A benchmark of optimally folded protein structures using integer programming and the 3D-HP-SC model

The Protein Structure Prediction (PSP) problem comprises, among other issues, forecasting the three-dimensional native structure of proteins using only their primary structure information. Most computational studies in this area use synthetic data instead of real biological data. However, the closer to the real-world, the more the impact of results and their applicability. This work presents 17 real protein sequences extracted from the Protein Data Bank for a benchmark to the PSP problem using the tri-dimensional Hydrophobic-Polar with Side-Chains model (3D-HP-SC). The native structure of these proteins was found by maximizing the number of hydrophobic contacts between the side-chains of amino acids. The problem was treated as an optimization problem and solved by means of an Integer Programming approach. Although the method optimally solves the problem, the processing time has an exponential trend. Therefore, due to computational limitations, the method is a proof-of-concept and it is not applicable to large sequences. For unknown sequences, an upper bound of the number of hydrophobic contacts (using this model) can be found, due to a linear relationship with the number of hydrophobic residues. The comparison between the predicted and the biological structures showed that the highest similarity between them was found with distance thresholds around 5.2–8.2 Å. Both the dataset and the programs developed will be freely available to foster further research in the area.     

Synthesis,spectroscopic studies,thermal analyses,biological activity of tridentate-coordinated transition-metal complexes [M(L)X2] and crystal structure of [ZnBr2(2,6-bis(tert-butylthiomethyl)pyridine)]

A new terdentate acyclic pincer ligand, 2,6-bis(tert-butylthiomethyl)pyridine (tbtmp), was synthesized and reacted with several complexes of iron, zinc, nickel, cobalt, and copper. The ligand and its coordination compounds were characterized using elemental analysis, infrared, ¹H- and ¹³C-NMR-spectroscopy, thermal analyses, plus—for the Zn complex—single-crystal X-ray diffractometry. The structure of [Zn(L)Br₂] was solved in the tetragonal crystal system, chiral space groups P4₁2₁2 and P4₃2₁2 (No. 92 and No. 96, a = 947.2(1) pm, c = 2265.2(5) pm), revealing five-fold coordination of the metal atoms. According to spectroscopy, all complexes share the same coordination environment around the metal atoms, consisting of two halide anions and a sulfur-methylene-pyridine-methylene-sulfur entity; tbtmp acts as a tridentate ligand with the pyridine N atom and both tert-butylthio S atoms coordinating to the metal ions (NS2). The analysis results indicate that the metal ions are coordinated as distorted pseudo-bipyramids, LMX₂, with the chelate ligand meridionally arranged. One of the complexes contains ethanol as an additional ligand, resulting in a pseudo-octahedral coordination sphere [Ni(L)Cl₂EtOH]. The latter was obtained in the form of green crystals, which turn into a red powder with loss of the ethanol molecule. Fe (III), Co(II), Ni(II) and Cu(II) metal complexes [M(L)Cl₂] were screened for their antibacterial activity against B. subtilis G(+) and Escherichia coli G(−) bacteria, and fungus (Candida albicans and Aspergillus flavus).     

Quantification of myo‐inositol, 1,5‐anhydro‐ D‐sorbitol,and D‐chiro‐inositol using high‐performance liquid chromatography with electrochemical detection in very small volume clinical samples

Inositol is a six‐carbon sugar alcohol and is one of nine biologically significant isomers of hexahydroxycyclohexane. Myo‐inositol is the primary biologically active form and is present in higher concentrations in the fetus and newborn than in adults. It is currently being examined for the prevention of retinopathy of prematurity in newborn preterm infants. A robust method for quantifying myo‐inositol (MI), D ‐chiro‐inositol (DCI) and 1,5‐anhydro‐ D ‐sorbitol (ADS) in very small‐volume (25 μL) urine, blood serum and/or plasma samples was developed. Using a multiple‐column, multiple mobile phase liquid chromatographic system with electrochemical detection, the method was validated with respect to (a) selectivity, (b) accuracy/recovery, (c) precision/reproducibility, (d) sensitivity, (e) stability and (f) ruggedness. The standard curve was linear and ranged from 0.5 to 30 mg/L for each of the three analytes. Above‐mentioned performance measures were within acceptable limits described in the Food and Drug Administration's Guidance for Industry: Bioanalytical Method Validation. The method was validated using blood serum and plasma collected using four common anticoagulants, and also by quantifying the accuracy and sensitivity of MI measured in simulated urine samples recovered from preterm infant diaper systems. The method performs satisfactorily measuring the three most common inositol isomers on 25 μL clinical samples of serum, plasma, milk, and/or urine. Similar performance is seen testing larger volume samples of infant formulas and infant formula ingredients. MI, ADS and DCI may be accurately tested in urine samples collected from five different preterm infant diapers if the urine volume is greater than 2–5 mL. Copyright © 2015 John Wiley & Sons, Ltd.     

The application of the Lattice Boltzmann method to the one-dimensional modeling of pulse waves in elastic vessels

The one-dimensional nonlinear equations for the blood flow motion in distensible vessels are considered using the kinetic approach. It is shown that the Lattice Boltzmann (LB) model for non-ideal gas is asymptotically equivalent to the blood flow equations for compliant vessels at the limit of low Knudsen numbers. The equations of state for non-ideal gas are transformed to the pressure-luminal area response. This property allows to model arbitrary pressure-luminal area relations. Several test problems are considered: the propagation of a sole nonlinear wave in an elastic vessel, the propagation of a pulse wave in a vessel with varying mechanical properties (artery stiffening) and in an artery bifurcation, in the last problem Resistor–Capacitor–Resistor (RCR) boundary conditions are considered. The comparison with the previous results shows a good precision.     

Microfunnel‐filter‐based emulsification microextraction followed by gas chromatography for simple determination of organophosphorus pesticides in environmental water samples

A simple and fast method named microfunnel‐filter‐based emulsification microextraction is introduced for an efficient determination of some organophosphorus pesticides including diazinon, malathion, and chlorpyrifos in the environmental samples including the river, sea, and well water. This method is based upon the dispersion of a low‐toxicity organic solvent (dihexyl ether), as the extractant, in a high volume of an aqueous sample solution (45 mL). It is implemented without a centrifugation step, and using a syringe filter and a micro‐funnel, the phase separation and transfer of the enriched analytes to the gas chromatograph are simply achieved. By filtration of the extractant phase, a suitable sample clean‐up is obtained, and the total extraction time is just a few minutes. The factors influencing the extraction efficiency are optimized, and under the optimal conditions, the proposed method provides a good linearity (in the range of 15–1500 ng/mL (R² > 0.996). A high enrichment factor is obtained (in the range of 306–342), and the method provides low limits of detection and quantification (in the ranges of 4–8 and 15–25 ng/mL, respectively).     

Stable isotope dilution assay for the accurate determination of tricaine in fish samples by HPLC–MS–MS

Tricaine methanesulfonate is one of most commonly used anesthetics in fish during blood sampling, artificial propagation and long‐distance transportation. In this study, an accurate method for the quantitative determination of tricaine in fish samples by a stable isotope dilution assay coupled with high‐performance liquid chromatography–triple quadrupole mass spectrometry was developed. Tricaine‐D₅ was synthesized and used as an isotopically labeled internal standard for the determination of tricaine. The analytical performance of the method was validated for tricaine determination in marine fish and freshwater fish. The determination of tricaine was linear in the range of 2.0–200.0 μg L^?1. The limit of detection and limit of quantitation for fish muscle tissues were 1.0 and 4.0 μg kg^?1, respectively. Good recoveries were obtained in the range of 92.08–97.50%. The inter‐ and intra‐assay relative standard deviations (RSD values) were investigated, and the values were 0.39–3.01 and 0.85–2.77%, respectively. The values of CCα and CCβ were 10.21–10.43 and 10.42–10.87 μg kg^?1, respectively. The clearance of MS‐222 from grass carp was further studied using our method. The results demonstrate that MS‐222 could be well absorbed and rapidly eliminated after bath administration.     

Determination of four acidic nonsteroidal anti‐inflammatory drugs in wastewater samples by dispersive liquid–liquid microextraction based on solidification of floating organic droplet and high‐performance liquid chromatography

A simple, environmentally friendly, and sensitive dispersive liquid–liquid microextraction based on solidification of floating organic droplet for the extraction of four acidic nonsteroidal anti‐inflammatory drugs (ketoprofen, naproxen, ibuprofen, and diclofenac) from wastewater samples subsequent by high‐performance liquid chromatography analysis was developed. The influence of extraction parameters such as pH, the effect of solution ionic strength, type of extraction solvent, disperser solvent, and extraction solvent volume were studied. High enrichment factors (283–302) were obtained through the developed method. The method provides good linearity (r > 0.999) in a concentration range of 1–100 μg/L, good intra‐ and inter‐day precision (relative standard deviation < 7%) and low limits of quantification. The relative recoveries of the selected compounds were situated over 80% both in synthetic and real water samples. The developed method has been successfully applied for the analysis of the selected compounds in wastewater samples.     

Simple in‐house flow‐injection capillary electrophoresis with capacitively coupled contactless conductivity method for the determination of colistin

An in‐house flow‐injection capillary electrophoresis with capacitively coupled contactless conductivity detection method was developed for the direct measurement of colistin in pharmaceutical samples. The flow injection and capillary electrophoresis systems are connected by an acrylic interface. Capillary electrophoresis separation is achieved within 2 min using a background electrolyte solution of 5 mM 2‐morpholinoethanesulfonic acid and 5 mM histidine (pH 6). The flow‐injection section allows for convenient filling of the capillary and sample introduction without the use of a pressure/vacuum manifold. Capacitively coupled contactless conductivity detection is employed since colistin has no chromophore but is cationic at pH 6. Calibration curve is linear from 20 to 150 mg/L, with a correlation coefficient (r²) of 0.997. The limit of quantitation is 20 mg/L. The developed method provides precision, simplicity, and short analysis time.     

Preparation of 17β‐estradiol‐imprinted material by surface‐initiated atom transfer radical polymerization and its application

A novel 17β‐estradiol molecularly imprinted polymer was grafted onto the surface of initiator‐immobilized silica by surface‐initiated atom transfer radical polymerization. The resulting molecularly imprinted polymer was characterized by elemental analysis and thermogravimetric analysis. The binding property of molecularly imprinted polymer for 17β‐estradiol was also studied with both static and dynamic methods. The results showed that the molecularly imprinted polymer possessed excellent recognition capacity for 17β‐estradiol (180.65 mg/g at 298 K), and also exhibited outstanding selectivity for 17β‐estradiol over the other competitive compounds (such as testosterone and progesterone). Then, the determination of trace 17β‐estradiol in beef samples was successfully developed by using molecularly imprinted polymer solid‐phase extraction coupled with high‐performance liquid chromatography. The limit of detection was 0.25 ng/mL, and the amount of 17β‐estradiol in beef samples was detected at 2.83 ng/g. This work proposed a sensitive, rapid, reliable, and convenient approach for the determination of trace 17β‐estradiol in complicated beef samples.