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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Prey availability and temporal partitioning modulate felid coexistence in Neotropical forests
Santos, Fernanda ; Carbone, Chris ; Wearn, Oliver R. ; Rowcliffe, J.M. ; Espinosa, Santiago ; Moreira, Marcela Guimarães ; Ahumada, Jorge A. ; Gonçalves, André Luis Sousa ; Trevelin, Leonardo C. ; Alvarez-Loayza, Patricia ; Spironello, Wilson R. ; Jansen, Patrick A. ; Juen, Leandro ; Peres, Carlos A. - \ 2019
PLoS ONE 14 (2019)3. - ISSN 1932-6203

Carnivores have long been used as model organisms to examine mechanisms that allow coexistence among ecologically similar species. Interactions between carnivores, including competition and predation, comprise important processes regulating local community structure and diversity. We use data from an intensive camera-trapping monitoring program across eight Neotropical forest sites to describe the patterns of spatiotemporal organization of a guild of five sympatric cat species: jaguar (Panthera onca), puma (Puma concolor), ocelot (Leopardus pardalis), jaguarundi (Herpailurus yagouaroundi) and margay (Leopardus wiedii). For the three largest cat species, we developed multi-stage occupancy models accounting for habitat characteristics (landscape complexity and prey availability) and models accounting for species interactions (occupancy estimates of potential competitor cat species). Patterns of habitat-use were best explained by prey availability, rather than habitat structure or species interactions, with no evidence of negative associations of jaguar on puma and ocelot occupancy or puma on ocelot occupancy. We further explore temporal activity patterns and overlap of all five felid species. We observed a moderate temporal overlap between jaguar, puma and ocelot, with differences in their activity peaks, whereas higher temporal partitioning was observed between jaguarundi and both ocelot and margay. Lastly, we conducted temporal overlap analysis and calculated species activity levels across study sites to explore if shifts in daily activity within species can be explained by varying levels of local competition pressure. Activity patterns of ocelots, jaguarundis and margays were similarly bimodal across sites, but pumas exhibited irregular activity patterns, most likely as a response to jaguar activity. Activity levels were similar among sites and observed differences were unrelated to competition or intraguild killing risk. Our study reveals apparent spatial and temporal partitioning for most of the species pairs analyzed, with prey abundance being more important than species interactions in governing the local occurrence and spatial distribution of Neotropical forest felids.

Considerations and consequences of allowing DNA sequence data as types of fungal taxa
Zamora, Juan Carlos ; Svensson, Måns ; Kirschner, Roland ; Olariaga, Ibai ; Ryman, Svengunnar ; Parra, Luis Alberto ; Geml, József ; Rosling, Anna ; Adamčík, Slavomír ; Ahti, Teuvo ; Aime, M.C. ; Ainsworth, A.M. ; Albert, László ; Albertó, Edgardo ; García, Alberto Altés ; Ageev, Dmitry ; Agerer, Reinhard ; Aguirre-Hudson, Begoña ; Ammirati, Joe ; Andersson, Harry ; Angelini, Claudio ; Antonín, Vladimír ; Aoki, Takayuki ; Aptroot, André ; Argaud, Didier ; Sosa, Blanca Imelda Arguello ; Aronsen, Arne ; Arup, Ulf ; Asgari, Bita ; Assyov, Boris ; Atienza, Violeta ; Bandini, Ditte ; Baptista-Ferreira, João Luís ; Baral, Hans-Otto ; Baroni, Tim ; Barreto, Robert Weingart ; Beker, Henry ; Bell, Ann ; Bellanger, Jean-Michel ; Bellù, Francesco ; Bemmann, Martin ; Bendiksby, Mika ; Bendiksen, Egil ; Bendiksen, Katriina ; Benedek, Lajos ; Bérešová-Guttová, Anna ; Berger, Franz ; Berndt, Reinhard ; Bernicchia, Annarosa ; Biketova, Alona Yu. ; Bizio, Enrico ; Bjork, Curtis ; Boekhout, Teun ; Boertmann, David ; Böhning, Tanja ; Boittin, Florent ; Boluda, Carlos G. ; Boomsluiter, Menno W. ; Borovička, Jan ; Brandrud, Tor Erik ; Braun, Uwe ; Brodo, Irwin ; Bulyonkova, Tatiana ; Burdsall, Harold H. ; Buyck, Bart ; Burgaz, Ana Rosa ; Calatayud, Vicent ; Callac, Philippe ; Campo, Emanuele ; Candusso, Massimo ; Capoen, Brigitte ; Carbó, Joaquim ; Carbone, Matteo ; Castañeda-ruiz, Rafael F. ; Castellano, Michael A. ; Chen, Jie ; Clerc, Philippe ; Consiglio, Giovanni ; Corriol, Gilles ; Courtecuisse, Régis ; Crespo, Ana ; Cripps, Cathy ; Crous, Pedro W. ; Silva, Gladstone Alves Da ; Silva, Meiriele Da ; Dam, Marjo ; Dam, Nico ; Dämmrich, Frank ; Das, Kanad ; Davies, Linda ; Crop, Eske De; Kesel, Andre De; Kuijper, T.W.M. - \ 2018
IMA fungus 9 (2018)1. - ISSN 2210-6340 - p. 167 - 185.
Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
Adapter les pratiques agricoles aux différentes conditions pédoclimatiques : un outil pour agriculteurs et conseillers
Turpin, N. ; Perret, E. ; Berge, H.F.M. ten; Hose, T. D'; Evert, F.K. van - \ 2016
Sciences Eaux & Territoires Hors-série (2016)30. - ISSN 2109-3016 - 7 p.
Les pratiques agricoles qui réduisent la quantité de carbone dans le sol peuvent perturber son activité microbienne, modifier sa structure, et sa capacité à fournir eau et nutriments aux cultures. Elles peuvent aussi limiter la capacité des sols agricoles à lutter contre le changement climatique. Le projet de recherche européen Catch-C s’est interrogé sur la capacité des pratiques agricoles
alternatives à limiter ou contrebalancer ces problèmes. À partir des premiers résultats de l'analyse des effets de différentes pratiques en Europe, cet article nous présente la conception d'un outil d'aide à la décision pour les acteurs du monde agricole qui résume les avantages et inconvénients de ces modèles alternatifs, propose des recommandations validées scientifiquement, pour tendre
vers une gestion durable des sols agricoles, sur lesquelles de futures politiques pourront se reposer
First Report of Cadophora luteo-olivacea Causing Side Rot on ‘Conference’ Pears in the Netherlands
Wenneker, M. ; Pham, K.T.K. ; Lemmers, M.E.C. ; Boer, Astrid de; Leeuwen, Paul van; Hollinger, T.C. ; Haas, B.H. de; Köhl, J. - \ 2016
Plant Disease 100 (2016)10. - ISSN 0191-2917 - p. 2162 - 2162.
Pear (Pyrus communis) is an important fruit crop in the Netherlands. Symptoms of side rot disease of pear fruits were first observed in 2008 on cv. Conference in storage in the Netherlands. Typical round to oval, dark-brown, and slightly sunken spots (size 0.5 to 1.0 cm in diameter) appeared after six or more months of cold storage under controlled atmosphere. Lesions of rinsed pears were sprayed with 70% ethanol and tissue under the lesion was placed onto potato dextrose agar (PDA) at 20°C in the dark. Colonies obtained from single spores produced on PDA were flat, felty and cottony in the middle, with smooth margins, an even edge, and varying in color from white turning to gray/black-olivaceous. Under UV light, ellipsoid or elongate conidia were produced (2.2 to 2.3 × 4.9 to 6.5 µm). Both cultural and morphological characteristics of the pathogen were similar to those described for Cadophora sp. (Spadaro et al. 2011). Three representative isolates (PPO 11-1228, PPO 24-1234, and PPO 107-1267) were sequenced using primers ITS1/ITS4 and EF1-728F and EF1-986R (Carbone and Kohn 1999). MegaBLAST analysis revealed that the ITS sequences (GenBank accession nos. KT350591, KT350592, and KT350593) matched with 99.8 to 100% identity to Cadophora luteo-olivacea in GenBank (KU141394 and KU141395). The TEF1 sequences (KT350597, KT350598, and KT350599) were 100% identical with many other culture collection C. luteo-olivacea sequences in GenBank (HQ661071 and KF764576) and only 71 to 80% to other Cadophora species isolated from pear (KT350601 and KT350602). Alcohol surface sterilized fruits were inoculated in pathogenicity tests in two ways: i) with an agar disk (10 mm diameter) with actively growing mycelium of C. luteo-olivacea prepared from a 14-day-old culture grown on PDA (isolates PPO 11-1228, PPO 24-1234, and PPO 107-1267); and ii) with 20 µl of a spore suspension (105 conidia ml–1) prepared from a 21-day-old PDA culture after wounding with a needle (isolates PPO 11-1228 and PPO 107-1267). Both experiments were performed at 5 and 15°C, on 10 ‘Conference’ pears per isolate-temperature combination. Inoculated fruits were sealed in plastic bags and were incubated in darkness. Typical symptoms appeared 7 to 14 days and 4 to 6 weeks later, for fruits incubated at 15 and 5°C, respectively. Mock-inoculated controls with water and PDA-only controls remained symptomless. Fungi isolated from the lesions had morphological characteristics that resembled the original isolates from infected pears. The identity of the reisolations was confirmed as C. luteo-olivacea by sequencing, thus completing Koch’s postulates. Side rot of long-term stored pears has first been reported in Oregon, United States (Bertrand et al. 1977). The primary causal fungus was identified as C. malorum (syn. Phialophora malorum) (Sugar and Spotts 1992). Recently, a skin pitting disease of kiwifruit caused by C. luteo-olivacea has been reported from Italy (Spadaro et al. 2010). To our knowledge, this is the first report of side rot disease of pear fruits caused by C. luteo-olivacea.
Wildlife speed cameras: measuring animal travel speed and day range using camera traps
Rowcliffe, J.M. ; Jansen, P.A. ; Kays, R. ; Kranstauber, B. ; Carbone, C. - \ 2016
Remote Sensing in Ecology and Conservation 2 (2016)2. - ISSN 2056-3485 - p. 84 - 94.
Travel speed (average speed of travel while active) and day range (average speed over the daily activity cycle) are behavioural metrics that influence processes including energy use, foraging success, disease transmission and human-wildlife interactions, and which can therefore be applied to a range of questions in ecology and conservation. These metrics are usually derived from telemetry or direct observations. Here, we describe and validate an entirely new alternative approach, using camera traps recording passing animals to measure movement paths at very fine scale. Dividing the length of a passage by its duration gives a speed observation, and average travel speed is estimated by fitting size-biased probability distributions to a sample of speed observations. Day range is then estimated as the product of travel speed and activity level (proportion of time spent active), which can also be estimated from camera-trap data. We field tested the procedure with data from a survey of terrestrial mammals on Barro Colorado Island, Panama. Travel speeds and day ranges estimated for 12 species scaled positively with body mass, and were higher in faunivores than in herbivores, patterns that are consistent with those obtained using independent estimates derived from tracked individuals. Comparisons of our day range estimates with independent telemetry-based estimates for three species also showed very similar values in absolute terms. We conclude that these methods are accurate and ready to use for estimating travel speed and day range in wildlife. Key advantages of the methods are that they are non-invasive, and that measurements are made at very high resolution in time and space, yielding estimates that are comparable across species and studies. Combined with emerging techniques in computer vision, we anticipate that these methods will help to expand the range of species for which we can estimate movement rate in the wild.
Le Nouveau Métabolisme Urbain
Spiller, M. - \ 2015
Le1 hebdo 2015 (2015)54.
Chaque minute, chaque seconde, quelqu’un, quelque part dans la ville, participe au grand cycle ordinaire : on mange, on digère et on se libère. Autrement dit, nous « métabolisons », c’est-à-dire que dans les cellules de chacun de nous se déroulent des processus vitaux qui entraînent la transformation de la nourriture. Et parce que chacun de nous métabolise, les villes aussi métabolisent !

Les repas que nous absorbons ne sont que la partie émergée de l’iceberg de ce métabolisme urbain. Comme les individus, les villes dépendent d’un flux continu de ressources importées, dont la nourriture, l’eau, les matériaux (matériaux de construction, téléphones portables, tissus, etc.) et bien sûr les combustibles, qui répondent à nos besoins en électricité. Comme nous, les villes utilisent ces ressources et les transforment en déchets tels le dioxyde de carbone, la boue de vidange, la pollution des fleuves ou les déchets solides déposés dans d’immenses décharges.
Density estimation using camera trap surveys: the Random Encounter Model
Rowcliffe, J.M. ; Carbone, C. ; Kays, R. ; Kranstauber, B. ; Jansen, P.A. - \ 2014
In: Camera Trapping in Wildlife Management and Research / Meek, P., Ballard, A.G., Melbourne : CSIRO Publishing - p. 317 - 323.
Quantifying levels of animal activity using camera trap data
Rowcliffe, J.M. ; Kays, R. ; Kranstauber, B. ; Carbone, C. ; Jansen, P.A. - \ 2014
Methods in Ecology and Evolution 5 (2014)11. - ISSN 2041-210X - p. 1170 - 1179.
home-range size - predator avoidance - circadian activity - microtus-arvalis - activity pattern - common vole - time - food - determinants - ecology
1.Activity level (the proportion of time that animals spend active) is a behavioural and ecological metric that can provide an indicator of energetics, foraging effort and exposure to risk. However, activity level is poorly known for free-living animals because it is difficult to quantify activity in the field in a consistent, cost-effective and non-invasive way. 2.This article presents a new method to estimate activity level with time-of-detection data from camera traps (or more generally any remote sensors), fitting a flexible circular distribution to these data to describe the underlying activity schedule, and calculating overall proportion of time active from this. 3.Using simulations and a case study for a range of small- to medium-sized mammal species, we find that activity level can reliably be estimated using the new method. 4.The method depends on the key assumption that all individuals in the sampled population are active at the peak of the daily activity cycle. We provide theoretical and empirical evidence suggesting that this assumption is likely to be met for many species, but may be less likely met in large predators, or in high-latitude winters. Further research is needed to establish stronger evidence on the validity of this assumption in specific cases; however, the approach has the potential to provide an effective, non-invasive alternative to existing methods for quantifying population activity levels.
Fragmentation of an aflatoxin-like gene cluster in a forest pathogen
Bradshaw, R.E. ; Slot, J.C. ; Moore, G.G. ; Chettri, P. ; Wit, P.J.G.M. de; Ehrlich, K.C. ; Ganley, A.R.D. ; Olson, M.A. ; Rokas, A. ; Carbone, I. ; Cox, M.P. - \ 2013
New Phytologist 198 (2013)2. - ISSN 0028-646X - p. 525 - 535.
aspergillus-parasiticus - dothistroma-septosporum - phylogenetic analyses - biosynthetic-pathway - recombination events - secondary metabolism - functional-analysis - horizontal transfer - filamentous fungi - evolution
Plant pathogens use a complex arsenal of weapons, such as toxic secondary metabolites, to invade and destroy their hosts. Knowledge of how secondary metabolite pathways evolved is central to understanding the evolution of host specificity. The secondary metabolite dothistromin is structurally similar to aflatoxins and is produced by the fungal pine pathogen Dothistroma septosporum. Our study focused on dothistromin genes, which are widely dispersed across one chromosome, to determine whether this unusual distributed arrangement evolved from an ancestral cluster. We combined comparative genomics and population genetics approaches to elucidate the origins of the dispersed arrangement of dothistromin genes over a broad evolutionary time-scale at the phylum, class and species levels. Orthologs of dothistromin genes were found in two major classes of fungi. Their organization is consistent with clustering of core pathway genes in a common ancestor, but with intermediate cluster fragmentation states in the Dothideomycetes fungi. Recombination hotspots in a D.septosporum population matched sites of gene acquisition and cluster fragmentation at higher evolutionary levels. The results suggest that fragmentation of a larger ancestral cluster gave rise to the arrangement seen in D.septosporum. We propose that cluster fragmentation may facilitate metabolic retooling and subsequent host adaptation of plant pathogens.
Letter to the Editor : Clarifying Assumptions Behind the Estimation of Animal Density From Camera Trap Rates
Rowcliffe, J.M. ; Carbone, C. ; Jansen, P.A. - \ 2013
Journal of Wildlife Management 77 (2013)6. - ISSN 0022-541X - p. 876 - 876.
Bias in estimating animal travel distance: the effect of sampling frequency
Rowcliffe, J.M. ; Carbone, C. ; Kays, R. ; Kranstauber, B. ; Jansen, P.A. - \ 2012
Methods in Ecology and Evolution 3 (2012)4. - ISSN 2041-210X - p. 653 - 662.
bialowieza-primeval-forest - correlated random-walk - gps telemetry data - home ranges - movement data - body-size - behavior - models - poland - error
1. The distance travelled by animals is an important ecological variable that links behaviour, energetics and demography. It is usually measured by summing straight-line distances between intermittently sampled locations along continuous animal movement paths. The extent to which this approach underestimates travel distance remains a rarely addressed and unsolved problem, largely because true movement paths are rarely, if ever, available for comparison. Here, we use simulated movement paths parameterized with empirical movement data to study how estimates of distance travelled are affected by sampling frequency. 2. We used a novel method to obtain fine-scale characteristics of animal movement from camera trap videos for a set of tropical forest mammals and used these characteristics to generate detailed movement paths. We then sampled these paths at different frequencies, simulating telemetry studies, and quantified the accuracy of sampled travel distance estimation. 3. For our focal species, typical telemetry studies would underestimate distances travelled by 67–93%, and extremely high sampling frequencies (several fixes per minute) would be required to get tolerably accurate estimates. The form of the relationship between tortuosity, sample frequency, and distance travelled was such that absolute distance cannot accurately be estimated by the infrequent samples used in typical tracking studies. 4. We conclude that the underestimation of distance travelled is a serious but underappreciated problem. Currently, there is no reliable, widely applicable method to obtain approximately unbiased estimates of distance travelled by animals. Further research on this problem is needed.
Camera Traps as Sensor Networks for Monitoring Animal Communities
Kays, R.W. ; Tilak, S. ; Kranstauber, B. ; Jansen, P.A. ; Carbone, C. ; Rowcliff, M.J. ; Fountain, T. ; Eggert, J. ; He, Z. - \ 2011
International Journal of Research and Reviews in Wireless Sensor Networks 1 (2011)2. - ISSN 2047-0037 - p. 19 - 29.
Studying animal movement and distribution is of critical importance to addressing environmental challenges including invasive species, infectious diseases, climate and land-use change. Motion sensitive camera traps offer a visual sensor to record the presence of a broad range of species providing location – specific information on movement and behavior. Modern digital camera traps that record video present not only new analytical opportunities, but also new data management challenges. This paper describes our experience with a terrestrial animal monitoring system at Barro Colorado Island, Panama. Our camera network captured the spatio-temporal dynamics of terrestrial bird and mammal activity at the site - data relevant to immediate science questions, and long-term conservation issues. We believe that the experience gained and lessons learned during our year-long deployment and testing of the camera traps as well as the developed solutions are applicable to broader sensor network applications and are valuable for the advancement of the sensor network research. We suggest that the continued development of these hardware, software, and analytical tools, in concert, offer an exciting sensor-network solution to monitoring of animal populations which could realistically scale over larger areas and time spans
Quantifying the sensitivity of camera traps:an adapted distance sampling approach
Rowcliffe, M. ; Carbone, C. ; Jansen, P.A. ; Kays, R.W. ; Kranstauber, B. - \ 2011
Methods in Ecology and Evolution 2 (2011)5. - ISSN 2041-210X - p. 464 - 476.
neotropical forests - photographic rates - estimate densities - cryptic mammals - population - tigers - landscape - design - birds
1. Abundance estimation is a pervasive goal in ecology. The rate of detection by motion-sensitive camera traps can, in principle, provide information on the abundance of many species of terrestrial vertebrates that are otherwise difficult to survey. The random encounter model (REM, Rowcliffe et al. 2008) provides a means estimating abundance from camera trap rate but requires camera sensitivity to be quantified. 2. Here, we develop a method to estimate the area effectively monitored by cameras, which is one of the most important codeterminants of detection rate. Our method borrows from distance sampling theory, applying detection function models to data on the position (distance and angle relative to the camera) where the animals are first detected. Testing the reliability of this approach through simulation, we find that bias depends on the effective detection angle assumed but was generally low at less than 5% for realistic angles typical of camera traps. 3. We adapted standard detection functions to allow for the possibility of smaller animals passing beneath the field of view close to the camera, resulting in reduced detection probability within that zone. Using a further simulation to test this approach, we find that detection distance can be estimated with little or no bias if detection probability is certain for at least some distance from the camera. 4. Applying this method to a 1-year camera trapping data set from Barro Colorado Island, Panama, we show that effective detection distance is related strongly positively to species body mass and weakly negatively to species average speed of movement. There was also a strong seasonal effect, with shorter detection distance during the wet season. Effective detection angle is related more weakly to species body mass, and again strongly to season, with a wider angle in the wet season. 5. This method represents an important step towards practical application of the REM, including abundance estimation for relatively small (
Stockage de carbone dans les sols sous systèmes de culture en semis direct sous couvert vègètal (SCV) dans diffèrents contextes pèdoclimatiques à Madagascar
Razafimbelo, T. ; Albrecht, A. ; Feller, C. ; Ravelojaona, H. ; Moussa, N. ; Razanamparany, C. ; Rakotoarinivo, C. ; Razafintsalama, H. ; Michellon, R. ; Naudin, K. ; Rabeharisoa, L. - \ 2010
Etude et Gestion des Sols 17 (2010)2. - ISSN 1252-6851 - p. 143 - 158.
Intra-lake stable isotope ratio variation in selected fish species and their possible carbon sources in Lake Kyoga (Uganda): implications for aquatic food web studies
Mbabazi, D. ; Makanga, B. ; Orach-Meza, F. ; Hecky, R.E. ; Balirwa, J.S. ; Ogutu-Ohwayo, R. ; Verburg, P.H. ; Chapman, L. ; Muhumuza, E. - \ 2010
African Journal of Ecology 48 (2010)3. - ISSN 0141-6707 - p. 667 - 675.
trophic structure - east-africa - mwanza gulf - nitrogen - diet - delta-n-15 - victoria - ecosystem - specialization - delta-c-13
The stable isotopes of nitrogen (delta 15N) and carbon (delta 13C) provide powerful tools for quantifying trophic relationships and carbon flow to consumers in food webs; however, the isotopic signatures of organisms vary within a lake. Assessment of carbon and nitrogen isotopic signatures in a suite of plants, invertebrates, and fishes in Lake Kyoga, indicated significant variation between two sites for delta 13C (paired t = 6.305; df = 14, P <0.001 and delta 15N paired t = 1.292; df = 14; P <0.05). The fish fauna in Bukungu was generally more 13C enriched (mean delta 13C = -16.37 +/- 1.64 parts per thousand) than in Iyingo (mean delta 13C = -20.80 +/- 2.41 parts per thousand) but more delta 15N depleted (mean delta 15N = 5.57 +/- 0.71 parts per thousand) than in Iyingo (mean delta 15N = 6.92 +/- 0.83 parts per thousand). The simultaneous shifts in phytoplankton and consumer signatures confirmed phytoplankton as the major source of carbon for the food chain leading to fish. Limited sampling coverage within lakes may affect lake wide stable isotope signatures, and the same error is transferred into trophic position estimation. Consideration of potential intra-lake spatial variability in isotope ratios and size is essential in evaluating the spatial and trophic structure of fish assemblages.Resume Les isotopes stables d'azote (delta 15N) et de carbone (delta 13C) sont des outils interessants pour quantifier les relations trophiques et le flux de carbone vers les consommateurs de chaines alimentaires; cependant, la signature isotopique des organismes varie au sein d'un meme lac. L'evaluation des signatures isotopiques du carbone et de l'azote dans une suite de plantes, d'invertebres et de poissons du lac Kyoga indiquait une variation significative entre deux sites pour delta 13C (test t apparie = 6.305; df = 14; P <0.05). La faune piscicole de Bukungu etait generalement plus enrichie en delta 13C (moyenne de delta 13C = -16.37 +/- 1.64 parts per thousand) qu'a Iyingo (moyenne de delta 13C = -20.80 +/- 2.41 parts per thousand) mais plus depourvue de delta 15N (moyenne de delta 15N = 5.57 +/- 0.71 parts per thousand) qu'Inyingo (moyenne de delta 15N = 6.92 +/- 0.83 parts per thousand). Les glissements simultanes des signatures du phytoplancton et des consommateurs confirmaient que le phytoplancton est la source principale de carbone de la chaine alimentaire qui aboutit aux poissons. Une couverture limitee de l'echantillonnage dans les lacs peut affecter la signature des isotopes stables de tout le lac, et cette meme erreur est reportee dans l'estimation de la situation trophique. Il est essentiel de tenir compte de la variabilite spatiale possible des taux et de la taille des isotopes dans les lacs lorsque l'on evalue la structure spatiale et trophique des assemblages de poissons.
Developmental, genetic and environmental factors affect the expression of flavonoid genes, enzymes and metabolites in strawberry fruits
Carbone, F. ; Preuss, A. ; Vos, C.H. de; Amico, E. d'; Perrotta, G. ; Bovy, A.G. ; Martens, S. ; Rosati, C. - \ 2009
Plant, Cell & Environment 32 (2009)8. - ISSN 0140-7791 - p. 1117 - 1131.
fragaria x ananassa - cellular-localization - phenolic-compounds - quality traits - biosynthesis - arabidopsis - pathway - proanthocyanidins - accumulation - dioxygenases
The influence of internal (genetic and developmental) and external (environmental) factors on levels of flavonoid gene transcripts, enzyme activity and metabolites was studied in fruit of six cultivated strawberry (Fragaria × ananassa Duch.) genotypes grown at two Italian locations. Gene expression and enzyme activity showed development- and genotype-associated patterns, revealing gene coordination. Analysis clarified the regulation mechanism of the hydroxylation status of the B-ring of the major flavonoid pools and pointed out examples of genotype-specific post-transcriptional regulation mechanisms and key steps of pathway regulation in strawberry fruits. Metabolite profiles were strongly affected by development and genotype. Flavan-3-ols, their proanthocyanidin (PA) derivatives and anthocyanins were the most abundant metabolites. Flavonol levels and PA-associated traits (epicatechin/catechin ratio and mean degree of polymerization) showed significant environmental effects. Multivariate and correlation analyses determined the relationships among genes, enzymes and metabolites. The combined molecular and biochemical information elucidated more in depth the role of genetic and environmental factors on flavonoid metabolism during strawberry fruit development, highlighting the major impact of developmental processes, and revealing genotype-dependent differences and environmental effects on PA-related traits.
A Meta-Regression Analysis of Forest Carbon Offset Costs
Kooten, G.C. van; Laaksonen-Craig, S. ; Wang, Y. - \ 2009
Canadian Journal of Forest Research 39 (2009)11. - ISSN 0045-5067 - p. 2153 - 2167.
fossil-fuel substitution - sequestering carbon - accounting methods - agricultural land - western canada - climate-change - co2 storage - sequestration - sinks - metaanalysis
The main focus of efforts to mitigate climate change is on the avoidance of fossil fuel emissions. However, the Kyoto Protocol rules permit the use of forestry activities that create carbon offset credits. These could obviate the need for lifestyle-changing reductions in fossil fuel use. Therefore, it is necessary for policy purpose to determine the cost effectiveness of creating forest sink carbon credits. In this study, meta-regression analyses with 1047 observations from 68 studies are used to determine factors that affect carbon sequestration costs. Results indicate that forest plantations and use of harvested biomass for energy make forestry activities more attractive. It also turns out that forestry activities are competitive with emissions reduction in tropical regions and, perhaps, boreal regions but certainly not in Europe. Finally, the regression estimates are used to project the potential costs of carbon uptake for various forest management scenarios— costs range from 0 to over 200US$/t CO2. Le principal objectif des efforts visant à atténuer les changements climatiques consiste à éviter les émissions de combustibles fossiles. Cependant, les règles de le protocole de Kyoto permettent d'utiliser les activités forestières qui génèrent des crédits pour compenser les émissions de carbone, ce qui pourrait éviter de devoir réduire l'utilisation de combustibles fossiles qui entraînerait un changement de style de vie. Par conséquent, pour établir des politiques il est nécessaire de déterminer le rapport coût-efficacité de la création de crédits en utilisant la forêt comme puits de carbone. Dans cette étude, des analyses de méta-régression avec 1047 observations provenant de 68 études sont utilisées pour déterminer les facteurs qui influencent les coûts de séquestration du carbone. Les résultats indiquent que les plantations forestières et l'utilisation de la biomasse qui est récoltée pour produire de l'énergie rendent les activités forestières plus attrayantes. De plus, les activités forestières sont compétitives avec la réduction des émissions dans les régions tropicales et possiblement dans les régions boréales, mais certainement pas en Europe. Finalement, les estimations des régressions sont utilisées pour prédire le coût potentiel de la séquestration du carbone associé à différents scénarios d'aménagement forestier; les coûts varient de 0 à 200 $US par tonne de CO2.
Camera traps as sensor networks for monitoring animal communities
Kays, R.W. ; Kranstauber, B. ; Jansen, P.A. ; Carbone, C. ; Rowcliffe, M. ; Fountain, T. ; Tilak, S. - \ 2009
In: Proceedings of the 4th IEEE International Workshop on Practical Issues in Building Sensor Network Applications (SenseApp) and the IEEE 34th Conference on Local Computer Networks (LCN 2009), Zurich, Switzerland, 20-23 October 2009. - - p. 811 - 818.
Studying animal movement and distribution is of critical importance to addressing environmental challenges including invasive species, infectious diseases, climate and land-use change. Motion sensitive camera traps offer a visual sensor to record the presence of a species at a location, recording their movement in the Eulerian sense. Modern digital camera traps that record video present new analytical opportunities, but also new data management challenges. This paper describes our experience with a year-long terrestrial animal monitoring system at Barro Colorado Island, Panama. The data gathered from our camera network shows the spatio-temporal dynamics of terrestrial bird and mammal activity at the site-data relevant to immediate science questions, and long-term conservation issues. We believe that the experience gained and lessons learned during our year long deployment and testing of the camera traps are applicable to broader sensor network applications and are valuable for the advancement of the sensor network research. We suggest that the continued development of these hardware, software, and analytical tools, in concert, offer an exciting sensor-network solution to monitoring of animal populations which could realistically scale over larger areas and time spans
Correlated effects of selection for immunity in White Leghorn chicken lines on natural antibodies and specific antibody responses to KLH and M. butyricum
Minozzi, G. ; Parmentier, H.K. ; Mignon-Grasteau, S. ; Nieuwland, M.G.B. ; Bed'hom, B. ; Gourichon, D. ; Minvielle, F. ; Pinard-van der Laan, M.H. - \ 2008
BMC Genetics 9 (2008). - ISSN 1471-2156
keyhole limpet hemocyanin - red-blood-cells - antigen - hens - lipopolysaccharide - adjuvant - gal
Background - The effect of selection for three general immune response traits on primary antibody responses (Ab) to Mycobacterium butyricum or keyhole limpet hemocyanin (KLH) was studied in four experimental lines of White Leghorn chicken. Birds underwent 12 generations of selection for one of three different general immune criteria; high antibody response to Newcastle disease virus 3 weeks after vaccination (ND3), high cell-mediated immune response, using the wing web response to phytohemglutinin (PHA) and high phagocytic activity, measured as carbone clearance (CC). Line ND3-L was selected on ND3, line PHA-L was selected on PHA, and line CC-L on CC, but all lines were measured for all three traits. The fourth line was a contemporary random bred control maintained throughout the selection experiment. Principal component analysis was used to distinguish clusters based on the overall set of immune measures. Results - In the KLH immunised group, no differences were present between lines for natural antibodies binding to KLH and LPS, and, lines ND3-L and PHA-L had higher titers to LTA and anti-Gal titers measured before the immunisation protocol. The measure of ND3 was correlated positively with LPS titers measured post KLH immunisation and with the difference between LPS titers measured at day 0 and 7 post immunisation. In the M. butyricum immunised group, Line ND3-L showed significantly higher specific antibody response to M. butyricum, and this result agrees well with the hypothesis that the Th-1 pathway was expected to be selected for in this line. Conclusion - This study has shown that the two different antigens KLH and M. butyricum gave rise to different responses in the set of selected lines, and that the response was only enhanced for the antigen associated with the same response mechanism as that for the trait (ND3, PHA or CC) for which the line was selected. Interactions between innate and acquired immunity have been observed mainly for the high antibody selected trait, indicating there was a specific interaction due to the selection criterion. Furthermore, the results confirmed the independence between the three selected traits. Finally, principal component analysis contributed to visually discriminate high and low responders to the two new antigens in the four lines. Background - Selection for general immune response in poultry has been proposed as a sustainable alternative to selection for resistance against specific diseases, because progress with the selection for resistance approach might be hindered by interactions between host and pathogen which would lead to continuous adaptability on both sides. In addition, it would not be feasible to select for disease resistance against the tremendous number of different pathogens that an animal could face in his entire life cycle. Several general immune traits were experimentally selected for in chicken lines [1] revealing that the different immune response mechanisms may have different genetic components [2]. This study was based on three lines of White Leghorn Chickens that have been selected for 12 generations for one of three different immune response traits, high antibody response (ND3), cell mediated activity (PHA) and phagocytic activity (CC). Line ND3-L was selected on ND3, line PHA-L was selected for PHA, and line CC-L for CC, but all lines were measured for all three traits. The fourth line was a contemporary random bred Control maintained throughout the selection experiment. The results of the selection have been described by Pinard van der Laan [2]. Briefly, 200 chicks per line were hatched (800 chicks in total) in a single batch every year. Selection for each trait was done by within-family mass selection based on individual phenotype. Heritabilities estimated for the three selection criteria ND3, PHA and CC were 0.35, 0.13 and 0.15, respectively, and correlations between the traits were not significant [2]. The assessment of the disease resistance capability of the selected lines is currently under investigation and must be completed before any transposition of the results of the present work to the industry may be developed. The question that arose from this long term selection experiment was to determine if the in-vivo selection had changed the level of other immune response traits, which is to test correlated effects, with the overall aim to investigate whether the selection was trait, antigen, mechanism or pathway specific. This might result in adding other antigens or mechanisms in the long term selection experiment. The second question was to determine whether the response for the three selection criteria had modified the levels of the humoral components of the innate immune system (natural antibodies). Finally, we were interested in estimating the associations between the immune response traits under artificial selection and the newly measured ones. First, we investigated if the selected lines differed in their immune capabilities to mount an immune response to two other complex T-cell dependent antigens: Keyhole Limpet hemocyanin (KLH) and Mycobacterium butyricum, respectively. KLH is a copper-containing high molecular weight protein, found in the sea mollusc Megathura crenulata, which is commonly used as a soluble model protein known to induce a TH-2 like response [3]. Mycobacterium is a solubilized particulate antigen that induces a TH-1 response in rodents [4]. Significant differences were found previously between high and low chicken lines selected for SRBC (Sheep Red Blood Cells), for antibody response to M. butyricum [5] and for KLH [6,7], and chickens from the high antibody response line showed higher titers, irrespective of the antigen. Secondly, the level of natural antibodies binding two different T-cell independent antigens, Lipopolysaccharide (LPS) and Lipoteichoic acid (LTA), were measured to identify if the selection had changed the levels of the humoral components of the innate immune system. Both LPS and LTA are cell wall components, and represent associated patterns of gram negative (LPS) and gram positive (LTA) bacteria, respectively. In addition, as a further measure of the innate immunity, natural anti-Gal antibodies were measured. These antibodies represent IgM antibodies binding surface carbohydrate structures shared by a variety of pathogens [8]. Natural anti-¿-Gal antibodies were measured in plasma samples by rabbit agglutinin levels, indicating antibodies reactive with Gal ¿ 1-3Galß-1-4GlcNAc-R, otherwise identified as the ¿-gal epitope. Their presence in the avian species has been previously demonstrated [9]. Chickens as well as primates lack the functional ¿1, 3-galactosyltransferase gene and consequently produce high levels of anti-¿-Gal antibodies in response to the colonisation of the intestinal micro flora with galactosil bearing bacteria [10,11]. Previous studies on lines divergently selected for antibody titers to SRBC, demonstrated positive and moderately high correlation between RRBC (rabbit red blood cell) and SRBC titers [12]. Furthermore, a recent study reported equally high levels of anti-gal antibodies in bile of high and low diet-efficient hens [13]. In the present work, a total of 400 birds from the 12th generation of selection were studied. Half of the birds were immunized with KLH and the other half with M. butyricum particles. Levels of Ab to all antigens were measured before and 7 or 11 days after immunization, and correlations between them were tested. Principal component analysis was performed on the measures of immune response to better visualize the association between the new measures and the three selected lines ND3-L, PHA-L and CC-L. Results - Group immunized with KLH (Group A) Mean values and results of the analyses of variance are listed in Table 1. As expected from the past selection, lines had different (P ¿ 0.001) mean values for the selected traits, but there were also significant line effects (P ¿ 0.05 to P ¿ 0.001) on four of the other measures of immunity.
Characterization of major enzymes and genes involved in flavonoid and proanthocyanidin biosynthesis during fruit development in strawberry (Fragaria x ananassa).
Almeida, J.R. ; Amico, E. d'; Preuss, A. ; Carbone, F. ; Vos, C.H. de - \ 2007
Archives of Biochemistry and Biophysics 465 (2007)1. - ISSN 0003-9861 - p. 61 - 71.
dihydroflavonol 4-reductases - leucoanthocyanidin reductase - anthocyanidin reductases - heterologous expression - antioxidant activity - molecular-cloning - quality traits - synthase - identification - leaves
The biosynthesis of flavonoids and proanthocyanidins was studied in cultivated strawberry (Fragaria x ananassa) by combining biochemical and molecular approaches. Chemical analyses showed that ripe strawberries accumulate high amounts of pelargonidin-derived anthocyanins, and a larger pool of 3',4'-hydroxylated proanthocyanidins. Activities and properties of major recombinant enzymes were demonstrated by means of in vitro assays, with special emphasis on specificity for the biologically relevant 4'- and 3',4'-hydroxylated compounds. Only leucoanthocyanidin reductase showed a strict specificity for the 3',4'-hydroxylated leucocyanidin, while other enzymes accepted either hydroxylated substrate with different relative activity rates. The structure of late flavonoid pathway genes, leading to the synthesis of major compounds in ripe fruits, was elucidated. Complex developmental and spatial expression patterns were shown for phenylpropanoid and flavonoid genes in fruits throughout ripening as well as in leaves, petals and roots. Presented results elucidate key steps in the biosynthesis of strawberry flavonoid end products. (c) 2007 Elsevier Inc. All rights reserved.
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