92 research outputs found
The environmental release and fate of antibiotics
No full textAntibiotics have been used as medical remedies for over 50 years and have recently emerged as new pollutants in the environment. This review encompasses the fate of several antibiotics in the environment, including sulfonamides, nitrofurans, terfenadines, cephalosporins and cyclosporins. It investigates the cycle of transfer from humans and animals including their metabolic transformation. The results show that antibiotic metabolites are of considerable persistence and are localized to ground-water and drinking water supplies. Furthermore, the results also show that several phases of the cycle of antibiotics in the environment are not well understood, such as how low concentrations of antibiotic metabolites in the diet affect humans and animals. This review also shows that improved wastewater decontamination processes are remediating factors for these emerging pollutants. The results obtained here may help legislators and authorities in understanding the fate and transformation of antibiotics in the environment. (C) 2014 Elsevier Ltd. All rights reserved.</p
Studies of enzymes from two protease families: Tissue Kallikreins, ADAMs and MMPs.
No full textThe human kallikrein family is a family of proteolytic enzymes, classified as serine proteases, that derive from chromosome 19, locus 13.3-13.4. These enzymes are widespread in pathophysiological processes such as cancer and neurodegenerative diseases; hence studies of catalytic sites and inhibitors are important in relation to the longer term of design of therapeutic drugs. One member of the family, human kallikrein 4 (hK4) which is thought to carry out crucial functions in the prostate, was expressed in this study as a secreted protein in a baculovirus expression system, bearing a His-tag and V5-epitope that were used for purification and detection respectively. Its mass was estimated to be 35kDa, ~2kDa less than the equivalent product expressed in monkey kidney cells. The protein was purified to 50-90% purity with a yield of 0.93mg/L-4.8mg/L based on methods derived from computational prediction of its properties, such as pI. Computational analysis was extended by applying high-performing computing techniques, such as molecular dynamics, and flexible ligand docking, to predict antigenic regions, the likely substrate specificity and putative inhibitors. These results show that hK4 has a loop, between Leu83-Ser94 that shows promise as a specific segment that can be exploited for generation of antibodies. Preferred substrates were also predicted to bear hydrophobic residues at the P'-region of the scissile bond and amphiphilic residues at the P-region. At the S-region, hK4 potentially involves its unique PLYH-motif in recognizing the P4/P5 position from the substrate. Flexible ligand-docking studies indicate that hK4 can be inhibited by inhibitors that carry a modified bulky hydrophobic sidechain with a guanidinium group at the P1-position and its own putative autoactivation region residues at the P2, P1' and P2' position. The computational study was extended to other members of the kallikrein family, predicting distinctions between these that could be used for future studies. These results show that 8 of the fifteen kallikrein members are very homologous in terms of specificity bearing typical trypsinlike activity and specificity, except for hK2, hK3, hK4, hK5, hK7, hK9, hK15 that retain certain distinct signatures in the binding pocket in terms of secondary specificity. The principles of substrate-specificity analysis that were developed were further applied on three metzincins, MMP-3, ADAM-9 and ADAM-10. These three enzymes are metalloproteases, which are involved in tissue remodeling, intracellular signalling and cell-to-cell mediation. The substrate-specificity analysis was carried out on all three metzincins using the structure of a crystallized complex of the MMP-3 enzyme with the TIMP-1 natural inhibitor as template. In this specific enzyme-substrate complex, the challenge was to model and suggest a possible orientation of the P-region, which is not known. The interactions on the P/S-region are therefore unclear and need to be clarified. In order to suggest the arrangement of the enzyme-substrate complex and the undefined S-subsites, four new residues were added in an extended beta-sheet conformation to the P1' residue (derived originally from the TIMP-1 inhibitor) to create a full-length modeled substrate spanning P4'-P4. This new modeled region, in particular, was bound through backbone H-bonds with the enzyme at position 169 (MMP nomenclature) suggesting a new crucial residue for substrate binding, and satisfied steric and chemical restraints in the S'-region of the enzyme. This modeling approach also indicated a putative presence of an S2/S3-pocket on these metzincins which is composed of different residues for MMP-3, ADAM-9 and ADAM-10, and which could prove useful for future drug design projects. Furthermore, the data argue against the involvement of a polarizable water molecule in catalysis, a mechanism that has been postulated by various groups. A new catalytic mechanism is suggested to involve an oxyanion anhydride transition state. This study is a demonstration of the power of combining bioinformatics with wet-lab biochemistry
Accumulation of perfluorinated alkyl substances (PFAS) in agricultural plants: A review
No full textPFASs are a class of compounds that include perfluoroalkyl and polyfluoroalkyl substances, some of the most
persistent pollutants still allowed - or only partially restricted - in several product fabrications and industrial
applications worldwide. PFASs have been shown to interact with blood proteins and are suspected of causing a
number of pathological responses, including cancer. Given this threat to living organisms, we carried out a broad
review of possible sources of PFASs and their potential accumulation in agricultural plants, from where they can
transfer to humans through the food chain. Analysis of the literature indicates a direct correlation between PFAS
concentrations in soil and bioaccumulation in plants. Furthermore, plant uptake largely changes with chain
length, functional group, plant species and organ. Low accumulations of perfluorooctanoic acid (PFOA) and
perfluorooctane sulfonic acid (PFOS) have been found in peeled potatoes and cereal seeds, while short-chain
compounds can accumulate at high levels in leafy vegetables and fruits. Significant variations in PFAS buildup in
plants according to soil amendment are also found, suggesting a particular interaction with soil organic matter.
Here, we identify a series of challenges that PFASs pose to the development of a safe agriculture for future
generations
State-of-the-art developments in metal and carbon-based semiconducting nanomaterials: applications and functions in spintronics, nanophotonics, and nanomagnetics
No full textNanomaterials composed of metals and metal alloys are the most valuable components in emerging micro-and nano-electronic devices and innovations to date. The composition of these nanomaterials, their quantum chemical and physical properties, and their production methods are in critical need of summarization, so that a complete state of the art of the present and future of nanotechnologies can be presented. In this review, we report on the most recent activities and results in the fields of spintronics, nanophotonics, and nanomagnetics, with particular emphasis on metallic nanoparticles in alloys and pure metals, as well as in organic combinations and in relation to carbon-based nanostructures. This review shows that the combinatory synthesis of alloys with rare metals, such as scandium, yttrium, and rare earths imparts valuable qualities to high-magnetic-field compounds, and provides unique properties with emphasis on nanoelectronic and computational components. In this review, we also shed light on the methods of synthesis and the background of spintronic, nanomagnetic, and nanophotonic materials, with applications in optics, diagnostics, nanoelectronics, and computational nanotechnology. The review is important for the industrial development of novel materials, and for summarizing both fabrication and manufacturing methods, as well as principles and functions of metallic nanoparticles
Emerging carbon-based nanosensor devices: structures, functions and applications
No full textBionanosensors and nanosensors have been devised in recent years with the use of various materials including carbon-based nanomaterials, for applications in diagnostics, environmental science and microelectronics. Carbon-based materials are critical for sensing applications, as they have physical and electronic properties which facilitate the detection of substances in solutions, gaseous compounds and pollutants through their conductive properties and resonance-frequency transmission capacities. In this review, a series of recent studies of carbon nanotubes (CNTs) based nanosensors and optical systems are reported, with emphasis on biochemical, chemical and environmental detection. This study also encompasses a background and description of the various properties of the nanomaterials, and the operation mechanism of the manufactured nanosensors. The use of computational chemistry is applied in describing the electronic properties and molecular events of the included nanomaterials during operation. This review shows that resonance-based sensing technologies reach detection limits for gases, such as ammonia down to 10(-24) level. The study also shows that the properties of the carbon nanomaterials give them unique features that are critical for designing new sensors based on electrocatalysis and other reactive detection mechanisms. Several research fields can benefit from the described emerging technologies, such as areas of research in environmental monitoring, rapid-on site diagnostics, in situ analyses, and blood and urine sampling in medical and sport industry. Carbon nanomaterials are critical for the operational sensitivity of nanosensors. Considering the low cost of fabrication, carbon nanomaterials can represent an essential step in the manufacturing of tomorrow's commercial sensors
Quantum chemical calculations of the active site of the solute-binding protein PsaA from Streptococcus pneumoniae explain electronic selectivity of metal binding
No full textStreptococcus pneumoniae is the world’s foremost bacterial pathogen. Virulence in the host is dependent on manganese acquisition via the PsaBCA permease. Crystallographic studies of its solute-binding protein component, PsaA, have previously shown that the nature of the metal ion bound by the protein modulates the conformational changes associated with its function. Notably, manganese and cadmium ions can be bound in a reversible manner, facilitating transport via PsaA, whereas zinc binds in an essentially irreversible manner preventing release to the permease. All three ionic species show a similar coordination in the PsaA crystal structures. A set of quantum chemical calculations have here been performed in order to differentiate between the ions in terms of electronic configuration. Based on natural bond orbital (NBO) analysis, the results show that manganese and cadmium bind more strongly to the protein than zinc, in that their coordination to the enzyme involves more shared electrons. Manganese has the highest indirect indicator of bonding strength and provides an unpaired electron that induces the formation of three bonds to the enzyme active site. Cadmium binds more strongly than zinc, though more weakly than manganese, and forms only ionic bonds in its ligand framework. These calculations indicate a concrete differentiation of the bonding states of the three active sites; however, bonding energies which can give more accurate estimates have not been computed presently. The calculations further show that the ionic radii are critical for the bonding state between the enzyme and the metal and that the conformational motions responsible for the PsaA’s functional cycle may depend on the ion binding strongly to the enzyme. Our results add important information of the PsaA-metal ion binding architecture to the existing crystallography data and aid in understanding the function of this protein.</p
Mathematical Modeling of Rogue Waves : A Survey of Recent and Emerging Mathematical Methods and Solutions
No full textAnomalous waves and rogue events are closely associated with irregularities and unexpected events occurring at various levels of physics, such as in optics, in oceans and in the atmosphere. Mathematical modeling of rogue waves is a highly active field of research, which has evolved over the last few decades into a specialized part of mathematical physics. The applications of the mathematical models for rogue events is directly relevant to technology development for the prediction of rogue ocean waves and for signal processing in quantum units. In this survey, a comprehensive perspective of the most recent developments of methods for representing rogue waves is given, along with discussion of the devised forms and solutions. The standard nonlinear Schrödinger equation, the Hirota equation, the MMT equation and other models are discussed and their properties highlighted. This survey shows that the most recent advancement in modeling rogue waves give models that can be used to establish methods for the prediction of rogue waves in open seas, which is important for the safety and activity of marine vessels and installations. The study further puts emphasis on the difference between the methods and how the resulting models form the basis for representing rogue waves in various forms, solitary or with a wave background. This review has also a pedagogic component directed towards students and interested non-experts and forms a complete survey of the most conventional and emerging methods published until recently
An investigation into the physical, chemical and thermochemical properties of Niobium nanoclusters
No full textThe search for spin-polarized metal clusters, energetic crystals and conductive materials is a paramount part of Nanotechnology. Adapting quantum chemistry and quantum mechanics methods to study and endeavor the electronic and lattice properties of groups of atoms in nanoclusters is a central approach, which aids in revealing crucial electronic properties that serve to develop and synthesize nanomaterials, nanometals and metal clusters. This project investigates the energy landscape of Niobium clusters (Nb n), in order to shed light on their electronic, dipole, and magnetic properties. The clusters are studied with the XTB Tight-binding software coupled with hybrid DFT functionals. The results show that Niobium clusters in nanosized particles (10-61 atoms) bear ultra-low orbital gaps, with promising properties for hyperconnects and nanoparticle-based electronics
Heavy metal pollution in the Baltic Sea, from the North European coast to the Baltic states, Finland and the Swedish coastline to Norway
No full textEnvironmental pollution and contamination is a continuous challenge that industrialized and developing countries are facing, affecting entire ecosystems, threatening biodiversity, reducing health and life quality of humans and contributing to the extinction of endangered species. The oceans and seas are the most vulnerable ecosystems to anthropogenic impacts, where heavy metals and other pollutants affect the viability of marine species. In this review, the focus is put on the widespread contamination of heavy metals on the Baltic sea and its marine ecosystems. Three parts are considered: the industrial sources of heavy metals in along the entire Baltic coast and in the Baltic sea, the levels and concentrations of heavy metals found in various phases of the environment (sediments, rivers, lakes and seas) and the accumulation of heavy metals in fish as well as avian species. The results from this review show that the heavy metal-releasing industries impact the marine environment for several decades, and that more efforts are required to restitute the Baltic sea to its original state.Computational Ecotoxicolog
Derivation and Numerical analysis of an Attenuation Operator for non-relativistic waves
No full textQuantum mechanical models for particles are strictly dependent on the Schrödinger equation, where the solutions and the Hermitian polynomials form a mathematical foundation to derive expectation values for observables. As for all quantum systems, the solutions are derived in discrete energy levels, and yield probability density, the kinetic energy and average momentum. In this study however, an attenuation Hamiltonian is derived by the algebraic relation of the momentum and position operators, and the derived equation, where the attenuation of kinetic energy is the eigenvalue, is studied numerically. The numerical solutions suggest that the change in kinetic energy from one transition to the next proceed in an undular fashion, and not in a definite manner. This suggests that any sub-atomic particle which experiences a transition from one level to the next, does so by both gaining and losing energy in an undular manner before reaching an equilibrium with a new and stabilized kinetic energy. The results show also that the phase of the change in kinetic energy between transitions differs between high and low momenta and that higher levels of momentum attenuate more smoothly than transitions between lower energy levels. The investigated attenuation operator may be important for future pinning and quasipinning approaches and play a role in future quantum information processing. Future research is required on the spectrum of the operator and on its potential analytical solutions
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