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Search results for: NON-PROTEIN NITROGEN
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Role of nitrogen in optical and electrical band gaps of hydrogenated/hydrogen free carbon nitride film
PublicationWe report the optical and electrical band gap energy of amorphous hydrogenated carbon nitride (a-HCNx) and carbon nitride (a-CNx) as a function of nitrogen concentration (N/C). The optical band gap of a-HCNx and a-CNx films has been determined by means of Ellipsometry and UV-VIS. Both optical and electrical band gaps increase with elevated nitrogen concentration. Experimentally obtained electrical band gap is compared with the...
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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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Characteristics and fate of organic nitrogen in municipal biological nutrient removal wastewater treatment plants
PublicationThe aim of this study was to investigate the occurrence and fate of colloidal and dissolved organic nitrogen (CON and DON) across biological nutrient removal (BNR) activated sludge bioreactors. Primary and secondary effluent total nitrogen (TN) measurements and component fractionation, CON and DON concentration profiles across BNR bioreactors, and laboratory batch experiments with the process mixed liquor were carried out at several...
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Biomass-Derived Nitrogen Functionalized Carbon Nanodots and Their Anti-Biofouling Properties
PublicationThe prevalence of the antibiotic resistant bacteria remains a global issue. Cheap, sustainable and multifunctional antibacterial membranes are at the forefront of filtrating materials capable of treating multiple flow streams, such as water cleansing treatments. Carbon nanomaterials are particularly interesting objects shown to enhance antibacterial properties of composite materials. In this article, amino-functionalized, photoluminescent...
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Application of mechanistic and data-driven models for nitrogen removal in wastewater treatment systems
PublicationIn this dissertation, the application of mechanistic and data-driven models in nitrogen removal systems including nitrification and deammonification processes was evaluated. In particular, the influential parameters on the activity of the Nitrospira activity were assessed using response surface methodology (RSM). Various long-term biomass washout experiments were operated in two parallel sequencing batch reactor (SBR) with a different...
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Non-isolating bondage in graphs
PublicationA dominating set of a graph $G = (V,E)$ is a set $D$ of vertices of $G$ such that every vertex of $V(G) \setminus D$ has a neighbor in $D$. The domination number of a graph $G$, denoted by $\gamma(G)$, is the minimum cardinality of a dominating set of $G$. The non-isolating bondage number of $G$, denoted by $b'(G)$, is the minimum cardinality among all sets of edges $E' \subseteq E$ such that $\delta(G-E') \ge 1$ and $\gamma(G-E')...
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Effect of Functionalization of Reduced Graphene Oxide Coatings with Nitrogen and Sulfur Groups on Their Anti-Corrosion Properties
PublicationElectrophoretic production of anticorrosion carbonaceous coatings on copper could be successfully performed by anodic oxidation of negatively charged graphene platelets suspended in an aqueous solution. The various platelets were synthesized by Hummer’s method followed by a hydrothermal reduction in the presence of NH4SCN which was expected to substitute some parts of graphene structure with nitrogen and sulfur groups. X-ray photoelectron...
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Modeling the pH effects on nitrogen removal in the anammox-enriched granular sludge
PublicationThe aim of the study was to determine the pH effects on nitrogen removal in the anammox-enriched granular sludge. The experimental data were extracted from a 4L completely-mixed batch reactor with the granular sludge at different initial pH values (6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5) and constant temperature T=30℃. Simulations were run in GPS-X 6.4 using a comprehensive mechanistic model Mantis2. Two kinetic parameters, including...
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MODELING THE pH EFFECTS ON NITROGEN REMOVAL IN THE ANAMMOX-ENRICHED GRANULAR SLUDGE
PublicationThe aim of the study was to determine the pH effects on nitrogen removal in the anammox-enriched 10 granular sludge. The experimental data were extracted from a 4L completely-mixed batch reactor with the 11 granular sludge at different initial pH values (6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5) and constant temperature 12 T=30℃. Simulations were run in GPS-X 6.4 using a comprehensive mechanistic model Mantis2. Two 13 kinetic parameters,...
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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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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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Assembly of Lipopolysaccharide in Escherichia coli Requires the Essential LapB Heat Shock Protein
PublicationHere, we describe two new heat shock proteins involved in the assembly of LPS in Escherichia coli, LapA and LapB (lipopolysaccharide assembly protein A and B). lapB mutants were identified based on an increased envelope stress response. Envelope stress responsive pathways control key steps in LPS biogenesis and respond to defects in the LPS assembly. Accordingly, the LPS content in ΔlapB or Δ(lapA lapB) mutants was elevated, with...
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Coupling transformation of carbon, nitrogen and sulfur in a long-term operated full-scale constructed wetland
PublicationThe coupling transformation of carbon, nitrogen and sulfur compounds has been studied in lab-scale and pilot-scale constructed wetlands (CWs), but few studies investigated full-scale CW. In this study, we used batch experiments to investigate the potentials of carbon, nitrogen and sulfur transformation in a long-term operated, full-scale horizontal subsurface flow wetland. The sediments collected from the HSFW were incubated for...
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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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Salt melt synthesis of curved nitrogen-doped carbon nanostructures: ORR kinetics boost
PublicationImplementing metal-free electrocatalysts for the oxygen reduction reaction (ORR) and revealing crucial chemical or topographical parameters driving their activity are vital for the development of power cells. The carbon-based catalysts are very often synthesized through carbonization of biopolymers, in particular, those one containing nitrogen groups such as chitosan. Unfortunately, the resulting carbonaceous materials usually...
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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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Electrocatalytic nitrogen dioxide sensor.
PublicationOpisano konstrukcję i właściwości elektrokatalitycznego czujnika gazów na bazie domieszkowanego samarem tlenku ceru. Pomiary przeprowadzono w mieszaninie syntetycznego powietrza i dwutlenku azotu. Kształt odpowiedzi prądowo - napięciowej zależy od stężenia NO2.
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An advanced synergy of partial denitrification-anammox for optimizing nitrogen removal from wastewater: A review
PublicationAnammox is a widely adopted process for energy-efficient removal of nitrogen from wastewater, but challenges with NOB suppression and NO3− accumulation have led to a deeper investigation of this process. To address these issues, the synergy of partial denitrification and anammox (PD-anammox) has emerged as a promising solution for sustainable nitrogen removal in wastewater. This paper presents a comprehensive review of recent developments...
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Role of nitrogen in evolution of sp2/sp3 bonding and optical band gap in hydrogenated carbon nitride
PublicationDrastic changes in the bonding are found in amorphous hydrogenated carbon nitride (a-CNx:H) film as a function of nitrogen concentration (or N/C ratio). The total C-sp3 fraction and hardness shows a sharp decrease (at N/C = 0.40) whereas optical band gap and resistivity shows a gradual increase as nitrogen concentration increases from 0.07 to 0.58. Raman spectrum of a-CNx:H film is fitted with both Gaussian (integrated intensity...
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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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Influence of composition of raw wastewater on removal of nitrogen compounds in multistage treatment wetlands
PublicationInfluence of composition of raw wastewater on the efficiency of organic matter and nitrogen removal in multistage treatment wetlands has been examined. Commonly used indicators, like COD/BOD5 and BOD5/TN ratio, determining wastewater susceptibility to biodegradation in conventional treatment technologies were assessed. It was confirmed that multistage treatment wetland may be used for treatment of wastewater with high loads of...
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Temperature Impact of Nitrogen Transformation in Technological System: Vertical Flow Constructed Wetland and Polishing Pond
PublicationThe article describes the results of the research, purpose of which was to evaluate influence of the temperature on the effectiveness of nitrification and denitrification in the sewage treatment system consisting of vertical flow constructed wetland and polishing pond. During the analysed period, the efficiency of removing total nitrogen was low and amounted to 12.7%. In the polishing pond in the summer period, content of total...
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A highly thermostable, homodimeric single-stranded DNA-binding protein from Deinococcus radiopugnans
PublicationWe report the identification and characterization of the single-stranded DNA-binding protein (SSB) from the mesophile and highly radiation-resistant Deinococcus radiopugnans (DrpSSB). PCR-derived DNA fragment containing the complete structural gene for DrpSSB protein was cloned and expressed in Escherichia coli. The gene consisting of an open reading frame of 900 nucleotides encodes a protein of 300 amino acids with a calculated...
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Nitrogen-Incorporated Boron-Doped Nanocrystalline Diamond Nanowires for Microplasma Illumination
PublicationThe origin of nitrogen-incorporated boron-doped nanocrystalline diamond (NB-NCD) nanowires as a function of substrate temperature (Ts) in H2/CH4/B2H6/N2 reactant gases is systematically addressed. Because of Ts, there is a drastic modification in the dimensional structure and microstructure and hence in the several properties of the NB-NCD films. The NB-NCD films grown at low Ts (400 °C) contain faceted diamond grains. The morphology...
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Non-isolating 2-bondage in graphs
PublicationA 2-dominating set of a graph G=(V,E) is a set D of vertices of G such that every vertex of V(G)D has at least two neighbors in D. The 2-domination number of a graph G, denoted by gamma_2(G), is the minimum cardinality of a 2-dominating set of G. The non-isolating 2-bondage number of G, denoted by b_2'(G), is the minimum cardinality among all sets of edges E' subseteq E such that delta(G-E') >= 1 and gamma_2(G-E') > gamma_2(G)....
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The Protein Folding Problem
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Impact of aeration conditions on the removal of low concentrations of nitrogen in a tertiary partially aerated biological filter
PublicationA submerged biological aerated filter (BAF) partially aerated was used to study the removal of low concentrations of ammonia nitrogen (0.3 g N/m3 to 30.5 g N/m3) typically found in nutrient enriched river and lake waters, and treated effluents. Four series of experiments were performed with a synthetic wastewater at ammonia loading rates between 6 g N/m3 d and 903 g N/m3 d and C/N ratios from 2 to 20. The results showed that ammonia...
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Electrical and noise responses of carbon nanotube networks enhanced by UV light for nitrogen dioxide sensing
Open Research DataNetworks consisting of randomly oriented carbon nanotubes (CNN) were investigated toward nitrogen dioxide detection by means of electrical and low-frequency noise measurements. UV-activation of CNN layers improved gas sensitivity and reduced the limit of detection, especially by employing 275 nm-LED. This data set includes DC resistance measurements...
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublicationAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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Justification of quasi-stationary approximation in models of gene expression of a self-regulating protein
PublicationWe analyse a model of Hes1 gene transcription and protein synthesis with a negative feedback loop. The effect of multiple binding sites in the Hes1 promoter as well as the dimer formation process are taken into account. We consider three, possibly different, time scales connected with: (i) the process of binding to/dissolving from a binding site, (ii) formation and dissociation of dimers, (iii) production and degradation of Hes1...
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PROTEIN AND PEPTIDE LETTERS
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Zarządzanie organizacjami non profit NSTC 24/25
e-Learning Courses -
Zarządzanie organizacjami non profit 23/24 STC
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Fractionation and origin of dissolved and colloidal organic nitrogen in BNR plant effluent
PublicationThe characteristics of effluent dissolved and colloidal organic nitrogen (DON and CON) as well as their origin, fate and biodegradability in wastewater treatment plants and receiving waters were identified as the major issues that limit the ability to achieve low total N in the effluent. This study presents the results of a comprehensive survey, which was conducted in eight biological nutrient removal (BNR) WWTPs in northern Poland....
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
PublicationRNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA....
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X-ray and UV Radiation Damage of dsDNA/Protein Complexes
PublicationRadiation 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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Electrical responses of nanoporous NiO films for light-activated nitrogen dioxide and acetone gas sensing
Open Research DataThe chemoresistive sensor response of nanoporous NiO films prepared by advanced gas deposition was investigated with and without simultaneous light irradiation, to detect nitrogen dioxide and acetone gases. The presented data show electrical responses presented as sensor resistance or relative changes in sensor resistance under selected environment...
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CURRENT PROTEIN & PEPTIDE SCIENCE
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Journal of Non-Oxide Glasses
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Non-coding RNA Research
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Current Protocols in Protein Science
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JOURNAL OF NON-EQUILIBRIUM THERMODYNAMICS
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Non-Coding RNA Investigation
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Non-linear FEM analysis of pounding-involved response of buildings under non-uniform earthquake excitation
PublicationThe aim of the paper is to show the results of the study investigating the influence of non-uniform earthquake excitation, due to spatial seismic effects connected with the propagation of seismic wave, on the pounding-involved response of two buildings. The three-dimensional non-linear FEM analysis has been conducted using the detailed models of colliding structures. Acceleration records for different structural supports have been...
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublicationWe present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups...
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Evolution towards simplicity in bacterial small heat shock protein system
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 two...