We report experimental measurements of the salt dependence of ion transport and DNA translocation through solid-state nanopores. The ionic conductance shows a three-order-of-magnitude decrease with ...decreasing salt concentrations from 1 M to 1 μM, strongly deviating from bulk linear behavior. The data are described by a model that accounts for a salt-dependent surface charge of the pore. Subsequently, we measure translocation of 16.5-μm-long dsDNA for 50 mM to 1 M salt concentrations. DNA translocation is shown to result in either a decrease (KCl > 0.4 M) or increase of the ionic current (KCl < 0.4 M). The data are described by a model where current decreases result from the partial blocking of the pore and current increases are attributed to motion of the counterions that screen the charge of the DNA backbone. We demonstrate that the two competing effects cancel at a KCl concentration of 370 ± 40 mM.
Recent studies have demonstrated that the anti-diabetic drug, metformin, can exhibit direct antitumoral effects, or can indirectly decrease tumor proliferation by improving insulin sensitivity. ...Despite these recent advances, the underlying molecular mechanisms involved in decreasing tumor formation are not well understood. In this study, we examined the antiproliferative role and mechanism of action of metformin in MCF-7 cancer cells treated with 10 mM of metformin for 24, 48, and 72 hours. Using BrdU and the MTT assay, it was found that metformin demonstrated an antiproliferative effect in MCF-7 cells that occurred in a time- and concentration-dependent manner. Flow cytometry was used to analyze markers of cell cycle, apoptosis, necrosis and oxidative stress. Exposure to metformin induced cell cycle arrest in G0-G1 phase and increased cell apoptosis and necrosis, which were associated with increased oxidative stress. Gene and protein expression were determined in MCF-7 cells by real time RT-PCR and western blotting, respectively. In MCF-7 cells metformin decreased the activation of IRβ, Akt and ERK1/2, increased p-AMPK, FOXO3a, p27, Bax and cleaved caspase-3, and decreased phosphorylation of p70S6K and Bcl-2 protein expression. Co-treatment with metformin and H2O2 increased oxidative stress which was associated with reduced cell number. In the presence of metformin, treating with SOD and catalase improved cell viability. Treatment with metformin resulted in an increase in p-p38 MAPK, catalase, MnSOD and Cu/Zn SOD protein expression. These results show that metformin has an antiproliferative effect associated with cell cycle arrest and apoptosis, which is mediated by oxidative stress, as well as AMPK and FOXO3a activation. Our study further reinforces the potential benefit of metformin in cancer treatment and provides novel mechanistic insight into its antiproliferative role.
For a hundred years or more, oil and natural gas has supplied fuel and other raw chemicals to support economic growth. In the last decades their shrinking reservoirs and the increasing cost of ...production has become obvious, leading researchers to look for alternative substitutes of all the chemical materials presently derived from oil and gas. This review is focused on xylan, the second most abundant plant polysaccharide on our planet. Some xylan-derived products have already found commercial applications (ethanol, xylitol, xylo-oligosaccharides) while others could have a great future in a wide range of industries. The chemical and structural variations of xylans produced by different plants, and the concentration of xylan in various plant resources are summarized. This review discusses the latest research developments in extraction and purification methodologies, and chemical modification, as well as the analytical methods necessary for xylan related research.
Despite gel electrophoresis being one of the main workhorses of molecular biology, the physics of polyelectrolyte electrophoresis in a strongly confined environment remains poorly understood. Theory ...indicates that forces in electrophoresis result from interplay between ionic screening and hydrodynamics, but these ideas could so far be addressed only indirectly by experiments based on macroscopic porous gels. Here, we provide a first direct experimental test by measuring the electrophoretic force on a single DNA molecule threading through a solid-state nanopore as a function of pore size. The stall force gradually decreases on increasing the nanopore diameter from 6 to 90 nm, inconsistent with expectations from simple electrostatics and strikingly demonstrating the influence of the hydrodynamic environment. We model this process by applying the coupled Poisson-Boltzmann and Stokes equations in the nanopore geometry and find good agreement with the experimental results.
Exocellular (1→6)-β-d-glucan (lasiodiplodan) produced by the fungus
MMPI was derivatized by carboxymethylation using different concentrations of a derivatizing agent. Lasiodiplodan was derivatized by ...carboxymethylation in an attempt to increase its solubility and enhance its biological activities. Carboxymethylglucans with degrees of substitution (DS) of 0.32, 0.47, 0.51, 0.58, and 0.68 were produced and characterized. FTIR analysis showed a band of strong intensity at 1600 cm
and an absorption band at 1421 cm
, resulting from asymmetric and symmetrical stretching vibrations, respectively, of the carboxymethyl group COO- in the carboxymethylated samples. Thermal analysis showed that native lasiodiplodan (LN) and carboxymethylated derivatives (LC) exhibited thermal stability up to 200-210 °C. X-ray diffractometry demonstrated that both native and carboxymethylated lasiodiplodan presented predominantly an amorphous nature. Scanning electron microscopy revealed that carboxymethylation promoted morphological changes in the biopolymer and increased porosity, and alveolar structures were observed along the surface. The introduction of carboxymethyl groups in the macromolecule promoted increased solubility and potentiated the hydroxyl radical-scavenging activity, suggesting a correlation between degree of substitution and antioxidant activity.
Noise in solid-state nanopores Smeets, R.M.M; Keyser, U.F; Dekker, N.H ...
Proceedings of the National Academy of Sciences - PNAS,
01/2008, Letnik:
105, Številka:
2
Journal Article
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Odprti dostop
We study ionic current fluctuations in solid-state nanopores over a wide frequency range and present a complete description of the noise characteristics. At low frequencies (f less, similar 100 Hz) ...we observe 1/f-type of noise. We analyze this low-frequency noise at different salt concentrations and find that the noise power remarkably scales linearly with the inverse number of charge carriers, in agreement with Hooge's relation. We find a Hooge parameter α = (1.1 ± 0.1) x 10⁻⁴. In the high-frequency regime (f greater, similar 1 kHz), we can model the increase in current power spectral density with frequency through a calculation of the Johnson noise. Finally, we use these results to compute the signal-to-noise ratio for DNA translocation for different salt concentrations and nanopore diameters, yielding the parameters for optimal detection efficiency.
Torsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrapping and thereby the progression of polymerases. However, the propagation of ...twist in condensed chromatin remains yet unresolved. Here, we measure how force and torque impact chromatin fibers with a nucleosome repeat length of 167 and 197. We find that both types of fibers fold into a left-handed superhelix that can be stabilized by positive torsion. We observe that the structural changes induced by twist were reversible, indicating that chromatin has a large degree of elasticity. Our direct measurements of torque confirmed the hypothesis of chromatin fibers as a twist buffer. Using a statistical mechanics-based torsional spring model, we extracted values of the chromatin twist modulus and the linking number per stacked nucleosome that were in good agreement with values measured here experimentally. Overall, our findings indicate that the supercoiling generated by DNA-processing enzymes, predicted by the twin-supercoiled domain model, can be largely accommodated by the higher-order structure of chromatin.
The RelA-mediated stringent response is at the heart of bacterial adaptation to starvation and stress, playing a major role in the bacterial cell cycle and virulence. RelA integrates several ...environmental cues and synthesizes the alarmone ppGpp, which globally reprograms transcription, translation, and replication. We have developed and implemented novel single-molecule tracking methodology to characterize the intracellular catalytic cycle of RelA. Our single-molecule experiments show that RelA is on the ribosome under nonstarved conditions and that the individual enzyme molecule stays off the ribosome for an extended period of time after activation. This suggests that the catalytically active part of the RelA cycle is performed off, rather than on, the ribosome, and that rebinding to the ribosome is not necessary to trigger each ppGpp synthesis event. Furthermore, we find fast activation of RelA in response to heat stress followed by RelA rapidly being reset to its inactive state, which makes the system sensitive to new environmental cues and hints at an underlying excitable response mechanism.
The overall consumption of ultra-processed food (UPF) has previously been associated with type 2 diabetes. However, due to the substantial heterogeneity of this food category, in terms of their ...nutritional composition and product type, it remains unclear whether previous results apply to all underlying consumption patterns of UPF.
Of 70,421 participants (35-70 years, 58.6% women) from the Lifelines cohort study, dietary intake was assessed with a food frequency questionnaire. UPF was identified according to the NOVA classification. Principal component analysis (PCA) was performed to derive UPF consumption patterns. The associations of UPF and adherence to UPF consumption patterns with incidence of type 2 diabetes were studied with logistic regression analyses adjusted for age, sex, diet quality, energy intake, alcohol intake, physical activity, TV watching time, smoking status, and educational level.
During a median follow-up of 41 months, a 10% increment in UPF consumption was associated with a 25% higher risk of developing type 2 diabetes (1128 cases; OR 1.25 95% CI 1.16, 1.34). PCA revealed four habitual UPF consumption patterns. A pattern high in cold savory snacks (OR 1.16 95% CI 1.09, 1.22) and a pattern high in warm savory snacks (OR 1.15 95% CI 1.08, 1.21) were associated with an increased risk of incident type 2 diabetes; a pattern high in traditional Dutch cuisine was not associated with type 2 diabetes incidence (OR 1.05 95% CI 0.97, 1.14), while a pattern high in sweet snacks and pastries was inversely associated with type 2 diabetes incidence (OR 0.82 95% CI 0.76, 0.89).
The heterogeneity of UPF as a general food category is reflected by the discrepancy in associations between four distinct UPF consumption patterns and incident type 2 diabetes. For better public health prevention, research is encouraged to further clarify how different UPF consumption patterns are related to type 2 diabetes.
β-Glucans are biomacromolecules well known, among other biological activities, for their immunomodulatory potential. Similarly, extracts of
also possess biological properties and are used in folk ...medicine for the treatment of inflammation, ulcers, and hepatic diseases. Microparticles containing (1→6)-β-d-glucan (lasiodiplodan) and
extract were produced and characterized. A 2
factorial design was employed to define the conditions of production of microparticles by atomization. Lasiodiplodan associated with maltodextrin and gum arabic was studied as a matrix material. Microparticles of 0.4 μm mean size and high phenolics content (3157.9 μg GAE/g) were obtained under the optimized conditions. The microparticle size ranged from 0.23 to 1.21 µm, and the mathematical model that best represented the release kinetics of the extract was the Korsmeyer-Peppas model. Diffusional exponent (n) values of 0.64 at pH 7.7 and 1.15 at pH 2.61 were found, indicating particles with a non-Fickian or anomalous transport system, and Super Case II transport, respectively. Thermal analysis indicated that the microparticles demonstrated high thermal stability. The X-ray diffraction analyses revealed an amorphous structure, and HPLC-DAD analysis showed microparticles rich in phenolic compounds: caffeic acid, p-coumaric acid, and catechin. The microparticles obtained comprise a new biomaterial with biological potential for applications in different fields.
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