@article{BaruchaMauchDucksteinetal.2022,
  author    = {Barucha, Anton and Mauch, Renan Marrichi and Duckstein, Franziska and Zagoya, Carlos and Mainz, Jochen G.},
  title     = {The potential of volatile organic compound analysis for pathogen detection and disease monitoring in patients with cystic fibrosis},
  series = {Expert review of respiratory medicine},
  volume    = {16},
  journal   = {Expert review of respiratory medicine},
  number    = {7},
  publisher = {Routledge, Taylor \& Francis Group},
  address   = {Abingdon},
  issn      = {1747-6348},
  doi       = {10.1080/17476348.2022.2104249},
  pages     = {723 -- 735},
  year      = {2022},
  abstract  = {Introduction Airway infection with pathogens and its associated pulmonary exacerbations (PEX) are the major causes of morbidity and premature death in cystic fibrosis (CF). Preventing or postponing chronic infections requires early diagnosis. However, limitations of conventional microbiology-based methods can hamper identification of exacerbations and specific pathogen detection. Analyzing volatile organic compounds (VOCs) in breath samples may be an interesting tool in this regard, as VOC-biomarkers can characterize specific airway infections in CF. Areas covered We address the current achievements in VOC-analysis and discuss studies assessing VOC-biomarkers and fingerprints, i.e. a combination of multiple VOCs, in breath samples aiming at pathogen and PEX detection in people with CF (pwCF). We aim to provide bases for further research in this interesting field. Expert opinion Overall, VOC-based analysis is a promising tool for diagnosis of infection and inflammation with potential to monitor disease progression in pwCF. Advantages over conventional diagnostic methods, including easy and non-invasive sampling procedures, may help to drive prompt, suitable therapeutic approaches in the future. Our review shall encourage further research, including validation of VOC-based methods. Specifically, longitudinal validation under standardized conditions is of interest in order to ensure repeatability and enable inclusion in CF diagnostic routine.},
  language  = {en}
}
@article{HampfNendelStreyetal.2021,
  author    = {Hampf, Anna and Nendel, Claas and Strey, Simone and Strey, Robert},
  title     = {Biotic yield losses in the Southern Amazon, Brazil},
  series = {Frontiers in plant science : FPLS},
  volume    = {12},
  journal   = {Frontiers in plant science : FPLS},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {1664-462X},
  doi       = {10.3389/fpls.2021.621168},
  pages     = {16},
  year      = {2021},
  abstract  = {Pathogens and animal pests (P\&A) are a major threat to global food security as they directly affect the quantity and quality of food. The Southern Amazon, Brazil's largest domestic region for soybean, maize and cotton production, is particularly vulnerable to the outbreak of P\&A due to its (sub)tropical climate and intensive farming systems. However, little is known about the spatial distribution of P\&A and the related yield losses. Machine learning approaches for the automated recognition of plant diseases can help to overcome this research gap. The main objectives of this study are to (1) evaluate the performance of Convolutional Neural Networks (ConvNets) in classifying P\&A, (2) map the spatial distribution of P\&A in the Southern Amazon, and (3) quantify perceived yield and economic losses for the main soybean and maize P\&A. The objectives were addressed by making use of data collected with the smartphone application Plantix. The core of the app's functioning is the automated recognition of plant diseases via ConvNets. Data on expected yield losses were gathered through a short survey included in an "expert" version of the application, which was distributed among agronomists. Between 2016 and 2020, Plantix users collected approximately 78,000 georeferenced P\&A images in the Southern Amazon. The study results indicate a high performance of the trained ConvNets in classifying 420 different crop-disease combinations. Spatial distribution maps and expert-based yield loss estimates indicate that maize rust, bacterial stalk rot and the fall armyworm are among the most severe maize P\&A, whereas soybean is mainly affected by P\&A like anthracnose, downy mildew, frogeye leaf spot, stink bugs and brown spot. Perceived soybean and maize yield losses amount to 12 and 16\%, respectively, resulting in annual yield losses of approximately 3.75 million tonnes for each crop and economic losses of US\$2 billion for both crops together. The high level of accuracy of the trained ConvNets, when paired with widespread use from following a citizen-science approach, results in a data source that will shed new light on yield loss estimates, e.g., for the analysis of yield gaps and the development of measures to minimise them.},
  language  = {en}
}
@article{MogrovejoAriasBrillWagner2020,
  author    = {Mogrovejo Arias, Diana Carolina and Brill, Florian H. H. and Wagner, Dirk},
  title     = {Potentially pathogenic bacteria isolated from diverse habitats in Spitsbergen, Svalbard},
  series = {Environmental earth sciences},
  volume    = {79},
  journal   = {Environmental earth sciences},
  number    = {5},
  publisher = {Springer},
  address   = {Berlin ; Heidelberg},
  issn      = {1866-6280},
  doi       = {10.1007/s12665-020-8853-4},
  pages     = {9},
  year      = {2020},
  abstract  = {The Arctic ecosystem, a reservoir of genetic microbial diversity, represents a virtually unlimited source of microorganisms that could interact with human beings. Despite continuous exploration of Arctic habitats and description of their microbial communities, bacterial phenotypes commonly associated with pathogenicity, such as hemolytic activity, have rarely been reported. In this study, samples of snow, fresh and marine water, soil, and sediment from several habitats in the Arctic archipelago of Svalbard were collected during Summer, 2017. Bacterial isolates were obtained after incubation on oligotrophic media at different temperatures and their hemolytic potential was assessed on sheep blood agar plates. Partial (alpha) or true (beta) hemolysis was observed in 32 out of 78 bacterial species. Genes expressing cytolytic compounds, such as hemolysins, likely increase the general fitness of the producing microorganisms and confer a competitive advantage over the availability of nutrients in natural habitats. In environmental species, the nutrient-acquisition function of these compounds presumably precedes their function as toxins for mammalian erythrocytes. However, in the light of global warming, the presence of hemolytic bacteria in Arctic environments highlights the possible risks associated with these microorganisms in the event of habitat melting/destruction, ecosystem transition, and re-colonization.},
  language  = {en}
}
@article{AlluBrotmanXueetal.2016,
  author    = {Allu, Annapurna Devi and Brotman, Yariv and Xue, Gang-Ping and Balazadeh, Salma},
  title     = {Transcription factor ANAC032 modulates JA/SA signalling in response to Pseudomonas syringae infection},
  series = {EMBO reports},
  volume    = {17},
  journal   = {EMBO reports},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {1469-221X},
  doi       = {10.15252/embr.201642197},
  pages     = {1578 -- 1589},
  year      = {2016},
  abstract  = {Responses to pathogens, including host transcriptional reprogramming, require partially antagonistic signalling pathways dependent on the phytohormones salicylic (SA) and jasmonic (JA) acids. However, upstream factors modulating the interplay of these pathways are not well characterized. Here, we identify the transcription factor ANAC032 from Arabidopsis thaliana as one such regulator in response to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pst). ANAC032 directly represses MYC2 activation upon Pst attack, resulting in blockage of coronatine-mediated stomatal reopening which restricts entry of bacteria into plant tissue. Furthermore, ANAC032 activates SA signalling by repressing NIMIN1, a key negative regulator of SA-dependent defence. Finally, ANAC032 reduces expression of JA-responsive genes, including PDF1.2A. Thus, ANAC032 enhances resistance to Pst by generating an orchestrated transcriptional output towards key SA- and JA-signalling genes coordinated through direct binding of ANAC032 to the MYC2, NIMIN1 and PDF1.2A promoters.},
  language  = {en}
}
@article{ShahnejatBushehriNobmannAlluetal.2016,
  author    = {Shahnejat-Bushehri, Sara and Nobmann, Barbara and Allu, Annapurna Devi and Balazadeh, Salma},
  title     = {JUB1 suppresses Pseudomonas syringae-induced defense responses through accumulation of DELLA proteins},
  series = {Journal of trace elements in medicine and biology},
  volume    = {11},
  journal   = {Journal of trace elements in medicine and biology},
  publisher = {Elsevier},
  address   = {Philadelphia},
  issn      = {1559-2316},
  doi       = {10.1080/15592324.2016.1181245},
  pages     = {7},
  year      = {2016},
  abstract  = {Phytohormones act in concert to coordinate plant growth and the response to environmental cues. Gibberellins (GAs) are growth-promoting hormones that recently emerged as modulators of plant immune signaling. By regulating the stability of DELLA proteins, GAs intersect with the signaling pathways of the classical primary defense hormones, salicylic acid (SA) and jasmonic acid (JA), thereby altering the final outcome of the immune response. DELLA proteins confer resistance to necrotrophic pathogens by potentiating JA signaling and raise the susceptibility to biotrophic pathogens by attenuating the SA pathway. Here, we show that JUB1, a core element of the GA - brassinosteroid (BR) - DELLA regulatory module, functions as a negative regulator of defense responses against Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) and mediates the crosstalk between growth and immunity.},
  language  = {en}
}