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Behavioural response of grey seals to pile-driving
Aarts, Geert ; Brasseur, Sophie ; Kirkwood, Roger - \ 2018
Den Helder : Wageningen Marine Research (Wageningen Marine Research report C006/18) - 54
Secreted venom allergen-like proteins of helminths: Conserved modulators of host responses in animals and plants
Wilbers, R.H.P. ; Schneiter, Roger ; Holterman, M.H.M. ; Drurey, Claire ; Smant, G. ; Asojo, Oluwatoyin A. ; Maizels, Rick M. ; Lozano Torres, J.L. - \ 2018
PLoS Pathogens 14 (2018)10. - ISSN 1553-7366
Despite causing considerable damage to host tissue at the onset of parasitism, invasive helminths establish remarkably persistent infections in both animals and plants. Secretions released by these obligate parasites during host invasion are thought to be crucial for their persistence in infection. Helminth secretions are complex mixtures of molecules, most of which have unknown molecular targets and functions in host cells or tissues. Although the habitats of animal- and plant-parasitic helminths are very distinct, their secretions share the presence of a structurally conserved group of proteins called venom allergen-like proteins (VALs). Helminths abundantly secrete VALs during several stages of parasitism while inflicting extensive damage to host tissue. The tight association between the secretion of VALs and the onset of parasitism has triggered a particular interest in this group of proteins, as improved knowledge on their biological functions may assist in designing novel protection strategies against parasites in humans, livestock, and important food crops.
Understanding meta-population trends of the Australian fur seal, with insights for adaptive monitoring
McIntosh, Rebecca R. ; Kirkman, Steve P. ; Thalmann, Sam ; Sutherland, Duncan R. ; Mitchell, Anthony ; Arnould, John P.Y. ; Salton, Marcus ; Slip, David J. ; Dann, Peter ; Kirkwood, Roger - \ 2018
PLoS One 13 (2018)9. - ISSN 1932-6203 - p. e0200253 - e0200253.
Effective ecosystem-based management requires estimates of abundance and population trends of species of interest. Trend analyses are often limited due to sparse or short-term abundance estimates for populations that can be logistically difficult to monitor over time. Therefore it is critical to assess regularly the quality of the metrics in long-term monitoring programs. For a monitoring program to provide meaningful data and remain relevant, it needs to incorporate technological improvements and the changing requirements of stakeholders, while maintaining the integrity of the data. In this paper we critically examine the monitoring program for the Australian fur seal (AFS) Arctocephalus pusillus doriferus as an example of an ad-hoc monitoring program that was co-ordinated across multiple stakeholders as a range-wide census of live pups in the Austral summers of 2002, 2007 and 2013. This 5-yearly census, combined with historic counts at individual sites, successfully tracked increasing population trends as signs of population recovery up to 2007. The 2013 census identified the first reduction in AFS pup numbers (14,248 live pups, -4.2% change per annum since 2007), however we have limited information to understand this change. We analyse the trends at breeding colonies and perform a power analysis to critically examine the reliability of those trends. We then assess the gaps in the monitoring program and discuss how we may transition this surveillance style program to an adaptive monitoring program than can evolve over time and achieve its goals. The census results are used for ecosystem-based modelling for fisheries management and emergency response planning. The ultimate goal for this program is to obtain the data we need with minimal cost, effort and impact on the fur seals. In conclusion we identify the importance of power analyses for interpreting trends, the value of regularly assessing long-term monitoring programs and proper design so that adaptive monitoring principles can be applied.
Adverse Outcome Pathway-Driven Analysis of Liver Steatosis in Vitro : A Case Study with Cyproconazole
Luckert, Claudia ; Braeuning, Albert ; Sousa, Georges De; Durinck, Sigrid ; Katsanou, Efrosini S. ; Konstantinidou, Parthena ; Machera, Kyriaki ; Milani, Emanuela S. ; Peijnenburg, Ad A.C.M. ; Rahmani, Roger ; Rajkovic, Andreja ; Rijkers, Deborah ; Spyropoulou, Anastasia ; Stamou, Marianna ; Stoopen, Geert ; Sturla, Shana ; Wollscheid, Bernd ; Zucchini-Pascal, Nathalie ; Lampen, Alfonso - \ 2018
Chemical Research in Toxicology 31 (2018)8. - ISSN 0893-228X - p. 784 - 798.

Adverse outcome pathways (AOPs) describe causal relationships between molecular perturbation and adverse cellular effects and are being increasingly adopted for linking in vitro mechanistic toxicology to in vivo data from regulatory toxicity studies. In this work, a case study was performed by developing a bioassay toolbox to assess key events in the recently proposed AOP for chemically induced liver steatosis. The toolbox is comprised of in vitro assays to measure nuclear receptor activation, gene and protein expression, lipid accumulation, mitochondrial respiration, and formation of fatty liver cells. Assay evaluation was performed in human HepaRG hepatocarcinoma cells exposed to the model compound cyproconazole, a fungicide inducing steatosis in rodents. Cyproconazole dose-dependently activated RARα and PXR, two molecular initiating events in the steatosis AOP. Moreover, cyproconazole provoked a disruption of mitochondrial functions and induced triglyceride accumulation and the formation of fatty liver cells as described in the AOP. Gene and protein expression analysis, however, showed expression changes different from those proposed in the AOP, thus suggesting that the current version of the AOP might not fully reflect the complex mechanisms linking nuclear receptor activation and liver steatosis. Our study shows that cyproconazole induces steatosis in human liver cells in vitro and demonstrates the utility of systems-based approaches in the mechanistic assessment of molecular and cellular key events in an AOP. AOP-driven in vitro testing as demonstrated can further improve existing AOPs, provide insight regarding molecular mechanisms of toxicity, and inform predictive risk assessment.

Erratum: Assessing the impact of underwater clearance of unexploded ordnance on harbour porpoises (Phocoena phocoena) in the Southern North Sea
Benda-Beckmann, Alexander M. von; Aarts, Geert ; Sertlek, H. ; Lucke, Klaus ; Verboom, Wim C. ; Kastelein, Ronald A. ; Ketten, Darlene R. ; Bemmelen, Rob van; Lam, Frans Peter A. ; Kirkwood, Roger J. ; Ainslie, Michael A. - \ 2018
Aquatic mammals 44 (2018)3. - ISSN 0167-5427 - p. 340 - 341.
This erratum concerns Figure 9 of the original article in which the line delimiting two effect types ("Permanent hearing loss increasingly likely" and "Permanent hearing loss very likely") was misplaced. This error, which has now been corrected, affects neither the main text nor the conclusion of the study. The authors apologize for the error.
Crystal structure of Brugia malayi venom allergen-like protein-1 (BmVAL-1), a vaccine candidate for lymphatic filariasis
Darwiche, Rabih ; Lugo, Fernanda ; Drurey, Claire ; Varossieau, Koen ; Smant, Geert ; Wilbers, Ruud H.P. ; Maizels, Rick M. ; Schneiter, Roger ; Asojo, Oluwatoyin A. - \ 2018
International Journal for Parasitology 48 (2018)5. - ISSN 0020-7519 - p. 371 - 378.
Brugia malayi is a causative agent of lymphatic filariasis, a major tropical disease. The infective L3 parasite stage releases immunomodulatory proteins including the venom allergen-like proteins (VALs), which are members of the SCP/TAPS (Sperm-coating protein/Tpx/antigen 5/pathogenesis related-1/Sc7) superfamily. BmVAL-1 is a major target of host immunity with >90% of infected B. malayi microfilaraemic cases being seropositive for antibodies to BmVAL-1. This study is part of ongoing efforts to characterize the structures and functions of important B. malayi proteins. Recombinant BmVAL-1 was produced using a plant expression system, crystallized and the structure was solved by molecular replacement and refined to 2.1 Å, revealing the characteristic alpha/beta/alpha sandwich topology of eukaryotic SCP/TAPS proteins. The protein has more than 45% loop regions and these flexible loops connect the helices and strands, which are longer than predicted based on other parasite SCP/TAPS protein structures. The large central cavity of BmVAL-1 is a prototypical CRISP cavity with two histidines required to bind divalent cations. The caveolin-binding motif (CBM) that mediates sterol binding in SCP/TAPS proteins is large and open in BmVAL-1 and is N-glycosylated. N-glycosylation of the CBM does not affect the ability of BmVAL-1 to bind sterol in vitro. BmVAL-1 complements the in vivo sterol export phenotype of yeast mutants lacking their endogenous SCP/TAPS proteins. The in vitro sterol-binding affinity of BmVAL-1 is comparable with Pry1, a yeast sterol transporting SCP/TAPS protein. Sterol binding of BmVAL-1 is dependent on divalent cations. BmVAL-1 also has a large open palmitate-binding cavity, which binds palmitate comparably to tablysin-15, a lipid-binding SCP/TAPS protein. The central cavity, CBM and palmitatebinding cavity of BmVAL-1 are interconnected within the monomer with channels that can serve as pathways for water molecules, cations and small molecules.
Heligmosomoides polygyrus Venom Allergen-like Protein-4 (HpVAL-4) is a sterol binding protein
Asojo, Oluwatoyin A. ; Darwiche, Rabih ; Gebremedhin, Selam ; Smant, Geert ; Lozano-Torres, Jose L. ; Drurey, Claire ; Pollet, Jeroen ; Maizels, Rick M. ; Schneiter, Roger ; Wilbers, Ruud H.P. - \ 2018
International Journal for Parasitology 48 (2018)5. - ISSN 0020-7519 - p. 359 - 369.
Heligmosomoides polygyrus bakeri is a model parasitic hookworm used to study animal and human helminth diseases. During infection, the parasite releases excretory/secretory products that modulate the immune system of the host. The most abundant protein family in excretory/secretory products comprises the venom allergen-like proteins (VALs), which are members of the SCP/TAPS (sperm-coating protein/ Tpx/antigen 5/pathogenesis related-1/Sc7) superfamily. There are >30 secreted Heligmosomoides polygyrus VAL proteins (HpVALs) and these proteins are characterised by having either one or two 15 kDa CAP (cysteine-rich secretory protein (CRISP)/antigen 5/pathogenesis related-1) domains. The first known HpVAL structure, HpVAL-4, refined to 1.9 Å is reported. HpVAL-4 was produced as a homogeneously glycosylated protein in leaves of Nicotiana benthamiana infiltrated with recombinant plasmids, making this plant expression platform amenable for the production of biological products. The overall topology of HpVAL-4 is a three layered aba sandwich between a short N-terminal loop and a C-terminal cysteine rich extension. The C-terminal cysteine rich extension has two strands stabilized by two disulfide bonds and superposes well with the previously reported extension from the human hookworm Necator americanus Ancylostoma secreted protein-2 (Na-ASP-2). The N-terminal loop is connected to alpha helix 2 via a disulfide bond previously observed in Na-ASP-2. HpVAL-4 has a central cavity that is more similar to the Nterminal CAP domain of the two CAP Na-ASP-1 from Necator americanus. Unlike Na-ASP-2, mammalian CRISP, and the C-terminal CAP domain of Na-ASP-1, the large central cavity of HpVAL-4 lacks the two histidines required to coordinate divalent cations. HpVAL-4 has both palmitate-binding and sterol-binding cavities and is able to complement the in vivo sterol export phenotype of yeast mutants lacking their endogenous CAP proteins. More studies are required to determine endogenous binding partners of HpVAL-4 and unravel the possible impact of sterol binding on immune-modulatory functions.
Antibodies to in silico selected GPI-anchored Theileria parva proteins neutralize sporozoite infection in vitro
Nyagwange, James ; Nene, Vishvanath ; Mwalimu, Stephen ; Henson, Sonal ; Steinaa, Lucilla ; Nzau, Benjamin ; Tijhaar, Edwin ; Pelle, Roger - \ 2018
Veterinary Immunology and Immunopathology 199 (2018). - ISSN 0165-2427 - p. 8 - 14.
Antigens - Neutralizing antibodies - Sporozoites - Theileria - Vaccine
East Coast fever (ECF) caused by Theileria parva kills cattle in East, Central and Southern Africa leading to significant economic losses. Vaccination is used as a control strategy against ECF and is presently dependent on deliberate infection with live sporozoites and simultaneous treatment with a long-acting oxytetracycline. Although effective, this method has serious limitations; the immunity is parasite strain specific and immunized cattle can become life-long asymptomatic carriers of the parasite, posing risk for the spread of the disease. In efforts to develop a subunit vaccine, the role of antibodies in the neutralization of T. parva sporozoites infection of host cells has been investigated and a circumsporozoite protein, p67, is able to induce such neutralizing antibodies. However, the p67 protein only protects a proportion of immunized cattle against T. parva challenge and such protection might be improved by inclusion of additional parasite antigens that neutralize sporozoite infection. In an attempt to identify such antigens, we searched the re-annotated T. parva genome for genes predicted to contain GPI anchor signals, since they are likely to be located on the cell surface, and expressed fragments of six of the selected genes in E. coli. The recombinant proteins were used to raise antisera in mice. Antisera to two proteins, TpMuguga_01g00876 and TpMuguga_01g00939, neutralized sporozoite infectivity to a high degree, while antisera to two additional proteins, TpMuguga_01g00095 and TpMuguga_04g00437, exhibited moderate neutralizing capacity. We conclude that these four antigens are potential vaccine candidates, which should be evaluated further in cattle.
The discovery of nickel hyperaccumulation in the New Caledonian tree Pycnandra acuminata 40 years on : an introduction to a Virtual Issue
Jaffré, Tanguy ; Reeves, Roger D. ; Baker, Alan J.M. ; Schat, Henk ; Ent, Antony van der - \ 2018
New Phytologist 218 (2018)2. - ISSN 0028-646X - p. 397 - 400.
hyperaccumulator - metallophyte - New Caledonia - nickel - phytomining - virtual issue
Seal monitoring and evaluation for the Gemini offshore windfarm: Tconstruction - 2015 report
Brasseur, Sophie ; Kirkwood, Roger ; Aarts, Geert - \ 2018
Yerseke : Wageningen Marine Research (Wageningen Marine Research report C004/18) - 64
Echoes from the past : Regional variations in recovery within a harbour seal population
Brasseur, Sophie M.J.M. ; Reijnders, Peter J.H. ; Cremer, Jenny ; Meesters, Erik ; Kirkwood, Roger ; Jensen, Lasse Fast ; Jeβ, Armin ; Galatius, Anders ; Teilmann, Jonas ; Aarts, Geert - \ 2018
PLoS One 13 (2018)1. - ISSN 1932-6203
Terrestrial and marine wildlife populations have been severely reduced by hunting, fishing and habitat destruction, especially in the last centuries. Although management regulations have led to the recovery of some populations, the underlying processes are not always well understood. This study uses a 40-year time series of counts of harbour seals (Phoca vitulina) in the Wadden Sea to study these processes, and demonstrates the influence of historical regional differences in management regimes on the recovery of this population. While the Wadden Sea is considered one ecologically coupled zone, with a distinct harbour seal population, the area is divided into four geo-political regions i.e. the Netherlands, Lower Saxony including Hamburg, Schleswig-Holstein and Denmark. Gradually, seal hunting was banned between 1962 and 1977 in the different regions. Counts of moulting harbour seals and pup counts, obtained during aerial surveys between 1974 and 2014, show a population growth from approximately 4500 to 39,000 individuals. Population growth models were developed to assess if population growth differed between regions, taking into account two Phocine Distemper Virus (PDV) epizootics, in 1988 and 2002 which seriously affected the population. After a slow start prior to the first epizootic, the overall population grew exponentially at rates close to assumed maximum rates of increase in a harbour seal population. Recently, growth slowed down, potentially indicative of approaching carrying capacity. Regional differences in growth rates were demonstrated, with the highest recovery in Netherlands after the first PDV epizootic (i.e. 17.9%), suggesting that growth was fuelled by migration from the other regions, where growth remained at or below the intrinsic growth rate (13%). The seals’ distribution changed, and although the proportion of seals counted in the German regions declined, they remained by far the most important pupping region, with approximately 70% of all pups being born there. It is hypothesised that differences in hunting regime, preceding the protection in the 1960’s and 1970’s, created unbalance in the distribution of breeding females throughout the Wadden Sea, which prevailed for decades. Breeding site fidelity promoted the growth in pup numbers at less affected breeding sites, while recolonisation of new breeding areas would be suppressed by the philopatry displayed by the animals born there. This study shows that for long-lived species, variable management regimes in this case hunting regulations, across a species’ range can drive population dynamics for several generations.
Characterization of the Theileria parva sporozoite proteome
Nyagwange, James ; Tijhaar, Edwin ; Ternette, Nicola ; Mobegi, Fredrick ; Tretina, Kyle ; Silva, Joana C. ; Pelle, Roger ; Nene, Vishvanath - \ 2018
International Journal for Parasitology 48 (2018)3-4. - ISSN 0020-7519 - p. 265 - 273.
Antigens - East Coast fever - MudPIT - Proteomics - Sporozoites - Theileria
East Coast fever is a lymphoproliferative disease caused by the tick-borne protozoan parasite Theileria parva. The sporozoite stage of this parasite, harboured and released from the salivary glands of the tick Rhipicephalus appendiculatus during feeding, invades and establishes infection in bovine lymphocytes. Blocking this initial stage of invasion presents a promising vaccine strategy for control of East Coast fever and can in part be achieved by targeting the major sporozoite surface protein p67. To support research on the biology of T. parva and the identification of additional candidate vaccine antigens, we report on the sporozoite proteome as defined by LC-MS/MS analysis. In total, 4780 proteins were identified in an enriched preparation of sporozoites. Of these, 2007 were identified as T. parva proteins, representing close to 50% of the total predicted parasite proteome. The remaining 2773 proteins were derived from the tick vector. The identified sporozoite proteins include a set of known T. parva antigens targeted by antibodies and cytotoxic T cells from cattle that are immune to East Coast fever. We also identified proteins predicted to be orthologs of Plasmodium falciparum sporozoite surface molecules and invasion organelle proteins, and proteins that may contribute to the phenomenon of bovine lymphocyte transformation. Overall, these data establish a protein expression profile of T. parva sporozoites as an important starting point for further study of a parasitic species which has considerable agricultural impact.
De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
Schmidt, Maximilian H.W. ; Vogel, Alexander ; Denton, Alisandra K. ; Istace, Benjamin ; Wormit, Alexandra ; Geest, H.C. van de; Bolger, Marie E. ; Alseekh, Saleh ; Mass, Janina ; Pfaff, Christian ; Schurr, Ulrich ; Chetelat, Roger ; Maumus, Florian ; Aury, Jean-Mary ; Koren, Sergey ; Fernie, Alisdair Robert ; Zamir, Dani ; Bolger, Anthony ; Usadel, Björn - \ 2017
The Plant Cell 29 (2017)10. - ISSN 1040-4651 - p. 2336 - 2348.
Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii. We describe the assembly of its genome to a contig N50 of 2.5 MB. The assembly pipeline comprised initial read correction with Canu and assembly with SMARTdenovo. The resulting raw nanopore-based de novo genome is structurally highly similar to that of the reference S. pennellii LA716 accession but has a high error rate and was rich in homopolymer deletions. After polishing the assembly with Illumina reads, we obtained an error rate of <0.02% when assessed versus the same Illumina data. We obtained a gene completeness of 96.53%, slightly surpassing that of the reference S. pennellii. Taken together, our data indicate that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.
Getting by or getting ahead: : Resettlement inputs and social capital in involuntary resettlement
Navarra, Melissa ; Zetter, Roger ; Niehof, A. ; Zhao, Feng - \ 2017
Journal of Population and Social Studies 25 (2017)2. - ISSN 0857-717X - p. 99 - 118.
This study goes beyond the conventional evaluative measurement of involuntary resettlement impacts by utilizing the institutions interventions perspective and social capital theory as tools for understanding the extent to which resettled populations in the Philippines and Indonesia are able to restore their socio-economic well-being. The paper outlines how the interplay between the resettlement inputs and social capital changed from the first year in the relocation site to several years later and how the changes provide evidence of the evolving well-being of the households. The cases examined in the study reveal that resettlement inputs and social capital work hand in hand in fostering improvement in the households' living conditions. The research also demonstrates that the value and relevance of household social ties could be context-specific. While the Philippine case presents a 'getting by' picture of households' well-being, the Indonesian case illustrates a combination of 'getting by' and 'getting ahead'.
Facile functionalization of peptide nucleic acids (PNAs) for antisense and single nucleotide polymorphism detection
Gahtory, Digvijay ; Murtola, Merita ; Smulders, Maarten M.J. ; Wennekes, Tom ; Zuilhof, Han ; Strömberg, Roger ; Albada, Bauke - \ 2017
Organic & Biomolecular Chemistry 15 (2017)32. - ISSN 1477-0520 - p. 6710 - 6714.

In this report, we show how a convenient on-resin copper-click functionalization of azido-functionalized peptide nucleic acids (PNAs) allows various PNA-based detection strategies. Firstly, a thiazole orange (TO) clicked PNA probe facilitates a binary readout when combined with F/Q labeled DNA, giving increased sensitivity for antisense detection. Secondly, our TO-PNA conjugate also allows single nucleotide polymorphism detection. Since antisense detection is also possible in the absence of the TO label, our sensing platform based on azido-d-ornithine containing PNA even allows for additional and more advanced functionalization and sensing strategies.

Considering healthiness promotes healthier choices but modulates medial prefrontal cortex differently in children compared with adults
Meer, Floor van; Laan, Laura N. van der; Viergever, Max A. ; Adan, Roger A.H. ; Smeets, Paul A.M. - \ 2017
NeuroImage 159 (2017). - ISSN 1053-8119 - p. 325 - 333.
Children - Decision making - Development - fMRI - Food choice
Childhood obesity is a rising problem worldwide mainly caused by overconsumption, which is driven by food choices. In adults, food choices are based on a value signal encoded in the medial prefrontal cortex (mPFC). This signal is modulated by the dorsolateral prefrontal cortex (dlPFC), which is involved in self-control. We aimed to examine the neural correlates of food choice in children, and how considering healthiness affects neural activity and choice behavior. 24 children and 28 adults performed a food choice task while being scanned with fMRI and provided health and taste ratings of the foods afterwards. During the choice task participants considered either the healthiness or tastiness of the food or chose naturally. Health rating was a positive predictor of choice in adults, but a negative predictor in children. Children had weaker dlPFC activation than adults during yes vs. no independent of health or taste condition. Both children and adults made healthier choices when considering healthiness. Taste rating modulated mPFC activation in both children and adults. When considering the healthiness, health rating positively modulated mPFC activation in adults, but negatively in children. Considering the healthiness increased connectivity between dlPFC and mPFC in adults, but not in children. In conclusion, considering healthiness can promote healthier choices in both children and adults, but is accompanied by an opposing pattern of brain activation in the mPFC. Since the absolute number of healthy choices remained lower in children, this suggests that children may not yet be geared to modify their choices away from their natural tendency to choose unhealthy tasty foods. Thus, this study suggests that it may be promising to develop interventions that increase children's preference for healthy food, for example by increasing the habitual consumption of healthy foods from a young age.
Humusica 1, article 4 : Terrestrial humus systems and forms-Specific terms and diagnostic horizons
Zanella, Augusto ; Ponge, Jean François ; Jabiol, Bernard ; Sartori, Giacomo ; Kolb, Eckart ; Gobat, Jean Michel ; Bayon, Renée Claire Le ; Aubert, Michael ; Waal, Rein de; Delft, Bas van; Vacca, Andrea ; Serra, Gianluca ; Chersich, Silvia ; Andreetta, Anna ; Cools, Nathalie ; Englisch, Michael ; Hager, Herbert ; Katzensteiner, Klaus ; Brethes, Alain ; Nicola, Cristina De ; Testi, Anna ; Bernier, Nicolas ; Graefe, Ulfert ; Juilleret, Jérôme ; Banas, Damien ; Garlato, Adriano ; Obber, Silvia ; Galvan, Paola ; Zampedri, Roberto ; Frizzera, Lorenzo ; Tomasi, Mauro ; Menardi, Roberto ; Fontanella, Fausto ; Filoso, Carmen ; Dibona, Raffaella ; Bolzonella, Cristian ; Pizzeghello, Diego ; Carletti, Paolo ; Langhor, Roger ; Cattaneo, Dina ; Nardi, Serenella ; Nicolini, Gianni ; Viola, Franco - \ 2017
Applied Soil Ecology 122 (2017)1. - ISSN 0929-1393 - p. 56 - 74.
Humic component - Humipedon - Humus - Humus classification - Humus diagnostic horizon - Humusica - Recognizable remains - Terrestrial humus - Zoogenically transformed material
Knowledge of a little number of specific terms is necessary to investigate and describe humipedons. This "new vocabulary" allows individuating and circumscribing particular diagnostic horizons, which are the fundamental bricks of the humipedon. Few "components" defined by specific terms characterize a specific "humipedon horizon"; few "humipedon horizons" compose a given "humus form" and some similar "humus forms" are grouped in a functional "humus system". In this article, specific terms and humus horizons are listed and explained one by one. Field difficulties are illustrated and resolved. The aim of the article is to present in a manner as simple as possible how to distinguish in the field the soil structures allowing a morpho-functional classification of terrestrial (aerated, not submerged) humipedons.
Het is waar maar het klopt niet
Turnhout, Esther ; Metze, Tamara - \ 2017

Hoogleraar aan de Universiteit Wageningen Esther Turnhout schrijft in haar essay Integere relaties in het dossier ‘De beroepstrots van academici’ dat dit ideaal ‘is gebaseerd op een strikte scheiding tussen enerzijds de productie van kennis in het domein van de wetenschap en anderzijds het gebruik van die kennis door beleid, politiek en andere maatschappelijke en private actoren’. Ze wijst erop dat dit ideaal van de wetenschap als autonoom en zelfregulerend ’veelvuldig is bekritiseerd’. Bijvoorbeeld door de Amerikaanse hoogleraar Daniel Sarewitz die betoogt dat ‘juist die autonomie van de wetenschap ervoor heeft gezorgd dat de wetenschap de relatie met de maatschappij uit het oog is verloren’. Sarewitz schrijft: ‘Afgeschermd van elke verantwoordingsplicht behalve die aan zichzelf, begint het “vrije spel van vrije intellectuelen” meer te lijken op een vrijbrief voor onverschilligheid en onverantwoordelijkheid. De tragische ironie is hier dat de geblokkeerde verbeelding van mainstream wetenschap een gevolg is van precies die autonomie waarvan wetenschappers zeggen dat het de kern is van hun succes.’ Elders schrijft hij zelfs: ‘De wetenschap is niet zelfreinigend, ze is zelfdestructief.’

Turnhout stelt dat ‘deze overmoed niet alleen binnen de wetenschap wordt gecultiveerd en in stand wordt gehouden. De maatschappij verlangt van wetenschappers dat ze problemen oplossen. (…) De financiering van onderzoek is in belangrijke mate gebaseerd op het principe van maatschappelijke impact. Zo houden wetenschap en samenleving elkaar gevangen in een onhoudbaar verhaal waarin feiten en waarden van elkaar te scheiden zijn en waarin wetenschappelijke kennis eenduidig kan worden vertaald in oplossingen. (…) Dit onhoudbare verhaal voedt steeds weer zowel de hoogmoed van de wetenschap als de verwachtingen van de maatschappij. Het leidt ook steeds tot teleurstelling bij de maatschappij over de niet ingeloste beloftes die zijn gedaan, en bij de wetenschap over de manier waarop maatschappelijke actoren in plaats van de feiten, interpretaties en opties van wetenschappers over te nemen hun eigen interpretaties verbinden aan kennis.’

Ondertussen wordt in de wetenschappelijke praktijk gewerkt aan nieuwe vormen van onderzoek die proberen los te breken uit dit ‘onhoudbare verhaal’. In hoeverre ziet het werk van wetenschappelijk onderzoeker Tamara Metze van de Universiteit Wageningen er anders uit dan dat van een traditioneel onderzoeker? ‘Ik laat me in mijn onderzoek uitvoerig informeren door zogenaamde communities of practice’, vertelt ze. ‘Dat betekent dat organisaties en mensen die betrokken zijn bij een bepaald probleem reflecteren op hun werk en op hun praktijken. Neem het Rijksinstituut voor Volksgezondheid en Milieu. Dat loopt er in de vaccinatiediscussie tegenaan dat het niet meer als de onbetwiste expert wordt gezien. De mededeling “Onderzoek toont aan dat je kinderen moet laten vaccineren” blijkt niet meer genoeg te zijn. Door breed te kijken in het hele veld onderzoeken we wat de rol is van emoties in zo’n discussie. We zoeken naar oplossingen, proberen ze ook uit, waarvan we dan direct weer verder leren. Het is transdisciplinair, meteen relevant en leerzaam.’

Metze baseert zich op de verschillende rollen die de politicoloog Roger Pielke onderscheidt voor de wetenschapper. Ten eerste is er de traditionele wetenschapper die afstandelijk is en min of meer als scheidsrechter functioneert. Hij of zij doet fundamenteel onderzoek in een nauwkeurig afgebakende discipline. Maar daarnaast zijn er ook rollen die aan de uiteindelijke ontvangers van het onderzoek meer keuzes geven. Zo eindigt veel beleidsonderzoek met verschillende scenario’s. Beleidsmakers kunnen dan kiezen of ze inzetten op een laag, midden of hoog scenario. Dan heb je als derde rol van de wetenschapper de issue-advocate die echt een normatief standpunt inneemt. Denk aan Albert Jan Kruiter die over zichzelf inderdaad zegt dat hij ‘rete-normatief’ is (‘ik gá voor die kwetsbare groep’). Dat kan volgens Metze nog steeds best onafhankelijk onderzoek zijn, als je maar duidelijk maakt vanuit welk normatief uitgangspunt je bent begonnen. Ten slotte heb je als vierde rol de kennismakelaar die met allerlei verschillende belanghebbenden praat en die kennis vervolgens probeert te integreren. Die laatste rol neemt Metze veelal in.

Onset and duration of gray seal (Halichoerus grypus) molt in the Wadden Sea, and the role of environmental conditions
Schop, Jessica ; Aarts, Geert ; Kirkwood, Roger ; Cremer, Jenny S.M. ; Brasseur, Sophie M.J.M. - \ 2017
Marine Mammal Science 33 (2017)3. - ISSN 0824-0469 - p. 830 - 846.
Halichoerus grypus - Annual life cycle - Dutch Wadden Sea - Gray seals - Haul-out - North Sea - Peak molt - Phocid seals - Population monitoring

Surveys of gray seals (Halichoerus grypus) during the molt period, when they are abundant on land, can be used to monitor changes in population size, but accurate interpretation of results requires an understanding of the molt process and how it may vary between years. This study investigates variability in onset (start date) and duration of visible molt by gray seals in the Wadden Sea, and the influence of environmental conditions on the onset. Molt was monitored in nine captive seals and observed molt phases were applied to wild seals over seven annual molt periods between 2004 and 2010, monitored using aerial photography. The onset of visible molt varied significantly between years, for example it differed 28 d between 2008 and 2009. Model selection by AIC retained one environmental variable that correlated with molt onset; however, its effect was inconsistent within the molt season and did not explain some of the apparent observed annual variation. Hence, the main causes of interannual variability in the onset of molt remain unclear and warrant further study. Researchers should account for annual variability in the onset of molt when interpreting survey results based on molt counts.

Consensus statement : Virus taxonomy in the age of metagenomics
Simmonds, Peter ; Adams, Mike J. ; Benk, Mária ; Breitbart, Mya ; Brister, J.R. ; Carstens, Eric B. ; Davison, Andrew J. ; Delwart, Eric ; Gorbalenya, Alexander E. ; Harrach, Balázs ; Hull, Roger ; King, Andrew M.Q. ; Koonin, Eugene V. ; Krupovic, Mart ; Kuhn, Jens H. ; Lefkowitz, Elliot J. ; Nibert, Max L. ; Orton, Richard ; Roossinck, Marilyn J. ; Sabanadzovic, Sead ; Sullivan, Matthew B. ; Suttle, Curtis A. ; Tesh, Robert B. ; Vlugt, René A. Van Der; Varsani, Arvind ; Murilo Zerbini, F. - \ 2017
Nature Reviews Microbiology 15 (2017)3. - ISSN 1740-1526 - p. 161 - 168.
The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.
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