Recent Submissions

  • Journal Article

    An ancestral apical brain region contributes to the central complex under the control of foxQ2 in the beetle Tribolium 

    He, Bicheng; Buescher, Marita; Farnworth, Max Stephen; Strobl, Frederic; Stelzer, Ernst HK; Koniszewski, Nikolaus DB; Muehlen, Dominik; Bucher, Gregor
    eLife 2019; 8: Art. e49065
    The genetic control of anterior brain development is highly conserved throughout animals. For instance, a conserved anterior gene regulatory network specifies the ancestral neuroendocrine center of animals and the apical organ of marine organisms. However, its contribution to the brain in non-marine animals has remained elusive. Here, we study the function of the Tc-foxQ2 forkhead transcription factor, a key regulator of the anterior gene regulatory network of insects. We characterized four distinct types of Tc-foxQ2 positive neural progenitor cells based on differential co-expression with Tc-six3/optix, Tc-six4, Tc-chx/vsx, Tc-nkx2.1/scro, Tc-ey, Tc-rx and Tc-fez1. An enhancer trap line built by genome editing marked Tc-foxQ2 positive neurons, which projected through the primary brain commissure and later through a subset of commissural fascicles. Eventually, they contributed to the central complex. Strikingly, in Tc-foxQ2 RNAi knock-down embryos the primary brain commissure did not split and subsequent development of midline brain structures stalled. Our work establishes foxQ2 as a key regulator of brain midline structures, which distinguish the protocerebrum from segmental ganglia. Unexpectedly, our data suggest that the central complex evolved by integrating neural cells from an ancestral anterior neuroendocrine center.
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  • Journal Article

    Anaemia among men in India: a nationally representative cross-sectional study 

    Didzun, Oliver; De Neve, Jan-Walter; Awasthi, Ashish; Dubey, Manisha; Theilmann, Michaela; Bärnighausen, Till; Vollmer, Sebastian; Geldsetzer, Pascal
    The Lancet Global Health 2019; 7(12) p.e1685-e1694
    BACKGROUND: Population-based studies on anaemia in India have mostly focused on women and children, with men with anaemia receiving much less attention despite anaemia's adverse effect on health, wellbeing, and economic productivity. This study aimed to determine the national prevalence of anaemia among men in India; how the prevalence of anaemia in men varies across India among states and districts and by sociodemographic characteristics; and whether the geographical and sociodemographic variation in the prevalence of anaemia among men is similar to that among women to inform whether anaemia reduction efforts for men should be coupled with existing efforts for women. METHODS: In this cross-sectional study, we analysed data from a nationally representative household survey carried out from January, 2015, to December, 2016, among men aged 15-54 years and women aged 15-49 years in all 29 states and seven Union Territories of India. Haemoglobin concentration was measured using the portable HemoCue Hb 201+ (HemoCue AB, Ängelholm, Sweden) and a capillary blood sample. In addition to disaggregating anaemia prevalence (separately in men and women) by state and age group, we used mixed-effects Poisson regression to determine individual-level and district-level predictors of anaemia. FINDINGS: 106 298 men and 633 305 women were included in our analysis. In men, the prevalence of any anaemia was 23·2% (95% CI 22·7-23·7), moderate or severe anaemia was 5·1% (4·9-5·4), and severe anaemia was 0·5% (0·5-0·6). An estimated 21·7% (20·9-22·5) of men with any degree of anaemia had moderate or severe anaemia compared with 53·2% (52·9-53·5) of women with any anaemia. Men aged 20-34 years had the lowest probability of having anaemia whereas anaemia prevalence among women was similar across age groups. State-level prevalence of any anaemia in men varied from 9·2% (7·7-10·9) in Manipur to 32·9% (31·0-34·7) in Bihar. The individual-level predictors of less household wealth, lower education, living in a rural area, smoking, consuming smokeless tobacco, and being underweight and the district-level predictors of living in a district with a lower rate of primary school completion, level of urbanisation, and household wealth were all associated with a higher probability of anaemia in men. Although some important exceptions were noted, district-level and state-level prevalence of anaemia among men correlated strongly with that among women. INTERPRETATION: Anaemia among men in India is an important public health problem. Because of the similarities in the patterns of geographical and sociodemographic variation of anaemia between men and women, future efforts to reduce anaemia among men could target similar population groups as those targeted in existing efforts to reduce anaemia among women.
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  • Journal Article

    Spectral Patterns Reveal Early Resistance Reactions of Barley Against Blumeria graminis f. sp. hordei 

    Kuska, Matheus Thomas; Brugger, Anna; Thomas, Stefan; Wahabzada, Mirwaes; Kersting, Kristian; Oerke, Erich-Christian; Steiner, Ulrike; Mahlein, Anne-Katrin
    Phytopathology 2017; 107(11) p.1388-1398
    Differences in early plant-pathogen interactions are mainly characterized by using destructive methods. Optical sensors are advanced techniques for phenotyping host-pathogen interactions on different scales and for detecting subtle plant resistance responses against pathogens. A microscope with a hyperspectral camera was used to study interactions between Blumeria graminis f. sp. hordei and barley (Hordeum vulgare) genotypes with high susceptibility or resistance due to hypersensitive response (HR) and papilla formation. Qualitative and quantitative assessment of pathogen development was used to explain changes in hyperspectral signatures. Within 48 h after inoculation, genotype-specific changes in the green and red range (500 to 690 nm) and a blue shift of the red-edge inflection point were observed. Manual analysis indicated resistance-specific reflectance patterns from 1 to 3 days after inoculation. These changes could be linked to host plant modifications depending on individual host-pathogen interactions. Retrospective analysis of hyperspectral images revealed spectral characteristics of HR against B. graminis f. sp. hordei. For early HR detection, an advanced data mining approach localized HR spots before they became visible on the RGB images derived from hyperspectral imaging. The link among processes during pathogenesis and host resistance to changes in hyperspectral signatures provide evidence that sensor-based phenotyping is suitable to advance time-consuming and cost-expensive visual rating of plant disease resistances
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  • Journal Article

    Comparing Open-Source Toolboxes for Processing and Analysis of Spike and Local Field Potentials Data 

    Unakafova, Valentina A.; Gail, Alexander
    Frontiers in Neuroinformatics 2019; 13: Art. 57
    Analysis of spike and local field potential (LFP) data is an essential part of neuroscientific research. Today there exist many open-source toolboxes for spike and LFP data analysis implementing various functionality. Here we aim to provide a practical guidance for neuroscientists in the choice of an open-source toolbox best satisfying their needs. We overview major open-source toolboxes for spike and LFP data analysis as well as toolboxes with tools for connectivity analysis, dimensionality reduction and generalized linear modeling. We focus on comparing toolboxes functionality, statistical and visualization tools, documentation and support quality. To give a better insight, we compare and illustrate functionality of the toolboxes on open-access dataset or simulated data and make corresponding MATLAB scripts publicly available.
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  • Journal Article

    Library of actions: Implementing a generic robot execution framework by using manipulation action semantics 

    Aein, Mohamad Javad; Aksoy, Eren Erdal; Wörgötter, Florentin
    The International Journal of Robotics Research 2019; 38(8) p.910-934
    When a robot has to imitate an observed action sequence, it must first understand the inherent characteristic features of the individual actions. Such features need to reflect the semantics of the action with a high degree of invariance between different demonstrations of the same action. At the same time the machine needs to be able to execute the action sequence in any appropriate situation. In this study, we introduce a new library of actions, which is a generic framework for executing manipulation actions on robotic systems by combining features that capture action semantics with a framework for execution. We focus on manipulation actions and first create a generic representation consisting of symbolic and subsymbolic components. To link these two domains we introduce a finite state machine allowing for sequential execution with error handling. The framework is developed from observing humans which provides us with a high degree of grounding. To quantitatively evaluate the scalability of the proposed approach, we conducted a large set of experiments involving different actions performed either individually or sequentially with various types of objects in different scene contexts.
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  • Journal Article

    Soil biota in vineyards are more influenced by plants and soil quality than by tillage intensity or the surrounding landscape 

    Buchholz, Jacob; Querner, Pascal; Paredes, Daniel; Bauer, Thomas; Strauss, Peter; Guernion, Muriel; Scimia, Jennifer; Cluzeau, Daniel; Burel, Françoise; Kratschmer, Sophie; et al.
    Winter, SilviaPotthoff, MartinZaller, Johann G.
    Scientific Reports 2017; 7(1)
    Tillage is known for its adverse effects on soil biota, at least in arable agroecosystems. However, in vineyards effects might differ as tillage is often performed during dry periods or only in every other inter-row allowing species to re-colonise disturbed areas. We examined the response of earthworms (lumbricids), springtails (collembola) and litter decomposition to periodically mechanically disturbed (PMD) and permanently green covered (PGC) vineyard inter-rows and assessed whether site effects are altered by the surrounding landscape. In commercial vineyards in Austria we sampled earthworms by handsorting, springtails by soil coring and pitfall trapping and installed litter decomposition bags. Earthworm species diversity increased with plant biomass under PMD but not under PGC; earthworm density was unaffected by tillage but increased with plant biomass mainly at high soil quality (soil fertility index). Springtail species diversity was unaffected by tillage; springtail densities (mainly larger species) were reduced under PGC. Litter decomposition was little affected by investigated parameters. Landscape heterogeneity affected the functional diversity of surface springtails, but did not influence soil-dwelling springtails, earthworms or litter decomposition. We conclude that effects on soil biota of periodical tillage in vineyards need not necessarily be detrimental and will be modified by plant biomass and soil quality.
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  • Journal Article

    Local field potentials are induced by visually evoked spiking activity in macaque cortical area MT 

    Esghaei, Moein; Daliri, Mohammad Reza; Treue, Stefan
    Scientific Reports 2017; 7(1)
    Local field potentials (LFP) have been the focus of many recent studies in systems neuroscience. However, the exact neural basis of these signals remains unclear. To address this question, we determined the relationship between LFP signals and another, much better understood, signature of neural activity: action potentials. Specifically, we focused on the relationship between the amplitude of stimulus-induced LFPs and the magnitude of spiking activity in visual cortex of non-human primates. Our trial-by-trial correlation analyses between these two components of extracellular signals in macaque visual cortex show that the spike rate is coupled to the LFP amplitude with a surprisingly long latency, typically 50 ms. Our analysis shows that the neural spike rate is a significant predictor of the LFP amplitude. This limits the functional interpretation of LFP signals beyond that based on spiking activities.
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  • Journal Article

    yRACK1/Asc1 proxiOMICs—Towards Illuminating Ships Passing in the Night 

    Schmitt, Kerstin; Valerius, Oliver
    Cells 2019; 8(11): Art. 1384
    Diverse signals and stress factors regulate the activity and homeostasis of ribosomes in all cells. The Saccharomyces cerevisiae protein Asc1/yRACK1 occupies an exposed site at the head region of the 40S ribosomal subunit (hr40S) and represents a central hub for signaling pathways. Asc1 strongly affects protein phosphorylation and is involved in quality control pathways induced by translation elongation arrest. Therefore, it is important to understand the dynamics of protein formations in the Asc1 microenvironment at the hr40S. We made use of the in vivo protein-proximity labeling technique Biotin IDentification (BioID). Unbiased proxiOMICs from two adjacent perspectives identified nucleocytoplasmic shuttling mRNA-binding proteins, the deubiquitinase complex Ubp3-Bre5, as well as the ubiquitin E3 ligase Hel2 as neighbors of Asc1. We observed Asc1-dependency of hr40S localization of mRNA-binding proteins and the Ubp3 co-factor Bre5. Hel2 and Ubp3-Bre5 are described to balance the mono-ubiquitination of Rps3 (uS3) during ribosome quality control. Here, we show that the absence of Asc1 resulted in massive exposure and accessibility of the C-terminal tail of its ribosomal neighbor Rps3 (uS3). Asc1 and some of its direct neighbors together might form a ribosomal decision tree that is tightly connected to close-by signaling modules.
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  • Journal Article

    Effects of forest‐use intensity on vascular epiphyte diversity along an elevational gradient 

    Guzmán‐Jacob, Valeria; Zotz, Gerhard; Craven, Dylan; Taylor, Amanda; Krömer, Thorsten; Monge‐González, María Leticia; Kreft, Holger
    Diversity and Distributions
    Aim: Understanding patterns of tropical plant diversity and their vulnerability to anthropogenic disturbance at different spatial scales remains a great challenge in ecology and conservation. Here, we study how the effects of forest‐use intensity on vascular epiphyte diversity vary along a tropical elevational gradient. Location: 3,500‐m elevational gradient along the eastern slopes of Cofre de Perote, Mexico. Methods: We studied the effects of forest‐use intensity on alpha, beta and gamma diversity of vascular epiphyte assemblages in old‐growth, degraded and secondary forests at eight study sites at 500‐m intervals along the elevational gradient. At each elevation and in each of the three forest‐use intensity levels, we established five 400‐m2 plots yielding a total of 120 plots. Results: Interactive effects of elevation and forest‐use intensity strongly impacted local‐scale patterns of vascular epiphyte diversity. Species diversity peaked at 500 as well as 1,500 m above sea level, which deviates from the previously reported humpshaped pattern. In most cases, alpha diversity did not differ significantly among forest‐ use intensity levels. However, gamma diversity was always lower in secondary forests compared to old‐growth forests across the entire elevational gradient. Within each elevational belt, beta diversity was dominated by species turnover along the forest‐use intensity gradient in the lowlands and declined with increasing elevation, where community composition became increasingly nested. Along the elevational gradient, the spatial turnover of vascular epiphyte community composition was similar among forest‐use intensity levels. Main conclusions: Our results reveal a strong interaction between forest‐use intensity and elevation, making it difficult to extrapolate findings from one elevational belt to another. Our findings highlight the value of old‐growth forest for epiphyte diversity, but also show that degraded and secondary forests—depending on the elevational belt—may maintain a high species diversity and thus play an important role in conservation planning.
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  • Working Paper

    Geschlechtergerechte Sprache in der Wissenschaft: Gebrauch und Motivation 

    Ivanov, Christine; Lange, Maria B.; Tiemeyer, Tabea; Ptok, Martin
    gender<ed> thoughts; 2
    Göttinger Centrum für Geschlechterforschung, 2019
    Seit den 1970ern ist geschlechtergerechte Sprache (ggS) im deutschen Sprachraum ein Thema. Die Diskussionen wandelten sich dabei stark. Ging es erst vorrangig um Sichtbarkeit von Frauen, stehen seit den 1990ern Heteronormativitätskritik und die Suche nach inklusiven Sprachformen im Vordergrund. Die vertretenen Positionen haben sich nicht abgelöst, sondern ergänzen sich teilweise oder stehen nebeneinander (in Konflikt). Trotz einer gewissen Institutionalisierung hat ggS ins wissenschaftliche Register kaum Aufnahme gefunden. Dabei ist Sprachwandel besonders wirksam, wenn statushohe Gruppen ihn vorleben. Zudem ist ggS exakter als ‚generische‘ Maskulina. Über ihren Gebrauch von ggS sowie ihre Präferenz bestimmter Formen, bzw. Hinderungsgründe für deren Verwendung, wurden in einer Online-Erhebung 290 Wissenschaftler_innen aus Geschlechterforschung und Medizin befragt. Die Ergebnisse wurden deskriptiv ausgewertet und dann hinsichtlich geschlechtertheoretischer Überlegungen reflektiert.
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  • Journal Article

    Spontaneous termination of chaotic spiral wave dynamics in human cardiac ion channel models 

    Aron, Marcel; Herzog, Sebastian; Parlitz, Ulrich; Luther, Stefan; Lilienkamp, Thomas
    PLOS ONE 2019; 14(8): Art. e0221401
    Chaotic spiral or scroll wave dynamics can be found in diverse systems. In cardiac dynamics, spiral or scroll waves of electrical excitation determine the dynamics during life-threatening arrhythmias like ventricular fibrillation. In numerical studies it was found that chaotic episodes of spiral and scroll waves can be transient, thus they terminate spontaneously. We show in this study that this behavior can also be observed using models which describe the ion channel dynamics of human cardiomyocytes (Bueno-Orovio-Cherry-Fenton model and the Ten Tusscher-Noble-Noble-Panfilov model). For both models we find that the average lifetime of the chaotic transients grows exponentially with the system size. With this behavior, we classify the systems into the group of type-II supertransients. We observe a significant difference of the breakup behavior between the models, which results in a distinct dynamics during the final phase just before the termination. The observation of a (temporally) stable single-spiral state affects the prevailing description of the dynamics of type-II supertransients as being "quasi-stationary" and also the feasibility of predicting the spontaneous termination of the spiral wave dynamics. In the long term, the relation between the breakup behavior of spiral waves and properties of chaotic transients like predictability or average transient lifetime may contribute to an improved understanding and classification of cardiac arrhythmias.
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  • Journal Article

    Development of a DNA Microarray-Based Assay for the Detection of Sugar Beet Root Rot Pathogens 

    Liebe, Sebastian; Christ, Daniela S.; Ehricht, Ralf; Varrelmann, Mark
    Phytopathology 2016; 106(1) p.76-86
    Sugar beet root rot diseases that occur during the cropping season or in storage are accompanied by high yield losses and a severe reduction of processing quality. The vast diversity of microorganism species involved in rot development requires molecular tools allowing simultaneous identification of many different targets. Therefore, a new microarray technology (ArrayTube) was applied in this study to improve diagnosis of sugar beet root rot diseases. Based on three marker genes (internal transcribed spacer, translation elongation factor 1 alpha, and 16S ribosomal DNA), 42 well-performing probes enabled the identification of prevalent field pathogens (e.g., Aphanomyces cochlioides), storage pathogens (e.g., Botrytis cinerea), and ubiquitous spoilage fungi (e.g., Penicillium expansum). All probes were proven for specificity with pure cultures from 73 microorganism species as well as for in planta detection of their target species using inoculated sugar beet tissue. Microarray-based identification of root rot pathogens in diseased field beets was successfully confirmed by classical detection methods. The high discriminatory potential was proven by Fusarium species differentiation based on a single nucleotide polymorphism. The results demonstrate that the ArrayTube constitute an innovative tool allowing a rapid and reliable detection of plant pathogens particularly when multiple microorganism species are present.
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  • Journal Article

    Effect of Environment and Sugar Beet Genotype on Root Rot Development and Pathogen Profile During Storage 

    Liebe, Sebastian; Varrelmann, Mark
    Phytopathology 2016; 106(1) p.65-75
    Storage rots represent an economically important factor impairing the storability of sugar beet by increasing sucrose losses and invert sugar content. Understanding the development of disease management strategies, knowledge about major storage pathogens, and factors influencing their occurrence is crucial. In comprehensive storage trials conducted under controlled conditions, the effects of environment and genotype on rot development and associated quality changes were investigated. Prevalent species involved in rot development were identified by a newly developed microarray. The strongest effect on rot development was assigned to environment factors followed by genotypic effects. Despite large variation in rot severity (sample range 0 to 84%), the spectrum of microorganisms colonizing sugar beet remained fairly constant across all treatments with dominant species belonging to the fungal genera Botrytis, Fusarium, and Penicillium. The intensity of microbial tissue necrotization was strongly correlated with sucrose losses (R² = 0.79 to 0.91) and invert sugar accumulation (R² = 0.91 to 0.95). A storage rot resistance bioassay was developed that could successfully reproduce the genotype ranking observed in storage trials. Quantification of fungal biomass indicates that genetic resistance is based on a quantitative mechanism. Further work is required to understand the large environmental influence on rot development in sugar beet.
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  • Journal Article

    Assessment of Fusarium Infection and Mycotoxin Contamination of Wheat Kernels and Flour Using Hyperspectral Imaging 

    Alisaac, Elias; Behmann, Jan; Rathgeb, Anna; Karlovsky, Petr; Dehne, Heinz-Wilhelm; Mahlein, Anne-Katrin
    Toxins 2019; 11(10): Art. 556
    Fusarium head blight (FHB) epidemics in wheat and contamination with Fusarium mycotoxins has become an increasing problem over the last decades. This prompted the need for non-invasive and non-destructive techniques to screen cereal grains for Fusarium infection, which is usually accompanied by mycotoxin contamination. This study tested the potential of hyperspectral imaging to monitor the infection of wheat kernels and flour with three Fusarium species. Kernels of two wheat varieties inoculated at anthesis with F. graminearum, F. culmorum, and F. poae were investigated. Hyperspectral images of kernels and flour were taken in the visible-near infrared (VIS-NIR) (400-1000 nm) and short-wave infrared (SWIR) (1000-2500 nm) ranges. The fungal DNA and mycotoxin contents were quantified. Spectral reflectance of Fusarium-damaged kernels (FDK) was significantly higher than non-inoculated ones. In contrast, spectral reflectance of flour from non-inoculated kernels was higher than that of FDK in the VIS and lower in the NIR and SWIR ranges. Spectral reflectance of kernels was positively correlated with fungal DNA and deoxynivalenol (DON) contents. In the case of the flour, this correlation exceeded r = -0.80 in the VIS range. Remarkable peaks of correlation appeared at 1193, 1231, 1446 to 1465, and 1742 to 2500 nm in the SWIR range.
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  • Journal Article

    In-Field Detection of Yellow Rust in Wheat on the Ground Canopy and UAV Scale 

    Bohnenkamp, David; Behmann, Jan; Mahlein, Anne-Katrin
    Remote Sensing 2019; 11(21): Art. 2495
    The application of hyperspectral imaging technology for plant disease detection in the field is still challenging. Existing equipment and analysis algorithms are adapted to highly controlled environmental conditions in the laboratory. However, only real time information from the field scale is able to guide plant protection measures and to optimize the use of resources. At the field scale, many parameters such as the optimal measurement distance, informative feature sets, and suitable algorithms have not been investigated. In this study, the hyperspectral detection and quantification of yellow rust in wheat was evaluated using two measurement platforms: a ground-based vehicle and an unmanned aerial vehicle (UAV). Di erent disease development stages and disease severities were provided in a plot-based field experiment. Measurements were performed weekly during the vegetation period. Data analysis was performed by three prediction algorithms with a focus on the selection of optimal feature sets. In this context, the across-scale application of optimized feature sets, an approach of information transfer between scales, was also evaluated. Relevant aspects for an on-line disease assessment in the field integrating a ordable sensor technology, sensor spatial resolution, compact analysis models, and fast evaluation have been outlined and reflected upon. For the first time, a hyperspectral imaging observation experiment of a plant disease was comparatively performed at two scales, ground canopy and UAV.
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  • Journal Article

    Infrared Thermography as a Non-Invasive Tool to Explore Differences in the Musculoskeletal System of Children with Hemophilia Compared to an Age-Matched Healthy Group 

    Seuser, Axel; Kurnik, Karin; Mahlein, Anne-Katrin
    Sensors 2018; 18(2): Art. 518
    Recurrent joint bleeds and silent bleeds are the most common clinical feature in patients with hemophilia. Every bleed causes an immediate inflammatory response and is the leading cause of chronic crippling arthropathy. With the help of infrared thermography we wanted to detect early differences between a group of clinical non-symptomatic children with hemophilia (CWH) with no history of clinically detected joint bleeds and a healthy age-matched group of children. This could help to discover early inflammation and help implement early treatment and preventative strategies. It could be demonstrated that infrared thermography is sensitive enough to detect more signs of early inflammatory response in the CWH than in healthy children. It seems to detect more side differences in temperature than clinical examination of silent symptoms detects tender points. Silent symptoms/tender points seem to be combined with early local inflammation. Using such a non-invasive and sensor-based early detection, prevention of overloading and bleeding might be achieved.
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  • Journal Article

    Quantitative assessment of disease severity and rating of barley cultivars based on hyperspectral imaging in a non-invasive, automated phenotyping platform 

    Thomas, Stefan; Behmann, Jan; Steier, Angelina; Kraska, Thorsten; Muller, Onno; Rascher, Uwe; Mahlein, Anne-Katrin
    Plant Methods 2018; 14(1)
    Background: Phenotyping is a bottleneck for the development of new plant cultivars. This study introduces a new hyperspectral phenotyping system, which combines the high throughput of canopy scale measurements with the advantages of high spatial resolution and a controlled measurement environment. Furthermore, the measured barley canopies were grown in large containers (called Mini-Plots), which allow plants to develop field-like phenotypes in greenhouse experiments, without being hindered by pot size. Results: Six barley cultivars have been investigated via hyperspectral imaging up to 30 days after inoculation with powdery mildew. With a high spatial resolution and stable measurement conditions, it was possible to automatically quantify powdery mildew symptoms through a combination of Simplex Volume Maximization and Support Vector Machines. Detection was feasible as soon as the first symptoms were visible for the human eye during manual rating. An accurate assessment of the disease severity for all cultivars at each measurement day over the course of the experiment was realized. Furthermore, powdery mildew resistance based necrosis of one cultivar was detected as well. Conclusion: The hyperspectral phenotyping system combines the advantages of field based canopy level measurement systems (high throughput, automatization, low manual workload) with those of laboratory based leaf level measurement systems (high spatial resolution, controlled environment, stable conditions for time series measurements). This allows an accurate and objective disease severity assessment without the need for trained experts, who perform visual rating, as well as detection of disease symptoms in early stages. Therefore, it is a promising tool for plant resistance breeding.
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  • Journal Article

    Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes 

    Capistrano-Gossmann, Gina G.; Ries, D.; Holtgräwe, D.; Minoche, A.; Kraft, T.; Frerichmann, S.L.M.; Rosleff Soerensen, T.; Dohm, J. C.; González, I.; Schilhabel, M.; et al.
    Varrelmann, M.Tschoep, H.Uphoff, H.Schütze, K.Borchardt, D.Toerjek, O.Mechelke, W.Lein, J. C.Schechert, A. W.Frese, L.Himmelbauer, H.Weisshaar, B.Kopisch-Obuch, F. J.
    Nature Communications 2017; 8(1): Art. 15708
    Rapid identification of agronomically important genes is of pivotal interest for crop breeding. One source of such genes are crop wild relative (CWR) populations. Here we used a CWR population of <200 wild beets (B. vulgaris ssp. maritima), sampled in their natural habitat, to identify the sugar beet (Beta vulgaris ssp. vulgaris) resistance gene Rz2 with a modified version of mapping-by-sequencing (MBS). For that, we generated a draft genome sequence of the wild beet. Our results show the importance of preserving CWR in situ and demonstrate the great potential of CWR for rapid discovery of causal genes relevant for crop improvement. The candidate gene for Rz2 was identified by MBS and subsequently corroborated via RNA interference (RNAi). Rz2 encodes a CC-NB-LRR protein. Access to the DNA sequence of Rz2 opens the path to improvement of resistance towards rhizomania not only by marker-assisted breeding but also by genome editing.
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  • Journal Article

    Monitoring wound healing in a 3D wound model by hyperspectral imaging and efficient clustering 

    Wahabzada, Mirwaes; Besser, Manuela; Khosravani, Milad; Kuska, Matheus Thomas; Kersting, Kristian; Mahlein, Anne-Katrin; Stürmer, Ewa
    PLOS ONE 2017; 12(12): Art. e0186425
    Wound healing is a complex and dynamic process with different distinct and overlapping phases from homeostasis, inflammation and proliferation to remodelling. Monitoring the healing response of injured tissue is of high importance for basic research and clinical practice. In traditional application, biological markers characterize normal and abnormal wound healing. Understanding functional relationships of these biological processes is essential for developing new treatment strategies. However, most of the present techniques (in vitro or in vivo) include invasive microscopic or analytical tissue sampling. In the present study, a non-invasive alternative for monitoring processes during wound healing is introduced. Within this context, hyperspectral imaging (HSI) is an emerging and innovative non-invasive imaging technique with different opportunities in medical applications. HSI acquires the spectral reflectance of an object, depending on its biochemical and structural characteristics. An in-vitro 3-dimensional (3-D) wound model was established and incubated without and with acute and chronic wound fluid (AWF, CWF), respectively. Hyperspectral images of each individual specimen of this 3-D wound model were assessed at day 0/5/10 in vitro, and reflectance spectra were evaluated. For analysing the complex hyperspectral data, an efficient unsupervised approach for clustering massive hyperspectral data was designed, based on efficient hierarchical decomposition of spectral information according to archetypal data points. It represents, to the best of our knowledge, the first application of an advanced Data Mining approach in context of non-invasive analysis of wounds using hyperspectral imagery. By this, temporal and spatial pattern of hyperspectral clusters were determined within the tissue discs and among the different treatments. Results from non-invasive imaging were compared to the number of cells in the various clusters, assessed by Hematoxylin/Eosin (H/E) staining. It was possible to correlate cell quantity and spectral reflectance during wound closure in a 3-D wound model in vitro.
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  • Journal Article

    Comparison and Combination of Thermal, Fluorescence, and Hyperspectral Imaging for Monitoring Fusarium Head Blight of Wheat on Spikelet Scale 

    Mahlein, Anne-Katrin; Alisaac, Elias; Al Masri, Ali; Behmann, Jan; Dehne, Heinz-Wilhelm; Oerke, Erich-Christian
    Sensors 2019; 19(10): Art. 2281
    Optical sensors have shown high capabilities to improve the detection and monitoring of plant disease development. This study was designed to compare the feasibility of different sensors to characterize Fusarium head blight (FHB) caused by Fusarium graminearum and Fusarium culmorum. Under controlled conditions, time-series measurements were performed with infrared thermography (IRT), chlorophyll fluorescence imaging (CFI), and hyperspectral imaging (HSI) starting 3 days after inoculation (dai). IRT allowed the visualization of temperature differences within the infected spikelets beginning 5 dai. At the same time, a disorder of the photosynthetic activity was confirmed by CFI via maximal fluorescence yields of spikelets (Fm) 5 dai. Pigment-specific simple ratio PSSRa and PSSRb derived from HSI allowed discrimination between Fusarium-infected and non-inoculated spikelets 3 dai. This effect on assimilation started earlier and was more pronounced with F. graminearum. Except the maximum temperature difference (MTD), all parameters derived from different sensors were significantly correlated with each other and with disease severity (DS). A support vector machine (SVM) classification of parameters derived from IRT, CFI, or HSI allowed the differentiation between non-inoculated and infected spikelets 3 dai with an accuracy of 78, 56 and 78%, respectively. Combining the IRT-HSI or CFI-HSI parameters improved the accuracy to 89% 30 dai.
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