First Detection of Gas-phase Methanol in a Protoplanetary Disk

The first detection of gas-phase methanol in a protoplanetary disk (TW Hya) is presented. In addition to being one of the largest molecules detected in disks to date, methanol is also the first disk organic molecule with an unambiguous ice chemistry origin. The stacked methanol emission, as observed with the Atacama Large Millimeter/submillimeter Array, is spectrally resolved and detected across six velocity channels (>3σ), reaching a peak signal-to-noise of 5.5σ, with the kinematic pattern expected for TW Hya. Using an appropriate disk model, a fractional abundance of 3 x 10^-12 – 4 x 10^-11 (with respect to H₂) reproduces the stacked line profile and channel maps, with the favored abundance dependent upon the assumed vertical location (midplane versus molecular layer). The peak emission is offset from the source position, suggesting that the methanol emission has a ring-like morphology: the analysis here suggests it peaks at ≈30 au, reaching a column density ≈3–6 x 10¹² cm⁻². In the case of TW Hya, the larger (up to millimeter-sized) grains, residing in the inner 50 au, may thus host the bulk of the disk ice reservoir. The successful detection of cold gas-phase methanol in a protoplanetary disk implies that the products of ice chemistry can be explored in disks, opening a window into studying complex organic chemistry during planetary system formation.

Satellite DNA as a target for TaqMan real-time PCR detection of the pinewood nematode, Bursaphelenchus xylophilus

The pinewood nematode (PWN), Bursaphelenchus xylophilus , is a major pathogen of conifers, which impacts on forest health, natural ecosystem stability and international trade. As a consequence, it has been listed as a quarantine organism in Europe. A real-time PCR approach based on TaqMan chemistry was developed to detect this organism. Specific probe and primers were designed based on the sequence of the Msp I satellite DNA family previously characterized in the genome of the nematode. The method proved to be specific in tests with target DNA from PWN isolates from worldwide origin. From a practical point of view, detection limit was 1 pg of target DNA or one individual nematode. In addition, PWN genomic DNA or single individuals were positively detected in mixed samples in which B. xylophilius was associated with the closely related non-pathogenic species B. mucronatus , up to the limit of 0.01% or 1% of the mixture, respectively. The real-time PCR assay was also used in conjunction with a simple DNA extraction method to detect PWN directly in artificially infested wood samples. These results demonstrate the potential of this assay to provide rapid, accurate and sensitive molecular identification of the PWN in relation to pest risk assessment in the field and quarantine regulation.

A rapid staining-assisted wood sampling method for PCR-based detection of pine wood nematode Bursaphelenchus xylophilus in Pinus massoniana wood tissue

For reasons of unequal distribution of more than one nematode species in wood, and limited availability of wood samples required for the PCR-based method for detecting pinewood nematodes in wood tissue of Pinus massoniana, a rapid staining-assisted wood sampling method aiding PCR-based detection of the pine wood nematode Bursaphelenchus xylophilus (Bx) in small wood samples of P. massoniana was developed in this study. This comprised a series of new techniques: sampling, mass estimations of nematodes using staining techniques, and lowest limit Bx nematode mass determination for PCR detection. The procedure was undertaken on three adjoining 5-mg wood cross-sections, of 0.5 · 0.5 · 0.015 cm dimension, that were cut from a wood sample of 0.5 · 0.5 · 0.5 cm initially, then the larger wood sample was stained by acid fuchsin, from which two 5-mg wood cross-sections (that adjoined the three 5-mg wood cross-sections, mentioned above) were cut. Nematode-staining-spots (NSSs) in each of the two stained sections were counted under a microscope at 100· magnification. If there were eight or more NSSs present, the adjoining three sections were used for PCR assays. The B. xylophilus – specific amplicon of 403 bp (DQ855275) was generated by PCR assay from 100.00% of 5-mg wood cross-sections that contained more than eight Bx NSSs by the PCR assay. The entire sampling procedure took only 10 min indicating that it is suitable for the fast estimation of nematode numbers in the wood of P. massonina as the prelimary sample selections for other more expensive Bx-detection methods such as PCR assay.

Detection of non-steroidal anti-inflammatory drugs in aqueous effluents using ionic liquids

Significant improvements in human health have been achieved through the increased consumption of pharmaceutical drugs. However, most of these active pharmaceutical ingredients (APIs) are excreted by mammals (in a metabolized or unchanged form) into the environment. The presence of residual amounts of these contaminants was already confirmed in aqueous streams since treatment processes either wastewater treatment plants (WWTPs) or sewage treatment plants (STPs) are not specifically designed for this type of pollutants. Although they are present in aqueous effluents, they are usually at very low concentrations, most of the times below the detection limits of analytical equipment used for their quantification, hindering their accurate monitoring. Therefore, the development of a pre-concentration technique in order to accurately quantify and monitor these components in aqueous streams is of major relevance. This work addresses the use of liquid-liquid equilibria, applying ionic liquids (ILs), for the extraction and concentration of non-steroidal anti-inflammatory drugs (NSAIDs) from aqueous effluents. Particularly, aqueous biphasic systems (ABSs) composed of ILs and potassium citrate were investigated in the extraction and concentration of naproxen, diclofenac and ketoprofen from aqueous media. Both the extraction efficiency and concentration factor achievable by these systems was determined and evaluated. Within the best conditions, extraction efficiencies of 99.4% and concentration factors up to 13 times were obtained.

Detection of trasformer intermittent winding faults by the on-load exciting current Park`s vector approach

This paper presents the application of the on-load exciting current Park's Vector Approach for diagnosing permanent and intermittent turn-to-turn winding faults in operating power transformers. First, an experimental investigation of the behaviour of the transformer under the occurrence of both permanent and intermittent winding faults is presented. Finally, experimental test results demonstrate the effectiveness of the proposed diagnostic technique, which is based on the on-line monitoring of the on-load exciting current Park's Vector patterns.

Detection of mineralized structures in very early stages of development of Marine Teleostei using a modified Alcian blue-Alizarin red double staining technique for bone and cartilage

We have developed a procedure for staining cartilage and bone in fish larvae as small as 2 mm (notochord length), for which standard alcian blue/alizarin red procedures did not give positive and/or consistent results. Small calcified structures only 100-200 pm in length can be clearly visualized. The method is suitable for both ontogenic studies during early stages of skeletal development in most marine fishes (e.g., Sparus aurata L., Solea senegalensis Kaup), whose larvae at hatching are often only a few millimeters long and for detecting skeletal abnormalities in small larvae. This procedure can also be used for specimens that have been preserved in 1000/0 ethanol for up to two years.

Application of molecular tools for detection of plant viruses

Grapevine leafroll disease (GLRD) is one of the most important virus diseases of grapevines worldwide, causing major economical impact. The disease has a complex aetiology and currently eleven phloem-limited viruses, termed in general Grapevine leafroll-associated virus (GLRaVs), have been identified. Two of the GLRaVs, GLRaV-1 and GLRaV-3, are included in the European certification scheme of propagation material. However, the flawed notion that GLRaV-3 is more frequent than GLRaV-1 and that all other GLRaVs are possibly not as relevant for GLRD, has until now precluded the development of specific serological and molecular detection assays and limited the scope of molecular characterization of the viruses known to be associated with the disease. Hence, few studies have addressed the phylodynamics of GLRaVs or even characterized the genetic structure of their natural populations. This generalized lack of molecular information, in turn underlie the deficient capacity to detect the viruses. The phylogenetic analyses were conducted on the basis of the heat shock protein 70 homologue (HSP70h) and the coat protein (CP) genes for GLRaV-1 and the HSP70h, the heat shock protein 90 homologue (HSP90h) and the CP genes for GLRaV-5. The data obtained for GLRaV-1 contributed 83 new CP sequences. This information was combined with previous analysis by other authors and used for the production of new polyclonal IgG, capable of detecting CP variants from all the phylogroups observed. Successful testing of this new tool included tissue print immunoblotting (TPIB) and in situ immunoassay (ISIA). The data obtained for GLRaV-5, contributed 61 new CP and 28 new HSP90h gene sequences. Eight phylogenetic groups were identified on the basis of the CP. Characterization of the genetic structure of the isolates revealed a higher diversity than previously reported and allowed the identification of dominant virus variants. For both GLRaV-1 and GLRaV-5, the effect of vegetative propagation on the virus transmission dynamics was addressed.

Detection of explosive vapors using organic thin-film transistors

Field effect transistors (FETs) based on organic materials were investigated as sensors for detecting 2,4,6-trinitrotoluene (TNT) vapors. Several FET devices were fabricated using two types of semiconducting organic materials, solution processed polymers deposited by spin coating and, oligomers (or small molecules) deposited by vacuum sublimation. When vapors of nitroaromatic compounds bind to thin films of organic materials which form the transistor channel, the conductivity of the thin film increases and changes the transistor electrical characteristic. The use of the amplifying properties of the transistor represents a major advantage over conventional techniques based on simple changes of resistance in polymers frequently used in electronic noses.

Detection of Incipient Thermal Damage Of Carbon Fiber/Epoxy Composites Using Fluorescent Thermal Damage Probes

Thesis (Ph.D.)--University of Washington, 2013

Detection of MegaTAL-induced HIV pol Mutation By Droplet Digital PCR

Thesis (Master's)--University of Washington, 2015

Next-generation sequencing is highly sensitive for the detection of beta-catenin mutations in desmoid-type fibromatoses

Desmoid-type fibromatoses are locally aggressive and frequently recurrent tumours, and an accurate diagnosis is essential for patient management. The majority of sporadic lesions harbour beta-catenin (CTNNB1) mutations. We used next-generation sequencing to detect CTNNB1 mutations and to compare the sensitivity and specificity of next-generation sequencing with currently employed mutation detection techniques: mutation-specific restriction enzyme digestion and polymerase chain reaction amplification. DNA was extracted from formalin-fixed paraffin-embedded needle biopsy or resection tissue sections from 144 patients with sporadic desmoid-type fibromatoses, four patients with syndrome-related desmoid-type fibromatoses and 11 morphological mimics. Two primer pairs were designed for CTNNB1 mutation hotspots. Using ≥10 ng of DNA, libraries were generated by Fluidigm and sequenced on the Ion Torrent Personal Genome Machine. Next-generation sequencing had a sensitivity of 92.36 % (133/144, 95 % CIs: 86.74 to 96.12 %) and a specificity of 100 % for the detection of CTNNB1 mutations in desmoid-type fibromatoses-like spindle cell lesions. All mutations detected by mutation-specific restriction enzyme digestion were identified by next-generation sequencing. Next-generation sequencing identified additional mutations in 11 tumours that were not detected by mutation-specific restriction enzyme digestion, two of which have not been previously described. Next-generation sequencing is highly sensitive for the detection of CTNNB1 mutations. This multiplex assay has the advantage of detecting additional mutations compared to those detected by mutation-specific restriction enzyme digestion (sensitivity 82.41 %). The technology requires minimal DNA and is time- and cost-efficient.

A Fuzzy-Wavelet Neural Network Model for the Detection of Meat Spoilage using an Electronic Nose

Food product safety is one of the most promising areas for the application of electronic noses. The performance of a portable electronic nose has been evaluated in monitoring the spoilage of beef fillet stored aerobically at different storage temperatures (0, 4, 8, 12, 16 and 20°C). This paper proposes a fuzzy-wavelet neural network model which incorporates a clustering pre-processing stage for the definition of fuzzy rules. The dual purpose of the proposed modeling approach is not only to classify beef samples in the respective quality class (i.e. fresh, semi-fresh and spoiled), but also to predict their associated microbiological population directly from volatile compounds fingerprints. Comparison results indicated that the proposed modeling scheme could be considered as a valuable detection methodology in food microbiology

Investigating the causal role of rightOFA in holistic detection of Mooney faces and objects: an fMRI-guided TMS study

Background The right occipital face area (rOFA) is known to be involved in face discrimination based on local featural information. Whether this region is involved in global, holistic stimulus processing is not known. Objective We used fMRI-guided transcranial magnetic stimulation (TMS) to investigate whether rOFA is causally implicated in stimulus detection based on holistic processing, by the use of Mooney stimuli. Methods Two studies were carried out: In Experiment 1, participants performed a detection task involving Mooney faces and Mooney objects; Mooney stimuli lack distinguishable local features and can be detected solely via holistic processing (i.e. at a global level) with top-down guidance from previously stored representations. Experiment 2 required participants to detect shapes which are recognized via bottom-up integration of local (collinear) Gabor elements and was performed to control for specificity of rightOFA's implication in holistic detection. Results In Experiment 1, TMS over rOFA and rLO impaired detection of all stimulus categories, with no category-specific effect. In Experiment 2, shape detection was impaired when TMS was applied over rLO but not over rOFA. Conclusions Our results demonstrate that rOFA is causally implicated in the type of top-down holistic detection required by Mooney stimuli and that such role is not face-selective. In contrast, rOFA does not appear to play a causal role in in detection of shapes based on bottom-up integration of local components, demonstrating that its involvement in processing non-face stimuli is specific for holistic processing.

A Rapid Detection of Meat Spoilage using an Electronic Nose and Fuzzy-Wavelet systems

Freshness and safety of muscle foods are generally considered as the most important parameters for the food industry. To address the rapid detection of meat spoilage microorganisms during aerobic or modified atmosphere storage, an electronic nose with the aid of fuzzy wavelet network has been considered in this research. The proposed model incorporates a clustering pre-processing stage for the definition of fuzzy rules. The dual purpose of the proposed modelling approach is not only to classify beef samples in the respective quality class (i.e. fresh, semi-fresh and spoiled), but also to predict their associated microbiological population directly from volatile compounds fingerprints. Comparison results against neural networks and neurofuzzy systems indicated that the proposed modelling scheme could be considered as a valuable detection methodology in food microbiology

Molecular imprinted nanoelectrodes for ultra sensitive detection of ovarian cancer marker

The relentless discovery of cancer biomarkers demands improved methods for their detection. In this work, we developed protein imprinted polymer on three-dimensional gold nanoelectrode ensemble (GNEE) to detect epithelial ovarian cancer antigen-125 (CA 125), a protein biomarker associated with ovarian cancer. CA 125 is the standard tumor marker used to follow women during or after treatment for epithelial ovarian cancer. The template protein CA 125 was initially incorporated into the thin-film coating and, upon extraction of protein from the accessible surfaces on the thin film, imprints for CA 125 were formed. The fabrication and analysis of the CA 125 imprinted GNEE was done by using cyclic voltammetry (CV), differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS) techniques. The surfaces of the very thin, protein imprinted sites on GNEE are utilized for immunospecific capture of CA 125 molecules, and the mass of bound on the electrode surface can be detected as a reduction in the faradic current from the redox marker. Under optimal conditions, the developed sensor showed good increments at the studied concentration range of 0.5–400 U mL−1. The lowest detection limit was found to be 0.5 U mL−1. Spiked human blood serum and unknown real serum samples were analyzed. The presence of non-specific proteins in the serum did not significantly affect the sensitivity of our assay. Molecular imprinting using synthetic polymers and nanomaterials provides an alternative approach to the trace detection of biomarker proteins.