Capillary and microelectrophoretic separations of ligase detection reaction products produced from low-abundant point mutations in genomic DNA

Capillary gel electrophoresis (CGE) and polymer-based microelectrophoretic platforms were investigated to analyze low-abundant point mutations in certain gene fragments with high diagnostic value for colorectal cancers. The electrophoretic separations were carried out on single-stranded DNA (ssDNA) products generated from an allele-specific ligation assay (ligase detection reaction, LDR), which was used to screen for a single base mutation at codon 12 in the K-ras oncogene. The presence of the mutation generated a ssDNA fragment that was >40 base pairs (bp) in length, while the primers used for the ligation assay were <30 bp in length. Various separation matrices were investigated, with the success of the matrix assessed by its ability to resolve the ligation product from the large molar excess of unligated primers when the mutant allele was lower in copy number compared to the wild-type allele. Using CGE, LDR product models (44 and 51 bp) could be analyzed in a cross-linked polyacrylamide gel with a 1000-fold molar excess of LDR primers (25 bp) in approximately 45 min. However, when using linear polyacrylamide gels, these same fragments could not be detected due to significant electrokinetic biasing during injection. A poly(methylmethacrylate) (PMMA) microchip of 3.5 cm effective column length was used with a 4% linear polyacrylamide gel to analyze the products generated from an LDR. When the reaction contained a 100-fold molar excess of wild-type DNA compared to a G12.2D mutant allele, the 44 bp ligation product could be effectively resolved from unligated primers in under 120 s, nearly 17 times faster than the CGE format. In addition, sample cleanup was simplified using the microchip format by not requiring desalting of the LDR prior to loading.     

Synthesis of oligonucleotides containing thiazole and thiazole N-oxide nucleobases

[reaction: see text] The thiazole C-nucleoside analogue was synthesized by the Hantzsch cyclization method to form the thiazole ring and was then converted to the thiazole N-oxide C-nucleoside analogue by peracid oxidation of the heterocycle nitrogen. Incorporation of the thiazole and thiazole N-oxide phosphoramidites into DNA was successful though significant deoxygenation of the N-oxide occurred during DNA assembly. The mechanism proposed for the reduction of the thiazole N-oxide to thiazole involves the formation of an N-oxide phosphite ester.     

The diffraction of elastic waves by an imperfect fusion bond

We consider diffraction by a semi-infinite crack located alonga fusion interface between two differing elastic media. Twotypes of crack, namely open and partially closed cracks, areinvestigated. An open crack is modelled by a stress-free contactboundary condition and a partially closed crack is modelledby a spring contact boundary condition. For the latter, thejump in the stress across the crack is assumed to be proportionalto the jump in the displacement across the crack. This situationarises in, for example, a K-weld where the fine grain of theparent material (for example, ferritic or forged austeniticsteel) is in stark contrast with the coarse-grained weld metal(for example, austenitic weld metal). In the metal weld thedirection of the grain axis varies through the metal. However,diffraction is a local phenomenon and so the austenitic steelis assumed to have a zonal axis so that it may be modelled bya transversely isotropic composite. The ferritic or forged austeniticsteel will be modelled as an isotropic material.     

The non-destructive identification of solid over-the-counter medications using single particle aerosol mass spectrometry

Single over-the-counter medication tablets were analyzed in real time using Single Particle Aerosol Mass Spectrometry (SPAMS). Dual-polarity time-of-flight mass spectra were obtained for micrometer-sized single particles dislodged from a single tablet without destroying the shape or markings of each tablet. The solid tablet was placed in a modified-top glass vial and shaken to dislodge and introduce micrometer-sized particles into the SPAMS system. Unique spectra from these particles were obtained in less than 1 s for single tablets of aspirin, ibuprofen, pseudoephedrine, phenylephrine, loratadine, or diphenhydramine. The signals obtained allowed the non-destructive identification of an individual tablet in seconds. SPAMS presents an ideal system for high-throughput analysis of solid drugs.     

Approaching real-time molecular diagnostics: single-pair fluorescence resonance energy transfer (spFRET) detection for the analysis of low abundant point mutations in K-ras oncogenes

The aim of this study was to develop new strategies for analyzing molecular signatures of disease states approaching real-time using single pair fluorescence resonance energy transfer (spFRET) to rapidly detect point mutations in unamplified genomic DNA. In addition, the detection process was required to discriminate between normal and mutant (minority) DNAs in heterogeneous populations. The discrimination was carried out using allele-specific primers, which flanked the point mutation in the target gene and were ligated using a thermostable ligase enzyme only when the genomic DNA carried this mutation. The allele-specific primers also carried complementary stem structures with end-labels (donor/acceptor fluorescent dyes, Cy5/Cy5.5, respectively), which formed a molecular beacon following ligation. We coupled ligase detection reaction (LDR) with spFRET to identify a single base mutation in codon 12 of a K-ras oncogene that has high diagnostic value for colorectal cancers. A simple diode laser-based fluorescence system capable of interrogating single fluorescent molecules undergoing FRET was used to detect photon bursts generated from the molecular beacon probes formed upon ligation. LDR-spFRET provided the necessary specificity and sensitivity to detect single-point mutations in as little as 600 copies of human genomic DNA directly without PCR at a level of 1 mutant per 1000 wild type sequences using 20 LDR thermal cycles. We also demonstrate the ability to rapidly discriminate single base differences in the K-ras gene in less than 5 min at a frequency of 1 mutant DNA per 10 normals using only a single LDR thermal cycle of genomic DNA (600 copies). Real-time LDR-spFRET detection of point mutations in the K-ras gene was accomplished in PMMA microfluidic devices using sheath flows.     

ON AVOIDANCE ACTIVITIES IN FISHERY ENFORCEMENT MODELS

Compliance and enforcement in fisheries are important issues from an economic point of view since management measures are useless without a certain level of enforcement. These conclusions come from the well‐established theoretical literature on compliance and enforcement problems within fisheries and a common result is that, it is efficient to set fines as high as possible and monitoring as low as possible, when fines are costless and offenders are risk neutral. However, this result is sensitive to the assumption that fishermen cannot engage in avoidance activities, e.g., activities to reduce the likelihood of being detected when noncomplying. The paper presents a model of fisheries that allows the fishermen to engage in avoidance activities. The conclusions from the model are that, under certain circumstances, fines are costly transfers to society since they not only have a direct positive effect on the level of deterrence, but also an indirect negative effect in the form of increased avoidance activities to reduce the probability of detection. The paper contributes to the literature on avoidance activities by introducing the externality from the illegal behavior as an endogenous effect on other offenders. For an externality, that has an exogenous effect on other actors, Malik shows that fines are only costly transfers for conditional deterrence (when one actor is deterred while another actor is not). For fisheries, we show that fines are also costly transfers under no deterrence (when no agents are deterred).     

Human breath analysis: methods for sample collection and reduction of localized background effects

Solid-phase microextraction (SPME) was applied, in conjunction with gas chromatography–mass spectrometry, to the analysis of volatile organic compounds (VOCs) in human breath samples without requiring exhaled breath condensate collection. A new procedure, exhaled breath vapor (EBV) collection, involving the active sampling and preconcentration of a breath sample with a SPME fiber fitted inside a modified commercial breath-collection device, the RTube™, is described. Immediately after sample collection, compounds are desorbed from the SPME fiber at 250 °C in the GC-MS injector. Experiments were performed using EBV collected at −80 °C and at room temperature, and the results compared to the traditional method of collecting exhaled breath condensate at −80 °C followed by passive SPME sampling of the collected condensate. Methods are compared in terms of portability, ease-of-use, speed of analysis, and detection limits. The need for a clean air supply for the study subjects is demonstrated using several localized sources of VOC contaminants including nail polish, lemonade, and gasoline. Various simple methods to supply clean inhaled air to a subject are presented. Chemical exposures are used to demonstrate the importance of providing cleaned air (organic vapor respirator) or an external air source (tubing stretched to a separate room). These techniques allow for facile data interpretation by minimizing background contaminants. It is demonstrated herein that this active SPME breath-sampling device provides advantages in the forms of faster sample collection and data analysis, apparatus portability and avoidance of power or cooling requirements, and performance for sample collection in a contaminated environment.      

焙烧硼钠钙石在高固液比氯化铵溶液中的溶解动力学

Boron is available in the form of metal borates, especially of sodium and calcium, in nature[1]. The production of boron compounds has substantially increased recently due to increasing uses of these compounds in nuclear technology, in rocket engines as f…