Acquisition of subcortical auditory potentials with around-the-Ear cEEGrid technology in normal and hearing impaired listeners

Even though the principles of recording brain electrical activity remain unchanged since their discovery, their acquisition has seen major improvements. The cEEGrid, a recently developed flex-printed multi-channel sensory array, can be placed around the ear and successfully record well-known cortical electrophysiological potentials such as late auditory evoked potentials (AEPs) or the P300. Due to its fast and easy application as well as its long-lasting signal recording window, the cEEGrid technology offers great potential as a flexible and 'wearable' solution for the acquisition of neural correlates of hearing. Early potentials of auditory processing such as the auditory brainstem response (ABR) are already used in clinical assessment of sensorineural hearing disorders and envelope following responses (EFR) have shown promising results in the diagnosis of suprathreshold hearing deficits. This study evaluates the suitability of the cEEGrid electrode configuration to capture these AEPs. cEEGrid potentials were recorded and compared to cap-EEG potentials for young normal-hearing listeners and older listeners with high-frequency sloping audiograms to assess whether the recordings are adequately sensitive for hearing diagnostics. ABRs were elicited by presenting clicks (70 and 100-dB peSPL) and stimulation for the EFRs consisted of 120 Hz amplitudemodulated white noise carriers presented at 70-dB SPL. Data from nine bipolar cEEGrid channels and one classical cap-EEG montage (earlobes to vertex) were analysed and outcome measures were compared. Results show that the cEEGrid is able to record ABRs and EFRs with comparable shape to those recorded using a conventional capEEG recording montage and the same amplifier. Signal strength is lower but can still produce responses above the individual neural electrophysiological noise floor. This study shows that the application of the cEEGrid can be extended to the acquisition of early auditory evoked potentials

I can't wait! Neural reward signals in impulsive individuals exaggerate the difference between immediate and future rewards

Waiting for rewards is difficult, and highly impulsive individuals with low self-control have an especially hard time with it. Here, we investigated whether neural responses to rewards in a delayed gratification task predict impulsivity and self-control. The EEG was recorded from participants engaged in a guessing game in which on each trial they could win either a large or small reward, paid either now or after 6 months. Ratings confirmed that participants preferred immediate, large rewards over small, delayed rewards. Electrophysiological reward signals reflecting the difference between immediate and future rewards predicted self-report measures of impulsivity and self-control. Further, these signals were highly reliable across two sessions over a 1-week interval, showing high temporal stability like stable personality traits. These results suggest that greater valuation of immediate rewards causes impulsive individuals to redirect control away from delayed rewards, indicating why it is so hard for them to wait

Development of a multiplex amplicon-sequencing assay to detect low-frequency mutations in poinsettia (Euphorbia pulcherrima) breeding programmes

Poinsettia is an economically important ornamental potted plant in which certain bract colour variants are often obtained by mutation breeding. Previously, in poinsettia, we identified Bract1, a GST gene involved in the sequestration and transport of anthocyanins to the vacuole. This gene carries a short, highly mutable 4-bp repeat in its coding region. Loss of one repeat unit leads to a loss of function for Bract1, and in homozygous mutants, anthocyanin-based coloration is absent, resulting in white or cream-coloured bracts. Although mutation induction through ionizing radiation leads to a high frequency of mutations in Bract1, mutants are difficult to obtain from homozygous red genotypes. In this study, we used Bract1-specific amplicon sequencing as a tool to identify mutations in pools of tissues, which enabled the detection of mutations in dilutions of up to one mutant in 50 nonmutated samples. This approach enabled efficient screening of recalcitrant homozygous genotypes for mutated alleles and the reduction of the mutation load in the application of ionizing radiation in mutation breeding programmes

Using Explainable AI to Understand Bond Excess Returns

Recent empirical evidence indicates that bond excess returns can be predicted using machine learning models. While the predictive power of machine learning models is intriguing, they typically lack transparency. We introduce SHapley Additive exPlanations (SHAP), a state-of-the-art explainable artificial technique, to open the black box of these models. Our analysis identifies the key determinants that drive the predictions of bond excess returns in machine learning models and how these determinants are related to bond excess returns. Thereby, our approach facilitates an in-depth interpretation of the predictions of bond excess returns made by machine learning models

A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication

Background: Black spot is one of the most severe and damaging diseases of garden roses. We present the draft genome sequence of its causative agent Diplocarpon rosae as a working tool to generate molecular markers and to analyze functional and structural characteristics of this fungus. Results: The isolate DortE4 was sequenced with 191x coverage of different read types which were assembled into 2457 scaffolds. By evidence supported genome annotation with the MAKER pipeline 14,004 gene models were predicted and transcriptomic data indicated that 88.5% of them are expressed during the early stages of infection. Analyses of k-mer distributions resulted in unexpectedly large genome size estimations between 72.5 and 91.4 Mb, which cannot be attributed to its repeat structure and content of transposable elements alone, factors explaining such differences in other fungal genomes. In contrast, different lines of evidences demonstrate that a huge proportion (approximately 80%) of genes are duplicated, which might indicate a whole genome duplication event. By PCR-RFLP analysis of six paralogous gene pairs of BUSCO orthologs, which are expected to be single copy genes, we could show experimentally that the duplication is not due to technical error and that not all isolates tested possess all of the paralogs. Conclusions: The presented genome sequence is still a fragmented draft but contains almost the complete gene space. Therefore, it provides a useful working tool to study the interaction of D. rosae with the host and the influence of a genome duplication outside of the model yeast in the background of a phytopathogen

Isolation, molecular characterization, and mapping of four rose MLO orthologs

Powdery mildew is a major disease of economic importance in cut and pot roses. As an alternative to conventional resistance breeding strategies utilizing single-dominant genes or QTLs, mildew resistance locus o (MLO)-based resistance might offer some advantages. In dicots such as Arabidopsis, pea, and tomato, loss-of-function mutations in MLO genes confer high levels of broad-spectrum resistance. Here, we report the isolation and characterization of four MLO homologs from a large rose EST collection isolated from leaves. These genes are phylogenetically closely related to other dicot MLO genes that are involved in plant powdery mildew interactions. Therefore, they are candidates for MLO genes involved in rose powdery mildew interactions. Two of the four isolated genes contain all of the sequence signatures considered to be diagnostic for MLO genes. We mapped all four genes to three linkage groups and conducted the first analysis of alternative alleles. This information is discussed in regards to a reverse genetics approach aimed at the selection of rose plants that are homozygous for loss-of-function in one or more MLO genes.BMBF/0315542ANatural Science Foundation of China/No31160403Natural Science Foundation of Yunnan/2011FB12

Evolution of the Rdr1 TNL-cluster in roses and other Rosaceous species

Background: The resistance of plants to pathogens relies on two lines of defense: a basal defense response and a pathogen-specific system, in which resistance (R) genes induce defense reactions after detection of pathogen-associated molecular patterns (PAMPS). In the specific system, a so-called arms race has developed in which the emergence of new races of a pathogen leads to the diversification of plant resistance genes to counteract the pathogens' effect. The mechanism of resistance gene diversification has been elucidated well for short-lived annual species, but data are mostly lacking for long-lived perennial and clonally propagated plants, such as roses. We analyzed the rose black spot resistance gene, Rdr1, in five members of the Rosaceae: Rosa multiflora, Rosa rugosa, Fragaria vesca (strawberry), Malus x domestica (apple) and Prunus persica (peach), and we present the deduced possible mechanism of R-gene diversification.Results: We sequenced a 340.4-kb region from R. rugosa orthologous to the Rdr1 locus in R. multiflora. Apart from some deletions and rearrangements, the two loci display a high degree of synteny. Additionally, less pronounced synteny is found with an orthologous locus in strawberry but is absent in peach and apple, where genes from the Rdr1 locus are distributed on two different chromosomes. An analysis of 20 TIR-NBS-LRR (TNL) genes obtained from R. rugosa and R. multiflora revealed illegitimate recombination, gene conversion, unequal crossing over, indels, point mutations and transposable elements as mechanisms of diversification.A phylogenetic analysis of 53 complete TNL genes from the five Rosaceae species revealed that with the exception of some genes from apple and peach, most of the genes occur in species-specific clusters, indicating that recent TNL gene diversification began prior to the split of Rosa from Fragaria in the Rosoideae and peach from apple in the Spiraeoideae and continued after the split in individual species. Sequence similarity of up to 99% is obtained between two R. multiflora TNL paralogs, indicating a very recent duplication.Conclusions: The mechanisms by which TNL genes from perennial Rosaceae diversify are mainly similar to those from annual plant species. However, most TNL genes appear to be of recent origin, likely due to recent duplications, supporting the hypothesis that TNL genes in woody perennials are generally younger than those from annuals. This recent origin might facilitate the development of new resistance specificities, compensating for longer generation times in woody perennials.DFG/DE 511/4-1DFG/DE 511/4-

Inheritance genetics of the trait vector competence in Frankliniella occidentalis (Western flower thrips) in the transmission of Tomato spotted wilt virus

The complexity of tospovirus–vector–host plant interaction is linked to a range of factors influencing vector's efficacy in virus transmission, leading to high variability in the transmission efficiency within vector populations. Main shortcomings of most studies are the missing information on the intrinsic potential of individual insects to serve as efficient vectors, both at phenotypic and at genotypic levels. Moreover, detailed analysis of vector competence heredity and monitoring the splitting of both genotypes and phenotypes in filial generations has not been reported. In this study, using the model system Frankliniella occidentalis and Tomato spotted wilt virus, we evaluated the inheritance and stability of the trait vector competence in a population through basic crossings of individually characterized partners, as well as virgin reproduction. We hypothesized that the trait is heritable in F. occidentalis and is controlled by a recessive allele. From the results, 83% and 94% of competent and noncompetent males respectively, inherited their status from their mothers. The trait was only expressed when females were homozygous for the corresponding allele. Furthermore, the allele frequencies were different between males and females, and the competent allele had the highest frequency in the population. These suggest that the trait vector competence is inherited in single recessive gene in F. occidentalis, for which the phenotype is determined by the haplodiploid mechanism. These findings are fundamental for our understanding of the temporal and spatial variability within vector populations with respect to the trait vector competence and at the same time offer an essential basis for further molecular studies.DFG/207/37-

The type of ploidy of chrysanthemum is not black or white: a comparison of a molecular approach to published cytological methods

Polyploidy is a widespread phenomenon among higher plants and a major factor shaping the structure and evolution of plant genomes. The important ornamental chrysanthemum (Chrysanthemum indicum hybrid) possesses a hexaploid genome with 54 chromosomes and was classified based on its evolutionary origin and cytological methods as an allopolyploid. However, it is questionable whether cytological methods are sufficient to determine the type of ploidy, and there are more informative methods available based on molecular marker analyses. Therefore, we collected segregation data for 406 dominant molecular marker alleles [327 amplified fragment length polymorphism (AFLPs), 65 single-strand conformation polymorphism (SSCPs) and 14 microsatellites (EST-SSRs)] in a biparental F1 population of 160 individuals. We analyzed these data for the characteristics that differ between allopolyploids and autopolyploids, including the segregation ratio of each marker, the ratio of single-dose (SD) to multi-dose (MD) markers, the ratio of SD markers in coupling to those in repulsion and the banding patterns of the SSRs. Whereas the analysis of the segregation ratio of each polymorphic marker indicated disomic (13 markers) as well as hexasomic (eight markers) inheritance, the ratio of SD markers in coupling to those in repulsion was 1:0, which is characteristic of autopolyploids. The observed ratio of SD to MD markers was 0.67:0.33 which is significantly different to the expected segregation for auto- and allohexaploids. Furthermore, the three EST-SSR alleles were inherited in all possible combinations and were not independent of each other, as expected for fixed heterozygosity in allopolyploids. Combining our results with published cytological data indicates that cultivated chrysanthemums should be classified as segmental allohexaploids.BMEL

Faster evaluation of induced floral sterility in transgenic early flowering poplar

A major concern over the use of transgenic trees is the potential for transgene dispersal through pollen and seeds. The incorporation of sterility inducing genes into transgenic lines of trees has been proposed to reduce or even avoid gene flow of transgenes into non-transgenic interbreeding species. The evaluation of strategies for the induction of sterility in transgenic forest tree species has been hindered by their long vegetative phases. In this study an early flowering 35