A rapid PCR protocol for marker assisted detection of heterozygotes in segregating generations involving 1BL/1RS translocation and normal wheat lines

A rapid and reliable polymerase chain reaction (PCR)-based protocol was developed for detecting zygosity of the 1BL/1RS translocation in hexaploid wheat. The protocol involved a multiplex PCR with 2 pairs of oligonucleotide primers, rye-specific Ris-1 primers, and consensus 5S intergenic spacer (IGS) primers, and digestion of the PCR products with the restriction enzyme, MseI. A small piece of alkali-treated intact leaf tissue is used as a template for the PCR, thereby eliminating the necessity for DNA extraction. The test is simple, highly sensitive, and rapid compared with the other detection systems of 1BS1RS heterozygotes in hexaploid wheat. PCR results were confirmed with AFLP analyses. Diagnostic tests for 1BL/1RS translocation based on Sec-1-specific ELISA, screening for chromosome arm 1RS controlled rust resistance locus Yr9, and the PCR test differed in their ability to detect heterozygotes. The PCR test and rust test detected more heterozygotes than the ELISA test. The PCR test is being used to facilitate S1 family recurrent selection in the Germplasm Enhancement Program of the Australian Northern Wheat Improvement Program. A combination of the PCR zygosity test with other markers currently being implemented in the breeding program makes this test economical for 1BL/1RS characterisation of S1 families.

Detection of Influenza type A virus by LightCycler RT-PCR

Using the Roche LightCycler we developed a real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay using the Influenza A LightCycler RT-PCR (FA-LC-RTPCR) for the rapid detection of Influenza A. The assay was used to examine 178 nasopharyngeal aspirate (NPA) samples, from patients with clinically recognised respiratory tract infection, for the presence of Influenza A RNA. The results were then compared to a testing algorithm combining direct immunofluorescent assy (DFA) and a culture augmented DFA (CA-DFA) assay. In total, 76 (43%) specimens were positive and 98 (55%) specimens were negative by both the FA-LC-RTPCR and the DFA and CA-DFA algorithm. In addition, the FA-LC-RTPCR detected a further 4 (2%) positive specimens, which were confirmed by a conventional RT-PCR method. The high level of sensitivity and specificity, combined with the rapid turnaround time for results, makes the LC-RT-PCR assay suitable for the detection of Influenza A in clinical specimens.

Quantitation of alternatively spliced NMDA receptor NR1 isoform mRNA transcripts in human brain by competitive RT-PCR

The N-methyl-D-aspartate (NMDA)-selective subtype of ionotropic glutamate receptor is of importance in neuronal differentiation and synapse consolidation, activity-dependent forms of synaptic plasticity, and excitatory amino acid-mediated neuronal toxicity [Neurosci. Res. Program, Bull. 19 (1981) 1; Lab. Invest. 68 (1993) 372]. NMDA receptors exist in vivo as tetrameric or pentameric complexes comprising proteins from two families of homologous subunits, designated NR1 and NR2(A-D) [Biochem. Biophys. Res. Commun. 185 (1992) 826]. The gene coding for the human NR1 subunit (hNR1) is composed of 21 exons, three of which (4, 20 and 21) can be differentially spliced to generate a total of eight distinct subunit variants. We detail here a competitive RT-PCR (cRT-PCR) protocol to quantify endogenous levels of hNR1 splice variants in autopsied human brain. Quantitation of each hNR1 splice variant is performed using standard curve methodology in which a known amount of synthetic ribonucleic acid competitor (internal standard) is co-amplified against total RNA. This method can be used for the quantitation of hNR1 mRNA levels in response to acute or chronic disease states, in particular in the glutamatergic-associated neuronal loss observed in Alzheimer's disease [J. Neurochem. 78 (2001) 175]. Furthermore, alterations in hNR1 mRNA expression may be reflected at the translational level, resulting in functional changes in the NMDA receptor. (C) 2003 Elsevier Science B.V. All rights reserved.

Quantitation of human brain GABAA receptor isoforms by competitive RT-PCR

We have developed a competitive RT-PCR assay, adapted from Lewohl et al. [Brain Res. Brain Res. Protoc. 1 (1997) 347]. for the quantitation of GABA, receptor beta isoforms in human brain using an internal standard that shares high sequence homology to the targets. The internal standard is identical to the beta(1) sequence except for a 61 bp deletion and the incorporation of a Hind III restriction enzyme site. Unlike traditional competitive RT-PCR, which requires a range of internal standard concentrations to be titrated against a constant amount of unknown, this method relies on a standard curve for quantitation of each sample and thus permits increased sample throughput. This method is suitable for the quantitation of beta(1), beta(2) and beta(3) isoforms of the GABA(A) receptor in human alcoholic and control brain. (C) 2003 Elsevier Science B.V. All rights reserved.

Preliminary comparison of three lightcycler pcr assays for the detection of herpes simplex virus in swab specimens

Three Herpes Simplex Virus LightCycler polymerase chain reaction assays were compared for the detection of herpes simplex virus in 48 swab specimens. The assays comprised of one in-house assay and two commercial kits: the Artus HSV LC RealArt PCR kit and the Roche LightCycler HSV 1/2 Detection kit. On the whole, the three assays had comparable sensitivities. However, differentiation of herpes simplex virus types 1 and 2 by melting curve analysis was problematic in all assays. Overall, the results highlight the limitations of typing herpes simplex virus by melting curve analysis.

An SNP-based PCR assay to differentiate between Listeria monocytogenes lineages derived from phylogenetic analysis of the sigB gene

The alternative sigma factor sigB gene is involved in the stress response regulation of Listeria monocytogenes, and contributes towards growth and survival in adverse conditions. This gene was examined to determine if it could be a useful indicator of lineage differentiation, similar to the established method based on ribotyping. The sigB sequence was resolved in four local L. monocytogenes strains and the phylogenetic relationship among these, and a further 21 sigB gene sequences from strains of different serotype and lineage including two Listeria innocua strains, obtained from the GenBank database were determined. The sigB nucleotide sequences of these 25 Listeria strains were then examined for single nucleotide polymorphic (SNP) sites that could differentiate between the three lineages. Based on nucleotide sequences L. monocytogenes lineage F serotype 1/2b and 4b clustered together, lineage II/serotype 1/2a and 1/2c strains clustered together, lineage III/serotypes 4a and 4c strains clustered together and L. innocua strains clustered together as an outgroup. SNPs differentiating the three lineages were identified. Individual allele-specific PCR reactions based on these polymorphisms were successful in grouping known and a further 37 local L. monocytogenes isolates into the three lineages. (C) 2003 Elsevier B.V. All fights reserved.

Gene flow in great bustard populations across the Strait of Gibraltar as elucidated from excremental PCR and mtDNA sequencing

Recent advances in molecular biology have made it possible to use the trace amounts of DNA in faeces to non-invasively sample endangered species for genetic studies. Here we use faeces as a source of DNA and mtDNA sequence data to elucidate the relationship among Spanish and Moroccan populations of great bustards. 834 bp of combined control region and cytochrome-b mtDNA fragments revealed four variable sites that defined seven closely related haplotypes in 54 individuals. Morocco was fixed for a single mtDNA haplotype that occurs at moderate frequency (28%) in Spain. We could not differentiate among the sampled Spanish populations of Caceres and Andalucia but these combined populations were differentiated from the Moroccan population. Estimates of gene flow (Nm = 0.82) are consistent with extensive observations on the southern Iberian peninsular indicating that few individuals fly across the Strait of Gibraltar. We demonstrate that both this sea barrier and mountain barriers in Spain limit dispersal among adjacent great bustard populations to a similar extent. The Moroccan population is of high ornithological significance as it holds the only population of great bustards in Africa. This population is critically small and genetic and observational data indicate that it is unlikely to be recolonised via immigration from Spain should it be extirpated. In light of the evidence presented here it deserves the maximum level of protection.

Estudo da corrosão e inibição dos aços carbono AISI 1010, inoxidável AISI 316 e duplex UNS S31803 em meio de solução de íons cloreto

O comportamento da corrosão e inibição à corrosão dos aços carbono AISI 1010, inox AISI 316 e duplex UNS S31803 foi estudado em meio de solução de íons cloreto à 3,0% (m/v), na ausência e presença do benzimidazol e imidazol como inibidores. A caracterização química e morfológica dos aços foi realizada por meio das técnicas de espectrometria de emissão ótica, difração de raios X (DRX), microscopia ótica, microscopia eletrônica de varredura (MEV) e energia dispersiva de raios X (EDX). As análises eletroquímicas foram realizadas através das técnicas de polarização potenciodinâmica e espectroscopia de impedância eletroquímica. As análises de DRX e de metalografia mostraram as fases presentes em cada aço, sendo o aço AISI 1010 composto pela fase ferrita, o aço AISI 316 pelas fases de FeNi e Cr e o aço UNS S31803 pelas fases austenita e ferrita. Além disso, a metalografia e as análises de MEV e EDX permitiram identificar regiões e certos elementos presentes nos aços que propiciam à ocorrência da corrosão, tais como inclusões. Os inibidores foram testados em diferentes concentrações (25 ppm, 50 ppm, 100 ppm, 500 ppm e 1000 ppm) para os três aços, através das curvas de polarização e impedância eletroquímica, e verificou-se que para todas as concentrações houve aumento da resistência à corrosão dos aços. Pelas curvas de polarização verificou-se que o benzimidazol proporcionou aos aços AISI 1010, AISI 316 e UNS S31803, eficiências de inibição de cerca de 51%, 71% e 75%, respectivamente. Enquanto que o imidazol apresentou eficiência de cerca de 73%, 95% e 86%, respectivamente. Os resultados de impedância eletroquímica mostraram que as eficiências de inibição do benzimidazol foram de aproximadamente 52%, 73% e 71%, respectivamente, para os aços AISI 1010, AISI 316 e UNS S31803. E por sua vez, o imidazol apresentou eficiências de aproximadamente 96% para os aços AISI 1010 e AISI 316 e 85% para o aço UNS S31803. O teste de perda de massa mostrou que para o aço AISI 1010 tanto o benzimidazol quanto e o imidazol inibiram a corrosão, sendo que reduziram a corrosão em cerca de 17% e 24%, respectivamente. Nas análises das curvas de polarização em estudos com a água do mar observou-se que os inibidores foram menos eficientes do que em meio de solução de cloreto. O benzimidazol obteve eficiências de cerca de 14%, 50% e 33%, respectivamente, para os aços AISI 1010, AISI 316 e UNS S31803. Enquanto que o imidazol apresentou eficiências de aproximadamente 21%, 59% e 34%, respectivamente. Em todas as análises eletroquímicas e análise de perda de massa, o imidazol se mostrou o melhor inibidor para os aços estudados.

Perfis de tensão residual do aço duplex UNS S32304 submetido a diferentes processos de soldagem TIG e condições de tratamento térmico

Visando a aplicação do aço UNS S32304 em embalados para transporte de material radioativo, amostras soldadas por processo TIG, com diferentes gases de proteção, foram submetidas a tratamentos térmicos nas temperaturas de 475°C, 600°C e 750°C por 8 horas, seguidas de resfriamento ao ar, a fim de analisar o efeito de temperaturas críticas no perfil de tensões residuais e microestrutura. A difratometria de raios X foi utilizada para determinação das tensões residuais, em diferentes condições (amostras como recebidas e apenas tratadas termicamente) e o perfil de tensões residuais total das amostras soldadas é apresentado para cada fase (austenita e ferrita). As tensões residuais das fases foram determinadas pela técnica sen2ψ, utilizando um difratômetro com fonte de radiação CuKα (<λ