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Wyniki wyszukiwania dla: PROTEINS
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CaZnO-based nanoghosts for the detection of ssDNA, pCRISPR and recombinant SARS-CoV-2 spike antigen and targeted delivery of doxorubicin
PublikacjaOverexpression of proteins/antigens and other gene-related sequences in the bodies could lead to significant mutations and refractory diseases. Detection and identification of assorted trace concentrations of such proteins/antigens and/or gene-related sequences remain challenging, affecting different pathogens and making viruses stronger. Correspondingly, coronavirus (SARS-CoV-2) mutations/alterations and spread could lead to overexpression...
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Impact of high-pressure processing on the bioactive compounds of milk - A comprehensive review
PublikacjaHigh-pressure processing (HPP) is a promising alternative to thermal pasteurization. Recent studies highlighted the effectivity of HPP (400–600 MPa and exposure times of 1–5 min) in reducing pathogenic microflora for up to 5 logs. Analysis of modern scientific sources has shown that pressure affects the main components of milk including fat globules, lactose, casein micelles. The behavior of whey proteins under HPP is very important...
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Characterization of Bioactivity of Selective Molecules in Fruit Wines by FTIR and NMR Spectroscopies, Fluorescence and Docking Calculations
PublikacjaFourier transform infrared (FTIR) and proton nuclear magnetic resonance (1H NMR) spectroscopies were applied to characterize and compare the chemical shifts in the polyphenols’ regions of some fruit wines. The obtained results showed that FTIR spectra (1800–900 cm−1) and 1H NMR (δ 6.5–9.3 ppm) of different fruit wines can be used as main indices of the year of vintage and quality of fruit wines. In addition to the classical determination...
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Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli
PublikacjaDr fimbriae are homopolymeric adhesive organelles of uropathogenic Escherichia coli composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond...
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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
PublikacjaIn 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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A mechanistically approached review upon assorted cell lines stimulated by athermal electromagnetic irradiation
PublikacjaThe probable influence of electromagnetic irradiation on cancer treatment has been deduced from the interaction of artificial electromagnetic emissions with biological organisms. Nonetheless, the suspected health effects induced by electromagnetic-based technology imply that such a treatment may contaminate the adjacent healthy cells. Thus, gaining mechanistic insights into the problem is required to avoid athermal health hazards....
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A new division of bacterial UvrA homologues
PublikacjaThe UvrA protein is a DNA-binding and damage-recognition enzyme which participates in the prokaryotic type nucleotide excision repair (NER) pathway. It has recently been noted that some bacterial genomes comprise additional uvrA genes which encode five distinct types of UvrA homologue. We investigated the sequences of over 2400 bacterial genomes and found 130 examples of bacteria containing uvrA 2 genes. The sequence analyses conducted...
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Proteomic and Metabolomic Changes in Psoriasis Preclinical and Clinical Aspects
PublikacjaSkin diseases such as psoriasis (Ps) and psoriatic arthritis (PsA) are immune-mediated inflammatory diseases. Overlap of autoinflammatory and autoimmune conditions hinders diagnoses and identifying personalized patient treatments due to different psoriasis subtypes and the lack of verified biomarkers. Recently, proteomics and metabolomics have been intensively investigated in a broad range of skin diseases with the main purpose...
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The hydration of the protein stabilizing agents: trimethylamine-N-oxide, glycine and its N-methylderivatives - the volumetric and compressibility studies
PublikacjaThe densities at T = (288.15, 293.15, 298.15, 303.15, and 308.15) K and sound velocities at T = 298.15 K have been measured for aqueous solutions of trimethylamine-N-oxide, glycine, N-methylglycine (sarcosine), N,N-dimethylglycine, N,N,N-trimethylglycine (betaine). From these data the apparent molar volumes, VΦ, the apparent molar isentropic compressions, KS,Φ, and the solvation numbers of solutes have been determined. The concentration...
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Antifungal dipeptides incorporating an inhibitor of homoserine dehydrogenase
PublikacjaThe antifungal activity of 5‐hydroxy‐4‐oxo‐L‐norvaline (HONV), exhibited under conditions mimicking human serum, may be improved upon incorporation of this amino acid into a dipeptide structure. Several HONV‐containing dipeptides inhibited growth of human pathogenic yeasts of the Candida genus in the RPMI‐1640 medium, with minimal inhibitory concentration values in the 32 to 64 μg mL−1 range. This activity was not affected by multidrug...
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The impact of lipophilicity on environmental processes, drug delivery and bioavailability of food components
PublikacjaLipophilic properties of the compound allow to predict its fate in living organisms and to propose the models of chemicals transport and accumulation in the ecosystem. Lipophilicity is also useful as the characteristic of chemicals in respect to their optimal attributes for specific biological and non-biological tasks. The lipophilicity descriptors define the potency of endo- and xenobiotics to metabolic transformations and their...
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Characterization of a single-stranded DNA-binding-like Protein from Nanoarchaeum equitans - a nucleic acid binding protein with broad substrate specificity
PublikacjaBackground SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized,...
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Characterization of a cryptic plasmid pSFKW33 from Shewanella sp. 33b
PublikacjaA 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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PARP inhibition potentiates the cytotoxic activity of C-1305, a selective inhibitor of topoisomerase II, in human BRCA1-positive breast cancer cells
PublikacjaTwo cellular proteins encoded by the breast and ovarian cancer type 1 susceptibility (BRCA1 and BRCA2) tumor suppressor genes are essential for DNA integrity and the maintenance of genomic stability.Approximately 5-10% of breast and ovarian cancers result from inherited alterations or mutations in these genes.Remarkably, BRCA1/BRCA2-deficient cells are hypersensitive to selective inhibition of poly(ADPribose) polymerase 1 (PARP-1),...
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Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity
PublikacjaWater molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel...
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Protein thermal stabilization in aqueous solutions of osmolytes
PublikacjaProteins’ 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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Cell-penetrating peptides – mechanism of transduction and synthesis – short review
PublikacjaPotential antimicrobial agents may be effective if they are delivered efficiently to their site of action. In many cases, lack of permeability through the cell membrane is the main problem. One of the possible solutions could be a novel intracellular delivery system involving cell-penetrating peptides (CPPs), which may improve the efficiency of many new biophar-maceuticals. Among other things, CPPs are capable of trans-porting...
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Inhibition of amyloid fibril formation of hen egg white lysozyme by trimethylamine N-oxide at low pH
PublikacjaIn vitro inhibition of the formation of fibrous aggregates of proteins (amyloids) has gained increasing attention due to the number of diseases associated with protein misfolding and fibrillation. An interesting group of compounds for which pronounced activity against this phenomenon can be expected consists of low molecular weight substances (osmolytes) which have the ability to change protein stability. Here we investigate the...
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Partial characterization of three Korean white lotus cultivars
PublikacjaThe nutritional and bioactive values of Korean white lotus cultivars (Muan, Chungyang, and Garam)extracted with methanol, water, and acetone solvents were evaluated by the contents of their bioactive compounds and antioxidant activity determined by ABTS, CUPRAC, FRAP, DPPH, and β-carotene-linoleic acid assays. HPLC, fluorometry, and FTIR spectroscopy were employed for evaluation of polyphenols and fatty acids. All lotus cultivar...
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Computational methods for calculation of binding free energy for ligand-receptor complexes
PublikacjaAccurate description of the molecular complexes energetic influence is required for understanding of many biological functions carried out by proteins. Therefore, estimation of binding free energy for ligand-receptor complexes is of highest importance for structure-based ligand design and drug discovery approaches.Experimental methods of determination of difference in Gibbs'es free energy have many limitations. Thus, computational...
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Effect of convection and microwave heating on the retention of bioactive components in human milk
PublikacjaBioactive substances are very important components of human milk (HM), especially for premature newborns. The effects of convection (CH) and microwave heating (MWH) at 62.5 and 66 °C, on the level of selected bioactive components of HM: lysozyme (LZ), lactoferrin (LF), secretory immunoglobulin A (sIgA), basal lipase (BL), cytokine TGF-2, vitamin C and total antioxidant capacity (TAC) was compared. Regardless of the used heating methods...
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Ligand-Modified Boron-Doped Diamond Surface: DFT Insights into the Electronic Properties of Biofunctionalization
PublikacjaWith the increasing power of computation systems, theoretical calculations provide a means for quick determination of material properties, laying out a research plan, and lowering material development costs. One of the most common is Density Functional Theory (DFT), which allows us to simulate the structure of chemical molecules or crystals and their interaction. In developing a new generation of biosensors, understanding the nature...
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Peptide dendrimers as antifungal agents and carriers for potential antifungal agent—N3‐(4‐methoxyfumaroyl)‐(S)‐2,3‐ diaminopropanoic acid—synthesis and antimicrobial activity
PublikacjaA series of peptide dendrimers and their conjugates with antimicrobial agent FMDP (N3‐(4‐methoxyfumaroyl)‐(S)‐2,3‐diamino‐propanoic acid) were synthesized. The obtained compounds were tested for the antibacterial and antifungal activity. All novel dendrimers displayed much better activity against the tested strains than FMDP itself. Moreover, their conjugates with FMDP also exhibited antimicrobial activity. The most promising molecules...
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Interaction of the conserved region 4.2 of sigma(E) with the RseA anti-sigma factor
PublikacjaEo-E RNA polymerase transcribes a regulon of folding factors for the bacterial envelope and is induced by physical and chemical stresses. The RseA anti-sigma factor inhibits the activity of Esigma(E) RNA, polymerase. It is shown here that the N-terminal portion of sigma(E), residues 1-153, binds core RNA polymerase. RseA interacts with residues 154-191 of sigma(E), a site that is homologous to region 4, the sigma factor binding...
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X-ray and UV Radiation Damage of dsDNA/Protein Complexes
PublikacjaRadiation and photodynamic therapies are used for cancer treatment by targeting DNA. However, efficiency is limited due to physico-chemical processes and the insensitivity of native nucleobases to damage. Thus, incorporation of radio- and photosensitizers into these therapies should increase both efficacy and the yield of DNA damage. To date, studies of sensitization processes have been performed on simple model systems, e.g.,...
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Chiral Pyrazolo[4,3-e][1,2,4]triazine Sulfonamides—Their Biological Activity, Lipophilicity, Protein Affinity, and Metabolic Transformations
PublikacjaReferring to our previous laboratory results related to the tyrosinase and urease inhibition by pyrazolo[4,3-e][1,2,4]triazine sulfonamides, we examined here in silico the mechanism of action at the molecular level of the investigated pyrazolotriazine sulfonamides by the molecular docking method. The studied compounds being evaluated for their cytotoxic effect against cancer cell lines (MCF-7, K-562) and for recombinant Abl and...
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General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublikacjaThe 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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The optimal mixture of Toxoplasma gondii recombinant antigens (GRA1, P22, ROP1) for diagnosis of ovine toxoplasmosis
PublikacjaToxoplasmosis, caused by Toxoplasma gondii, is the major parasitic disease affecting sheep. Infection not only results in significant reproductive losses in these animals, but has public health implications since consumption of infected meat can facilitate zoonotic transmission. Although several serological tests are currently used for diagnosis of ovine toxoplasmosis, production of reliable reagents is a constraint and therefore...
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MutS3: a MutS homologue of unknown biological function
PublikacjaThe homologues of MutS proteins are widespread among both Prokaryotes and Eukaryotes. MutS designated as MutS1 is a part of MMR (mismatch repair) system which is responsible for removal of mispaired bases and small insertion/deletion loops in DNA. Initially, the only MutS homologues known were those engaged in mismatch repair and these were later designated as MutS1. Subsequently, the MutS2 homologue was distinguished. MutS2 does...
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Biofilm formation and its regulation in Staphylococcus aureus
PublikacjaInfections caused by the major human and animal pathogen, Staphylococcus aureus are becoming an important problem due to its emerging resistance mechanisms and variety of virulence factors. Biofilm formation is considered to be one of the most important factor attributed to high pathogenicity of S. aureus. Described in the literature methods used in identification of biofilm forming abilities of bacteria consist of phenotypic and...
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Toxoplasma gondii recombinant antigens as tools for serodiagnosis of human toxoplasmosis: current status of studies
PublikacjaToxoplasma gondii is a parasitic protozoan which is the cause of toxoplasmosis. Although human toxoplasmosis in healthy adults is usually asymptomatic, serious disease can occur in the case of congenital infections and immunocompromised individuals. Furthermore, despite the exact recognition of its etiology, it still presents a diagnostic problem. Diagnosis of toxoplasmosis is mainly based on the results of serological tests detecting...
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Genetic predisposition to inflammatory bowel disease
PublikacjaInflammatory bowel disease (IBD) is a chronic, incurable inflammatory disease of the digestive system. The two main disease entities included in the IBD are ulcerative colitis and Crohn's disease. According to epidemiological studies there are more and more new cases every year. In especially among the youngest patients with symptoms of malnutrition and growth inhibition to land up in hospitalwith cancer suspected. The purpose...
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Synthesis of amides under microwave irradiation
PublikacjaAmides belong to the most important carboxylic acid derivatives. They are constituents of natural compounds like peptides and proteins. They found applications in many branches of science and industry, especially in pharmaceutical and polymer science. Conventional procedures for amide preparation involve reaction between amine and carboxylic acid or their more active derivatives such as acid chlorides, acid anhydrides or esters....
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9,10-Dioxoanthracenyldithiocarbamates effectively inhibit the proliferation of non-small cell lung cancer by targeting multiple protein tyrosine kinases
PublikacjaAnthraquinones have attracted considerable interest in the realm of cancer treatment owing to their potent anticancer properties. This study evaluates the potential of a series of new anthraquinone derivatives as anticancer agents for non-small-cell lung cancer (NSCLC). The compounds were subjected to a range of tests to assess their cytotoxic and apoptotic properties, ability to inhibit colony formation, pro-DNA damage functions,...
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In silico epitope prediction of Borrelia burgdorferi sensu lato antigens for the detection of specific antibodies
PublikacjaDespite many years of research, serodiagnosis of Lyme disease still faces many obstacles. Difficulties arise mainly due to the low degree of amino acid sequence conservation of the most immunogenic antigens among B. burgdorferi s.l. genospecies, as well as differences in protein production depending on the environment in which the spirochete is located. Mapping B-cell epitopes located on antigens allows for a better understanding...
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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublikacjaGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublikacjaIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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Cancer immune escape: the role of antigen presentation machinery
PublikacjaThe mechanisms of antigen processing and presentation play a crucial role in the recognition and targeting of cancer cells by the immune system. Cancer cells can evade the immune system by downregulating or losing the expression of the proteins recognized by the immune cells as antigens, creating an immunosuppressive microenvironment, and altering their ability to process and present antigens. This review focuses on the mechanisms...
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Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublikacjaPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
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Structural changes of a simple peptide—Trpzip-1—in aqueous solutions and the corresponding hydration phenomena under the influence of temperature
PublikacjaTrpzip-1, a simple β-hairpin, is a rare example of peptide with stable secondary structure and can be a convenient model to study temperature-related processes that potential prion or amyloid proteins undergo. Although its sequence is simple, the exact processes which the peptide undergoes in aqueous solutions are quite complex and not well understood. The selection of well-established experimental (DSC, FTIR) and theoretical methods...
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By-Products from Food Industry as a Promising Alternative for the Conventional Fillers for Wood–Polymer Composites
PublikacjaThe present paper describes the application of two types of food-industry by-products, brewers’ spent grain (BSG), and coffee silverskin (ŁK) as promising alternatives for the conventional beech wood flour (WF) for wood–polymer composites. The main goal was to investigate the impact of partial and complete WF substitution by BSG and ŁK on the processing, structure, physicochemical, mechanical, and thermal properties of resulting...
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Chicken feather keratin as a source of bioactive peptides useful in prevention of metabolic disorders – in silico and in vitro hydrolysis
PublikacjaProtein derived bioactive peptides not only serve as nutrients but can also exert drug-like activity, e.g. antidiabetic, antihypertensive, or antimicrobial, to name a few. Most biopeptides have beneficial effects on health that make them attractive for nutraceutical applications. The majority of bioactive peptides have been obtained from food proteins, but protein-rich by-products generated by agriculture...
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A new human IgG avidity test, using mixtures of recombinant antigens (rROP1, rSAG2, rGRA6), for the diagnosis of difficult-to-identify phases of toxoplasmosis
PublikacjaThe preliminary diagnostic utility of two mixtures of Toxoplasma gondii recombinant antigens (rROP1+rSAG2 and rROP1+rGRA6) in IgG ELISA and IgG avidity test has been evaluated. A total of 173 serum samples from patients with toxoplasmosis and seronegative people were examined. The sensitivity of IgG ELISA for rROP1+rSAG2 and rROP1+rGRA6 was 91.1% and 76.7%, respectively, while the reactivity for sera from patients where acute toxoplasmosis...
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In vitro antioxidative and binding properties of phenolics in traditional, citrus and exotic fruits
PublikacjaMany polyphenols bind proteins, therefore our research was focused on the potential of protein binding to polyphenols of investigated fruits and their health-related effects. The contents of polyphenols and related antioxidant activities of traditional, citrus and exotic fruits were compared. The presence of polyphenols (flavonoids and phenolic acids) in the investigated samples and their interaction with human serum albumin (HSA)...
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Studies on applicability of new solid-phase microextraction fibers for the selective extraction and determination of short - chain monocarboksylic acids
PublikacjaShort-chain monocarobxylic acids, sometimes referred to as volatile fatty acids (VFA), are a group of low molecular weight alkyl monocarboxylic acids that are widely distributed within the environment. These molecules contain any from 2 to 8 carbon atoms and originate from the anaerobic biodegradation of organic matter such as carbohydrates, proteins, and fats. These compounds are commonly found in the effluents from animal farming,...
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Cyanogenic Compounds and Estrogen Disruptors
PublikacjaBalanced diet consists largely of plants containing cyanogenic compounds in the form of the more common cyanogenic glycosides and sometimes lipids. Maize, wheat, rye, apples, barley, oats, sugar cane and yet many other plants consumed by humans contain cyanogenic compounds. However the risk of poisoning is negligible as it is very easy to remove the toxic HCN by grinding and drying in air or soaking in water and an additional...
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Genetic and pharmacologic proteasome augmentation ameliorates Alzheimer’s-like pathology in mouse and fly APP overexpression models
PublikacjaThe proteasome has key roles in neuronal proteostasis, including the removal of misfolded and oxidized proteins, presynaptic protein turnover, and synaptic efficacy and plasticity. Proteasome dysfunction is a prominent feature of Alzheimer’s disease (AD). We show that prevention of proteasome dysfunction by genetic manipulation delays mortality, cell death, and cognitive deficits in fly and cell culture AD models. We developed...
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublikacjaThe 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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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
PublikacjaThe structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA...
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MP3vec: A Reusable Machine-Constructed Feature Representation for Protein Sequences
Publikacja—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...