Treatment- and Population-Dependent Activity Patterns of Behavioral and Expression QTLs

Genetic control of gene expression and higher-order phenotypes is almost invariably dependent on environment and experimental conditions. We use two families of recombinant inbred strains of mice (LXS and BXD) to study treatment- and genotype-dependent control of hippocampal gene expression and behavioral phenotypes. We analyzed responses to all combinations of two experimental perturbations, ethanol and restraint stress, in both families, allowing for comparisons across 8 combinations of treatment and population. We introduce the concept of QTL activity patterns to characterize how associations between genomic loci and traits vary across treatments. We identified several significant behavioral QTLs and many expression QTLs (eQTLs). The behavioral QTLs are highly dependent on treatment and population. We classified eQTLs into three groups: cis-eQTLs (expression variation that maps to within 5 Mb of the cognate gene), syntenic trans-eQTLs (the gene and the QTL are on the same chromosome but not within 5 Mb), and non-syntenic trans-eQTLs (the gene and the QTL are on different chromosomes). We found that most non-syntenic trans-eQTLs were treatment-specific whereas both classes of syntenic eQTLs were more conserved across treatments. We also found there was a correlation between regions along the genome enriched for eQTLs and SNPs that were conserved across the LXS and BXD families. Genes with eQTLs that co-localized with the behavioral QTLs and displayed similar QTL activity patterns were identified as potential candidate genes associated with the phenotypes, yielding identification of novel genes as well as genes that have been previously associated with responses to ethanol

A Genome-Wide Survey of Imprinted Genes in Rice Seeds Reveals Imprinting Primarily Occurs in the Endosperm

Genomic imprinting causes the expression of an allele depending on its parental origin. In plants, most imprinted genes have been identified in Arabidopsis endosperm, a transient structure consumed by the embryo during seed formation. We identified imprinted genes in rice seed where both the endosperm and embryo are present at seed maturity. RNA was extracted from embryos and endosperm of seeds obtained from reciprocal crosses between two subspecies Nipponbare (Japonica rice) and 93-11 (Indica rice). Sequenced reads from cDNA libraries were aligned to their respective parental genomes using single-nucleotide polymorphisms (SNPs). Reads across SNPs enabled derivation of parental expression bias ratios. A continuum of parental expression bias states was observed. Statistical analyses indicated 262 candidate imprinted loci in the endosperm and three in the embryo (168 genic and 97 non-genic). Fifty-six of the 67 loci investigated were confirmed to be imprinted in the seed. Imprinted loci are not clustered in the rice genome as found in mammals. All of these imprinted loci were expressed in the endosperm, and one of these was also imprinted in the embryo, confirming that in both rice and Arabidopsis imprinted expression is primarily confined to the endosperm. Some rice imprinted genes were also expressed in vegetative tissues, indicating that they have additional roles in plant growth. Comparison of candidate imprinted genes found in rice with imprinted candidate loci obtained from genome-wide surveys of imprinted genes in Arabidopsis to date shows a low degree of conservation, suggesting that imprinting has evolved independently in eudicots and monocots

Highly multiplexed quantitative PCR-based platform for evaluation of chicken immune responses

To address the need for sensitive high-throughput assays to analyse avian innate and adaptive immune responses, we developed and validated a highly multiplexed qPCR 96.96 Fluidigm Dynamic Array to analyse the transcription of chicken immune-related genes. This microfluidic system permits the simultaneous analysis of expression of 96 transcripts in 96 samples in 6 nanolitre reactions and the 9,216 reactions are ready for interpretation immediately. A panel of 89 genes was selected from an RNA-seq analysis of the transcriptional response of chicken macrophages, dendritic cells and heterophils to agonists of innate immunity and from published transcriptome data. Assays were confirmed to be highly specific by amplicon sequencing and melting curve analysis and the reverse transcription and preamplification steps were optimised. The array was applied to RNA of various tissues from a commercial line of broiler chickens housed at two different levels of biosecurity. Gut-associated lymphoid tissues, bursa, spleen and peripheral blood leukocytes were isolated and transcript levels for immune-related genes were defined. The results identified blood cells as a potentially reliable indicator of immune responses among all the tissues tested with the highest number of genes significantly differentially transcribed between birds housed under varying biosecurity levels. Conventional qPCR analysis of three differentially transcribed genes confirmed the results from the multiplex qPCR array. A highly multiplexed qPCR-based platform for evaluation of chicken immune responses has been optimised and validated using samples from commercial chickens. Apart from applications in selective breeding programmes, the array could be used to analyse the complex interplay between the avian immune system and pathogens by including pathogen-specific probes, to screen vaccine responses, and as a predictive tool for immune robustness

Surface damage on 6H-SiC by highly-charged Xeq+ ions irradiation

Surface damage on 6H-SiC irradiated by highly-charged Xeq+ (q = 18, 26) ions to different fiuences in two geometries was studied by means of AFM, Raman scattering spectroscopy and FTIR spectrometry. The FTIR spectra analysis shows that for Xe26+ ions irradiation at normal incidence, a deep reflection dip appears at about 930 cm(-1). Moreover, the reflectance on top of reststrahlen band decreases as the ion fluence increases, and the reflectance at tilted incidence is larger than that at normal incidence. The Raman scattering spectra reveal that for Xe26+ ions at normal incidence, surface reconstruction occurs and amorphous stoichiometric SiC and Si-Si and C-C bonds are generated and original Si-C vibrational mode disappears. And the intensity of scattering peaks decreases with increasing dose. The AFM measurement shows that the surface swells after irradiation. With increasing ion fluence, the step height between the irradiated and the unirradiated region increases for Xe18+ ions irradiation; while for Xe-26+ ions irradiation, the step height first increases and then decreases with increasing ion fluence. Moreover, the step height at normal incidence is higher than that at tilted incidence by the irradiation with Xe18+ to the same ion fluence. A good agreement between the results from the three methods is found. (C) 2014 Elsevier B.V. All rights reserved

Structures and optical properties of Kr23+ and Ne8+-irradiated GaN epi-layers

Epitaxial GaN layers grown by MOCVD on c-plane sapphire substrates were irradiated with 5.3 MeV Kr23+ and 2.3 MeV Ne8+ ions to various fluences. The pristine and the irradiated GaN samples were characterized using high resolution X-ray diffraction (HRXRD), UV-visible transmittance spectrum and Raman scattering spectrum analysis. The HRXRD results show an obvious increase in the FWHM and a decrease in the intensity of the GaN (0002) peak with increasing ion fluences. Meanwhile the UV-visible transmittance spectra show a decrease in the band gap value after irradiation. The Raman scattering spectrum shows that new Raman bands around 300 and 670 cm(-1) appear with increasing ion fluences. The new Raman bands can be ascribed to disorder-activated Raman scattering (DARS) from the highest acoustic-phonon branch and the optical-phonon branch at the brillouin zone boundaries, respectively. (C) 2013 Elsevier B.V. All rights reserved