The Contribution of the Activation Entropy to the Gas-Phase Stability of Modified Nucleic Acid Duplexes

Tricyclo-DNA (tcDNA) is a sugar-modified analogue of DNA currently tested for the treatment of Duchenne muscular dystrophy in an antisense approach. Tandem mass spectrometry plays a key role in modern medical diagnostics and has become a widespread technique for the structure elucidation and quantification of antisense oligonucleotides. Herein, mechanistic aspects of the fragmentation of tcDNA are discussed, which lay the basis for reliable sequencing and quantification of the antisense oligonucleotide. Excellent selectivity of tcDNA for complementary RNA is demonstrated in direct competition experiments. Moreover, the kinetic stability and fragmentation pattern of matched and mismatched tcDNA heteroduplexes were investigated and compared with non-modified DNA and RNA duplexes. Although the separation of the constituting strands is the entropy-favored fragmentation pathway of all nucleic acid duplexes, it was found to be only a minor pathway of tcDNA duplexes. The modified hybrid duplexes preferentially undergo neutral base loss and backbone cleavage. This difference is due to the low activation entropy for the strand dissociation of modified duplexes that arises from the conformational constraint of the tc-sugar-moiety. The low activation entropy results in a relatively high free activation enthalpy for the dissociation comparable to the free activation enthalpy of the alternative reaction pathway, the release of a nucleobase. The gas-phase behavior of tcDNA duplexes illustrates the impact of the activation entropy on the fragmentation kinetics and suggests that tandem mass spectrometric experiments are not suited to determine the relative stability of different types of nucleic acid duplexes.

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Two low-cost digital camera-based platforms for quantitative creatinine analysis in urine

In clinical analysis creatinine is a routine biomarker for the assessment of renal and muscular dysfunctions. Although several techniques have been proposed for a fast and accurate quantification of creatinine in human serum or urine, most of them require expensive or complex apparatus, advanced sample preparation or skilled operators. To circumvent these issues, we propose two home-made platforms based on a CD Spectroscope (CDS) and Computer Screen Photo-assisted Technique (CSPT) for the rapid assessment of creatinine level in human urine. Both systems display a linear range (r² = 0.9967 and 0.9972, respectively) from 160 μmol L⁻¹ to 1.6 mmol L⁻¹ for standard creatinine solutions (n = 15) with respective detection limits of 89 μmol L⁻¹ and 111 μmol L⁻¹. Good repeatability was observed for intra-day (1.7–2.9%) and inter-day (3.6–6.5%) measurements evaluated on three consecutive days. The performance of CDS and CSPT was also validated in real human urine samples (n = 26) using capillary electrophoresis data as reference. Corresponding Partial Least-Squares (PLS) regression models provided for mean relative errors below 10% in creatinine quantification.     

Novel poly(lactic acid)–poly(ethylene oxide) chain‐linked copolymer and its application in nano‐encapsulation

The work presented here investigates the synthesis of poly(lactic acid)–poly(ethylene oxide) diisocyanate chain‐linked copolymer, and its application in the nano‐encapsulation of bioactive compounds. Study was conducted on the effect of the type of chain‐linking agent, along with molecular weight, thermal properties and hydrophilic/hydrophobic behavior, through the methods of gel permeation chromatography, Fourier transform infrared spectroscopy–attenuated total reflectance, differential scanning calorimetry, light scattering, water uptake experimentation, and water contact angle measurements. Nanoparticle formation was performed via a single solvent evaporation process, and the particles obtained were characterized by dynamic light scattering and scanning electron microscopy. Results show the significantly enhanced molecular weight of the final product after the chain‐linking reaction (up to 300,000 g/mol), as well as the non‐linear nature of the sample due to broad polydispersity, ranging from 4–13. The final products exhibited glass transition temperatures of between 30 and 44 °C, while their crystalline quality was either significantly suppressed or a completely amorphous attribute was observed. Nanoparticles in the range of 300 nm that contained metazachlor were successfully prepared, and their releasing behavior exhibited first order release kinetics. A slower rate of release was observed in samples containing 4,4′‐methylenebis(phenyl isocyanate) as a chain‐linker. Copyright © 2014 John Wiley & Sons, Ltd.     

Influence of laser photobiomodulation upon connective tissue remodeling during wound healing

The modulation of collagen fibers during experimental skin wound healing was studied in 112 Wistar rats submitted to laser photobiomodulation treatment. A standardized 8mm-diameter wound was made on the dorsal skin of all animals. In half of them, 0.2ml of a silica suspension was injected along the border of the wound in order to enhance collagen deposition and facilitate observation. The others received saline as vehicle. The treatment was carried out by means of laser rays from an aluminum-gallium arsenide diode semiconductor with 9mW applied every other day (total dose=4J/cm(2)) on the borders of the wound. Tissue sections obtained from four experimental groups representing sham-irradiated animals, laser, silica and the association of both, were studied after 3, 7, 10, 15, 20, 30 and 60 days from the laser application. The wounded skin area was surgically removed and submitted to histological, immunohistochemical, ultrastructural, and immunofluorescent studies. Besides the degree and arrangement of collagen fibers and of their isotypes, the degree of edema, the presence of several cell types especially pericytes and myofibroblasts, were described and measured. The observation of Sirius-red stained slides under polarized microscopy revealed to be of great help during the morphological analysis of the collagen tissue dynamic changes. It was demonstrated that laser application was responsible for edema regression and a diminution in the number of inflammatory cells (p<0.05). An evident increase in the number of actin-positive cells was observed in the laser-treated wounds. Collagen deposition was less than expected in silica-treated wounds, and laser treatment contributed to its better differentiation and modulation in all irradiated groups. Thus, laser photobiomodulation was able to induce several modifications during the cutaneous healing process, especially in favoring newly-formed collagen fibers to be better organized and compactedly disposed.     

Isolation of polymerase chain reaction-ready bacterial DNA from Lake Baikal sediments by carboxyl-functionalised magnetic polymer microspheres

Carboxyl group-containing magnetic nonporous poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate) (P(HEMA-co-EDMA)) microspheres were used for the isolation of polymerase chain reaction (PCR)-ready DNA from samples of Baikal sediments. DNA was isolated using the phenol extraction method or the Soil DNA Isolation Kit. The occurrence of false-negative results in PCR caused by the presence of extracellular inhibitors in DNA samples was solved using solid phase reversible DNA immobilisation. PCR-ready DNA was reversibly adsorbed to the microspheres in the presence of 8.0% (w/v) poly(ethylene glycol) (PEG 6000) and 2.0M sodium chloride concentrations. The adsorbed DNA was released from the microspheres in a low ionic strength TE buffer. The quality of isolated DNA was checked by PCR amplification.     

Trap-assisted tunnelling current in MIM structures

A new model is presented of current transport in Metal Insulator Metal (MIM) structures by quantum mechanical tunnelling. In addition to direct tunnelling through an insulating layer, tunnelling via defects present in the insulating layer plays an important role. Examples of the influence of the material and thickness of the insulating layer, energy distribution of traps, and metal work functions are also provided.     

Incorporating ergonomic risks into assembly line balancing

In manufacturing, control of ergonomic risks at manual workplaces is a necessity commanded by legislation, care for health of workers and economic considerations. Methods for estimating ergonomic risks of workplaces are integrated into production routines at most firms that use the assembly-type of production. Assembly line re-balancing, i.e., re-assignment of tasks to workers, is an effective and, in case that no additional workstations are required, inexpensive method to reduce ergonomic risks. In our article, we show that even though most ergonomic risk estimation methods involve nonlinear functions, they can be integrated into assembly line balancing techniques at low additional computational cost. Our computational experiments indicate that re-balancing often leads to a substantial mitigation of ergonomic risks.