is crucial for the proper functioning of telomere, which could be blocked by our novel modified peptide molecules....
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ADVANCES IN PROTEIN CHEMISTRY
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JOURNAL OF PROTEIN CHEMISTRY
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EPAS1 resistance to miRNA-based regulation contributes to prolonged expression of HIF-2 during hypoxia in human endothelial cells
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General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublicationThe stability of proteins in an aqueous solution can be modified by the presence of osmolytes. The hydration sphere of stabilizing osmolytes is strikingly similar to the enhanced hydration sphere of a protein. This similarity leads to an increase in the protein stability. Moreover, the hydration sphere of destabilizing osmolytes is significantly different. These solutes generate in their surroundings so-called “structurally different...
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Protein overproduction alters exosome secretion in Chinese hamster ovary cells
PublicationDespite the abundance of available cell lines, nearly 70% of all recombinant therapeutic proteins today are produced in Chi-nese hamster ovary (CHO) cells. The impact of protein overproduction on the secretion of exosomes by CHO cells has been investigated here. Increased secretion of extracellular vesicles (EVs) by protein overexpressing CHO cells was demonstrated with protein content assay, nanoparticle tracking analysis, and...
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Molecular targets for antifungals in amino acid and protein biosynthetic pathways
PublicationFungi cause death of over 1.5 million people every year, while cutaneous mycoses are among the most common infections in the world. Mycoses vary greatly in severity, there are long-term skin (ringworm), nail or hair infections (tinea capitis), recurrent like vaginal candidiasis or severe, life-threatening systemic, multiorgan infections. In the last few years, increasing importance is attached to the health and economic problems...
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Production of Toxoplasma gondii MAG1 recombinant antigen in Leishmania tarentolae expression system
PublicationThe results of the work associated with the production of the Toxoplasma gondii matrix antigen 1 (MAG1) in the eukaryotic expression system of Leishmania tarentolae are shown.
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The Relationship between Gene Activity and Nitrous Oxide Production during Nitrification in Activated Sludge Systems
PublicationNitrite is an important factor which inhibits the first stage of the nitrification, the effect is stronger with the decrease of the DO concentrations. NO2- presence at concentration above 15 mg N – NO2 in the aeration tanks stimulates N2O production regardless of the DO concentration. The significant nirS gene induction, observed especially during the experiments with the nitrite addition indicates that N2O production is basically...
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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublicationA simple microplate method was designed for rapid testing DNA-binding activity of proteins. The principle of the assay involves binding of tested DNA by his-tagged protein immobilized on a nickel-coated ELISA plate, following colorimetric detection of biotinylated DNA with avidin conjugated to horseradish peroxidase. The method was used to compare DNA mismatch binding activities of MutS proteins from three bacterial species. The...
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New, fast and cheap prediction tests for BRCA1 gene mutations identification in clinical samples.
PublicationDespite significant progress in cancer therapy, cancer is still the second cause of mortality in the world. The necessity to make quick therapeutic decisions forces the development of procedures allowing to obtain a reliable result in a quick and unambiguous manner. Currently, detecting predictive mutations, including BRCA1, is the basis for effectively treating advanced breast cancer. Here, we present new insight on gene mutation...
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MUTL PROTEIN AS A COMMON CONSTITUENT OF VSP, BER, NER AND MMR REPAIR SYSTEMS
PublicationMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mismatch repair system (MMR). However, there is growing evidence that MMR system is not the only field of action of these proteins. Moreover, involvement in MMR does not even have to be their primary function. There are some reports indicating involvement of MutL in BER, NER and VSP (very short patch repair). MutL protein...
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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublicationIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
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Homocitrate synthase gene as a new molecular target in diagnostics of Candida spp. infections
PublicationNew potential molecular target which will be investigated during this research (homocitrate synthase gen) is the innovative target other than ribosomal DNA. This gene encodes enzyme present only in fungi and some Archaea what significantly increases specificity. It also reduces risk of contamination or influence of other factors (reaction with other DNA present in sample derived from bacteria or host cells) what excludes false...
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Novel primosomal protein B from thermophilic bacterium Thermoanerobacter tengcongensis
PublicationWe report the identification and characterization of theprimosomal protein B (PriB) from thermophilic bacteriumThermoanerobacter tengcongensis (TtePriB). It is the largestknown bacterial PriB protein consisting 216 amino acidresidues with a calculated molecular mass of 25 kDa. Surprisingly,it is functional as monomer containing two single-stranded DNA binding domain (OB-fold) and it is thecompletely new kind structure of SSB protein....
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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublicationOsmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress, and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical...
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A New Expression for the 3-D Dyadic FDTD-Compatible Green's Function Based on Multidimensional Z-Transform
PublicationIn this letter, a new analytic expression for the time-domain discrete Green's function (DGF) is derived for the 3-D finite-difference time-domain (FDTD) grid. The derivation employs the multidimensional Z-transform and the impulse response of the discretized scalar wave equation (i.e., scalar DGF). The derived DGF expression involves elementary functions only and requires the implementation of a single function in the multiple-precision...
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Chitosan-protein scaffolds loaded with lysostaphin as potential antistaphylococcal wound dressing materials.
PublicationAIMS: The development of technology for preparing chitosan-protein scaffolds loaded with lysostaphin, which potentially could be used as dressing for wound treatment and soft tissue infections caused by Staphylococcus aureus. METHODS AND RESULTS: The unique technology of chitosan solubilization using gaseous CO(2) instead of organic or inorganic acids was used for the incorporation of lysostaphin, the enzyme that exhibits bactericidal...
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Proteolysis of whey protein isolates in nanoemulsion systems: impact of nanoemulsification and additional synthetic emulsifiers
PublicationNanoemulsions are currently of interest in the functional food sector because their small droplet size (100–500 nm) provides a number of potential advantages over conventional emulsions. This study concerned the behavior of nanoemulsions stabilized with whey proteins and two synthetic emulsifiers (Tween 80 and Croduret), and exposed to conditions simulating the human upper gastrointestinal tract. In particular, the effect of synthetic...
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Unusual structural properties of water within the hydration shell of hyperactive antifreeze protein
PublicationMany hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were...
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CURRENT GENE THERAPY
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CANCER GENE THERAPY
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HUMAN GENE THERAPY
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JOURNAL OF GENE MEDICINE
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Prokaryotic expression systems
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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Methodology of Selecting the Optimal Receptor to Create an Electrochemical Immunosensor for Equine Arteritis Virus Protein Detection
PublicationThe study reports a methodology of selecting the optimal receptor to create an electrochemical immunosensor for equine arteritis virus (EAV) protein detection. The detection was based on antigen recognition by antibodies immobilized on gold electrodes. Modification steps were controlled by electrochemical impedance spectroscopy and cyclic voltammetry measurements. In order to obtain the impedance immunosensor with the best parameters,...
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Methodology of Selecting the Optimal Receptor to Create an Electrochemical Immunosensor for Equine Arteritis Virus Protein Detection
PublicationThe study reports a methodology of selecting the optimal receptor to create an electrochemical immunosensor for equine arteritis virus (EAV) protein detection. The detection was based on antigen recognition by antibodies immobilized on gold electrodes. Modification steps were controlled by electrochemical impedance spectroscopy and cyclic voltammetry measurements. In order to obtain the impedance immunosensor with the best parameters,...
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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Influence of Escherichia coli on Expression of Selected Human Drug Addiction Genes
PublicationThe impact of enteric microflora on the expression of genes associated with cocaine and amphetamine addiction was described. Human genome-wide experiments on RNA transcripts expressed in response to three selected Escherichia coli strains allowed for significant alteration (p > 0.05) of the linear regression model between HT-29 RNA transcripts associated with the KEGG pathway:hsa05030:Cocaine addiction after 3 h stimulation with...
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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublicationInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
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Induction of immune responses in sheep by vaccination with liposome-entrapped DNA complexes encoding Toxoplasma gondii MIC3 gene
PublicationToxoplasma gondii is a parasite that has been extensively studied due to its medical and veterinary importance in terminating pregnancies. Consequently, a satisfactory vaccine is required to control itsadverse effects on pregnant animals. The microneme protein, MIC3, is a major adhesion protein that binds to the surface of host cells and parasites, and is therefore a potential vaccine against T. gondii.The viability of MIC3 as...
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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublicationWe present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...
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Human UDP-Glucuronosyltransferases: Effects of altered expression in breast and pancreatic cancer cell lines.
PublicationIncreased aerobic glycolysis and de novo lipid biosynthesis are common characteristics of invasive cancers. UDP-glucuronosyltransferases (UGTs) are phase II drug metabolizing enzymes that in normal cells possess the ability to glucuronidate these lipids and speed their excretion; however, de-regulation of these enzymes in cancer cells can lead to an accumulation of bioactive lipids, which further fuels cancer progression. We hypothesize...