Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays

We describe a method for multiplex detection of mutations in which the solid-phase minisequencing principle is applied to an oligonucleotide array format. The mutations are detected by extending immobilized primers that anneal to their template sequences immediately adjacent to the mutant nucleotide positions with single labeled dideoxynucleoside triphosphates using a DNA polymerase. The arrays were prepared by coupling one primer per mutation to be detected on a small glass area. Genomic fragments spanning nine disease mutations, which were selected as targets for the assay, were amplified in multiplex PCR reactions and used as templates for the minisequencing reactions on the primer array. The genotypes of homozygous and heterozygous genomic DNA samples were unequivocally defined at each analyzed nucleotide position by the highly specific primer extension reaction. In a comparison to hybridization with immobilized allele-specific probes in the same assay format, the power of discrimination between homozygous and heterozygous genotypes was one order of magnitude higher using the minisequencing method. Therefore, single-nucleotide primer extension is a promising principle for future high-throughput mutation detection and genotyping using high density DNA-chip technology.     

The effect of shaking on magnetic shields

The increase of the shielding factor due to shaking was measured in a scale model for a magnetically shielded room. The increase was found to be 7 dB for a single-layer square cylinder biased by the Earth's magnetic field. The shielding factor of a large-volume three-layer Mumetal^®room was estimated to increase by a factor of 30, thus confirming the feasibility of shaking in magnetic shields. The shaking parameters, amplitude, and frequency are not critical according to the experiments. Winding the shaking coils along the edges of the cubic shield leads to minimum disturbances inside the cube, and the winding can also be applied to demagnetize the shield by an alternating field of 25 A/m, 50 Hz. The relative incremental permeability of Mumetal was studied as a function of the shaking and biasing fields. The permeability was found to increase considerably by shaking and by decreasing the biasing field. With zero biasing and with shaking field of Hs= 5 A/m root mean square (rms), 50 Hz, the permeability reached its maximum value of 89 000, which is sevenfold the value without shaking.     

Focused multi-task learning in a Gaussian process framework

Multi-task learning, learning of a set of tasks together, can improve performance in the individual learning tasks. Gaussian process models have been applied to learning a set of tasks on different data sets, by constructing joint priors for functions underlying the tasks. In these previous Gaussian process models, the setting has been symmetric in the sense that all the tasks have been assumed to be equally important, whereas in settings such as transfer learning the goal is asymmetric, to enhance performance in a target task given the other tasks. We propose a focused Gaussian process model which introduces an ??explaining away?? model for each of the additional tasks to model their non-related variation, in order to focus the transfer to the task-of-interest. This focusing helps reduce the key problem of negative transfer, which may cause performance to even decrease if the tasks are not related closely enough. In experiments, our model improves performance compared to single-task learning, symmetric multi-task learning using hierarchical Dirichlet processes, transfer learning based on predictive structure learning, and symmetric multi-task learning with Gaussian processes.     

Interactions of sulphur anions and stainless steels at kraft pulp digesting temperature

Interactions of certain stainless steels (S30400, S31600, S31803, S32304) and sulphur anions, separately and in combination, at concentrations typical of kraft liquors were investigated using XRF and CER techniques. IC, ISE and ABC titration were applied in the modelling of behaviour of the sulphur anions. Nickel and sulphur enriched to the steel surfaces in all experiments. Abilities of molybdenum and chromium to remain in the surfaces appeared to be better than those of iron. Adhesion of sulphur onto austenitic grades was probably stronger than that of the duplex grades. Sulphide and combination of sulphur anions formed durable films, but films formed by thiosulphate possessed some gliding properties. For the solution, real amount of the sulphide was less than the added amount. Thiosulphate had a tendency to convert into sulphite.     

Effect of ageing on transformation kinetics and internal friction of Ni-rich Ni–Ti alloys

In Ni-rich Ni–Ti alloys the ageing treatments create finely dispersed Ti₃Ni₄ precipitates in the B2-based matrix. Formed precipitates are known to influence the phase transformation temperatures and to facilitate the R-phase transformation. In addition to the change in the phase transformation behaviour, the ageing treatments are also reported to affect internal friction and mechanical properties of Ni–Ti alloys.In the present work, by means of systematic DSC and DMA studies the effects of the ageing treatments on the phase transformation as well as on the internal friction and mechanical properties of Ni-rich Ni–Ti alloy were studied. As an extension to earlier studies, the present study concentrates both on the effects of the ageing time and the ageing temperature systematically. By combining the results of the DSC measurements of phase transformation behaviour to the DMA measurements of internal friction and mechanical behaviour of the Ni-rich Ni–Ti alloy, the present study gives yet unpublished information about the comprehensive effects of the ageing treatments on these alloys. These results enable to control the phase transformation temperatures, internal friction and mechanical properties of the Ni-rich Ni–Ti alloy by selecting the suitable ageing treatment.Results showed that the noticed effects of the ageing treatments on mechanical properties could be explained with the changes in the size, distribution, density and coherency of the formed Ti₃Ni₄ precipitates. The high internal friction values can be explained as the contribution of the internal stress fields and increased amount of mobile interfaces as the result of the formed Ti₃Ni₄ precipitates. The amount of mobile interfaces seems to be more dominant factor for the increased internal friction value than the effect of the internal stress fields. Therefore, the optimal internal friction values can be obtained with a proper aging treatment which will yield a high density of small Ti₃Ni₄ precipitates.     

Updated survey of Fusarium species and toxins in Finnish cereal grains

The aim of the project was to produce updated information during 2005–14 on the Fusarium species found in Finnish cereal grains, and the toxins produced by them, as the last comprehensive survey study of Fusarium species and their toxins in Finland was carried out at the turn of the 1960s and the 1970s. Another aim was to use the latest molecular and chemical methods to investigate the occurrence and correlation of Fusarium species and their mycotoxins in Finland. The most common Fusarium species found in Finland in the FinMyco project 2005 and 2006 were F. avenaceum, F. culmorum, F. graminearum, F. poae, F. sporotrichioides and F. langsethiae. F. avenaceum was the most dominant species in barley, spring wheat and oat samples. The occurrence of F. culmorum and F. graminearum was high in oats and barley. Infection by Fusarium fungi was the lowest in winter cereal grains. The incidence of Fusarium species in 2005 was much higher than in 2006 due to weather conditions. F. langsethiae has become much more common in Finland since 2001. F. graminearum has also risen in the order of importance. A highly significant correlation was found between Fusarium graminearum DNA and deoxynivalenol (DON) levels in Finnish oats, barley and wheat. When comparing the FinMyco data in 2005–06 with the results of the Finnish safety monitoring programme for 2005–14, spring cereals were noted as being more susceptible to infection by Fusarium fungi and the formation of toxins. The contents of T-2 and HT-2 toxins and the frequency of exceptionally high DON concentrations all increased in Finland during 2005–14. Beauvericin (BEA), enniatins (ENNs) and moniliformin (MON) were also very common contaminants of Finnish grains in 2005–06. Climate change is leading to warmer weather, and this may indicate more changes in Finnish Fusarium mycobiota and toxin contents and profiles in the near future.     

Determination of malachite green residues in rainbow trout muscle with liquid chromatography and liquid chromatography coupled with tandem mass spectrometry

A method for the determination of malachite green and its major metabolite leucomalachite green in rainbow trout muscle is reported with limits of detection of 0.8 and 0.6 μg kg^-1, respectively. Residues were extracted with an acetonitrile-acetate buffer mixture and partitioned into methylene chloride. Clean-up of the extracts was performed on alumina and propylsulfonic acid solid-phase extraction columns using the automated solid-phase extraction system. The chromatographic separation of malachite green and leucomalachite green was achieved on a Chromspher 5B column using an acetonitrile-acetate buffer mobile phase. Leucomalachite green was converted to malachite green by post-column oxidation before spectrophotometric detection at 600 nm. The mean recoveries of malachite green and leucomalachite green from control rainbow trout muscle spiked at 2-50 μg kg^-1 were 65% (range 63.4-65.9%, relative standard deviation 3.9-16.1%) and 74% (range 58.3-82.6%, relative standard deviation 3.3-11.4%), respectively. Qualitative confirmation of the determined residues was performed with liquid chromatography coupled with tandem mass spectrometry detection with limits of detection of 2.5 and 1 μg kg^-1 for malachite green and leucomalachite green, respectively.     

Determination of Fusarium mycotoxins beauvericin and enniatins (A,A1, B,B1) in eggs of laying hens using liquid chromatography–tandem mass spectrometry (LC–MS/MS)

An existing sample preparation technique used for the determination of ionophoric coccidiostats was modified to permit the analysis of Fusarium mycotoxins beauvericin and enniatins in egg samples. The validation results indicated that the sample preparation method developed is well applicable to the determination of the related compounds in eggs. The presence and contamination levels of beauvericin and enniatins A, A1, B and B1 were studied in Finnish egg samples in 2004–2005. The egg sample analyses (112 whole eggs and 367 egg yolk) revealed that the occurrence of beauvericin as well as enniatins B and B1 is very common in Finnish eggs. The contaminations were, however, in most cases in trace-levels (<limit of quantification). Enniatin A and A1 were not found in any of the whole egg samples, and furthermore enniatin B1 was present only in samples from 2004. The general contamination levels of beauvericin and enniatins in whole egg samples were similar in 2004 and 2005. The prevalence and concentration levels of mycotoxins were higher in the market samples (egg yolk) as compared to samples collected in the national residue monitoring programme (whole egg) samples suggesting that there may be bioaccumulation of these mycotoxin contaminants in egg yolk. This is the first study to report the presence of Fusarium mycotoxins beauvericin and enniatins in egg samples.