Recent Submissions

  • Journal Article

    3D virtual pathohistology of lung tissue from Covid-19 patients based on phase contrast X-ray tomography 

    Eckermann, Marina; Frohn, Jasper; Reichardt, Marius; Osterhoff, Markus; Sprung, Michael; Westermeier, Fabian; Tzankov, Alexandar; Werlein, Christopher; Kühnel, Mark; Jonigk, Danny; et al.
    Salditt, Tim
    eLife 2020; 9 p.1-25: Art. e60408
    We present a three-dimensional (3D) approach for virtual histology and histopathology based on multi-scale phase contrast x-ray tomography, and use this to investigate the parenchymal architecture of unstained lung tissue from patients who succumbed to Covid-19. Based on this first proof-of-concept study, we propose multi-scale phase contrast x-ray tomography as a tool to unravel the pathophysiology of Covid-19, extending conventional histology by a third dimension and allowing for full quantification of tissue remodeling. By combining parallel and cone beam geometry, autopsy samples with a maximum cross section of 8 mm are scanned and reconstructed at a resolution and image quality, which allows for the segmentation of individual cells. Using the zoom capability of the cone beam geometry, regions-of-interest are reconstructed with a minimum voxel size of 167 nm. We exemplify the capability of this approach by 3D visualization of diffuse alveolar damage (DAD) with its prominent hyaline membrane formation, by mapping the 3D distribution and density of lymphocytes infiltrating the tissue, and by providing histograms of characteristic distances from tissue interior to the closest air compartment.
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  • Journal Article

    Revisiting wind speed measurements using actively heated fiber optics: a wind tunnel study 

    van Ramshorst, Justus G. V.; Coenders-Gerrits, Miriam; Schilperoort, Bart; van de Wiel, Bas J. H.; Izett, Jonathan G.; Selker, John S.; Higgins, Chad W.; Savenije, Hubert H. G.; van de Giesen, Nick C.
    Atmospheric Measurement Techniques 2020; 13(10) p.5423-5439
    Near-surface wind speed is typically only measured by point observations. The actively heated fiber-optic (AHFO) technique, however, has the potential to provide high-resolution distributed observations of wind speeds, allowing for better spatial characterization of fine-scale processes. Before AHFO can be widely used, its performance needs to be tested in a range of settings. In this work, experimental results on this novel observational wind-probing technique are presented. We utilized a controlled wind tunnel setup to assess both the accuracy and the precision of AHFO under a range of operational conditions (wind speed, angles of attack and temperature difference). The technique allows for wind speed characterization with a spatial resolution of 0.3 m on a 1 s timescale. The flow in the wind tunnel was varied in a controlled manner such that the mean wind ranged between 1 and 17 m s$^{−1}$. The AHFO measurements are compared to sonic anemometer measurements and show a high coefficient of determination (0.92–0.96) for all individual angles, after correcting the AHFO measurements for the angle of attack. Both the precision and accuracy of the AHFO measurements were also greater than 95 % for all conditions. We conclude that AHFO has the potential to measure wind speed, and we present a method to help choose the heating settings of AHFO. AHFO allows for the characterization of spatially varying fields of mean wind. In the future, the technique could potentially be combined with conventional distributed temperature sensing (DTS) for sensible heat flux estimation in micrometeorological and hydrological applications.
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  • Journal Article

    BioSounds: an open-source, online platform for ecoacoustics 

    Darras, Kevin; Pérez, Noemí; -, Mauladi; Hanf-Dressler, Tara
    F1000Research 2020; 9 p.1-12: Art. 1224
    Passive acoustic monitoring of soundscapes and biodiversity produces vast amounts of audio recordings. However, the management of these raw data presents technical challenges and their analysis suffers from bottlenecks. A multitude of software solutions exist, but none can perform all the data processing needed by ecologists for analysing large acoustic data sets. The field of ecoacoustics needs a software tool that is free, evolving, and accessible. We take a step in that direction and present BioSounds: an open-source, online platform for ecoacoustics designed by ecologists and built by software engineers. Biosounds can be used for archiving and sharing recordings, manually creating and reviewing annotations of sonant animals in soundscapes, analysing audio in time and frequency, and storing reference recordings for different taxa. We present its features and structure, and compare it with similar software. We describe its operation mode and the workflow for typical use cases such as the analysis of bird and bat communities sampled in soundscape recordings. BioSounds is available from: https://github.com/nperezg/biosounds
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  • Journal Article

    Knowledge of Student Teachers on Sustainable Land Use Issues–Knowledge Types Relevant for Teacher Education 

    Richter-Beuschel, Lisa; Bögeholz, Susanne
    Sustainability 2020; 12(20) p.1-20: Art. 8332
    For restructuring educational processes and institutions toward Sustainable Development, teachers’ knowledge and competences are crucial. Due to the high relevance of teachers’ content knowledge, this study aimed to (i) assess Sustainable Development-relevant knowledge by differentiating between situational, conceptual and procedural knowledge, (ii) find out via item response theory modelling how these theoretically distinguished knowledge types can be empirically supported, and (iii) link the knowledge dimension(s) to related constructs. We developed a paper-and-pencil test to assess these three knowledge types (N = 314). A two-dimensional structure that combines situational and conceptual knowledge and that distinguishes situational/conceptual knowledge from procedural knowledge, fits the data best (EAP/PV situational/conceptual: 0.63; EAP/PV procedural: 0.67). Student teachers at master level outperformed bachelor level students in situational/conceptual knowledge but master level students did not differ from students at bachelor level regarding procedural knowledge. We observed only slight correlations between the two knowledge dimensions and the content-related motivational orientations of professional action competence. Student teachers’ deficits in procedural knowledge can be attributed to the small number of Education for Sustainable Development-relevant courses attended. Systematically fostering procedural knowledge in teacher education could promote achieving cognitive learning objectives associated with Sustainable Development Goals in the long term.
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  • Journal Article

    Arguments for Construct Validity of the Self-Efficacy Beliefs of Interdisciplinary Science Teaching (SElf-ST) Instrument 

    Handtke, Kevin
    European Journal of Educational Research 2020; 9(4) p.1435-1453
    Current research on self-efficacy beliefs of interdisciplinary science teaching indicates shortcomings in facing recent teaching challenges in secondary education and corresponding valid instruments. Thus, we designed the Self-Efficacy Beliefs of Interdisciplinary Science Teaching (SElf-ST) instrument based on a pedagogical content knowledge model for science teaching. We ensured the factorial validity of ten factors. To bring construct validity down to a round figure, we examined convergent and divergent validity in this paper. For answering the overall research question regarding arguments for the convergent and divergent validity of the interpretation of the SElf-ST instrument’s test values (and related hypotheses), we analyzed data of pre-service, trainee, and in-service biology, chemistry, and physics teachers (n = 590) in a cross-sectional study. While the strong latent correlations of the ten SElf-ST factors with self-efficacy beliefs of interdisciplinary science teaching in primary education (r = 0.40 – 0.63, p < 0.01) indicate convergent validity, the rather weak correlations with self-efficacy beliefs of general teaching (r = 0.17 – 0.54, p < 0.01), self-rated content knowledge in science (r = 0.13 – 0.40, p < 0.01), and perceived stress (r = -0.13 – -0.19, p < 0.01) support different divergent validity intensities. Thus, assumed relations within the nomological net surrounding the self-efficacy beliefs of interdisciplinary science teaching construct were confirmed for secondary education. In sum, we shed light on a rarely explored aspect of construct validity in science education research regarding self-efficacy beliefs. Doing so, we gained strong arguments that the SElf-ST instrument’s test values can serve as indicators of self-efficacy beliefs of interdisciplinary science teaching in secondary education.
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  • Journal Article

    Selection markers for transformation of the sequenced reference monokaryon Okayama 7/#130 and homokaryon AmutBmut of Coprinopsis cinerea 

    Dörnte, Bastian; Peng, Can; Fang, Zemin; Kamran, Aysha; Yulvizar, Cut; Kües, Ursula
    Fungal Biology and Biotechnology. 2020 Oct 12;7(1):15
    Abstract Background Two reference strains have been sequenced from the mushroom Coprinopsis cinerea, monokaryon Okayama 7/#130 (OK130) and the self-compatible homokaryon AmutBmut. An adenine-auxotrophy in OK130 (ade8-1) and a para-aminobenzoic acid (PABA)-auxotrophy in AmutBmut (pab1-1) offer selection markers for transformations. Of these two strains, homokaryon AmutBmut had been transformed before to PABA-prototrophy and with the bacterial hygromycin resistance marker hph, respectively. Results Gene ade8 encodes a bifunctional enzyme with an N-terminal glycinamide ribonucleotide synthase (GARS) and a C-terminal aminoimidazole ribonucleotide synthase (AIRS) domain required for steps 2 and 5 in the de novo biosynthesis of purines, respectively. In OK130, a missense mutation in ade8-1 rendered residue N231 for ribose recognition by the A loop of the GARS domain into D231. The new ade8+ vector pCcAde8 complements the auxotrophy of OK130 in transformations. Transformation rates with pCcAde8 in single-vector and co-transformations with ade8+-selection were similarly high, unlike for trp1+ plasmids which exhibit suicidal feedback-effects in single-vector transformations with complementation of tryptophan synthase defects. As various other plasmids, unselected pCcAde8 helped in co-transformations of trp1 strains with a trp1+-selection vector to overcome suicidal effects by transferred trp1+. Co-transformation rates of pCcAde8 in OK130 under adenine selection with nuclear integration of unselected DNA were as high as 80% of clones. Co-transformation rates of expressed genes reached 26–42% for various laccase genes and up to 67% with lcc9 silencing vectors. The bacterial gene hph can also be used as another, albeit less efficient, selection marker for OK130 transformants, but with similarly high co-transformation rates. We further show that the pab1-1 defect in AmutBmut is due to a missense mutation which changed the conserved PIKGT motif for chorismate binding in the C-terminal PabB domain to PIEGT in the mutated 4-amino-4-deoxychorismate synthase. Conclusions ade8-1 and pab1-1 auxotrophic defects in C. cinerea reference strains OK130 and AmutBmut for complementation in transformation are described. pCcAde8 is a new transformation vector useful for selection in single and co-transformations of the sequenced monokaryon OK130 which was transformed for the first time. The bacterial gene hph can also be used as an additional selection marker in OK130, making in combination with ade8+ successive rounds of transformation possible.
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  • Journal Article

    Correction to: Unexpected high frequency of neurofibroma in the celiac ganglion of German cattle 

    Dammann, Insa; Wemheuer, Wiebke M.; Wrede, Arne; Wemheuer, Wilhelm E.; Campe, Amely; Petschenka, Jutta; Schulze-Sturm, Ulf; Hahmann, Uwe; Czerny, Claus P.; Münster, Pia; et al.
    Brenig, BertramKreienbrock, LotharHerden, ChristianeSchulz-Schaeffer, Walter J.
    Veterinary Research. 2020 Oct 15;51(1):130
    An amendment to this paper has been published and can be accessed via the original article.
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  • Journal Article

    Protection of Citrus Fruits from Postharvest Infection with Penicillium digitatum and Degradation of Patulin by Biocontrol Yeast Clavispora lusitaniae 146 

    Díaz, Mariana Andrea; Pereyra, Martina María; Santander, Fabricio Fabián Soliz; Perez, María Florencia; Córdoba, Josefina María; Alhussein, Mohammad; Karlovsky, Petr; Dib, Julián Rafael
    Microorganisms 2020; 8(10) p.1-12: Art. 1477
    Fungal rots are one of the main causes of large economic losses and deterioration in the quality and nutrient composition of fruits during the postharvest stage. The yeast Clavispora lusitaniae 146 has previously been shown to efficiently protect lemons from green mold caused by Penicillium digitatum. In this work, the effect of yeast concentration and exposure time on biocontrol efficiency was assessed; the protection of various citrus fruits against P. digitatum by C. lusitaniae 146 was evaluated; the ability of strain 146 to degrade mycotoxin patulin was tested; and the effect of the treatment on the sensory properties of fruits was determined. An efficient protection of lemons was achieved after minimum exposure to a relatively low yeast cell concentration. Apart from lemons, the yeast prevented green mold in grapefruits, mandarins, oranges, and tangerines, implying that it can be used as a broad-range biocontrol agent in citrus. The ability to degrade patulin indicated that strain 146 may be suitable for the control of further Penicillium species. Yeast treatment did not alter the sensory perception of the aroma of fruits. These results corroborate the potential of C. lusitaniae 146 for the control of postharvest diseases of citrus fruits and indicate its suitability for industrial-scale fruit processing.
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  • Journal Article

    Time-continuous and time-discrete SIR models revisited: theory and applications 

    Wacker, Benjamin; Schlüter, Jan
    Advances in Difference Equations. 2020 Oct 07;2020(1):556
    Since Kermack and McKendrick have introduced their famous epidemiological SIR model in 1927, mathematical epidemiology has grown as an interdisciplinary research discipline including knowledge from biology, computer science, or mathematics. Due to current threatening epidemics such as COVID-19, this interest is continuously rising. As our main goal, we establish an implicit time-discrete SIR (susceptible people–infectious people–recovered people) model. For this purpose, we first introduce its continuous variant with time-varying transmission and recovery rates and, as our first contribution, discuss thoroughly its properties. With respect to these results, we develop different possible time-discrete SIR models, we derive our implicit time-discrete SIR model in contrast to many other works which mainly investigate explicit time-discrete schemes and, as our main contribution, show unique solvability and further desirable properties compared to its continuous version. We thoroughly show that many of the desired properties of the time-continuous case are still valid in the time-discrete implicit case. Especially, we prove an upper error bound for our time-discrete implicit numerical scheme. Finally, we apply our proposed time-discrete SIR model to currently available data regarding the spread of COVID-19 in Germany and Iran.
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  • Journal Article

    Validating the Efficiency of the FeS$_2$ Method for Elucidating the Mechanisms of Contaminant Removal Using Fe$_0$/H$_2$O Systems 

    Xiao, Minhui; Cui, Xuesong; Hu, Rui; Gwenzi, Willis; Noubactep, Chicgoua
    Processes 2020; 8(9) p.1-16: Art. 1162
    There is growing interest in using pyrite minerals (FeS$_2$) to enhance the efficiency of metallic iron (Fe$^0$) for water treatment (Fe$^0$/H$_2$O systems). This approach contradicts the thermodynamic predicting suppression of FeS$_2$ oxidation by Fe$^0$ addition. Available results are rooted in time series correlations between aqueous and solid phases based on data collected under various operational conditions. Herein, the methylene blue method (MB method) is used to clarify the controversy. The MB method exploits the differential adsorptive affinity of MB onto sand and sand coated with iron corrosion products to assess the extent of Fe$^0$ corrosion in Fe$^0$/H$_2$O systems. The effects of the addition of various amounts of FeS$_2$ to a Fe$^0$/sand mixture (FeS$_2$ method) on MB discoloration were characterized in parallel quiescent batch experiments for up to 71 d (pH$_0$ = 6.8). Pristine and aged FeS$_2$ specimens were used. Parallel experiments with methyl orange (MO) and reactive red 120 (RR120) enabled a better discussion of the achieved results. The results clearly showed that FeS$_2$ induces a pH shift and delays Fe precipitation and sand coating. Pristine FeS$_2$ induced a pH shift to values lower than 4.5, but no quantitative MB discoloration occurred after 45 d. Aged FeS$_2$ could not significantly shift the pH value (final pH ≥ 6.4) but improved the MB discoloration. The used systematic sequence of experiments demonstrated that adsorption and coprecipitation are the fundamental mechanisms of contaminant removal in Fe$^0$/H$_2$O systems. This research has clarified the reason why a FeS$_2$ addition enhances the efficiency of Fe$^0$ environmental remediation.
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  • Journal Article

    Flesh ID: Nanopore Sequencing Combined with Offline BLAST Search for the Identification of Meat Source 

    Kissenkötter, Jonas; Böhlken-Fascher, Susanne; Abd El Wahed, Ahmed
    Foods 2020; 9(10) p.1-13: Art. 1392
    Detection of animal species in meat product is crucial to prevent adulterated and unnecessary contamination during processing, in addition to avoid allergy and religious consequences. Gold standard is the real-time PCR assays, which has a limited target capability. In this study, we have established a rapid sequencing protocol to identify animal species within hours. Sequencing was achieved by nanopore sequencing and data analysis via offline BLAST search. The whole procedure was conducted in a mobile suitcase lab. As per national and international regulations, the developed assay detected adulteration of pork meat with 0.1% of horse, chicken, turkey, cattle, sheep, duck, rabbit, goat, and donkey. The developed test could be used on-site as a rapid and mobile detection system to determine contamination of meat products
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  • Journal Article

    Phenotypic Responses, Reproduction Mode and Epigenetic Patterns under Temperature Treatments in the Alpine Plant Species Ranunculus kuepferi (Ranunculaceae) 

    Syngelaki, Eleni; Daubert, Mareike; Klatt, Simone; Hörandl, Elvira
    Biology 2020; 9(10) p.1-20: Art. 315
    Plant life in alpine habitats is shaped by harsh abiotic conditions and cold climates. Phenotypic variation of morphological characters and reproduction can be influenced by temperature stress. Nevertheless, little is known about the performance of different cytotypes under cold stress and how epigenetic patterns could relate to phenotypic variation. Ranunculus kuepferi, a perennial alpine plant, served as a model system for testing the effect of cold stress on phenotypic plasticity, reproduction mode, and epigenetic variation. Diploid and autotetraploid individuals were placed in climate growth cabinets under warm and cold conditions. Morphological traits (height, leaves and flowers) and the proportion of well-developed seeds were measured as fitness indicators, while flow cytometric seed screening (FCSS) was utilized to determine the reproduction mode. Subsequently, comparisons with patterns of methylation-sensitive amplified fragment-length polymorphisms (AFLPs) were conducted. Diploids grew better under warm conditions, while tetraploids performed better in cold treatments. Epigenetic patterns were correlated with the expressed morphological traits. Cold stress reduced the reproduction fitness but did not induce apomixis in diploids. Overall, our study underlines the potential of phenotypic plasticity for acclimation under environmental conditions and confirms the different niche preferences of cytotypes in natural populations. Results help to understand the pattern of geographical parthenogenesis in the species.
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  • Journal Article

    Metagenome-Assembled Genome Sequences from an Anoxygenic Photosynthetic Consortium Involved in Sulfur Cycling 

    Winkler, Lucia; Münker, Marc F.; Brunotte, Susanne; Rohlmann, Lina; Diez Alfageme, Alvaro; Poehlein, Anja; Hoppert, Michael; Reitner, Joachim; Nacke, Heiko
    Microbiology Resource Announcements 2020; 9(40) p.1-3: Art. e00819-20
    We sequenced the metagenome of an anoxygenic photosynthetic consortium originating from pond water and reconstructed four metagenome-assembled genomes. These genomes include Desulfocapsa, Paludibacter, Lamprocystis, and Rhodocyclaceae representatives and indicate the presence of genes for dissimilatory sulfate reduction and oxidation of reduced sulfur compounds.
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  • Journal Article

    Can We Use Gene-Editing to Induce Apomixis in Sexual Plants? 

    Scheben, Armin; Hojsgaard, Diego
    Genes 2020; 11(7) p.1-28: Art. 781
    Apomixis, the asexual formation of seeds, is a potentially valuable agricultural trait. Inducing apomixis in sexual crop plants would, for example, allow breeders to fix heterosis in hybrid seeds and rapidly generate doubled haploid crop lines. Molecular models explain the emergence of functional apomixis, i.e., apomeiosis + parthenogenesis + endosperm development, as resulting from a combination of genetic or epigenetic changes that coordinate altered molecular and developmental steps to form clonal seeds. Apomixis-like features and synthetic clonal seeds have been induced with limited success in the sexual plants rice and maize by using gene editing to mutate genes related to meiosis and fertility or via egg-cell specific expression of embryogenesis genes. Inducing functional apomixis and increasing the penetrance of apomictic seed production will be important for commercial deployment of the trait. Optimizing the induction of apomixis with gene editing strategies that use known targets as well as identifying alternative targets will be possible by better understanding natural genetic variation in apomictic species. With the growing availability of genomic data and precise gene editing tools, we are making substantial progress towards engineering apomictic crops.
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  • Journal Article

    Meta-analyses of genome wide association studies in lines of laying hens divergently selected for feather pecking using imputed sequence level genotypes 

    Falker-Gieske, Clemens; Iffland, Hanna; Preuß, Siegfried; Bessei, Werner; Drögemüller, Cord; Bennewitz, Jörn; Tetens, Jens
    BMC Genetics. 2020 Oct 01;21(1):114
    Abstract Background Feather pecking (FP) is damaging behavior in laying hens leading to global economic losses in the layer industry and massive impairments of animal welfare. The objective of the study was to discover genetic variants and affected genes that lead to FP behavior. To achieve that we imputed low-density genotypes from two different populations of layers divergently selected for FP to sequence level by performing whole genome sequencing on founder and half-sib individuals. In order to decipher the genetic structure of FP, genome wide association studies and meta-analyses of two resource populations were carried out by focusing on the traits ‘feather pecks delivered’ (FPD) and the ‘posterior probability of a hen to belong to the extreme feather pecking subgroup’ (pEFP). Results In this meta-analysis, we discovered numerous genes that are affected by polymorphisms significantly associated with the trait FPD. Among them SPATS2L, ZEB2, KCHN8, and MRPL13 which have been previously connected to psychiatric disorders with the latter two being responsive to nicotine treatment. Gene set enrichment analysis revealed that phosphatidylinositol signaling is affected by genes identified in the GWAS and that the Golgi apparatus as well as brain structure may be involved in the development of a FP phenotype. Further, we were able to validate a previously discovered QTL for the trait pEFP on GGA1, which contains variants affecting NIPA1, KIAA1211L, AFF3, and TSGA10. Conclusions We provide evidence for the involvement of numerous genes in the propensity to exhibit FP behavior that could aid in the selection against this unwanted trait. Furthermore, we identified variants that are involved in phosphatidylinositol signaling, Golgi metabolism and cell structure and therefore propose changes in brain structure to be an influential factor in FP, as already described in human neuropsychiatric disorders.
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  • Journal Article

    Understanding German Pig Farmers’ Intentions to Design and Construct Pig Housing for the Improvement of Animal Welfare 

    Winkel, Carolin; von Meyer-Höfer, Marie; Heise, Heinke
    Animals 2020; 10(10) p.1-22: Art. 1760
    Improving farm animal welfare requires modifications to the behavior of many stakeholders. Investments in more animal-friendly barns to improve animal welfare have already been made by some farmers. However, more farmers must be persuaded to modernize their barns. The marketing of animal-friendly products is the responsibility of retailers, and consumers have to purchase these products. Currently, little is known about what (and how) underlying psychological factors influence a farmer’s intention to construct pig housing to improve farm animal welfare. Pig farmers in Germany were questioned via an online questionnaire in May 2020 (n = 424). Based on the Theory of Planned Behavior (TPB), partial least squares path modeling was used. The constructs: attitude, subjective norm, direct and indirect experience associated with the construction of pig housing substantially influenced the farmers’ behaviors. As expected, the impact of perceived behavioral control on intention was negative but was also very low and only slightly significant. Contrary to expectations, the perceived behavioral control had no significant influence on farmers’ behaviors. Pig farmers who have already rebuilt their pigs’ housing should be motivated to share their experiences to influence their colleagues’ intentions to construct. Our results will encourage policy makers to consider the important role of the different psychological and intrinsic factors influencing pig farmers. Thus, the sustainability of pig farming can be improved by giving politicians a better understanding of farmers´ behaviors.
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  • Journal Article

    Point-Of-Care or Point-Of-Need Diagnostic Tests: Time to Change Outbreak Investigation and Pathogen Detection 

    Hansen, Sören; Abd El Wahed, Ahmed
    Tropical Medicine and Infectious Disease 2020; 5(4) p.1-15: Art. 151
    In the recent years, the progress of international trade and travel has led to an increased risk of emerging infections. Around 75 percent of the pathogens causing these infections are of animal origin. Point-of-care tests (POCT) and point-of-need tests (PONT) have been established in order to directly provide accurate and rapid diagnostics at field level, the patient bed-side or at the site of outbreaks. These assays can help physicians and decision makers to take the right action without delay. Typically, POCT and PONT rely on genomic identification of pathogens or track their immunological fingerprint. Recently, protocols for metagenomic diagnostics in the field have been developed. In this review, we give an overview of the latest developments in portable diagnostic methods. In addition, four mobile platforms for the implementation of these techniques at point-of-care and point-of-need are described. These approaches can provide reliable diagnostics and surveillance, especially in low resource settings as well as at the level of one health.
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  • Journal Article

    Pan-genomic open reading frames: A potential supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction 

    Li, Zhengcao; Simianer, Henner
    PLOS Genetics 2020; 16(8) p.1-19: Art. e1008995
    Pan-genomic open reading frames (ORFs) potentially carry protein-coding gene or coding variant information in a population. In this study, we suggest that pan-genomic ORFs are promising to be utilized in estimation of heritability and genomic prediction. A Saccharomyces cerevisiae dataset with whole-genome SNPs, pan-genomic ORFs, and the copy numbers of those ORFs is used to test the effectiveness of ORF data as a predictor in three prediction models for 35 traits. Our results show that the ORF-based heritability can capture more genetic effects than SNP-based heritability for all traits. Compared to SNP-based genomic prediction (GBLUP), pan-genomic ORF-based genomic prediction (OBLUP) is distinctly more accurate for all traits, and the predictive abilities on average are more than doubled across all traits. For four traits, the copy number of ORF-based prediction(CBLUP) is more accurate than OBLUP. When using different numbers of isolates in training sets in ORF-based prediction, the predictive abilities for all traits increased as more isolates are added in the training sets, suggesting that with very large training sets the prediction accuracy will be in the range of the square root of the heritability. We conclude that pan-genomic ORFs have the potential to be a supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction.
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  • Journal Article

    Chloroplast Haplotypes of Northern Red Oak (Quercus rubra L.) Stands in Germany Suggest Their Origin from Northeastern Canada 

    Götz, Jeremias; Krutovsky, Konstantin V.; Leinemann, Ludger; Müller, Markus; Rajora, Om P.; Gailing, Oliver
    Forests 2020; 11(9) p.1-15: Art. 1025
    Northern red oak (Quercus rubra L.) is one of the most important foreign tree species in Germany and considered as a major candidate for prospective sustainable forestry in the face of climate change. Therefore, Q. rubra was subject of many previous studies on its growth traits and attempts to infer the origin of various populations of this species using nuclear and chloroplast DNA markers. However, the exact geographic origin of German red oak stands has still not been identified. Its native range widely extends over North America, and the species can tolerate a broad range of environmental conditions. We genotyped individual trees in 85 populations distributed in Germany and North America using five chloroplast microsatellite and three novel chloroplast CAPS markers, resulting in the identification of 29 haplotypes. The new marker set enabled the identification of several new red oak haplotypes with restricted geographic origin. Some very rare haplotypes helped us narrow down the origin of Q. rubra stands in Germany, especially some stands from North Rhine-Westphalia, to the northern part of the species’ natural distribution area including the Peninsula of Nova Scotia, where the most similar haplotype composition was observed, compared to distinct German stands.
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  • Journal Article

    Extreme Climate Event and Its Impact on Landscape Resilience in Gobi Region of Mongolia 

    Vova, Oyudari; Kappas, Martin; Renchin, Tsolmon; Fassnacht, Steven R.
    Remote Sensing 2020; 12(18) p.1-21: Art. 2881
    The dzud, a specific type of climate disaster in Mongolia, is responsible for serious environmental and economic damage. It is characterized by heavy snowfall and severe winter conditions, causing mass livestock deaths that occur through the following spring. These events substantially limit socioeconomic development in Mongolia. In this research, we conducted an analysis of several dzud events (2000, 2001, 2002, and 2010) to understand the spatial and temporal variability of vegetation conditions in the Gobi region of Mongolia. The present paper also establishes how these extreme climatic events affect vegetation cover and local grazing conditions using the seasonal aridity index ($_a$AI$_Z$), time-series Moderate Resolution Imaging Spectroradiometer (MODIS) Normalized Difference Vegetation Index (NDVI), and livestock data. We also correlated $_a$AI$_Z$, NDVI, and seasonal precipitation in the varied ecosystems of the study area. The results illustrate that under certain dzud conditions, rapid regeneration of vegetation can occur. A thick snow layer acting as a water reservoir combined with high livestock losses can lead to an increase of the maximum August NDVI. The Gobi steppe areas showed the highest degree of vulnerability to climate, with a drastic decline of grassland in humid areas. Another result is that snowy winters can cause a 10 to 20-day early peak in NDVI and a following increase in vegetation growth. During a drought year with dry winter conditions, the vegetation growth phase begins later due to water deficiency, which leads to weaker vegetation growth. Livestock loss and the reduction of grazing pressure play a crucial role in vegetation recovery after extreme climatic events in Mongolia.
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