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Regulation of the First Committed Step in Lipopolysaccharide Biosynthesis Catalyzed by LpxC Requires the Essential Protein LapC (YejM) and HslVU Protease
PublicationWe previously showed that lipopolysaccharide (LPS) assembly requires the essential LapB protein to regulate FtsH-mediated proteolysis of LpxC protein that catalyzes the first committed step in the LPS synthesis. To further understand the essential function of LapB and its role in LpxC turnover, multicopy suppressors of ΔlapB revealed that overproduction of HslV protease subunit prevents its lethality by proteolytic degradation...
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Checkpoints that regulate balanced biosynthesis of lipopolysaccharide and its essentiality in Escherichia coli
PublicationThe outer membrane (OM) of Gram-negative bacteria, such as Escherichia coli, is essential for their viability. Lipopolysaccharide (LPS) constitutes the major component of OM, providing the permeability barrier, and a tight balance exists between LPS and phospholipids amounts as both of these essential components use a common metabolic precursor. Hence, checkpoints are in place, right from the regulation of the first committed step...
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The impact of hydrological research, municipal authorities, and residents on rainwater management in Gdańsk (Poland) in the process of adapting the city to climate change
PublicationAim of the study The city of Gdańsk faces changing climatic conditions that result in a higher frequency of extreme weather events. In response to the increasingly frequent appearance of flash floods, scientific research was carried out on changes in the probability of the occurrence of maximum daily precipitation in Gdańsk. The purpose of this paper is to show the role of hydrological research (science), decisions of local authorities...
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Flood-Triggering Rainfall and Potential Losses—The Copula-Based Approach on the Example of the Upper Nysa Kłodzka River
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Comparative Analysis of Developed Rainfall Intensity–Duration–Frequency Curves for Erbil with Other Iraqi Urban Areas
PublicationRainfall Intensity–Duration–Frequency (IDF) relationships are widely used in water infrastructure design and construction. IDF curves represent the relationship between rainfall intensity, duration, and frequency, and are obtained by analyzing observed data. These relationships are critical for the safe design of flood protection structures, storm sewers, culverts, bridges, etc. In this study, the IDF curves and empirical IDF formulas...
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Application of Multinomial Logistic Regression to Model the Impact of Rainfall Genesis on the Performance of Storm Overflows: Case Study
PublicationIn this study, a mathematical model was proposed to analyze the performance of storm overfows. The model included the infuence of rainfall genesis on the duration of storm overfow, its volume, and the maximum instantaneous fow. The multinomial logistic regression model, which has not been used so far to model objects located in a stormwater system, was proposed to simulate the duration of storm overfow. The Iman–Conover method,...
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Development of cluster analysis methodology for identification of model rainfall hyetographs and its application at an urban precipitation field scale
PublicationDespite growing access to precipitation time series records at a high temporal scale, in hydrology, and particularly urban hydrology, engineers still design and model drainage systems using scenarios of rainfall temporal distributions predefined by means of model hyetographs. This creates the need for the availability of credible statistical methods for the development and verification of already locally applied model hyetographs....
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Assessment of Trace Metals Leaching During Rainfall Events from Building Rooftops with Different Types of Coverage – Case Study
PublicationRunoff water is an important medium transporting various types of pollution originating from the atmosphere and washed out from roofing materials. The study presents a quality assessment of runoff from different roofs in the context of trace metal concentrations. The analysed rooftops were covered with copper, tar paper and ceramic tile. The quality of the rain water collected at the same time satisfies the demands of the first...
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Relationship between Visibility, Air Pollution Index and Annual Mortality Rate in Association with the Occurrence of Rainfall—A Probabilistic Approach
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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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Escherichia coli K-12 suppressor-free mutants lacking early glycosyltransferases and late acyltransferases. Minimal lipopolysaccharide structure and induction of envelope stress response.
PublicationTo elucidate the minimal lipopolysaccharide (LPS) structure needed for the viability of Escherichia coli, suppressor-free strains lacking either the 3-deoxy-d-manno-oct-2-ulosonic acid transferase waaA gene or derivatives of the heptosyltransferase I waaC deletion with lack of one or all late acyltransferases (lpxL/M/P) and/or various outer membrane biogenesis factors were constructed. Δ(waaC lpxL lpxM lpxP) and waaA mutants exhibited...
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On thinning ice: Effects of atmospheric warming, changes in wind speed and rainfall on ice conditions in temperate lakes (Northern Poland)
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Comparison of conductivity averaging methods for one-dimensional unsaturated flow in layered soils
PublicationW artykule przedstawiono numeryczne rozwiązania równania Richardsa, opisującego nieustalony przepływ wody w uwarstwionym gruncie nienasyconym. Przeanalizowano różne metody obliczania średniej przewodności hydraulicznej między węzłami siatki numerycznej oraz różne możliwości położenia węzłów względem granic warstw gruntu. Najlepsze wyniki otrzymano stosując metodę uśredniania stanowiącą adaptację wcześniejszej propozycji jednego...
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Multiple transcriptional factors regulate transcription of the rpoE gene in Escherichia coli under different growth conditions and when the lipopolysaccharide biosynthesis is defective.
PublicationThe RpoE sigma factor is essential for the viability of Escherichia coli. RpoE regulates extracytoplasmic functions including lipopolysaccharide (LPS) translocation and some of its non-stoichiometric modifications. Transcription of the rpoE gene is positively autoregulated by EσE and by unknown mechanisms that control the expression of its distally located promoter(s). Mapping of 5′ ends of rpoE mRNA identified five new transcriptional...
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Identification of Substrates of Cytoplasmic Peptidyl-Prolyl Cis/Trans Isomerases and Their Collective Essentiality in Escherichia Coli
PublicationProtein folding often requires molecular chaperones and folding catalysts, such as peptidyl-prolyl cis/trans isomerases (PPIs). The Escherichia coli cytoplasm contains six well-known PPIs, although a requirement of their PPIase activity, the identity of their substrates and relative enzymatic contribution is unknown. Thus, strains lacking all periplasmic and one of the cytoplasmic PPIs were constructed. Measurement of their PPIase...
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Multicopy Suppressor Analysis of Strains Lacking Cytoplasmic Peptidyl-Prolyl cis/trans Isomerases Identifies Three New PPIase Activities in Escherichia coli That Includes the DksA Transcription Factor
PublicationConsistent with a role in catalyzing rate-limiting step of protein folding, removal of genes encoding cytoplasmic protein folding catalysts belonging to the family of peptidyl-prolyl cis/trans isomerases (PPIs) in Escherichia coli confers conditional lethality. To address the molecular basis of the essentiality of PPIs, a multicopy suppressor approach revealed that overexpression of genes encoding chaperones (DnaK/J and GroL/S),...
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Dissection of σE‐dependent cell lysis in Escherichia coli: roles of RpoE regulators RseA, RseB and periplasmic folding catalyst PpiD
PublicationTo understand the mechanism of sigma(E)-dependent cell lysis, we examined the consequences of deletion derivatives of rpoE regulators rseA, rseB and rseC on sigma(E) transcription, on levels of free versus membrane-bound sigma(E) and on OMP-biogenesis limiting factor(s) that could impact cell lysis. RT-PCR showed that individual nonpolar DeltarseA and DeltarseB increased the rpoE expression to varying extents, with pronounced induction...
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Molecular and structural basis of inner core lipopolysaccharide alterations in Escherichia coli: incorporation of glucuronic acid and phosphoethanolamine in the heptose region.
PublicationIt is well established that lipopolysaccharide (LPS) often carries nonstoichiometric substitutions in lipid A and in the inner core. In this work, the molecular basis of inner core alterations and their physiological significance are addressed. A new inner core modification of LPS is described, which arises due to the addition of glucuronic acid on the third heptose with a concomitant loss of phosphate on the second heptose. This...
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Suppressors of lapC mutation identify new regulators of LpxC, which mediates the first committed step in lipopolysaccharide biosynthesis
PublicationGram-negative bacteria, such as Escherichia coli, are characterized by an asymmetric outer membrane (OM) with lipopolysaccharide (LPS) located in the outer leaflet and phospholipids facing the inner leaflet. E. coli recruits LPS assembly proteins LapB, LapC and LapD in concert with FtsH protease to ensure a balanced biosynthesis of LPS and phospholipids. We recently reported that bacteria either lacking the periplasmic domain of...
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A new factor LapD is required for the regulation of LpxC amounts and lipopolysaccharide trafficking
PublicationLipopolysaccharide (LPS) constitutes the major component of the outer membrane and is essential for bacteria, such as Escherichia coli. Recent work has revealed the essential roles of LapB and LapC proteins in regulating LPS amounts; although, if any additional partners are involved is unknown. Examination of proteins co-purifying with LapB identified LapD as a new partner. The purification of LapD reveals that it forms a complex...
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Upscaling unsaturated flow in binary porous media with air entry pressure effects
PublicationArtykuł dotyczy przepływu w gruntach nienasyconych, zawierających soczewki (inkluzje) materiału gruboziarnistego. Materiał inkluzji charakteryzuje się niższą wartością ciśnienia wejścia powietrza niż materiał tła. Podczas infiltracji część powietrza zostaje zamknięta w inkluzjach, po całkowitym wypełnieniu wodą materiału tła. Z drugiej strony, drenaż inkluzji rozpoczyna się dopiero wtedy, gdy przekroczone zostanie ciśnienie wejścia...
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Ellipsometric study of carbon nitride films deposited by DC-magnetron sputtering
PublicationWe report the optical properties of a carbon nitride (CNx) film as a function of nitrogen concentration (N/C) of the deposited film. As nitrogen concentration is increased (N/C ratio) in a CNx film, the refractive index and band gap also increase. The real and imaginary parts, n and k (refractive index and extinction coefficient) of the complex refraction index of carbon nitride films were determined by spectroscopic ellipsometry...
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Two-phase flow in heterogeneous porous media with non-wetting phase trapping
PublicationThis article presents amathematical model describing flowof two fluid phases in a heterogeneous porous medium. Zaproponowano model matematyczny przepływu dwufazowego w drobnoziarnistym ośrodku porowatym zawierającym inkluzje gruboziarniste. Inkluzje charakteryzują się niższą wartością ciśnienia wejścia dla płynu niezwilżającego (np. powietrze, ropa naftowa) niż materiał podstawowy. Podczas nawadniania takiego ośrodka dochodzi do...
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Influence of heterogeneous air entry pressure on large scale unsaturated flow in porous media
PublicationThe paper presents numerical simulations of water infiltration in unsaturated porous media containing coarse-textured inclusions embed- ded in fine-textured background material. The calculations are performed using the two-phase model for water and air flow and a simplified model known as the Richards equation. It is shown that the Richards equation cannot correctly describe flow in the presence of heterogeneities. How- ever, its...
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Ellipsometric study of carbon nitride films deposited by DC-magnetron sputtering
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An evaluation of endemic exposure of citizens living in near a Gdańsk Phosphatic Fertilizer Plant
PublicationPrzeprowadzono ocenę wpływu Gdańskich Zakładów Nawozów Fosforowych FOSFORY na mieszkańców różnych dzielnic Gdańska. Oznaczono - za pomocą Neutronowej Analizy Aktywacyjnej (NAA) stężenia Al, As, Au, Br, Ca, Cl, Cu, Dy, I, In, K, La, Mg, Mn, Mo, Na, S, Sb, Sm, U, V, Zn w próbkach włosów i paznokci stóp, zebranych od 22 osób mieszkających w sąsiedztwie Zakładów oraz od jedenastoosobowej grupy kontrolnej. Podstawowe różnice pomiędzy...
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Poziomy stężeń lotnych związków chlorowcoorganicznych w wodach opadowych na terenie dużej aglomeracji miejskiej = Measurement of volatile chloroorganic compounds in urban rainwater (Gdańsk, Sopot, Gdynia)
PublicationW 105 próbkach opadów atmosferycznych (deszcz, deszcz ze śniegiem) zebranych z terenu Trójmiasta w okresie od listopada 2000 r. do maja 2001 r. oznaczano chloro - i bromopochodne metanu, etanu i etenu (7 różnych związków). Najczęściej wykrywanymi i oznaczanymi były: chloroform i czterochlorek węgla, (bardzo popularne rozpuszczalniki stosowane jako środki chłodzące i czyszczące). Najwyższe stężenia obserwowano w przypadku chloroformu,...
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Immunization with an anti-idiotypic antibody against the broadly lipopolysaccharide-reactive antibody WN1 222-5 induces Escherichia coli R3-core-type specific antibodies in rabbits
PublicationThe mouse monoclonal antibody (mAb) WN1 222-5 recognizes a carbohydrate epitope in the inner core region of LPS that is shared by all strains of Escherichia coli and Salmonella enterica and is able to neutralize their endotoxic activity in vitro and in vivo. Immunization of mice with mAb WN1 222-5 yielded several anti-idiotypic mAbs one of which (mAb S81-19) competitively inhibited binding of mAb WN1 222-5 to E. coli and Salmonella...
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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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Modeling two phase flow in large scale fractured porous media with an extended multiple interacting continua method
PublicationWe present a two phase flow conceptual model, the corresponding simulator (2pMINC) and a workflow for large-scale fractured reservoirs, based on a continuum fracture approach which uses the multiple interacting continua (MINC) method complemented with an improved upscaling technique. The complex transient behavior of the flow processes in fractured porous media is captured by subgridding the coarse blocks in nested volume elements...
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Evaluation of occupational exposure in a slide bearings factory on the basis of urine and blood sample analyses
PublicationZbadano wpływ pracy w zakładach łożysk ślizgowych na zdrowie pracowników. Przeprowadzono analizę próbek moczu i krwi pobranych od 42 pracowników i 6 osób zatrudnionych w administracji przedsiębiorstwa, stanowiących grupę kontrolną. Oznaczono zawartość Al, Cu, Pb i Zn we krwi i moczu pracowników dwukrotnie, przed i po terapii za pomocą chelatowania, stosując ICP-MS oraz metodę dodatku wzorca. Istotność różnic w zawartości pierwiastków...
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Interaction of the conserved region 4.2 of sigma(E) with the RseA anti-sigma factor
PublicationEo-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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Assessment of atmospheric inorganic pollution in the urban region of Gdańsk, Northern Poland
PublicationProjekt wykonano w przemysłowej części Gdańska w celu zidentyfikowania głównych źródeł zanieczyszczeń. Próbki suchego oraz żywego (w hodowli hydroponicznej) mchu eksponowano równolegle w celu określenia ich właściwości kumulacji w aspekcie badań biomonitoringowych. Analizę chemiczną składu próbek mchu wykonano dzięki zastosowaniu techniki aktywacji neutronowej i reaktorze badawczym w Delft (Holandia). Uzyskane wyniki wskazują,...
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Nuclear Activation Methods in the Estimation of Environmental Pollution and the Assessment of the Industrial Plant Impact on the Citizens of Gdansk (Poland)
PublicationNeutronowa Analiza Aktywacyjna została wykorzystana do oceny stanu jakości powietrza atmosferycznego na podstawie badań analitycznych stopnia kumulacji zanieczyszczeń nieorganicznych w mchu torfowca, a także składu wód opadowych. Ponadto przedstawiono wyniki badań dotyczących szacowania ryzyka zawodowego pracowników zakładów przemysłowych na podstawie analizy próbek materiału biologicznego pobranego od osób narażonych.
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Assessment of phosphatic fertilizer production impact on occupational staff based on NAA of hair, nails, and inhald particles
PublicationW pracy przedstawiono wyniki badań nad wpływem zakładów fosforowych na zdrowie pracowników. W celu oszacowania narażenia zawodowego oznaczano 25 pierwiastków w próbkach włosów, paznokci i w cząstkach pyłu pobranych od pracowników i od grupy kontrolnej. Otrzymane wyniki badań porównano za pomocą testów statystycznych (t-studenta i nieparametrycznego testu U Manna - Whitneya).
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Crystal structures of the DsbG disulfide isomerase reveal an unstable disulfide
PublicationDsb proteins control the formation and rearrangement of disulfide bonds during the folding of secreted and membrane proteins in bacteria. DsbG, a member of this family, has disulfide bond isomerase and chaperone activity. Here, we present two crystal structures of DsbG at 1.7- and 2.0-Angstrom resolution that are meant to represent the reduced and oxidized forms, respectively. The oxidized structure, however, reveals a mixture...
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Reactive deposition of TiNx layers in a DC-magnetron discharge
PublicationTiNx layers have been deposited in 'balanced mode' and 'unbalanced mode' of a reactive DC-magnetron plasma (carrier gas argon, reactive gas nitrogen) under different conditions. Discharge power and reactive gas flow have been varied. The layers have been examined by X-ray photoelectron spectroscopy (XPS), X-ray reflectometry (XR), and spectroscopic ellipsometry (SE). The results of the layer analyses were combined with plasma investigations...
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Optical and chemical characterization of thin TiNx films deposited by DC-magnetron sputtering
PublicationThin titanium nitride (tinx) films were deposited on silicon substrates by means of a reactive dc-magnetron plasma. Layers were synthesized under various conditions of discharge power and nitrogen flows in two operation modes of the magnetron (the so-called "balanced" and "unbalanced" modes). The optical constants of the tinx films were investigated by spectroscopic ellipsometry (se). X-ray photoelectron spectroscopy (xps) was...
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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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Experimental and Numerical Analysis of Air Trapping in a Porous Medium with Coarse Textured Inclusions
PublicationThe paper presents a 2D upward infiltration experiment performed on a model porous medium consisting of fine sand background with two inclusions made of coarser sands. The purpose of the experiment was to investigate the effects of structural air trapping, which occurs during infiltration as a result of heterogeneous material structure. The experiment shows that a significant amount of air becomes trapped in each of the inclusions. Numerical...
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Deposition and characterization of organic polymer thin films using a dielectric barrier discharge with different C2Hm/N2 (m = 2, 4, 6) gas mixtures
PublicationOrganic polymer thin films have been deposited on Si(100) and aluminum coated glass substrates by a dielectric barrier discharge (DBD) operated at medium pressure using different C2Hm/N2 (m = 2, 4, 6) gas mixtures. The deposited films were characterized by various spectroscopic techniques. Fourier transform infrared reflection absorption spectroscopy (FT-IRRAS) revealed the chemical functional groups present in the films. The surface...
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Assessment of the impact of a phosphatic fertilizer plant on the adjecent environment using fuzzy logic
PublicationZbadano wpływ zakładów nawozów fosforowych na otaczające środowisko. W próbkach trawy i gleby oraz produktów i produktu ubocznego oznaczono wybrane pierwiastki ziem rzadkich, metale ciężkie i metaloidy. Zbadano rozkład stężeń pierwiastków oznaczonych w próbkach gleby i trawy wzdłuż południowego i wschodniego kierunku, porównując ją ze stężeniami oznaczonymi w glebie i trawie z terenu zakładów oraz w substratach i produktach. Wyniki...
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Fatty acyl benzamido antibacterials based on inhibition of DnaK-catalyzed protein folding
PublicationWe have reported that the hsp70 chaperone DnaK from Escherichia coli might assist protein folding by catalyzing the cis/trans isomerization of secondary amide peptide bonds in unfolded or partially folded proteins. In this study a series of fatty acylated benzamido inhibitors of the cis/trans isomerase activity of DnaK was developed and tested for antibacterial effects in E. coli MC4100 cells. Nα-[Tetradecanoyl-(4-aminomethylbenzoyl)]-l-asparagine...
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Dehydration converts DsbG crystal diffraction from low to high resolution
PublicationDiffraction quality crystals are essential for crystallographic studies of protein structure, and the production of poorly diffracting crystals is often regarded as a dead end in the process. Here we show a dramatic improvement of poorly diffracting DsbG crystals allowing high-resolution diffraction data measurement. Before dehydration, the crystals are fragile and the diffraction pattern is streaky, extending to 10 Å resolution....
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KU812 basophils express urocortin, CRH-R, MC1R and steroidogenic enzymes and secrete progesterone
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Effect of nitrogen doping on TiOxNy thin film formation at reactive high-power pulsed magnetron sputtering
PublicationThe paper is focused on a study of formation of TiOxNy thin films prepared by pulsed magnetron sputtering of metallic Ti target. Oxygen and nitrogen were delivered into the discharge in the form of reactive gases O2 and N2. The films were deposited by high-power impulse magnetron sputtering working with discharge repetition frequency f = 250 Hz at low (p = 0.75 Pa) and high (p = 10 Pa) pressure. The substrates were on floating...
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Spectroscopic Study of Plasma Polymerized a-C:H Films Deposited by a Dielectric Barrier Discharge
PublicationPlasma polymerized a-C:H thin films have been deposited on Si (100) and aluminum coated glass substrates by a dielectric barrier discharge (DBD) operated at medium pressure using C2Hm/Ar (m = 2, 4, 6) gas mixtures. The deposited films were characterized by Fourier transform infrared reflection absorption spectroscopy (FT-IRRAS), Raman spectroscopy, and ellipsometry. FT-IRRAS revealed the presence of sp3 and sp2 C–H stretching and...
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Discussion:Horizontal stress increase induced by deep vibratory compaction
PublicationDeep compaction control of granular material using the results of field tests. The analysis include the CPTU and DMT tests terformed before and after compaction works.
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Influence of reactive oxygen species during deposition of iron oxide films by high power impulse magnetron sputtering.
PublicationIron oxide films were deposited using high power impulse magnetron sputtering (HiPIMS) of an iron cathode in an argon/oxygen gas mixture at different gas pressures (0.5~Pa, 1.5~Pa, and 5.0~Pa). The HiPIMS system was operated at a repetition frequency $f = 100$~Hz with a duty cycle of 1~\%. A main goal is a comparison of film growth during conventional and electron cyclotron wave resonance-assisted HiPIMS. The deposition plasma...
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Role of size scale of ZnO nanoparticles and microparticles on toxicity toward bacteria and osteoblast cancer cells
PublicationThe specific role of size scale, surface capping, and aspect ratio of zinc oxide (ZnO) particles on toxicity toward prokaryotic and eukaryotic cells was investigated. ZnO nano and microparticles of controlled size and mor- phology were synthesized by wet chemical methods. Cytotoxicity toward mammalian cells was studied using a human osteoblast cancer cell line and antibacterial activity using Gram-negative bacteria (Escherichia...