Using color histograms and SPA-LDA to classify bacteria

In this work, a new approach is proposed to verify the differentiating characteristics of five bacteria (Escherichia coli, Enterococcus faecalis, Streptococcus salivarius, Streptococcus oralis, and Staphylococcus aureus) by using digital images obtained with a simple webcam and variable selection by the Successive Projections Algorithm associated with Linear Discriminant Analysis (SPA-LDA). In this sense, color histograms in the red–green–blue (RGB), hue-saturation-value (HSV), and grayscale channels and their combinations were used as input data, and statistically evaluated by using different multivariate classifiers (Soft Independent Modeling by Class Analogy (SIMCA), Principal Component Analysis-Linear Discriminant Analysis (PCA-LDA), Partial Least Squares Discriminant Analysis (PLS-DA) and Successive Projections Algorithm-Linear Discriminant Analysis (SPA-LDA)). The bacteria strains were cultivated in a nutritive blood agar base layer for 24 h by following the Brazilian Pharmacopoeia, maintaining the status of cell growth and the nature of nutrient solutions under the same conditions. The best result in classification was obtained by using RGB and SPA-LDA, which reached 94 and 100 % of classification accuracy in the training and test sets, respectively. This result is extremely positive from the viewpoint of routine clinical analyses, because it avoids bacterial identification based on phenotypic identification of the causative organism using Gram staining, culture, and biochemical proofs. Therefore, the proposed method presents inherent advantages, promoting a simpler, faster, and low-cost alternative for bacterial identification. Figure

Summary of the new proposed methodology for bacteria classification by using color histograms and SPA-LDA     

High-level Expression of a Manganese Superoxide Dismutase (PoMn-SOD) from Pleurotus ostreatus in Pichia pastoris

The full-length cDNA of Pleurotus ostreatus superoxide dismutase (PoMn-SOD) was cloned and successfully expressed by using the pPIC9K vector under the control of alcohol oxidase 1 promoter with a secretion signal peptide (α-factor) in Pichia pastoris. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting demonstrated that recombinant PoMn-SOD, a 21.8 kDa protein, was secreted into the culture medium. Nondenaturing PAGE experiments confirmed that recombinant PoMn-SOD was secreted in a functionally active form and the expression system did not require any acid activation process. The factors affecting the expression level were optimized in shaking flask cultures. The maximum enzyme activity (156.9 U/mg) was observed under the following conditions: Initial medium pH was 6.0, induction time point was at the 6th day, and methanol concentration was 0.7 % (v/v). This was the first report on secretory expression of recombinant PoMn-SOD in P. pastoris, which might provide a reference for further practical applications.     

Ultrasensitive detection and identification of BRAF V600 mutations in fresh frozen,FFPE, and plasma samples of melanoma patients by E-ice-COLD-PCR

A number of molecular diagnostic methods have been developed for the detection and identification of mutations in tumor samples, which are important for the choice of treatment in the context of personalized medicine. For the treatment of metastatic melanoma, Vemurafenib is recommended for patients with BRAF V600 activating mutations. However, the different assays developed to date for the detection of these mutations lack sensitivity or specificity or do not allow a sequencing-based identification or validation of the mutation. Recently, enhanced improved and complete enrichment co-amplification at lower denaturation temperature-polymerase chain reaction (E-ice-COLD-PCR) has been developed as a sensitive method for the detection and identification of mutations in KRAS codons 12/13. Here, we present the first E-ice-COLD-PCR assay for the detection and identification of BRAF codon 600 mutations, which has a large dynamic range, as 25 pg to 25 ng can be used as DNA input without any reduction in mutation enrichment efficiency, and which can detect down to 0.01 % of mutated alleles in a wild-type background. The assay has been validated on fresh frozen, formalin-fixed paraffin-embedded (FFPE), and plasma samples of melanoma patients and has allowed the detection and identification of BRAF mutations present in samples appearing as wild type using standard pyrosequencing, endpoint genotyping, or Sanger sequencing. Thus, the BRAF V600 E-ice-COLD-PCR assay is currently one of the most powerful molecular diagnostic tools for the ultrasensitive detection and identification of BRAF codon 600 mutations.     

Preparation of immobilized sepharose-micrococcal nuclease derivatives: activity and stability

Micrococcal nuclease has been covalently attached to CNBr-activated Sepharose 4B by coupling through three different enzyme functions: (a) amino groups; (b) carboxyl groups; and (c) tyrosyl or histidyl residues. On the basis of coupling yield and catalytic efficiency, Sepharose-(NH₂) nuclease derivatives were chosen for further activity andstability studies. The activity of the insoluble enzyme has been evaluated with macromolecular (DNA) and small (synthetic nucleotide) substrates; with the latter the enzyme retains 70% of native enzyme activity. Good enhancement of enzyme stability in the 4–40°C range has been observed.     

Lariat ethers in the chiral recognition of amino acid esters:electrospray ionization mass spectrometry investigation

The ability of the crown ethers (1–4), containing the ortho- or para- methoxyphenoxy-methyl substituents in their structure, to chiral recognition in reference to amino acid esters has been investigated by electrospray ionization mass spectrometry (ESI-MS). The method allows registering the diastereomeric complexes between the studied crowns as hosts and the protonated alanine, phenylglycine and phenylalanine methyl esters as guests in the gas phase. ESI-MS experiments using isotopically labeled guests provide robust and reproducible results, indicating a moderate degree of chiral discrimination in the series of the studied crown ethers. ESI-MS experiments using achiral amine as a reference yielded the results comparable with the previous method. It has been found that (S)-enantiomers of the crowns bind predominately (S)-enantiomers of the amino acid esters, and vice-versa. It has been shown that the chiral ortho-substituted crown (S)-1 demonstrates the more pronounced values for chiral discrimination as compared with the para-substituted crown (S)-2. This fact indicates the interrelationship between the chiral recognition and the lariat nature of crown 1. Increasing the size of the cavity and the presence of a flat aromatic moiety in crowns 3 and 4 strengthens their complexing ability, simultaneously weakening the enantioselectivity of the complexation.     

Purification,Characterisation and Cloning of a 2S Albumin with DNase,RNase and Antifungal Activities from Putranjiva Roxburghii

The present study reports the characterisation of a novel ~12-kDa heterodimeric protein, designated as putrin, from the seeds of Putranjiva roxburghii. The purification of putrin to homogeneity was accomplished using DEAE-sepharose where protein was unbound, CM-sepharose and Cibacron blue 3GA where it was bound and appeared as single peak on a size-exclusion chromatography column. A 15 % sodium dodecyl sulphate polyacrylamide electrophoresis gel, under reducing condition, demonstrated that putrin is made of two polypeptide chains of approximately 4.5 and 7.5 kDa. Circular dichroism studies demonstrated the helical nature and conformational stability of protein at increasing temperatures. Putrin exhibited both RNase and DNase activities and exerted antifungal activity but possessed relatively weak translation–inhibitory activity in cell-free system. The cloning and sequence analysis revealed a 414 bp open reading frame encoding a preproprotein of 137 amino acid residues. The amino acid sequence comparisons and phylogenetic analysis of putrin showed significant homology to 2S seed storage family proteins. The results demonstrated that putrin belongs to 2S albumin family and exhibits a spectrum of biotechnologically exploitable functions.     

Polarography of hexavalent molybdenum in hypophosphorous acid solutions

The polarographic behaviour and determination of Mo(VI) in hypophosphorous acid solutions of concentrations varying from 0.1 to 5.0 mol l^?1 andT=25±0.1 °C have been investigated. It was shown that reduction of MoO ₄ ^2? takes place along a single or two waves depending upon the acid concentration. Microcoulometric experiments have been performed at the limiting region of the different waves obtained at different acid concentrations. A scheme for the mechanism of reduction occuring at theDME has been deduced. A method for analytical determination of Mo(VI) on both the micro- and macro-scales in hypophosphorous acid solutions has been reported. Analysis of a binary mixture Mo(VI)/Cd(II) and a tertiary mixture Mo(VI)/Cd(II)/Zn(II) in mol l^?1 hypophosphorous acid has been investigated.     

Heat of reaction and curing of epoxy resin

The heat of reaction and kinetics of curing of diglycidyl ether of bisphenol-A (DGEBA) type of epoxy resin with catalytic amounts of ethylmethylimidazole (EMI) have been studied by differential power-compensated calorimetry as a part of the program for the study of process monitoring for composite materials. The results were compared with those from 1∶1 and 1∶2 molar mixtures of DGEBA and EMI. A method of determination of heat of reaction from dynamic thermoanalytical instruments was given according to basic thermodynamic principles. The complicated mechanism, possibly involving initial ionic formation, has also been observed in other measurements, such as by time-domain dielectric spectroscopy. The behavior of commercially available DGEBA resin versus purified monomeric DGEBA were compared. The melting point of purified monomeric DGEBA crystals is 41.4 °C with a heat of fusion of 81 J/g. The melt of DGEBA is difficult to crystallize upon cooling. The glass transition of purified DGEBA monomer occurs around ?22 °C with aΔC _p of 0.60 J/K/g.     

A Mathematical Analysis of the Selective Enrichment of NECEEM-Based Non-SELEX

Non-Systematic Evolution of Ligands by EXponential enrichment (SELEX)selection of aptamers, a novel technology for aptamer selection from libraries of random DNA (or RNA) sequences, involves repetitive steps of partitioning without polymerase chain reaction (PCR) amplification between them. This selection is based on non-equilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) and has exceptionally high efficiency. In this paper, a mathematical analysis was carried out to predict the levels of enrichment of non-SELEX selection under different conditions such as different protein concentrations and different efficiencies of partitioning. Investigated results suggest that the magnitude of the bulk affinity (k _d) being 10⁴ or 10⁵ μM for the initial pool has no obvious effect on selective enrichment and that the first, second, and third rounds of non-SELEX selection have different optimum protein concentration values [T _f] that give maximum enrichment levels when [T _f] ranges from 0.0005 to 0.5 μM. The significance of analyzing selective enrichment of NECEEM-based non-SELEX with the efficiency of partitioning target-bound ligands from free ligands has been demonstrated.     

Functional Microgels Assisted Tryptic Digestion and Quantification of Cytochrome c Through Internal Standard Mass Spectrometry

Quantitation of cytochrome c (Cyt c) in cell lysates through surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) using gold nanoparticles (Au NPs) as the matrix and GR-10 peptide as an internal standard has been demonstrated. To shorten digestion time, temperature sensitive microgels containing trypsin (TR) and Au NPs have been employed. As-prepared functional microgels (TR/Au NPs/MGs) allow digestion of Cyt c within 15 s under microwave irradiation. The internal standard SALDI-MS approach provides linearity (R² = 0.98) of MS signal ratio (I _1168.6/I _1067.6) of the tryptic digested peptide (m/z 1168.6) to GR-10 peptide (m/z 1067.6) against the concentration of Cyt c ranging from 25 to 200 nM, with a limit of detection (at a signal-to-noise ratio of 3) of 10 nM. This approach has been validated by the analysis of the lysates of HeLa cells, with an average concentration of 13.7?±?3.5 μM for cytoplasmic Cyt c. Increased concentrations of Cyt c in the HeLa cells treated with etoposide (a commercial drug) or carbon dots (potential drug) have been revealed through this simple, sensitive, and rapid SALDI-MS approach, supporting the drugs induced Cyt c-mediated apoptosis of the cells. This study has shown that this internal standard SALDI-MS approach holds great potential for cell study. Graphical Abstract

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Preparation of Cu (II)/PEI–QPEI/SiO2 nanopowder as antibacterial material

The silica nanoparticles were prepared by the sol–gel process, and then twice modified and grafted by polyethylenimine (PEI) on their surface. After quaternary ammonium reaction and chelated copper reaction, the PEI/SiO₂, QPEI/SiO₂, PEI–QPEI/SiO₂ and Cu (II)/PEI–QPEI/SiO₂ nanopowders were obtained in turn. The morphology and structure of the products were characterized through SEM, EDX, HRTEM, FTIR and element analysis. At the same time, the antibacterial activity of the products to E. coli and Candida were evaluated through quantification and qualitative ways, e.g. microcalorimetric method and culture dish method. The results suggested that the Cu (II)/PEI–QPEI/SiO₂, a novel three-component functional nanopowder, presented the best antibacterial activity to both E. coli and Candida duo to the synergistic sterilization capability of the ammonium salt and copper ions, compared with other products. It indicated that the Cu (II)/PEI–QPEI/SiO₂ nanopowder could be a novel antibacterial nanomaterial to widely application in preventing and minimizing bacteria of the organism and environment in future.     

Corrosion inhibition investigations of 3-acetylpyridine semicarbazone on carbon steel in hydrochloric acid medium

The corrosion inhibition efficiency of 3-acetylpyridine-semicarbazide (3APSC) on carbon steel (CS) in 1.0 M HCl solution has been investigated using weight loss measurements, electrochemical impedance spectroscopy (EIS) and potentiodynamic polarization studies. The results show that inhibition efficiency on metal increases with the inhibitor concentration. 3APSC exhibited marked inhibition towards carbon steel in HCl medium even at low concentrations. The adsorption of inhibitor on the surfaces of the corroding metal obeys the Langmiur isotherm and thermodynamic parameters (K _ads, ?G _ads ⁰ ) were calculated. Activation parameters of the corrosion process (E _a, ?H* and ?S*) were also calculated from the corrosion rates. Polarization studies revealed that 3APSC act as a mixed-type inhibitor. Surface analysis of the metal specimens was performed by scanning electron microscopy.     

Investigation of volatile metabolites during growth of Escherichia coli and Pseudomonas aeruginosa by needle trap-GC-MS

A new method for the growth-dependent headspace analysis of bacterial cultures by needle trap (NT)-gas chromatography-mass spectrometry (GC-MS) was established. NTs were used for the first time as enrichment technique for volatile organic compounds (VOCs) in the headspace of laboratory cultures. Reference strains of Escherichia coli and Pseudomonas aeruginosa were grown in different liquid culture media for 48 h at 36 °C. In the course of growth, bacterial culture headspace was analysed by NT-GC-MS. In parallel, the abiotic release of volatile organic compounds (VOC) from nutrient media was investigated by the same method. By examination of microbial headspace samples in comparison with those of uninoculated media, it could be clearly differentiated between products and compounds which serve as substrates. Specific microbial metabolites were detected and quantified during the stationary growth phase. P. aeruginosa produced dimethyl sulfide (max. 125 μg L^?1??1) and 2-nonanone (max. 200 μg L^?1), whereas E. coli produced carbon disulfide, butanal and indole (max. 149 mg L^?1). Both organisms produced isoprene. Graphical Abstract

MVOCs produced by P. aeruginosa and E. coli at T = 36 °C in autoclaved LB + TRP medium      

Selective visual detection of Pb(II) ion via gold nanoparticles coated with a dithiocarbamate-modified 4′-aminobenzo-18-crown-6

We have developed a crown ether based selective colorimetric sensing scheme for the determination of Pb(II) ion by using gold nanoparticles modified with dithiocarbamate derivative of 4′-aminobenzo-18-crown-6 that acts as a colorimetric probe. Monodisperse Au-NPs were prepared by reacting 4′-aminobenzo-18-crown-6 with carbon disulfide to generate the dithiocarbamate ligand which was then added to the Au-NPs to form a supramolecular assembly on their surface. The Au-NPs modified in this way undergo aggregation in the presence of Pb(II) ions, and this causes the color to change from red to blue. The Pb(II)-induced aggregation can be monitored by using UV-visible spectrometry and even with the bare eye. The absorbance ratio (A_650nm/A_520nm) is linearly related to the concentration of Pb(II) in the 0.1 to 75 μM range (with a correlation coefficient of 0.9957), and the detection limit is 50 nM which is lower than the allowable level (75 nM) as defined by the US EPA. The method was successfully applied to the determination of Pb(II) in spiked water samples. Figure

Schematic representation of Pb²⁺ ion-induced DTC-CE-Au NPs aggregation via sandwich complex formation.     

Modification in physical properties of organo clay filled polyurethane nanocomposites

Polyurethane (PU) have been prepared by using polyether polyol (jagropol oil) and 1,6-hexamethylene diisocyanate (HMDI) as a cross-linker. The organically modified montmorillonite clay (o-MMT) is well dispersed into urethane matrix by in-situ polymerization method. A series of PU/o-MMT nanocomposites have been prepared by varying amounts viz., 1, 3, 5 and 6 wt % of nanoclay. The mechanical properties such as tensile strength, percentage elongation at break and tensile modulus of the composites were experimentally determined. The swelling behavior of the composites has been studied in different organic solvents. It was noticed that the swelling data of the composites significantly depends on the solubility parameters of the solvents. Microcrystalline parameters such as, lattice strain (g in %), average number of unit cells (〈N〉) in direction perpendicular to Bragg plane, surface weighted crystal size (D _s) and interplanar distance (d _hkl ), were calculated from X-ray patterns. These parameters were computed using Exponential asymmetric column length distribution functions. Morphological features of cryofractured PU/o-MMT composites were also analyzed using scanning electron microscopy (SEM).     

Dehydrogenation of 4-aryl(hetaryl) spinacine derivatives with dimethyl sulfoxide

Aromatization of 4-aryl(hetaryl)tetrahydroimidazo[4,5-c]pyridine-6-carboxylic acids and their lithium salts by the action of dimethyl sulfoxide has been revealed for the first time. Heating of these compounds in DMSO for 5–7 h at 90–95°C leads to the formation of 4-aryl(hetaryl)imidazo[4,5-c]pyridine derivatives as a result of dehydrogenation and decarboxylation. Heating of the corresponding lithium salts generated in situ (DMSO, 90–95°C, 3–5 h) affords difficultly accessible 4-aryl(hetaryl)imidazo[4,5-c]pyridine-6-carboxylic acids.     

The evolution of properties of recycled poly(ethylene terephthalate) as function of chain extenders,the extrusion cycle and heat treatment

Poly(ethylene terephthalate) (PET) is the most widely used plastic in beverages packaging. It is also the most recycled plastic in the world. It is estimated that 6 million tons of PET are recycled (rPET) each year worldwide. Recycling of this material by melt processing has been the subject of many studies, in order to limit the degradation processes that lead to a significant decrease in the molecular weight (viscosity). Two key points are highlighted: The former is the presence of impurities like adhesive, glue and Poly Vinyl Chloride etc. The latter is the presence of water. These were therefore the main factors of the degradation of rPET. The impurities can be eliminated by a selective recovery and the moisture by a suitable drying combined with the addition of chain extenders namely Caprolactam (CAP) and/or Trimellitic anhydride (TMA). This combination has proved to be very promising since extruded mixtures (rPET/TMA or CAP) have quite acceptable rheological properties especially in terms of intrinsic viscosity, dynamic viscosity and melt flow index (MFI) at low concentration of chain extender. Rheological and FTIR analysis showed that the degradation of rPET becomes more significant from the second extrusion cycle. Finally, DSC analysis showed that T _g were not affected by extrusion cycle number; However, cold crystallization temperature T _cc2 were significantly affected by heat treatment. The DSC analysis showed also that from the 2nd extrusion cycle, a conversion of heating crystallization temperature (T _c) which appeared during the first heating (1st scan) to a melting temperature (T _m1) that appeared during the second heating (3rd scan) occurred due to the change of the decomposition mechanism environment (from oxygen environment to that of nitrogen).     

Kinetics and possible mechanism of hydrogen chloride oxidation over supported copper-containing salt catalysts: II. Kinetics of HCl oxidation in the deacon and methane oxychlorination reactions over the CuCl2-KCl-LaCl3 catalyst

The kinetics of HCl oxidation at 350–425°C over the supported CuCl₂-KCl-LaCl₃ catalyst has been investigated using a gradientless technique. The HCl oxidation kinetics in the Deacon and methane oxychlorination reactions has been studied in order to substantially extend the \(Cl_2 \left( {P_{Cl_2 } } \right)\) partial pressure variation range. When the reaction rate is independent of P _HCl, HCl oxidation on the copper-potassium catalysts is described by the same rate equation, irrespective of whether the catalyst contains lanthanum or not. The introduction of lanthanum chloride increases the HCl oxidation rate by one order of magnitude. The rate equation obtained has significant advantages over the equation corresponding to the Kenney-Slama equation. The kinetic features of HCl oxidation over the lanthanum-containing catalyst, whether the process depends on P _HCl or not, can be explained in terms of the superposition of the Kenney-Slama dissociative mechanism and the catalytic mechanism suggested here. The role of lanthanum chloride in both HCl oxidation pathways is considered.     

Simultaneous determination of bufadienolides and phenolic compounds in sea squill (Drimia maritima (L.) Stearn) by HPLC-DAD-MSn as a means to differentiate individual plant parts and developmental stages

Mediterranean sea squill (Drimia maritima (L.) Stearn) is used in the production of medicinal products. Current HPLC methods comprise tedious sample clean-up and have been merely focused on the analysis of cardiac glycosides, whereas a thorough characterization of D. maritima considering both the latter compound class and more hydrophilic secondary metabolites in one HPLC run has not been performed so far. Consequently, a novel HPLC-DAD-MSⁿ method has been developed allowing the simultaneous determination of both cardiac glycosides and phenolic compounds, which is characterized by simplified sample preparation. This method was applied to characterize sea squill, revealing a complex profile of its extractive compounds derived from the two classes. Furthermore, the potential of the method reported here to quantitate the predominant compounds, i.e., dihydroquercetin derivatives and bufadienolides, was demonstrated. The occurrence of phenolic compounds, not described for sea squill so far, and of characteristic compounds specific to individual plant parts or vegetation stages was further addressed. The data revealed that classification of various vegetation phases based on quantitative evaluation of bufadienolides and dihydroquercetin derivatives applying principal component analysis (PCA) appears possible. Thus, the methodology presented here forms the basis for future routine application in quality control of raw materials and pharmaceutical preparations derived from sea squill. This will allow systematic comparison of different plant parts, vegetation stages and origins based on an extended sample set. Figure

Red sea squill with inflorescence and cross-section of a fresh bulb     

Extraction of chromium(VI) with blue tetrazolium chloride and tetranitrotetrazolium blue chloride

The optimum conditions for extraction of microquantities of chromium(VI) as an ion-association complex with blue tetrazolium chloride (BTC) and tetranitrotetrazolium blue chloride (TNBT) has been determined. The extracted species was a 1: 2 of the BTC and TNBT cation and the chlorochromate anion. Beer’s law was obeyed in the range of 0.04–0.8 μg/mL Cr(VI) for BTC and 0.1–1.6 μg/mL Cr(VI) for TNBT. The molar absorptivities were ?₂₅₅ = 7.77 × 10⁴ L/(mol cm) (for BTC) and ?₂₇₅ = 2.04 × 10⁴ L/(mol cm) (for TNBT). Sandell’s sensitivity of the systems were found to be 6.69 × 10^?4 μg/cm² (for BTC) and 2.55 × 10^?3 μg/cm² (for TNBT). Limit of detection (LOD) is 8.55 ng/mL and limit of quantitation (LOQ) is 0.028 μg/mL Cr(VI) for BTC. For TNBT, LOD is 0.031 μg/mL and LOQ is 0.103 μg/mL. The characteristic values for the extraction equilibrium and the equilibrium in the aqueous phase have been determined. A sensitive method for determination of trace of chromium(VI) in plants has been developed.