Variable Substrate Research Articles

Frequency of irrigation with saline water in sugar-apple seedlings produced on substrate with polymer

ABSTRACT The objective of this work was to evaluate the growth of sugar-apple seedlings under irrigation management with saline water in a substrate with soil amendment. Treatments were obtained from the arrangement between polymer doses (0, 0.2, 0.6, 1.0 and 1.2 g dm-3) and levels of irrigation water electrical conductivity (0.3, 1.1, 2.7, 4.3 and 5.0 dS m-1), associated with irrigation frequencies (daily and every alternate day), and two additional treatments to evaluate container volume (1.30 and 0.75 dm3), using a randomized complete block design, with four replicates. At 120 days after sowing, the variables substrate salinity, stem diameter, plant height, number of leaves and Dickson quality index were determined. Data were submitted to analyses of variance, regression and contrast. Substrate salinity increased with the increase in irrigation water electrical conductivity and polymer doses. Growth and quality of the seedlings were reduced with increasing irrigation water salinity, and highest values of the variables were obtained in seedlings under daily irrigation. Container with larger volume led to higher growth. The use of hydrated polymer at the adopted levels had no effect on growth and quality of seedlings, requiring further studies. To produce sugar-apple seedlings with better quality, irrigation frequency should be daily and water electrical conductivity should be lower than 2 dS m-1.

An alkali tolerant α-l-rhamnosidase from Fusarium moniliforme MTCC-2088 used in de-rhamnosylation of natural glycosides

Analkali tolerant α-l-rhamnosidase has been purified to homogeneity from the culture filtrate of a new fungal strain, Fusarium moniliforme MTCC-2088, using concentration by ultrafiltration and cation exchange chromatography on CM cellulose column. The molecular mass of the purified enzyme has been found to be 36.0 kDa using SDS-PAGE analysis. The Km value using p-nitrophenyl-α-l-rhamnopyranoside as the variable substrate in 0.2 M sodium phosphate buffer pH10.5 at50 °C was 0.50 mM. The catalytic rate constant was15.6 s−1giving the values of kcat/Km is 3.12 × 104M−1 s−1. The pH and temperature optima of the enzyme were 10.5 and 50 °C, respectively. The purified enzyme had better stability at 10 °C in basic pH medium. The enzyme derhamnosylated natural glycosides like naringin to prunin, rutin to isoquercitrin and hesperidin to hesperetin glucoside. The purified α-l-rhamnosidase has potential for enhancement of wine aroma.

Stabilizing a homoclinic stripe

For a large class of reaction-diffusion systems with large diffusivity ratio, it is well known that a two-dimensional stripe (whose cross-section is a one-dimensional homoclinic spike) is unstable and breaks up into spots. Here, we study two effects that can stabilize such a homoclinic stripe. First, we consider the addition of anisotropy to the model. For the Schnakenberg model, we show that (an infinite) stripe can be stabilized if the fast-diffusing variable (substrate) is sufficiently anisotropic. Two types of instability thresholds are derived: zigzag (or bending) and break-up instabilities. The instability boundaries subdivide parameter space into three distinct zones: stable stripe, unstable stripe due to bending and unstable due to break-up instability. Numerical experiments indicate that the break-up instability is supercritical leading to a 'spotted-stripe' solution. Finally, we perform a similar analysis for the Klausmeier model of vegetation patterns on a steep hill, and examine transition from spots to stripes.This article is part of the theme issue 'Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 2)'.

Metabolic modeling and response surface analysis of an Escherichia coli strain engineered for shikimic acid production

BackgroundClassic metabolic engineering strategies often induce significant flux imbalances to microbial metabolism, causing undesirable outcomes such as suboptimal conversion of substrates to products. Several mathematical frameworks have been developed to understand the physiological and metabolic state of production strains and to identify genetic modification targets for improved bioproduct formation. In this work, a modeling approach was applied to describe the physiological behavior and the metabolic fluxes of a shikimic acid overproducing Escherichia coli strain lacking the major glucose transport system, grown on complex media.ResultsThe obtained flux distributions indicate the presence of high fluxes through the pentose phosphate and Entner-Doudoroff pathways, which could limit the availability of erythrose-4-phosphate for shikimic acid production even with high flux redirection through the pentose phosphate pathway. In addition, highly active glyoxylate shunt fluxes and a pyruvate/acetate cycle are indicators of overflow glycolytic metabolism in the tested conditions. The analysis of the combined physiological and flux response surfaces, enabled zone allocation for different physiological outputs within variant substrate conditions. This information was then used for an improved fed-batch process designed to preserve the metabolic conditions that were found to enhance shikimic acid productivity. This resulted in a 40% increase in the shikimic acid titer (60 g/L) and 70% increase in volumetric productivity (2.45 gSA/L*h), while preserving yields, compared to the batch process.ConclusionsThe combination of dynamic metabolic modeling and experimental parameter response surfaces was a successful approach to understand and predict the behavior of a shikimic acid producing strain under variable substrate concentrations. Response surfaces were useful for allocating different physiological behavior zones with different preferential product outcomes. Both model sets provided information that could be applied to enhance shikimic acid production on an engineered shikimic acid overproducing Escherichia coli strain.

Role of Musa paradisiaca ascorbate peroxidase in the transformation of methyl phenyl sulfide to its sulfoxide

An ascorbate peroxidase from a new source Musa paradisiaca leaf juice has been purified to homogeneity using a simple procedure involving concentration by ultra filtration and anion exchange chromatography on diethyl amino ethyl [DEAE] cellulose column. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis [SDS-PAGE] analysis of the purified enzyme has shown a single protein band of molecular mass 208.9 kDa which has been confirmed by native-PAGE and intact mass analysis by mass spectrometry. The Km and kcat values of the enzyme using ascorbate and H2O2 as the variable substrates were 0.13 m mol L−1, 40.42 s−1 and 0.23 m mol L−1, 27.24 s−1, respectively. The pH and temperature optima of the enzyme were 7.0 and 298 K, respectively. The enzyme transformed approximately 97% methyl phenyl sulfide to its sulfoxide. The product was racemic mixture.

Studying and Simulation of a Different Formation of U Shape with T and L shapes of Plasmonic Nanoantennas with Variable Substrates

Studying and Simulation of a Different Formation of U Shape with T and L shapes of Plasmonic Nanoantennas with Variable Substrates

Studying and Simulation of a Different Formation of U Shape with T and L Shapes of Plasmonic Nanoantennas With Variable Substrates

Studying and Simulation of a Different Formation of U Shape with T and L Shapes of Plasmonic Nanoantennas With Variable Substrates

Optimization of Nutrition Therapy with the Use of Calorimetry to Determine and Control Energy Needs in Mechanically Ventilated Critically Ill Patients: The ONCA Study, a Randomized, Prospective Pilot Study.

Adequate nutrition therapy in critically ill patients poses a challenge because of the variable energy and substrate needs. The objective was to investigate whether nutrition therapy involving indirect calorimetry (IC), instead of equations for assessment of energy needs, could improve the nutrition status of critically ill patients. Forty mechanically ventilated patients were randomized into a group in which energy needs were controlled by calorimetry (IC group) and a group treated with a formula-based approach reflecting standard care (SC group). The primary outcome was change in the phase angle (PhA), a bioelectrical impedance parameter related to nutrition status and prognosis. The mean IC-based energy requirement was lower than the formula-based estimate (21.1 ± 6.4 versus [vs] 25kcal/kg/d, P < .01). The IC group reached 98% ± 8% of the energy goal, whereas the SC group reached only 79% ± 29% (P < 0.05), although mean intake was similar in both groups. The protein intake goal was better met in the IC group (91% ± 24%) than the SC group (73% ± 33%). The PhA of the IC group did not change during treatment, whereas that of the SC group tended to decrease by 0.36° ± 0.86° (P = .077). A shorter length of stay in intensive care was observed in the IC than in the SC group (13 ± 8 vs 24 ± 20 days, P < .05). Intensified individual nutrition therapy involving IC appears to be useful for improving nutrition status in critically ill patients.

Piezoelectric modulation of nonlinear optical response in BaTiO3 thin film

We study the nonlinear optical response in a strained thin film ferroelectric oxide BaTiO3 using piezoelectric Pb(Mg1/3Nb2/3)O3-PbTiO3 (001) as a variable strain substrate and La-doped SrTiO3 as a conductive buffer layer. The rotation-anisotropic second harmonic intensity profile shows hysteretic modulation corresponding to the strain variation from the inverse piezoelectric response of the substrate. An enhancement of 15% is observed at 1.2 kV/cm, while a control sample shows negligible change as a function of piezovoltage. Reflection high-energy electron diffraction, x-ray photoelectron spectroscopy, and high-resolution scanning transmission electron microscopy reveal the epitaxial interface. X-ray diffraction and piezoresponse force microscopy confirm tetragonal distortion and ferroelectricity of the BaTiO3 overlayer. Our results suggest a promising route to enhance the performance of nonlinear optical oxides for the development of future nano-opto-mechanical devices.

Hydrological Performance and Runoff Water Quality of Experimental Green Roofs

Within the scope of the conducted experiment the authors analysed the efficiency of runoff reduction by the system of extensive type green roofs. The observations were based on storm events in the area of Lower Silesia at the Agro and Hydrometeorology Station Wrocław-Swojec. The authors analysed the thickness of plant substrate, and also estimated the quality of runoff waters under the conditions of periodic atmospheric deposition. Also considered were such indicators as electrolytic conductivity, N, NO3−, NO2−, NH4+, P, PO43−. The experiment included roof substrates designed in two variants, with known hydraulic and physical properties of the soil material. The analysis was performed for models with vegetation layer based on pumice and zelolite, covered with five plant species from the sedum family. The modelling of the hydraulic properties was conducted with variably saturated medium, using the Hydrus 1D software. The performance of systems with primary layer thickness of 11 cm and 9, 8, 7, 6 and 5 cm was estimated. The designed models reduced the average peak flows to 89%, and in addition they caused a delay in the initiation of the runoff which was dependent on the intensity and distribution of rainfalls in time, and on the initial moisture of the profiles. Simulations, performed for variable substrate thickness, permit the conclusion that in the case of thin-layer profiles (5 cm), the relative retention index was decidedly lower and amounted to 35.9% for the substrate with zeolite (originally 60.6%) and 41% for the substrate with pumice (originally 65.7%). In the case of total nitrogen and phosphates, statistical analysis revealed significant differences (p &lt; 0.05) in relation to specific concentrations in the rainwater and in the control surface. The total nitrogen in the runoff from the green roof was nearly twice as high as that in the rainwater and amounted to, on average, 8.3 mg L−1.

Bandgap Engineering in $$\hbox {TiO}_{2}$$ TiO 2 –Ge Nanocomposite Thin Films

Titanium dioxide–germanium ( $$\hbox {TiO}_{2}$$ –Ge) composite thin films were prepared by pulse laser deposition technique using third harmonic (355 nm) of Nd:YAG laser at fluence of $$12.73\,\hbox {J/cm}^{2}$$ . Films were grown on n-type Si (100) substrate using $$\hbox {TiO}_{2}$$ –Ge composite target. The bandgap was tailored by varying the composition of $$\hbox {TiO}_{2}$$ –Ge composite films based on the variable substrate–target distance from 5–8 cm. Ge concentration in $$\hbox {TiO}_{2}$$ matrix was measured through electron-dispersive X-ray spectroscopy and concentration variation from 0.9–25.3% was observed. Crystalline structure of thin films was analysed through X-ray diffraction, whereas micro-strains and dislocation density is also calculated through different X-ray diffraction peaks. A detailed study of the various polymorphs of $$\hbox {TiO}_{2}$$ and presence of Ge in crystalline form was carried out through Raman spectroscopy. Direct and indirect absorption transitions were observed through ultraviolet and visible spectroscopy. Absorption edge shifted to visible region of electromagnetic spectrum is associated with a possible quantum confinement effect in Ge or strain generated due to lattice mismatch of Si substrate and Ge with $$\hbox {TiO}_{2}$$ . Absorption transitions of thin film containing 2.6% Ge were observed in visible region along with the emission in the same spectral region observed through photoluminescence spectra.

What's a picture really worth? On the use of drone aerial imagery to estimate intertidal rocky shore mussel demographic parameters

Describing distribution patterns of organisms on the rocky intertidal zone is crucial to generate ecological models of broad scope and validity. Our aim was to combine 3D photogrammetric models and spectral analysis derived from aerial images, with ground-based quadrat sampling to provide realistic measurements of mussel (Mytilus galloprovincialis) density, size and reproductive output. A remotely piloted aircraft (drone) was used to conduct intertidal photographic surveys during low tides (<0.4 m) over 8 study sites along the Portuguese central west coast. At each site, high pixel resolution photographs were collected at 30 m altitude (82–247 photographs, 80% overlap, with a ground spatial resolution of approximately 0.8 cm/pixel), encompassing an average intertidal area of 15200 m2 per survey location. A mosaic was created from the images and these were georeferenced and a 3D photogrammetric model was constructed for each location. An analysis of the spectral signature for the different ground cover types was used to perform a maximum likelihood supervised classification with overall high classification accuracy (86.5% ± 4.3%, mean ± SD). Additionally, we analysed the effect of environmental variables (substrate complexity and wave exposure) on mussel density on rocky substrate and size. Maximum mussel density occurred at intermediate values of wave exposure while smaller sized mussels were found at high values of wave exposure. Density, size and reproductive output maps were predicted for the study region. This information allows the validation of metapopulation models dealing with the persistence of spatially-structured populations within patchy habitats and so enables the management of pivotal conservation areas.

Transitions in DNA polymerase β μs-ms dynamics related to substrate binding and catalysis.

DNA polymerase β (pol β) plays a central role in the DNA base excision repair pathway and also serves as an important model polymerase. Dynamic characterization of pol β from methyl-TROSY 13C-1H multiple quantum CPMG relaxation dispersion experiments of Ile and Met sidechains and previous backbone relaxation dispersion measurements, reveals transitions in μs-ms dynamics in response to highly variable substrates. Recognition of a 1-nt-gapped DNA substrate is accompanied by significant backbone and sidechain motion in the lyase domain and the DNA binding subdomain of the polymerase domain, that may help to facilitate binding of the apoenzyme to the segments of the DNA upstream and downstream from the gap. Backbone μs-ms motion largely disappears after formation of the pol β–DNA complex, giving rise to an increase in uncoupled μs-ms sidechain motion throughout the enzyme. Formation of an abortive ternary complex using a non-hydrolyzable dNTP results in sidechain motions that fit to a single exchange process localized to the catalytic subdomain, suggesting that this motion may play a role in catalysis.

Claw morphometrics in monitor lizards: Variable substrate and habitat use correlate to shape diversity within a predator guild.

Numerous studies investigate morphology in the context of habitat, and lizards have received particular attention. Substrate usage is often reflected in the morphology of characters associated with locomotion, and, as a result, claws have become well‐studied ecomorphological traits linking the two. The Kimberley predator guild of Western Australia consists of 10 sympatric varanid species. The purpose of this study was to quantify claw size and shape in the guild using geometric morphometrics, and determine whether these features correlated with substrate use and habitat. Each species was assigned a Habitat/substrate group based on the substrate their claws interact with in their respective habitat. Claw morphometrics were derived for both wild caught and preserved specimens from museum collections, using a 2D semilandmark analysis. Claw shape significantly separated based on Habitat/substrate group. Varanus gouldii and Varanus panoptes claws were associated with sprinting and extensive digging. Varanus mertensi claws were for shallow excavation. The remaining species’ claws reflected specialization for some form of climbing, and differed based on substrate compliance. Varanus glauerti was best adapted for climbing rough sandstone, whereas Varanus scalaris and Varanus tristis had claws ideal for puncturing wood. Phylogenetic signal also significantly influenced claw shape, with Habitat/substrate group limited to certain clades. Positive size allometry allowed for claws to cope with mass increases, and shape allometry reflected a potential size limit on climbing. Claw morphology may facilitate niche separation within this trophic guild, especially when considered with body size. As these varanids are generalist predators, morphological traits associated with locomotion may be more reliable candidates for detecting niche partitioning than those associated directly with diet.

Structural basis for Acinetobacter baumannii biofilm formation

Acinetobacter baumannii-a leading cause of nosocomial infections-has a remarkable capacity to persist in hospital environments and medical devices due to its ability to form biofilms. Biofilm formation is mediated by Csu pili, assembled via the "archaic" chaperone-usher pathway. The X-ray structure of the CsuC-CsuE chaperone-adhesin preassembly complex reveals the basis for bacterial attachment to abiotic surfaces. CsuE exposes three hydrophobic finger-like loops at the tip of the pilus. Decreasing the hydrophobicity of these abolishes bacterial attachment, suggesting that archaic pili use tip-fingers to detect and bind to hydrophobic cavities in substrates. Antitip antibody completely blocks biofilm formation, presenting a means to prevent the spread of the pathogen. The use of hydrophilic materials instead of hydrophobic plastics in medical devices may represent another simple and cheap solution to reduce pathogen spread. Phylogenetic analysis suggests that the tip-fingers binding mechanism is shared by all archaic pili carrying two-domain adhesins. The use of flexible fingers instead of classical receptor-binding cavities is presumably more advantageous for attachment to structurally variable substrates, such as abiotic surfaces.

Ellipsometry-based combination of isothermal sorption-desorption measurement and temperature programmed desorption technique: A probe for interaction of thin polymer films with solvent vapor.

An environmental chamber equipped with an in situ spectroscopic ellipsometer, programmatic vapor pressure control, and variable temperature substrate holder has been designed for studying polymer coating behavior during an exposure to a solvent vapor and also for probing the residual solvent in the film afterwards. Both sorption-desorption cycle at a constant temperature and temperature programmed desorption (TPD) of the residual solvent manifest themselves as a change of the film thickness. Monitoring of ellipsometric angles of the coating allows us to determine the thickness as a function of the vapor pressure or sample temperature. The solvent vapor pressure is precisely regulated by a computer-controlled pneumatics. TPD spectra are recorded during heating of the film in an oil-free vacuum. The vapor pressure control system is described in detail. The system has been tested on 6-170 nm thick polystyrene, poly(methyl methacrylate), and poly(2-vinyl pyridine) films deposited on silicon substrates. Liquid toluene, water, ethanol, isopropanol, cyclohexane, 1,2-dichloroethane, and chlorobenzene were used to create a vapor atmosphere. Typical sorption-desorption and TPD curves are shown. The instrument achieves sub-monolayer sensitivity for adsorption studies on flat surfaces. Polymer-solvent vapor systems with strong interaction demonstrate characteristic absorption-desorption hysteresis spanning from vacuum to the glass transition pressure. Features on the TPD curves can be classified as either glass transition related film contraction or low temperature broad contraction peak. Typical absorption-desorption and TPD dependencies recorded for the 6 nm thick polystyrene film demonstrate the possibility to apply the presented technique for probing size effects in extremely thin coatings.

Subthreshold Modeling of Tri-Gate Junctionless Transistors With Variable Channel Edges and Substrate Bias Effects

In this paper, subthreshold channel potential, current, swing, threshold voltage, and drain-induced barrier lowering models of short-channel tri-gate junctionless field-effect transistors are presented. The models incorporate the effects of both substrate-induced surface potential and variable edges of channel. The quasi-3-D approach is used for the modeling of minimum of channel potential that is subsequently used in the drift–diffusion equation to obtain the current expression in subthreshold regime. Threshold voltage and subthreshold swing models are also based on the minimum of channel potential. The analytical results are compared with the simulation data obtained using 3-D visual TCAD device simulator from Cogenda Pvt., Ltd.

Portable standoff spectrometer for hazard identification using integrated quantum cascade laser arrays from 65 to 11 µm

This article presents new spectroscopic results in standoff chemical detection that are enabled by monolithic arrays of Distributed Feedback (DFB) Quantum Cascade Lasers (QCLs), with each array element at a slightly different wavelength than its neighbor. The standoff analysis of analyte/substrate pairs requires a laser source with characteristics offered uniquely by a QCL Array. This is particularly true for time-evolving liquid chemical warfare agent (CWA) analysis. In addition to describing the QCL array source developed for long wave infrared coverage, a description of an integrated prototype standoff detection system is provided. Experimental standoff detection results using the man-portable system for droplet examination from 1.3 meters are presented using the CWAs VX and T-mustard as test cases. Finally, we consider three significant challenges to working with droplets and liquid films in standoff spectroscopy: substrate uptake of the analyte, time-dependent droplet spread of the analyte, and variable substrate contributions to retrieved signals.

Mechanistic and structural insights into the in vitro inhibitory action of hypericin on glutathione reductase purified from baker's yeast.

This work aims at studying the interaction between glutathione reductase (GR) and hypericin. The type of inhibition was determined by measuring changes in GR activity at increasing concentrations of hypericin as well as at varying concentrations of glutathione disulfide (GSSG) and nicotinamide adenine dinucleotide phosphate (NADPH), and the binding pose of hypericin was predicted by molecular docking. Accordingly, hypericin emerges as an effective inhibitor of GR. When the variable substrate is GSSG, the type of inhibition is competitive. When the variable substrate is NADPH, however, the type of inhibition appears to be linear mixed-type competitive. Our computational analyses suggest that hypericin binds in the large intermonomer cavity of GR, and that it may interfere with the normal positioning/functioning of the redox-active disulfide center at the enzyme's active site. Overall, besides its contributory role in promoting oxidative stress via the formation of reactive oxygen species in photodynamic therapy, hypericin can also weaken cancer cells through inhibiting GR.

Characterization of AiiK, an AHL lactonase, from Kurthia huakui LAM0618T and its application in quorum quenching on Pseudomonas aeruginosa PAO1

N-Acyl homoserine lactones (AHLs) act as the key quorum sensing (QS) signal molecules in gram-negative bacteria, which coordinates gene expression and then activates various processes, including biofilm formation and production of virulence factors in some pathogens. Quorum quenching (QQ), which is the inactivation of the signal molecules by means of enzymatic degradation or modification, inhibits the processes of QS rather than killing the pathogens and is a promising antipathogenic strategy to control the bacterial pathogens. In this study, an AHL lactonase gene (named aiiK) was cloned from Kurthia huakuii LAM0618T and the AHL lactonase AiiK was expressed by Escherichia coli. AiiK exhibits a variable substrate spectrum and efficient degradation of the AHL compounds. The enzyme assays demonstrated that AiiK behaves as an AHL lactonase that can hydrolyze the lactone bond of the AHLs. The total hydrolytic efficiency of AiiK for C10-HSL is 3.9 s−1·mM−1. AiiK can also maintain 20% activity after 12 h incubation at 37 °C and demonstrate great resistance to α-chymotrypsin, trypsin, and protease K. Furthermore, AiiK significantly inhibits the biofilm formation and attenuates extracellular proteolytic activity and pyocyanin production of Pseudomonas aeruginosa PAO1, which indicates the potential application of AiiK as a biocontrol agent or an anti-pathogenic drug.