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Search Results: 1 - 10 of 30998 matches for " Thomas Debener "
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Identification of superior reference genes for data normalisation of expression studies via quantitative PCR in hybrid roses (Rosa hybrida)
Maik Klie, Thomas Debener
BMC Research Notes , 2011, DOI: 10.1186/1756-0500-4-518
Abstract: We used three different algorithms (BestKeeper, geNorm and NormFinder) to validate the expression stability of nine candidate reference genes in different rose tissues from three different genotypes of Rosa hybrida and in leaves treated with various stress factors. The candidate genes comprised the classical "housekeeping genes" (Actin, EF-1α, GAPDH, Tubulin and Ubiquitin), and genes showing stable expression in studies in Arabidopsis (PP2A, SAND, TIP and UBC). The programs identified no single gene that showed stable expression under all of the conditions tested, and the individual rankings of the genes differed between the algorithms. Nevertheless the new candidate genes, specifically, PP2A and UBC, were ranked higher as compared to the other traditional reference genes. In general, Tubulin showed the most variable expression and should be avoided as a reference gene.Reference genes evaluated as suitable in experiments with Arabidopsis thaliana were stably expressed in roses under various experimental conditions. In most cases, these genes outperformed conventional reference genes, such as EF1-α and Tubulin. We identified PP2A, SAND and UBC as suitable reference genes, which in different combinations may be used for normalisation in expression analyses via qPCR for different rose tissues and stress treatments. However, the vast genetic variation found within the genus Rosa, including differences in ploidy levels, might also influence expression stability of reference genes, so that future research should also consider different genotypes and ploidy levels.Roses are one of the economically most important ornamentals worldwide. They are produced as cut and potted plants and garden and landscaping plants with a production value of 24 billion Euros from 1995 to 2007 [1]. Other, less prominent uses include medicinal applications or the consumption in teas and soups [2]. Apart from the beauty of their flowers, roses are also admired for their delicate scent. Their scent
The type of ploidy of chrysanthemum is not black or white: a comparison of a molecular approach to published cytological methods
Maik Klie,Marcus Linde,Thomas Debener
Frontiers in Plant Science , 2014, DOI: 10.3389/fpls.2014.00479
Abstract: 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 close to 0.7:0.3 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 allo-hexaploids.
Molecular Markers for Genetic Diversity Studies in African Leafy Vegetables  [PDF]
Emmanuel O. Omondi, Thomas Debener, Marcus Linde, Mary Abukutsa-Onyango, Fekadu F. Dinssa, Traud Winkelmann
Advances in Bioscience and Biotechnology (ABB) , 2016, DOI: 10.4236/abb.2016.73017
Abstract: African leafy vegetables are becoming important crops in tackling nutrition and food security in many parts of sub-Saharan Africa, since they provide important micronutrients and vitamins, and help resource-poor farm families bridge lean periods of food shortage. Genetic diversity studies are essential for crop improvement programmes as well as germplasm conservation efforts, and research on genetic diversity of these vegetables using molecular markers has been increasing over time. Diversity studies have evolved from the use of morphological and biochemical markers to molecular markers. Molecular markers provide valuable data, since they detect mostly selectively neutral variations at the DNA level. They are well established and their strengths and limitations have been described. New marker types are being developed from a combination of the strengths of the basic techniques to improve sensitivity, reproducibility, polymorphic information content, speed and cost. This review discusses the principles of some of the established molecular markers and their application to genetic diversity studies of African leafy vegetables with a main focus on the most common Solanum, Amaranthus, Cleome and Vigna species.
Evolution of the Rdr1 TNL-cluster in roses and other Rosaceous species
Terefe-Ayana Diro,Kaufmann Helgard,Linde Marcus,Debener Thomas
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-409
Abstract: 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 perennial
Defensin-Like ZmES4 Mediates Pollen Tube Burst in Maize via Opening of the Potassium Channel KZM1
Suseno Amien,Irina Kliwer,Mihaela L. Márton,Thomas Debener,Dietmar Geiger,Dirk Becker,Thomas Dresselhaus
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1000388
Abstract: In contrast to animals and lower plant species, sperm cells of flowering plants are non-motile and are transported to the female gametes via the pollen tube, i.e. the male gametophyte. Upon arrival at the female gametophyte two sperm cells are discharged into the receptive synergid cell to execute double fertilization. The first players involved in inter-gametophyte signaling to attract pollen tubes and to arrest their growth have been recently identified. In contrast the physiological mechanisms leading to pollen tube burst and thus sperm discharge remained elusive. Here, we describe the role of polymorphic defensin-like cysteine-rich proteins ZmES1-4 (Zea mays embryo sac) from maize, leading to pollen tube growth arrest, burst, and explosive sperm release. ZmES1-4 genes are exclusively expressed in the cells of the female gametophyte. ZmES4-GFP fusion proteins accumulate in vesicles at the secretory zone of mature synergid cells and are released during the fertilization process. Using RNAi knock-down and synthetic ZmES4 proteins, we found that ZmES4 induces pollen tube burst in a species-preferential manner. Pollen tube plasma membrane depolarization, which occurs immediately after ZmES4 application, as well as channel blocker experiments point to a role of K+-influx in the pollen tube rupture mechanism. Finally, we discovered the intrinsic rectifying K+ channel KZM1 as a direct target of ZmES4. Following ZmES4 application, KZM1 opens at physiological membrane potentials and closes after wash-out. In conclusion, we suggest that vesicles containing ZmES4 are released from the synergid cells upon male-female gametophyte signaling. Subsequent interaction between ZmES4 and KZM1 results in channel opening and K+ influx. We further suggest that K+ influx leads to water uptake and culminates in osmotic tube burst. The species-preferential activity of polymorphic ZmES4 indicates that the mechanism described represents a pre-zygotic hybridization barrier and may be a component of reproductive isolation in plants.
Mining Disease-Resistance Genes in Roses: Functional and Molecular Characterization of the Rdr1 Locus
Diro Terefe-Ayana,Aneela Yasmin,Thanh Loan Le,Marcus Linde,Thomas Debener
Frontiers in Plant Science , 2011, DOI: 10.3389/fpls.2011.00035
Abstract: The interaction of roses with the leaf spot pathogen Diplocarpon rosae (the cause of black spot on roses) is an interesting pathosystem because it involves a long-lived woody perennial, with life history traits very different from most model plants, and a hemibiotrophic pathogen with moderate levels of gene flow. Here we present data on the molecular structure of the first monogenic dominant resistance gene from roses, Rdr1, directed against one isolate of D. rosae. Complete sequencing of the locus carrying the Rdr1 gene resulted in a sequence of 265,477 bp with a cluster of nine highly related TIR–NBS–LRR (TNL) candidate genes. After sequencing revealed candidate genes for Rdr1, we implemented a gene expression analysis and selected five genes out of the nine TNLs. We then silenced the whole TNL gene family using RNAi (Rdr1–RNAi) constructed from the most conserved sequence region and demonstrated a loss of resistance in the normally resistant genotype. To identify the functional TNL gene, we further screened the five TNL candidate genes with a transient leaf infiltration assay. The transient expression assay indicated a single TNL gene (muRdr1H), partially restoring resistance in the susceptible genotype. Rdr1 was found to localize within the muRdr1 gene family; the genes within this locus contain characteristic motifs of active TNL genes and belong to a young cluster of R genes. The transient leaf assay can be used to further analyze the rose black spot interaction and its evolution, extending the analyses to additional R genes and to additional pathogenic types of the pathogen.
Defensin-Like ZmES4 Mediates Pollen Tube Burst in Maize via Opening of the Potassium Channel KZM1
Suseno Amien equal contributor,Irina Kliwer equal contributor,Mihaela L. Márton,Thomas Debener,Dietmar Geiger,Dirk Becker,Thomas Dresselhaus
PLOS Biology , 2010, DOI: 10.1371/journal.pbio.1000388
Abstract: In contrast to animals and lower plant species, sperm cells of flowering plants are non-motile and are transported to the female gametes via the pollen tube, i.e. the male gametophyte. Upon arrival at the female gametophyte two sperm cells are discharged into the receptive synergid cell to execute double fertilization. The first players involved in inter-gametophyte signaling to attract pollen tubes and to arrest their growth have been recently identified. In contrast the physiological mechanisms leading to pollen tube burst and thus sperm discharge remained elusive. Here, we describe the role of polymorphic defensin-like cysteine-rich proteins ZmES1-4 (Zea mays embryo sac) from maize, leading to pollen tube growth arrest, burst, and explosive sperm release. ZmES1-4 genes are exclusively expressed in the cells of the female gametophyte. ZmES4-GFP fusion proteins accumulate in vesicles at the secretory zone of mature synergid cells and are released during the fertilization process. Using RNAi knock-down and synthetic ZmES4 proteins, we found that ZmES4 induces pollen tube burst in a species-preferential manner. Pollen tube plasma membrane depolarization, which occurs immediately after ZmES4 application, as well as channel blocker experiments point to a role of K+-influx in the pollen tube rupture mechanism. Finally, we discovered the intrinsic rectifying K+ channel KZM1 as a direct target of ZmES4. Following ZmES4 application, KZM1 opens at physiological membrane potentials and closes after wash-out. In conclusion, we suggest that vesicles containing ZmES4 are released from the synergid cells upon male-female gametophyte signaling. Subsequent interaction between ZmES4 and KZM1 results in channel opening and K+ influx. We further suggest that K+ influx leads to water uptake and culminates in osmotic tube burst. The species-preferential activity of polymorphic ZmES4 indicates that the mechanism described represents a pre-zygotic hybridization barrier and may be a component of reproductive isolation in plants.
ERP evidence for the recognition of emotional prosody through simulated cochlear implant strategies
Agrawal Deepashri,Timm Lydia,Viola Filipa,Debener Stefan
BMC Neuroscience , 2012, DOI: 10.1186/1471-2202-13-113
Abstract: Background Emotionally salient information in spoken language can be provided by variations in speech melody (prosody) or by emotional semantics. Emotional prosody is essential to convey feelings through speech. In sensori-neural hearing loss, impaired speech perception can be improved by cochlear implants (CIs). Aim of this study was to investigate the performance of normal-hearing (NH) participants on the perception of emotional prosody with vocoded stimuli. Semantically neutral sentences with emotional (happy, angry and neutral) prosody were used. Sentences were manipulated to simulate two CI speech-coding strategies: the Advance Combination Encoder (ACE) and the newly developed Psychoacoustic Advanced Combination Encoder (PACE). Twenty NH adults were asked to recognize emotional prosody from ACE and PACE simulations. Performance was assessed using behavioral tests and event-related potentials (ERPs). Results Behavioral data revealed superior performance with original stimuli compared to the simulations. For simulations, better recognition for happy and angry prosody was observed compared to the neutral. Irrespective of simulated or unsimulated stimulus type, a significantly larger P200 event-related potential was observed for happy prosody after sentence onset than the other two emotions. Further, the amplitude of P200 was significantly more positive for PACE strategy use compared to the ACE strategy. Conclusions Results suggested P200 peak as an indicator of active differentiation and recognition of emotional prosody. Larger P200 peak amplitude for happy prosody indicated importance of fundamental frequency (F0) cues in prosody processing. Advantage of PACE over ACE highlighted a privileged role of the psychoacoustic masking model in improving prosody perception. Taken together, the study emphasizes on the importance of vocoded simulation to better understand the prosodic cues which CI users may be utilizing.
Temporal Feature Perception in Cochlear Implant Users
Lydia Timm, Deepashri Agrawal, Filipa C. Viola, Pascale Sandmann, Stefan Debener, Andreas Büchner, Reinhard Dengler, Matthias Wittfoth
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0045375
Abstract: For the perception of timbre of a musical instrument, the attack time is known to hold crucial information. The first 50 to 150 ms of sound onset reflect the excitation mechanism, which generates the sound. Since auditory processing and music perception in particular are known to be hampered in cochlear implant (CI) users, we conducted an electroencephalography (EEG) study with an oddball paradigm to evaluate the processing of small differences in musical sound onset. The first 60 ms of a cornet sound were manipulated in order to examine whether these differences are detected by CI users and normal-hearing controls (NH controls), as revealed by auditory evoked potentials (AEPs). Our analysis focused on the N1 as an exogenous component known to reflect physical stimuli properties as well as on the P2 and the Mismatch Negativity (MMN). Our results revealed different N1 latencies as well as P2 amplitudes and latencies for the onset manipulations in both groups. An MMN could be elicited only in the NH control group. Together with additional findings that suggest an impact of musical training on CI users’ AEPs, our findings support the view that impaired timbre perception in CI users is at partly due to altered sound onset feature detection.
Auditory Processing under Cross-Modal Visual Load Investigated with Simultaneous EEG-fMRI
Christina Regenbogen, Maarten De Vos, Stefan Debener, Bruce I. Turetsky, Carolin M??nang, Andreas Finkelmeyer, Ute Habel, Irene Neuner, Thilo Kellermann
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0052267
Abstract: Cognitive task demands in one sensory modality (T1) can have beneficial effects on a secondary task (T2) in a different modality, due to reduced top-down control needed to inhibit the secondary task, as well as crossmodal spread of attention. This contrasts findings of cognitive load compromising a secondary modality’s processing. We manipulated cognitive load within one modality (visual) and studied the consequences of cognitive demands on secondary (auditory) processing. 15 healthy participants underwent a simultaneous EEG-fMRI experiment. Data from 8 participants were obtained outside the scanner for validation purposes. The primary task (T1) was to respond to a visual working memory (WM) task with four conditions, while the secondary task (T2) consisted of an auditory oddball stream, which participants were asked to ignore. The fMRI results revealed fronto-parietal WM network activations in response to T1 task manipulation. This was accompanied by significantly higher reaction times and lower hit rates with increasing task difficulty which confirmed successful manipulation of WM load. Amplitudes of auditory evoked potentials, representing fundamental auditory processing showed a continuous augmentation which demonstrated a systematic relation to cross-modal cognitive load. With increasing WM load, primary auditory cortices were increasingly deactivated while psychophysiological interaction results suggested the emergence of auditory cortices connectivity with visual WM regions. These results suggest differential effects of crossmodal attention on fundamental auditory processing. We suggest a continuous allocation of resources to brain regions processing primary tasks when challenging the central executive under high cognitive load.
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