Purification of genomic DNA by short monolithic columns

The isolation and purification of nucleic acids is essential for many procedures in molecular biology. After showing that bacterial and eukaryotic genomic DNA can be specifically bound to the CIM DEAE monolithic column, this characteristic was exploited in development of a simple and fast chromatographic procedure for isolation and purification of genomic DNA from cell lysates that does not include the usage of toxic organic solutions. The purity and the quality of the isolate as well as the duration of the procedure was similar to other chromatographic methods used today for isolation of genomic DNA, but the initial sample volume was not restricted.     

Discovery of new therapeutic targets by the informational spectrum method

The field of bioinformatics has become a major part of the drug discovery pipeline playing a key role in improvement and acceleration of this time and money consuming process. Here we review the application of the informational spectrum method (ISM), a virtual spectroscopy method for structure/function analysis of proteins, in identification of functional protein domains representing candidate therapeutic targets for drugs against human immunodeficiency virus (HIV)-1, anthrax, highly pathogenic influenza virus H5N1 and cardiovascular diseases.     

Redox Speciation of Vanadium in Estuarine Waters Using Improved Methodology Based on Anion Exchange Chromatography Coupled to HR ICP-MS System

An improved methodology was developed for V redox speciation in estuarine waters using a hyphenated technique consisting of ion chromatograph (IC) with an anion exchange column and a high-resolution inductively coupled plasma mass spectrometer (HR ICP-MS). This approach enables the direct determination of V(V), whereas reduced species (mainly V(IV)) are calculated by subtracting V(V) concentrations from the measured total V concentration. Based on the “on-column” V(V) chelation mechanism by EDTA, with the eluent composed of 40 mmol L⁻¹ ammonium bicarbonate, 40 mmol L⁻¹ ammonium sulphate, 8 mmol L⁻¹ ethylenediaminetetraacetic acid and 3% acetonitrile, the method was successfully used for analyses of V redox speciation in samples taken in the vertical salinity gradient of the highly stratified Krka River estuary. Due to the matrix effects causing different sensitivities, a standard addition method was used for V(V) quantification purposes. The limit of detection (LOD) was also found to be matrix related: 101.68 ng L⁻¹ in the seawater and 30.56 µg L⁻¹ in the freshwater. Performed stability tests showed that V redox speciation is preserved at least 7 days in un-treated samples, possibly due to the stabilization of V-reduced species with natural organic matter (NOM). The dominant V form in the analysed samples was V(V) with the reduced V(IV) accounting for up to 26% of the total dissolved pool. The concentration of V(IV) was found to correlate negatively with the oxygen concentration. Significant removal of dissolved V was detected in oxygen depleted zones possibly related to the particle scavenging.     

Part per trillion determination of atrazine in natural water samples by a surface plasmon resonance immunosensor

A new immunoassay for continuously monitoring atrazine in water has been developed. It uses a portable biosensor platform based on surface plasmon resonance (SPR) technology. This immunoassay is based on the binding inhibition format with purified polyclonal antibodies, with the analyte derivative covalently immobilized on a gold sensor surface. An alkanethiol self-assembled monolayer (SAM) was formed on the gold-coated sensor surface in order to obtain a reusable sensing surface. The low detection limit for the optimized assay, calculated as the concentration that produces a 10% decrease in the blank signal, is 20 ng/L. A complete assay cycle, including regeneration, is accomplished in 25 min. Additionally, a study of the matrix effects of different types of wastewater was performed. All measurements were carried out with the SPR sensor system (β-SPR) commercialised by the company Sensia, S.L. (Spain). The small size and low response time of the β-SPR platform would allow it to be used in real contaminated locations. The immunosensor was evaluated and validated by measuring the atrazine content of 26 natural samples collected from Ebro River. Solid-phase extraction followed by gas chromatography coupled to mass spectrometric detection (SPE–GC–MS) was used to validate the new immunoassay.     

Discriminatory power, typability, and accuracy of single nucleotide extension microarrays

Despite great conceptual promise, the use of microarrays in typing approaches has not yet gained wide acceptance. The establishment of proper criteria for determining discriminatory power as well as typability and the accuracy of microarray data remains to be solved. Purely experimental estimations of these parameters would far exceed what is experimentally practical. We therefore used simulations in combination with experimental results in parameter estimations. Our assay was based on 26 single nucleotide polymorphisms (SNPs) identified in the Campylobacterjejuni Multi Locus Sequence Typing (MLST) database (http:///pubmist.org/campylobacter/). The SNPs were detected using a single nucleotide extension (SNE) typing microarray. Unknown isolates were assigned to the known sequence type(s) by calculating weighted sum of matches minus a weighted sum of mismatches between predicted and candidate genotype. The weights were set according to the Bayesian posterior probability of the SNP classification. These studies showed that any typing or profiling method based on binary data requires an accuracy of <2-3% error for each datapoint (in our case SNPs) to classify the isolates to the correct allelic profile in 90% of the cases. The classification error for our experimental data was 3.2% (after removing 5 high error SNPs). We therefore conclude that SNE microarrays are promising for future high-throughput typing of bacteria.     

Self-delivering nanoemulsions for dual fluorine-19 MRI and fluorescence detection

We report the design, synthesis, and biological testing of highly stable, nontoxic perfluoropolyether (PFPE) nanoemulsions for dual 19F MRI-fluorescence detection. A linear PFPE polymer was covalently conjugated to common fluorescent dyes (FITC, Alexa647 and BODIPy-TR), mixed with pluronic F68 and linear polyethyleneimine (PEI), and emulsified by microfluidization. Prepared nanoemulsions (<200 nm) were readily taken up by both phagocytic and non-phagocytic cells in vitro after a short (approximately 3 h) co-incubation. Following cell administration in vivo, 19F MRI selectively visualizes cell migration. Exemplary in vivo MRI images are presented of T cells labeled with a dual-mode nanoemulsion in a BALB/c mouse. Fluorescence detection enables fluorescent microscopy and FACS analysis of labeled cells, as demonstrated in several immune cell types including Jurkat cells, primary T cells and dendritic cells. The intracellular fluorescence signal is directly proportional to the 19F NMR signal and can be used to calibrate cell loading in vitro.     

Phenolics,Antioxidant Potentials,and Antimicrobial Activities of Six Wild Boletaceae Mushrooms

Since mushrooms are important sources of bioactive compounds such as phenolic acids, their identification and quantification were performed by high-performance liquid chromatography resulting in total concentrations between 2.9161?±?0.0829?mg/kg (Boletus fechtneri) and 51.4480?±?1.0333?mg/kg (Boletus appendiculatus). The antioxidant properties of methanol extracts and corresponding hydrolysates were estimated using 2,2-diphenyl-1-picrylhydrazyl, 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), total reducing power, ferric-reducing antioxidant power, cupric-reducing antioxidant capacity, and total phenolic content assays. The Xerocomus badius methanol extract showed the highest antioxidant potential, while among hydrolysates, the highest antioxidant potential was observed for Xerocomellus chrysenteron. The antimicrobial activities of methanol extracts of studied mushrooms against pathogenic bacterial and fungal strains were measured and the highest values were obtained for B. fechtneri and B. appendiculatus extracts against Pseudomonas aeruginosa. Principal component analyses and agglomerative hierarchical clustering were used to display the correlation between the parameters and their relationships with the mushroom species.     

Halochromic cellulose textile obtained via dyeing with biocolorant isolated from Streptomyces sp. strain NP4

Cellulose - Halochromic (pH-responsive) material was obtained by dyeing functionalized viscose fabric with a crude extract from Streptomyces sp. strain NP4. The functionalization of the fabric...     

Bis(phosphinimino)methanide Borohydride Complexes of the Rare‐Earth Elements as Initiators for the Ring‐Opening Polymerization of ε‐Caprolactone: Combined Experimental and Computational Investigations

Rare‐earth‐metal borohydrides are known to be efficient catalysts for the polymerization of apolar and polar monomers. The bis‐borohydrides [{CH(PPh₂NSiMe₃)₂}La(BH₄)₂(THF)] and [{CH(PPh₂NSiMe₃)₂}Ln(BH₄)₂] (Ln=Y, Lu) have been synthesized by two different synthetic routes. The lanthanum and the lutetium complexes were prepared from [Ln(BH₄)₃(THF)₃] and K{CH(PPh₂NSiMe₃)₂}, whereas the yttrium analogue was obtained from in situ prepared [{CH(PPh₂NSiMe₃)₂}YCl₂]₂ and NaBH₄. All new compounds were characterized by standard analytical/spectroscopic techniques, and the solid‐state structures were established by single‐crystal X‐ray diffraction. The ring‐opening polymerization (ROP) of ε‐caprolactone initiated by [{CH(PPh₂NSiMe₃)₂}La(BH₄)₂(THF)] and [{CH(PPh₂NSiMe₃)₂}Ln(BH₄)₂] (Ln=Y, Lu) was studied. At 0 °C the molar mass distributions determined were the narrowest values (M?_w/M?_n=1.06–1.11) ever obtained for the ROP of ε‐caprolactone initiated by rare‐earth‐metal borohydride species. DFT investigations of the reaction mechanism indicate that this type of complex reacts in an unprecedented manner with the first B? H activation being achieved within two steps. This particularity has been attributed to the metallic fragment based on the natural bond order analysis.