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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Mimosoid legume plastome evolution : IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP
Dugas, D.V. ; Hernandez, David ; Koenen, Erik J.M. ; Schwarz, Erika ; Straub, Shannon ; Hughes, C.E. ; Jansen, R.K. ; Nageswara-Rao, Madhugiri ; Staats, Martijn ; Trujillo, J.T. ; Hajrah, N.H. ; Alharbi, N.S. ; Al-Malki, A.L. ; Sabir, J.S.M. ; Bailey, C.D. - \ 2015
Scientific Reports 5 (2015). - ISSN 2045-2322 - 13 p.

The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis), and discuss the results in the context of other legume and rosid plastid genomes. Mimosoid plastomes have a typical angiosperm gene content and general organization as well as a generally slow rate of protein coding gene evolution, but they are the largest known among legumes. The increased length results from tandem repeat expansions and an unusual 13 kb IR-SSC boundary shift in Acacia and Inga. Mimosoid plastomes harbor additional interesting features, including loss of clpP intron1 in Inga, accelerated rates of evolution in clpP for Acacia and Inga, and dN/dS ratios consistent with neutral and positive selection for several genes. These new plastomes and results provide important resources for legume comparative genomics, plant breeding, and plastid genetic engineering, while shedding further light on the complexity of plastome evolution in legumes and angiosperms.

Mestgedrag voor- en na spenen in Vair varkenshuis
Reimert, I. ; Bartels, A.C. ; Alphen, M. van; Koenen, M. ; Nooijen, M. - \ 2015
Adaptation Physiology Group, Wageningen University - 19 p.
mestgedrag - varkenshuis - varkenstoilet
Recently evolved diversity and convergent radiations of rainforest mahoganies (Meliaceae) shed new light on the origins of rainforest hyperdiversity
Koenen, E.J.M. ; Clarkson, J.J. ; Pennington, T.D. ; Chatrou, L.W. - \ 2015
New Phytologist 207 (2015)2. - ISSN 0028-646X - p. 327 - 339.
plastid dna-sequences - plant diversity - molecular phylogenetics - south-america - rapid diversification - evolutionary history - tropical forests - guarea meliaceae - global patterns - east dispersal
•Tropical rainforest hyperdiversity is often suggested to have evolved over a long time-span (the ‘museum’ model), but there is also evidence for recent rainforest radiations. The mahoganies (Meliaceae) are a prominent plant group in lowland tropical rainforests world-wide but also occur in all other tropical ecosystems. We investigated whether rainforest diversity in Meliaceae has accumulated over a long time or has more recently evolved. •We inferred the largest time-calibrated phylogeny for the family to date, reconstructed ancestral states for habitat and deciduousness, estimated diversification rates and modeled potential shifts in macro-evolutionary processes using a recently developed Bayesian method. •The ancestral Meliaceae is reconstructed as a deciduous species that inhabited seasonal habitats. Rainforest clades have diversified from the Late Oligocene or Early Miocene onwards. Two contemporaneous Amazonian clades have converged on similar ecologies and high speciation rates. •Most species-level diversity of Meliaceae in rainforest is recent. Other studies have found steady accumulation of lineages, but the large majority of plant species diversity in rainforests is recent, suggesting (episodic) species turnover. Rainforest hyperdiversity may best be explained by recent radiations from a large stock of higher level taxa.
To pool or not to pool? Impact of the use of individual and pooled fecal samples for in vitro fermentation studies
Aguirre, M. ; Ramiro Garcia, J. ; Koenen, M.E. ; Venema, K. - \ 2014
Journal of Microbiological Methods 107 (2014). - ISSN 0167-7012 - p. 1 - 7.
human large-intestine - gut microbiota - model - bacteria - oligosaccharides - metabolism - products - patterns - starch - core
This study investigated the stability and the activity of the microbiota from a single and a pool of donors in the TNO in vitro model of the colon (TIM-2 system). Our findings demonstrate the suitability of the preparation of a pool of fecal sample to be used for fermentation experiments.
Nieuwe koe laat geen vieze boeren. Kaaskoe en boterkoe uit beeld
Dongen, A. van; Arendonk, J.A.M. van; Koenen, E. - \ 2014
De Gelderlander 13-06-2014 (2014). - 2 p.
Scientific Opinion concerning a Multifactorial approach on the use of animal and non-animal-based measures to assess the welfare of pigs
Authie, E. ; Berg, C. ; Bøtner, A. ; Browman, H. ; Capua, I. ; Koeijer, A.A. de; Depner, K. ; Domingo, M. ; Edwards, S. ; Fourichon, C. ; Koenen, F. ; More, S. ; Raj, M.A.B. ; Sihvonen, L. ; Spoolder, H.A.M. ; Stegeman, J.A. ; Thulke, H.H. ; Vågsholm, I. ; Velarde, A. ; Willeberg, P. ; Zientara, S. - \ 2014
EFSA Journal 12 (2014)5. - 101 p.
Pigs have a need for manipulable materials to satisfy a range of behavioural needs, which can be different in different classes of pig. When these needs are not met, a range of adverse welfare consequences result, one of these being an increased risk for tail-biting in weaners and rearing pigs. The ability to control the risk of tail- biting is essential when aiming to avoid tail-docking. Based on available scientific information this Opinion identifies the multiple interactions between risk factors, welfare consequences and animal and non-animal-based measures on the two subjects requested (i) the absence of functional manipulable materials, for pigs at different stages in life and (ii) tail-biting, for weaners and rearing pigs only. An attempt is made to quantify the relationships between the identified interactions by carrying out a statistical analysis of information from available databases, those being an international dataset collected using the Welfare Quality® protocol, which was not designed to evaluate risk factors for tail-biting and therefore, it had limitations in fitness for this analysis, and a large Finnish dataset with undocked pigs. Based on the current state of knowledge, the AHAW Panel proposes two simple tool-boxes for on farm use to assess (i) the functionality of the supplied manipulable material and (ii) the presence and strength of risk factors for tail biting. Both proposed tool-boxes include a combination of the most important resource-based and animal-based measures. Further development and validation of decision–support tools for customised farm assessment is strongly recommended and a proposal for harmonised data collection across the range of European farming circumstances is presented. A series of further recommendations are made by the AHAW Panel.
Scientific Opinion on the use of low atmosphere pressure system (LAPS) for stunning poultry
Authie, E. ; Berg, C. ; Bøtner, A. ; Browman, H. ; Capua, I. ; Koeijer, A.A. de; Depner, K. ; Domingo, M. ; Edwards, S. ; Fourichon, C. ; Koenen, F. ; More, S. ; Raj, M.A.B. ; Sihvonen, L. ; Spoolder, H.A.M. ; Stegeman, J.A. ; Thulke, H.H. ; Vågsholm, I. ; Velarde, A. ; Willeberg, P. ; Zientara, S. - \ 2014
EFSA Journal 12 (2014)1. - 27 p.
The EFSA's Panel on Animal Health and Welfare (AHAW Panel) was asked to deliver a scientific opinion on the use of a low atmosphere pressure system (LAPS) for stunning poultry. Four documents were provided by the European Commission (EC) as the basis for an assessment of the extent to which the LAPS is able to provide a level of animal welfare at least equivalent to that ensured by the current allowed methods for stunning poultry. The LAPS is described as rendering poultry unconscious by gradually reducing oxygen tension in the atmosphere leading to progressive hypoxia in the birds. In order to be allowed in the EU, new stunning methods must ensure 1) absence of pain, distress and suffering until the onset of unconsciousness, and 2) that the animal remains unconscious until death. The submitted studies were peer-reviewed by the AHAW Panel as outlined in its “Guidance on the assessment criteria for studies evaluating the effectiveness of stunning intervention regarding animal protection at the time of killing”. It is unclear from the submitted documents whether the rate of decompression used in LAPS induces unconsciousness and death without causing avoidable pain and suffering in poultry. The assessed studies did not pass the eligibility assessment and, therefore, no further assessment was undertaken.
Towards a new classification system for legumes: Progress report from the 6th International Legume Conference
Pontes Coelho Borges, L.M. ; Bruneau, A. ; Cardoso, D. ; Crisp, M. ; Delgado-Salinas, A. ; Doyle, J.J. ; Egan, A. ; Herendeen, P.S. ; Hughes, C. ; Kenicer, G. ; Klitgaard, B. ; Koenen, E. ; Lavin, M. ; Lewis, G. ; Luckow, M. ; Mackinder, B. ; Malecot, V. ; Miller, J.T. ; Pennington, R.T. ; Queiroz, L.P. de; Schrire, B. ; Simon, M.F. ; Steele, K. ; Torke, B. ; Wieringa, J.J. ; Wojciechowski, M.F. ; Boatwright, S. ; Estrella, M. de la; Mansano, V.D. ; Prado, D.E. ; Stirton, C. ; Wink, M. - \ 2013
South African Journal of Botany 89 (2013). - ISSN 0254-6299 - p. 3 - 9.
caesalpinioid legumes - phylogeny - leguminosae - evolution - diversification - dipsacales - sequences - lineages - gene - rbcl
Legume systematists have been making great progress in understanding evolutionary relationships within the Leguminosae (Fabaceae), the third largest family of flowering plants. As the phylogenetic picture has become clearer, so too has the need for a revised classification of the family. The organization of the family into three subfamilies and 42 tribes is outdated and evolutionarily misleading. The three traditionally recognized subfamilies, Caesalpinioideae, Mimosoideae, and Papilionoideae, do not adequately represent relationships within the family. The occasion of the Sixth International Legume Conference in Johannesburg, South Africa in January 2013, with its theme "Towards a new classification system for legumes," provided the impetus to move forward with developing a new classification. A draft classification, based on current phylogenetic results and a set of principles and guidelines, was prepared in advance of the conference as the basis for discussion. The principles, guidelines, and draft classification were presented and debated at the conference. The objectives of the discussion were to develop consensus on the principles that should guide the development of the classification, to discuss the draft classification's strengths and weaknesses and make proposals for its revision, and identify and prioritize phylogenetic deficiencies that must be resolved before the classification could be published. This paper describes the collaborative process by a large group of legume systematists, publishing under the name Legume Phylogeny Working Group, to develop a new phylogenetic classification system for the Leguminosae. The goals of this paper are to inform the broader legume community, and others, of the need for a revised classification, and spell out clearly what the alternatives and challenges are for a new classification system for the family. (C) 2013 SAAB. Published by Elsevier B.V. All rights reserved.
Scientific Opinion on monitoring procedures at slaughterhouses for sheep and goats
Authie, E. ; Berg, C. ; Bøtner, A. ; Browman, H. ; Capua, I. ; Koeijer, A.A. de; Depner, K. ; Domingo, M. ; Edwards, S. ; Fourichon, C. ; Koenen, F. ; More, S. ; Raj, M.A.B. ; Sihvonen, L. ; Spoolder, H.A.M. ; Stegeman, J.A. ; Thulke, H.H. ; Vågsholm, I. ; Velarde, A. ; Willeberg, P. ; Zientara, S. - \ 2013
EFSA Journal 11 (2013)12. - 65 p.
This scientific opinion proposes toolboxes of welfare indicators for developing monitoring procedures at slaughterhouses for sheep and goats stunned with the head-only electrical method or slaughtered without stunning. In particular, the opinion proposes welfare indicators together with their corresponding outcomes of consciousness, unconsciousness or death. In the case of slaughter with head-only electrical stunning, the opinion proposes a toolbox to assess consciousness at three key stages of monitoring: (a) after electrical stunning and during shackling and hoisting, (b) during neck cutting and (c) during bleeding. For slaughter without stunning, another toolbox is proposed for (a) assessing unconsciousness before releasing the animals from restraint, and (b) confirming death before carcass dressing begins. Various activities—including a systematic literature review, an online survey and stakeholders‘ and hearing experts‘ meetings—were conducted to gather information about the sensitivity, specificity and feasibility of the indicators. On the basis of such information, a methodology was developed to select the most appropriate indicators to be used in the monitoring procedures. The frequency of checking differs according to the role of each person with responsibility for ensuring animal welfare. The personnel performing stunning, shackling, hoisting and/or bleeding will have to check all the animals and confirm that they are not conscious following stunning or before releasing from the restraint. For the animal welfare officer, who has the overall responsibility for animal welfare, a mathematical model for the sampling protocols is proposed, giving some allowance to set the sample size of animals to be checked at a given throughput rate (total number of animals slaughtered in the slaughterhouses) and threshold failure rate (number of potential failures—proportion of animals that are conscious after stunning). Finally, different risk factors and scenarios are proposed to define a =normal‘ or a =reinforced‘ monitoring protocol, according to the needs of the slaughterhouse.
Scientific Opinion on monitoring procedures at slaughterhouses for poultry
Authie, E. ; Berg, C. ; Bøtner, A. ; Browman, H. ; Capua, I. ; Koeijer, A.A. de; Depner, K. ; Domingo, M. ; Edwards, S. ; Fourichon, C. ; Koenen, F. ; More, S. ; Raj, M.A.B. ; Sihvonen, L. ; Spoolder, H.A.M. ; Stegeman, J.A. ; Thulke, H.H. ; Vågsholm, I. ; Velarde, A. ; Willeberg, P. ; Zientara, S. - \ 2013
EFSA Journal 11 (2013)12. - 65 p.
This scientific opinion proposes toolboxes of welfare indicators, and their corresponding outcomes of consciousness, unconsciousness or death, for developing monitoring procedures at slaughterhouses for poultry stunned using electrical waterbaths and gas mixtures or slaughtered without stunning. For waterbath stunning, the opinion proposes a toolbox of indicators for assessing consciousness in poultry at two key stages of monitoring: (a) between the exit from the waterbath stunner and neck cutting and (b) during bleeding. For gas stunning, the opinion proposes a toolbox of indicators for assessing consciousness in poultry at two key stages of monitoring: (a) during shackling and (b) during bleeding. For slaughter without stunning, a toolbox is proposed for confirming death prior to entering scald tanks. Various activities—including a systematic literature review, an online survey and stakeholders‘ and hearing experts‘ meetings—were conducted to gather information about the specificity, sensitivity and feasibility of the indicators. On the basis of such information, a methodology was developed to select the most appropriate indicators to be used in the monitoring procedures. The frequency of checking differs according to the role of each person with responsibility for ensuring poultry welfare. The personnel will have to check all the birds and confirm that they are not conscious following stunning with electrical waterbaths or gas mixtures and that they are dead before entering scald tanks. For the animal welfare officer, a mathematical model for the sampling protocols is proposed, giving some allowance to set the sample size of birds that he/she needs to check at a given throughput rate (total number of birds slaughtered in the slaughterhouses) and threshold failure rate (number of potential failures—birds that are conscious after stunning). Finally, different risk factors and scenarios are proposed to define a =normal‘ or a =reinforced‘ monitoring protocol, according to the needs of the slaughterhouse.
Scientific Opinion on monitoring procedures at slaughterhouses for pigs
Authie, E. ; Berg, C. ; Bøtner, A. ; Browman, H. ; Capua, I. ; Koeijer, A.A. de; Depner, K. ; Domingo, M. ; Edwards, S. ; Fourichon, C. ; Koenen, F. ; More, S. ; Raj, M.A.B. ; Sihvonen, L. ; Spoolder, H.A.M. ; Stegeman, J.A. ; Thulke, H.H. ; Vågsholm, I. ; Velarde, A. ; Willeberg, P. ; Zientara, S. - \ 2013
EFSA Journal 11 (2013)12. - 62 p.
This scientific opinion proposes toolboxes of welfare indicators for developing monitoring procedures at slaughterhouses for pigs stunned with the head-only electrical method or carbon dioxide at high concentration. In particular, the opinion proposes welfare indicators together with their corresponding outcomes of consciousness, unconsciousness or death. The opinion proposes a toolbox of indicators and the outcomes to be used to assess consciousness in pigs at three key stages of monitoring: (a) after stunning and during shackling and hoisting, (b) during sticking and (c) during bleeding. Various activities—including a systematic literature review, an online survey and stakeholders‘ and hearing experts‘ meetings—were conducted to gather information about specificity, sensitivity and feasibility of the indicators that are to be included in the toolboxes for monitoring welfare. On the basis of information gathered during these activities, a methodology was developed to select the most appropriate indicators that could be used in the monitoring procedures. The frequency of checking differs according to the role of each person with responsibility for ensuring animal welfare at slaughter. The personnel performing stunning, shackling, hoisting and/or bleeding will have to check all the animals and confirm that they are not conscious following stunning. For the animal welfare officer, who has the overall responsibility for animal welfare, a mathematical model for the sampling protocols is proposed, giving some allowance to set the sample size of animals that he/she needs to check at a given throughput rate (total number of animals slaughtered in the slaughterhouses) and tolerance level (number of potential failures—animals that are conscious after stunning; animals that are not unconscious or not dead after slaughter without stunning). The model can also be applied to estimate threshold failure rate at a chosen throughput rate and sample size. Finally, different risk factors and scenarios are proposed to define a =normal‘ or a =reinforced‘ monitoring protocol, according to the needs of the slaughterhouse.
Guidance on the assessment criteria for studies evaluating the effectiveness of stunning interventions regarding animal protection at the time of killing
Authie, E. ; Berg, C. ; Bøtner, A. ; Browman, H. ; Capua, I. ; Koeijer, A.A. de; Depner, K. ; Domingo, M. ; Edwards, S. ; Fourichon, C. ; Koenen, F. ; More, S. ; Raj, M.A.B. ; Sihvonen, L. ; Spoolder, H.A.M. ; Stegeman, J.A. ; Thulke, H.H. ; Vågsholm, I. ; Velarde, A. ; Willeberg, P. ; Zientara, S. - \ 2013
EFSA Journal 11 (2013)12. - 41 p.
This guidance defines the assessment process and the criteria that will be applied by the Animal Health and Welfare Panel to studies on known new or modified legal stunning interventions to determine their suitability for further assessment. The criteria that need to be fulfilled are eligibility criteria, reporting quality criteria and methodological quality criteria. The eligibility criteria are based upon the legislation and previously published scientific data. They focus on the intervention and the outcomes of interest, i.e. immediate onset of unconsciousness and insensibility or absence of avoidable pain, distress and suffering until the loss of consciousness and sensibility, and duration of the unconsciousness and insensibility (until death). If a study fulfils the eligibility criteria, it will be assessed regarding a set of reporting quality criteria that are based on the REFLECT and the STROBE statements. As a final step in this first assessment phase, the methodological quality of the submitted study will be assessed. If the criteria regarding eligibility, reporting quality and methodological quality are fulfilled, a full assessment of the animal welfare implications of the proposed alternative stunning intervention, including both pre-stunning and stunning phases, and an evaluation of the quality, strength and external validity of the evidence presented would be carried out at the next level of the assessment. In the case that the criteria regarding eligibility and reporting quality and methodological quality are not fulfilled, the assessment report of the panel will highlight the shortcomings and indicate where improvements are required before the study can be assessed further. In addition to the assessment criteria, the guidance also specifies general aspects applicable to studies on stunning interventions that should be considered when studying the effectiveness of stunning interventions.
Scientific Opinion on monitoring procedures at slaughterhouses for bovines
Authie, E. ; Berg, C. ; Bøtner, A. ; Browman, H. ; Capua, I. ; Koeijer, A.A. de; Depner, K. ; Domingo, M. ; Edwards, S. ; Fourichon, C. ; Koenen, F. ; More, S. ; Raj, M.A.B. ; Sihvonen, L. ; Spoolder, H.A.M. ; Stegeman, J.A. ; Thulke, H.H. ; Vågsholm, I. ; Velarde, A. ; Willeberg, P. ; Zientara, S. - \ 2013
EFSA Journal 11 (2013)12. - 65 p.
This scientific opinion proposes toolboxes of welfare indicators for developing monitoring procedures at slaughterhouses for bovines stunned with penetrative captive bolt or slaughtered without stunning. In particular, the opinion proposes welfare indicators together with their corresponding outcomes of consciousness, unconsciousness or death. In the case of slaughter with captive bolt stunning, the opinion proposes a toolbox of indicators and the outcomes to be used to assess consciousness in bovine animals at three key stages of monitoring: (a) after stunning and during shackling and hoisting; (b) during neck cutting or sticking; and (c) during bleeding. For slaughter of bovines without stunning, a set of indicators and outcomes are proposed in another toolbox to be used for (a) assessing unconsciousness, before releasing bovines from restraint; and (b) confirming death before carcass dressing begins. Various activities—including a systematic literature review, an online survey and stakeholders’ and hearing experts’ meetings—were conducted to gather information about the specificity, sensitivity and feasibility of the indicators that can be included in the toolboxes. The frequency of checking differs according to the role of each person responsible for ensuring animal welfare. Personnel performing stunning, shackling, hoisting and/or bleeding will have to check all the animals and confirm that they are not conscious following stunning or before release from the restraint. For the animal welfare officer, who has the overall responsibility for animal welfare, a mathematical model for the sampling protocols is proposed, giving some allowance to set the sample size of animals that he/she needs to check at a given throughput rate (total number of animals slaughtered in the slaughterhouse) and tolerance level (number of potential failures). Finally, different risk factors and scenarios are proposed to define a ‘normal’ or a ‘reinforced’ monitoring protocol, according to the needs of the slaughterhouse.
Alles ging fout wat fout kon gaan (interview met Sanne Koenen)
Imares, - \ 2013
Efficacy of chimeric Pestivirus vaccine candidates against Classical Swine Fever: protection and DIVA characteristics
Eble, P.L. ; Geurts, Y. ; Quak, J. ; Moonen-Leusen, H.W.M. ; Blome, S. ; Hofmann, M.A. ; Koenen, F. ; Beer, M. ; Loeffen, W.L.A. - \ 2013
Veterinary Microbiology 162 (2013)2-4. - ISSN 0378-1135 - p. 437 - 446.
subunit marker vaccine - hog-cholera virus - monoclonal-antibodies - pigs - transmission - differentiation - strains - infection - virulent - induce
Currently no live DIVA (Differentiating Infected from Vaccinated Animals) vaccines against classical swine fever (CSF) are available. The aim of this study was to investigate whether chimeric pestivirus vaccine candidates (CP7_E2alf, Flc11 and Flc9) are able to protect pigs against clinical signs, and to reduce virus shedding and virus transmission, after a challenge with CSF virus (CSFV), 7 or 14 days after a single intramuscular vaccination. In these vaccine candidates, either the E2 or the Erns encoding genome region of a bovine viral diarrhoea virus strain were combined with a cDNA copy of CSFV or vice versa. Furthermore, currently available serological DIVA tests were evaluated. The vaccine candidates were compared to the C-strain. All vaccine candidates protected against clinical signs. No transmission to contact pigs was detected in the groups vaccinated with C-strain, CP7_E2alf and Flc11. Limited transmission occurred in the groups vaccinated with Flc9. All vaccine candidates would be suitable to stop on-going transmission of CSFV. For Flc11, no reliable differentiation was possible with the current Erns-based DIVA test. For CP7_E2alf, the distribution of the inhibition percentages was such that up to 5% false positive results may be obtained in a large vaccinated population. For Flc9 vaccinated pigs, the E2 ELISA performed very well, with an expected 0.04% false positive results in a large vaccinated population. Both CP7_E2alf and Flc9 are promising candidates to be used as live attenuated marker vaccines against CSF, with protection the best feature of CP7_E2alf, and the DIVA principle the best feature of Flc9.
Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species-rich clades
Bruneau, A. ; Doyle, J.J. ; Herendeen, P. ; Hughes, C. ; Kenicer, G. ; Lewis, G. ; Mackinder, B.A. ; Pennington, R.T. ; Sanderson, M.J. ; Wojciechowski, M.F. ; Boatwright, S. ; Brown, G. ; Cardoso, D. ; Crips, M. ; Egan, A. ; Fortunato, R. ; Hawkins, J. ; Kajita, T. ; Klitgaard, B.B. ; Koenen, E. ; Lavin, M. ; Luckow, M. ; Marazzi, B. ; McMahon, M.M. ; Miller, J.T. ; Murphy, D.J. ; Ohashi, H. ; Queiroz, L.P. de; Rico, L. ; Särkinen, T. ; Schrire, B. ; Simon, M.F. ; Souza, E.R. ; Steele, K. ; Torke, B.M. ; Wieringa, J.J. ; Wijk, B.E. - \ 2013
Taxon 62 (2013)2. - ISSN 0040-0262 - p. 217 - 248.
swartzia leguminosae-papilionoideae - tribe millettieae leguminosae - chloroplast dna regions - southern south-america - intron spacer regions - matk coding sequence - plastid trnl-f - molecular phylogenetics - divergence times - s.l. leguminosae
The Leguminosae, the third-largest angiosperm family, has a global distribution and high ecological and economic importance. We examine how the legume systematic research community might join forces to produce a comprehensive phylogenetic estimate for the ca. 751 genera and ca. 19,500 species of legumes and then translate it into a phylogeny-based classification. We review the current state of knowledge of legume phylogeny and highlight where problems lie, for example in taxon sampling and phylogenetic resolution. We review approaches from bioinformatics and next-generation sequencing, which can facilitate the production of better phylogenetic estimates. Finally, we examine how morphology can be incorporated into legume phylogeny to address issues in comparative biology and classification. Our goal is to stimulate the research needed to improve our knowledge of legume phylogeny and evolution; the approaches that we discuss may also be relevant to other species-rich angiosperm clades
Evaluation of classical swine fever virus antibody detection assays with an emphasis on the differentiation of infected from vaccinated animals
Schroeder, S. ; Rosen, T. von; Blome, S. ; Loeffen, W.L.A. ; Haegeman, A. ; Koenen, F. ; Uttenthal, A. - \ 2012
Revue scientifique et technique / Office International des Epizooties 31 (2012)3. - ISSN 0253-1933 - p. 997 - 1010.
The aim of this study was to evaluate the general characteristics of
commercially available enzyme-linked immunosorbent assays (ELISAs) to detect
antibody against classical swine fever (CSF), as well as to assess their potential
use as accompanying marker tests able to differentiate infected from vaccinated
animals (DIVA).
The Chekit* CSF-Sero and the HerdChek* CSFV Ab, both of which detect
antibodies against the E2 protein of classical swine fever virus (CSFV), had the
highest sensitivity. Both tests were practicable and showed good reproducibility.
Comparable sensitivity was shown by the Chekit* CSF-Marker, an Erns ELISA.
However, this test does not allow differentiation between antibodies directed
against ruminant pestiviruses and those against CSFV. Therefore, it is not
suitable for use with the chimeric marker vaccines tested.
The PrioCHECK® CSFV Erns was the only ELISA suitable for use in DIVA with
marker vaccines containing Erns proteins from ruminant pestiviruses. However,
this test was less sensitive and selective than the E2-ELISAs and cannot be
recommended.
Autophagy activity is up-regulated in adipose tissue of obese individuals and modulates proinflammantory cytokine expression.
Jansen, H.J. ; Essen, P. van; Koenen, T. ; Joosten, L.A. ; Netea, M.G. ; Tack, C.J. ; Stienstra, R. - \ 2012
Endocrinology 153 (2012)12. - ISSN 0013-7227 - p. 5866 - 5874.
insulin-resistance - inflammation - adipocytes - mice - interleukin-1-beta - differentiation - adipogenesis - biogenesis - immunity - cells
Autophagy, an evolutionary conserved process aimed at recycling damaged organelles and protein aggregates in the cell, also modulates proinflammatory cytokine production in peripheral blood mononuclear cells. Because adipose tissue inflammation accompanied by elevated levels of proinflammatory cytokines is characteristic for the development of obesity, we hypothesized that modulation of autophagy alters adipose tissue inflammatory gene expression and secretion. We tested our hypothesis using ex vivo and in vivo studies of human and mouse adipose tissue. Levels of the autophagy marker LC3 were elevated in sc adipose tissue of obese vs. lean human subjects and positively correlated to both systemic insulin resistance and morphological characteristics of adipose tissue inflammation. Similarly, autophagic activity levels were increased in adipose tissue of obese and insulin resistant animals as compared with lean mice. Inhibition of autophagy by 3-methylalanine in human and mouse adipose tissue explants led to a significant increase in IL-1ß, IL-6, and IL-8 mRNA expression and protein secretion. Noticeably, the enhancement in IL-1ß, IL-6, and keratinocyte-derived chemoattractant (KC) by inhibition of autophagy was more robust in the presence of obesity. Similar results were obtained by blocking autophagy using small interfering RNA targeted to ATG7 in human Simpson-Golabi-Behmel syndrome adipocytes. Our results demonstrate that autophagy activity is up-regulated in the adipose tissue of obese individuals and inhibition of autophagy enhances proinflammatory gene expression both in adipocytes and adipose tissue explants. Autophagy may function to dampen inflammatory gene expression and thereby limit excessive inflammation in adipose tissue during obesity.
A taxonomic revision of the reinstated genus Leplaea and the newly recognized genus Neoguarea (Meliaceae, Sapindales): the exclusion of Guarea from Africa
Koenen, E.J.M. ; Wilde, J.J.F.E. de - \ 2012
Plant Ecology and Evolution 145 (2012)2. - ISSN 2032-3913 - p. 209 - 241.
iucn red list - tropical forests
Background and aims - The taxonomy of the African representatives of the genus Guarea, among them a number of timber species, is badly understood. The group is revised. Methods - Standard herbarium taxonomy practices were used. Specimens from fifteen different herbaria were studied. Using a GIS application and geo-referenced herbarium specimens, IUCN Red List categories are assessed for each species. Key results - Morphological studies show that the group is distinct from the South-American members of Guarea and deserves generic status. This is supported by molecular data. Therefore the genus Leplaea is reinstated to accommodate five of the species formerly placed in Guarea and the new combinations are presented. Furthermore, two new species, L. adenopunctata E.J.M.Koenen & J.J.de Wilde and L. cauliflora E.J.M.Koenen & J.J.de Wilde are formally described. In addition to de Wilde's (2007) revision of Heckeldora, one more species, G. leonensis, is transferred to this genus and the new combination made. G. glomerulata is shown to be morphologically distinct and to deserve generic status as well. This is endorsed by molecular data. As a consequence, Guarea sect. Neoguarea Harms is granted generic rank to accommodate this species; the new genus is described and the new combination made. A generic key to the African Guareeae is provided, as well as a key to the species of Leplaea; botanical drawings, distribution maps and IUCN Red List categories are presented.
Comparative evaluation of live marker vaccine candidates "CP7_E2alf" and "flc11" along with C-strain "Riems" after oral vaccination
Blome, S. ; Aebischer, A. ; Lange, E. ; Hofmann, M. ; Leifer, I. ; Loeffen, W.L.A. ; Koenen, F. ; Beer, M. - \ 2012
Veterinary Microbiology 158 (2012)1-2. - ISSN 0378-1135 - p. 42 - 59.
classical-swine-fever - time rt-pcr - e-rns - virus - pestiviruses - differentiation - pigs - e2
Due to the tremendous socio-economic impact of classical swine fever (CSF) outbreaks, emergency vaccination scenarios are continuously under discussion. Unfortunately, all currently available vaccines show restrictions either in terms of marker capacities or immunogenicity. Recent research efforts were therefore directed at the design of new modified live marker vaccines. Among the most promising candidates the chimeric pestiviruses “CP7_E2alf” and “flc11” were identified. Within an international research project, these candidates were comparatively tested in challenge experiments after a single oral vaccination. Challenge infection was carried out with highly virulent CSF virus strain “Koslov”, 14 or 21 days post vaccination (dpv), respectively. Safety, efficacy, and marker potential were addressed. All assessments were done in comparison with the conventional “gold standard” C-strain “Riems” vaccine. In addition to the challenge trials, multiple vaccinations with both candidates were performed to further assess their marker vaccine potential. All vaccines were safe and yielded full protection upon challenge 21 days post vaccination. Neither serological nor virological investigations showed major differences among the three vaccines. Whereas CP7_E2alf also provided clinical protection upon challenge at 14 days post vaccination, only 50% of animals vaccinated with flc11, and 83% vaccinated with C-strain “Riems” survived challenge at this time point. No marked differences were seen in protected animals. Despite the fact that all multiple-vaccinated animals stayed sero-negative in the accompanying marker test, the discriminatory assay remains a weak point due to delayed or inexistent detection of some of the vaccinated and subsequently infected animals. Nevertheless, the potential as live marker vaccines could be confirmed for both vaccine candidates. Future efforts will therefore be directed at the licensing of “Cp7_E2alf” as the first live marker vaccine for CSF
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