Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Typology of vulnerability of wheat farmers in Northeast Iran and implications for their adaptive capacity
    Nazari Nooghabi, Saeedeh ; Fleskens, Luuk ; Sietz, Diana ; Azadi, Hossein - \ 2019
    Climate and Development (2019). - ISSN 1756-5529
    climate risk - patterns - Socio-ecological - vulnerability scoping diagram - wheat farmers

    This study is focused on understanding sources and patterns of vulnerability of wheat smallholder farmers in Northeast Iran. We conducted a farm household survey and recorded multiple environmental and socio-economic attributes of 391 wheat smallholder farmers. A Vulnerability Scoping Diagram and Principal Component Analysis served to identify key factors determining wheat farmer's vulnerability. Also, we performed a cluster analysis to classify wheat farmers into three vulnerability types. Although drought affects all types as main environmental stressor, only for Cluster 2 was it the key vulnerability factor. For Clusters 1 and 3 socio-economic vulnerability components prevailed: for farmers categorized in Cluster 1 land consolidation was the main problem, while the current wheat import policy was the key problem for Cluster 3 farmers. Multiple tailored policies are needed that reduce the vulnerability of wheat farmers in all clusters. Supportive government policies should for example focus on avoiding price distortions from wheat imports for Cluster 3, land consolidation for Cluster 1 and collective tackling of pests and weeds for Cluster 2. Simultaneous provision of farm advisory services will benefit farmers of Clusters 1 and 3, while availability of improved seeds (drought-tolerant varieties) and other inputs will lower the environmental vulnerability of all farmers.

    Modeling spatial pattern formation in plant development
    Adibi, Milad - \ 2017
    Wageningen University. Promotor(en): V. dos Santos, co-promotor(en): C. Fleck. - Wageningen : Wageningen University - ISBN 9789462956896 - 209
    plant development - mathematical models - patterns - arabidopsis thaliana - vascular system - xylem - auxins - modeling - systems biology - plantenontwikkeling - wiskundige modellen - patronen - arabidopsis thaliana - vaatsysteem - xyleem - auxinen - modelleren - systeembiologie

    Modern biological research is accumulating an ever-increasing amount of information on genes and their functions. It is apparent that biological functions can very rarely be attributed to a single genes, but rather arise from complex interaction within networks that comprise many genes. A fundamentally important challenge in contemporary biology is to extract mechanistic understanding about the complex behavior of genetic networks from the available data. The interactions within a genetic network are often exceedingly complex and no-linear in nature, and thus are not open to intuitive understanding. This situation has given rise to a host of mathematical and computational approaches aimed at in-depth analysis of genetic network topologies and dynamics. In particular these approaches focus on system level proprieties of these networks, not directly derivable from their constituent components. To a large extent the power of these theoretical approaches rely on meaningful reduction in complexity by utilizing justified simplifications and abstractions. The underlying principle is that in order to comprehend a mechanism, it is not necessary to take into account all the available information about the mechanism. Given this, Computational models that follow this approach focus on incorporating core components that are essential in answering a specific biological question, while simplifying/omitting the less relevant processes. A fundamental question is this regard is what simplifying concept should be employed when developing a theoretical model of a genetic network.

    A successful approach to address this question is the notion of network motif analysis. This approach is based on the core idea that most genetic networks are not arbitrary nor unique, instead they can be categorized into common network dynamics and topologies that perform core functions. Analogous to components of an electric circuit (resistors, capacitor, etc.) these network motifs have distinct properties that are independent of the network that they are embedded in. Therefore analysis of genetic networks in terms of their constituent motifs can potentially be an effective mean in obtaining mechanistic understanding about them.

    In this thesis the network motif approach is utilized to study two instances of pattern formation in plant tissues. The first study focuses on organization of stem cells within the shoot apical meristem of the model plant, Arabidopsis thaliana. The results demonstrate that three interconnected network motifs can account for a range of experimental observations regarding this system. Furthermore through an exhaustive exploration of the available data, candidate genes and interactions corresponding to these motifs are outlined, thus paving the way for future interdisciplinary investigations.

    The second study explores the development of vasculature during arabidopsis embryogenesis. In contrast to shoot apical mersitem in mature plant, the cell number and arrangement of vasculature in highly dynamic during its embryonic development. To account for this feature, a computational framework was utilized that is capable of capturing the interplay between genes and cell growth and division. The outcome revealed that two interlocking networks motifs dynamically control both patterning and growth of the vascular tissue. The study revealed novel spatial features of a motif previously studies exclusively in non-spatial settings. Furthermore the study resulted in a compelling example of model-driven discovery, where theoretical analysis predicted a specific cellular arrangement to be crucial for the correct development of vasculature. Subsequent analysis of experimental data confirmed the existence of this cellular arrangement in the embryo.

    The projects presented in this thesis exemplify successful applications of the network motif approach in studying spatial genetic network. In both cases the networks were successfully examined in terms of their constituent motifs, which subsequently lead to increased mechanistic understanding of them. Ultimately the work presented in this thesis demonstrates the effectiveness of studying genetic networks by a combination of careful examination of available biological data and a reductionist modeling approach guided by the concept of network motifs.

    The interplay between mouth and mind : explaining variation in taste-related brain activation
    Rijn, Inge van - \ 2016
    Wageningen University. Promotor(en): Kees de Graaf, co-promotor(en): Paul Smeets. - Wageningen : Wageningen University - ISBN 9789462579040 - 156
    taste research - magnetic resonance imaging - brain - patterns - satiety - hunger - calories - smaakonderzoek - kernspintomografie - hersenen - patronen - verzadigdheid - honger - calorieën

    Food does not always ‘taste’ the same. During hunger, for example, food may be tastier compared to during satiety. Many other internal and external factors affect the way we experience our food and make it a dynamic process. Our brain is responsible for weighing and integrating these factors and forms the final consumption experience. Mapping the impact of all factors that influence the consumption experience is of fundamental importance for understanding why we eat the way we eat. Important drivers for food consumption are its rewarding capacity, healthiness and caloric content. Furthermore, in the current supermarket environment, advertisements and food claims are omnipresent, and may exert influence on our consumption experience by triggering all kinds of cognitive processes. Therefore, in this thesis we aimed to assess the effect of food content (caloric content and sugar type), character (personality trait reward sensitivity and attitude health-interest) and cognitive effects (labeling/claim effects and selective attention to food properties) on brain activation during tasting. Such taste-related brain responses were obtained with the use of functional Magnetic Resonance Imaging while administering small sips of liquid to young, normal weight female participants in a MRI scanner.

    To begin with, we focussed on the effect of caloric content on taste responses (Chapter 2). An important function of eating is ingesting energy, and the ability to sense energy in the oral cavity would therefore be biologically relevant. However, in this thesis we showed that oral exposure to caloric (maltodextrin and maltodextrin + sucralose) and non-caloric (sucralose) stimuli does not elicit discriminable responses in the brain when averaged over hunger and satiety. Nevertheless, energy content did interact with hunger state in several brain regions involved in inhibition (approach-avoidance behaviors) and gustation: the middle cingulate cortex, ventrolateral prefrontal cortex, anterior insula and thalamus. Thus, brain activation in response to oral calories, irrespective of sweetness, seems to be dependent on hunger state.

    In addition to the detection of oral calories in general, we examined whether different sugar types, glucose and fructose, can be sensed in the oral cavity (Chapter 3). Tasting glucose compared to fructose evoked greater food reward (anterior cingulate cortex, ACC) activation during hunger and greater food motivation (precentral gyrus) activation during hunger and satiety. Responses to oral fructose relative to glucose were greater only during satiety in an area associated with inhibitory control (superior frontal gyrus). It appears that oral glucose and fructose evoke differential brain responses, independent of sweetness.

    Secondly, we investigated in how far reward sensitivity, a personality trait, affected brain responses to calories in the oral cavity (Chapter 4). This because a food’s reward value is highly dependent on its caloric content. Sensitivity to rewards was measured with the Behavioral Activation System Drive scale and was correlated with oral calorie activation from a simple maltodextrin solution and a sucrose sweetened soft drink. Oral calorie activation was obtained by subtracting activation by a non-caloric solution (sucralose solution/non-caloric soft drink) from that by a caloric solution (maltodextrin + sucralose/sucrose sweetened soft drink). We found that neural responses to oral calories from a maltodextrin solution are modulated by reward sensitivity in reward-related areas such as the caudate, amygdala, and ACC. For soft drinks, we found no correlations with reward sensitivity in any reward related area. This discrepancy may be due to the direct detection of maltodextrin, but not sucrose in the oral cavity. However, the absence of this effect in a familiar soft drink warrants further research into its relevance for real life ingestive behavior.

    In the last part of this thesis we explored how cognitions modulate the consumption experience. Perceived, rather than actual caloric content, inflicted by calorie food labels, induces cognitive processes that may influence the consumption experience on their own. We tested this in an experiment and found that receipt of a beverage perceived as low- compared to high-caloric induced more activation in the dorsal striatum, a region involved in coding food reward (Chapter 5). As low-calorie labels may appeal especially to the health-minded consumers, we correlated brain responses to the receipt of a beverage perceived as low- compared to high-caloric with health interest (measured with the General health interest subscale of the Health and Taste Attitude Scales). Indeed, health interest scores correlated positively with activation in the dorsal striatum.

    Rather than focussing participants’ attention on differences within one food aspect, in Chapter 6 we focussed on selective attention to different food aspects, i.e. pleasantness versus taste intensity versus calories. In the supermarket, food labels and claims often do the same. In the first place, paying attention to hedonics, caloric content or taste intensity predominantly resulted in common brain activation in regions involved in the neural processing of food stimuli, e.g. the insula and thalamus. This likely resulted from ‘bottom-up’ sensory effects, which are more prominent than ‘top-down’ attentional effects. However, small differences were also observed; taste activation was higher during selective attention to intensity compared to calories in the right middle orbitofrontal cortex and during selective attention to pleasantness compared to intensity in the right putamen, right ACC and bilateral middle insula. Overall, these results indicate that statements regarding food properties can alter the consumption experience through attention-driven effects on the activation of gustatory and reward regions.

    Finally, the general discussion (Chapter 7) describes main finding and conclusions of this thesis. In sum, we showed that food energy content, sugar type, trait reward sensitivity, health interest, food labels and selective attention all modulate taste-related brain activation. In conclusion, these findings indicate that the formation of the final consumption experience is a very multifaceted process that dependents on numerous factors integrated by the brain, of which we are just beginning to grasp its complexity.

    Environmental proxies of antigen exposure explain variation in immune investment better than indices of pace of life
    Horrocks, N.P.C. ; Hegemann, A. ; Ostrowski, S. ; Ndithia, H. ; Shobrak, M. ; Williams, J.B. ; Matson, K.D. ; Tieleman, B.I. - \ 2015
    Oecologia 177 (2015)1. - ISSN 0029-8549 - p. 281 - 290.
    female pied flycatchers - tropical birds - trade-offs - ecological immunology - microbial diversity - natural antibodies - aridity gradient - south-africa - history - patterns
    Investment in immune defences is predicted to covary with a variety of ecologically and evolutionarily relevant axes, with pace of life and environmental antigen exposure being two examples. These axes may themselves covary directly or inversely, and such relationships can lead to conflicting predictions regarding immune investment. If pace of life shapes immune investment then, following life history theory, slow-living, arid zone and tropical species should invest more in immunity than fast-living temperate species. Alternatively, if antigen exposure drives immune investment, then species in antigen-rich tropical and temperate environments are predicted to exhibit higher immune indices than species from antigen-poor arid locations. To test these contrasting predictions we investigated how variation in pace of life and antigen exposure influence immune investment in related lark species (Alaudidae) with differing life histories and predicted risks of exposure to environmental microbes and parasites. We used clutch size and total number of eggs laid per year as indicators of pace of life, and aridity, and the climatic variables that influence aridity, as correlates of antigen abundance. We quantified immune investment by measuring four indices of innate immunity. Pace of life explained little of the variation in immune investment, and only one immune measure correlated significantly with pace of life, but not in the predicted direction. Conversely, aridity, our proxy for environmental antigen exposure, was predictive of immune investment, and larks in more mesic environments had higher immune indices than those living in arid, low-risk locations. Our study suggests that abiotic environmental variables with strong ties to environmental antigen exposure can be important correlates of immunological variation.
    Minor differences in body condition and immune status between avian influenza virus-infected and noninfected mallards: a sign of coevolution?
    Dijk, J.G.B. van; Fouchier, R.A.M. ; Klaassen, M. ; Matson, K.D. - \ 2015
    Ecology and Evolution 5 (2015)2. - ISSN 2045-7758 - p. 436 - 449.
    a virus - anas-platyrhynchos - natural antibodies - stable hydrogen - wild birds - vice-versa - ducks - patterns - migration - isotopes
    Wildlife pathogens can alter host fitness. Low pathogenic avian influenza virus (LPAIV) infection is thought to have negligible impacts on wild birds; however, effects of infection in free-living birds are largely unstudied. We investigated the extent to which LPAIV infection and shedding were associated with body condition and immune status in free-living mallards (Anas platyrhynchos), a partially migratory key LPAIV host species. We sampled mallards throughout the species' annual autumn LPAIV infection peak, and we classified individuals according to age, sex, and migratory strategy (based on stable hydrogen isotope analysis) when analyzing data on body mass and five indices of immune status. Body mass was similar for LPAIV-infected and noninfected birds. The degree of virus shedding from the cloaca and oropharynx was not associated with body mass. LPAIV infection and shedding were not associated with natural antibody (NAbs) and complement titers (first lines of defense against infections), concentrations of the acute phase protein haptoglobin (Hp), ratios of heterophils to lymphocytes (H:L ratio), and avian influenza virus (AIV)-specific antibody concentrations. NAbs titers were higher in LPAIV-infected males and local (i.e., short distance) migrants than in infected females and distant (i.e., long distance) migrants. Hp concentrations were higher in LPAIV-infected juveniles and females compared to infected adults and males. NAbs, complement, and Hp levels were lower in LPAIV-infected mallards in early autumn. Our study demonstrates weak associations between infection with and shedding of LPAIV and the body condition and immune status of free-living mallards. These results may support the role of mallards as asymptomatic carriers of LPAIV and raise questions about possible coevolution between virus and host.
    Is green infrastructure an effective climate adaption strategy for conserving biodiversity? A case study with the great crested newt
    Teeffelen, A.J.A. van; Vos, C.C. ; Jochem, R. ; Baveco, J.M. ; Meeuwsen, H. ; Hilbers, J.P. - \ 2015
    Landscape Ecology 30 (2015)5. - ISSN 0921-2973 - p. 937 - 954.
    population viability analysis - triturus-cristatus - amphibian populations - extinction risk - habitat - conservation - landscapes - management - dynamics - patterns
    Context Increasing the amount of green infrastructure, defined as small-scale natural landscape elements, has been named as a climate adaptation measure for biodiversity. While green infrastructure strengthened ecological networks in some studies, it is not known whether this effect also holds under climate change, and how it compares to other landscape adaptation options. Objectives We assessed landscape adaptation options under scenarios of climate change for a dispersal-limited and climate-sensitive species: great crested newt, Triturus cristatus. Methods A spatially-explicit modelling framework was used to simulate newt metapopulation dynamics in a case study area in the Netherlands, under alternative spatial configurations of 500 ha to-be-restored habitat. The framework incorporated weather-related effects on newt recruitment, following current and changing climate conditions. Results Mild climate change resulted in slightly higher metapopulation viability, while more severe climate change (i.e. more frequent mild winters and summer droughts) had detrimental effects on metapopulation viability. The modelling framework revealed interactions between climate and landscape configuration on newt viability. Restoration of ponds and terrestrial habitat may reduce the negative effects of climate change, but only when certain spatial requirements (habitat density, connectivity) as well as abiotic requirements (high ground water level) are met. Conclusions Landscape scenarios where habitat was added in the form of green infrastructure were not able to meet these multiple conditions, as was the case for a scenario that enlarged core areas. The approach allowed a deduction of landscape design rules that incorporated both spatial and abiotic requirements resulting in more effective climate adaptation options.
    Survival, reproduction, and immigration explain the dynamics of a local Red-backed Shrike population in the Netherlands
    Hemerik, L. ; Geertsma, M. ; Waasdorp, S. ; Middelveld, R.P. ; Kleef, H. van; Klok, T.C. - \ 2015
    Journal of Ornithology 156 (2015)1. - ISSN 2193-7192 - p. 35 - 46.
    lanius-collurio - marked animals - birds - consequences - dispersal - patterns - weather
    Populations of many bird species strongly declined in Western Europe in the late twentieth century. One such species is the Red-backed Shrike in the Netherlands. In one of the last strongholds of this species, the Bargerveen Reserve, the breeding population flourished in the 1990s due to rewetting management. However, further development of the area has led to a decline in breeding numbers such that the population is now less than half the size it was in the 1990s. Here, we analyze the vital rates of the Red-backed Shrike population in the Bargerveen. In 2001–2008, nestlings in this population were individually marked, and resighting data was collected during the breeding seasons of 2002–2009. We used estimates of vital rates based on monitoring in 2001 until 2009 to diagnose the population dynamics. Mark–recapture data were analyzed with the program MARK. The most parsimonious model gave age- and gender-specific survival probabilities of 0.12 for first-year females, 0.64 for older females, 0.20 for first-year males, and 0.54 for older males (with overlapping confidence intervals for the gender-specific adult survival values). The estimated yearly resighting probabilities were gender specific, with a higher probability observed for males (0.81) than for females (0.53). For 2001–2009, we computed an average number of offspring per breeding pair of 2.91 (with 72 % of the pairs breeding successfully). Using these vital rates, we parameterized a simple matrix model. The resulting yearly growth was 0.80. Adult survival had an elasticity of 0.83, while juvenile survival and reproduction both had an elasticity of 0.20. Because the population numbers have stabilized since 2005, the observed yearly population growth suggests that 20 % of the Red-backed Shrikes breeding in the Bargerveen are immigrants. Comparison with data on other Red-backed Shrike populations indicates that juvenile and adult survival rates can be improved in the Bargerveen Reserve. Appropriate management measures to accomplish this are discussed.
    Short communication: Effect of straw inclusion rate in a dry total mixed ration on the behavior of weaned dairy calves
    Groen, M.J. ; Steele, M.A. ; DeVries, T.J. - \ 2015
    Journal of Dairy Science 98 (2015). - ISSN 0022-0302 - p. 2693 - 2700.
    feed delivery method - heifers - cows - management - patterns - exposure - fiber
    The primary objective of this study was to determine the effect of straw inclusion levels on the feeding behavior of young, weaned calves adapted to a dry total mixed ration (TMR) composed of a multitextured concentrate and chopped straw. A secondary objective was to determine how developed feeding patterns persist after calves were switched to a conventional silage-based diet. Ten Holstein bull calves (91 ± 2.4 d of age, weighing 136 ± 12.3 kg) were assigned to 1 of 2 treatments: a TMR containing [dry matter (DM) basis] either (1) 85% concentrate and 15% chopped straw for 10 wk (wk 1 to 10) or (2) 85% concentrate and 15% chopped straw for 5 wk (wk 1 to 5), then 70% concentrate and 30% chopped straw for 5 wk (wk 6 to 10). After 10 wk, all animals were transitioned to a TMR containing (DM basis) 42.3% corn silage and 57.7% haylage for 2 wk (wk 11 to 12). During wk 1 to 5, all calves had similar DMI (5.5 kg/d), average daily gain (1.7 kg/d), feed efficiency (3.5 kg of DM/kg of gain), and eating time (151.9 min/d). During wk 6 to 10, calves transitioned to the 70% diet ate less DM (5.5 vs. 7.4 kg/d), grew more slowly (1.3 vs. 1.6 kg/d), sorted more against long forage particles (62.8 vs. 103.8%), and had greater feeding times (194.9 vs. 102.6 min/d). The difference in feeding time occurred only during the first 8 h after feed delivery. Despite similar DMI (5.2 kg/d) and average daily gain (1.1 kg/d) in wk 11 to 12, differences in behavior were observed resulting from previous diets. In wk 11 to 12, calves previously fed the 70% diet continued to have a longer meal immediately after feed delivery. Overall, the results indicate that diluting a dry TMR containing a multitextured concentrate and chopped straw with more straw resulted in calves spending more time feeding and having longer meals immediately after feed delivery; this feeding pattern carried over after calves were transitioned to a silage-based ration.
    Eating behaviour explains differences between individuals in dynamic texture perception of sausages
    Devezeaux de Lavergne, M.S.M. ; Derks, J.A.M. ; Ketel, E.C. ; Wijk, R.A. de; Stieger, M.A. - \ 2015
    Food Quality and Preference 41 (2015). - ISSN 0950-3293 - p. 189 - 200.
    swallowing threshold - food texture - bite size - age - bolus - patterns - young - gels
    Texture perception of foods has been demonstrated to be influenced by age, dental health and oral processing behaviour. Eating duration is a significant factor contributing to and determining food oral processing behaviour. The influence of eating duration on dynamic texture perception, oral processing behaviour and properties of the food bolus have not been investigated extensively. The aims of this study are (i) to determine the influence of naturally preferred eating duration on dynamic texture perception of sausages and (ii) to explain differences in dynamic texture perception between short and long duration eaters by chewing behaviour and bolus properties. Two groups of subjects were selected based on their natural eating duration for a controlled portion size of two sausages. The group of “long duration eaters” (n = 11) took on average twice as long to consume a piece of sausage compared to the group of “short duration eaters” (n = 12). Independent of eating duration, short and long eating duration subjects chewed sausages with the same chewing frequency (p = 0.57) and muscle effort rate (p = 0.15) during oral processing. Total muscle effort and total number of chews were significantly higher (p <0.05 for both) for long duration eaters mainly due to the longer eating time compared to short duration eaters. Bolus properties showed that short duration eaters did not break down the boli as much as long duration eaters resulting in fewer (p <0.001) and larger (p <0.05) sausage bolus fragments, firmer (p <0.001) and less adhesive (p <0.001) boli with lower fat content (p <0.05) and less saliva incorporation (p <0.001) at swallow compared to the bolus properties of long duration eaters. These differences in bolus properties influenced dynamic texture perception of the sausages as the bolus of short duration eaters revealed different properties than the bolus of long duration eaters. Temporal dominance of sensations (TDS) showed that short and long duration eaters perceived the same sausage similarly in the early stages of oral processing, but started to perceive the texture of the same sausage differently from the middle of oral processing towards the end. We conclude that short duration eaters did not compensate for their shorter eating duration by chewing more efficiently but were comfortable swallowing a less broken down bolus than long duration eaters. Moreover, we conclude that differences in eating behaviour between subjects can lead to differences in bolus properties of sausages causing differences in dynamic texture perception of the same sausage.
    An exploratory analysis of land abandonment drivers in areas prone to desertification
    Kosmas, C. ; Kairis, O. ; Karavitis, C. ; Hessel, R. ; Ritsema, C.J. - \ 2015
    Catena 128 (2015). - ISSN 0341-8162 - p. 252 - 261.
    soil-erosion - europe - indicators - patterns - spain - risk
    The abandonment of land is a global problemwith environmental and socioeconomic implications. An approach to assess the relationship between land abandonment and a large set of indicators was illustrated in the present study by using data collected in the framework of the European Union DESIRE research project from 808 field sites located in 10 study sites in the Mediterranean region, Eastern Europe, Latin America, Africa and Asia. A total of 48 indicators provided information for biophysical conditions and socioeconomic characteristics measured at the plot level. The selected indicators refer to farm characteristics (family status, land tenure, present and previous types of land-use, soil depth, slope gradient, tillage operations) and to site-specific characteristics including annual rainfall, rainfall seasonality and water availability. Classes were designated for each indicator and a sensitivity score was assigned to each class based on existing research or empirically assessing the importance of each indicator to the land abandonment issue. Questionnaires for each process of land degradation were prepared and datawere collected at field site level in collaboration with land users. Based on correlation statistics and multivariate analyses more than ten indicators out of 48 resulted as significant in affecting land abandonment in the studied field sites. Among them, the most important were rainfall seasonality, elderly index, land fragmentation, farm size, selected soil properties, and the level of policy implementation. Results contribute to the development of appropriate tools for assessing the effectiveness of land management practices for contrasting land abandonment.
    Soil biodiversity and DNA barcodes: opportunities and challenges
    Orgiazzi, A. ; Bonnet Dunbar, M. ; Panagos, P. ; Groot, G.A. de; Lemanceau, P. - \ 2015
    Soil Biology and Biochemistry 80 (2015)1. - ISSN 0038-0717 - p. 244 - 250.
    molecular microbial ecology - bacterial communities - ecosystem services - diversity - fungal - patterns - identification - assemblages - resilience - extraction
    Soils encompass a huge diversity of organisms which mostly remains to be characterized due to a number of methodological and logistical issues. Nonetheless, remarkable progress has been made in recent years toward developing strategies to characterize and describe soil biodiversity, especially thanks to the development of molecular approaches relying on direct DNA extraction from the soil matrix.Metabarcoding can be applied to DNA from any environment or organism, and is gaining increasing prominence in biodiversity studies. This approach is already commonly used to characterize soil microbial communities and its application is now being extended to other soil organisms, i.e. meso- and macro-fauna.These developments offer unprecedented scientific and operational opportunities in order to better understand soil biodiversity distribution and dynamics, and to propose tools and strategies for biodiversity diagnosis. However, these opportunities also come with challenges that the scientific community must face. Such challenges are related to i) clarification of terminology, (ii) standardisation of methods and further methodological development for additional taxonomic groups, (iii) development of a common database, and (iv) ways to avoid waste of information and data derived from metabarcoding. In order to facilitate common application of metabarcoding in soil biodiversity assessment, we discuss these opportunities and challenges and propose solutions towards a more homogeneous framework.
    Temporal aggregation of bottom trawling and its implication for the impact on the benthic ecosystem
    Denderen, P.D. van; Hintzen, N.T. ; Kooten, T. van; Rijnsdorp, A.D. - \ 2015
    ICES Journal of Marine Science 72 (2015)3. - ISSN 1054-3139 - p. 952 - 961.
    southern north-sea - solea-solea l - beam trawl - fishing disturbance - fishery management - species richness - chesapeake bay - burying depth - vms data - patterns
    Understanding trawling impacts on the benthic ecosystem depends to a large extent on the ability to estimate trawling activity at the appropriate scale. Several studies have assessed trawling at fine spatial scales yearly, largely ignoring temporal patterns. In this study, we analysed these temporal patterns in beam trawl effort intensity at 90 stations of the Dutch continental shelf of the North Sea for a period of 10 years, at a fine temporal (weekly) and spatial (110 × 70 m) scale using Vessel Monitoring by Satellite (VMS) data. Our results show that trawling is aggregated in time and shows clear seasonality, related to the behavior of the fleet and migration patterns of the target fish species. The temporal patterns affect the overall impact on and the recovery of the benthic community, as is illustrated with a benthic population model. Our results imply that trawling impact studies using high-resolution data like VMS should take account of the possibility of temporal aggregation and seasonality in trawling to improve the assessment of the impact of trawling on the population dynamics of benthos.
    Time-dependent effects of climate and drought on tree growth in a Neotropical dry forest: Short-term tolerance vs. long-term sensitivity
    Mendivelso, H.A. ; Camarero, J.J. ; Gutierrez, E. ; Zuidema, P. - \ 2014
    Agricultural and Forest Meteorology 188 (2014). - ISSN 0168-1923 - p. 13 - 23.
    tropical forests - ring chronologies - rain-forest - santa-cruz - water-use - phenology - patterns - bolivia - precipitation - coordination
    We analyzed the effects of climate and drought on radial growth using dendrochronology in seven deciduous tree species coexisting in a Bolivian tropical dry forest subjected to seasonal drought. Precipitation, temperature and a multiscalar drought index were related to tree-ring width data at different time-scales (from one month to 42 years). Precipitation affected positively tree growth in all species, mainly during the wet season, while temperature affected it negatively in five species. Tree growth responses to precipitation and temperature were species-specific and peaked at short-time scales, specifically from one to nine months. At inter-annual scales tree growth always responded positively to less dry conditions at short-time scales, particularly from two to seven months, and also at long-time scales from six to 30 years. Tree growth was mainly sensitive to multi-annual droughts and such sensitivity differed among species. Our findings suggest that tree species of the studied tropical dry forest are predominantly sensitive in terms of growth reduction to long-lasting droughts. This time-dependency of growth responses to drought should be explicitly considered as an additional constraint of the community dynamics in evaluations of the future responses of tropical dry forests to climate warming. (C) 2014 Elsevier B.V. All rights reserved.
    Soil inorganic carbon stock under different soil types and land uses on the Loess Plateau region of China
    Tan, W.F. ; Zhang, R. ; Cao, H. ; Huang, C.Q. ; Yang, Q.K. ; Wang, M.K. ; Koopal, L.K. - \ 2014
    Catena 121 (2014). - ISSN 0341-8162 - p. 22 - 30.
    organic-carbon - storage - sequestration - grasslands - deposition - dynamics - patterns - nitrogen - climate - caliche
    The soil carbon reservoir is the largest carbon reservoir in terrestrial ecosystems and consists of soil organic and inorganic carbon stocks. Previous studies have mainly focused on the soil organic carbon (SOC) stock, and limited information is available about the soil inorganic carbon (SIC) stock. The Chinese Loess Plateau (CLP), which is located in the arid and semi-arid region of China, is an important inorganic carbon reservoir, with a thick soil layer that is rich in calcium carbonate. However, there are few reports on the SIC stock and its spatial distribution in this region. In the current study, the SIC densities and stocks for various soil types and land use patterns were evaluated based on 495 profiles with 2470 soil samples across the CLP, which were collected from the Chinese Second National Soil Survey. The results showed that in the top 1 m of soil across the CLP, the average SIC density is 17.04 kg/m(2), and the total SIC stock is approximately 10.20 Pg C (1 Pg = 10(15) g). The SIC stock of the CLP accounts for approximately 18.4% of the total SIC stock throughout China. The average values of the SIC stock in the 0-20, 20-50 and 50-100 cm depths of the CLP are 2.39, 2.92 and 4.89 Pg, respectively. Under different land use patterns, the order of the average SIC density is farmland approximate to grassland > forest in all soil layers. For the various soil types, the SIC density in the 0-100 cm layer is the highest in alkaline soil and lowest in subalpine meadow soil, whereas the SIC stock is highest in loessial soil, eolian sandy soil and sierozem, and the lowest in subalpine meadow soil. These differences are largely a result of the area occupied by each soil type and the climate conditions. The results of this study provide basic information about carbon reservoir in China and contribute to our understanding of the SIC stock on the CLP as it relates to the carbon balance of terrestrial ecosystems. (C) 2014 Elsevier B.V. All rights reserved.
    Public Perception of Water Consumption and Its Effects on Water Conservation Behavior
    Fan, L.X. ; Wang, F. ; Liu, G.B. ; Yang, X. ; Qin, W. - \ 2014
    Water 6 (2014)6. - ISSN 2073-4441 - p. 1771 - 1784.
    end uses - patterns - households - buildings - attitudes - recall - diary
    The usual perception of consumers regarding water consumption is that their bills do not match their actual water consumption. However, this mismatch has been insufficiently studied; particularly for cases related to specific water-use patterns, water conservation practices, and user socio-demographics. In this study, a total of 776 households in 16 villages situated in the rural Wei River Basin are investigated to address the gap in the literature. Questionnaires and 3-day water diaries are used for data collection and comparison. Results show that significant relations exist between perceived water consumption and actual water consumption. Participants have different perceptions of specific water-use patterns. Participants tend to underestimate their outdoor and kitchen water consumption and overestimate their indoor water consumption. Females and elder consumers accurately estimate their water consumption, whereas consumers with high education levels and incomes underestimate their actual water consumption. The groups who can accurately estimate water consumption have better water conservation consciousness and water conservation practices than those who underestimate their water consumption. The huge disparities highlighted by the results suggest that community policies and programs to improve public water conservation consciousness or practices must be implemented to enhance consumer understanding of water consumption.
    Genetic and morphological diversity of okra (Abelmoschus esculentus [L.] Moench.) genotypes and their possible relationships, with particular reference to Greek landraces
    Kyriakopoulou, O.G. ; Arens, P.F.P. ; Pelgrom, K.T.B. ; Karapanos, I. ; Bebeli, P. ; Passam, H.C. - \ 2014
    Scientia Horticulturae 171 (2014). - ISSN 0304-4238 - p. 58 - 70.
    numerical-analysis - germplasm - aflp - collection - cultivars - stability - patterns - distance - markers - plants
    Despite its high economic value in many countries (especially in developing regions of the tropics and sub-tropics), okra has received little attention with respect to its source of origin and genetic diversity, particularly at the molecular level. Phenotypic description (morphology, pod characteristics and seed germination) and AFLP (amplified fragment length polymorphism) analysis were performed on Greek and international genotypes. Whereas morphological descriptors did not separate the accessions according to their geographical origin, AFLP analysis revealed a low level (12%) of polymorphism and distinct geographical groupings. Greek germplasm separated into three distinct groups with no overlap between them on the basis of molecular markers. A higher degree of genetic heterogeneity was found (UPGMA analysis) among the accessions of the Boyiatiou group than in the Pylaias group, whereas the occurrence of some common phylogenetic characteristics made separation on the basis of morphology alone difficult. The results from AFLP markers indicate that Greek germplasm constitutes a significant pool of variation with respect to morphological parameters, pod characteristics and seed germinability. Moreover, differences in seed germination among phenotypes may relate to their geographical origin (mainland or islands).
    Cross-Sectional Associations of Objectively Measured Physical Activity, Cardiorespiratory Fitness and Anthropometry in European Adults
    Wientzek, A. ; Diaz, M.J.T. ; Castano, J.M.H. ; Amiano, P. ; Arriola, L. ; Overvad, K. ; Ostergaard, J.N. ; Charles, M.A. ; Fagherazzi, G. ; Palli, D. ; Bendinelli, B. ; Skeie, G. ; Borch, K.B. ; Wendel-Vos, W. ; Hollander, E.L. de; May, A.M. ; Ouden, M.E.M. den; Trichopoulou, A. ; Valanou, E. ; Soderberg, S. ; Franks, P.W. ; Brage, S. ; Vigl, M. ; Boeing, H. ; Ekelund, U. - \ 2014
    Obesity 22 (2014)5. - ISSN 1930-7381 - p. E127 - E134.
    activity energy-expenditure - body-mass index - heart-rate - abdominal obesity - aerobic fitness - weight - accelerometry - indicators - behaviors - patterns
    Objective: To quantify the independent associations between objectively measured physical activity (PA), cardiorespiratory fitness (CRF), and anthropometry in European men and women. Methods: 2,056 volunteers from 12 centers across Europe were fitted with a heart rate and movement sensor at 2 visits 4 months apart for a total of 8 days. CRF (ml/kg/min) was estimated from an 8 minute ramped step test. A cross-sectional analysis of the independent associations between objectively measured PA (m/s(2)/d), moderate and vigorous physical activity (MVPA) (% time/d), sedentary time (% time/d), CRF, and anthropometry using sex stratified multiple linear regression was performed. Results: In mutually adjusted models, CRF, PA, and MVPA were inversely associated with all anthropometric markers in women. In men, CRF, PA, and MVPA were inversely associated with BMI, whereas only CRF was significantly associated with the other anthropometric markers. Sedentary time was positively associated with all anthropometric markers, however, after adjustment for CRF significant in women only. Conclusion: CRF, PA, MVPA, and sedentary time are differently associated with anthropometric markers in men and women. CRF appears to attenuate associations between PA, MVPA, and sedentary time. These observations may have implications for prevention of obesity.
    Prolonged isolation and persistence of a common endemic on granite outcrops in both mesic and semi-arid environments
    Tapper, S.L. ; Byrne, M. ; Yates, C.J. ; Keppel, G. ; Hopper, S.D. ; Niel, K.P. Van; Schut, A.G.T. ; Mucina, L. ; Wardell-Johnson, G.W. - \ 2014
    Journal of Biogeography 41 (2014)11. - ISSN 0305-0270 - p. 2032 - 2044.
    population-structure - climate-change - genetic diversity - dna polymorphism - plant diversity - cpdna variation - phylogeography - chloroplast - myrtaceae - patterns
    Granite outcrops may be able to act as refugia for species during adverse climate change, owing to their topographic complexity. We assessed this hypothesis by examining phylogeographical patterns in a common, geographically widespread granite endemic, Stypandra glauca (Hemerocallidaceae).
    Changes of bat activity, species richness, diversity and community composition over an altitudinal gradient in the Soutpansberg range, South Africa
    Linden, V.M.G. ; Weier, S.M. ; Gaigher, I. ; Kuipers, H.J. ; Weterings, M.J.A. ; Taylor, P. - \ 2014
    Acta Chiropterologica 16 (2014)1. - ISSN 1508-1109 - p. 27 - 40.
    small mammal diversity - higher-taxon richness - elevational gradient - habitat preferences - model selection - extinction risk - climate-change - biodiversity - chiroptera - patterns
    Bats are important indicator species which can help in identifying areas where conservation efforts should be concentrated and whether these areas are affected by ongoing climate change. To elucidate factors limiting and influencing the elevational distribution of bats in a recognised biodiversity hotpot, the Soutpansberg mountain range (in Vhembe Biosphere Reserve) of northern South Africa, we collected data in and around the Luvhondo Private Nature Reserve, by catching and acoustically monitoring bats over an altitudinal gradient from 900 to 1,748 m. A total of 18 different species could be recorded. Two species, namely Pipistrellus hesperidus and Chaerephon cf. ansorgei appeared to be present and dominant at all altitudes. Activity, species richness and diversity significantly decreased with increasing altitude, whereas community composition was not related to altitude and no endemics to either low or high altitude were detected. It is likely that the change of species richness and diversity over altitude is caused by other factors correlated with altitude such as vegetation type, area size, energy availability and climatic differences. Our research demonstrated that lower altitudes are richer and more diverse in bat species and since no highland endemics have been discovered, conservation efforts in the area, regarding bats, should not ignore these lower altitudes which are most susceptible to human impacts leading to habitat degradation due to over-grazing, bush encroachment, cultivation and denudation of large trees for firewood collection.
    using genetic profiles of african forest elephants to infer population structure, movements, and habitat use in a conservation and development landscape in gabon
    Eggert, L.S. ; Buij, R. ; Lee, M.E. ; Campbell, P. ; Dallmeier, F. ; Fleischer, R.C. ; Alonso, A. ; Maldonado, J. - \ 2014
    Conservation Biology 28 (2014)1. - ISSN 0888-8892 - p. 107 - 118.
    loxodonta-africana - savanna elephants - protected areas - national-park - relatedness - demography - patterns - crisis - loci
    Conservation of wide-ranging species, such as the African forest elephant (Loxodonta cyclotis), depends on fully protected areas and multiple-use areas (MUA) that provide habitat connectivity. In the Gamba Complex of Protected Areas in Gabon, which includes 2 national parks separated by a MUA containing energy and forestry concessions, we studied forest elephants to evaluate the importance of the MUA to wide-ranging species. We extracted DNA from elephant dung samples and used genetic information to identify over 500 individuals in the MUA and the parks. We then examined patterns of nuclear microsatellites and mitochondrial control-region sequences to infer population structure, movement patterns, and habitat use by age and sex. Population structure was weak but significant, and differentiation was more pronounced during the wet season. Within the MUA, males were more strongly associated with open habitats, such as wetlands and savannas, than females during the dry season. Many of the movements detected within and between seasons involved the wetlands and bordering lagoons. Our results suggest that the MUA provides year-round habitat for some elephants and additional habitat for others whose primary range is in the parks. With the continuing loss of roadless wilderness areas in Central Africa, well-managed MUAs will likely be important to the conservation of wide-ranging species.
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