### Recent Submissions

• Journal Article

#### Molecular and Serological Footprints of Mycobacterium avium Subspecies Infections in Zoo Animals ﻿

Veterinary Sciences 2020; 7(3) p.1-14: Art. 117
Background: Mycobacteria of the Mycobacterium avium complex (MAC) pose a significant risk to zoological collections. Mycobacterium avium subspecies paratuberculosis (MAP) is a member of MAC and the causative agent of Johne’s disease. Despite many reports in animals kept in zoological gardens, systemic surveillance has rarely been reported. Methods: In this study, archived serum samples collected from animal species at the Wilhelma Zoological and Botanical Gardens in Stuttgart, Germany, were screened for the presence of antibodies against MAC and MAP. In addition, molecular investigations were performed on necropsy, fecal, and environmental samples. Results: In total, 30/381 serum samples of various mammalian species were positive for MAC antibodies in ELISA, while one sample of a reticulated giraffe (Giraffa camelopardalis reticulata) was positive in MAP-specific ELISA. Samples from many species were positive in pan-Mycobacterium real-time PCR (40/43 fecal samples, 27/43 environmental samples, and 31/90 necropsy samples). Surprisingly, no sample was positive in the MAP-specific molecular assays. However, two environmental samples from primate enclosures were positive in Mycobacterium avium subspecies hominissuis (MAH)-specific real-time PCR. Conclusions: The results reveal serological indications of MAC infections in the zoological collection. However, the presence of a MAP-contaminated environment by a high-shedding individual animal or MAP-infected population is unlikely.
• Journal Article

#### Meat Quality Parameters and Sensory Properties of One High-Performing and Two Local Chicken Breeds Fed with Vicia faba ﻿

Foods 2020; 9(8) p.1-18: Art. 1052
The current practices of the poultry industry have raised concerns among consumers. Among these is the culling of day-old male chicks of laying hybrids; a suitable alternative for this could be the use of dual-purpose breeds where both sexes are used. Another practice that causes concern is the import of large quantities of soybeans for feedstuff production. Substitutes for these soybean-based products are regional protein crops, such as faba beans (Vicia faba L.; FBs). The objective of this study was to test the suitability of FB as a locally produced soybean meal replacement for two local dual-purpose chicken breeds and one high-performing layer line. The breast and leg meat of male Bresse Gauloise (BG), Vorwerkhuhn (VH), and White Rock (WR) animals was evaluated for different meat quality parameters: pH, color, water holding capacity, and tenderness. Sensory properties of the samples were evaluated by a trained panel with a conventional descriptive analysis. Results show different effects of FB diets on meat quality parameters in the different breeds. The attributes mostly affected by the diet are related to aroma, flavor, and texture, particularly in VH and WR. Overall, faba beans appear to be an acceptable dietary protein source for rearing these breeds for meat production.
• Journal Article

#### The Effect of Algae or Insect Supplementation as Alternative Protein Sources on the Volatile Profile of Chicken Meat ﻿

Foods 2020; 9(9) p.1-15: Art. 1235
The aim of this study was to investigate the differences in the volatile profile of meat from chickens fed with alternative protein diets (such as algae or insect) through two different trials. In Trial 1, broiler chicken at one day of age were randomly allocated to three experimental groups: a basal control diet (C) and two groups in which the soybean meal was replaced at 75% (in the starter phase) and 50% (in the grower phase) with partially defatted Hermetia illucens (HI) larvae or Arthrospira platensis (SP). In Trial 2, broiler chickens were housed and reared similar to Trial 1, with the exception that the experimental diets replaced soybean meal with either 100% partially defatted HI or 100% SP. In both trials, chickens were slaughtered at day 35. Per group, 10 chickens were submitted to volatile analysis by using solid-phase microextraction (HS-SPME) and gas chromatography–mass spectrometry (GC-MS) analysis. Results in both trials showed that levels of several lipid-derived compounds were found to be lower in chickens fed an HI diet, which could be linked to a possibly lower level of polyunsaturated fatty acid content in HI-fed chicken. In addition, the dietary treatments could be discriminated based on the volatile profile, i.e., the substitution of soy with HI or SP distinctively affected the levels of flavor compounds.
• Journal Article

#### Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data ﻿

BMC Genomics. 2020 Sep 11;21(1):624
• Journal Article

#### Buffalopox Virus: An Emerging Virus in Livestock and Humans ﻿

Pathogens 2020; 9(9) p.1-9: Art. 676
Buffalopox virus (BPXV) is the cause of buffalopox, which was recognized by the FAO/WHO Joint Expert Committee on Zoonosis as an important zoonotic disease. Buffalopox was first described in India, later in other countries, and has become an emerging contagious viral zoonotic disease infecting milkers with high morbidity among affected domestic buffalo and cattle. BPXV is a member of the genus Orthopoxvirus and a close variant of the vaccinia virus (VACV). Recent genome data show that BPXV shares a most recent common ancestor of VACV Lister strain, which had been used for inoculating buffalo calves to produce a Smallpox vaccine. Over time, VACV evolved into BPXV by establishing itself in buffaloes to be increasingly pathogenic to this host and to make infections in cattle and humans. Together with the current pandemic of SARS-COV2/COVID 19, BPXV infections illustrate how vulnerable the human population is to the emergence and re-emergence of viral pathogens from unsuspected sources. In view that majority of the world population are not vaccinated against smallpox and are most vulnerable in the event of its re-emergence, reviewing and understanding the biology of vaccinia-like viruses are necessary for developing a new generation of safer smallpox vaccines in the smallpox-free world.
• Journal Article

#### Egg Production and Bone Stability of Local Chicken Breeds and Their Crosses Fed with Faba Beans ﻿

Animals 2020; 10(9) p.1-20: Art. 1480
Poultry production is raising concerns within the public regarding the practice of culling day-old chicks and the importation of soy from overseas for feedstuff. Therefore, an alternative approach to poultry production was tested. In two consecutive experiments, two traditional chicken breeds, Vorwerkhuhn and Bresse Gauloise, and White Rock as a commercial layer genotype as well as crossbreds thereof were fed diets containing either 20% vicin-rich or vicin-poor faba beans, though addressing both subjects of debate. Hen performance traits and bone stability were recorded. All parameters were considerably influenced by the genotype with White Rock showing the significantly highest (p < 0.05) laying performance (99.4% peak production) and mean egg weights (56.6 g) of the purebreds, but the lowest bone breaking strength (tibiotarsus 197.2 N, humerus 230.2 N). Regarding crossbreds, the Bresse Gauloise × White Rock cross performed best (peak production 98.1%, mean egg weight 58.0 g). However, only limited dietary effects were found as only the feeding of 20% vicin-rich faba beans led to a significant reduction of egg weights of at most 1.1 g (p < 0.05) and to a significant reduction of the shell stability in the crossbred genotypes. In terms of dual-purpose usage, crossing of Bresse Gauloise with White Rock seems to be the most promising variant studied here.
• Journal Article

#### Quantitative Modelling and Perspective Taking: Two Competencies of Decision Making for Sustainable Development ﻿

Sustainability 2020; 12(17) p.1-32: Art. 6980
Land use change, natural resource use and climate change are challenging Sustainable Development issues (SDGs 13–15). Fostering the competencies to deal with such issues is one core task for current educational endeavors. Among these competencies, decision-making competencies are central. In detail, we investigate how learners evaluate alternative decision-making options to improve existing competence models. We exemplify our competence modelling approach using the designation of a Marine Protected Area. The cross-sectional sample consists of secondary school students and student teachers (N = 760). Partial Credit modelling shows that quantitative modelling of decision-making options is a different competence dimension than perspective taking if contextualized for Sustainable Development. In quantitative modelling, mathematical modelling is used to evaluate and reflect on decision-making options. Perspective taking covers the ability to consider different normative perspectives on Sustainable Development issues. Both dimensions show plausible (latent) correlations with related constructs within the nomological net, i.e., with qualitative arguing, economic literacy, mathematical competencies, reading competencies and analytical problem solving. Furthermore, person-abilities increase with level of education for both dimensions. The identified competence dimensions quantitative modelling and perspective taking were successfully modelled and shown to be distinct; the resulting measuring instrument is reliable and valid.
• Journal Article

#### Analysis of the brain transcriptome in lines of laying hens divergently selected for feather pecking ﻿

BMC Genomics. 2020 Aug 27;21(1):595
Abstract Background Feather pecking (FP) in laying hens reduces animal welfare and leads to economic losses for the layer industry. FP is considered a heritable condition that is influenced by dysregulation of neurotransmitter homeostasis, the gut microbiome, and the immune system. To identify genes and biological pathways responsible for FP behavior we compared the brain transcriptomes of 48 hens divergently selected for FP. In addition, we tested if high feather peckers (HFP) and low feather peckers (LFP) respond differently to light since light has been shown to trigger FP behavior. Results Of approximately 48 million reads/sample an average of 98.4% were mapped to the chicken genome (GRCg6a). We found 13,070 expressed genes in the analyzed brains of which 423 showed differential expression between HFP and LFP. Genes of uncertain function and non-coding RNAs were overrepresented among those transcripts. Functional analyses revealed the involvement of cholinergic signaling, postsynaptic activity, membrane channels, and the immune system. After the light stimulus, 28 genes were found to be differentially expressed. These included an interaction cluster of core components of the circadian clock. However, differences in the response to light between HFP and LFP were not detectable. Conclusions Genes involved in cholinergic signaling, channel activity, synaptic transmission, and immune response were found to be involved in FP behavior. We propose a model in which the gut microbiota modulates the immune system, which in turn affects cholinergic signaling. This might have an influence on monoamine signaling with possible involvement of GABA or glutamate signaling.
• Journal Article

#### Impact of a Ration Negative in Dietary Cation–Anion Difference and Varying Calcium Supply Fed before Calving on Colostrum Quality of the Dams and Health Status and Growth Performance of the Calves ﻿

Animals 2020; 10(9) p.1-17: Art. 1465
• Journal Article

#### The Impact of Behavioral Drivers on Adoption of Sustainable Agricultural Practices: The Case of Organic Farming in Turkey ﻿

Sustainability 2020; 12(17) p.1-20: Art. 6875
Adoption decisions represent a crucial topic in sustainable agriculture research, particularly in the organic agriculture sector; to understand farmers’ decision-making, research has to delve more deeply into the influences of farmers’ behavior. The aim of this study, therefore, is to determine the behavioral intentions of Turkish sultana raisin producers toward organic farming practices. The proposed model integrates basic elements of the Theory of Planned Behavior and the technology acceptance model, which is then tested with survey data gathered from conventional and organic farmers by applying structural equation modeling, a powerful multivariate statistical technique. The results reveal that organic agriculture is perceived as a useful low-cost innovation by conventional farmers. Relating the results to group comparisons indicates that members of the conventional group are significantly more likely to have a positive intention towards adopting organic farming practices. Our results suggest possible interventions that policymakers should implement not only to stimulate adoption intentions of conventional farmers, but also to sustain continuance of organic practices by current operators.
• Journal Article

#### Survey data to identify the selection criteria used by breeders of four strains of Pakistani beetal goats ﻿

Data in Brief 2020; 32 p.1-4: Art. 106051
This article presents raw data from a survey conducted to identify the selection criteria of breeders raising either of four strains of Beetal goats, namely Beetal Faisalabadi, Beetal Makhi-Cheeni, Beetal Nuqri, and Beetal Rahim Yar Khan. After a pre-survey, a questionnaire was developed and a survey was conducted at four sites of the Punjab province of Pakistan: Faisalabad/Sahiwal, Bahawalpur/Bahawalnagar, Rajanpur, and Rahim Yar Khan. Each of these sites was the home tract of one strain. During the survey breeders (n = 162) were asked to rank the traits of their selection criteria based on the relative importance of those traits. Furthermore, the prevailing production system was also characterized by the breeders. For the interpretation of the results of this survey the readers are referred to Ref. [1]. The raw data set provided in this article can be extended in the future to include more strains of Beetal goats as well as other goat breeds. The selection criteria of breeders can change over time. This data set can also be used in future studies to investigate the temporal changes in the relative importance of different traits for the breeders. The factors potentially influencing those changes can also be investigated. This data set can further be utilized to design community based breeding plans tailored to the needs of the goat farming community.
• Journal Article

#### An Innovative Concept for a Multivariate Plausibility Assessment of Simultaneously Recorded Data ﻿

Animals 2020; 10(8) p.1-22: Art. 1412
The aim of this work was to develop an innovative multivariate plausibility assessment (MPA) algorithm in order to differentiate between ‘physiologically normal’, ‘physiologically extreme’ and ‘implausible’ observations in simultaneously recorded data. The underlying concept is based on the fact that different measurable parameters are often physiologically linked. If physiologically extreme observations occur due to disease, incident or hormonal cycles, usually more than one measurable trait is affected. In contrast, extreme values of a single trait are most likely implausible if all other traits show values in a normal range. For demonstration purposes, the MPA was applied on a time series data set which was collected on 100 cows in 10 commercial dairy farms. Continuous measurements comprised climate data, intra-reticular pH and temperature, jaw movement and locomotion behavior. Non-continuous measurements included milk yield, milk components, milk mid-infrared spectra and blood parameters. After the application of the MPA, in particular the pH data showed the most implausible observations with approximately 5% of the measured values. The other traits showed implausible values up to 2.5%. The MPA showed the ability to improve the data quality for downstream analyses by detecting implausible observations and to discover physiologically extreme conditions even within complex data structures. At this stage, the MPA is not a fully developed and validated management tool, but rather corresponds to a basic concept for future works, which can be extended and modified as required.
• Journal Article

#### Combining Random Forests and a Signal Detection Method Leads to the Robust Detection of Genotype-Phenotype Associations ﻿

Genes 2020; 11(8) p.1-16: Art. 892
Genome wide association studies (GWAS) are a well established methodology to identify genomic variants and genes that are responsible for traits of interest in all branches of the life sciences. Despite the long time this methodology has had to mature the reliable detection of genotype–phenotype associations is still a challenge for many quantitative traits mainly because of the large number of genomic loci with weak individual effects on the trait under investigation. Thus, it can be hypothesized that many genomic variants that have a small, however real, effect remain unnoticed in many GWAS approaches. Here, we propose a two-step procedure to address this problem. In a first step, cubic splines are fitted to the test statistic values and genomic regions with spline-peaks that are higher than expected by chance are considered as quantitative trait loci (QTL). Then the SNPs in these QTLs are prioritized with respect to the strength of their association with the phenotype using a Random Forests approach. As a case study, we apply our procedure to real data sets and find trustworthy numbers of, partially novel, genomic variants and genes involved in various egg quality traits.
• Journal Article

#### The Impact of Local Agrobiodiversity and Food Interventions on Cost, Nutritional Adequacy, and Affordability of Women and Children's Diet in Northern Kenya: A Modeling Exercise ﻿

Frontiers in Nutrition 2020; 7 p.1-12: Art. 129
Wild plant species are often excellent sources of micronutrients and have the potential to promote healthy living, yet they are under-exploited. Distribution of micronutrient powders as diet supplements can play an effective role in reducing micronutrient deficiencies among infants and young children. However, assessing their effects in ensuring a nutritious diet at low cost have been limited. This study assessed the impact of including wild plant species and micronutrient powders in modeled optimized lowest-cost diets for women and children in rural Kenya. Market surveys, focus group discussions in six villages and a 24-h dietary intake recall were used to collect data that were subsequently entered in the cost of diet linear programming tool to model lowest-cost nutritious diets for women and children in Turkana County, Kenya. Three wild vegetables, three wild fruits, and micronutrient powder were added to the models to assess their impact on the cost and the nutrient adequacy of the diets. A locally adapted cost optimized nutritious diet without any intervention costs between 50 and 119 Kenyan shillings (KES) daily ($0.5 to$1.2) for children between 6 and 23 months and 173 to 305 KES ($1.8 to$2.9) for women. Addition of the three wild vegetables resulted in cost reductions between 30 and 71% as well as making up for iron and zinc gaps. The micronutrient powder had an insignificant effect on diet cost and filling nutrient gaps. Edible wild plant species, specifically wild vegetables, can reduce diet costs in considerable proportions while filling nutrient gaps year-round. However, affordability of a nutritious diet remains a major challenge in Turkana County, irrespective of the wealth group.
• Journal Article

#### Effects of Modern Food Retailers on Adult and Child Diets and Nutrition ﻿

Nutrients 2020; 12(6) p.1-17: Art. 1714
In many developing countries, food environments are changing rapidly, with modern retailers—such as supermarkets—gaining in importance. Previous studies have suggested that the rise of modern retailers contributes to overweight and obesity. Effects of modern retailers on dietary quality have not been analyzed previously due to the unavailability of individual-level dietary data. Here, we address this research gap with data from randomly selected households in Lusaka, Zambia. Anthropometric and food-intake data from 930 adults and 499 children were analyzed to estimate effects of purchasing food in modern retailers on body weight, height, and dietary quality while controlling for income and other confounding factors. The food expenditure share spent in modern retailers was found to be positively associated with overweight in adults, but not in children. For children, a positive association between expenditures in modern retailers and height was identified. Modern retailers contribute to higher consumption of ultra-processed foods and calories. But they also increase protein and micronutrient intakes among adults and children, mainly through higher consumption of meat and dairy. The findings underline that modern retailers can influence diets and nutrition in positive and negative ways. Differentiated regulatory policies are needed to shape food environments for healthy food choices and nutrition.
• Journal Article

#### Effects of Different Farrowing and Rearing Systems on Post-Weaning Stress in Piglets ﻿

Agriculture 2020; 10(6) p.1-13: Art. 230
This study aimed to investigate how farrowing and rearing systems affect skin lesions, serum cortisol, and aggressive behavior as indicators for weaning stress of piglets. Between May 2016 and March 2018, in total 3144 weaning piglets from three different farrowing systems were examined: farrowing crates (FC), single-housing free-farrowing pens (FF), and group-housing of lactating sows and litters (GH). After weaning and regrouping, piglets were relocated to conventional rearing pens (conv; 5.7 m$^2$) or to wean-to-finish pens (w-f; 12.4 m$^2$). Skin lesions were scored 24 h after weaning. Blood samples were taken one week before and 24 h after weaning to analyze the individual difference in serum cortisol. Behavior was observed for 24 h after relocation. Animals raised in FC and FF had significantly more skin lesions than that of GH animals. Piglets born in GH showed lower cortisol differences and fought less and for shorter periods compared to FC and FF piglets. Piglets weaned to w-f pens showed greater cortisol changes and fought significantly longer than piglets in conv pens. Group housing during the suckling period reduced weaning stress for piglets in terms of skin lesions, serum cortisol, and aggressive behavior. Greater space allowance (w-f vs. conv) was not beneficial with regard to the investigated parameters.
• Journal Article

#### Reliable Discrimination of Green Coffee Beans Species: A Comparison of UV-Vis-Based Determination of Caffeine and Chlorogenic Acid with Non-Targeted Near-Infrared Spectroscopy ﻿

Foods 2020; 9(6) p.1-14: Art. 788
Species adulteration is a common problem in the coffee trade. Several attempts have been made to differentiate among species. However, finding an applicable methodology that would consider the various aspects of adulteration remains a challenge. This study investigated an ultraviolet–visible (UV-Vis) spectroscopy-based determination of caffeine and chlorogenic acid contents, as well as the applicability of non-targeted near-infrared (NIR) spectroscopy, to discriminate between green coffee beans of the Coffea arabica (Arabica) and Coffea canephora (Robusta) species from Java Island, Indonesia. The discrimination was conducted by measuring the caffeine and chlorogenic acid content in the beans using UV-Vis spectroscopy. The data related to both compounds was processed using linear discriminant analysis (LDA). Information about the diffuse reflectance (log 1/R) spectra of intact beans was determined by NIR spectroscopy and analyzed using multivariate analysis. UV-Vis spectroscopy attained an accuracy of 97% in comparison to NIR spectroscopy’s accuracy by selected wavelengths of LDA (95%). The study suggests that both methods are applicable to discriminate reliably among species.
• Journal Article

#### Root growth in light of changing magnesium distribution and transport between source and sink tissues in potato (Solanum tuberosum L.) ﻿

Scientific Reports 2020; 10(1) p.1-14: Art. 8796
This study depicts relations between magnesium (Mg) transport and re-translocation, photoassimilate partitioning, cation and ion concentrations, and finally root growth of potato under different Mg supplies. Potato plants were grown in a hydroponic culture system under different Mg regimes while investigating Mg concentrations, the expression of various Mg transporters, soluble sugars, and cations and anions in source and sink organs at different growth stages. Reports from literature about the impact of Mg deficiency on root growth are inconsistent. As Mg is known to be a phloem mobile nutrient, it is expected to be re-translocated under restricted availability of Mg from source to sink organs. Thus, we assume that plants can tolerate a slight Mg restriction without severe root growth reduction. However, under severe Mg deficiency, the process of Mg re-translocation is hampered, resulting in an impaired photoassimilate partitioning, and finally root growth. This might also explain the findings of studies claiming that Mg deficiency does not impair root growth as plants of these studies likely only suffered a slight Mg restriction. Finally, this study gives indications that an interruption of the process of Mg-re-translocation in early plant growth could be an indicator for growth reductions of the plant at a later growth stage.
• Journal Article

#### Target‐oriented habitat and wildlife management: estimating forage quantity and quality of semi‐natural grasslands with Sentinel‐1 and Sentinel‐2 data ﻿

Remote Sensing in Ecology and Conservation p.1-18
Semi‐natural grasslands represent ecosystems with high biodiversity. Their conservation depends on the removal of biomass, for example, through grazing by livestock or wildlife. For this, spatially explicit information about grassland forage quantity and quality is a prerequisite for efficient management. The recent advancements of the Sentinel satellite mission offer new possibilities to support the conservation of semi‐natural grasslands. In this study, the combined use of radar (Sentinel‐1) and multispectral (Sentinel‐2) data to predict forage quantity and quality indicators of semi‐natural grassland in Germany was investigated. Field data for organic acid detergent fibre concentration (oADF ), crude protein concentration (CP ), compressed sward height (CSH ) and standing biomass dry weight (DM ) collected between 2015 and 2017 were related to remote sensing data using the random forest regression algorithm. In total, 102 optical‐ and radar‐based predictor variables were used to derive an optimized dataset, maximizing the predictive power of the respective model. High $R^2$ values were obtained for the grassland quality indicators oADF ($R^2$ = 0.79, RMSE = 2.29%) and CP ($R^2$ = 0.72, RMSE = 1.70%) using 15 and 8 predictor variables respectively. Lower R 2 values were achieved for the quantity indicators CSH ($R^2$ = 0.60, RMSE = 2.77 cm) and DM ($R^2$ = 0.45, RMSE = 90.84 g/m²). A permutation‐based variable importance measure indicated a strong contribution of simple ratio‐based optical indices to the model performance. In particular, the ratios between the narrow near‐infrared and red‐edge region were among the most important variables. The model performance for oADF , CP and CSH was only marginally increased by adding Sentinel‐1 data. For DM , no positive effect on the model performance was observed by combining Sentinel‐1 and Sentinel‐2 data. Thus, optical Sentinel‐2 data might be sufficient to accurately predict forage quality, and to some extent also quantity indicators of semi‐natural grassland.
• Journal Article

#### Identification of Regulatory SNPs Associated with Vicine and Convicine Content of Vicia faba Based on Genotyping by Sequencing Data Using Deep Learning ﻿

Genes 2020; 11(6) p.1-16: Art. 614
Faba bean (Vicia faba) is a grain legume, which is globally grown for both human consumption as well as feed for livestock. Despite its agro-ecological importance the usage of Vicia faba is severely hampered by its anti-nutritive seed-compounds vicine and convicine (V+C). The genes responsible for a low V+C content have not yet been identified. In this study, we aim to computationally identify regulatory SNPs (rSNPs), i.e., SNPs in promoter regions of genes that are deemed to govern the V+C content of Vicia faba. For this purpose we first trained a deep learning model with the gene annotations of seven related species of the Leguminosae family. Applying our model, we predicted putative promoters in a partial genome of Vicia faba that we assembled from genotyping-by-sequencing (GBS) data. Exploiting the synteny between Medicago truncatula and Vicia faba, we identified two rSNPs which are statistically significantly associated with V+C content. In particular, the allele substitutions regarding these rSNPs result in dramatic changes of the binding sites of the transcription factors (TFs) MYB4, MYB61, and SQUA. The knowledge about TFs and their rSNPs may enhance our understanding of the regulatory programs controlling V+C content of Vicia faba and could provide new hypotheses for future breeding programs.