Polymeric microspheres as support to co-immobilized Agaricus bisporus and Trametes versicolor laccases and their application in diazinon degradation

The laccase enzymes of Agaricus bisporus and Trametes versicolor were successfully covalently co-immobilized on poly(glycidyl methacrylate) microspheres. The enzyme load reached after the co-immobilization of both enzymes was 6.75 U g⁻¹ carrier. The resulting biocatalyst showed the combined properties of both immobilized enzymes, increasing their optimum pH and temperature ranges. The storage and operational stabilities were also improved after co-immobilization. In presence of mediator (ABTS) the organophosphate pesticide diazinon was 100% biodegraded after 48 h of reaction with 0.2 U/mL of co-immobilized enzymes (at the two maximum activity pH values: 2.0 and 3.0). In the absence of a mediator, the degradation percentages were above 88%. Data showed that, compared with single enzymatic immobilization, the co-immobilization of the two laccases is an easy, efficient, and low cost alternative to expanding the range of work of the biocatalyst, thereby improving the stability and some biochemical properties to generate a powerful alternative for pesticide degradation in a wide range of conditions.     

MALDI-FTICR MS Imaging as a Powerful Tool to Identify Paenibacillus Antibiotics Involved in the Inhibition of Plant Pathogens

Nowadays, microorganisms are more and more often used as biocontrol agents for crop protection against diseases. Among them, bacteria of Bacillus and Paenibacillus genders are already used as commercial biocontrol agents. Their mode of action is supposed to be related to their production of antibiotics, such as cyclic lipopeptides, which exhibit great antimicrobial activities. We chose to work with a Paenibacillus polymyxa strain (Pp56) very resistant to various microorganisms. The bacteria were grown simultaneously with Fusarium oxysporum and we applied matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance (MALDI-FTICR) mass spectrometry to identify the antibiotics compounds present in the fungus growth inhibition area. We, therefore, identified fusaricidins A, B, and C and numerous members of the LI-F antibiotics family. MALDI-FTICR mass spectrometry imaging was then used to follow the diffusion of lipopeptides involved in the inhibitory activity over time. We analyzed the molecular content of the inhibitory area at different Pp56 and Fusarium incubation durations and concluded that some lipopeptides such as fusaricidin B and a mixture of LI-F05b/06b/08a were mainly involved in the defense mechanism of Pp56. Our study confirms that MALDI imaging may be a powerful tool to quickly determine which molecular species is involved in an antagonism with another microorganism, avoiding time-consuming steps of extraction, purification, and activity tests, which are still commonly used in microbiology.

Peptidyl-Resin Substrates as a Tool in the Analysis of Caspase Activity

Caspases, proteolytic enzymes belonging to the group of cysteine proteases, play a crucial role in apoptosis. Understanding their activity and substrate specificity is extremely important. Fluorescence-based approaches, including fluorogenic substrates, are generally used to confirm cleavage preferences. Here we present a new method of substrate specificity and activity analysis based on the application of fix-charge tagged peptides located on the resin. The proteolysis of peptide bond on the resin, occurring even with low efficiency, results in the formation of N-terminal fragments of model peptide containing ionization enhancers in the form of quaternary ammonium groups, allowing for ultrasensitive and reliable analysis by LC-MS/MS. The possibility of application of the proposed solution was tested through the analysis of substrate specificity and activity of caspase 3 or 7. The obtained results confirm the known substrate specificity of executioner caspases. Our solution also allowed us to observe that caspases can hydrolyze peptides shorter than those presented to date in the scientific literature.     

Computing and Interpreting Specific Production Rates in a Chemostat in Steady State According to the Luedeking-Piret model

The Luedeking–Piret model is an empirical relationship which is very widely used in cell cultures to evaluate specific production rates of some products (metabolites or others). It constitutes a very common method of calculation as much in fundamental as in applied research and especially for designing and optimizing industrial processes in very varied fields. However, this model appears to be frequently deficient and has to be greatly adapted, practically, one might say, for each individual case. Obviously, this is a very great drawback, requiring a great deal of time spent on it and one that greatly lessens the ‘universality’ of the model. This work reveals that it is possible to give the initial Luedeking–Piret model a much more general scope. The used method revealed metabolic switches that have never been suspected until now. Confirmation of the method would certainly give a precious general tool both to optimize production processes and to increase understanding of some physiological states of cells in chemostat.     

Dynamic Environments as a Tool to Preserve Desired Output in a Chemical Reaction Network

Current efforts to design functional molecular systems have overlooked the importance of coupling out-of-equilibrium behaviour with changes in the environment. Here, the authors use an oscillating reaction network and demonstrate that the application of environmental forcing, in the form of periodic changes in temperature and in the inflow of the concentration of one of the network components, removes the dependency of the periodicity of this network on temperature or flow rates and enforces a stable periodicity across a wide range of conditions. Coupling a system to a dynamic environment can thus be used as a simple tool to regulate the output of a network. In addition, the authors show that coupling can also induce an increase in behavioural complexity to include quasi-periodic oscillations.     

FTIR Spectroscopy as a Tool to Study Age-Related Changes in Cardiac and Skeletal Muscle of Female C57BL/6J Mice

Studying aging is important to further understand the molecular mechanisms underlying this physiological process and, ideally, to identify a panel of aging biomarkers. Animals, in particular mice, are often used in aging studies, since they mimic important features of human aging, age quickly, and are easy to manipulate. The present work describes the use of Fourier Transform Infrared (FTIR) spectroscopy to identify an age-related spectroscopic profile of the cardiac and skeletal muscle tissues of C57BL/6J female mice. We acquired ATR-FTIR spectra of cardiac and skeletal muscle at four different ages: 6; 12; 17 and 24 months (10 samples at each age) and analyzed the data using multivariate statistical tools (PCA and PLS) and peak intensity analyses. The results suggest deep changes in protein secondary structure in 24-month-old mice compared to both tissues in 6-month-old mice. Oligomeric structures decreased with age in both tissues, while intermolecular β-sheet structures increased with aging in cardiac muscle but not in skeletal muscle. Despite FTIR spectroscopy being unable to identify the proteins responsible for these conformational changes, this study gives insights into the potential of FTIR to monitor the aging process and identify an age-specific spectroscopic signature.     

Ultracentrifuge as a Versatile Tool to Study Preferential Interaction of Polymers in Mixed Solvents

Abstract

Over the past five decades the analytical ultracentrifuge has been a versatile tool in the study of macromolecules and colloidal particles. Several textbooks [1–4] and review articles [5–10] deal with experimental techniques and theories for complete characterization of macromolecular species. However, the first published articles on the analytical ultracentrifuge dealt with the analysis of particle size distributions in suspensions of inorganic colloids. The emphasis has now shifted to organic polymers following the discovery that a large number of such polymers exist in nature. Before the development of the ultracentrifuge, the existence of such giant molecules was not recognized; the molecular kinetic units of proteins and of high organic polymers in solution were simply thought of as clusters of much smaller molecules, forming particles of undefined mass. Beginning with the elegant investigations of Svedberg [11, 12] on ultracentrifugation, such substances were revealed to be macromolecules, large because they contain a huge number of atoms connected together by primary chemical bonds [13]. Following a long and fruitful series of investigations in the early twenties and thirties, Svedberg wrote in one of his articles [12], “the proteins are built up of particles possessing the hallmark of individuality and therefore are in reality giant molecules. We have reason to believe that the particles in the protein solutions and the protein crystals are built up according to a plan which makes every atom in them indispensable for the completion of the structure.” Almost at the same time, it was Staudinger [14] who clearly demonstrated that substances such as polystyrene and natural rubber exist in solution without change in molecular weight regardless of the solvent employed .     

Non-thermal Plasma as a Priming Tool to Improve the Yield of Pea in Outdoor Conditions

Seed priming is a pre-treatment of seeds leading to the improvement of their germination, the plant growth, and the product yield. In this study we investigated the possibility of the use of non-thermal plasma operating in atmospheric pressure air for seed priming with the objective to improve the yield of pea seeds. Two priming ways were used: an indirect way by using plasma activated water (PAW) generated by the transient spark discharge with water electrospray or the glow discharge batch treatment and a direct exposure of seeds to the pulsed corona discharge. After treatment, the seeds were planted in the outdoor field for about 14 weeks until harvest. The direct plasma treatment resulted in two key results: the strong effectiveness of the pulsed corona plasma improving the yield, and the long-term effect of the plasma seed treatment. The results of the indirect treatment showed that the pea plants from the seeds primed using PAW gained some improved growth parameters, especially the number of seeds per pod and the total number of seeds per plant. The scanning electron microscopy analysis showed that PAW and direct treatment induced some morphology changes at the surface of the pea seeds. This study documents a long-term effect of non-thermal plasma seed priming and contributes to the plasma agriculture applications by suggesting the implementation of non-thermal plasma direct or indirect treatments into the field.

     

X-Ray Crystallography as a Tool to Determine Three-Dimensional Structures of Commercial Enzymes Subjected to Treatment in Pressurized Fluids

The study of enzyme function often involves a multi-disciplinary approach. Several techniques are documented in the literature towards determining secondary and tertiary structures of enzymes, and X-ray crystallography is the most explored technique for obtaining three-dimensional structures of proteins. Knowledge of three-dimensional structures is essential to understand reaction mechanisms at the atomic level. Additionally, structures can be used to modulate or improve functional activity of enzymes by the production of small molecules that act as substrates/cofactors or by engineering selected mutants with enhanced biological activity. This paper presentes a short overview on how to streamline sample preparation for crystallographic studies of treated enzymes. We additionally revise recent developments on the effects of pressurized fluid treatment on activity and stability of commercial enzymes. Future directions and perspectives on the the role of crystallography as a tool to access the molecular mechanisms underlying enzymatic activity modulation upon treatment in pressurized fluids are also addressed.     

Photoreactive DNA as a Tool to Study Replication Protein A Functioning in DNA Replication and Repair

Replication protein A (RPA), eukaryotic single-stranded DNA-binding protein, is a key player in multiple processes of DNA metabolism including DNA replication, recombination and DNA repair. Human RPA composed of subunits of 70-, 32- and 14-kDa binds ssDNA with high affinity and interacts specifically with multiple proteins. The RPA heterotrimer binds ssDNA in several modes, with occlusion lengths of 8–10, 13–22 and 30 nucleotides corresponding to global, transitional and elongated conformations of protein. Varying the structure of photoreactive DNA, the intermediates of different stages of DNA replication or DNA repair were designed and applied to identify positioning of the RPA subunits on the specific DNA structures. Using this approach, RPA interactions with various types of DNA structures attributed to replication and DNA repair intermediates were examined. This review is dedicated to blessed memory of Prof. Alain Favre who contributed to the development of photoreactive nucleotide derivatives and their application for the study of protein–nucleic acids interactions.     

Electrochemical Sensing of Dissolved Hydrogen in Aqueous Solutions as a Tool to Monitor Magnesium Alloy Corrosion

Magnesium and its alloys have been the focus of the development of biodegradable metallic implant materials for years. Since water is reduced to form hydrogen gas during their corrosion, the amount and rate of hydrogen evolution, and therefore the dissolved hydrogen, could be used as an indicator to monitor and compare the corrosion. Here we report on a commercially available Clark‐Type amperometric microsensor and a simple potentiometric sensor for hydrogen to monitor the corrosion of a magnesium alloy in aqueous solutions. The sensors were compared using rare‐earth containing Mg alloy discs (Mg with 4 % Y, 2 % Nd, 0.5 % Ga, 0.5 % Dy) immersed in phosphate buffered saline (pH 7.4) and 3.5 % NaCl.     

Use of the Gaussian Distribution Function as a Tool to Estimate Continuous Heterogeneity in Adsorbing Systems

In environmental engineering, adsorption and desorption are phenomena commonly referred to as responsible for pollution dispersion, retention, or retardation in soils, aquifers, and hydrologic systems. They are also used to remove organic pollutants from water or odorous compounds in gas deodorization. Most often, the characterization of the aqueous adsorption systems that are of engineering interest involves a narrow adsorbate concentration range and low values of the adsorbate concentration. The practice is to use the Freundlich equation that best fits most data and is considered sufficient to design adsorption contactors. However, no physical or chemical meaning can be associated with the values taken by the parameters. The present paper gives a new way of analyzing adsorption data, using an extension of the Freundlich equation and the Gaussian distribution function that makes it possible to associate parameter values of this extension with the adsorbate–adsorbent normal interaction energy, its heterogeneity, and to some extent the adsorbate–adsorbate lateral interaction energy.     

Seed Priming with Non-thermal Plasma Modified Plant Reactions to Selenium or Zinc Oxide Nanoparticles: Cold Plasma as a Novel Emerging Tool for Plant Science

Plasma Chemistry and Plasma Processing - This research explored the capability of seed priming with the non-thermal plasma to modify reactions of Melissa officinalis, an important medicinal plant,...     

Diffuse Reflectance Spectroscopy as a Tool to Measure the Absorption Coefficient in Skin: South African Skin Phototypes

In any laser skin treatment, the optical properties (absorption and scattering coefficients) are important parameters. The melanin content of skin influences the absorption of light in the skin. The spread in the values of the absorption coefficients for the South African skin phototypes are not known. A diffuse reflectance probe consisting of a ring of six light delivery fibers and a central collecting fiber was used to measure the diffused reflected light from the arms of 30 volunteers with skin phototypes I–V (on the Fitzpatrick scale). The absorption coefficient was calculated from these measurements. This real‐time in vivo technique was used to determine the absorption coefficient of sun‐exposed and ‐protected areas on the arm. The range of typical absorption coefficients for the South African skin phototypes is reported. The values for the darker South African skin types were much higher than was previously reported for darker skin phototypes. In the analysis, the contributions of the eumelanin and pheomelanin were separated, which resulted in improved curve fitting for volunteers of southern Asian ethnicity without compromising the other groups.     

Changes in fluorescent emission due to non-covalent interactions as a general detection procedure for thin-layer chromatography

Changes in fluorescence emission due to non-covalent analyte-fluorophore interactions in silica gel plates are studied and used as a general detection procedure for thin-layer chromatography (TLC). The presence of the analyte modifies the microenvironment of the fluorophore and thus changes the balance between radiative (k(r)) and non-radiative (k(nr)) emission constants. A model is proposed for analyte-fluorophore induced electrostatic interactions, which depend on analyte polarizability and are responsible for fluorescence enhancements. As consequence of these induced interactions, the analyte creates an apolar environment that prevents non-fluorescent decay mechanisms, decreasing k(nr). On the other hand, the effect of an increase in refractive index on k(r) is investigated, as it contributes to some extent to fluorescence enhancements in silica gel medium. Changes in fluorescence emission should be regarded as a general property of fluorophores in the presence of analytes, and criteria that fluorophores should meet to be used as sensitive TLC probes are discussed here.     

Ion Implantation Standards as a Spark Source Mass Spectrometric Surface Analysis Calibration Technique: The Analysis of B in Irradiated Zircaloy-2

Abstract

Ion implantation standards were used to calibrate a spark source mass spectrometer (SSMS) near surface region analytical method. Standards were prepared by ion implanting ¹¹B⁺ at 100 keV into Zircaloy-2 at doses in the 3 × 10¹⁵ to 3 × 10^{16 11}B atoms/cm² range. The analytical method was predicated on the idea that both standards and samples could be sparked in a SSMS under essentially identical and reproducible conditions. Calibration plots gave linear log-log results for plots of ¹¹B⁺/¹²²Sn⁺ versus B concentration in the standards. Calibration plots were determined on the basis of 5 to 6 replicate determinations for 3 different implant standard concentration levels. A series of irradiated Zircaloy-2 cladding samples were analyzed and shown to contain not more than 0.06 μg/cm² total B in the near surface region.     

Cation Exchange Liquid Chromatography with Amperometric Detection as a Method for the Analysis of Endogenous Catecholamine Concentrations in Plasma or Serum

Abstract

A chromatographic system which permits determination of catecholamines, isolated from a few ml of plasma or serum, is described in detail. Some factors of importance for the improvement of the signal-to-noise ratio at subpicomole detection levels have been carefully investigated.     

Co-Fermentation of Cheese Whey and Crude Glycerol in EGSB Reactor as a Strategy to Enhance Continuous Hydrogen and Propionic Acid Production

This study evaluated the production of hydrogen and propionic acid in an expanded granular sludge bed (EGSB) reactor by co-fermentation of cheese whey (CW) and crude glycerol (CG). The reactor was operated at hydraulic retention time (HRT) of 8 h by changing the CW/CG ratio from 5:1 to 5:2, 5:3, 5:4, and 5:5. At the ratio of 5:5, HRT was reduced from 8 to 0.5 h. The maximum hydrogen yield of 0.120 mmol H₂ g COD^?1 was observed at the CW/CG ratio of 5:1. Increasing the CG concentration repressed hydrogen production in favor of propionic acid, with a maximum yield of 6.19 mmol HPr g COD^?1 at the CW/CG ratio of 5:3. Moreover, by reducing HRT of 8 to 0.5 h, the hydrogen production rate was increased to a maximum value of 42.5 mL H₂ h^?1 L^?1at HRT of 0.5 h. The major metabolites were propionate, 1,3-propanediol, acetate, butyrate, and lactate.     

Radial stratification of ions as a function of mass to charge ratio in collisional cooling radio frequency multipoles used as ion guides or ion traps

Collisional cooling in radio frequency (RF) ion guides has been used in mass spectrometry as an intermediate step during the transport of ions from high pressure regions of an ion source into high vacuum regions of a mass analyzer. Such collisional cooling devices are also increasingly used as 'linear', two-dimensional (2D) ion traps for ion storage and accumulation to achieve improved sensitivity and dynamic range. We have used the effective potential approach to study m/z dependent distribution of ions in the devices. Relationships obtained for the ideal 2D multipole demonstrate that after cooling the ion cloud forms concentric cylindrical layers, each of them composed of ions having the same m/z ratio; the higher the m/z, the larger is the radial position occupied by the ions. This behavior results from the fact that the effective RF focusing is stronger for ions of lower m/z, pushing these ions closer to the axis. Radial boundaries of the layers are more distinct for multiply charged ions, compared to singly charged ions having the same m/z and charge density. In the case of sufficiently high ion density and low ion kinetic energy, we show that each m/z layer is separated from its nearest neighbor by a radial gap of low ion density. The radial gaps of low ion population between the layers are formed due to the space charge repulsion. Conditions for establishing the m/z stratified structure include sufficiently high charge density and adequate collisional relaxation. These conditions are likely to occur in collisional RF multipoles operated as ion guides or 2D ion traps for external ion accumulation. When linear ion density increases, the maximum ion cloud radius also increases, and outer layers of high m/z ions approach the multipole rods and may be ejected. This 'overfilling' of the multipole capacity results in a strong discrimination against high m/z ions. A relationship is reported for the maximum linear ion density of a multipole that is not overfilled.     

N-terminus 4-Chloromethyl Thiazole Peptide as a Macrocyclization Tool in the Synthesis of Cyclic Peptides: Application to the Synthesis of Conformationally Constrained RGD-Containing Integrin Ligands

The synthesis of conformationally constrained RGD-containing integrin ligands via an efficient solid-phase intramolecular thioalkylation reaction is described. The reaction of S-nucleophiles with newly generated N-terminal 4-chloromethyl thiazoles leads to the desired cyclic RGD products 5 in high purities and good overall yields.