Electrical Current Signatures of DNA Base Modifications in Single Molecules Immobilized in the α-Hemolysin Ion Channel

Nanopore technology holds high potential for next-generation DNA sequencing. This method operates by drawing an individual single-stranded DNA molecule through a nanoscale pore, while monitoring the current deflections that occur as the DNA passes through. Individual current levels for the four DNA nucleotides have been established by immobilization of an end biotinylated strand in the pore, in which the nucleotide of interest is suspended at the most sensitive region of the ion channel. Due to the inherent reactivity of DNA bases, many modified nucleotides in the genome exist as a result of oxidative and UV insults, among others. Herein, the current levels for common DNA damage lesions 8-oxo-7,8-dihydroguanine, spiroiminodihydantoin, guanidinohydantoin, uridine, abasic sites, thymine dimers, thymine glycol, and 5-iodocytosine were assessed through immobilization experiments. In some cases, the current difference between the damaged and canonical nucleotides was not well resolved; therefore, we took advantage of the chemical reactivity of the new functional groups present to make amine adducts that shifted the current levels outside the range of the native nucleotides. Among the adducts studied, only the 2-aminomethyl-18-crown-6 adduct was able to give a large current shift in the immobilization experiment, as well as being observed in a translocation experiment. The results show potential in providing current-level modulators for identification of some types of DNA damage. In principle, any DNA base modification that can be converted chemically or enzymatically into an abasic site could be identified in this way.     

LAS glass–ceramic scaffolds by three-dimensional printing

Highly porous (>60% open porosity) glass–ceramic scaffolds with remarkable mechanical properties (compression strength of ～15 MPa) were produced by indirect 3D printing. Precursor glass powders were printed into 3D ordered structures and then heat treated to sinter and develop crystalline phases. The final glass–ceramic contained a β-spodumene solid solution together with a secondary phase of lithium disilicate.The precision of the printed geometry and the density of the struts in the scaffold depended on several processing parameters (e.g. powder size and flowability, layer thickness) and were improved by increasing the binder saturation and drying time. Two types of powders with different particle size distribution (PSD) and flowability were used. Powders with a larger PSD, could be processed within a wider range of printing parameters due to their good flowability; however, the printing precision and the struts density were lower compared to the scaffolds printed using the powder in a smaller average PSD.     

Authenticity Assessment of Extra Virgin Olive Oil: Evaluation of Desmethylsterols and Triterpene Dialcohols

Extra virgin olive oil (EVOO) has a long history of economic adulteration, the detection of which presents significant challenges due to the diverse composition of cultivars grown around the world and the limitations of existing methods for detecting adulteration. In this study, using Method COI/T.20/Doc. No. 30/Rev. 1 of the International Olive Council, the authenticity of 88 market samples of EVOO was evaluated by comparing total sterol contents, desmethylsterol composition, and contents of triterpene dialcohols (erythrodiol and uvaol) with purity criteria specified in the United States Standards for grades of olive oil and olive‐pomace oil. Three of the 88 samples labeled as EVOO failed to meet purity criteria, indicating possible adulteration with commodity oil and/or solvent‐extracted olive oil. Detection of adulteration was also evaluated by spiking an EVOO sample with commodity oil at the 10 % level. As expected, eight of the spiked samples (canola, corn, hazelnut, peanut, safflower, soybean, and sunflower oils, and palm olein) failed to meet purity criteria. Two of the three samples spiked with 10 % hazelnut oil went undetected for adulteration. Overall, a low occurrence rate of adulteration (<5 %), based on purity criteria for desmethylsterols and triterpene dialcohols, was detected for the 88 products labeled as EVOO.     

Molecular dynamics simulations of enantiomeric separations as an interfacial process in HPLC

Since chromatographic separation is a dynamic process, with the interactions between the drug and the chiral stationary phase mediated by the solvent, no single interacting structure, such as could be found by minimizing the energy, could possibly describe and account for the ratio of residence times in the chromatographic column for the enantiomeric pair. We describe the use of explicit-solvent fully atomistic molecular dynamics simulations, permitting all the interactions between the atoms constituting the chiral stationary phase, solvent molecules and the drug molecule. This allows us to better understand the molecular dynamic chiral recognition that provides the discrimination, which results in the separation of enantiomers by high performance liquid chromatography. It also provides a means of predicting, for a given set of conditions, which enantiomer elutes first and an estimate of the expected separation factor. In this review, we consider the use of molecular dynamics toward this understanding and prediction.     

High-Fat Diet Aggravates Cerebral Infarct,Hemorrhagic Transformation and Neuroinflammation in a Mouse Stroke Model

Background: Stroke in context of type 2 diabetes (T2D) is associated with a poorer outcome than in non-diabetic conditions. We aimed at creating a new reproducible mouse model of stroke in impaired glucose tolerance conditions induced by high-fat diet. Methods: Adult C57BL6 mice were fed for 2 months with either normal diet (ND) or high-fat diet (HFD). We used a model of Middle Cerebral Artery Occlusion (MCAO) for 90 min. Oral Glucose Tolerance Test (OGTT) and Insulin Tolerance Test (ITT) were used to assess pre-diabetic status. Brain infarct volume, hemorrhagic transformation (HT) as well as systemic and cerebral inflammatory markers were evaluated. Results: HFD was associated with an increased body weight and glycemia following OGTT. The HFD group presented a significant increase in brain infarct volume (38.7 (IQR 30–46.7%) vs. 28.45 (IQR 21–30%); p = 0.016) and HT (HFD: 2 (IQR 1–5) vs. ND: 0 (IQR 0–1); p = 0.012) and higher levels of IL-6 and MCP-1 in infarcted hemisphere compared to the ND group. Conclusion: Two months of HFD in adult mice were sufficient to alter the lipid profile and the control of hyperglycemia. These metabolic perturbations were significantly associated with increased infarct volume and hemorrhagic complications.     

Activation of the NLRP3 Inflammasome Increases the IL-1β Level and Decreases GLUT4 Translocation in Skeletal Muscle during Insulin Resistance

Low-grade chronic inflammation plays a pivotal role in the pathogenesis of insulin resistance (IR), and skeletal muscle has a central role in this condition. NLRP3 inflammasome activation pathways promote low-grade chronic inflammation in several tissues. However, a direct link between IR and NLRP3 inflammasome activation in skeletal muscle has not been reported. Here, we evaluated the NLRP3 inflammasome components and their role in GLUT4 translocation impairment in skeletal muscle during IR. Male C57BL/6J mice were fed with a normal control diet (NCD) or high-fat diet (HFD) for 8 weeks. The protein levels of NLRP3, ASC, caspase-1, gasdermin-D (GSDMD), and interleukin (IL)-1β were measured in both homogenized and isolated fibers from the flexor digitorum brevis (FDB) or soleus muscle. GLUT4 translocation was determined through GLUT4myc-eGFP electroporation of the FBD muscle. Our results, obtained using immunofluorescence, showed that adult skeletal muscle expresses the inflammasome components. In the FDB and soleus muscles, homogenates from HFD-fed mice, we found increased protein levels of NLRP3 and ASC, higher activation of caspase-1, and elevated IL-1β in its mature form, compared to NCD-fed mice. Moreover, GSDMD, a protein that mediates IL-1β secretion, was found to be increased in HFD-fed-mice muscles. Interestingly, MCC950, a specific pharmacological NLRP3 inflammasome inhibitor, promoted GLUT4 translocation in fibers isolated from the FDB muscle of NCD- and HFD-fed mice. In conclusion, we found increased NLRP3 inflammasome components in adult skeletal muscle of obese insulin-resistant animals, which might contribute to the low-grade chronic metabolic inflammation of skeletal muscle and IR development.     

Chemical analysis and significance of heterocyclic aromatic amines

 Levels of known heterocyclic amines vary from undetectable in many meats sold in fast food restaurants, to over 10 ng/g for meats prepared in restaurants that cook food to order, to hundreds of nanograms per gram for some meats cooked under certain home or laboratory conditions. To simulate the dry reactions that seem to occur at the meat surface we developed a model system to mimic these processes. Mixtures of free amino acids, creatinine and glucose, simulating the composition of beef or chicken, heated at 200  °C, form eight heterocyclic amines. Besides the commonly found 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline, 2-amino-3-methylimidazo[4,5-f]quinoline, 2-amino-3,4-dimethylimidazo[4,5-f]quinoline, 2-amino-3,4,8-trimethylimidazo[4,5-f]quinoxaline and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine, 2-amino-1,6-dimethylimidazo[4,5-b]pyridine, 2-amino-1,5,6-trimethylimidazo[4,5-b]pyridine and 2-amino-1,6-dimethylfuro[3,2-e]imidazo[4,5-b]pyridine were also found. The calculated risk of consumption of heterocyclic amines is determined by the dietary dose, the extrapolation of carcinogenic potencies from rodents to humans, and the extrapolation of high rodent doses to low human exposures. Results suggest that DNA binding is linear with dose, but that the human DNA forms more adducts per unit dose than that of the rat. Altogether, the risk appears to be equivalent to that for many carcinogens that are regulated. Received: 23 April 1998     

Chemical analysis and significance of heterocyclic aromatic amines

 Levels of known heterocyclic amines vary from undetectable in many meats sold in fast food restaurants, to over 10 ng/g for meats prepared in restaurants that cook food to order, to hundreds of nanograms per gram for some meats cooked under certain home or laboratory conditions. To simulate the dry reactions that seem to occur at the meat surface we developed a model system to mimic these processes. Mixtures of free amino acids, creatinine and glucose, simulating the composition of beef or chicken, heated at 200  °C, form eight heterocyclic amines. Besides the commonly found 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline, 2-amino-3-methylimidazo[4,5-f]quinoline, 2-amino-3,4-dimethylimidazo[4,5-f]quinoline, 2-amino-3,4,8-trimethylimidazo[4,5-f]quinoxaline and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine, 2-amino-1,6-dimethylimidazo[4,5-b]pyridine, 2-amino-1,5,6-trimethylimidazo[4,5-b]pyridine and 2-amino-1,6-dimethylfuro[3,2-e]imidazo[4,5-b]pyridine were also found. The calculated risk of consumption of heterocyclic amines is determined by the dietary dose, the extrapolation of carcinogenic potencies from rodents to humans, and the extrapolation of high rodent doses to low human exposures. Results suggest that DNA binding is linear with dose, but that the human DNA forms more adducts per unit dose than that of the rat. Altogether, the risk appears to be equivalent to that for many carcinogens that are regulated. Received: 23 April 1998     

Prevalence of Salmonella in two Botswana abattoir environments

A 1-year study was carried out to investigate the prevalence of Salmonella in two abattoir environments coded "A" and "B" in Gaborone, Botswana. The total number of environmental samples collected from abattoirs A and B was 250 and 300, respectively. The samples were taken from soils in the corrals, knife blades, saw blades, cattle-drinking water, cattle feces, and feed. Preenrichment, enrichment, and selective/differential media, which enabled the favorable growth of Salmonella, were used in the study. Salmonellae were present in all sampled environments. The most common serotypes found in the environment at abattoir A were E1, C1, C2, and B. Serotypes B, C1, C2, C3, and E1 were common in abattoir B. Antigenic characterization of the salmonellae isolates showed that Salmonella Anatum, Salmonella Azteca, Salmonella Saintpaul, Salmonella Cerro, and Salmonella Westhampton were predominant in abattoir A, whereas Salmonella Anatum, Salmonella Mbandaka, Salmonella Molade, Salmonella Reading, and Salmonella Oranienburg were dominant in abattoir B. Implementing hazard analysis critical control point principles in work procedures would definitely reduce the gross contamination taking place in abattoirs.     

Insights into the cITP process using on-line NMR spectroscopy

Recently, capillary isotachophoresis (cITP) has been coupled on-line with nuclear magnetic resonance (NMR) to enhance analysis of dilute charged analytes through sample concentration and separation. This study focuses on the unique detection capabilities of NMR to noninvasively examine the cITP process and obtain diagnostic information. With their enhanced mass sensitivity, microcoil NMR probes provide optimal detection for cITP/NMR. Whereas previous studies used deuterated buffers, a 1H NMR observable leading electrolyte, tetramethylammonium acetate, is employed here to better track cITP progression. Fortuitously, the 1H chemical shift of the acetate methyl resonance depends on pD. Hence, by using a calibration curve, the solution pD can be determined on-line during cITP. Similarly, intracapillary temperature can be measured in cITP/NMR by observing the HOD chemical shift. To obtain accurate chemical shift measurements, charge-neutral tert-butyl alcohol is added to all cITP electrolyte solutions as an internal reference. As an ancillary benefit, line width measurements of the ubiquitous tert-butyl alcohol enable NMR spectral resolution to be examined throughout the experiment. Capable of providing quantitative results, NMR simultaneously determines the concentrations of the leading ion, sample, and counterion over the course of the cITP experiment.