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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Analysis of metabolome changes in the bile acid pool in feces and plasma of antibiotic-treated rats
Behr, C. ; Slopianka, M. ; Haake, V. ; Strauss, V. ; Sperber, S. ; Kamp, H. ; Walk, T. ; Beekmann, K. ; Rietjens, I.M.C.M. ; Ravenzwaay, B. van - \ 2019
Toxicology and Applied Pharmacology 363 (2019). - ISSN 0041-008X - p. 79 - 87.
Antibiotics - Bile acid profiling - Gut microbiome - Metabolomics - Microbiome-related metabolites - Repeated dose oral toxicity study

The bile acid-liver-gut microbiota axis plays an important role in the host's health. The gut microbiota has an impact on the bile acid pool, but also the bile acids themselves can influence the gut microbiota composition. In this study, six antibiotics from five different classes (i.e. lincosamides, glycopeptides, macrolides, fluoroquinolones, aminoglycosides) were used to modulate microbial communities of Wistar rats to elucidate changes in the bile acid metabolism and to identify key metabolites in the bile acid pool related to gut microbial changes. 20 primary and secondary bile acids were analyzed in plasma and feces of control and treated animals. Antibiotics treatment induced significant changes in primary and secondary bile acids in both matrices. Taurine-conjugated primary bile acids significantly increased in plasma and feces. Contrary, cholic acid and most of the analyzed secondary bile acids significantly decreased in plasma, and cholic acid accumulated in the feces after treatment with all antibiotics but roxithromycin. Despite the different activity spectra of the antibiotics applied against gut microbes, the overall effect on the bile acid pool tended to be similar in both matrices except for streptomycin. These results show that changes in the gut microbial community affect the bile acid pool in plasma and feces and that changes in the bile acid profile can be indicative of alterations of the gut microbiome. Due to the important role of bile acids for the host, changes in the bile acid pool can have severe consequences for the host.

Impact of lincosamides antibiotics on the composition of the rat gut microbiota and the metabolite profile of plasma and feces
Behr, C. ; Ramírez-Hincapié, S. ; Cameron, H.J. ; Strauss, V. ; Walk, T. ; Herold, M. ; Beekmann, K. ; Rietjens, I.M.C.M. ; Ravenzwaay, B. van - \ 2018
Toxicology Letters 296 (2018). - ISSN 0378-4274 - p. 139 - 151.
Antibiotics - Gut microbiome - Metabolomics - Microbiome-related metabolites - Repeated dose oral toxicity study - Taxonomic profiling

The importance of the gut microorganisms and their wide range of interactions with the host are well-acknowledged. In this study, lincomycin and clindamycin were used to modulate microbial communities of Wistar rats to gain a comprehensive understanding of the implications of microbiome alterations. A metabolomics approach and taxonomic profiling were applied to characterize the effects of these antibiotics on the functionality of the microbiome and to identify microbiome-related metabolites. After treatment, the diversity of the microbial community was drastically reduced. Bacteroidetes and Verrucomicrobia were drastically reduced, Tenericutes and Deferribacteres completely disappeared, while abundance of Firmicutes and Proteobacteria were highly increased. Changes in plasma and feces metabolites were observed for metabolites belonging mainly to the class of complex lipids, fatty acids and related metabolites as well as amino acids and related compounds. Bile acid metabolism was markedly affected: taurocholic acid, glycochenodeoxycholic acid and cholic acid presented abrupt changes showing a specific metabolite pattern indicating disruption of the microbial community. In both plasma and feces taurocholic acid was highly upregulated upon treatment whereas glycochenodeoxycholic acid was downregulated. Cholic acid was upregulated in feces but downregulated in plasma. These results show that changes in the gut microbial community lead to alterations of the metabolic profile in blood and feces of the host and can be used to identify potentially microbiome-related metabolites. This implies that metabolomics could be a suitable tool to estimate the extent of changes induced in the intestinal microbiome with respect to consequences for the host.

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 (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.

Microbiome-related metabolite changes in gut tissue, cecum content and feces of rats treated with antibiotics
Behr, C. ; Sperber, S. ; Jiang, X. ; Strauss, V. ; Kamp, H. ; Walk, T. ; Herold, M. ; Beekmann, K. ; Rietjens, I.M.C.M. ; Ravenzwaay, B. van - \ 2018
Toxicology and Applied Pharmacology 355 (2018). - ISSN 0041-008X - p. 198 - 210.
Antibiotics - Gut content and tissue - Gut microbiome - Metabolite profiling - Metabolomics - Repeated dose oral toxicity study

The metabolic functionality of the gut microbiota contributes to the metabolism and well-being of its host, although detailed insight in the microbiota's metabolism is lacking. Omics technologies could facilitate unraveling metabolism by the gut microbiota. In this study, we performed metabolite profiling of different matrices of the gut, after antibiotic treatment of rats in order to evaluate metabolite changes observed at different dose levels and in different sexes, and to identify the best tissue matrix for further investigations regarding an assessment of metabolic effects of new compounds with antibiotic activity. Three different antibiotics (vancomycin, streptomycin and roxithromycin) were administered orally to rats for 28 days according to the OECD 407 guideline with a subsequent metabolic profiling in feces, cecum content and gut tissue (jejunum, ileum, cecum, colon and rectum). The data were analyzed in the MetaMap®Tox database. Treatment-related effects could be observed in the metabolite profile of feces and cecum content, but not of the different gut tissues. The metabolite profile showed compound specific effects on the microbiome. In line with the activity spectra of the antibiotics tested, vancomycin showed the largest effects, followed by roxithromycin and then by streptomycin for which changes were modest. In general, for all antibiotics the largest changes were observed for the classes of lipids (increase up to 94-fold), bile acids (increase up to 33-fold), amino acids (increase up to 200-fold) and amino acid related (increase up to 348-fold). The most relevant changes in metabolite values were similar in feces and cecum content and among sexes. The results of this targeted analysis indicate that the metabolic profiles of male and female animals in the gut microbiome are comparable. Concluding, taking other samples than feces does not add any extra information. Thus, as a non-invasive sampling method, feces provide a suitable matrix for studies on metabolism by the gut microbiota.

Gut microbiome-related metabolic changes in plasma of antibiotic-treated rats
Behr, C. ; Kamp, H. ; Fabian, E. ; Krennrich, G. ; Mellert, W. ; Peter, E. ; Strauss, V. ; Walk, T. ; Rietjens, I.M.C.M. ; Ravenzwaay, B. van - \ 2017
Archives of Toxicology 91 (2017)10. - ISSN 0340-5761 - p. 3439 - 3454.
Antibiotics - Metabolomics - Microbiome - Plasma metabolite profiling - Repeated dose oral toxicity study

The intestinal microbiota contributes to the metabolism of its host. Adequate identification of the microbiota’s impact on the host plasma metabolites is lacking. As antibiotics have a profound effect on the microbial composition and hence on the mammalian-microbiota co-metabolism, we studied the effects of antibiotics on the “functionality of the microbiome”—defined as the production of metabolites absorbed by the host. This metabolomics study presents insights into the mammalian-microbiome co-metabolism of endogenous metabolites. To identify plasma metabolites related to microbiome changes due to antibiotic treatment, we have applied broad-spectrum antibiotics belonging to the class of aminoglycosides (neomycin, gentamicin), fluoroquinolones (moxifloxacin, levofloxacin) and tetracyclines (doxycycline, tetracycline). These were administered orally for 28 days to male rats including blood sampling for metabolic profiling after 7, 14 and 28 days. Fluoroquinolones and tetracyclines can be absorbed from the gut; whereas, aminoglycosides are poorly absorbed. Hippuric acid, indole-3-acetic acid and glycerol were identified as key metabolites affected by antibiotic treatment, beside changes mainly concerning amino acids and carbohydrates. Inter alia, effects on indole-3-propionic acid were found to be unique for aminoglycosides, and on 3-indoxylsulfate for tetracyclines. For each class of antibiotics, specific metabolome patterns could be established in the MetaMap®Tox data base, which contains metabolome data for more than 550 reference compounds. The results suggest that plasma-based metabolic profiling (metabolomics) could be a suitable tool to investigate the effect of antibiotics on the functionality of the microbiome and to obtain insight into the mammalian-microbiome co-metabolism.

Population-level effects and recovery of aquatic invertebrates after multiple applications of an insecticide
Dohmen, P. ; Preuss, T.G. ; Hamer, M. ; Galic, N.G. ; Strauss, T. ; Brink, P.J. van den - \ 2016
Integrated Environmental Assessment and Management 12 (2016)1. - ISSN 1551-3793 - p. 67 - 81.
Standard risk assessment of plant protection products (PPP) combines “worst-case” exposure scenarios with effect thresholds using assessment (safety) factors to account for uncertainties. If needed, risks can be addressed applying more realistic conditions at higher tiers, which refine exposure and/or effect assessments using additional data. However, it is not possible to investigate the wide range of potential scenarios experimentally. In contrast, ecotoxicological mechanistic effect models do allow for addressing a multitude of scenarios. Furthermore, they may aid the interpretation of experiments such as mesocosm studies, allowing extrapolation to conditions not covered in experiments. Here, we explore how to use mechanistic effect models in the aquatic risk assessment of a model insecticide (Modelmethrin), applied several times per season but rapidly dissipating between applications. The case study focuses on potential effects on aquatic arthropods, the most sensitive group for this substance. The models provide information on the impact of a number of short exposure pulses on sensitive and/or vulnerable populations and, when impacted, assess recovery. The species to model were selected based on their sensitivity in laboratory and field (mesocosm) studies. The general unified threshold model for survival (GUTS) model, which describes the toxicokinetics and toxicodynamics of chemicals in individuals, was linked to 3 individual-based models (IBM), translating individual survival of sensitive organisms into population-level effects. The impact of pulsed insecticide exposures on populations were modeled using the spatially explicit IBM metapopulation model for assessing spatial and temporal effects of pesticides (MASTEP) for Gammarus pulex, the Chaoborus IBM for populations of Chaoborus crystallinus, and the “IdamP” model for populations of Daphnia magna. The different models were able to predict the potential effects of Modelmethrin applications to key arthropod species inhabiting different aquatic ecosystems; the most sensitive species were significantly impacted unless respective mitigation measures were implemented (buffer zones resulting in reduced exposure). As expected the impact was stronger in shallow ditches as compared to deeper pond scenarios. Furthermore, as expected, recovery depended on factors such as temperature (affecting population growth rate and number of generations) and the occurence of nonimpacted aquatic ecosystems (their frequency and connectivity). These model predictions were largely in line with field observations and/or the results of a mesocosm study, providing additional evidence on the suitability and reliability of the models for risk assessment purposes. Because of their flexibility, models may predict the likelihood of unacceptable effects—based on previously defined protection goals—for a range of insecticide exposure scenarios and freshwater habitats
Ecological Recovery Potential of Freshwater Organisms: Consequences for Environmental Risk Asseswsment of Chemicals
Gergs, A. ; Classen, S. ; Strauss, T. ; Ottermans, R. ; Brock, T.C.M. ; Ratte, H.T. ; Hommen, U. ; Preuss, T.G. - \ 2016
In: Reviews of Environmental Contamination and Toxicology / de Voogt, P., Springer (Reviews of Environmental Contamination and Toxicology 236) - ISBN 9783319200125 - p. 259 - 294.
Chemical contaminants released into the in the environment may have adverse effects on (non-target) species, populations and communities. The return of a stressed system to its pre-disturbance or other reference state, i.e. the ecological recovery, may depend on various factors related to the affected taxon, the ecosystem of concern and the type of stressor with consequences for the assessment and management of risks associated with chemical contaminants. Whereas the effects caused by short-term exposure might be acceptable to some extent, the conditions under which ecological recovery can serve as a decision criterion in the environmental risk assessment of chemical stressors remains to be evaluated. For a generic consideration of recovery in the risk assessment of chemicals, we reviewed case studies of natural and artificial aquatic systems and evaluate five aspects that might cause variability in population recovery time: (1) taxonomic differences and life-history variability, (2) factors related to ecosystem type and community processes, (3) type of disturbance, (4) comparison of field and semi-field studies, and (5) effect magnitude, i.e., the decline in population size following disturbance. We discuss our findings with regard to both retrospective assessments and prospective risk assessment.
State of the art in mechanistic effect modelling for aquatic risk assessment of plant protection products
Preuss, T.G. ; Baveco, J.M. ; Focks, A. ; Hommen, U. ; Strauss, T. ; Thorbek, P. - \ 2015
In: Abstract Book, SETAC Europe 25th Annual Meeting. - SETAC
The minimum detectable difference (MDD) and the interpretation of treatmentr related effects of pesticides in experimental ecosystems
Brock, T.C.M. ; Hammers-Wirtz, M. ; Hommen, U. ; Preuss, T.G. ; Ratte, H.T. ; Roessink, I. ; Strauss, T. ; Brink, P.J. van den - \ 2015
Environmental Science and Pollution Research 22 (2015)2. - ISSN 0944-1344 - p. 1160 - 1174.
zero dose control - risk-assessment - insecticide - mesocosms - models - replicability - microcosms - responses - recovery - systems
In the European registration procedure for pesticides, microcosm and mesocosm studies are the highest aquatic experimental tier to assess their environmental effects. Evaluations of microcosm/mesocosm studies rely heavily on no observed effect concentrations (NOECs) calculated for different population-level endpoints. Ideally, a power analysis should be reported for the concentration–response relationships underlying these NOECs, as well as for measurement endpoints for which significant effects cannot be demonstrated. An indication of this statistical power can be provided a posteriori by calculated minimum detectable differences (MDDs). The MDD defines the difference between the means of a treatment and the control that must exist to detect a statistically significant effect. The aim of this paper is to expand on the Aquatic Guidance Document recently published by the European Food Safety Authority (EFSA) and to propose a procedure to report and evaluate NOECs and related MDDs in a harmonised way. In addition, decision schemes are provided on how MDDs can be used to assess the reliability of microcosm/mesocosm studies and for the derivation of effect classes used to derive regulatory acceptable concentrations. Furthermore, examples are presented to show how MDDs can be reduced by optimising experimental design and sampling techniques.
Miscellaneous standard methods for Apis mellifera research
Human, H. ; Brodschneider, R. ; Dietemann, V. ; Dively, G. ; Ellis, J.D. ; Forsgren, E. ; Fries, I. ; Hatjina, F. ; Hu, F.L. ; Jaffe, R. ; Jensen, A.B. ; Kohler, A. ; Magyar, J.P. ; Ouml;zkyrym, A. ; Pirk, C.W.W. ; Rose, R. ; Strauss, U. ; Tanner, G. ; Tarpy, D.R. ; Steen, J.J.M. van der; Vaudo, A. ; Vejsnaes, F. ; Wilde, J. de; Williams, G.R. ; Zheng, H.Q. - \ 2013
Journal of Apicultural Research 52 (2013)4. - ISSN 0021-8839
honey-bee workers - greatheadii var. davyana - low-temperature narcosis - varroa-jacobsoni oud - carbon-dioxide - nosema-ceranae - developmental stages - nutritional content - drone congregation - natural conditions
A variety of methods are used in honey bee research and differ depending on the level at which the research is conducted. On an individual level, the handling of individual honey bees, including the queen, larvae and pupae are required. There are different methods for the immobilising, killing and storing as well as determining individual weight of bees. The precise timing of developmental stages is also an important aspect of sampling individuals for experiments. In order to investigate and manipulate functional processes in honey bees, e. g. memory formation and retrieval and gene expression, microinjection is often used. A method that is used by both researchers and beekeepers is the marking of queens that serves not only to help to locate her during her life, but also enables the dating of queens. Creating multiple queen colonies allows the beekeeper to maintain spare queens, increase brood production or ask questions related to reproduction. On colony level, very useful techniques are the measurement of intra hive mortality using dead bee traps, weighing of full hives, collecting pollen and nectar, and digital monitoring of brood development via location recognition. At the population level, estimation of population density is essential to evaluate the health status and using beelines help to locate wild colonies. These methods, described in this paper, are especially valuable when investigating the effects of pesticide applications, environmental pollution and diseases on colony survival.
Vertebrate time-tree elucidates the biogeographic pattern of a major biotic change around the K–T boundary in Madagascar
Crottini, A. ; Madsen, Ole ; Poux, C. ; Strauß, A. ; Vieites, D.R. ; Vences, M. - \ 2012
Cretaceous-Tertiary - historical biogeography - lineage diversification - rainforest adaptation - overseas dispersal
The geographic and temporal origins of Madagascar's biota have long been in the center of debate. We reconstructed a time-tree including nearly all native nonflying and nonmarine vertebrate clades present on the island, from DNA sequences of two single-copy protein-coding nuclear genes (BDNF and RAG1) and a set of congruent time constraints. Reconstructions calculated with autocorrelated or independent substitution rates over clades agreed in placing the origins of the 31 included clades in Cretaceous to Cenozoic times. The two clades with sister groups in South America were the oldest, followed by those of a putative Asian ancestry that were significantly older than the prevalent clades of African ancestry. No colonizations from Asia occurred after the Eocene, suggesting that dispersal and vicariance of Asian/Indian groups were favored over a comparatively short period during, and shortly after, the separation of India and Madagascar. Species richness of clades correlates with their age but those clades that have a large proportion of species diversity in rainforests are significantly more species-rich. This finding suggests an underlying pattern of continuous speciation through time in Madagascar's vertebrates, with accelerated episodes of adaptive diversification in those clades that succeeded radiating into the rainforests.
Tradeoffs between characteristics of good participatory processes: initial insights from European River Basin Scenario Workshops
Sarkki, S. ; Varjopuro, R. ; Vliet, M. van - \ 2011
In: Society, Environment and Place in Northern Regions / Nuttall, M., Strauss, H., Tervo-Kankare, K., Oulu : University of Oulu, Thule Institute - ISBN 9789514297410 - p. 61 - 74.
Energy advantages of orientation to solar radiation in three African ruminants
Hetem, R.S. ; Maartin Strauss, W. ; Heusinkveld, B.G. ; Bie, S. de; Prins, H.H.T. ; Wieren, S.E. van - \ 2011
Journal of Thermal Biology 36 (2011)7. - ISSN 0306-4565 - p. 452 - 460.
grazing winter range - behavioral thermoregulation - magnetic alignment - black wildebeest - body orientation - thermal balance - heat gain - cattle - temperature - sun
Animal orientation relative to incident solar radiation allows an animal to effectively adjust the amount of radiant heat gained from an environment. Yet recent literature found ruminants to primarily orientate north/south and proposed magnetic alignment as the most parsimonious explanation. To test whether such northerly orientation has an energy advantage, we used heated cylindrical models to estimate energy costs of thermoregulation associated with north and east orientations of three species of African ruminants under cool winter conditions. Concurrent behavioural observations revealed that eland, blue wildebeest and impala did not preferentially orientate north/south during warm summer or cool winter conditions. Instead, all three species preferred to orientate perpendicular to incident solar radiation during winter and parallel to incident solar radiation during summer, throughout the day. On clear winter days with little wind, more than 60% of animal orientation preference could be accounted for by the energy savings associated with that orientation. Thus energy demands are likely to be the primary driver of animal orientation preferences.
Empirical and theoretical challenges in aboveground-belowground ecology
Putten, W.H. van der; Bardgett, R.D. ; Ruiter, P.C. de; Hol, W.H.G. ; Meyer, K.M. ; Bezemer, T.M. ; Bradford, M.A. ; Christensen, S. ; Eppinga, M.B. ; Fukami, T. ; Hemerik, L. ; Molofsky, J. ; Schädler, M. ; Scherber, C. ; Strauss, S.Y. ; Vos, M. ; Wardle, D.A. - \ 2009
Oecologia 161 (2009)1. - ISSN 0029-8549 - p. 1 - 14.
plant-soil feedback - increased competitive ability - climate-change - community composition - trophic interactions - insect herbivory - enemy release - food-web - terrestrial ecosystems - grassland ecosystems
A growing body of evidence shows that aboveground and belowground communities and processes are intrinsically linked, and that feedbacks between these subsystems have important implications for community structure and ecosystem functioning. Almost all studies on this topic have been carried out from an empirical perspective and in specific ecological settings or contexts. Belowground interactions operate at different spatial and temporal scales. Due to the relatively low mobility and high survival of organisms in the soil, plants have longer lasting legacy effects belowground than aboveground. Our current challenge is to understand how aboveground¿belowground biotic interactions operate across spatial and temporal scales, and how they depend on, as well as influence, the abiotic environment. Because empirical capacities are too limited to explore all possible combinations of interactions and environmental settings, we explore where and how they can be supported by theoretical approaches to develop testable predictions and to generalise empirical results. We review four key areas where a combined aboveground¿belowground approach offers perspectives for enhancing ecological understanding, namely succession, agro-ecosystems, biological invasions and global change impacts on ecosystems. In plant succession, differences in scales between aboveground and belowground biota, as well as between species interactions and ecosystem processes, have important implications for the rate and direction of community change. Aboveground as well as belowground interactions either enhance or reduce rates of plant species replacement. Moreover, the outcomes of the interactions depend on abiotic conditions and plant life history characteristics, which may vary with successional position. We exemplify where translation of the current conceptual succession models into more predictive models can help targeting empirical studies and generalising their results. Then, we discuss how understanding succession may help to enhance managing arable crops, grasslands and invasive plants, as well as provide insights into the effects of global change on community re-organisation and ecosystem processes
Inducible colony formation within the Scenedesmaceae: Adaptive responses to infochemicals from two different herbivore taxa
Verschoor, A.M. ; Stap, I. ; Helmsing, N.R. ; Lürling, M.F.L.L.W. ; Donk, E. van - \ 2004
Journal of Phycology 40 (2004)5. - ISSN 0022-3646 - p. 808 - 814.
green-alga scenedesmus - daphnia - chlorophyceae - defenses - zooplankton - morphology - chlorococcales - substances - induction - obliquus
We studied the occurrence of colony formation within 40 different strains of Scenedesmaceae (Chlorococcales, Chlorophyta) in response to grazing-released infochemicals from the herbivorous zooplankters Brachionus calyciflorus Pallas (Rotifera) and Daphnia magna Strauss (Cladocera). With the exception of two strains, all strains showed similar responses to both B. calyciflorus and D. magna infochemicals, either no response or inducible colony formation. Colony size was found to increase with B. calyciflorus infochemical concentration and could be described by a sigmoid function. The increase in colony size was more pronounced in the Scenedesmus species tested than in Desmodesmus species, which was probably due to higher threshold infochemical concentrations for colony induction in Desmodesmus. Therefore, the adaptivity of colony formation to the herbivory threat only holds above the threshold concentration for colony induction and as long as maximum colony size has not been attained. Taking this into account, our results suggest that inducible colony formation is a common adaptive response of many Scenedesmaceae to the threat of herbivory.
Informal Security Systems in Southern Africa and Approaches to Strengthen them through Policy Measures
Benda-Beckmann, F. von; Kirsch, R. - \ 1999
In: The Real World of Social Policy. An anthology of project experience / Freiberg-Strauss, J., Meyer, K., Wiesbaden : Universum Verlagsanstalt - p. 22 - 40.
The capacity of social security systems in Southern Africa : conditions, constellations and socio-political relevance : [seminar, Mangochi, Malawi, September 11 - 15, 1995]
Benda-Beckmann, F. von; Kirsch, R. ; Freiberg-Strauss, J. - \ 1997
Eschborn : GTZ - 72 p.
Baculovirus DNA replication
Kool, M. - \ 1994
Agricultural University. Promotor(en): R.W. Goldbach; J. Tramper; Just Vlak. - S.l. : Kool - ISBN 9789054852629 - 200
baculovirus - kernpolyedervirussen - moleculaire genetica - replicatie - translatie - eiwitsynthese - nuclear polyhedrosis viruses - molecular genetics - replication - translation - protein synthesis
<p>Baculoviruses are attractive biological agents for the control of insect pests. They are highly specific for insects and cause a fatal disease (Granados and Federici, 1986). in addition, baculoviruses are successfully exploited as expression vectors for the production of heterologous proteins for various applications (Luckow and Summers, 1988; Luckow, 1991). In both cases large-scale systems for the production of baculoviruses are important. Production in insect larvae is difficult to scale up and to control. Insect-cell cultures offer an attractive alternative. Moreover, in the case of pharmaceuticals and diagnostics in human and veterinary medicine insect-cell systems have to be applied since such systems are well defined.<p>Due to the great interest in baculoviruses as biological insecticides and expression vectors for foreign genes, the molecular genetic aspects of especially the <em>Autographa californica</em> multiple nucleocapsid nuclear polyhedrosis virus (AcMNPV), the type member of the <em>Baculoviridae,</em> have been studied in much detail (Blissard and Rohrmann, 1990). Chapter 2 of this thesis presents, as of March 1994, an overview of the structural and functional organization of the AcMNPV genome. The genomes of AcMNPV (R.D. Possee, pers. comm.) and <em>Bombyx mori</em> MNPV (BmMNPV) (S. Maeda, pers. comm.) have been completely sequenced but are awaiting publication. In contrast to other large DNA viruses such as adenovirus, herpesviruses, and vacciniavirus (Fields and Knipe, 1990), the process of baculovirus DNA replication of AcMNPV is poorly understood. At the start of this study a few genes were found which were thought to be involved in AcMNPV DNA replication such as a helicase and a DNA polymerase. Sequences representing the origin of AcMNPV DNA replication were not known.<p>Baculoviruses can be produced on a large scale in insect-cell cultures using batch (Maiorella <em>et al.,</em> 1988), semicontinuous (Hink and Strauss, 1980) <em></em> and continuous reactors (Kompier <em>et al.,</em> 1988). <em></em> Continuous production of wild-type (wt) AcMNPV and recombinants thereof was achieved in a system consisting of one bioreactor producing insect cells in series with a second bioreactor for virus infection and protein production (Kompier <em>et al.,</em> 1988; <em></em> Van Lier <em>et al.,</em> 1992). <em></em> After a few weeks of continuous operation, however, the productivity decreased to a low level. In the case of wt AcMNPV, the number of polyhedra per cell, the fraction of cells containing polyhedra, and the concentration of extracellular virus were found to be decreased (Kompier <em>et al.,</em> 1988). Continuous production of an AcMNPV recombinant where the polyhedrin gene was replaced by the lacZ gene of <em>Escherichia coli</em> essentially gave the same results (Van Lier <em>et al.,</em> 1992). <em></em> The decrease of virus production was ascribed to a phenomenon known as passage effect (Tramper and Vlak, 1986), <em></em> but the underlying mechanism remained unknown.<p>Analysis of samples obtained from continuous bioreactor systems (Chapter <em>3)</em> showed that with ongoing production a mutant AcMNPV became dominant. This mutant lacked about <em>43%</em> of the original genome. The deleted DNA included the polyhedrin gene and several genes essential for DNA replication. The replication of the mutant appeared to be dependent on the presence of an intact helper AcMNPV. The passage effect in the continuous system is thus thought to be the result of interference between the deletion mutant and helper virus. These so-called defective interfering particles (DIPs) can only accumulate when the concentration of the intact virus is high enough to support the replication of these DIPs. Thus, for a successful continuous production of baculoviruses low multiplicities of infection should be used to avoid the accumulation of DIPs.<p>One of the regions of the AcMNPV genome putatively involved in the generation of the DIPs is located in the EcoRI-C fragment of AcMNPV. Deletion mutants often lacked a considerable portion of <em>Eco</em> RI-C, but also maintained a consistent segment of this fragment that may be essential for replication and/or encapsidation. To investigate the genetic functions of the EcoRI-C fragment in the defective genomes and their possible role in the generation of these genomes, the nucleotide sequence of a <em>7.3</em> kilobase pair region of the right part of the <em>Eco</em> RI-C fragment was determined (Chapter 4). <em></em> Eight putative open reading frames (ORFs) were identified and their respective amino acid sequences compared with a number of data libraries, The product of ORF 1227 <em></em> corresponded with GP41, <em></em> a virion protein, and its predicted protein sequence was found to be 55 amino acids longer at its C-terminus than reported previously (Whitford and Faulkner, 1992). The majority of ORF 1227, including the additional 55 amino acids, moreover, showed a high degree of homology with protein P40 of <em>Helicoverpa zea</em> SNPV, also a structural virion protein (Ma <em>et al.,</em> 1993). Three other ORFs in the analyzed AcMNPV region showed homology with ORF's in the HzSNPV sequence, indicating that the general organization of this region is similar in both viruses, and possibly between MNPVs and SNPVs. However, no sequences have yet been identified within this region that may play a role in the generation and/or encapsidation of the DIPs.<p>The generation and characterization of DIPs was further investigated in Chapter 5. Three small separate regions, representing only 5 % of the original AcMNPV genome, were found to be retained in DNA of defective genomes after 40 serial passages in insect cells with undiluted inocula. Independently, Lee and Krell (1992) showed that after 80 serial passages of AcMNPV, DIPs were found which contained tandem repeats of DNA, mainly derived from a small region of the AcMNPV genome, located in the <em>Hin</em> dIII-K fragment. Since all these defective genomes were still able to replicate in insect cells, although only with the help of intact virus, they must have retained essential cis-acting elements necessary for DNA replication. Therefore, a replication assay was developed to study whether these regions, retained in the defective genomes, contained <em>cis</em> -acting elements such as an origin ( <em>ori</em> ) of DNA replication. Transfection of <em>Spodoptera frugiperda</em> cells with plasmids containing these sequences followed by superinfection with intact helper AcMNPV resulted in amplification of these plasmids, as demonstrated by the <em>Dpn</em> I sensitivity <em></em> assay. In order to demonstrate replicating activity of these plasmids, it appeared essential to transfect the cells well (24 h) before superinfection with helper virus, and for an optimal replication result the multiplicity used for superinfection had to be I or lower (Chapters 5 and 6). Using this assay seven putative origins of DNA replication were identified in the AcMNPV genome (Chapters 5, 6, and 7).<p>Six of the seven putative <em>ori's</em> were found in the homologous regions <em>hr</em> 1, <em>hr</em> 2, <em>hr</em> 3, <em>hr</em> 4a, <em>hr</em> 4b, and <em>hr</em> 5 of AcMNPV (Chapter 6), which are interspersed along the genome (Cochran and Faulkner, 1983; Guarino <em>et al.,</em> 1986). Recently, another <em>hr</em> region, <em>hr</em> 1a, has been identified in the AcMNPV genome, that could also serve as <em>ori</em> in a replication assay (Leisy and Rohrmann, 1993). Initial studies demonstrated that the <em>hr</em> regions function as enhancers for transcription, when placed in <em>cis</em> to the promoter of early baculovirus genes (Guarino <em>et</em><em>al.,</em> 1986; Guarino and Summers, 1986). <em></em> Rodems and Friesen (1993) demonstrated that <em>hr</em> regions also function as enhancers <em>in vivo</em> . These results together with the data of this thesis imply that all <em>hr's</em> in AcMNPV may be bifunctional <em>in vivo</em> , i.e. have both enhancer and <em>ori</em> activity. Sequence analysis has shown that <em>hr's</em> contain two to eight 30 bp imperfect palindromes, interspaced by other repeated sequences, and that each palindrome contains a naturally occurring <em>Eco</em> RI site at its core (Guarino <em>et al.,</em> 1986; Guarino and Summers, 1986). <em></em> One copy of such a palindrome appeared to be sufficient for either enhancer function or <em>ori</em> activity (Guarino et al., 1986; Pearson <em>et al.</em> , 1992).<p>In addition to the seven <em>hr's,</em> the <em>Hin</em> dIII-K fragment of AcMNPV was also found to carry a putative <em>ori</em> , although this fragment does not contain an <em>hr</em> region (Chapter 6). <em></em> The <em>Hin</em> dIII-K ori had a complex structure (Chapter 7), resembling those of other large DNA viruses. This <em>ori</em> contained several regions, some of which were found to be essential for its activity, whereas others contain auxiliary sequences, that enhance <em>ori</em> activity. Sequence analysis of these regions identified several structures often found in other viral replication <em>ori's</em> , such as palindromes and other repeated motifs (DePamphilis, <em>1993).</em> Recently an <em>ori</em> , also with a complex structure, but different from AcMNPV <em>hr's,</em> has been identified in another baculovirus, <em>Orgyia pseudotsugata</em> MNPV (OpMNPV) (Pearson <em>et al.,</em> 1993).<p>The individual role of all these <em>ori's</em> during viral DNA replication, and whether they are all active simultaneously <em>in vivo</em> , is unclear. Deletion of <em>hr</em> 5 from the AcMNPV genome or the closely related <em>Bombyx mori</em> MNPV (BmMNPV) genome had no effect on the replication of these viruses (Rodems and Friesen, 1993; Majima <em>et al.,</em> 1993) <em>.</em> Also from the experiments with DIPs generated by serial passaging it can be deduced that not all the <em>ori's</em> are necessary for replication of the genome. After 40 serial, undiluted passages three small segments of the genome were predominantly found to be retained, harbouring only the <em>hr</em> 1, <em>hr</em> 3, and <em>hr</em> 5 <em></em> regions (Chapter 5). Deletion of all <em>hr's</em> would indicate the importance of these regions for virus replication <em>in vivo.</em><p>The importance of the <em>ori</em> in the <em>Hin</em> dIII-K fragment <em></em> is supported by sequence data of the corresponding region in the closely related BmMNPV (Kamita <em>et al.,</em> 1993). Although most of the auxiliary sequences of this <em>ori</em> were found to be deleted in the BmMNPV genome, the essential part of this <em>ori</em> , containing the palindromes and the A/T rich region, was retained suggesting that these elements could not be deleted. These sequence data and the observation that after prolonged serial passage of AcMNPV (80 passages) large replicating DNA molecules are found in which repeated sequences from the <em>Hin</em> dIII-K fragment accumulate (Lee and Krell, 1992), may be a reflection of the importance of this region as genuine <em>ori</em><em>in vivo</em> (Chapter 7).<p>The occurrence of multiple <em>ori's</em> is not unique for baculoviruses, but has also been reported for herpesviruses and Chilo iridescent virus (CIV). The genome of herpes simplex virus I (HSV-1) contains three <em>ori's</em> , <em>ori</em><sub><font size="-2">L</font></sub> , and two copies of <em>ori</em> , (for review, see Fields and Knipe, 1990) and it has been shown that the presence of a single <em>ori</em> , independent which one, is sufficient for replication (Longnecker and Roizman, 1986; Polvino-Bodnar <em>et al.</em> , 1987; Igarashi <em>et al.</em> , 1993). In CIV at least six putative <em>ori's</em> have been identified (Handermann <em>et al.</em> , 1992). It remains to be seen whether in the case of baculoviruses each of the eight putative <em>ori's</em> is necessary for viral replication. When the <em>ori's</em> are indeed functionally redundant, the presence of multiple <em>ori's</em> in the viral genome may increase the frequency of initiation and thus increase the speed of DNA replication. Analysis of intermediates of DNA replication may shed more light on the nature of <em>in vivo ori's</em> .<p>The experiments in Chapter 6 also supported the view that a circular topology is a prerequisite for replication of <em>ori</em> -containing plasmids. Linear DNA, even if it contained an <em>ori</em> , did not replicate. These results are in line with the circular nature of baculovirus DNA and suggest a model for baculovirus replication involving a theta structure or a rolling circle. The latter model is supported by data of Leisy and Rohrmann (1993), who demonstrated that replicating plasmids form large concatemeric molecules. In addition, the finding of defective genomes with many reiterations (concatemers) of a 2.8 kbp segment, mainly mapping in the AcMNPV <em>Hin</em> dIII-K fragment (Lee and Krell, 1992), supported also a rolling circle as model for DNA replication.<p>Not only <em>cis</em> -acting elements, but also <em>trans</em> -acting factors are important for DNA replication. Chapters 8 and 9 describe the functional mapping of AcMNPV genes required for DNA replication. A transient complementation assay was employed, in which, instead of AcMNPV infection, four co-transfected cosmid clones, encompassing almost the entire genome, provided all the essential <em>trans</em> -acting factors for plasmid DNA replication. No replication of plasmids occurred when one of the cosmids was omitted from the transfection mixture. This result indicated that this assay was a valid and powerful approach to identify the AcMNPV replication genes. The assay was first used to define essential regions in the four cosmids (Chapter 8). Six essential regions were retrieved and these were further subcloned and tested (Chapter 9). Initially in this assay, plasmid replication appeared to be independent of the presence, in <em>cis</em> , of a viral <em>ori</em> , when cloned genes or viral DNA were used instead of complete virus to supply essential <em>trans</em> -acting factors (Chapter 8). However, this was caused by employing high gene copy numbers in the transfections (Chapter 9). As a consequence, a relative abundance of proteins is produced, which may lead to a saturation of specific origins with these proteins. The excess of proteins thus can bind to other originlike structures, even when the affinities are low, and hence cause replication of any plasmid.<p>Nine genes involved in DNA replication were identified in the AcMNPV genome (Chapter 9). Six genes, specifying <em>helicase, dna pol, ie-1, lef-1, lef-2,</em> and <em>lef-3</em> , were found to be essential, while three genes, <em>p35, ie-2</em> , and <em>pe38</em> , stimulated DNA replication. No stimulation was observed by the <em>pcna</em> -like protein gene. Two of the three identified stimulatory genes, <em>ie-2</em> and <em>pe38</em> , are known as transactivators for transcription (Carson <em>et al.</em> , 1988; Lu and Carstens, 1993), whereas the third stimulating gene, <em>p35</em> , has previously been identified as inhibitor of virus-induced apoptosis in <em>S. frugiperda cells</em> (Clem <em>et al.</em> , 1991). However, the observation that infection with a <em>p35</em> deletion mutant in <em>Trichoplusia ni</em> cells did not result in a reduction of virus production (Clem <em>et al.</em> , 1991) suggests that the stimulating effect of <em>p35</em> in the transient replication assays is not based on activation of the replication process, but is due to inhibiting apoptosis, which may be induced by the expression of one or more of the replication genes.<p>Of the six essential AcMNPV DNA replication proteins, putative functions could only be attributed for the helicase and DNA polymerase, based on their homology with other known helicases and DNA polymerases (Lu and Carstens, 1991; Tomalski <em>et al.</em> , 1988). Studying other viral systems, a number of striking similarities was noticed between <em>Baculoviridae</em> and <em>Herpesviridae</em> . Although these two viral families have traditionally been separated based on their different morphology and host specificity, they both have a large double stranded DNA genome, which replicates in the host cell nucleus, and has a circular form in at least one stage of their replication cycle. Their genomes may also replicate in a similar manner as transfection of origin-containing plasmids into infected cells resulted in large concatemers of input plasmid DNA (Leisy and Rohrmann, 1993; Hammerschmidt and Mankertz, 1991). Most strikingly, the number of essential replication genes is similar for both baculoviruses and herpesviruses. An attempt was made to relate the other four, hitherto unassigned, baculovirus replication proteins, IE-1, LEF-1, LEF-2, and LEF-3 with proteins involved in herpesvirus DNA replication (Chapter 10).<p>Firstly, the sequences of replication proteins of five different herpesviruses were aligned, which resulted in the identification of a number of conserved motifs in these proteins. Many of these conserved motifs showed (distant) homology with the four baculovirus replication proteins and, most importantly, in the same linear spatial organization as in their putative herpesvirus homologues. Using these conserved motifs as markers the four replication proteins IE-1, LEF-1, LEF- 2, and LEF-3 of AcMNPV were aligned with herpesvirus homologues (Chapter 10). These alignments suggest that <em>ie-1</em> codes for a single stranded DNA binding protein (SSB), <em>lef-1</em> for a primase-associated protein, <em>lef-2</em> for a DNA polymerase processivity factor, and <em>lef-3</em> for a primase. The assignment to <em>ie-1</em> to code for a SSB was further supported by the finding of a conserved known single stranded DNA binding sequence motif in six baculovirus IE-1, proteins, which is also found in many other prokaryotic and eukaryotic SSBs (Chapter 10). Further computer-assisted examination and biochemical analysis has to be done to confirm the suggested functions for the four baculovirus replication proteins.<p>The similarity between <em>Baculoviridae</em> and <em>Herpesviridae</em> in DNA structure and mechanism of DNA replication, added to the employment of an identical kind and amount of essential replication genes, poses the question whether these two groups of viruses share a common lineage. On the basis of the mutation rate of the conserved baculovirus polyhedrin genes as compared to the insect species in which they occur (Vlak and Rohrmann, 1985) it has been postulated that baculoviruses are ancient viruses that have evolved along with the insects. The relationship among replication genes could imply that herpesviruses have evolved from baculoviruses along with their invertebrate hosts towards vertebrates. Alternatively, the emergence of herpesviruses may be the result of an independent, parallel evolutionary event in ancient vertebrates. Since viral DNA replication in nuclear environments is a conserved process, conserved host replication genes may have been. independently transduced into different ancient viral genomes.
Conjugal gene transfer between bacteria in soil and rhizosphere
Smit, E. - \ 1994
Agricultural University. Promotor(en): W.M. de Vos; J.D. van Elsas. - S.l. : Smit - ISBN 9789054852193 - 140
micro-organismen - bacteriën - classificatie - taxonomie - genetische modificatie - recombinant dna - heritability - genetica - overerving - microorganisms - bacteria - classification - taxonomy - genetic engineering - genetics - inheritance
<p>The extent of possible conjugal transfer of recombinant DNA present in genetically engineered microorganisms (GEMs) was studied. Occurrence of transfer of recombinant DNA is only one of the concerns regarding the use of GEMs (Chapter 2). Other potential hazards preventing the application of GEMs for agricultural purposes are (1) possible pathogenicity, (2) disturbance of ecological balance, (3) unwanted biochemical reactions, and (4) negative effects on diversity and specific populations (Levin and Strauss, 1991). The fate of GEMs introduced into soil is not very predictable, since knowledge on most of the aforementioned aspects is scarce. In most countries strict regulations limit large scale field studies with GEMs, which slows down research.<p>Research was focused on (1) development of sensitive detection techniques to study GEMs in soil, (2) detection of conjugal plasmid transfer to indigenous bacteria in soil, (2) assessing the fate of recombinant DNA present in different genomic locations. The soil isolate <em>Pseudomonas fluorescens</em> R2f was chosen as model microorganism. All studies were done <em>in vitro</em> and in soil microcosms which were planted whith wheat.<p>Studying conjugal transfer between homologous donor and recipient strains introduced into soil we found that matings could occur on the transconjugant selective plates, thus obscuring the real number of transconjugants in soil (Chapter 3). The use of nalidixic acid instead of streptomycin (in conjunction with rifampicin) to select for recipients which received the plasmid and to counterselect the donor, was shown to prevent these plate matings. The use of nalidixic acid to prevent plate mating was later confirmed by Walter et al., (1991). Employing this donor counterselection, it was shown that the number of transconjugants decreased with decreasing numbers of introduced donor and recipient cells. However, transconjugants could only be detected when the soil was amended with nutrients or bentonite clay or when plant roots were present. The fact that plasmid transfer between <em>P.</em><em>fluorescens</em> R2f strains was enhanced in the rhizosphere was not entirely surprising since this organism was originally isolated from the rhizosphere. Stimulation of plasmid transfer by addition of nutrients or the presence of plant roots was also found by others (Stotzky, 1989; Edwards, 1993).<p>Experiments in which both donor and recipient are introduced, might be indicative for factors affecting conjugal gene transfer, however they do not necessarily predict transfer to indigenous bacteria. Most potential indigenous recipients are generally in a different physiological state than the freshly cultured, metabolically active, introduced recipients. To detect transfer to indigenous bacteria, another donor counterselection method was developed (Chapter 4). A phage specific for the donor strain, ΦR2f, was isolated, which could be used to lyse the donor prior to plating on transconjugant-selective plates. The selftransmissible plasmid RP4p which containes suitable antibiotic resistance genes for selection, had been marked previously with an eukaryotic DNA fragment for hybridization purposes, giving RP4p. RP4p transfer to indigenous bacteria was observed in the rhizosphere of wheat (Chapter 5). The number of indigenous transconjugants detected was around 10 <sup><font size="-2">3</font></SUP>cfu/g of soil, while transconjugant numbers in the corresponding bulk soil were just below 10 <sup><font size="-2">2</font></SUP>cfu/g of soil. All indigenous transconjugants analysed contained the plasmid, and all were able to transfer RP4p to a <em>P.</em><em>fluorescens</em> recipient strain in control filter matings. The transconjugants were identified as belonging to the genera <em>Pseudomonas, Enterobacter, Comamonas</em> and <em>Alcaligenes.</em> These genera fit very well into the known host range of RP4 (Thomas, 1989).<p>Transfer of RP4p to indigenous bacteria was also studied in four different soils (Chapter 6). Highest numbers of transconjugants per g of dry soil were found in Montrond silt loam and Flevo silt loam (10 <sup><font size="-2">3</font></SUP>-10 <sup><font size="-2">4</font></SUP>), whereas in Ede loamy sand and Loss silt loam transconjugant numbers were around 10 <sup><font size="-2">2</font></SUP>. The presence of plant roots affected transconjugant numbers to a significant extent in Ede loamy sand and Loss silt loam but not in the other soils. High clay and organic matter contents as present in Flevo silt loam and Montrond silt loam might be favourable for conjugal transfer and obscure any stimulatory effect of the rhizosphere.<p>Since selftransmissible plasmids are not likely to be used as vectors for inserting recombinant DNA in GEMs, possible transfer of a marked IncQ plasmid was studied (Chapter 7). A marker cassette was constructed based on two antibiotic resistance genes, <em>npt</em> II <em></em> and <em>aad</em> B <em></em> conferring resistance against kanamycin and gentamycin, and part of a <em>Bacillus thuringiensis</em> endotoxin gene, <em>cry</em> IVB <em></em> was used as molecular marker. This marker cassette was cloned an IncQ plasmid (a RSF1010 derivative) wich resulted in plasmid pSKTG. Mobilization of the non-selftransmissible plasmid pSKTG was studied in filter matings, in sterile soil and in natural soil. In filter matings, pSKTG was only mobilized in the presence of RP4p. Transfer frequencies in bi- and tri-parental matings were in the same range, indicating that apparently cell-to-cell contact was not a limiting factor. In sterile soil, mobilization frequencies of pSKTG with RP4p present in the same strain were 100-fold lower then on filters (10 <sup><font size="-2">-4</font></SUP>). When RP4p was present in a separately introduced strain, (triparental) transfer was found to occur with a frequency of 10 <sup><font size="-2">-6</font></SUP>. In microcosms with non-sterile soil planted with wheat, mobilization of pSKTG to indigenous bacteria was detected only in the presence of RP4p. The results obtained in filter matings using using the total soil bacterial community suggested the occurence of genetic elements capable of plasmid mobilization. Such elements have been found by Hill et al. (1992) and Top (1993), elements with mobilizing capacity are probably present at low levels in natural soil, since pSKTG could not be shown to be mobilized <em>in situ</em> in the absence of RP4p.<p>The influence of the location of heterologous DNA in <em>Pseudomonas fluorescens</em> R2f on gene stability, expression and transfer following introduction into Ede loamy sand and Flevo silt loam was studied (Chapter 8). Three strains were used with markers on different genetic elements, i.e a selftransmissible plasmid (RP4p), a mobilizable plasmid (pSKTG), and a chromosomally inserted marker gene cassette (KTG). <em>In vitro</em> filter mating experiments showed that the selftransmissible plasmid was transferred with high frequencies (about 10 <sup><font size="-2">-2</font></SUP>) and that this plasmid could mobilize pSKTG with similar frequencies. The chromosomally inserted marker cassette could be mobilized by RP4p to a recipient strain with low frequency (10 <sup><font size="-2">-8</font></SUP>). In sterile soil, transfer of the chromosome could not be detected in the presence of RP4p. The three strains showed poor survival in Ede loamy sand and good survival in Flevo silt loam. Moreover, a partial, but significant loss of expression of the gentamycin resistance gene <em>aad</em> B was observed in Ede loamy sand, but not in Flevo silt loam.<p>RP4p was found to be transferred from an introduced donor to indigenous bacteria in both non- sterile soils planted to wheat, whereas transconjugants harbouring the mobilizable plasmid pSKTG or the chromosomally inserted marker cassette were not detected when using a donor strain without IncP1 plasmid.<p>A lot of data concering gene transfer in soil have been published since this project started in november 1988. At that time however, most knowledge on conjugal gene transfer had been obtained using selftransmissible plasmids and introduced donor and recipient strains. In this work we showed that care should be taken to avoid matings on selective plates when such experiments are performed. The experiment which showed that RP4p could transfer to indigenous bacteria in soil and rhizosphere was one of the first reports on this phenomenon. Later, we confirmed that RP4p could also transfer to indigenous bacteria in soils of different type and texture. This indicated that the soil environment is not a barrier for gene transfer. The observation that an IncQ plasmid could be mobilized <em>in situ</em> to indigenous bacteria by RP4p present in a different strain, showed that tri- parental matings could take place. Transfer of an IncQ plasmid, or markers present on the chromosome could not be detected when RP4p was not added. However, indications were found for the presence of selftransmissible genetic elements in soil bacteria which could mobilize an IncQ plasmid.<p>Transfer frequencies of recombinant DNA present on either a selftransmissible, a mobilizable plasmid, or on the chromosome can be compared (some are based on estimations) using the data obtained (See Table 1). Multiplication of the figures with the number of introduced donor cells (per gram of soil) gives, depending on the conditions in soil, the number of transconjugants per gram of soil. Since IncQ plasmids and chromosomal inserts cannot propagate their own transfer, we assumed the presence of selftransmissible plasmids in 10 <sup><font size="-2">4</font></SUP>indigenous bacteria per g of soil (total 10 <sup><font size="-2">8</font></SUP>cfu/g of soil) in soil, with the capability of plasmid and chromosome mobilization. Frequencies clearly indicate that transfer of both the IncQ plasmid and the insert by naturally occurring genetic elements is below the detection limit (which is between 10 and 100 bacteria per gram of soil) and that transfer of those elements is a very rare event. It is difficult to indicate up to what level transfer of heterologous genes is acceptable. We therefore propose that if bacteria containing heterologous genes are to be applied for agricultural purposes, the recombinant DNA will be inserted into the chromosome to prevent unnecessary transfer.<br/><img src="/wda/abstracts/i1727_1.gif" height="702" width="600"/>
Sensitive colorimetric determination of ammonium ion in water by laser photothermal detection.
Strauss, E. ; Favier, J.P. ; Bicanic, D.D. ; Asselt, K. van; Lubbers, M. - \ 1991
The Analyst 116 (1991). - ISSN 0003-2654 - p. 77 - 79.
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