Structure of the nitrogen-centered radical formed during inactivation of E. coli ribonucleotide reductase by 2'-azido-2'-deoxyuridine-5'-diphosphate: trapping of the 3'-ketonucleotide

Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides providing the monomeric precursors required for DNA replication and repair. The class I RNRs are composed of two homodimeric subunits: R1 and R2. R1 has the active site where nucleotide reduction occurs, and R2 contains the diiron tyrosyl radical (Y*) cofactor essential for radical initiation on R1. Mechanism-based inhibitors, such as 2'-azido-2'-deoxyuridine-5'-diphosphate (N(3)UDP), have provided much insight into the reduction mechanism. N(3)UDP is a stoichiometric inactivator that, upon interaction with RNR, results in loss of the Y* in R2 and formation of a nitrogen-centered radical (N*) covalently attached to C225 (R-S-N*-X) in the active site of R1. N(2) is lost prior to N* formation, and after its formation, stoichiometric amounts of 2-methylene-3-furanone, pyrophosphate, and uracil are also generated. On the basis of the hyperfine interactions associated with N*, it was proposed that N* is also covalently attached to the nucleotide through either the oxygen of the 3'-OH (R-S-N*-O-R') or the 3'-C (R-S-N*-C-OH). To distinguish between the proposed structures, the inactivation was carried out with 3'-[(17)O]-N(3)UDP and N* was examined by 9 and 140 GHz EPR spectroscopy. Broadening of the N* signal was detected and the spectrum simulated to obtain the [(17)O] hyperfine tensor. DFT calculations were employed to determine which structures are in best agreement with the simulated hyperfine tensor and our previous ESEEM data. The results are most consistent with the R-S-N*-C-OH structure and provide evidence for the trapping of a 3'-ketonucleotide in the reduction process.     

Review of the Sampling and Pretreatment Methods for Dioxins Determination in Solids,Liquids and Gases

The analytical requirements for the determination of dioxins (e.g. PCDD, PCDF) are unique in comparison with those for other routinely monitored chemicals: dioxins are measured in parts per trillion (ppt) and lower levels in technical and environmental samples, whereas other organics are measured in parts per million (ppm) or parts per billion (ppb). The ultra‐trace analysis of dioxins requires a high sample enrichment obtainable by the use of efficient extraction methods and highly selective purification/fractionation techniques. Furthermore, highly sensitive equipment (e.g. high resolution gas chromatography ‐ HRGC) with detection levels in the ppt range must be used to isolate and separate a huge number of dioxin congeners. The quantification of the dioxins by a high resolution mass detector (HRMS) requires the use of internal and labeled standards. This paper reviews and compares the classic and modern pretreatment methods, namely extraction and clean‐up, that are currently used in dioxin analysis in industrial samples and that were improved or developed in the last 25 years. In addition, the standard methods for dioxin sampling from an emission source (flue or stack gas) are examined and compared with new, automated techniques.     

Physicochemical Properties,Fatty Acid Composition,Volatile Compounds of Blueberries,Cranberries, Raspberries,and Cuckooflower Seeds Obtained Using Sonication Method

Every year, thousands of tons of fruit seeds are discarded as agro-industrial by-products around the world. Fruit seeds are an excellent source of oils, monounsaturated fatty acids, and n-6 and n-3 polyunsaturated essential fatty acids. This study aimed to develop a novel technology for extracting active substances from selected seeds that were obtained after pressing fruit juices. The proposed technology involved sonification with the use of ethyl alcohol at a low extraction temperature. Seeds of four species—blueberry (Vaccinium myrtillus L.), raspberry (Rubus idaeus), cranberry (Vaccinium macrocarpon), and cuckooflower (Cardamine pratensis)—were used for extraction. Following alcohol evaporation under nitrogen, the antioxidant activity, chemical composition, and volatile compounds of the obtained extracts were analyzed using chromatographic methods, including gas chromatography (GC)–mass spectrometry (MS) (GC–MS/MS), and high-performance liquid chromatography–MS. We analyzed physicochemical properties, fatty acid, and volatile compounds composition, sterol and tocochromanol content of blueberry, cranberry, raspberry, and cuckooflower seed oils obtained by sonication. This method is safe and effective, and allows for obtaining valuable oils from the seeds.     

Chemical Characteristics and Antioxidant Activity of Arctostaphylos uva-ursi L. Spreng. at the Southern Border of the Geographical Range of the Species in Europe

The bearberry (Arctostaphylos uva-ursi L. Spreng.) is a source of herbal material—bearberry leaf (Uvae ursi folium), which is highly valued and sought by pharmaceutical and cosmetic industries. For many years, leaves of this plant have been used in traditional medicine as a diuretic, antimicrobial, and anti-inflammatory agent for various diseases of the urogenital tract. The bearberry has also been proposed as a natural antioxidant additive due to the high contents of phenolic compounds in its leaves. The study was focused on characterization of the basic phytochemical composition and antioxidant activity of extracts derived from bearberry leaves collected from plants located at the southern border of the geographical range of the species in Europe. The investigated herbal material is characterized by a different chemical profile compared to the chemical profiles of bearberry found in other parts of the continent. Bearberry extracts from plants growing in two different habitat types—heathlands and pine forests showed a wide range of variation, especially in the concentration of hyperoside, corilagin, and methylartutin and the total flavonoid contents. In addition to arbutin, bearberry can be a valuable source of phenolic compounds, which are mainly responsible for the antioxidant properties of extracts. The high content of phenols and high values of antioxidant parameters indicate a high potential of bearberry leaves to be used as a powerful natural source of antioxidants in herbal preparations. Therefore, the A. uva-ursi populations can be a source of plant material for pharmaceutical, cosmetic, and food industries.     

Whole genome amplification induced bias in the detection of KRAS‐mutated cell populations during colorectal carcinoma tissue testing

Whole genome amplification replicates the entire DNA content of a sample and can thus help to circumvent material limitations when insufficient DNA is available for planned genetic analyses. However, there are conflicting data in the literature whether whole genome amplification introduces bias or reflects precisely the spectrum of starting DNA. We analyzed the origins of discrepancies in KRAS (Kirsten rat sarcoma viral oncogene homolog gene) mutation detection in six of ten samples amplified using the GenomePlex® Tissue Whole Genome Amplification kit 5 (WGA5; Sigma‐Aldrich, St. Louis, MO, USA) and KRAS StripAssay® (KRAS SA; ViennaLab Diagnostics, Vienna, Austria). We undertook reextraction, reamplification, retyping, authentication, reanalysis, and reinterpretation to determine whether the discrepancies originated during the preanalytical, analytical, and/or interpretative phase of genotyping. We conclude that a combination of glass slide/sample heterogeneity and biased amplification due to stochastic effects in the early phases of whole genome amplification (WGA) may have adversely affected the results obtained. Our findings are relevant for both forensic genetics testing and massively parallel sequencing using preamplification.     

Exact and approximation methods for dependability assessment of tram systems with time window

The transportation system examined in this paper is the city tram one, where failed trams are replaced by reliable spare ones. If failed tram is repaired and delivered, then it comes back on work. There is the time window that failed tram has to be either replaced (exchanged) by spare or by repaired and delivered within. Time window is therefore paramount to user perception of transport system unreliability. Time between two subsequent failures, exchange time, and repair together with delivery time, respectively, are described by random variables A, E, and D. A/E/D is selected as the notation for these random variables. There is a finite number of spare trams. Delivery time does not depend on the number of repair facilities. Hence, repair and delivery process can be treated as one with infinite number of facilities. Undesirable event called hazard is the event: neither the replacement nor the delivery has been completed in the time window. The goal of the paper is to find the following relationships: hazard probability of the tram system and mean hazard time as functions of number of spare trams. For systems with exponential time between failures, Weibull exchange and exponential delivery (so M/W/M in the proposed notation) two accurate solutions have been found. For systems with Weibull time between failures with shape in the range from 0.9 to 1.1, Weibull exchange and exponential delivery (i.e. W/W/M) a method yielding small errors has been provided. For the most general and difficult case in which all the random variables conform to Weibull distribution (W/W/W) a method returning moderate errors has been given.     

Ring-Opening Polymerization of Lactones Initiated with Metal Hydroxide-Activated Macrocyclic Ligands: Determination of Mechanism and Structure of Polymers

Anhydrous alkali metal hydroxide (KOH, NaOH, and LiOH)-activated macrocyclic ligand complexing metal cations, i.e., coronands 12C4, 15C5, 18C6, DCH24C8, and cryptand C222, were selected for initiation of β-butyrolactone (β-BL) and ε-caprolactone (ε-CL) polymerization. It was found that β-BL polymerizes in the presence of KOH/18C6, KOH/C222, and NaOH/C222 systems. The real initiators in this case are two salts, potassium 3-hydroxybutyrate and potassium trans-crotonate, which are responsible for the formation of two fractions of the obtained polymer. ε-CL underwent polymerization with KOH or NaOH activated by all ligands used or without the ligand but with LiOH/12C4. Using KOH-activated strong ligands, i.e., 15C5, 18C6, or C222, two polymer fractions were generated containing linear and, unexpectedly, also cyclic macromolecules. The mechanism of the studied processes is discussed.