Short-chain polyphosphates: Extraction effects on migration and size estimation of Saccharomyces cerevisiae extracts with polyacrylamide gel electrophoresis

Polyacrylamide gel electrophoresis is commonly used to characterize the chain length of polyphosphates (polyP), more generally called condensed phosphates. After separation, nonradioactive, optical polyP staining is limited to chain lengths greater than 15 ${\mathrm{PO}}_3^{-}$monomers with toluidine blue or 4′,6-diamidino-2-phenylindole. PolyP chain lengths longer than 62${\mathrm{PO}}_3^{-}$monomers were correlated to the shortest DNA ladders. In this study, synthetic linear polyPs (Sigma-Aldrich “Type 45”, estimated mean length of 45 ${\mathrm{PO}}_3^{-}$ monomers), trimetaphosphate (trimetaP: 3 ${\mathrm{PO}}_3^{-}$ ring), tripolyphosphate (tripolyP), pyrophosphate (PP_i), and inorganic orthophosphate (o-P_i) were visualized after separation by an in situ hydrolytic degradation process to o-P_i that was subsequently stained with methyl green. Statistically insignificant migration reduction of synthetic short-chain polyP after perchloric acid or phenol–chloroform extraction was confirmed with the Friedman test. ³¹P diffusion–ordered NMR spectroscopy confirmed that extraction also reduced PP_i diffusivity by <10%. Linear regression between the R_f peak migration value and the logarithm of synthetic polyP molecular weights enabled estimation of extracted polyP chain lengths from 2 to 45 ${\mathrm{PO}}_3^{-}$monomers. Linear polyP extracts from Saccharomyces cerevisiae grown in aerobic conditions were generally shorter than extracts cultured in anaerobic conditions. Extractions from both aerobic and anaerobic S. cerevisiae included tripolyP and o-P_i, but no PP_i.     

Dielectrophoresis microbial characterization and isolation of Staphylococcus aureus based on optimum crossover frequency

Characterization of antibiotic-resistant bacteria is a significant concern that persists for the rapid classification and analysis of the bacteria. A technology that utilizes the manipulation of antibiotic-resistant bacteria is key to solving the significant threat of these pathogenic bacteria by rapid characterization profile. Dielectrophoresis (DEP) can differentiate between antibiotic-resistant and susceptible bacteria based on their physical structure and polarization properties. In this work, the DEP response of two Gram-positive bacteria, namely, Methicillin-resistant Staphylococcus aureus (MRSA) and Methicillin-susceptible S. aureus (MSSA), was investigated and simulated. The DEP characterization was experimentally observed on the bacteria influenced by oxacillin and vancomycin antibiotics. MSSA control without antibiotics has crossover frequencies ($f_{x0}$) from 6 to 8 MHz, whereas MRSA control is from 2 to 3 MHz. The $f_{x0}$ changed when bacteria were exposed to the antibiotic. As for MSSA, the $f_{x0}$ decreased to 3.35 MHz compared to $f_{x0}$ MSSA control without antibiotics, MRSA, $f_{x0}$ increased to 7 MHz when compared to MRSA control. The changes in the DEP response of MSSA and MRSA with and without antibiotics were theoretically proven using MyDEP and COMSOL simulation and experimentally based on the modification to the bacteria cell walls. Thus, the DEP response can be employed as a label-free detectable method to sense and differentiate between resistant and susceptible strains with different antibiotic profiles. The developed method can be implemented on a single platform to analyze and identify bacteria for rapid, scalable, and accurate characterization.     

Nanostructure stability and swelling of ternary block copolymer/homopolymer blends: A direct comparison between dissipative particle dynamics and experiment

Ternary block copolymer (BCP)‐homopolymer (HP) blends offer a simple method for tuning nanostructure sizes to meet application‐specific demands. Comprehensive dissipative particle dynamic (DPD) simulations were performed to study the impact of polymer interactions, molecular weight, and HP volume fraction (φ_HP ) on symmetric ternary blend morphological stability and domain spacing. DPD reproduces key features of the experimental phase diagram, including lamellar domain swelling with increasing φ_HP , the formation of an asymmetric bicontinuous microemulsion at a critical HP concentration ${\phi }_{\mathrm{HP}}^{*}$, and macrophase separation with further HP addition. Simulation results matched experimental values for ${\phi }_{\mathrm{HP}}^{*}$ and lamellar swelling as a function of HP to BCP chain length ratio, α = N_HP/N_BCP . Structural analysis of blends with fixed φ_HP but varying α confirmed that ternary blends follow the wet/dry brush model of domain swelling with the miscibility of HPs and BCPs depending on α . Longer HPs concentrate in the center of domains, boosting their swelling efficiencies compared to shorter chains. These results advance our understanding of BCP‐HP blend phase behavior and demonstrate the value of DPD for studying polymeric blends. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 794–803     

Quantitative model for predicting the electroosmotic flow in dual-pole nanochannels

Developing and assessing nanofluidic systems is time-consuming and costly owing to the method's novelty; hence, modeling is essential to determine the optimal areas for implementation and to grasp its workings. In this work, we examined the influence of dual-pole surface and nanopore configuration on ion transfer simultaneously. To achieve this, the two trumpet and cigarette configuration were coated with a dual-pole soft surface so that the negative charge could be positioned in the nanopore's small aperture. Subsequently, the Poisson–Nernst–Planck and Navier–Stokes equations were simultaneously solved under steady-state circumstances using varied values physicochemical properties for the soft surface and electrolyte. The pore's selectivity was $S_{\mathrm{Trumpet}}>S_{\mathrm{Cigarette}}$, and the rectification factor, on the other hand, was , when the overall concentration was very low. When the ion partitioning effect is taken into account, we clearly show that the rectifying variables for the cigarette configuration and the trumpet configuration can reach values of 45 and 49.2, when the charge density and mass concentration were 100 mol/m³ and 1 mM, respectively. By using dual-pole surfaces, the controllability of nanopores’ rectifying behavior may be modified to produce superior separation performance.     

Analysis of the Binding of Cytokines to Highly Charged Polymer Networks

A model describing the binding of biological signaling proteins to highly charged polymer networks is presented. The networks are formed by polyelectrolyte chains for which the distance between two charges at the chain is smaller than the Bjerrum length. Counterion condensation on such highly charged chains immobilizes a part of the counterions. The Donnan-equilibrium between the polymer network and the aqueous solution with salt concentration $c_s^b$ is used to calculate the salt concentration of the co- and counterions $c_s^g$ entering the network. Two factors are decisive: i) The electrostatic interaction between the network and the protein is given by the Donnan-potential of the network and the net charge of the protein. In addition to this leading term, a second term describes the change in the Born-energy of the proteins when entering the network. ii) The interaction of the protein with the highly charged chains within the network is governed by counterion release: Patches of positive charge at the protein become multivalent counterions of the polyelectrolyte chains thus releasing a concomitant number of condensed counterions. The model compares favorably to experimental data obtained on a set of biohybrid polymer networks composed of crosslinked glycosaminoglycan chains that interact with a mixture of key signaling proteins.     

High-throughput dielectrophoretic separator based on printed circuit boards

The separation of particles with respect to their intrinsic properties is an ongoing task in various fields such as biotechnology and recycling of electronic waste. Especially for small particles in the lower micrometer or nanometer range, separation techniques are a field of current research since many existing approaches lack either throughput or selectivity. Dielectrophoresis (DEP) is a technique that can address multiple particle properties, making it a potential candidate to solve challenging separation tasks. Currently, DEP is mostly used in microfluidic separators and thus limited in throughput. Additionally, DEP setups often require expensive components, such as electrode arrays fabricated in the clean room. Here, we present and characterize a separator based on two inexpensive custom-designed printed circuit boards (80 × 120 mm board size). The boards consist of interdigitated electrode arrays with $250\mu$m electrode width and spacing. We demonstrate the separation capabilities using polystyrene particles ranging from 500 nm to $6\mu$m in monodisperse experiments. Further, we demonstrate selective trapping at flow rates up to 240 ml/h in the presented device for a binary mixture. Our experiments demonstrate an affordable way to increase throughput in electrode-based DEP separators.     

Inherent Adaptivity of Alzheimer Peptides to Crowded Environments

Amyloid β (Aβ) is the major constituent in senile plaques of Alzheimer's disease in which peptides initially undergo structural conversions to form elongated fibrils. The impact of crowding on the fibrillation pathways of Aβ₄₀ and Aβ₄₂, the most common peptide isoforms are studied. PEG and Ficoll are used as model crowders to mimic a macromolecular enriched surrounding. The fibrillar growth is monitored with the help of ThT-fluorescence assays in order to extract two rates describing primary and secondary processes of nucleation and growth. Techniques as fluorescence correlation spectroscopy and analytical ultracentrifugation are used to discuss oligomeric states; fibril morphologies are investigated using negative-staining transmission electron microscopy. While excluded volume effects imposed by macromolecular crowding are expected to always increase rates of intermolecular interactions and structural conversion, a vast variety of effects are found depending on the peptide, the crowder, or ionic strength of the solution. While investigations of the obtained rates with respect to a reactant-occluded model are capable to display specific surface interactions with the crowder, the employment of crystallization-like models reveal the crowder-induced entropic gain with $\mathrm{\Delta }\mathrm{\Delta }{G}_{\text{fib}}^{\text{crow}}=-116\pm 21k$J mol⁻¹ per volume fraction of the crowder.     

Modeling of a linear ion trap with driving rectangular waveforms

We consider the operation of a digital linear ion trap with resonant radial ejection. A sequence of rectangular voltage pulses with a dipole resonance signal is applied to the trap electrodes. The periodic waveform is piecewise constant, has zero mean, and is determined by an asymmetry parameter $d$: one value is taken on interval $\left(0,\mathit{dT}\right)$ and another on $\left(\mathit{dT},T\right)$, where $T$ is the RF period. Ion mass scanning is performed by varying the asymmetry parameter $d$ and amplitude of the negative pulse part with time. The ion oscillation frequencies and acceptance of the linear trap are calculated. The dependence of the ion mass to charge ratio $m/z$ on the parameter $d$ is $m/z~d^2$. The maximum value is about $m/z=30$ kDa for typical parameters of the linear trap: frequency 0.5 MHz, rod radius 4 mm, and negative pulse amplitude 1 kV. The dipolar excitation frequency is 0.125 MHz at which the LIT acceptance is maximal.     

Biologically inspired 3Fe4S cluster as structural mimics of FeMoco M-cluster

A 3Fe4S cluster related to M-cluster of Mo-nitrogenase is reported. [K(THF)₅][Fe₃(μ-bdt)₂(μ-PPh₂)(CO)₅] ( 1 ) is synthesized from photo-assisted structural rearrangement of [K(THF)₂][(μ,κ²-bdt)Fe₂(μ-PPh₂)(CO)₅] under visible light irradiation. The molecular structure of 1 consists of a Fe₃ core bearing one dithiolate bridge and the second dithiolate group capping onto the metallic plane. The structural motif of 1 is analogous to that of Mo-participated 3Fe4S unit in M-cluster of Mo-nitrogenase, with the similar Fe-Fe and Fe-S bond distances. Upon protonation in 193 K, a Fe-hydride species ( 1H ) is generated and characterized to possess the bridging hydride group (δ = −12.57 ppm) by ¹H-NMR spectroscopy and DFT calculation. In CH₃CN solution, complex 1 exhibits a reversible reduction and oxidation process at $E_{1/2}^{\mathrm{red}}$ = −1.94 V and $E_{1/2}^{\mathrm{ox}}$ = −0.18 V, respectively, at 273 K. The reduction behavior of 1 in CH₂Cl₂ solution at 243 K displays a slight modification in the presence of trifluoroacetic acid, revealing a moderate anodic potential shift (~50 mV). The current amplitude of the reduction wave is linearly increased with the increasement of acid added, indicative of the catalytic event.     

The confined helium atom: An information–theoretic approach

In this article, we study the helium atom confined in a spherical impenetrable cavity by using informational measures. We use the Ritz variational method to obtain the energies and wave functions of the confined helium atom as a function of the cavity radius $r_0$. As trial wave functions we use one uncorrelated function and five explicitly correlated basis sets in Hylleraas coordinates with different degrees of electronic correlation. We computed the Shannon entropy, Fisher information, Kullback–Leibler entropy, Tsallis entropy, disequilibrium and Fisher–Shannon complexity, as a function of $r_0$. We found that these entropic measures are sensitive to electronic correlation and can be used to measure it. As expected these entropic measures are less sensitive to electron correlation in the strong confinement regime ( a.u.).     

Effects of Ultraviolet Radiation (UV‐A+UV‐B) on the Antioxidant Metabolism of the Red Macroalga Species Acanthophora spicifera (Rhodophyta,Ceramiales) From Different Salinity and Nutrient Conditions

Acanthophora spicifera (M.Vahl) Børgesen is a macroalga of great economic importance. This study evaluated the antioxidant responses of two algal populations of A. spicifera adapted to different abiotic conditions when exposed to ultraviolet‐A+ultraviolet‐B radiation (UV‐A+UV‐B). Experiments were performed using the water at two collection points for 7 days of acclimatization and 7 days of exposure to UVR (3 h per day), followed by metabolic analyses. At point 1, water of 30 ± 1 practical salinity unit (psu) had concentrations of 1.06 ± 0.27 mm ${\text{NH}}_4^{+}$, 8.47 ± 0.01 mm ${\text{NO}}_3^{?}$, 0.17 ± 0.01 mm ${\text{PO}}_4^{?3}$ and pH 7.88. At point 2, water of 35 ± 1 psu had concentrations of 1.13 ± 0.05 mm ${\text{NH}}_4^{+}$, 3.73 ± 0.01 mm ${\text{NO}}_3^{?}$, 0.52 ± 0.01 mm ${\text{PO}}_4^{?3}$ and pH 8.55. Chlorophyll a, phycobiliproteins, carotenoids, mycosporins, polyphenolics and antioxidant enzymes (catalase, superoxide dismutase and guaiacol peroxidase) were evaluated. The present study demonstrates that ultraviolet radiation triggers antioxidant activity in the A. spicifera. However, such activation resulted in greater responses in samples of the point 1, with lower salinity and highest concentration of nutrients.     

Characterization of a convection-based support microstructure through a flow resistance parameter

Modern convection-based supports differ substantially in pore size, porosity, and microstructure topology. Due to such variability, it is challenging to evaluate the contribution of a particular microstructure topology on flow resistance. We demonstrated that the flow resistance parameter ($\varphi$) introduced decades ago can be used as a criterion to evaluate the effect of microstructure topology on a pressure drop when the pore size is used as a characteristic support dimension. Furthermore, the $\varphi$ value of simple cubic packing was calculated over the entire range of open porosity and compared to the $\varphi$ values determined for pressure drop models derived for particular convection-based supports and experimental values of various convection-based supports from the literature. It was shown that different convection-based supports become clustered into distinct groups when plotted according to their $\varphi$ and open porosity values, allowing their discrimination.     

Extending the power transform approach for recovering areas of overlapping peaks

Power functions, , are embedded in some modern chromatography detectors and software which not only alter the linear dynamic range of such detectors but also improve the cosmetic aspects of the chromatograms. These aspects include a reduction in baseline noise, improved peak symmetry, and better resolution. However, after raising the electronic output of a detector to a selected power (n > 1), the original peak area information is lost as are very small peaks. Recent advances in the peak processing protocol allow us to recover peak areas from overlapping peak areas, even in noisy environments using power functions. One of the primary protocol requirements of this approach was to have resolution factors ≥0.9. An increasing positive bias in the recovered area was observed as the resolution factors decreased below 0.9. In this work, we extend the capabilities of power function to lower resolution values. This bias is addressed by considering the increasing contributions in peak height coming from adjacent peaks. It is shown that the power function can now be used as long as the peak maxima are visible, making  = 0.5, the lower treatable resolution factor for two peaks of similar areas.     

Numerical study supplemented with simplified model on electrophoresis of a hydrophobic colloid incorporating finite ion size effects and ion-solvent interactions

We consider a modified electrokinetic model to study the electrophoresis of a hydrophobic particle by considering the finite sized ions. The mathematical model adopted in this study incorporates the ion steric repulsion, ion-solvent interactions as well as Maxwell stress on the electrolyte. The dielectric permittivity and viscosity of the electrolyte is considered to vary with the local ionic volume fraction. Based on this modified model for the electrokinetics we have analyzed the electrophoresis in a single as well as mixture of electrolytes of monovalent and non-$z:z$ electrolytes. The dependence of viscosity on local ionic volume fraction modifies the hydrodynamic drag as well as diffusivity of ions, which are ignored in existing studies on electrophoresis. A simplified model for electrophoresis of a hydrophobic particle incorporating the ion steric repulsion and ion-solvent interactions is developed based on the first-order perturbation on applied electric field. This simplified model is established to be efficient for a Debye layer thinner than the particle size and a smaller range of slip length. This model can be implemented for any number of ionic species as well as non-$z:z$ electrolytes. It is established that the ion steric interactions and dielectric decrement creates a counterion saturation in the Debye layer leading to an enhanced mobility compared to the standard model. However, experimental data for non-dilute cases often under predicts the theoretically determined mobility. The present modified model fills this lacuna and demonstrate that the consideration of finite ion size modifies the medium viscosity and hence, ionic mobility, which in combination lowers the mobility value.     

Minor amounts of glycerol improve the properties of polyisobutylene‐based polyurethane and its nanocomposites

The synthesis of primary hydroxyl‐telechelic polyisobutylene, HOCH₂‐PIB‐CH₂OH, often yields product the number average terminal functionality ( $f_{n,{\mathrm{CH}}_2\mathrm{OH}}$) of which is less than theoretical 2.0, typically $f_{n,{\mathrm{CH}}_2\mathrm{OH}}$ = 1.75–1.95. Polyurethane (PU) prepared with such low‐cost imperfect PIB‐diols, unsurprisingly, exhibit poor overall properties. Herein we report that mechanical, rheological, and thermal properties of polyisobutylene‐based polyurethane (PIB‐PU) and PIB‐PU reinforced with organically modified montmorillonite (OmMMT) prepared with PIB‐diol of $f_{n,{\mathrm{CH}}_2\mathrm{OH}}$ = 1.85 are significantly enhanced by glycerol. Specifically, we document that calculated minor amounts of glycerol substantially improves tensile strength, ultimate elongation, elastic modulus, toughness, rubbery plateau, flow temperature, creep, permanent set, rate of recovery after loading, and thermal properties of PIB‐PU and OmMMT‐reinforced PIB‐PU prepared with PIB‐diol of $f_{n,{\mathrm{CH}}_2\mathrm{OH}}$ = 1.85. The observations are summarized and discussed in terms of chemistry, micromorphology, and viscoelasticity. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019 , 57, 929–935     

Photodynamic Therapy Minimally Affects HEMA-DMAEMA Hydrogel Viscoelasticity

Soft matter implants are a rapidly growing field in medicine for reconstructive surgery, aesthetic treatments, and regenerative medicine. Though these procedures are efficacious, all implants carry risks associated with microbial infection which are often aggressive. Preventative and responsive measures exist but are limited in applicability to soft materials. Photodynamic therapy (PDT) presents a means to perform safe and effective antimicrobial treatments in proximity to soft implants. HEMA-DMAEMA hydrogels are prepared with the photosensitizer methylene blue included at 10 and 100 µM in solution used for swelling over 2 or 4 days. Thirty minutes or 5 h of LED illumination at $9.20\frac{mW}{c{m}^2}$ is then used for PDT-induced generation of reactive oxygen species in direct contact with hydrogels to test viable limits of treatment. Frequency sweep rheological measurements reveal minimal overall changes in terms of loss modulus and loss factor but a statistically significant drop in storage modulus for some PDT doses, though within the range of controls and biological variation. These mild impacts suggest the feasibility of PDT application for infection clearing in proximity to soft implants. Future investigation with additional hydrogel varieties and current implant models will further detail the safety of PDT in implant applications.     

Rapid prototyping of polydimethylsiloxane (PDMS) microchips using electrohydrodynamic jet printing: Application to electrokinetic assays

Polydimethylsiloxane (PDMS) based microfluidic devices have found increasing utility for electrophoretic and electrokinetic assays because of their ease of fabrication using replica molding. However, the fabrication of high-resolution molds for replica molding still requires the resource-intensive and time-consuming photolithography process, which precludes quick design iterations and device optimization. We here demonstrate a low-cost, rapid microfabrication process, based on electrohydrodynamic jet printing (EJP), for fabricating non-sacrificial master molds for replica molding of PDMS microfluidic devices. The method is based on the precise deposition of an electrically stretched polymeric solution of polycaprolactone in acetic acid on a silicon wafer placed on a computer-controlled motion stage. This process offers the high-resolution (order 10 $\mu$m) capability of photolithography and rapid prototyping capability of inkjet printing to print high-resolution templates for elastomeric microfluidic devices within a few minutes. Through proper selection of the operating parameters such as solution flow rate, applied electric field, and stage speed, we demonstrate microfabrication of intricate master molds and corresponding PDMS microfluidic devices for electrokinetic applications. We demonstrate the utility of the fabricated PDMS microchips for nonlinear electrokinetic processes such as electrokinetic instability and controlled sample splitting in ITP. The ability to rapid prototype customized reusable master molds with order 10 $\mu$m resolution within a few minutes can help in designing and optimizing microfluidic devices for various electrokinetic applications.     

Partial molar volume and partial molar compressibility of four homologous α-amino acids in aqueous sodium fluoride solutions at different temperatures

Density and ultrasonic speed of four amino acids (glycine, l-alanine, l-valine, and l-leucine) in aqueous sodium fluoride solutions {(0.1 to 0.5) M} have been measured at T = (308.15, 313.15, and 318.15) K. Apparent molar volumes (V_φ), partial molar volumes $\left(V_{\phi }^0\right)$, transfer volumes $\left(\mathrm{\Delta }{V}_{\phi }^0\right)$ and hydration number (n_H) are evaluated using density data. Adiabatic compressibility (β_s), change (Δβ_s), and relative change in compressibility (Δβ_s/β₀), apparent molar compressibility (K_φ), partial molar compressibility $\left(K_{\phi }^0\right)$, transfer compressibility $\left(\mathrm{\Delta }{K}_{\phi }^0\right)$, and hydration number (n_H) have been calculated using ultrasonic speed data. The linear correlation of $V_{\phi }^0\text{,}\mathrm{\Delta }{V}_{\phi }^0\text{,}{K}_{\phi }^0$ and $\mathrm{\Delta }{K}_{\phi }^0$ for a homologous series of amino acids have been used utilised to calculate the contribution of charged end groups (${\text{NH}}_3^{+}$, COO^?), CH₂ group and other alkyl chain of the amino acids. The analysis shows that the ion–ion interactions are much stronger than ion–hydrophobic interactions over the entire concentration range of sodium fluoride. It is observed that sodium fluoride has a strong dehydration effect on amino acids.     

Photo‐Fenton and Riboflavin‐photosensitized Processes of the Isoxaflutole Herbicide

The proherbicide Isoxaflutole (IXF) hydrolyzes spontaneously to diketonitrile (DKN) a phytotoxic compound with herbicidal activity. In this work, the sensitized degradation of IXF using Riboflavin (Rf), a typical environmentally friendly sensitizer, Fenton and photo‐Fenton processes has been studied. The results indicate that only the photo‐Fenton process produces a significant degradation of the IXF. Photolysis experiments of IXF sensitized by Riboflavin is not a meaningful process, IXF quenches the Rf excited triplet (³Rf*) state with a quenching rate constant of 1.5 · 10⁷ m ^?1 s^?1 and no reaction is observed with the species O₂(¹Δ_g) or ${\mathrm{O}}_2^{·?}$ generated from ³Rf*. The Fenton reaction produces no changes in the IXF concentration. While the photo‐Fenton process of the IXF, under typical conditions, it produces a degradation of 99% and a mineralization to CO₂ and H₂O of 88%. A rate constant value of 1.0 × 10⁹ m ^?1 s^?1 was determined for the reaction between IXF and HO˙. The photo‐Fenton process degradation products were identified by UHPLC‐MS/MS analysis.