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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    Development and analysis of the Soil Water Infiltration Global database
    Rahmati, Mehdi ; Weihermüller, Lutz ; Vanderborght, Jan ; Pachepsky, Yakov A. ; Mao, Lili ; Sadeghi, Seyed Hamidreza ; Moosavi, Niloofar ; Kheirfam, Hossein ; Montzka, Carsten ; Looy, Kris Van; Toth, Brigitta ; Hazbavi, Zeinab ; Yamani, Wafa Al; Albalasmeh, Ammar A. ; Alghzawi, M.Z. ; Angulo-Jaramillo, Rafael ; Antonino, Antônio Celso Dantas ; Arampatzis, George ; Armindo, Robson André ; Asadi, Hossein ; Bamutaze, Yazidhi ; Batlle-Aguilar, Jordi ; Béchet, Béatrice ; Becker, Fabian ; Blöschl, Günter ; Bohne, Klaus ; Braud, Isabelle ; Castellano, Clara ; Cerdà, Artemi ; Chalhoub, Maha ; Cichota, Rogerio ; Císlerová, Milena ; Clothier, Brent ; Coquet, Yves ; Cornelis, Wim ; Corradini, Corrado ; Coutinho, Artur Paiva ; Oliveira, Muriel Bastista De; Macedo, José Ronaldo De; Durães, Matheus Fonseca ; Emami, Hojat ; Eskandari, Iraj ; Farajnia, Asghar ; Flammini, Alessia ; Fodor, Nándor ; Gharaibeh, Mamoun ; Ghavimipanah, Mohamad Hossein ; Ghezzehei, Teamrat A. ; Giertz, Simone ; Hatzigiannakis, Evangelos G. ; Horn, Rainer ; Jiménez, Juan José ; Jacques, Diederik ; Keesstra, Saskia Deborah ; Kelishadi, Hamid ; Kiani-Harchegani, Mahboobeh ; Kouselou, Mehdi ; Jha, Madan Kumar ; Lassabatere, Laurent ; Li, Xiaoyan ; Liebig, Mark A. ; Lichner, Lubomír ; López, María Victoria ; Machiwal, Deepesh ; Mallants, Dirk ; Mallmann, Micael Stolben ; Oliveira Marques, Jean Dalmo De; Marshall, Miles R. ; Mertens, Jan ; Meunier, Félicien ; Mohammadi, Mohammad Hossein ; Mohanty, Binayak P. ; Pulido-Moncada, Mansonia ; Montenegro, Suzana ; Morbidelli, Renato ; Moret-Fernández, David ; Moosavi, Ali Akbar ; Mosaddeghi, Mohammad Reza ; Mousavi, Seyed Bahman ; Mozaffari, Hasan ; Nabiollahi, Kamal ; Neyshabouri, Mohammad Reza ; Ottoni, Marta Vasconcelos ; Ottoni Filho, Theophilo Benedicto ; Pahlavan-Rad, Mohammad Reza ; Panagopoulos, Andreas ; Peth, Stephan ; Peyneau, Pierre Emmanuel ; Picciafuoco, Tommaso ; Poesen, Jean ; Pulido, Manuel ; Reinert, Dalvan José ; Reinsch, Sabine ; Rezaei, Meisam ; Roberts, Francis Parry ; Robinson, David ; Rodrigo-Comino, Jesüs ; Rotunno Filho, Otto Corrêa ; Saito, Tadaomi ; Suganuma, Hideki ; Saltalippi, Carla ; Sándor, Renáta ; Schütt, Brigitta ; Seeger, Manuel ; Sepehrnia, Nasrollah ; Sharifi Moghaddam, Ehsan ; Shukla, Manoj ; Shutaro, Shiraki ; Sorando, Ricardo ; Stanley, Ajayi Asishana ; Strauss, Peter ; Su, Zhongbo ; Taghizadeh-Mehrjardi, Ruhollah ; Taguas, Encarnación ; Teixeira, Wenceslau Geraldes ; Vaezi, Ali Reza ; Vafakhah, Mehdi ; Vogel, Tomas ; Vogeler, Iris ; Votrubova, Jana ; Werner, Steffen ; Winarski, Thierry ; Yilmaz, Deniz ; Young, Michael H. ; Zacharias, Steffen ; Zeng, Yijian ; Zhao, Ying ; Zhao, Hong ; Vereecken, Harry - \ 2018
    Earth System Science Data 10 (2018)3. - ISSN 1866-3508 - p. 1237 - 1263.

    In this paper, we present and analyze a novel global database of soil infiltration measurements, the Soil Water Infiltration Global (SWIG) database. In total, 5023 infiltration curves were collected across all continents in the SWIG database. These data were either provided and quality checked by the scientists who performed the experiments or they were digitized from published articles. Data from 54 different countries were included in the database with major contributions from Iran, China, and the USA. In addition to its extensive geographical coverage, the collected infiltration curves cover research from 1976 to late 2017. Basic information on measurement location and method, soil properties, and land use was gathered along with the infiltration data, making the database valuable for the development of pedotransfer functions (PTFs) for estimating soil hydraulic properties, for the evaluation of infiltration measurement methods, and for developing and validating infiltration models. Soil textural information (clay, silt, and sand content) is available for 3842 out of 5023 infiltration measurements (∼76%) covering nearly all soil USDA textural classes except for the sandy clay and silt classes. Information on land use is available for 76ĝ€% of the experimental sites with agricultural land use as the dominant type (∼40%). We are convinced that the SWIG database will allow for a better parameterization of the infiltration process in land surface models and for testing infiltration models. All collected data and related soil characteristics are provided online in ∗.xlsx and ∗.csv formats for reference, and we add a disclaimer that the database is for public domain use only and can be copied freely by referencing it. Supplementary data are available at https://doi.org/10.1594/PANGAEA.885492 (Rahmati et al., 2018). Data quality assessment is strongly advised prior to any use of this database. Finally, we would like to encourage scientists to extend and update the SWIG database by uploading new data to it.

    Neutral and functionally important genes shed light on phylogeography and the history of high-altitude colonization in a widespread New World duck
    Lozano-Jaramillo, Maria ; McCracken, Kevin G. ; Cadena, Carlos Daniel - \ 2018
    Ecology and Evolution 8 (2018)13. - ISSN 2045-7758 - p. 6515 - 6528.
    adaptation - hypoxia - migration - natural selection

    Phylogeographic studies often infer historical demographic processes underlying species distributions based on patterns of neutral genetic variation, but spatial variation in functionally important genes can provide additional insights about biogeographic history allowing for inferences about the potential role of adaptation in geographic range evolution. Integrating data from neutral markers and genes involved in oxygen (O2)-transport physiology, we test historical hypotheses about colonization and gene flow across low- and high-altitude regions in the Ruddy Duck (Oxyura jamaicensis), a widely distributed species in the New World. Using multilocus analyses that for the first time include populations from the Colombian Andes, we also examined the hypothesis that Ruddy Duck populations from northern South America are of hybrid origin. We found that neutral and functional genes appear to have moved into the Colombian Andes from both North America and southern South America, and that high-altitude Colombian populations do not exhibit evidence of adaptation to hypoxia in hemoglobin genes. Therefore, the biogeographic history of Ruddy Ducks is likely more complex than previously inferred. Our new data raise questions about the hypothesis that adaptation via natural selection to high-altitude conditions through amino acid replacements in the hemoglobin protein allowed Ruddy Ducks to disperse south along the high Andes into southern South America. The existence of shared genetic variation with populations from both North America and southern South America as well as private alleles suggests that the Colombian population of Ruddy Ducks may be of old hybrid origin. This study illustrates the breadth of inferences one can make by combining data from nuclear and functionally important loci in phylogeography, and underscores the importance of complete range-wide sampling to study species history in complex landscapes.

    Laboratory testing of Beerkan infiltration experiments for assessing the role of soil sealing on water infiltration
    Prima, S. Di; Concialdi, P. ; Lassabatere, L. ; Angulo-Jaramillo, R. ; Pirastru, M. ; Cerdà, A. ; Keesstra, S. - \ 2018
    Catena 167 (2018). - ISSN 0341-8162 - p. 373 - 384.
    Beerkan infiltration experiment - BEST algorithms - Rainfall simulation - Saturated soil hydraulic conductivity - Soil sealing

    Soil surface sealing is a major cause of decreased infiltration rates and increased surface runoff and erosion during a rainstorm. The objective of this paper is to quantify the effect of surface sealing on infiltration for 3 layered soils with different textures for the upper layer and investigate the capability of BEST procedure to catch the formation of the seal and related consequences on water infiltration. Rainfall experiments were carried out to induce the formation of the seal. Meanwhile, Beerkan infiltration runs were carried out pouring water at different distances from the soil surface (BEST-H versus BEST-L runs, with a High and Low water pouring heights, respectively) for the same type of layered soils. Then, we determined saturated soil hydraulic conductivity, Ks, values from rainfall simulation and Beerkan infiltration experiments. Rainfall simulations carried out on soil layers having different depths allowed to demonstrate that infiltration processes were mainly driven by the seal and that Ks estimates were representative of the seal. Mean Ks values, estimated for the late-phase, ranged from 13.9 to 26.2 mm h−1. Soil sealing induced an increase in soil bulk density by 38.7 to 42.1%, depending on the type of soil. Rainfall-deduced Ks data were used as target values and compared with those estimated by the Beerkan runs. BEST-H runs proved more appropriate than BEST-L runs, those last triggering no seal formation. The predictive potential of the three BEST algorithms (BEST-slope, BEST-intercept and BEST-steady) to yield a proper Ks estimate for the seal was also investigated. BEST-slope yielded negative Ks values in 87% of the cases for BEST-H runs. Positive values were obtained in 100% of the cases with BEST-steady and BEST-intercept. However, poorer fits were obtained with the latter algorithm. The comparison of Ks estimates with rainfall-deduced estimates allowed to identify BEST-steady algorithm with BEST-H run as the best combination. The method proposed in this study could be used to easily measure the seal's saturated hydraulic conductivity of an initially undisturbed bare soil directly impacted by water with minimal experimental efforts, using small volumes of water and easily transportable equipment.

    Comparing transient and steady-state analysis of single-ring infiltrometer data for an abandoned field affected by fire in Eastern Spain
    Prima, Simone Di; Lassabatere, Laurent ; Rodrigo-Comino, Jesús ; Marrosu, Roberto ; Pulido, Manuel ; Angulo-Jaramillo, Rafael ; úbeda, Xavier ; Keesstra, Saskia ; Cerdà, Artemi ; Pirastru, Mario - \ 2018
    Water 10 (2018)4. - ISSN 2073-4441
    Bottomless bucket method - Data analysis procedures - Field-saturated soil hydraulic conductivity - Infiltration - Post-fire soil hydraulic characterization - Single-ring infiltrometer
    This study aimed at determining the field-saturated soil hydraulic conductivity, Kfs, of an unmanaged field affected by fire by means of single-ring infiltrometer runs and the use of transient and steady-state data analysis procedures. Sampling and measurements were carried out in 2012 and 2017 in a fire-affected field (burnt site) and in a neighboring non-affected site (control site). The predictive potential of different data analysis procedures (i.e., transient and steady-state) to yield proper Kfs estimates was investigated. In particular, the transient WU1 method and the BB, WU2 and OPD methods were compared. The cumulative linearization (CL) method was used to apply the WU1 method. Values of Kfs ranging from 0.87 to 4.21 mm·h-1 were obtained, depending on the considered data analysis method. The WU1 method did not yield significantly different Kfs estimates between the sampled sites throughout the five-year period, due to the generally poor performance of the CL method, which spoiled the soil hydraulic characterization. In particular, good fits were only obtained in 23% of the cases. The BB, WU2 and the OPD methods, with a characterization based exclusively on a stabilized infiltration process, yielded an appreciably lower variability of the Kfs data as compared with the WU1 method. It was concluded that steady-state methods were more appropriate for detecting slight changes of Kfs in post-fire soil hydraulic characterizations. Our results showed a certain degree of soil degradation at the burnt site with an immediate reduction of the soil organic matter and a progressive increase of the soil bulk density during the five years following the fire. This general impoverishment resulted in a slight but significant decrease in the field-saturated soil hydraulic conductivity.
    Comparing Beerkan infiltration tests with rainfall simulation experiments for hydraulic characterization of a sandy-loam soil
    Prima, Simone Di; Bagarello, Vincenzo ; Lassabatere, Laurent ; Angulo-Jaramillo, Rafael ; Bautista, Inmaculada ; Burguet, Maria ; Cerda Bolinches, Artemio ; Iovino, Massimo ; Prosdocimi, Massimo - \ 2017
    Hydrological Processes 31 (2017)20. - ISSN 0885-6087 - p. 3520 - 3532.
    Beerkan infiltration - height of water application - rainfall simulation - runoff - saturated soil hydraulic conductivity

    Saturated soil hydraulic conductivity, Ks, data collected by ponding infiltrometer methods and usual experimental procedures could be unusable for interpreting field hydrological processes and particularly rainfall infiltration. The Ks values determined by an infiltrometer experiment carried out by applying water at a relatively large distance from the soil surface could however be more appropriate to explain surface runoff generation phenomena during intense rainfall events. In this study, a link between rainfall simulation and ponding infiltrometer experiments was established for a sandy-loam soil. The height of water pouring for the infiltrometer run was chosen, establishing a similarity between the gravitational potential energy of the applied water, Ep, and the rainfall kinetic energy, Ek. To test the soundness of this procedure, the soil was sampled with the Beerkan estimation of soil transfer parameters procedure of soil hydraulic characterization and two heights of water pouring (0.03 m, i.e., usual procedure, and 0.34 m, yielding Ep = Ek). Then, a comparison between experimental steady-state infiltration rates, isR, measured with rainfall simulation experiments determining runoff production and Ks values for the two water pouring heights was carried out in order to discriminate between theoretically possible (isR ≥ Ks) and impossible (isR < Ks) situations. Physically possible Ks values were only obtained by applying water at a relatively large distance from the soil surface, because isR was equal to 20.0 mm h−1 and Ks values were 146.2–163.9 and 15.2–18.7 mm h−1 for a height of water pouring of 0.03 and 0.34 m, respectively. This result suggested the consistency between Beerkan runs with a high height of water pouring and rainfall simulator experiments. Soil compaction and mechanical aggregate breakdown were the most plausible physical mechanisms determining reduction of Ks with height. This study demonstrated that the height from which water is poured onto the soil surface is a key parameter in infiltrometer experiments and can be adapted to mimic the effect of high intensity rain on soil hydraulic properties.

    Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits
    Pérez-Jaramillo, Juan E. ; Carrión, Víctor J. ; Bosse, Mirte ; Ferrão, Luiz F.V. ; Hollander, Mattias de; Garcia, Antonio Augusto Franco ; Ramírez, Camilo A. ; Mendes, Rodrigo ; Raaijmakers, Jos M. - \ 2017
    ISME Journal 11 (2017)10. - ISSN 1751-7362 - p. 2244 - 2257.
    Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant-microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification. Diversity Array Technology-based genotyping and phenotyping of local common bean accessions showed significant genetic and root architectural differences between wild and modern accessions, with a higher specific root length for the wild accessions. Canonical Correspondence Analysis indicated that the divergence in rhizobacterial community composition between wild and modern bean accessions is associated with differences in specific root length. Along the bean genotypic trajectory, going from wild to modern, we observed a gradual decrease in relative abundance of Bacteroidetes, mainly Chitinophagaceae and Cytophagaceae, and an increase in relative abundance of Actinobacteria and Proteobacteria, in particular Nocardioidaceae and Rhizobiaceae, respectively. Collectively, these results establish a link between common bean domestication, specific root morphological traits and rhizobacterial community assembly.
    Impacts of thinning of a Mediterranean oak forest on soil properties influencing water infiltration
    Prima, Simone Di; Bagarello, Vincenzo ; Angulo-Jaramillo, Rafael ; Bautista, Inmaculada ; Cerda Bolinches, Artemio ; Campo, Antonio Del; González-Sanchis, María ; Iovino, Massimo ; Lassabatere, Laurent ; Maetzke, Federico - \ 2017
    Journal of Hydrology and Hydromechanics 65 (2017)3. - ISSN 0042-790X - p. 276 - 286.
    Forest soils - Saturated and near saturated hydraulic conductivity - Soil water repellency
    In Mediterranean ecosystems, special attention needs to be paid to forest-water relationships due to water scarcity. In this context, Adaptive Forest Management (AFM) has the objective to establish how forest resources have to be managed with regards to the efficient use of water, which needs maintaining healthy soil properties even after disturbance. The main objective of this investigation was to understand the effect of one of the AFM methods, namely forest thinning, on soil hydraulic properties. At this aim, soil hydraulic characterization was performed on two contiguous Mediterranean oak forest plots, one of them thinned to reduce the forest density from 861 to 414 tree per ha. Three years after the intervention, thinning had not affected soil water permeability of the studied plots. Both ponding and tension infiltration runs yielded not significantly different saturated, Ks, and unsaturated, K-20, hydraulic conductivity values at the thinned and control plots. Therefore, thinning had no an adverse effect on vertical water fluxes at the soil surface. Mean Ks values estimated with the ponded ring infiltrometer were two orders of magnitude higher than K-20 values estimated with the minidisk infiltrometer, revealing probably soil structure with macropores and fractures. The input of hydrophobic organic matter, as a consequence of the addition of plant residues after the thinning treatment, resulted in slight differences in terms of both water drop penetration time, WDPT, and the index of water repellency, R, between thinned and control plots. Soil water repellency only affected unsaturated soil hydraulic conductivity measurements. Moreover, K-20 values showed a negative correlation with both WDPT and R, whereas Ks values did not, revealing that the soil hydrophobic behavior has no impact on saturated hydraulic conductivity.
    High-throughput phenotyping and improvements in breeding cassava for increased carotenoids in the roots
    Belalcazar, John ; Dufour, Dominique ; Andersson, Meike S. ; Pizarro, Mónica ; Luna, Jorge ; Londoño, Luis ; Morante, Nelson ; Jaramillo, Angélica M. ; Pino, Lizbeth ; Becerra López-Lavalle, Luis A. ; Davrieux, Fabrice ; Talsma, Elise F. ; Ceballos, Hernán - \ 2016
    Crop Science 56 (2016)6. - ISSN 0011-183X - p. 2916 - 2925.

    Past research developed reliable equations to base selections for high β-carotene on nearinfrared spectroscopy (NIR) predictions (100 genotypes d−1) rather than with high-perfor-mance liquid chromatography (HPLC) (<10 samples d−1). During recent harvest, CIAT made selections based on NIR predictions for the first time. This innovation produced valuable information that will help other cassava (Manihot esculenta Crantz) breeding programs. A total of 284 samples were analyzed with NIR and HPLC for total β-carotene (TBC) and by the oven method for dry matter content (DMC). Results indicated that NIR reliably predicted TBC and DMC. In addition, 232 genotypes grown in preliminary yield trials (PYTs) were harvested at 8.5 and 10.5 mo after planting (one plant per genotype and age) and root quality traits analyzed (by NIR only). Repeatability of results at the two ages was excellent, suggesting reliable results from NIR. In contrast to previous reports, age of the plant did not influence carotenoids content in the roots. The availability of a high-throughput NIR protocol allowed comparing results (for the first time) from seedling and cloned plants from the same genotype. Results showed very little relationship for DMC between seedling and cloned plants (R2 = 0.09). There was a much better association for TBC (R2 = 0.48) between seedling and cloned plants. It is postulated that variation in the environmental conditions when seedling and cloned plants (from the same gen-otype) may be responsible for these weak associations. Important changes in selection strategies have been implemented to overcome problems related to a lengthy harvesting season.

    Towards bioeconomy development in Latin America and the Caribbean
    Trigo, E.J. ; Henry, G. ; Sanders, J.P.M. ; Schurr, U. ; Ingelbrecht, I. ; Revell, C. ; Santana, C. ; Rocha, P. - \ 2015
    In: Towards a Latin America and Caribbean knowledge based bio-economy in partnership with Europe / Hodson de Jaramillo, E., Bogota Colombia : Pontificia Universidad Javeriana - ISBN 9789587167429 - p. 15 - 41.
    Reported behavior, knowledge and awareness toward the potential for norovirus transmission by food handlers in Dutch catering companies and institutional settings in relation to the prevalence of norovirus
    Verhoef, Linda ; Jaramillo Gutierrez, Giovanna ; Koopmans, Marion ; Boxman, Ingeborg L.A. - \ 2013
    Food Control 34 (2013)2. - ISSN 0956-7135 - p. 420 - 427.
    Environmental samples - Environmental swabs - Food safety knowledge - Foodborne - Questionnaires

    Norovirus (NoV) in ready to eat food has recently been defined as one of the virus-food commodity combinations with greatest public health concern. The role of food handlers therein has well been recognized. The aim of this study was to identify gaps in food handlers' education and to investigate possible associations between reported behavior, knowledge and awareness of NoV, and environmental presence of NoV. For this, face-to-face interviews were conducted using structured questionnaires in 1023 catering companies (i.e. restaurants mainly), 101 non-hospital health care centers, 52 hospital central kitchens and in 102 hospital in-patient units. In addition, three surface swabs were taken at each setting. Multivariate logistic regression was performed on data restricted to NoV high season months only, in which NoV was present in 21/374 (6%) catering companies and 37/233 (16%) institutional settings (p<0.01). The two independent determinants of presence of NoV on environmental surfaces identified were being situated in an institutional setting and having an attitude to continue food handling while sick with vomiting complaints. Several gaps in education and training were identified, demonstrating that knowledge on NoV was low, although awareness of NoV was significantly higher among food handlers in institutional settings than in catering companies. This is the first time questionnaires and environmental testing have been combined in the same study to identify issues of improvement. Training on all important aspects of NoV according to the recently developed Codex Alimentarius guidelines to control viruses in food is strongly recommended.

    Land cover controls on river discharge in Sweden
    Velde, Y. van der; Vercauteren, N. ; Jaramillo, F. ; Dekker, S.C. ; Destouni, G. ; Lyon, S.W. - \ 2013
    Abstract As humans alter landscape, vegetation, climate and atmospheric composition, changes in the terrestrial water balance and fresh water resources are likely to occur. Understanding how climate, vegetation, humans and hydrology interact is key for accurate projections of future fresh water resources. In this study we focus on forest dominated Sweden where significant changes in climate and increasing human activity have co-occurred during the past 50 years. For 280 catchments in Sweden, we related runoff coefficients and change trends thereof to land-surface characteristics. With these relationships we created average and change trend maps for runoff and evapotranspiration across Sweden. All this information is summarized by plotting water use efficiency (actual evapotranspiration (ET)/precipitation) against energy use efficiency (actual ET/potential ET ) in a Budyko-type framework for areas with unique land cover across Sweden. This plot clearly shows that wetlands tend to have lower water and energy use efficiencies compared to “open waters”, forests and agriculture, and that agriculture and forests have comparable water and energy use efficiencies closest to those of “open waters”. These results demonstrate how a change in land cover driven by climate change or by humans is likely to alter land-cover-atmosphere interactions, thereby changing both the water and energy balance of catchments. Looking at runoff coefficient change trends during the last 50 years we see that forests tended to become more efficient in using water and energy (i.e. the fractions of water and energy converted into river runoff and heat decreased). As this behavior coincides with an increase in precipitation it signals an acceleration of the hydrological cycle of Swedish forests. In this presentation we will discuss these findings focusing on the impact of forests on river discharges and the implications for future water cycles.
    Computational protein design with electrostatic focusing: experimental characterization of a conditionally folded helical domain with a reduced amino acid alphabet
    Suarez Diez, M. ; Pujol, M. ; Matzapetakis, M. ; Jaramillo, A. ; Iranzo, O. - \ 2013
    Biotechnology Journal 8 (2013)7. - ISSN 1860-6768 - p. 855 - 864.
    solution nmr structure - structural basis - peptides - recognition - prediction - sequences - dynamics - energy - trifluoroethanol - optimization
    Automated methodologies to design synthetic proteins from first principles use energy computations to estimate the ability of the sequences to adopt a targeted structure. This approach is still far from systematically producing native-like sequences, due, most likely, to inaccuracies when modeling the interactions between the protein and its aqueous environment. This is particularly challenging when engineering small protein domains (with less polar pair interactions than with the solvent). We have re-designed a three-helix bundle, domain B, using a fixed backbone and a four amino acid alphabet. We have enlarged the rotamer library with conformers that increase the weight of electrostatic interactions within the design process without altering the energy function used to compute the folding free energy. Our synthetic sequences show less than 15% similarity to any Swissprot sequence. We have characterized our sequences in different solvents using circular dichroism and nuclear magnetic resonance. The targeted structure achieved is dependent on the solvent used. This method can be readily extended to larger domains. Our method will be useful for the engineering of proteins that become active only in a given solvent and for designing proteins in the context of hydrophobic solvents, an important fraction of the situations in the cell
    Interweaving monitoring activities and model development towards enhancing knowledge of the soil-plant-atmosphere continuum
    Romano, N. ; Angulo-Jaramillo, M. ; Javaux, M. ; Ploeg, M.J. van der - \ 2012
    Vadose Zone Journal 11 (2012)3. - ISSN 1539-1663 - 3 p.
    water - observatories - ecohydrology - systems
    The guest editors summarize the advances and challenges associated with monitoring and modeling of the soil–plant–atmosphere continuum. They introduce the contributions in the special section, with an emphasis on the scale addressed in each study. The study of water pathways from the soil to the atmosphere through plants—the so-called soil–plant–atmosphere continuum (SPAC)—has always been central to agronomy, hydrology, plant physiology, and other disciplines, using a wide range of approaches and tools. In recent years, we have been witnessing a rapid expansion of interweaving monitoring activities and model development related to SPAC in climatic, ecological, and applications other than the traditional agrohydrological, and it is therefore timely to review the current status of this topic and outline future directions of research. The initiative for the special section of Vadose Zone Journal on SPAC emanated from several sessions we recently organized in international conferences and meetings. With a view to the specific research questions covered in this special section, this article introduces and reviews SPAC underlying issues and then provides a brief overview of the invited contributions. We have grouped together the 15 contributions under three main sections related to the local, field, and landscape spatial scales of interests. Within these sections, the papers present their innovative results using different measuring techniques (from classic tensiometers and TDR sensors to more advanced and sophisticated equipment based on tomography and geophysics) and different modeling tools (from mechanistic models based on the Richards equation to more parametrically parsimonious hydrologic balance models). They provide a snapshot of the current state of the art while emphasizing the significant progress attained in this field of research. New technological developments and applications are also highlighted.
    Soil water repellency in arid and humid climates
    Jaramillo, D.F. ; Dekker, L.W. ; Ritsema, C.J. ; Hendrickx, J.M.H. - \ 2003
    In: Soil water repellency; occurrence, consequences, and amelioration / Ritsema, C.J., Dekker, L.W., Amsterdam : Elsevier - ISBN 9780444512697 - p. 93 - 98.
    Plaguicidas en el medio ambiente
    Stoorvogel, J.J. ; Jaramillo, R. ; Merino, R. ; Kosten, S. - \ 2003
    In: Los Plaguicidas. Impactos en produccion, salud y medio ambiente en Carchi, Ecuador / Yanggen, D., Crissman, C., Espinosa, P., Peru : Centro International de la Papa - ISBN 9789978222829 - p. 49 - 69.
    Carbofuran presence in soil leachate, groundwater, and surface water in the potato growing area in Carchi, Equador
    Jaramillo, R. ; Bowen, W. ; Stoorvogel, J.J. - \ 2001
    In: CIP Program Report 1999-2000 Lima : Int. Potato Center - p. 355 - 360.
    Occurrence of soil water repellency in arid and humid climates
    Jaramillo, D.F. ; Dekker, L.W. ; Ritsema, C.J. ; Hendrickx, J.M.H. - \ 2000
    Journal of Hydrology 231/232 (2000). - ISSN 0022-1694 - p. 105 - 111.
    bodemwater - hydratatie - afstoting - dehydratie - evaporatie - humide klimaatzones - soil water - hydration - repellency - dehydration - evaporation - humid zones
    Soil measurements during HAPEX-Sahel intensive observation period.
    Cuenca, R.H. ; Brouwer, J. ; Chanzy, A. ; Droogers, P. ; Galle, S. ; Gaze, S.R. ; Sicot, M. ; Stricker, J.N.M. ; Angulo-Jaramillo, R. ; Boyle, S.A. ; Bromley, J. ; Chebhouni, A.G. - \ 1997
    Journal of Hydrology 188/189 (1997). - ISSN 0022-1694 - p. 224 - 266.
    bodemwatergehalte - neerslag - hydrologie - sahel - soil water content - precipitation - hydrology - sahel
    This article describes measurements made at each site and for each vegetation cover as part of the soils program for the HAPEX-Sahel regional scale experiment. The measurements were based on an initial sampling scheme and included profile soil water content, surface soil water content, soil water potential, infiltration rates, additional measurements on core samples, and grain size analysis. The measurements were used to categorize the state of the surface and profile soil water regimes during the experiment and to derive functional relationships for the soil water characteristic curve, unsaturated hydraulic conductivity function, and infiltration function. Sample results for different supersites and different vegetation covers are presented showing soil water profiles and total soil water storage on days corresponding to the experimental 'Golden Days'. Sample results are also presented for spatial and temporal distribution of surface moisture content and infiltration tests. The results demonstrate that the major experimental objective of monitoring the supersites during the most rapid vegetative growth stage with the largest change of the surface energy balance following the rainy season was very nearly achieved. Separation of the effects of probable root activity and drainage of the soil profile is possible. The potential for localized advection between the bare soil and vegetation strips of the tiger bush sites is demonstrated.
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