Dealing with repetitions in sequencing by hybridization

DNA sequencing by hybridization (SBH) induces errors in the biochemical experiment. Some of them are random and disappear when the experiment is repeated. Others are systematic, involving repetitions in the probes of the target sequence. A good method for solving SBH problems must deal with both types of errors. In this work we propose a new hybrid genetic algorithm for isothermic and standard sequencing that incorporates the concept of structured combinations. The algorithm is then compared with other methods designed for handling errors that arise in standard and isothermic SBH approaches. DNA sequences used for testing are taken from GenBank. The set of instances for testing was divided into two groups. The first group consisted of sequences containing positive and negative errors in the spectrum, at a rate of up to 20%, excluding errors coming from repetitions. The second group consisted of sequences containing repeated oligonucleotides, and containing additional errors up to 5% added into the spectra. Our new method outperforms the best alternative procedures for both data sets. Moreover, the method produces solutions exhibiting extremely high degree of similarity to the target sequences in the cases without repetitions, which is an important outcome for biologists. The spectra prepared from the sequences taken from GenBank are available on our website http://bio.cs.put.poznan.pl/.     

Kinetic Spectrophotometric Determination of Chromium (VI) by Oxidation of Sodium Pyrogallol-5-sulphonate by Hydrogen Peroxide

Summary. A new selective, sensitive, and simple kinetic method is developed for the determination of trace amounts of chromium (VI). The method is based on the catalytic effect of Cr(VI) on the reaction of sodium pyrogallol-5-sulphonate (PS) with hydrogen peroxide. The reaction is followed spectrophotometrically by tracing the oxidation product at 437nm within 1min after addition of H₂O₂. The optimum reaction conditions are PS (1.32·10^–3mol·dm^–3), H₂O₂ (0.32mol·dm^–3), HClO₄ (2.6·10^–3mol·dm^–3) at 25°C. Following this procedure, chromium (VI) can be determined with a linear calibration graph up to 0.25ng·cm^–3 and a detection limit of 0.024ng·cm^–3, based on the 3 criterion. The interference effect of several species was also investigated and it was found that the most common cations and anions do not interfere with the determination. The developed procedure was successfully applied to the determination of Cr(VI) and total Cr in river waters and total Cr in herbal samples.     

Interface Amorphization of Two-Dimensional Black Phosphorus upon Treatment with Diazonium Salts

Two-dimensional (2D) black phosphorus (BP) represents one of the most appealing 2D materials due to its electronic, optical, and chemical properties. Many strategies have been pursued to face its environmental instability, covalent functionalization being one of the most promising. However, the extremely low functionalization degrees and the limitations in proving the nature of the covalent functionalization still represent challenges in many of these sheet architectures reported to date. Here we shine light on the structural evolution of 2D-BP upon the addition of electrophilic diazonium salts. We demonstrated the absence of covalent functionalization in both the neutral and the reductive routes, observing in the latter case an unexpected interface conversion of BP to red phosphorus (RP), as characterized by Raman, ³¹P-MAS NMR, and X-ray photoelectron spectroscopies (XPS). Furthermore, thermogravimetric analysis coupled to gas chromatography and mass spectrometry (TG-GC-MS), as well as electron paramagnetic resonance (EPR) gave insights into the potential underlying radical mechanism, suggesting a Sandmeyer-like reaction.     

X-ray analysis at 150?K, synthesis and theoretical calculations of 1-naphthaleneacrylic acid

The X-ray structure, synthesis, theoretical calculation and IR spectra of 1-naphthaleneacrylic acid are reported. The titled compound crystallizes in the monoclinic C 2/c space group with unit cell parameters: a = 14.556(3), b = 5.1332(10), c = 26.832(5) ?, β = 97.02(3)°, V = 1989.8(7) ?³, Z = 8 and form typical centrosymmetric hydrogen-bonded dimers. Theoretical calculations of 1-naphthylacrylic acid isolated molecule and hydrogen-bonded dimer have been carried out using density functional theory at the B3LYP level. For optimized structures the vibrational spectra have been then calculated and compared with experimental IR spectrum. The assignment and characterization of theoretical vibrational spectra were based on the potential energy distribution analysis. This comparison has shown that the theoretical spectrum for the dimer structure is in good agreement with the experimental one. Structural comparisons with naphthalene, and with some substituted 2-propenoic acids have shown influence of the substituent on conformation of the naphthalene ring or 2-propenoic moiety.     

Determination of traces of cobalt in the presence of nioxime and cetyltrimethylammonium bromide by adsorptive stripping voltammetry

A sensitive method of Co(II) determination by adsorptive stripping voltammetry is presented. The method exploits the enhancement of cobalt peak current observed in the system Co(II)-nioxime-cetyltrimethylammonium bromide-piperazine-N,N′-bis(2-ethanesulfonic acid). The calibration plot for an accumulation time of 60 s is linear from 5 × 10⁻¹¹ to 3 × 10⁻⁹ mol L⁻¹. The relative standard deviation is 3.8% for Co(II) determination at concentration 1 × 10⁻⁹ mol L⁻¹. The detection limit is 1.7 × 10⁻¹¹ mol L⁻¹. The validation of the method is performed by the analyses of certified reference materials and comparing the result of Co(II) determination in river water sample by the proposed method with those obtained by ET AAS. The main advantage of this new system is the micro-trace Co(II) determination by adsorptive stripping voltammetry, as compared to those described before, a low concentration of the supporting electrolyte used, and so commercially available reagents without additional purification can be used.     

α-CGRP disrupts amylin fibrillization and regulates insulin secretion: implications on diabetes and migraine

Despite being relatively benign and not an indicative signature of toxicity, fibril formation and fibrillar structures continue to be key factors in assessing the structure–function relationship in protein aggregation diseases. The inability to capture molecular cross-talk among key players at the tissue level before fibril formation greatly accounts for the missing link toward the development of an efficacious therapeutic intervention for Type II diabetes mellitus (T2DM). We show that human α-calcitonin gene-related peptide (α-CGRP) remodeled amylin fibrillization. Furthermore, while CGRP and/or amylin monomers reduce the secretion of both mouse Ins1 and Ins2 proteins, CGRP oligomers have a reverse effect on Ins1. Genetically reduced Ins2, the orthologous version of human insulin, has been shown to enhance insulin sensitivity and extend the life-span in old female mice. Beyond the mechanistic insights, our data suggest that CGRP regulates insulin secretion and lowers the risk of T2DM. Our result rationalizes how migraine might be protective against T2DM. We envision the new paradigm of CGRP : amylin interactions as a pivotal aspect for T2DM diagnostics and therapeutics. Maintaining a low level of amylin while increasing the level of CGRP could become a viable approach toward T2DM prevention and treatment.

CGRP concentration is elevated in migraine conditions. The protective effect of migraine against type 2 diabetes is attributed to the ability of CGRP to remodel human amylin aggregation and to suppress the secretion of mouse insulin 2 (the orthologue of human insulin).     

Sensitive voltammetric determination of gallium in aluminium materials using renewable mercury film silver based electrode

Simple cyclic renewable silver amalgam film electrode (Hg(Ag)FE), applied for the determination of gallium(III) using differential pulse anodic stripping voltammetry (DP ASV), is presented. The effects of various factors such as: preconcentration potential and time, pulse height, step potential and supporting electrolyte composition are optimised. The calibration graph is linear from 5?nM (0.35?µg?L^?1) to 80?nM (5.6?µg?L^?1) for a preconcentration time of 60?s, with correlation coefficient of 0.995. For a Hg(Ag)FE with a surface area of 9.9?mm² the detection limit for a preconcentration time of 120?s is as low as 0.1?µg?L^?1. The repeatability of the method at a concentration level of the analyte as low as 3.5?µg?L^?1, expressed as RSD is 3.2% (n?=?5). The proposed method was successfully applied by studying the synthetic samples and simultaneously recovery of Ga(III) from spiked aluminium samples.     

Urease adsorption and activity on magnetite nanoparticles functionalized with monofunctional and bifunctional surface layers

The surface of magnetite nanoparticles was coated with functional polysiloxane layers using reaction of hydrolytic copolycondensation of tetraethoxysilane and 3-aminopropyltriethoxysilane (or N-[3-trimethoxysilylpropyl]ethylendiamine), and also that of tetraethoxysilane, 3-aminopropyltriethoxysilane and methyltriethoxysilane (or n-propyltriethoxysilane). It was shown that these functionalized magnetically controllable particles (about 60–150 nm in size as aggregates), as opposed to magnetite, adsorb urease well from aqueous solutions (up to 1 g/g), and that the level of residual activity of adsorbed layers is up to 84 % in the case of a bifunctional sample. It was established that the activity of immobilized urease is normally gradually reduced during storage of the samples, but in the case of ethylenediamine functional group is not decreased for 45 days. The synthesized samples are promising for use as magnetically directed biocatalysts.