The Effect of Sample and Sample Matrix on DNA Processing: Mechanisms for the Detection and Management of Inhibition in Forensic Samples

The presence of inhibitory substances in biological forensic samples has, and continues to affect the quality of the data generated following DNA typing processes. Although the chemistries used during the procedures have been enhanced to mitigate the effects of these deleterious compounds, some challenges remain. Inhibitors can be components of the samples, the substrate where samples were deposited or chemical(s) associated to the DNA purification step. Therefore, a thorough understanding of the extraction processes and their ability to handle the various types of inhibitory substances can help define the best analytical processing for any given sample. A series of experiments were conducted to establish the inhibition tolerance of quantification and amplification kits using common inhibitory substances in order to determine if current laboratory practices are optimal for identifying potential problems associated with inhibition. DART mass spectrometry was used to determine the amount of inhibitor carryover after sample purification, its correlation to the initial inhibitor input in the sample and the overall effect in the results. Finally, a novel alternative at gathering investigative leads from samples that would otherwise be ineffective for DNA typing due to the large amounts of inhibitory substances and/or environmental degradation was tested. This included generating data associated with microbial peak signatures to identify locations of clandestine human graves. Results demonstrate that the current methods for assessing inhibition are not necessarily accurate, as samples that appear inhibited in the quantification process can yield full DNA profiles, while those that do not indicate inhibition may suffer from lowered amplification efficiency or PCR artifacts. The extraction methods tested were able to remove >90% of the inhibitors from all samples with the exception of phenol, which was present in variable amounts whenever the organic extraction approach was utilized. Although the results attained suggested that most inhibitors produce minimal effect on downstream applications, analysts should practice caution when selecting the best extraction method for particular samples, as casework DNA samples are often present in small quantities and can contain an overwhelming amount of inhibitory substances.

Material Evaluation of an Elastomer, Epoxy and Lightweight Concrete Rail Attachment System for Direct Fixation Light Rail Applications

Thesis (Master's)--University of Washington, 2016-08

Jointly event extraction and visualization on Twitter via probabilistic modelling

Event extraction from texts aims to detect structured information such as what has happened, to whom, where and when. Event extraction and visualization are typically considered as two different tasks. In this paper, we propose a novel approach based on probabilistic modelling to jointly extract and visualize events from tweets where both tasks benefit from each other. We model each event as a joint distribution over named entities, a date, a location and event-related keywords. Moreover, both tweets and event instances are associated with coordinates in the visualization space. The manifold assumption that the intrinsic geometry of tweets is a low-rank, non-linear manifold within the high-dimensional space is incorporated into the learning framework using a regularization. Experimental results show that the proposed approach can effectively deal with both event extraction and visualization and performs remarkably better than both the state-of-the-art event extraction method and a pipeline approach for event extraction and visualization.

Evaluation of five commercial methods for the extraction and purification of DNA from human faecal samples for downstream molecular detection of the enteric protozoan parasites Cryptosporidium spp., Giardia duodenalis, and Entamoeba spp

High quality, pure DNA is required for ensuring reliable and reproducible results in molecular diagnosis applications. A number of in-house and commercial methods are available for the extraction and purification of genomic DNA from faecal material, each one offering a specific combination of performance, cost-effectiveness, and easiness of use that should be conveniently evaluated in function of the pathogen of interest. In this comparative study the marketed kits QIAamp DNA stool mini (Qiagen), SpeedTools DNA extraction (Biotools), DNAExtract-VK (Vacunek), PowerFecal DNA isolation (MoBio), and Wizard magnetic DNA purification system (Promega Corporation) were assessed for their efficacy in obtaining DNA of the most relevant enteric protozoan parasites associated to gastrointestinal disease globally. A panel of 113 stool specimens of clinically confirmed patients with cryptosporidiosis (n = 29), giardiasis (n = 47) and amoebiasis by Entamoeba histolytica (n = 3) or E. dispar (n = 10) and apparently healthy subjects (n = 24) were used for this purpose. Stool samples were aliquoted in five sub-samples and individually processed by each extraction method evaluated. Purified DNA samples were subsequently tested in PCR-based assays routinely used in our laboratory. The five compared methods yielded amplifiable amounts of DNA of the pathogens tested, although performance differences were observed among them depending on the parasite and the infection burden. Methods combining chemical, enzymatic and/or mechanical lysis procedures at temperatures of at least 56 °C were proven more efficient for the release of DNA from Cryptosporidium oocysts.

Fixing, storage time and DNA extraction applied to dT-RFLP for ecological and molecular studies of marine nematodes assemblages

The application of molecular methods offers an alternative faster than traditional methods based on morphology It is nearly impossible to process all the samples in short period using traditional methods, and the deterioration of marine sediments rapidly occurs The dT-RFLP (directed Terminal-Restriction Fragment Length Polymorphism) allows a rapid assessment of biodiversity changes of nematodes assemblages The use of a not suitable fixing, storage time and DNA extraction could be a limitation in molecular analysis like dT-RFLP and real time PCR.Objetives: the best fixative •the level of DNA degradation over the time •the best DNA extraction method for marine nematodes and suitable for dT-RFLP analysis

Determination Of Flavanones In Orange Juices Obtained From Different Sources By Hplc/dad.

Flavanones (hesperidin, naringenin, naringin, and poncirin) in industrial, hand-squeezed orange juices and from fresh-in-squeeze machines orange juices were determined by HPLC/DAD analysis using a previously described liquid-liquid extraction method. Method validation including the accuracy was performed by using recovery tests. Samples (36) collected from different Brazilian locations and brands were analyzed. Concentrations were determined using an external standard curve. The limits of detection (LOD) and the limits of quantification (LOQ) calculated were 0.0037, 1.87, 0.0147, and 0.0066 mg 100 g(-1) and 0.0089, 7.84, 0.0302, and 0.0200 mg 100 g(-1) for naringin, hesperidin, poncirin, and naringenin, respectively. The results demonstrated that hesperidin was present at the highest concentration levels, especially in the industrial orange juices. Its average content and concentration range were 69.85 and 18.80-139.00 mg 100 g(-1). The other flavanones showed the lowest concentration levels. The average contents and concentration ranges found were 0.019, 0.01-0.30, and 0.12 and 0.1-0.17, 0.13, and 0.01-0.36 mg 100 g(-1), respectively. The results were also evaluated using the principal component analysis (PCA) multivariate analysis technique which showed that poncirin, naringenin, and naringin were the principal elements that contributed to the variability in the sample concentrations.

Dentine Bond Strength And Antimicrobial Activity Evaluation Of Adhesive Systems.

This study evaluated the dentine bond strength (BS) and the antibacterial activity (AA) of six adhesives against strict anaerobic and facultative bacteria. Three adhesives containing antibacterial components (Gluma 2Bond (glutaraldehyde)/G2B, Clearfil SE Protect (MDPB)/CSP and Peak Universal Bond (PUB)/chlorhexidine) and the same adhesive versions without antibacterial agents (Gluma Comfort Bond/GCB, Clearfil SE Bond/CSB and Peak LC Bond/PLB) were tested. The AA of adhesives and control groups was evaluated by direct contact method against four strict anaerobic and four facultative bacteria. After incubation, according to the appropriate periods of time for each microorganism, the time to kill microorganisms was measured. For BS, the adhesives were applied according to manufacturers' recommendations and teeth restored with composite. Teeth (n=10) were sectioned to obtain bonded beams specimens, which were tested after artificial saliva storage for one week and one year. BS data were analyzed using two-way ANOVA and Tukey test. Saliva storage for one year reduces the BS only for GCB. In general G2B and GCB required at least 24h for killing microorganisms. PUB and PLB killed only strict anaerobic microorganisms after 24h. For CSP the average time to eliminate the Streptococcus mutans and strict anaerobic oral pathogens was 30min. CSB showed no AA against facultative bacteria, but had AA against some strict anaerobic microorganisms. Storage time had no effect on the BS for most of the adhesives. The time required to kill bacteria depended on the type of adhesive and never was less than 10min. Most of the adhesives showed stable bond strength after one year and the Clearfil SE Protect may be a good alternative in restorative procedures performed on dentine, considering its adequate bond strength and better antibacterial activity.

Chemical composition, acetylcholinesterase inhibitory and antifungal activities of Pera glabrata (Schott) Baill. (Euphorbiaceae)

Pera glabrata (Schott) Baill. was selected for this study after showing a preliminary positive result in a screening of Atlantic Forest plant species in the search for acetylcholinesterase inhibitors and antifungal compounds. The bioassays were conducted with crude ethanol extract of the leaves using direct bioautography method for acetylcholinesterase and antifungal activities. This extract was partitioned with hexane, chloroform and ethyl acetate solvents. The active chloroform fraction was submitted to silica gel chromatography column affording 12 groups. Caffeine, an alkaloid, which showed detection limits of 0.1 and 1.0 µg for anticholinesterasic and antifungal activities, respectively, was isolated from group nine. After microplate analyses, only groups four, nine, 10, 11 and 12 showed acetylcholinesterase inhibitory activity of 40% or higher. The group 12 was purified by preparative layer chromatography affording four sub-fractions. Two sub-fractions from this group were analyzed by gas chromatography-mass spectrometry and gas chromatography-flame ionization detector. The first sub-fraction showed anticholinesterasic activity and contained two major compounds: 9-hydroxy-4-megastigmen-3-one (84%) and caffeine (6%). The second sub-fraction presented five major compounds identified as 9-hydroxy-4-megastigmen-3-one, isololiolide, (-) loliolide, palmitic acid and lupeol and did not show activity.

Consumo alimentar de micronutrientes entre pré-escolares no domicílio e em escolas de educação infantil do município de Caxias do Sul (RS)

OBJETIVO: Avaliar a ingestão alimentar de micronutrientes em pré-escolares no domicílio e em escolas de educação infantil públicas e particulares. MÉTODOS: Estudo transversal realizado com 362 pré-escolares entre dois e seis anos de idade, em Caxias do Sul (RS) Brasil, em 2007. A ingestão alimentar na escola foi avaliada por meio do método de pesagem direta individual, e no domicílio, por meio de registro alimentar realizado pelos pais ou responsáveis. Foi calculada a ingestão alimentar de cálcio, ferro, folato, vitamina A, vitamina C e zinco de acordo com o local da refeição e tipo de escola. RESULTADOS: Houve maior ingestão de alimentos contendo ferro, folato e vitamina C durante o período em que as crianças permaneceram na escola infantil, e maior ingestão de cálcio, vitamina A e zinco no domicílio. Houve significativamente maior ingestão de alimentos contendo ferro (p=0,03), folato (p=0,03), vitamina A (p<0,01) e vitamina C (p<0,01) pelas crianças da escola particular e maior ingestão de cálcio (p<0,01) e zinco (p<0,01) na escola pública. Quanto à prevalência de inadequação dos micronutrientes, as crianças não apresentaram risco deficiente para ingestão de ferro, folato, vitamina A e C e zinco, porém apenas 67,4% apresentaram ingestão de cálcio igual ou acima ao valor de referência. CONCLUSÃO: Os achados sugerem que o consumo de cálcio, vitamina A e zinco foi maior nos domicílios, apesar de as crianças permanecerem a maior parte do dia nas escolas. O consumo diário de micronutrientes de crianças de escolas públicas e particulares não diferiu significativamente, mesmo com diferenças nos cardápios.

Simplified models for cross-section stress demands on C-section purlins in uplift

The objective of this paper is to provide and verify simplified models that predict the longitudinal stresses that develop in C-section purlins in uplift. The paper begins with the simple case of flexural stress: where the force has to be applied at the shear center, or the section braced in both flanges. Restrictions on load application point and restraint of the flanges are removed until arriving at the more complex problem of bending when movement of the tension flange alone is restricted, as commonly found in purlin-sheeting systems. Winter`s model for predicting the longitudinal stresses developed due to direct torsion is reviewed, verified, and then extended to cover the case of a bending member with tension flange restraint. The developed longitudinal stresses from flexure and restrained torsion are used to assess the elastic stability behavior of typical purlin-sheeting systems. Finally, strength predictions of typical C-section purlins are provided for existing AISI methods and a newly proposed extension to the direct strength method that employs the predicted longitudinal stress distributions within the strength prediction. (C) 2009 Elsevier Ltd. All rights reserved.

New concept for lifting in onshore oil wells

This paper presents the development of a prototype of a tubular linear induction motor applied to onshore oil exploitation, named MAT AE OS (which is the Portuguese acronym for Tubular Asynchronous Motor for Onshore Oil Exploitation). The function of this motor is to directly drive the sucker-rod pump installed in the down hole of the oil well. Considering the drawbacks and operational costs of the conventional oil extraction method, which is based on the walking beam and rod, string system, the developed prototype is intended to become a feasible alternative from both technical and economic points of view. At the present time, the MAT AE OS prototype is installed in a test bench at the Applied Electromagnetism Laboratory at the Escola Politecnica da Universidade de Sao Paulo. The complete testing system is controlled and supervised by special software, enabling good flexibility in operation, data acquisition, and performance analysis. The test results indicate that the motor develops a constant lift force along the pumping cycle, as shown by the measured dynamometric charts. Also, the evaluated electromechanical performance seems to be superior to that obtained by the traditional method. The system utilizing the MAT AE OS prototype allows the complete elimination of the rod string sets required by the conventional equipment, indicating that the new system may advantageously replace the surface mechanical components presently utilized.

Carbon and Nitrogen Dynamics in an Oxisol as Affected by Liming and Crop Residues under No-Till

The short-term effects of surface lime application and black oat (Avena strigosa Schreb.) residues, with or without N fertilization, were evaluated in a long-term no-till (NT) system on a sandy clay loam, a kaolinitic, thermic Typic Hapludox from the state of Parana, Brazil. The main plot treatments were: control and dolomitic lime applied on soil surface at 8 Mg ha(-1). Three treatments with crop residues were evaluated on the subplots: (i) fallow, (ii) black oat residues, and (iii) black oat residues aft er N fertilization at 180 kg ha(-1). Black oat dry biomass was not affected by the treatments during 3 yr. Surface liming increased soil pH, microbial biomass, microbial activity, and bacterial/fungal ratio at the soil surface (0-5 cm), resulting in increased amino acid turnover, water-soluble humic substances formation, and N mineralization and nitrification. While the application of black oat did increase the soil pH, overall it had much less effect on soil biological processes and C and N pools than did lime. We concluded that black oat cannot replace the need for lime to optimize crop production in these tropical NT systems. In the long term, however, black oat should aid in the amelioration of acidity and replenishment of soil organic C pools and should help reduce erosion. Overall, this study suggests that overapplication of inorganic fertilizer N may occur in some tropical NT systems. Further experiments are required in NT systems to investigate the use of slow-release N fertilizers in combination with lime and black oat as a mechanism to reduce acidification and promote sustainability.

STRUCTURAL INTERDEPENDENCE AMONG COLOMBIAN DEPARTMENTS

This paper analyzes structural interdependence among Colombian departments. The results show that Bogota has a large influence on the other regional economies through the power of its purchases. Additionally, a center-periphery pattern emerges in the spatial concentration of the effects of the hypothetical extraction of any territory. From a policy point of view, the main findings reaffirm the role played by Bogota in the recent polarization process observed in the regional economies in Colombia. Any policy action oriented to reduce these regional disparities should take into account that, given the structural interdependence among Colombian departments, the effects of new investment in the lagged regions would flow through Bogota and the major regional economies.

Rapid isolation of total RNA and genomic DNA from Hakea actities

Tissues of the Australian native plant species Hakea actities (Proteaceae) contain numerous metabolites and structural compounds that hinder the isolation of nucleic acids. Separate RNA and genomic DNA extraction procedures were developed to isolate high quality nucleic acids from H. actities. Total RNA was extracted from leaves, roots and cluster roots of H. actities grown in low nutrient levels. Cluster root formation in H. actities only occurs when the plants are grown in low nutrient concentrations. However, under these conditions, nucleic acid extraction becomes increasingly difficult. The new procedures are faster than many of the published nucleic acid extraction protocols, and avoid the use of hazardous chemicals. The RNA extraction method was used successfully on another Australian species and a crop species, suggesting that the procedure is useful for molecular studies of a broad range of plants.

Desenvolvimento e padronização de um método para determinação da sensibilidade do mycobacterium tuberculosis a fármacos contra tuberculose

A resistência a fármacos antituberculose tem constituído uma grande ameaça ao controle da tuberculose em âmbito mundial. A sua detecção precoce permite ao médico instituir um esquema de tratamento mais adequado ao paciente e consequentemente quebrar a cadeia de transmissão dos bacilos. Os testes de sensibilidade a antimicrobianos atuais, embora eficientes, são caros e/ou demorados e/ou trabalhosos. Com base nesta premissa, nos propusemos a desenvolver e padronizar um método fenotípico direto para determinação da sensibilidade do Mycobacterium tuberculosis a antimicrobianos de primeira linha do tratamento da tuberculose. Para o desenvolvimento deste novo teste, utilizaram-se os princípios do método das proporções e do exame de cultura pelo método de Ogawa–Kudoh. O estudo foi dividido em duas fases. A primeira, caracterizada pelo desenvolvimento e padronização do método proposto e a segunda, pela análise da concordância entre o método desenvolvido e o método do MGIT (padrão-ouro). Na primeira fase, foram realizados diversos ensaios para definir: os volumes de absorção e de liberação de líquidos de diferentes tipos de swab, o meio de cultura, as concentrações dos antimicrobianos e o tempo de leitura/interpretação das culturas. Além disso, foi verificado se a amostra deveria ou não ser diluída. Com base nos resultados destes ensaios, padronizou-se o método com: swab comercial, em meio de cultura Ogawa- Kudoh contendo separadamente 0,2 μg/mL de isoniazida, 40,0 μg/mL de rifampicina, 10,0 μg/mL de estreptomicina e 500,0 μg/mL de ácido para-nitrobenzóico. Padronizou-se ainda a inoculação da amostra de escarro de forma direta, ou seja, sem diluir e a leitura/interpretação do resultado do teste no período entre 21 e 28 dias. A análise comparativa entre este método e o teste de sensibilidade a antimicrobianos no sistema MGIT realizada na segunda fase do projeto indicou um índice kappa igual a 1,000, ou seja, uma concordância muito boa em relação ao padrão-ouro. Diante desses resultados promissores, acreditamos que o método desenvolvido apresente um grande potencial para ser utilizado em laboratórios com pouca infra-estrutura, por ser de baixo custo, fácil execução e relativamente rápido.