Assessment of allelic diversity in intron-containing Mal d 1 genes and their association to apple allergenicity

<p>Abstract</p> <p>Background</p> <p>Mal d 1 is a major apple allergen causing food allergic symptoms of the oral allergy syndrome (OAS) in birch-pollen sensitised patients. The <it>Mal d 1 </it>gene family is known to have at least 7 intron-containing and 11 intronless members that have been mapped in clusters on three linkage groups. In this study, the allelic diversity of the seven intron-containing <it>Mal d 1 </it>genes was assessed among a set of apple cultivars by sequencing or indirectly through pedigree genotyping. Protein variant constitutions were subsequently compared with <b>S</b>kin <b>P</b>rick <b>T</b>est (SPT) responses to study the association of deduced protein variants with allergenicity in a set of 14 cultivars.</p> <p>Results</p> <p>From the seven intron-containing <it>Mal d 1 </it>genes investigated, <it>Mal d 1.01 </it>and <it>Mal d 1.02 </it>were highly conserved, as nine out of ten cultivars coded for the same protein variant, while only one cultivar coded for a second variant. <it>Mal d 1.04</it>, <it>Mal d 1.05 </it>and <it>Mal d 1.06 A, B </it>and <it>C </it>were more variable, coding for three to six different protein variants. Comparison of <it>Mal d 1 </it>allelic composition between the high-allergenic cultivar Golden Delicious and the low-allergenic cultivars Santana and Priscilla, which are linked in pedigree, showed an association between the protein variants coded by the <it>Mal d 1.04 </it>and <it>-1.06A </it>genes (both located on linkage group 16) with allergenicity. This association was confirmed in 10 other cultivars. In addition, <it>Mal d 1.06A </it>allele dosage effects associated with the degree of allergenicity based on prick to prick testing. Conversely, no associations were observed for the protein variants coded by the <it>Mal d 1.01 </it>(on linkage group 13), -<it>1.02</it>, -<it>1.06B, -1.06C </it>genes (all on linkage group 16), nor by the <it>Mal d 1.05 </it>gene (on linkage group 6).</p> <p>Conclusion</p> <p>Protein variant compositions of Mal d 1.04 and -1.06A and, in case of <it>Mal d 1.06A</it>, allele doses are associated with the differences in allergenicity among fourteen apple cultivars. This information indicates the involvement of qualitative as well as quantitative factors in allergenicity and warrants further research in the relative importance of quantitative and qualitative aspects of <it>Mal d 1 </it>gene expression on allergenicity. Results from this study have implications for medical diagnostics, immunotherapy, clinical research and breeding schemes for new hypo-allergenic cultivars.</p

Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq

Transcription is the first step connecting genetic information with an organism's phenotype. While expression of annotated genes in the human brain has been characterized extensively, our knowledge about the scope and the conservation of transcripts located outside of the known genes' boundaries is limited. Here, we use high-throughput transcriptome sequencing (RNA-Seq) to characterize the total non-ribosomal transcriptome of human, chimpanzee, and rhesus macaque brain. In all species, only 20–28% of non-ribosomal transcripts correspond to annotated exons and 20–23% to introns. By contrast, transcripts originating within intronic and intergenic repetitive sequences constitute 40–48% of the total brain transcriptome. Notably, some repeat families show elevated transcription. In non-repetitive intergenic regions, we identify and characterize 1,093 distinct regions highly expressed in the human brain. These regions are conserved at the RNA expression level across primates studied and at the DNA sequence level across mammals. A large proportion of these transcripts (20%) represents 3′UTR extensions of known genes and may play roles in alternative microRNA-directed regulation. Finally, we show that while transcriptome divergence between species increases with evolutionary time, intergenic transcripts show more expression differences among species and exons show less. Our results show that many yet uncharacterized evolutionary conserved transcripts exist in the human brain. Some of these transcripts may play roles in transcriptional regulation and contribute to evolution of human-specific phenotypic traits

Diversity arrays technology (DArT) markers in apple for genetic linkage maps

Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive PstI restriction enzyme, resulted in a high frequency of markers, although there was 52–54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55–76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage

Laser-induced plasma in methane and dimethyl ether for flame ignition and combustion diagnostics

In this paper we report the investigation of the laser-induced breakdown and ignition behaviour of methane/air and dimethyl ether (DME)/air mixtures. Moreover, the optical emission from the induced plasma is utilized for determining the mixture composition quantitatively by means of laser-induced breakdown spectroscopy (LIBS). To the best of the authors' knowledge, LIBS and laser ignition of DME have not been reported in literature before. The technique under investigation is finally employed for combustion diagnostics in laminar as well as turbulent flames. In the laminar premixed and non-premixed flames the LIBS spectra allow spatially resolved measurements of the equivalence ratio and enable studying the mixing of gases provided through the burner with the surrounding room air. In addition, the breakdown threshold of the applied laser pulse energy yields an estimate for the local temperature. In the turbulent cases single-shot LIBS spectra are recorded at fixed position allowing the derivation of local statistical fluctuations of the equivalence ratio in partially premixed jet flames. The results show that laser-induced breakdowns have a strong potential for flame diagnostics and, under suitable conditions, for the ignition of combustible mixtures

Floating choices: a generational perspective on intentions of rural – urban migrants in China

Using data from a 2005 survey of rural – urban migrants in Shenzhen, we investigate the intentions of two groups of migrants. We use the birth years from 1970 to 1980 as a reasonable range of dividing lines to separate the two groups. For each year we divide the sample into those born before that year and those born in or after that year. These are referred to as the old generation and the new generation, respectively. Three possible development trajectories are considered: settling in cities, returning home to seek a nonagricultural job, and returning home to farm. We find that members of the new generation have stronger desires to do nonfarm work, and that returning to seek a nonagricultural job has become the most important planned trajectory for this generation. Sharp differences exist between the two generations in the reasons that underlie their intentions. For the old generation, conditions such as age, family responsibility, and type of job are important determinants of intentions, while other conditions such as initial migration motives, social capital, and socioeconomic conditions of origin areas are important for the intentions of the new generation. Thus the new generation is more likely to view migration as a form of investment with the accumulation of human capital and social capital. Those migrants from the old generation who have higher education levels also intend to seek a nonfarm job. However, because of the combined effects of life cycle and the market transition in China, these intentions are not as strong as those of the new generation. We discuss economic and policy implications of our findings.

Local composition and temperature determination in laminar flames by laser-induced plasma diagnostics

We utilize laser-induced breakdown spectroscopy for measuring mixture composition and temperature in flames. Spectroscopy of the plasma emission yields concentration information, while temperature is derived from the breakdown threshold pulse energy

Laser-induced breakdown spectroscopy : A simple but versatile tool for combustion diagnostics

Laser-induced breakdown spectroscopy (LIBS) is an experimentally simple method capable of measuring elemental composition in a flame. Moreover, the breakdown threshold energy is temperature dependent. Hence, LIBS allows multiple parameter determination in combustion environments

Laser-induced breakdown flame thermometry

The determination of temperature distribution is an essential task when flames are characterized. We propose a new approach for flame thermometry based on laser-induced breakdown spectroscopy (LIBS) utilizing the temperature dependency of the breakdown threshold laser pulse energy. Calibration measurements are carried out in heated gas flows and post-combustion gases. Compositional effects on the breakdown threshold are corrected employing a straightforward procedure. For this purpose, the elemental composition is derived from the LIBS spectra and this information is then used for correcting the measured threshold laser pulse energy. A series of proof-of-concept measurements in a laminar methane/air flame on a Bunsen burner is conducted and compared to reference data from coherent anti-Stokes Raman scattering (CARS). The corrected LIBS temperatures show excellent agreement with those obtained by CARS. Therefore, our approach represents a simple and straightforward alternative to traditionally used thermometry methods. (C) 2012 The Combustion Institute. Published by Elsevier Inc. All rights reserved

Laser-induced breakdown spectroscopy in gases using ungated detection in combination with polarization filtering and online background correction

Quantitative and fast analysis of gas mixtures is an important task in the field of chemical, security and environmental analysis. In this paper we present a diagnostic approach based on laser-induced breakdown spectroscopy (LIBS). A polarization filter in the signal collection system enables sufficient suppression of elastically scattered light which otherwise reduces the dynamic range of the measurement. Running the detector with a doubled repetition rate as compared to the laser online background correction is obtained. Quantitative measurements of molecular air components in synthetic, ambient and expiration air are performed and demonstrate the potential of the method. The detection limits for elemental oxygen and hydrogen are in the order of 15 ppm and 10 ppm, respectively