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    Self-organized stress patterns drive state transitions in actin cortices 

    Tan, Tzer Han; Malik-Garbi, Maya; Abu-Shah, Enas; Li, Junang; Sharma, Abhinav; MacKintosh, Fred C.; Keren, Kinneret; Schmidt, Christoph F.; Fakhri, Nikta
    Science Advances 2018; 4(6): Art. eaar2847
    Biological functions rely on ordered structures and intricately controlled collective dynamics. This order in living systems is typically established and sustained by continuous dissipation of energy. The emergence of collective patterns of motion is unique to nonequilibrium systems and is a manifestation of dynamic steady states. Mechanical resilience of animal cells is largely controlled by the actomyosin cortex. The cortex provides stability but is, at the same time, highly adaptable due to rapid turnover of its components. Dynamic functions involve regulated transitions between different steady states of the cortex. We find that model actomyosin cortices, constructed to maintain turnover, self-organize into distinct nonequilibrium steady states when we vary cross-link density. The feedback between actin network structure and organization of stress-generating myosin motors defines the symmetries of the dynamic steady states. A marginally cross-linked state displays divergence-free long-range flow patterns. Higher cross-link density causes structural symmetry breaking, resulting in a stationary converging flow pattern. We track the flow patterns in the model actomyosin cortices using fluorescent single-walled carbon nanotubes as novel probes. The self-organization of stress patterns we have observed in a model system can have direct implications for biological functions.
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    Does the Optimal Dietary Methionine to Cysteine Ratio in Diets for Growing Chickens Respond to High Inclusion Rates of Insect Meal from Hermetia illucens? 

    Brede, Anne; Wecke, Christian; Liebert, Frank
    Animals 2018; 8(11): Art. 187
    The dietary methionine:cysteine (Met:Cys) ratio (MCR) is an important factor influencing the optimal growth of chickens. Therefore, this study aimed to contribute to the assessment of the optimal dietary MCR in diets with the complete replacement of soybean meal (SBM) by a partly defatted larvae meal of Hermetia illucens (HM). A growth study with 240 male meat-type chickens (Ross 308) was conducted, also assessing the body nutrient deposition both at the end of the starter (day 21) and the grower (day 35) period. Birds were fed experimental diets based on wheat, maize, and insect meal (23%/21% HM in starter/grower diets). Sulfur amino acids were created as the limiting AA in diets with graded MCR (40:60; 45:55; 50:50; 55:45; 60:40). The control diet contained SBM instead of HM with a MCR of 50:50. The current results based on growth parameters, dietary protein quality, and Met efficiency data gave support to the previous assumption of an ideal MCR of 50:50, which was also valid in diets with a high proportion of insect meal. The lowest MCR of 40:60 led to significantly impaired feed intake and growth of the birds, while the response to the highest MCR (60:40) was moderate.
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    Analysis of porcine body size variation using re-sequencing data of miniature and large pigs 

    Reimer, C.; Rubin, C.-J.; Sharifi, A. R.; Ha, N.-T.; Weigend, S.; Waldmann, K.-H.; Distl, O.; Pant, S. D.; Fredholm, M.; Schlather, M.; et al.
    Simianer, H.
    BMC Genomics 2018; 19(1): Art. 687
    BACKGROUND: Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in "SweepFinder", to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely FST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F2 individuals from a cross of Goettingen Minipigs and large pigs. RESULTS: Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F2 cross-breds. CONCLUSION: The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region.
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    Response of Collembola and Acari communities to summer flooding in a grassland plant diversity experiment 

    González-Macé, Odette; Scheu, Stefan
    PLOS ONE 2018; 13(8): Art. e0202862
    Flooding frequency is predicted to increase during the next decades in Europe. Therefore, it is important to understand how short-term disturbance events affect soil biota providing essential ecosystem functions and uncover factors modulating their response such as plant community composition. Here we report on the response of soil microarthropod communities (Collembola and Acari) to a severe summer flood in 2013, which affected major parts of central Europe. Collembola and Acari density and Collembola and Oribatida richness were strongly affected by the flood, but they recovered within three months. Effects of plant community composition on soil microarthropods disappeared after the flood, presumably due to homogenization of the field, but the effects of plant community were in a stage of being reasserted three months after the flood. Widespread, surface living and generalistic microarthropod species recolonized the field quickly. Prostigmata and Oribatida were more resilient or recovered to flooding than Astigmata and Gamasida. Long-term impacts, however, remain unknown and deserve further investigation.
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    Identification and validation of reference genes for qPCR in the terrestrial gastropod Cepaea nemoralis 

    Affenzeller, Susanne; Cerveau, Nicolas; Jackson, Daniel John
    PLOS ONE 2018; 13(8): Art. e0201396
    Identifying and understanding mechanisms that generate phenotypic diversity is a fundamental goal of evolutionary biology. With a diversity of pigmented shell morphotypes governed by Mendelian patterns of inheritance, the common grove snail Cepaea nemoralis (Linnaeus, 1758) has been a model for evolutionary biologists and population geneticists for decades. However, the genetic mechanisms by which C. nemoralis generates this pigmented shell diversity remain unknown. An important first step in investigating this pigmentation pattern is to establish a set of validated reference genes for differential gene expression assays. Here we have evaluated eleven candidate genes for reverse transcription quantitative polymerase chain reaction (qPCR) in C. nemoralis. Five of these were housekeeping genes traditionally employed as qPCR reference genes in other species, while six alternative genes were selected de novo from C. nemoralis transcriptome data based on the stability of their expression levels. We tested all eleven candidates for expression stability in four sub-adult tissues of C. nemoralis: pigmented mantle, unpigmented mantle, head and foot. We find that two commonly employed housekeeping genes (alpha tubulin, glyceraldehyde 3-phosphate dehydrogenase) are unsuitable for use as qPCR reference genes in C. nemoralis. The traditional housekeeping gene UBIquitin on the other hand performed very well. Additionally, an RNAdirected DNA polymerase (RNAP), a Potassium Channel Protein (KCHP) and a Prenylated Rab acceptor protein 1 (PRAP), identified de novo from transcriptomic data, were the most stably expressed genes in different tissue combinations. We also tested expression stability over two seasons and found that, although other genes are more stable within a single season, beta actin (BACT) and elongation factor 1 alpha (EF1α) were the most reliable reference genes across seasons.
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    Using imaging photoplethysmography for heart rate estimation in non-human primates 

    Unakafov, Anton M.; Möller, Sebastian; Kagan, Igor; Gail, Alexander; Treue, Stefan; Wolf, Fred
    PLOS ONE 2018; 13(8): Art. e0202581
    For humans and for non-human primates heart rate is a reliable indicator of an individual's current physiological state, with applications ranging from health checks to experimental studies of cognitive and emotional state. In humans, changes in the optical properties of the skin tissue correlated with cardiac cycles (imaging photoplethysmogram, iPPG) allow noncontact estimation of heart rate by its proxy, pulse rate. Yet, there is no established simple and non-invasive technique for pulse rate measurements in awake and behaving animals. Using iPPG, we here demonstrate that pulse rate in rhesus monkeys can be accurately estimated from facial videos. We computed iPPGs from eight color facial videos of four awake head-stabilized rhesus monkeys. Pulse rate estimated from iPPGs was in good agreement with reference data from a contact pulse-oximeter: the error of pulse rate estimation was below 5% of the individual average pulse rate in 83% of the epochs; the error was below 10% for 98% of the epochs. We conclude that iPPG allows non-invasive and non-contact estimation of pulse rate in non-human primates, which is useful for physiological studies and can be used toward welfare-assessment of non-human primates in research.
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    Analysis of Energy Dissipation Channels in a Benchmark System of Activated Dissociation: N2 on Ru(0001). 

    Shakouri, Khosrow; Behler, Jörg; Meyer, Jörg; Kroes, Geert-Jan
    The Journal of Physical Chemistry. C, Nanomaterials and Interfaces 2018; 122(41) p.23470-23480
    The excitation of electron-hole pairs in reactive scattering of molecules at metal surfaces often affects the physical and dynamical observables of interest, including the reaction probability. Here, we study the influence of electron-hole pair excitation on the dissociative chemisorption of N2 on Ru(0001) using the local density friction approximation method. The effect of surface atom motion has also been taken into account by a high-dimensional neural network potential. Our nonadiabatic molecular dynamics simulations with electronic friction show that the reaction of N2 is more strongly affected by the energy transfer to surface phonons than by the energy loss to electron-hole pairs. The discrepancy between the computed reaction probabilities and experimental results is within the experimental error both with and without friction; however, the incorporation of electron-hole pairs yields somewhat better agreement with experiments, especially at high collision energies. We also calculate the vibrational efficacy for the N2 + Ru(0001) reaction and demonstrate that the N2 reaction is more enhanced by exciting the molecular vibrations than by adding an equivalent amount of energy into translation.
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    Functional diversity changes over 100 yr of primary succession on a volcanic island: insights into assembly processes 

    Karadimou, E.; Kallimanis, A. S.; Tsiripidis, I.; Raus, T.; Bergmeier, E.; Dimopoulos, P.
    Ecosphere 2018; 9(9): Art. e02374
    Changes in species diversity following volcanic eruptions have been studied extensively, but our knowledge on functional diversity and community assembly under such conditions is very limited. Here, we study the processes following the destruction of vegetation after a volcanic eruption. Specifically, we investigate (1) the temporal patterns of taxonomic and functional diversity over time since a previous eruption (alpha diversity) and beta diversity, (2) the temporal patterns of 26 individual traits (vegetative characteristics, plant taxa ecological preferences, and regenerative characteristics) providing more detailed information on species strategies at the initial and later stages of succession, and (3) the processes driving species assembly and whether they changed over time since the eruption an eruption. We analyzed data recorded during five floristic censuses that took place between 1911 and 2011, calculated alpha and beta facets of taxonomic and functional diversity and examined how community structure changed over time, using 26 functional characteristics, based on their ability to discern primary from later colonists, including longevity, growth form, Ellenberg’s indicator values, seed production and weight, flower size and sex, pollination type, and dispersal mode. Null model analysis was used to test whether the observed functional diversity deviates from random expectations. Alpha diversity, both taxonomic and functional, increased over time after an eruption, while beta diversity did not display a clear trend. This finding indicates that mainly abiotic processes determine species assembly over time after an eruption (at least for the time span studied here), contrary to theoretical expectations. It is most interesting that, simultaneously, some aspects of diversity indicated the effect of biotic interactions (facilitation and competition) on the assembly of species a few years after an eruption. This finding implies a legacy effect, since a high percentage of perennial species was noticed in the assemblage right after the eruption, as well as the effect of the harsh environmental conditions on the assembly of the plant communities. In conclusion, our results indicate the role of legacy effects in succession (most probably through the survival of underground plant parts) and underline the importance of disturbance history in providing the context needed for understanding effects of past events on succession.
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    Conceptual model development using a generic Features, Events, and Processes (FEP) database for assessing the potential impact of hydraulic fracturing on groundwater aquifers 

    Tatomir, Alexandru; McDermott, Christopher; Bensabat, Jacob; Class, Holger; Edlmann, Katriona; Taherdangkoo, Reza; Sauter, Martin
    Advances in Geosciences 2018; 45 p.185-192
    Hydraulic fracturing for natural gas extraction from unconventional reservoirs has not only impacted the global energy landscape but has also raised concerns over its potential environmental impacts. The concept of “features, events and processes” (FEP) refers to identifying and selecting the most relevant factors for safety assessment studies. In the context of hydraulic fracturing we constructed a comprehensive FEP database and applied it to six key focused scenarios defined under the scope of FracRisk project (http://www.fracrisk.eu, last access: 17 August 2018). The FEP database is ranked to show the relevance of each item in the FEP list per scenario. The main goal of the work is to illustrate the FEP database applicability to develop a conceptual model for regional-scale stray gas migration.
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    Diffusion limitations and Michaelis–Menten kinetics as drivers of combined temperature and moisture effects on carbon fluxes of mineral soils 

    Moyano, Fernando Esteban; Vasilyeva, Nadezda; Menichetti, Lorenzo
    Biogeosciences 2018; 15(16) p.5031-5045
    CO2 production in soils responds strongly to changes in temperature and moisture, but the magnitude of such responses at different timescales remains difficult to predict. Knowledge of the mechanisms leading to the often observed interactions in the effects of these drivers on soil CO2 emissions is especially limited. Here we test the ability of different soil carbon models to simulate responses measured in soils incubated at a range of moisture levels and cycled through 5, 20, and 35 C. We applied parameter optimization methods while modifying two structural components of models: (1) the reaction kinetics of decomposition and uptake and (2) the functions relating fluxes to soil moisture. We found that the observed interactive patterns were best simulated by a model using Michaelis–Menten decomposition kinetics combined with diffusion of dissolved carbon (C) and enzymes. In contrast, conventional empirical functions that scale decomposition rates directly were unable to properly simulate the main observed interactions. Our best model was able to explain 87% of the variation in the data. Model simulations revealed a central role of Michaelis– Menten kinetics as a driver of temperature sensitivity variations as well as a decoupling of decomposition and respiration C fluxes in the short and mid-term, with general sensitivities to temperature and moisture being more pronounced for respiration. Sensitivity to different model parameters was highest for those affecting diffusion limitations, followed by activation energies, the Michaelis–Menten constant, and carbon use efficiency. Testing against independent data strongly validated the model (R2 D 0:99) and highlighted the importance of initial soil C pool conditions. Our results demonstrate the importance of model structure and the central role of diffusion and reaction kinetics for simulating and understanding complex dynamics in soil C.
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    Proglacial streams and their chronology in the glacier forefields of the Himalayas 

    Tombrink, Gerrit
    E&G Quaternary Science Journal 2018; 67(1) p.33-36
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    Does graded substitution of soy protein concentrate by an insect meal respond on growth and N-utilization in Nile tilapia (Oreochromis niloticus)? 

    Dietz, C.; Liebert, F.
    Aquaculture Reports 2018; 12 p.43-48
    Besides fishmeal, soybean protein is the most common protein source in aquafeed. However, the sustainability of soybean production is criticized. Due to the rapid development of aquaculture, the increasing demand for high value feed proteins has initiated research into alternative and more sustainable proteins for aquafeeds. In order to evaluate one promising alternative protein source, a growth study (56 days) was conducted with juvenile Nile tilapia (Oreochromis niloticus, 35 g on average) with a partial substitution of soybean protein by a partly defatted insect meal from black soldier fly larvae (Hermetia illucens). Growth performance, feed utilization and dietary protein quality parameters were evaluated based on analysed body protein deposition. A control feed (8% fish meal, 37% soy protein concentrate (SPC)) and three iso-nitrogenous and iso-energetic experimental feeds with 25, 50 or 100% replacement of SPC by partly defatted Hermetia meal (HM) were formulated. All feeds supplied essential amino acids as recommended for Nile tilapia. Growth response and protein utilization were examined in a semi-closed in-door water recirculation system. A comparative slaughter technique was applied to generate N deposition data for protein quality evaluation based on the standardized net protein utilization (NPUstd) according to the “Goettingen approach”. All feeds were very well accepted. Replacement of SPC by HM up to 50% improved feed protein quality and result in similar specific growth rate and feed conversion ratio, respectively. However, a higher inclusion rate of HM tended to impair growth, but not the observed protein quality. In conclusion, the replacement of SPC by partly defatted HM up to a level of 50% had no negative effect on growth performance and improved the dietary protein quality of tilapia feeds under study. Insect protein from Hermetia illucens could be a promising option to make aquafeed formulation more flexible and sustainable.
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    mRNA expression profiling in cotyledons reveals significant up-regulation of the two bovine pregnancy-associated glycoprotein genes boPAG-8 and boPAG-11 in early gestation 

    Wiedemann, Isabel; Krebs, Tony; Momberg, Niklas; Knorr, Christoph; Tetens, Jens
    Veterinary Medicine and Science
    The multigene family of pregnancy-associated glycoproteins (PAGs) belongs to a group of aspartic proteases that are exclusively expressed by trophoblast cells in the placenta of even-toed ungulates. In Bovidae, 22 different PAG genes (boPAGs) with a wide range of temporal and spatial expression- and glycosylation patterns have been reported to date. In this study we describe the mRNA expression patterns using real-time quantitative PCR (qPCR) for selected modern (boPAG-1, -9, -21) and ancient bovine PAGs (boPAG-2, -8, -10, -11, - 12) in cotyledonary tissue. The highest mean expression was detected in boPAG-8 and lowest in boPAG-10 (P < 0.05). Furthermore, boPAG-8 and -11 were significantly greater expressed in early gestation compared with later pregnancy stages. The characterization of boPAG mRNA-expression levels gives important insights for further protein analyses which will be valuable information for the development of new pregnancy detection systems.
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    N Balance Studies Emphasize the Superior Protein Quality of Pig Diets at High Inclusion Level of Algae Meal (Spirulina platensis) or Insect Meal (Hermetia illucens) when Adequate Amino Acid Supplementation Is Ensured 

    Neumann, Carmen; Velten, Susanne; Liebert, Frank
    Animals 2018; 8(10): Art. 172
    Two age-dependent nitrogen (N) balance studies (average body mass 25 and 60 kg) utilized 16 male castrated piglets and 16 barrows to measure N utilization parameters of diets with complete substitution of SBM by alternative protein sources (SM, HM), but different AA fortifications. Lysine supplementation up to 80% of the recommended lysine (Lys) supply in diets HM (A) and SM (A) yielded similar protein quality data (63.6 ± 2.1 and 63.7 ± 3.4). Surprisingly, only in piglet diet HM (AA) did the extended AA supplementation (Lys, methionine (Met), threonine (Thr)) enhance protein quality (72.8 ± 6.7) significantly (p = 0.004). Similar trends were observed in growing pigs. However, when the level of histidine (His) in diet SM (AA) was increased, feed protein quality (71.8 ± 1.3) was significantly (p < 0.001) improved indicating the importance of adequate His supply in diets with a complete substitution of SBM by the algae meal (SM) under study. AA efficiency data extend the possibilities to explain the observed responses on protein quality. When an adequate AA balancing in the diet is guaranteed, from nutritional point of view both of the alternative proteins may replace SBM in pig diets.
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    Carcass Quality, Meat Quality and Sensory Properties of the Dual-Purpose Chicken Lohmann Dual 

    Siekmann, Lisa; Meier-Dinkel, Lisa; Janisch, Sabine; Altmann, Brianne; Kaltwasser, Claudia; Sürie, Christian; Krischek, Carsten
    Foods 2018; 7(10): Art. 156
    Over 40 million day-old layer line cockerels are culled in Germany each year, due to economic reasons, leading to a recently instigated research focus on the potential of dual-purpose breeds as an alternative to conventional poultry husbandry, especially the practice of culling. This paper aims to explore and assess the dual-purpose chicken breed “Lohmann Dual” (LD) performance (n = 30) and sensory characteristics (n = 48). Carcass and meat quality traits are evaluated, and descriptive sensory analysis of breast muscles is conducted. To define the scope of characteristics, a market sample of “Ross” Line (n = 35) is adducted. LD carcasses are characterized by higher leg than breast yield; carcass, breast and leg weights are higher in Ross. LD meat has a lower pH, differs in color, has higher drip and thawing losses, but lower cooking loss. LD breast muscles are firmer as indicated by shear force measurements, which is confirmed through the sensory analysis. Appearance, odor and flavor differ between the lines. Overall, distinguishable differences are found between both breeds. Further research should focus on the marketing aspect of the dual-purpose line, as some characteristics could draw consumers to this product. Animal welfare and ethical concerns should further be considered when considering dual-purpose breeds as a feasible alternative to culling.
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    Grassland renovation has important consequences for C and N cycling and losses 

    Kayser, Manfred; Müller, Jürgen; Isselstein, Johannes
    Food and Energy Security: Art. e00146
    Sward degradation is a serious threat to the functioning of agricultural grassland and the provision of ecosystem services. Renovation measures are frequently applied to restore degraded swards. The success is highly variable, and substantial trade- offs can be related to the process of renovation. This paper starts with a general classifica- tion of renovation measures and then investigates the processes that are directly re- lated to renovation and lead to a change in botanical composition and affect soil functions and C and N fluxes. These processes are strongly interrelated and depend- ent on site, climate, and management condition as well as on the timescale. The more an existing and degraded sward is deliberately disturbed prior to a renovation meas- ure, for example, by ploughing, the stronger will be the change in sward composi- tion, and the stronger will be the potential yield and quality advantage. However, the risk of a release of soil organic C and N emissions to the environment will also in- crease. These emissions will usually decrease in time, but so will the positive effects on sward composition. This demonstrates that the renovation of swards is normally the second best solution and a proper and well- adapted grassland utilization and management should be adopted to avoid degradation in the first place.
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    How Rainforest Conversion to Agricultural Systems in Sumatra (Indonesia) Affects Active Soil Bacterial Communities 

    Berkelmann, Dirk; Schneider, Dominik; Engelhaupt, Martin; Heinemann, Melanie; Christel, Stephan; Wijayanti, Marini; Meryandini, Anja; Daniel, Rolf
    Frontiers in Microbiology 2018; 9: Art. 2381
    Palm oil production in Indonesia increased constantly over the last decades, which led to massive deforestation, especially on Sumatra island. The ongoing conversion of rainforest to agricultural systems results in high biodiversity loss. Here, we present the first RNA-based study on the effects of rainforest transformation to rubber and oil palm plantations in Indonesia for the active soil bacterial communities. For this purpose, bacterial communities of three different converted systems (jungle rubber, rubber plantation, and oil palm plantation) were studied in two landscapes with rainforest as reference by RT-PCR amplicon-based analysis of 16S rRNA gene transcripts. Active soil bacterial communities were dominated by Frankiales (Actinobacteria), subgroup 2 of the Acidobacteria and Alphaproteobacteria (mainly Rhizobiales and Rhodospirillales). Community composition differed significantly between the converted land use systems and rainforest reference sites. Alphaproteobacteria decreased significantly in oil palm samples compared to rainforest samples. In contrast, relative abundances of taxa within the Acidobacteria increased. Most important abiotic drivers for shaping soil bacterial communities were pH, calcium concentration, base saturation and C:N ratio. Indicator species analysis showed distinct association patterns for the analyzed land use systems. Nitrogen-fixing taxa including members of Rhizobiales and Rhodospirillales were associated with rainforest soils while nitrifiers and heat-resistant taxa including members of Actinobacteria were associated with oil palm soils. Predicted metabolic profiles revealed that the relative abundances of genes associated with fixation of nitrogen significantly decreased in plantation soils. Furthermore, predicted gene abundances regarding motility, competition or gene transfer ability indicated rainforest conversion-induced changes as well.
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    Urbanization Leads to Increases in pH, Carbonate, and Soil Organic Matter Stocks of Arable Soils of Kumasi, Ghana (West Africa) 

    Asabere, Stephen Boahen; Zeppenfeld, Thorsten; Nketia, Kwabena Abrefa; Sauer, Daniela
    Frontiers in Environmental Science 2018; 6: Art. 19
    Tropical soils typically have low cation exchange capacity and nutrient contents. Both are enhanced by soil organic matter (SOM), which is thus particularly important for the fertility of these soils. In this study, we assessed the influence of urbanization on SOM, carbonate contents and pH of arable soils of Kumasi (Ghana, West Africa), since rapid urban sprawl is widespread in West Africa, whereby in many West African cities urban farming is pivotal to the food security of their population. Based on satellite imagery for the year 1986, we defined long-term and short-term urban arable soils, whereby long-term urban soils were urban already in 1986 (thus ≥30 years, as soil sampling took place in 2016), and short-term urban soils became urban afterwards (<30 years). We took 618 undisturbed topsoil samples (0–10 cm) from 206 urban arable fields. The factors land-use (maize fields) and soil (Ferric Acrisols) were kept largely constant. The fine-earth was analyzed for pH (water), carbonate contents, loss on ignition (LOI), total C (TC) and N (TN). SOM contents were obtained from LOI (SOMLOI). All element contents were transformed to bulk soil element stocks per m2. Differences between short-term and long-term urban soils were identified by a set of linear mixed models. Coarse fragments were more abundant in the long-term (16%) compared to the short-term (10%) urban soils, because of solid municipal waste that accumulates over time in urban soils. TC and SOMLOI concentrations of the fine earth, pH and C/N ratios were all significantly higher in the long-term urban soils. SOC concentrations in the fine earth, as well as bulk soil stocks of TC, SOC, and SOMLOI were also higher in the long-term urban soils, but at a lower degree of confidence, due to variable bulk densities and contents of coarse fragments. We conclude that dumping of organic and inorganic waste (including ash, bones, egg shells, concrete and mortar) increases SOM stocks and soil pH, but also leads to accumulation of non-degradable solid materials (including plastic, metals etc.). These findings point to the need of an improved urban waste management system, separating degradable and non-degradable waste.
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    A perforated anodised aluminium slide for improved specimen clearing and imaging for confocal laser scanning microscopy 

    Quade, Felix S. C.; Preitz, Beate; Prpic, Nikola-Michael
    2018; 11(1): Art. 716
    Objective The bleaching, clearing and handling of tiny specimens with soft tissue and cuticular components for confocal laser scanning microscopy is difficult, because after cuticle bleaching and tissue clearing the specimens are virtually invisible. We have adjusted the design of the specimen container described by Smolla et al. (Arthropod Struct Dev 43:175–81, 2014) to handle tiny specimens. Results We describe a perforated and anodised aluminium slide that was designed to hold the distal tips of the pedipalp appendages of the spider Parasteatoda tepidariorum during clearing, and that can then be used directly for confocal laser scanning microscopy. We believe that this slide design will be helpful for others who want to visualise specimens between 500 and 800 µm with confocal laser scanning microscopy.
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    RAD sequencing resolved phylogenetic relationships in European shrub willows (Salix L. subg. Chamaetia and subg. Vetrix) and revealed multiple evolution of dwarf shrubs 

    Wagner, Natascha Dorothea; Gramlich, Susanne; Hörandl, Elvira
    Ecology and Evolution 2018; 8(16) p.8243-8255
    The large and diverse genus Salix L. is of particular interest for decades of biological research. However, despite the morphological plasticity, the reconstruction of phylogenetic relationships was so far hampered by the lack of informative molecular markers. Infrageneric classification based on morphology separates dwarf shrubs (subg. Chamaetia) and taller shrubs (subg. Vetrix), while previous phylogenetic studies placed species of these two subgenera just in one largely unresolved clade. Here we want to test the utility of genomic RAD sequencing markers for resolving relationships at different levels of divergence in Salix. Based on a sampling of 15 European species representing 13 sections of the two subgenera, we used five different RAD sequencing datasets generated by ipyrad to conduct phylogenetic analyses. Additionally we reconstructed the evolution of growth form and analyzed the genetic composition of the whole clade. The results showed fully resolved trees in both ML and BI analysis with high statistical support. The two subgenera Chamaetia and Vetrix were recognized as nonmonophyletic, which suggests that they should be merged. Within the Vetrix/Chamaetia clade, a division into three major subclades could be observed. All species were confirmed to be monophyletic. Based on our data, arctic-alpine dwarf shrubs evolved four times independently. The structure analysis showed five mainly uniform genetic clusters which are congruent in sister relationships observed in the phylogenies. Our study confirmed RAD sequencing as a useful genomic tool for the reconstruction of relationships on different taxonomic levels in the genus Salix.
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