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Search results for: PROTEIN SURFACE
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Tailoring Diffusional Fields in Zwitterion/Dopamine Copolymer Electropolymerized at Carbon Nanowalls for Sensitive Recognition of Neurotransmitters
PublicationThe importance of neurotransmitter sensing in the diagnosis and treatment of many psychological illnesses and neurodegenerative diseases is non-negotiable. For electrochemical sensors to become widespread and accurate, a long journey must be undertaken for each device, from understanding the materials at the molecular level to real applications in biological fluids. We report a modification of diamondized boron-doped carbon nanowalls...
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Simultaneous optical and electrochemical label-free biosensing with ITO-coated lossy-mode resonance sensor
PublicationIn this work we discuss a new label-free biosensing device based on indium tin oxide (ITO) overlaid section of a multimode optical fiber fused silica core. The sensor has been used to optical measurements also simultaneously interrogated electrochemically (EC). Due to optimized thickness and optical properties of ITO film, a lossy-mode resonance (LMR) could be observed in the optical domain, where electrical properties of the film...
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Optimization of vortex-assisted supramolecular solvent-based liquid liquid microextraction for the determination of mercury in real water and food samples
PublicationA novel method was developed for sample preparation for spectrophotometric determination of Hg(II) in water and food samples. The method was based on vortex-assisted supramolecular solvent-assisted liquid-liquid microextraction (VA-SUPRASs-LLME). Analytical parameters such as pH, chelating agent, solvent type and volume, vortex time and salting out effect were optimized. Surface and normal probability plots were drawn for the variables...
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Boron-doped diamond nanosheet volume-enriched screen-printed carbon electrodes: a platform for electroanalytical and impedimetric biosensor applications
PublicationThis paper focuses on the development of a novel electrode based on boron-doped diamond nanosheet full-volume-enriched screen-printed carbon electrodes (BDDPE) for use as an impedimetric biosensor. Impedimetric biosensors offer high sensitivity and selectivity for virus detection, but their use as point-of-care devices is limited by the complexity of nanomaterials’ architecture and the receptor immobilisation procedures. The study...
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Ageing-Time Dependent Changes of Angiotensin I-Converting Enzyme-Inhibiting Activity of Protein Hydrolysates Obtained from Dry-Cured Pork Loins Inoculated with Probiotic Lactic Acid Bacteria
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Karaś P., Kochanowicz K., Pitek M., Domański P., Obuchowski I., Tomiczek B., Liberek K.: Evolution towards simplicity in bacterial small heat shock protein system// eLife -, (2023), s.1-21
PublicationEvolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in an equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis, we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either...
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Biotechnological production and purification of Borrelia burgdorferi sl B1 protein
Open Research DataBorrelia burgdorferi B1 protein could be used in the detection of specific immunoglobulins from patients' sera with Lyme disease that may be infected with different genospecies of B. burgdorferii sl. The goal of the study was to obtain the highest possible yield of protein expression in prokaryotic cells and purified protein preparations. This dataset...
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Biotechnological production and purification of Borrelia burgdorferi sl B2 protein
Open Research DataBorrelia burgdorferi B2 protein could be used in the detection of specific immunoglobulins from patients' sera with Lyme disease that may be infected with different genospecies of B. burgdorferii sl. The goal of the study was to obtain the highest possible yield of protein expression in prokaryotic cells and purified protein preparations. This dataset...
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Biotechnological production and purification of Borrelia burgdorferi sl B12 protein
Open Research DataBorrelia burgdorferi B12 protein could be used in the detection of specific immunoglobulins from patients' sera with Lyme disease that may be infected with different genospecies of B. burgdorferii sl. The goal of the study was to obtain the highest possible yield of protein expression in prokaryotic cells and purified protein preparations. This dataset...
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Biotechnological production and purification of Borrelia burgdorferi sl B3 protein
Open Research DataBorrelia burgdorferi B3 protein could be used in the detection of specific immunoglobulins from patients' sera with Lyme disease that may be infected with different genospecies of B. burgdorferii sl. The goal of the study was to obtain the highest possible yield of protein expression in prokaryotic cells and purified protein preparations. This dataset...
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Biotechnological production and purification of Borrelia burgdorferi sl B6 protein
Open Research DataBorrelia burgdorferi B6 protein could be used in the detection of specific immunoglobulins from patients' sera with Lyme disease that may be infected with different genospecies of B. burgdorferii sl. The goal of the study was to obtain the highest possible yield of protein expression in prokaryotic cells and purified protein preparations. This dataset...
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Biotechnological production and purification of Borrelia burgdorferi sl P protein
Open Research DataBorrelia burgdorferi P protein could be used in the detection of specific immunoglobulins G (IgG) from patients' sera with Lyme disease that may be infected with different genospecies of B. burgdorferii sl. The goal of the study was to obtain the highest possible yield of protein expression in prokaryotic cells and purified protein preparations. This...
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Biotechnological production and purification of Borrelia burgdorferi sl F protein
Open Research DataBorrelia burgdorferi F protein could be used in the detection of specific immunoglobulins G (IgG) from patients' sera with Lyme disease that may be infected with different genospecies of B. burgdorferii sl. The goal of the study was to obtain the highest possible yield of protein expression in prokaryotic cells and purified protein preparations. This...
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Significant Decrease in Glycated Hemoglobin, 2h-Post-Load Glucose and High-Sensitivity C-Reactive Protein Levels in Patients with Abnormal Body Mass Index after Therapy with Manual Lymphatic Drainage
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Low-power microwave-induced fabrication of functionalised few-layer black phosphorus electrodes: A novel route towards Haemophilus Influenzae pathogen biosensing devices
PublicationIn this paper, various passivation schemes were applied at few-layer black phosphorus (FLBP) to achieve covalent functionalisation with 4-azidobenzoic acid, improving its electrochemical response intended for analytical and biosensing applications. The thermal and microwave assisted modification procedures in toluene and dime-thylformamide resulted in high reversibility of reactions on functionalised FLBP using a ferricyanide/ferrocya-nide...
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Analysis of the Factors Affecting Static In Vitro Pepsinolysis of Food Proteins
PublicationIn this meta-analysis, we collected 58 publications spanning the last seven decades that reported static in vitro protein gastric digestion results. A number of descriptors of the pepsinolysis process were extracted, including protein type; pepsin activity and concentration; protein concentration; pH; additives; protein form (e.g., ‘native’, ‘emulsion’, ‘gel’, etc.); molecular weight of the protein; treatment; temperature; and...
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Determination of viscosity changes of protein hydrolyzate solutions depending on shear rate
Open Research DataRheological characteristics of connective tissue protein solutions were made on the basis of viscosity measurement using a Brookfield viscometer using LV SC4 - 27 spindles and shear rate of 85 s-1 (Fig. 1). Solutions of protein hydrolysates with a concentration of 2% in 0.5M acetic acid were prepared.
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The structurally similar TRFH domain of TRF1 and TRF2 dimers shows distinct behaviour towards TIN2
PublicationThe telomere repeat binding-factor 1 and 2 (TRF1 and TRF2) proteins of the shelterin complex bind to duplex telomeric DNA as homodimers, and the homodimerization is mediated by their TRFH (TRF-homology) domains. We performed molecular dynamic (MD) simulations of the dimer forms of TRF1TRFH and TRF2TRFH in the presence/absence of the TIN2TBM (TIN2, TRF-interacting nuclear protein 2, TBM, TRF-binding motif) peptide. The MD results...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field
PublicationSecondary structure is a solid scaffold on which the three-dimensional structure of a protein is built. Therefore, care must be taken to reproduce the secondary structure as accurately as possible in the simulations of protein systems. In this chapter, we summarize the physics-based energy terms that govern secondary-structure formation, the auxiliary restraints on secondary structure derived from bioinformatics and from the experimental...
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Water-mediated long-range interactions between the internal vibrations of remote proteins
PublicationIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
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Characterization of a cryptic plasmid pSFKW33 from Shewanella sp. 33b
PublicationA cryptic plasmid pSFKW33 from psychrotrophic bacterium Shewanella sp. 33B, an isolate from the Gulf of Gdansk (the Baltic Sea), was sequenced and characterized. It is an 8021 bpcircular molecule with 38% GC content, which shows a distinctive nucleotide sequence without homology to other known plasmids. The nucleotide sequence analysis predicts eight open reading frames. The deduced amino acid sequence of ORF-1 shared significant...
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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublicationAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
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Data on solutions of Hes1 system
Open Research DataHes1 protein (hairy and enhancer of split 1) belongs to the helix-loop-helix (bHLH) family of transcription proteins, i.e. DNA-binding proteins in the promoter region or in another region where regulation of transcription processes occurs. The database collects data on solutions of the Hes1 systems with multiple binding sites and the dimer formation...
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Amyloid fibril formation in the presence of water structure-affecting solutes
PublicationThe impact of the differently hydrated non-electrolytes (protein structure destabilizers) on the fibrillation of hen egg white lysozyme (HEWL) was investigated. Two isomeric urea derivatives i.e. butylurea (BU) and N,N,N′,N′-tetramethylurea (TMU) were chosen as a tested compounds. The obtained results show that butylurea exerts greater impact on HEWL and its fibrillation than tetramethylurea. Both substances decrease the time of...
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The development of an indirect ELISA for the detection of goose parvovirus antibodies using specific VP3 subunits as the coating antigen
PublicationIn Poland, the leader in goose production in Europe, goose parovirus infection, or Derzsy’s disease (DD), must be reported to the veterinary administration due to the serious economic and epizootic threat to waterfowl production. Prophylactic treatment for DD includes attenuated live or inactivated vaccines. Moreover, the control of DD includes the monitoring of maternal derived antibody (MDA) levels in the offspring and antibody...
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Bodybuilders and high-level meat consumers’ behavior towards rabbit, beef, chicken, turkey, and lamb meat: A comparative review
PublicationIn bodybuilders’ diets, protein plays a crucial role in supporting muscle growth and repairing damaged muscle tissue. These individuals meet their protein needs by combining dietary sources with supplements. Animal-based proteins are often preferred over plant-based proteins because they are believed to better support muscle protein synthesis. This review explores the meat consumption patterns of bodybuilders and high-level meat...
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Construction, production and evaluation of the diagnostic utility of a recombinant Toxoplasma gondii chimeric antigen SAG1-SAG2-AMA1F
Open Research DataThe intracellular parasite Toxoplasma gondii has the ability to infect a wide range of warm-blooded animals, including humans. Currently, diagnosis of toxoplasmosis is based mainly on the use of the native antigens in enzyme immunoassay which allow for detection of IgG, IgM and IgA antibody classes. However, in some cases the performed studies give...
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Construction, production and evaluation of the diagnostic utility of a recombinant Toxoplasma gondii chimeric antigen SAG1-SAG2-MAG1L
Open Research DataThe intracellular parasite Toxoplasma gondii has the ability to infect a wide range of warm-blooded animals, including humans. Currently, diagnosis of toxoplasmosis is based mainly on the use of the native antigens in enzyme immunoassay which allow for detection of IgG, IgM and IgA antibody classes. However, in some cases the performed studies give...
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Fusion of DNA-binding domain of Pyrococcus furiosus ligase with TaqStoffel DNA polymerase as a useful tool in PCR with difficult targets
PublicationThe DNA coding sequence of TaqStoffel polymer- ase was fused with the DNA-binding domain of Pyrococcus furiosus ligase. The resulting novel recombinant gene was cloned and expressed in E. coli. The recombinant enzyme was purified and its enzymatic features were studied. The fusion protein (PfuDBDlig-TaqS) was found to have enhanced processivity as a result of the conversion of the Taq DNA polymerase from a relatively low processive...
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Overproduction of CaStr2p native and His-tag versions.
Open Research DataEnzyme of fungal L-methionine biosynthetic pathway: cystathionine-γ-synthase (CaStr2p) could be exploited as molecular target for antifungal chemotherapy. The goal of the study was to obtain conditions optimal for protein production with the use of prokaryotic cells. The constructed expression plasmids, designed in three different versions: encoding...
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Overproduction of CaMet15p native and His-tag versions.
Open Research DataEnzyme of fungal L-methionine biosynthetic pathway: O-acetylhomoserine sulfhydrylase (Met15p) could be exploited as molecular target for antifungal chemotherapy. The goal of the study was to obtain conditions optimal for protein production with the use of prokaryotic cells. The constructed expression plasmids, designed in three different versions: encoding...
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Overproduction of homoserine O-acetyltransferase (CaMet2p) native and His-tag versions.
Open Research DataEnzyme of fungal L-methionine biosynthetic pathway: homoserine O-acetyltransferase (Met2p) could be exploited as molecular target for antifungal chemotherapy. The goal of the study was to obtain conditions optimal for protein production with the use of prokaryotic cells. The constructed expression plasmids, designed in three different versions: encoding...
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Emulsification alters simulated gastrointestinal proteolysis of β-casein and β-lactoglobulin
PublicationWe have studied the effect of the adsorption of milk proteins at the oil-water interface on their digestibility in simulated gastrointestinal environment. The investigations aimed to characterize how both the breakdown of the adsorbed proteins and the interactions with physiological surfactants, phosphatidylcholine (PC) and bile salts (BS), influence structural transformations of model, protein-stabilized food emulsions in the...
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Extracting functional groups of ALLINI to design derivatives of FDA‐approved drugs: Inhibition of HIV‐1 integrase
PublicationHIV‐1 integrase (IN) is crucial for integration of viral DNA into the host genome and a promising target in development of antiretroviral inhibitors. In this work, six new compounds were designed by linking the structures of two different class of HIV‐1 IN inhibitors (active site binders and allosteric IN inhibitors (ALLINIs)). Among newly designed compounds, INRAT10b was found most potent HIV‐1 IN inhibitor considering different...
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DNA-reactive anticancer imidazoacridinone C-1311 is a new inhibitor of hypoxia-inducible factor 1 alpha, vascular endothelial growth factor and tumor angiogenesis
PublicationHypoxia-inducible factor 1 (HIF-1) plays a critical role for tumor adaptation to hypoxia and promotes angiogenesis. Antitumor imidazoacridinone C-1311 is a DNA reactive topoisomerase II and FLT3 receptor tyrosine kinase inhibitor selected for phase II clinical trials for breast cancer. Here, we demonstrate the new mechanism of C-1311 action involving HIF-1a, vascular endothelial growth factor (VEGF) and angiogenesis as additional...
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Triazoloacridone C-1305 impairs XBP1 splicing by acting as a potential IRE1α endoribonuclease inhibitor
PublicationInositol requiring enzyme 1 alpha (IRE1α) is one of three signaling sensors in the unfolding protein response (UPR) that alleviates endoplasmic reticulum (ER) stress in cells and functions to promote cell survival. During conditions of irrevocable stress, proapoptotic gene expression is induced to promote cell death. One of the three signaling stressors, IRE1α is an serine/threonine-protein kinase/endoribonuclease (RNase) that...
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Mechanism of Osmolyte Stabilization–Destabilization of Proteins: Experimental Evidence
PublicationIn this work, we investigated the influence of stabilizing (N,N,N-trimethylglycine) and destabilizing (urea) osmolytes on the hydration spheres of biomacromolecules in folded forms (trpzip-1 peptide and hen egg white lysozyme─hewl) and unfolded protein models (glycine─GLY and N-methylglycine─NMG) by means of infrared spectroscopy. GLY and NMG were clearly limited as minimal models for unfolded proteins and should be treated with...
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Solvation phenomena in ternary system tetramethylurea-methylacetamide-water: Insights from volumetric, compressibility and FTIR analysis
PublicationThe properties of the ternary systems N,N,N’,N’-tetramethylurea - N-methylacetamide - water were investigated using Fourier-transform infrared spectroscopy (FTIR), volumetric and compression measurements. Densities and sound velocities were determined in order to obtain the apparent molar volumes (VΦ) and apparent molar isentropic compressions (ΚS,Φ). These values were then extrapolated to infinite dilution. Additionally, interaction parameters...
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Functional similarities and differences among subunits of the nascent polypeptide-associated complex (NAC) of Saccharomyces cerevisiae
PublicationProtein factors bind ribosomes near the tunnel exit, facilitating protein trafficking and folding. In eukaryotes, the heterodimeric nascent polypeptide-associated complex (NAC) is the most abundant - equimolar to ribosomes. Saccharomyces cerevisiae has a minor β-type subunit (Nacβ2) in addition to abundant Nacβ1, and therefore two NAC heterodimers, α/β1 and α/β12. The additional beta NAC gene arose at the time of the whole genome...
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Scarabaeidae as human food – A comprehensive review
PublicationRising global population and sustainable protein demand have sparked interest in unique food sources. Entomophagy, or insect consumption, presents a solution and Scarab beetles, part of the Scarabaeidae family, offer a novel food option. The comprehensive review underscores their potential as human food, with strong nutrition, low environmental impact, and the ability to ease strain on conventional agriculture. Nutritional analysis...
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B-GALACTOSIDASE ARTHROBACTER SP. 32cB - OBTAINING THE GENE SEQUENCE, CONSTRUCTION OF THE EXPRESSION SYSTEM, BIOSYNTHESIS AND BIOCHEMICAL CHARACTERIZATION OF THE ENZYME
PublicationINTRODUCTION: β-Galactosidase is an enzyme which catalyzes the hydrolysis of O glycosidic bond in β-galactosides. Another activity of β galactosidase is a transglycosylation activity. The main industrial use of this protein is the hydrolysis of lactose in milk in a cooling conditions. Synthesis of galactooligosaccharides, which are mostly used as a prebiotics added to some foods or available as dietary supplements, is only one...
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Preparation and characterization of porous scaffolds from chitosan-collagen-gelatin composite
PublicationNovel porous scaffolds composed of chitosan, collagen and gelatin were prepared and characterized. For preparing scaffolds gelatin and collagen isolated from fish skins with various physicochemical properties were used. In order to reduce preparation solubility glutaraldehyde in the amount of 1%, w/w relative to the total biopolymers weight in solution was used. All obtained biomaterials showed a homogeneous porosity. Protein polymer...
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Hopf bifurcation in time‐delayed gene expression model with dimers
PublicationWe study a mathematical model of gene transcription and protein synthesis with negative feedback. We consider a system of equations taking into account the formation of dimers (i.e., complex formed by two protein monomers), the way in which dimers bind to DNA and time delay in translation process. For the model consisting of three ordinary differential equations with time delay, we derive conditions for stability of the positive...
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Early Stages of RNA-Mediated Conversion of Human Prions
PublicationPrion diseases are characterized by the conversion of prion proteins from a PrPC fold into a disease-causing PrPSC form that is self-replicating. A possible agent to trigger this conversion is polyadenosine RNA, but both mechanism and pathways of the conversion are poorly understood. Using coarse-grained molecular dynamic simulations we study the time evolution of PrPC over 600 μs. We find that both the D178N mutation and interacting...
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Cloning, expression, and biochemical characterization of a coldactive GDSL-esterase of a Pseudomonas sp. S9 isolated from Spitsbergen island soil
PublicationAn estS9 gene, encoding an esterase of the psychrotolerant bacterium Pseudomonas sp. S9 was cloned and sequenced. The deduced sequence revealed a protein of 636 amino acid residues with a molecular mass of 69 kDa.Further amino acid sequence analysis revealed that the EstS9 enzyme contained a G-D-S-L motif centered at a catalytic serine, an N-terminal catalytic domain and a C-terminal autotransporter domain. Two recombinant E. coli...
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Correlation between the number of Pro-Ala repeats in the EmrA homologue of Acinetobacter baumannii and resistance to netilmicin, tobramycin, imipenem and ceftazidime
PublicationAcinetobacter baumannii coccobacilli are dangerous to patients in intensive care units because of their multidrug resistance to antibiotics, developed mainly in the past decade. This study aimed to examine whether there is a significant correlation between the number of Pro-Ala repeats in the CAP01997 protein, the EmrA homologue of A. baumannii, and resistance to antibiotics. A total of 79 multidrug-resistant A. baumannii strains...
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Microencapsulation of fish oil – determination of optimal wall material and encapsulation methodology
PublicationFor the first time, we present a meta-analysis of experimental and literature data to determine which microencapsulation methodology, and which wall material are best suited to protect fish oil. Our analysis covered a period of several decades of research (1984–2018). The analysis was conducted on 196 literature data-points, and 16 data-points determined experimentally for this publication. PLS regression was used to determine...
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Effect of conventional cooking on changes in the contents of basic composition and glucosinolates in kale
PublicationBrassica vegetables have been strongly recommended as part of human diet because of its high content of bioactive sulphur compounds, eg glucosinolates. The nutrient and health promoting compounds in kale are significantly affected by traditional cooking. The study investigated changes in the levels of dry mass, ash, fat, total protein, dietary fibre as well as total and individual glucosinolates in the kale due to the traditional...
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Data regarding a new, vector-enzymatic DNA fragment amplification-expression technology for the construction of artificial, concatemeric DNA, RNA and proteins, as well as biological effects of selected polypeptides obtained using this method
PublicationApplications of bioactive peptides and polypeptides are emerging in areas such as drug development and drug delivery systems. These compounds are bioactive, biocompatible and represent a wide range of chemical properties, enabling further adjustments of obtained biomaterials. However, delivering large quantities of peptide derivatives is still challenging. Several methods have been developed for the production of concatemers –...