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    Defoliating Insect Mass Outbreak Affects Soil N Fluxes and Tree N Nutrition in Scots Pine Forests. 

    Grüning, Maren M.; Simon, Judy; Rennenberg, Heinz; L-M-Arnold, Anne
    Frontiers in plant science 2017; 8: Art. 954
    Biotic stress by mass outbreaks of defoliating pest insects does not only affect tree performance by reducing its photosynthetic capacity, but also changes N cycling in the soil of forest ecosystems. However, how insect induced defoliation affects soil N fluxes and, in turn, tree N nutrition is not well-studied. In the present study, we quantified N input and output fluxes via dry matter input, throughfall, and soil leachates. Furthermore, we investigated the effects of mass insect herbivory on tree N acquisition (i.e., organic and inorganic 15N net uptake capacity of fine roots) as well as N pools in fine roots and needles in a Scots pine (Pinus sylvestris L.) forest over an entire vegetation period. Plots were either infested by the nun moth (Lymantria monacha L.) or served as controls. Our results show an increased N input by insect feces, litter, and throughfall at the infested plots compared to controls, as well as increased leaching of nitrate. However, the additional N input into the soil did not increase, but reduce inorganic and organic net N uptake capacity of Scots pine roots. N pools in the fine roots and needles of infested trees showed an accumulation of total N, amino acid-N, protein-N, and structural N in the roots and the remaining needles as a compensatory response triggered by defoliation. Thus, although soil N availability was increased via surplus N input, trees did not respond with an increased N acquisition, but rather invested resources into defense by accumulation of amino acid-N and protein-N as a survival strategy.
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    Analyzing job satisfaction and preferences of employees: the case of horticultural companies in Germany 

    Meyerding, Stephan G. H.
    International Food and Agribusiness Management Review 2017; 20(5) p.765-788
    German horticulture, as well as horticulture and agriculture in other industrialized countries, faces increasing skilled labor shortage. Additionally family run businesses in horticulture and agriculture are lacking a new generation of entrepreneurs, leading to increased structural change. Insights about job attributes attractiveness as well as their impact on job satisfaction lead to a more transparent environment in which employers and employees can make better-informed decisions and redesign the professional environment, resulting in increased job satisfaction, performance and career sustainability. For this purpose, a survey was undertaken from August 2013 to February 2015 through a questionnaire examining the preferences and perception of employees (N=229) regarding job characteristics. The theoretical background of the study is Warr’s vitamin model, which assumes non-linear relationships between job characteristics and job satisfaction. The strongest connections with job satisfaction among employees are with future prospects and conflict between work-andfamily. The study is one of the first of its kind to provide a detailed overview of job satisfaction of different groups of employees in German horticulture.
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    Alterations in the Rumen Liquid-, Particle- and Epithelium-Associated Microbiota of Dairy Cows during the Transition from a Silage- and Concentrate-Based Ration to Pasture in Spring. 

    Schären, Melanie; Kiri, Kerstin; Riede, Susanne; Gardener, Mark; Meyer, Ulrich; Hummel, Jürgen; Urich, Tim; Breves, Gerhard; Dänicke, Sven
    Frontiers in microbiology 2017; 8: Art. 744
    In spring dairy cows are often gradually transitioned from a silage- and concentrate-based ration (total mixed ration, TMR) to pasture. Rumen microbiota adaptability is a key feature of ruminant survival strategy. However, only little is known on the temporal and spatial microbial alterations involved. This study aims to investigate how the rumen liquid (LAAB), particle (PAAB), and epithelium (EAAB) associated archaea and bacteria are influenced by this nutritional change. A 10-wk trial was performed, including 10 rumen-fistulated dairy cows, equally divided into a pasture- and a confinement- group (PG and CG). The CG stayed on a TMR-based ration, while the PG was gradually transitioned from TMR to pasture (wk 1: TMR-only, wk 2: 3 h/day on pasture, wk 3 & 4: 12 h/day on pasture, wk 5-10: pasture-only). In wk 1, wk 5, and wk 10 samples of solid and liquid rumen contents, and papillae biopsies were collected. The DNA was isolated, and PCR-SSCP and 16S rRNA gene amplicon sequencing analysis were performed. Cluster analysis revealed a higher similarity between LAAB and PAAB, compared to the EAAB, characterized by higher species diversity. At all three locations the microbiota was significantly influenced by the ration change, opposite the generally acknowledged hypothesis that the EAAB remain more consistent throughout dietary changes. Even though the animals in the PG were already on a full-grazing ration for 4-6 days in wk 5, the microbiota at all three locations was significantly different compared to wk 10, suggesting an adaptation period of several days to weeks. This is in line with observations made on animal level, showing a required time for adaptation of 2-3 weeks for production and metabolic variables. A large part of the rumen prokaryote species remained unaltered upon transition to pasture and exhibited a strong host influence, supporting the hypothesis that the rumen microbiota consists of a core and a variable microbiota. For the effect of the location as well as the ration change either very similar or opposite trends among member species of common taxa were observed, demonstrating that microbes that are phylogenetically close may still exhibit substantially different phenotypes and functions.
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    Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure. 

    Fleming, Damarius S.; Weigend, Steffen; Simianer, Henner; Weigend, Annett; Rothschild, Max; Schmidt, Carl; Ashwell, Chris; Persia, Mike; Reecy, James; Lamont, Susan J.
    G3 (Bethesda, Md.) 2017-05-05; 7(5) p.1525-1537
    Global climate change is increasing the magnitude of environmental stressors, such as temperature, pathogens, and drought, that limit the survivability and sustainability of livestock production. Poultry production and its expansion is dependent upon robust animals that are able to cope with stressors in multiple environments. Understanding the genetic strategies that indigenous, noncommercial breeds have evolved to survive in their environment could help to elucidate molecular mechanisms underlying biological traits of environmental adaptation. We examined poultry from diverse breeds and climates of Africa and Northern Europe for selection signatures that have allowed them to adapt to their indigenous environments. Selection signatures were studied using a combination of population genomic methods that employed FST , integrated haplotype score (iHS), and runs of homozygosity (ROH) procedures. All the analyses indicated differences in environment as a driver of selective pressure in both groups of populations. The analyses revealed unique differences in the genomic regions under selection pressure from the environment for each population. The African chickens showed stronger selection toward stress signaling and angiogenesis, while the Northern European chickens showed more selection pressure toward processes related to energy homeostasis. The results suggest that chromosomes 2 and 27 are the most diverged between populations and the most selected upon within the African (chromosome 27) and Northern European (chromosome 2) birds. Examination of the divergent populations has provided new insight into genes under possible selection related to tolerance of a population's indigenous environment that may be baselines for examining the genomic contribution to tolerance adaptions.
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    A Nonsense Variant in the ST14 Gene in Akhal-Teke Horses with Naked Foal Syndrome. 

    Bauer, Anina; Hiemesch, Theresa; Jagannathan, Vidhya; Neuditschko, Markus; Bachmann, Iris; Rieder, Stefan; Mikko, Sofia; Penedo, M Cecilia; Tarasova, Nadja; Vitková, Martina; et al.
    Sirtori, NicolòRoccabianca, PaolaLeeb, TossoWelle, Monika M.
    G3 (Bethesda, Md.) 2017; 7(4) p.1315-1321
    Naked foal syndrome (NFS) is a genodermatosis in the Akhal-Teke horse breed. We provide the first scientific description of this phenotype. Affected horses have almost no hair and show a mild ichthyosis. So far, all known NFS affected horses died between a few weeks and 3 yr of age. It is not clear whether a specific pathology caused the premature deaths. NFS is inherited as a monogenic autosomal recessive trait. We mapped the disease causing genetic variant to two segments on chromosomes 7 and 27 in the equine genome. Whole genome sequencing of two affected horses, two obligate carriers, and 75 control horses from other breeds revealed a single nonsynonymous genetic variant on the chromosome 7 segment that was perfectly associated with NFS. The affected horses were homozygous for ST14:c.388G>T, a nonsense variant that truncates >80% of the open reading frame of the ST14 gene (p.Glu130*). The variant leads to partial nonsense-mediated decay of the mutant transcript. Genetic variants in the ST14 gene are responsible for autosomal recessive congenital ichthyosis 11 in humans. Thus, the identified equine ST14:c.388G>T variant is an excellent candidate causative variant for NFS, and the affected horses represent a large animal model for a known human genodermatosis. Our findings will enable genetic testing to avoid the nonintentional breeding of NFS-affected foals.
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    Pitfall trap sampling bias depends on body mass, temperature, and trap number: insights from an individual-based model 

    Engel, Jan; Hertzog, Lionel; Tiede, Julia; Wagg, Cameron; Ebeling, Anne; Briesen, Heiko; Weisser, Wolfgang W.
    Ecosphere 2017; 8(4): Art. e01790
    The diversity and community composition of ground arthropods is routinely analyzed by pitfall trap sampling, which is a cost- and time-effective method to gather large numbers of replicates but also known to generate data that are biased by species-specific differences in locomotory activity. Previous studies have looked at factors that influence the sampling bias. These studies, however, were limited to one or few species and did rarely quantify how the species-specific sampling bias shapes community-level diversity metrics. In this study, we systematically quantify the species-specific and community-level sampling bias with an allometric individual-based model that simulates movement and pitfall sampling of 10 generic ground arthropod species differing in body mass. We perform multiple simulation experiments covering different scenarios of pitfall trap number, spatial trap arrangement, temperature, and population density. We show that the sampling bias decreased strongly with increasing body mass, temperature, and pitfall trap number, while population density had no effect and trap arrangement only had little effect. The average movement speed of a species in the field integrates body mass and temperature effects and could be used to derive reliable estimates of absolute species abundance. We demonstrate how unbiased relative species abundance can be derived using correction factors that need only information on species body mass. We find that community-level diversity metrics are sensitive to the particular community structure, namely the relation between body mass and relative abundance across species. Generally, pitfall trap sampling flattens the rank-abundance distribution and leads to overestimations of ground arthropod Shannon diversity. We conclude that the correction of the species-specific pitfall trap sampling bias is necessary for the reliability of conclusions drawn from ground arthropod field studies. We propose bias correction is a manageable task using either body mass to derive unbiased relative abundance or the average speed to derive reliable estimates of absolute abundance from pitfall trap sampling.
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    Social-ecological traps hinder rural development in southwestern Madagascar 

    Hänke, Hendrik; Barkmann, Jan; Coral, Claudia; Enfors Kaustky, Elin; Marggraf, Rainer
    Ecology and Society 2017; 22(1): Art. 42
    The semiarid Mahafaly region in southwestern Madagascar is not only a unique biodiversity hotspot, but also one of the poorest regions in the world. Crop failures occur frequently, and despite a great number of rural development programs, no effective progress in terms of improved yields, agricultural income, or well-being among farming households has been observed. In addition to the severe development challenges in the region, environmental degradation and the loss of biodiversity are prevailing issues. This paper takes a social-ecological systems perspective to analyze why the region appears locked in poverty. Specifically, we address the socialecological interaction between environmental factors such as low and variable precipitation, the lack of sustainable intensification in agriculture resulting in recalcitrant hunger, and several environmental degradation trends. The study is based on (i) longitudinal data from 150 farming households interviewed at high temporal resolution during the course of 2014, and (ii) extensive recall surveys from the southwestern Madagascar project region. The analysis reveals a complex interplay of pronounced seasonality in income generation due to recurrent droughts and crop failures making local farmers highly risk averse. This interplay results in a gradual depletion of environmental assets and hinders the accumulation of capital in the hands of smallholder farmers, and improvements in agricultural production even where environmental conditions would allow for it. As a result, households are insufficiently buffered and insured against repetitive income and food security shocks. This can be understood as a set of interacting, partly nested social-ecological traps, which entrench the Mahafalian smallholder population in deep poverty while the productivity of the environment declines. We provide new insights on the interplay between hunger, poverty, and loss of environmental assets in a global biodiversity hotspot. Finally, we propose a set of key issues that need to be considered to unlock this severe lock-in and enable transformation toward a more sustainable development in southwestern Madagascar.
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    Changing Structure and Sustainable Development for China’s Hog Sector 

    Zhang, Xiaoheng; Chu, Feng; Yu, Xiaohua; Zhou, Yingheng; Tian, Xu; Geng, Xianhui; Yang, Jinyang
    Sustainability 2017; 9(1): Art. 69
    Supply shortages and competitive disadvantages are the main problems faced by China’s hog sector. The non-essential import of pork products, triggered by competitive disadvantages, poses great challenges to hog farms. Structural changes are an important policy concern in China and elsewhere. Previous literature has ignored whether the ongoing structural changes from backyard to large farms can contribute to sustainable development. This study adopts the micro-level data of hog farms collected from Jiangsu Province, and uses a two-step metafrontier model and a primal system approach. The empirical results reveal that the ongoing structural changes are capable of boosting the growth in output in China’s hog sector, since the stronger increase in comparable technical efficiency compensates for the inappropriate technology. Furthermore, the ongoing structural changes are also beneficial in the reduction of production costs and in improving competitiveness in China’s hog sector. The decline in technical and allocative inefficiency costs, particularly for technical inefficiency costs, contributes to the cost advantage with the increasing farm size.
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    Seasonal changes in energy expenditure, body temperature and activity patterns in llamas (Lama glama). 

    Riek, Alexander; Brinkmann, Lea; Gauly, Matthias; Perica, Jurcevic; Ruf, Thomas; Arnold, Walter; Hambly, Catherine; Speakman, John R.; Gerken, Martina
    Scientific reports 2017-08-08; 7(1): Art. 7600
    Mammals typically keep their body temperature (Tb) within a narrow limit with changing environmental conditions. There are indications that some wild ungulates can exhibit certain forms of energy saving mechanisms when ambient temperatures are low and/or food is scarce. Therefore, the aim of the study was to determine if the llama, one of the most extensively kept domestic livestock species, exhibits seasonal adjustment mechanisms in terms of energy expenditure, Tb and locomotion. For that purpose llamas (N = 7) were kept in a temperate habitat on pasture. Locomotor activity, Tb (measured in the rumen) and the location of each animal were recorded continuously for one year using a telemetry system. Daily energy expenditure was measured as field metabolic rate (FMR). FMR fluctuated considerably between seasons with the lowest values found in winter (17.48 ± 3.98 MJ d-1, 402 kJ kg-0.75 d-1) and the highest in summer (25.87 ± 3.88 MJ d-1, 586 kJ kg-0.75 d-1). Llamas adjusted their energy expenditure, Tb and locomotor activity according to season and also time of day. Thus, llamas seem to have maintained the ability to reduce their energy expenditure and adjust their Tb under adverse environmental conditions as has been reported for some wild ungulates.
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    Nitrate application or P deficiency induce a decline in Medicago truncatula N2-fixation by similar changes in the nodule transcriptome. 

    Liese, Rebecca; Schulze, Joachim; Cabeza, Ricardo A.
    Scientific reports 2017-04-10; 7: Art. 46264
    Nitrogen fixation of Medicago truncatula is regulated by the nitrogen status of leaves through inducing a repeatedly occurring 24-h nodule activity rhythm that reduces per day nitrogen fixation. The hypotheses of the present study were that (1) long-term moderate whole-plant P deficiency in Medicago truncatula induces an according daily rhythm in nitrogenase activity comparable to that induced by nitrate application and (2), the changes in the nodule transcriptome that go along with a strong nitrogenase activity decline during the afternoon would be similar under P deficiency or after nitrate supply. The nodules of plants in a low P treatment developed a rhythmic pattern of activity that resembled the pattern following nitrate application. A comprehensive, RNAseq-based comparative transcriptome profiling of nodules during a repeated part of the rhythm revealed similarities between P deficiency versus nitrate supply. Under both treatments, the formation of nitrogenase was targeted by a reduction in the expression of genes for nodule-specific cysteine-rich peptides (NCR), and possibly also by a disturbance of the inner cell iron allocation. A strong reduction in the expression of leghemoglobin is likely to have restricted the supply of oxygen for respiration.
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    Adding Some Green to the Greening: Improving the EU's Ecological Focus Areas for Biodiversity and Farmers 

    Pe'er, Guy; Zinngrebe, Yves; Hauck, Jennifer; Schindler, Stefan; Dittrich, Andreas; Zingg, Silvia; Tscharntke, Teja; Oppermann, Rainer; Sutcliffe, Laura M.E.; Sirami, Clélia; et al.
    Schmidt, JennyHoyer, ChristianSchleyer, ChristianLakner, Sebastian
    Conservation Letters 2017; 10(5) p.517-530
    Ecological Focus Areas (EFAs) are one of the three new greening measures of the European Common Agricultural Policy (CAP). We used an interdisciplinary and European-scale approach to evaluate ecological effectiveness and farmers’ perception of the different EFA options. We assessed potential benefits of EFA options for biodiversity using a survey among 88 ecologists from 17 European countries. We further analyzed data on EFA uptake at the EU level and in eight EU Member States, and reviewed socio-economic factors influencing farmers’ decisions. We then identified possible ways to improve EFAs. Ecologists scored field margins, buffer strips, fallow land, and landscape features as most beneficial whereas farmers mostly implemented “catch crops and green cover,” nitrogen-fixing crops, and fallow land. Based on the expert inputs and a review of the factors influencing farmers’ decisions, we suggest that EFA implementation could be improved by (a) prioritizing EFA options that promote biodiversity (e.g., reducing the weight or even excluding ineffective options); (b) reducing administrative constraints; (c) setting stricter management requirements (e.g., limiting agrochemical use); and (d) offering further incentives for expanding options like landscape features and buffer strips. We finally propose further improvements at the next CAP reform, to improve ecological effectiveness and cost-effectiveness.
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    Nitrous oxide emissions from winter oilseed rape cultivation 

    Ruser, Reiner; Fuß, Roland; Andres, Monique; Hegewald, Hannes; Kesenheimer, Katharina; Köbke, Sarah; Räbiger, Thomas; Quinones, Teresa Suarez; Augustin, Jürgen; Christen, Olaf; et al.
    Dittert, KlausKage, HenningLewandowski, IrisProchnow, AnnetteStichnothe, HeinzFlessa, Heinz
    Agriculture, Ecosystems & Environment 2017; 249 p.57-69
    Winter oilseed rape (Brassica napus L., WOSR) is the major oil crop cultivated in Europe. Rapeseed oil is predominantly used for production of biodiesel. The framework of the European Renewable Energy Directive requires that use of biofuels achieves GHG savings of at least 50% compared to use of fossil fuel starting in 2018. However, N2O field emissions are estimated using emission factors that are not specific for the crop and associated with strong uncertainty. N2O field emissions are controlled by N fertilization and dominate the GHG balance of WOSR cropping due to the high global warming potential of N2O. Thus, field experiments were conducted to increase the data basis and subsequently derive a new WOSR-specific emission factor. N2O emissions and crop yields were monitored for three years over a range of N fertilization intensities at five study sites representative of German WOSR production. N2O fluxes exhibited the typical high spatial and temporal variability in dependence on soil texture, weather and nitrogen availability. The annual N2O emissions ranged between 0.24 kg and 5.48 kg N2O-N ha−1 a−1. N fertilization increased N2O emissions, particularly with the highest N treatment (240 kg N ha−1). Oil yield increased up to a fertilizer amount of 120 kg N ha−1, higher N-doses increased grain yield but decreased oil concentrations in the seeds. Consequently oil yield remained constant at higher N fertilization. Since, yield-related emission also increased exponentially with N surpluses, there is potential for reduction of the N fertilizer rate, which offers perspectives for the mitigation of GHG emissions. Our measurements double the published data basis of annual N2O flux measurements in WOSR. Based on this extended dataset we modeled the relationship between N2O emissions and fertilizer N input using an exponential model. The corresponding new N2O emission factor was 0.6% of applied fertilizer N for a common N fertilizer amount under best management practice in WOSR production (200 kg N ha−1 a−1). This factor is substantially lower than the linear IPCC Tier 1 factor (EF1) of 1.0% and other models that have been proposed.
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    Phenotypic diversity, major genes and production potential of local chickens and guinea fowl in Tamale, northern Ghana. 

    Brown, Michael Mensah; Alenyorege, Benjamin; Teye, Gabriel Ayum; Roessler, Regina
    Asian-Australasian journal of animal sciences 2017-10; 30(10) p.1372-1381
    OBJECTIVE: Our study provides information on phenotypes of local chickens and guinea fowl and their body measures as well as on major genes in local chickens in northern Ghana. METHODS: Qualitative and morphometric traits were recorded on 788 local chickens and 394 guinea fowl in urban households in Tamale, Ghana. RESULTS: The results showed considerable variation of color traits and numerous major genes in local chickens, while color variations and related genotypes in guinea fowl were limited. In local chickens, white was preferred for plumage, whereas dark colors were preferred for beak and shanks. More than half of the chickens carried at least one major gene, but the contributions of single gene carriers were low. All calculated allele frequencies were significantly lower than their expected Mendelian allele frequencies. We observed higher mean body weight and larger linear body measures in male as compared to female chickens. In female chickens, we detected a small effect of major genes on body weight and chest circumference. In addition, we found some association between feather type and plumage color. In guinea fowl, seven distinct plumage colors were observed, of which pearl grey pied and pearl grey were the most prevalent. Male pearl grey pied guinea fowl were inferior to pearl grey and white guinea fowl in terms of body weight, body length and chest circumference; their shank length was lower than that of pearl grey fowl. CONCLUSION: Considerable variation in qualitative traits of local chickens may be indicative of genetic diversity within local chicken populations, but major genes were rare. In contrast, phenotypic and genetic diversity in local guinea fowl is limited. Broader genetic diversity studies and evaluation of trait preferences of local poultry producers are required for the design of appropriate breeding programs.
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    Stochastic Frontier Analysis Using SFAMB for Ox 

    Holtkamp, Jonathan; Brümmer, Bernhard
    Journal of Statistical Software 2017; 81(6)
    SFAMB is a flexible econometric tool designed for the estimation of stochastic frontier models. Ox is a matrix language used in different modules, with a console version freely available to academic users. This article provides a brief introduction to the field of stochastic frontier analysis, with examples of code (input and output) as well as a technical documentation of member functions. SFAMB provides frontier models for both crosssectional data and panel data (focusing on fixed effects models). Member functions can be extended depending on the needs of the user.
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    Rural food security, subsistence agriculture, and seasonality. 

    Sibhatu, Kibrom T.; Qaim, Matin
    PloS one 2017; 12(10): Art. e0186406
    Many of the world's food-insecure and undernourished people are smallholder farmers in developing countries. This is especially true in Africa. There is an urgent need to make smallholder agriculture and food systems more nutrition-sensitive. African farm households are known to consume a sizeable part of what they produce at home. Less is known about how much subsistence agriculture actually contributes to household diets, and how this contribution changes seasonally. We use representative data from rural Ethiopia covering every month of one full year to address this knowledge gap. On average, subsistence production accounts for 58% of rural households' calorie consumption, that is, 42% of the calories consumed are from purchased foods. Some seasonal variation occurs. During the lean season, purchased foods account for more than half of all calories consumed. But even during the main harvest and post-harvest season, purchased foods contribute more than one-third to total calorie consumption. Markets are even more important for dietary quality. During all seasons, purchased foods play a much larger role for dietary diversity than subsistence production. These findings suggest that strengthening rural markets needs to be a key element in strategies to improve food security and dietary quality in the African small-farm sector.
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    Supermarket purchase contributes to nutrition-related non-communicable diseases in urban Kenya. 

    Demmler, Kathrin M.; Klasen, Stephan; Nzuma, Jonathan M.; Qaim, Matin
    PloS one 2017; 12(9): Art. e0185148
    BACKGROUND: While undernutrition and related infectious diseases are still pervasive in many developing countries, the prevalence of non-communicable diseases (NCD), typically associated with high body mass index (BMI), is rapidly rising. The fast spread of supermarkets and related shifts in diets were identified as possible factors contributing to overweight and obesity in developing countries. Potential effects of supermarkets on people's health have not been analyzed up till now. OBJECTIVE: This study investigates the effects of purchasing food in supermarkets on people's BMI, as well as on health indicators such as fasting blood glucose (FBG), blood pressure (BP), and the metabolic syndrome. DESIGN: This study uses cross-section observational data from urban Kenya. Demographic, anthropometric, and bio-medical data were collected from 550 randomly selected adults. Purchasing food in supermarkets is defined as a binary variable that takes a value of one if any food was purchased in supermarkets during the last 30 days. In a robustness check, the share of food purchased in supermarkets is defined as a continuous variable. Instrumental variable regressions are applied to control for confounding factors and establish causality. RESULTS: Purchasing food in supermarkets contributes to higher BMI (+ 1.8 kg/m2) (P<0.01) and an increased probability (+ 20 percentage points) of being overweight or obese (P<0.01). Purchasing food in supermarkets also contributes to higher levels of FBG (+ 0.3 mmol/L) (P<0.01) and a higher likelihood (+ 16 percentage points) of suffering from pre-diabetes (P<0.01) and the metabolic syndrome (+ 7 percentage points) (P<0.01). Effects on BP could not be observed. CONCLUSIONS: Supermarkets and their food sales strategies seem to have direct effects on people's health. In addition to increasing overweight and obesity, supermarkets contribute to nutrition-related NCDs. Effects of supermarkets on nutrition and health can mainly be ascribed to changes in the composition of people's food choices.
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    Gut microbiomes of mobile predators vary with landscape context and species identity. 

    Tiede, Julia; Scherber, Christoph; Mutschler, James; McMahon, Katherine D.; Gratton, Claudio
    Ecology and evolution 2017-10; 7(20) p.8545-8557
    Landscape context affects predator-prey interactions and predator diet composition, yet little is known about landscape effects on insect gut microbiomes, a determinant of physiology and condition. Here, we combine laboratory and field experiments to examine the effects of landscape context on the gut bacterial community and body condition of predatory insects. Under laboratory conditions, we found that prey diversity increased bacterial richness in insect guts. In the field, we studied the performance and gut microbiota of six predatory insect species along a landscape complexity gradient in two local habitat types (soybean fields vs. prairie). Insects from soy fields had richer gut bacteria and lower fat content than those from prairies, suggesting better feeding conditions in prairies. Species origin mediated landscape context effects, suggesting differences in foraging of exotic and native predators on a landscape scale. Overall, our study highlights complex interactions among gut microbiota, predator identity, and landscape context.
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    Performances of Different Fragment Sizes for Reduced Representation Bisulfite Sequencing in Pigs 

    Yuan, Xiao-Long; Zhang, Zhe; Pan, Rong-Yang; Gao, Ning; Deng, Xi; Li, Bin; Zhang, Hao; Sangild, Per Torp; Li, Jia-Qi
    Biological Procedures Online 2017; 19(5)
    Reduced representation bisulfite sequencing (RRBS) has been widely used to profile genome-scale DNA methylation in mammalian genomes. However, the applications and technical performances of RRBS with different fragment sizes have not been systematically reported in pigs, which serve as one of the important biomedical models for humans. The aims of this study were to evaluate capacities of RRBS libraries with different fragment sizes to characterize the porcine genome. We found that the MspI-digested segments between 40 and 220 bp harbored a high distribution peak at 74 bp, which were highly overlapped with the repetitive elements and might reduce the unique mapping alignment. The RRBS library of 110–220 bp fragment size had the highest unique mapping alignment and the lowest multiple alignment. The cost-effectiveness of the 40–110 bp, 110–220 bp and 40–220 bp fragment sizes might decrease when the dataset size was more than 70, 50 and 110 million reads for these three fragment sizes, respectively. Given a 50-million dataset size, the average sequencing depth of the detected CpG sites in the 110–220 bp fragment size appeared to be deeper than in the 40–110 bp and 40–220 bp fragment sizes, and these detected CpG sties differently located in gene- and CpG island-related regions. In this study, our results demonstrated that selections of fragment sizes could affect the numbers and sequencing depth of detected CpG sites as well as the cost-efficiency. No single solution of RRBS is optimal in all circumstances for investigating genome-scale DNA methylation. This work provides the useful knowledge on designing and executing RRBS for investigating the genome-wide DNA methylation in tissues from pigs.
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    An effective molecular approach for assessing cereal aphid-parasitoid-endosymbiont networks 

    Ye, Zhengpei; Vollhardt, Ines M. G.; Girtler, Susanne; Wallinger, Corinna; Tomanovic, Zeljko; Traugott, Michael
    Scientific Reports 2017; 7(1): Art. 3138 (2017)
    Molecular approaches are increasingly being used to analyse host-parasitoid food webs as they overcome several hurdles inherent to conventional approaches. However, such studies have focused primarily on the detection and identification of aphids and their aphidiid primary parasitoids, largely ignoring primary parasitoid-hyperparasitoid interactions or limiting these to a few common species within a small geographical area. Furthermore, the detection of bacterial secondary endosymbionts has not been considered in such assays despite the fact that endosymbionts may alter aphid-parasitoid interactions, as they can confer protection against parasitoids. Here we present a novel two-step multiplex PCR (MP-PCR) protocol to assess cereal aphid-primary parasitoid-hyperparasitoid-endosymbiont interactions. The first step of the assay allows detection of parasitoid DNA at a general level (24 primary and 16 hyperparasitoid species) as well as the species-specific detection of endosymbionts (3 species) and cereal aphids (3 species). The second step of the MP-PCR assay targets seven primary and six hyperparasitoid species that commonly occur in Central Europe. Additional parasitoid species not covered by the second-step of the assay can be identified via sequencing 16S rRNA amplicons generated in the first step of the assay. The approach presented here provides an efficient, highly sensitive, and cost-effective (~consumable costs of 1.3 € per sample) tool for assessing cereal aphid-parasitoid-endosymbiont interactions.
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    Soil nitrogen transformation responses to seasonal precipitation changes are regulated by changes in functional microbial abundance in a subtropical forest 

    Chen, Jie; Xiao, Guoliang; Kuzyakov, Yakov; Jenerette, G. Darrel; Ma, Ying; Liu, Wei; Wang, Zhengfeng; Shen, Weijun
    Biogeosciences 2017; 14(9) p.2513-2525
    The frequency of dry-season droughts and wet-season storms has been predicted to increase in subtropical areas in the coming decades. Since subtropical forest soils are significant sources of N2O and NO3−, it is important to understand the features and determinants of N transformation responses to the predicted precipitation changes. A precipitation manipulation field experiment was conducted in a subtropical forest to reduce dry-season precipitation and increase wet-season precipitation, with annual precipitation unchanged. Net N mineralization, net nitrification, N2O emission, nitrifying (bacterial and archaeal amoA) and denitrifying (nirK, nirS and nosZ) gene abundance, microbial biomass carbon (MBC), extractable organic carbon (EOC), NO3−, NH4+ and soil water content (SWC) were monitored to characterize and explain soil N transformation responses. Dry-season precipitation reduction decreased net nitrification and N mineralization rates by 13–20 %, while wet-season precipitation addition increased both rates by 50 %. More than 20 % of the total variation of net nitrification and N mineralization could be explained by microbial abundance and SWC. Notably, archaeal amoA abundance showed the strongest correlation with net N transformation rates (r  ≥  0.35), suggesting the critical role of archaeal amoA abundance in determining N transformations. Increased net nitrification in the wet season, together with large precipitation events, caused substantial NO3− losses via leaching. However, N2O emission decreased moderately in both dry and wet seasons due to changes in nosZ gene abundance, MBC, net nitrification and SWC (decreased by 10–21 %). We conclude that reducing dry-season precipitation and increasing wet-season precipitation affect soil N transformations through altering functional microbial abundance and MBC, which are further affected by changes in EOC and NH4+ availabilities.
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