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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Rarity of monodominance in hyperdiverse Amazonian forests
Steege, Hans Ter; Henkel, Terry W. ; Helal, Nora ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Huth, Andreas ; Groeneveld, Jürgen ; Sabatier, Daniel ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Irume, Mariana Victória ; Martins, Maria Pires ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Mendoza, Abel Monteagudo ; Ramos, José Ferreira ; Luize, Bruno Garcia ; Moraes de Leão Novo, Evlyn Márcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Venticinque, Eduardo Martins ; Manzatto, Angelo Gilberto ; Reis, Neidiane Farias Costa ; Terborgh, John ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Feldpausch, Ted R. ; Duque, Alvaro ; Costa, Flávia R.C. ; Arboleda, Nicolás Castaño ; Schöngart, Jochen ; Killeen, Timothy J. ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Assis, Rafael L. ; Baraloto, Chris ; Engel, Julien ; Petronelli, Pascal ; Castellanos, Hernán ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Camargo, José Luís ; Laurance, Susan G.W. ; Laurance, William F. ; Rincón, Lorena M. ; Schietti, Juliana ; Sousa, Thaiane R. ; Sousa Farias, Emanuelle de; Lopes, Maria Aparecida ; Magalhães, José Leonardo Lima ; Mendonça Nascimento, Henrique Eduardo ; Lima de Queiroz, Helder ; Aymard C, Gerardo A. ; Brienen, Roel ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Draper, Freddie ; García-Villacorta, Roosevelt ; Lopes, Aline ; Vicentini, Alberto ; Alonso, Alfonso ; Dallmeier, Francisco ; Gomes, Vitor H.F. ; Lloyd, Jon ; Neill, David ; Aguiar, Daniel Praia Portela de; Arroyo, Luzmila ; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho de; Amaral, Dário Dantas do; Feeley, Kenneth J. ; Gribel, Rogerio ; Pansonato, Marcelo Petratti ; Barlow, Jos ; Berenguer, Erika ; Ferreira, Joice ; Fine, Paul V.A. ; Guedes, Marcelino Carneiro ; Jimenez, Eliana M. ; Licona, Juan Carlos ; Peñuela Mora, Maria Cristina ; Villa, Boris ; Cerón, Carlos ; Maas, Paul ; Silveira, Marcos ; Stropp, Juliana ; Thomas, Raquel ; Baker, Tim R. ; Daly, Doug ; Dexter, Kyle G. ; Huamantupa-Chuquimaco, Isau ; Milliken, William ; Pennington, Toby ; Ríos Paredes, Marcos ; Fuentes, Alfredo ; Klitgaard, Bente ; Pena, José Luis Marcelo ; Peres, Carlos A. ; Silman, Miles R. ; Tello, J.S. ; Chave, Jerome ; Cornejo Valverde, Fernando ; Fiore, Anthony Di; Hilário, Renato Richard ; Phillips, Juan Fernando ; Rivas-Torres, Gonzalo ; Andel, Tinde R. van; Hildebrand, Patricio von; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Barbosa, Flávia Rodrigues ; Matos Bonates, Luiz Carlos de; Sá Carpanedo, Rainiellen de; Dávila Doza, Hilda Paulette ; Fonty, Émile ; GómeZárate Z, Ricardo ; Gonzales, Therany ; Gallardo Gonzales, George Pepe ; Hoffman, Bruce ; Junqueira, André Braga ; Malhi, Yadvinder ; Andrade Miranda, Ires Paula de; Pinto, Linder Felipe Mozombite ; Prieto, Adriana ; Jesus Rodrigues, Domingos de; Rudas, Agustín ; Ruschel, Ademir R. ; Silva, Natalino ; Vela, César I.A. ; Vos, Vincent Antoine ; Zent, Egleé L. ; Zent, Stanford ; Weiss Albuquerque, Bianca ; Cano, Angela ; Carrero Márquez, Yrma Andreina ; Correa, Diego F. ; Costa, Janaina Barbosa Pedrosa ; Flores, Bernardo Monteiro ; Galbraith, David ; Holmgren, Milena ; Kalamandeen, Michelle ; Nascimento, Marcelo Trindade ; Oliveira, Alexandre A. ; Ramirez-Angulo, Hirma ; Rocha, Maira ; Scudeller, Veridiana Vizoni ; Sierra, Rodrigo ; Tirado, Milton ; Umaña Medina, Maria Natalia ; Heijden, Geertje van der; Vilanova Torre, Emilio ; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Ahuite Reategui, Manuel Augusto ; Baider, Cláudia ; Balslev, Henrik ; Cárdenas, Sasha ; Casas, Luisa Fernanda ; Farfan-Rios, William ; Ferreira, Cid ; Linares-Palomino, Reynaldo ; Mendoza, Casimiro ; Mesones, Italo ; Torres-Lezama, Armando ; Giraldo, Ligia Estela Urrego ; Villarroel, Daniel ; Zagt, Roderick ; Alexiades, Miguel N. ; Oliveira, Edmar Almeida de; Garcia-Cabrera, Karina ; Hernandez, Lionel ; Palacios Cuenca, Walter ; Pansini, Susamar ; Pauletto, Daniela ; Ramirez Arevalo, Freddy ; Sampaio, Adeilza Felipe ; Valderrama Sandoval, Elvis H. ; Valenzuela Gamarra, Luis ; Levesley, Aurora ; Pickavance, Georgia ; Melgaço, Karina - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

Insight into the molecular mechanisms of organic acid pathways in Aspergillus niger
Laothanachareon, Thanaporn - \ 2019
Wageningen University. Promotor(en): V.A.P. Martins dos Santos, co-promotor(en): P.J. Schaap. - Wageningen : Wageningen University - ISBN 9789463950350 - 252
Macrophage-Specific NF-κB Activation Dynamics Can Segregate Inflammatory Bowel Disease Patients
Papoutsopoulou, Stamatia ; Burkitt, Michael D. ; Bergey, François ; England, Hazel ; Hough, Rachael ; Schmidt, Lorraine ; Spiller, David G. ; White, Michael H.R. ; Paszek, Pawel ; Jackson, Dean A. ; Martins Dos Santos, Vitor A.P. ; Sellge, Gernot ; Pritchard, D.M. ; Campbell, Barry J. ; Müller, Werner ; Probert, Chris S. - \ 2019
Frontiers in Immunology 10 (2019). - ISSN 1664-3224 - 11 p.
The heterogeneous nature of inflammatory bowel disease (IBD) presents challenges, particularly when choosing therapy. Activation of the NF-κB transcription factor is a highly regulated, dynamic event in IBD pathogenesis. Using a lentivirus approach, NF-κB-regulated luciferase was expressed in patient macrophages, isolated from frozen peripheral blood mononuclear cell samples. Following activation, samples could be segregated into three clusters based on the NF-κB-regulated luciferase response. The ulcerative colitis (UC) samples appeared only in the hypo-responsive Cluster 1, and in Cluster 2. Conversely, Crohn's disease (CD) patients appeared in all Clusters with their percentage being higher in the hyper-responsive Cluster 3. A positive correlation was seen between NF-κB-induced luciferase activity and the concentrations of cytokines released into medium from stimulated macrophages, but not with serum or biopsy cytokine levels. Confocal imaging of lentivirally-expressed p65 activation revealed that a higher proportion of macrophages from CD patients responded to endotoxin lipid A compared to controls. In contrast, cells from UC patients exhibited a shorter duration of NF-κB p65 subunit nuclear localization compared to healthy controls, and CD donors. Analysis of macrophage cytokine responses and patient metadata revealed a strong correlation between CD patients who smoked and hyper-activation of p65. These in vitro dynamic assays of NF-κB activation in blood-derived macrophages have the potential to segregate IBD patients into groups with different phenotypes and may therefore help determine response to therapy.
Implications of horizontal and vertical relationships on farmers performance in the Brazilian pork industry
Martins, Franco Müller ; Trienekens, Jacques ; Omta, Onno - \ 2019
Livestock Science 228 (2019). - ISSN 1871-1413 - p. 161 - 169.
Brazil - Contracts - Performance - Pork supply chain - Relationship characteristics

According to the literature, vertical and horizontal relationships are of key importance to farmer performance. However, most studies have examined these relationships using distinct models. This paper contributes with new insights to the supply chain management and network theories by using a single model to analyse how horizontal relationships impact on vertical relationships and how these jointly affect the performance of Brazilian pig farmers. Data were obtained from 269 farmers delivering pigs through contracts and spot markets in southern Brazil. The results demonstrate that both vertical and horizontal relationships can improve farmer performance. Moreover, horizontal relationships positively influence vertical relationships by improving the exchange of information between farmers and buyers. Furthermore, the findings suggest that these relationships are sensitive to the context (spot market or contracted production) in which the transactions are executed. The study draws relevant management implications for pig farmers, buyers and farmer associations.

Mild maternal hyperglycemia in INSC93S transgenic pigs causes impaired glucose tolerance and metabolic alterations in neonatal offspring
Renner, Simone ; Martins, Ana Sofia ; Streckel, Elisabeth ; Braun-Reichhart, Christina ; Backman, Mattias ; Prehn, Cornelia ; Klymiuk, Nikolai ; Bähr, Andrea ; Blutke, Andreas ; Landbrecht-Schessl, Christina ; Wünsch, Annegret ; Kessler, Barbara ; Kurome, Mayuko ; Hinrichs, Arne ; Koopmans, Sietse Jan ; Krebs, Stefan ; Kemter, Elisabeth ; Rathkolb, Birgit ; Nagashima, Hiroshi ; Blum, Helmut ; Ritzmann, Mathias ; Wanke, Rüdiger ; Aigner, Bernhard ; Adamski, Jerzy ; Hrabě de Angelis, Martin ; Wolf, Eckhard - \ 2019
Disease Models & Mechanisms 12 (2019)8. - ISSN 1754-8411
Developmental programming - Maternal diabetes - Metabolomics - Pig - Transgenic

Alongside the obesity epidemic, the prevalence of maternal diabetes is rising worldwide, and adverse effects on fetal development and metabolic disturbances in the offspring's later life have been described. To clarify whether metabolic programming effects are due to mild maternal hyperglycemia without confounding obesity, we investigated wild-type offspring of INSC93S transgenic pigs, which are a novel genetically modified large-animal model expressing mutant insulin (INS) C93S in pancreatic β-cells. This mutation results in impaired glucose tolerance, mild fasting hyperglycemia and insulin resistance during late pregnancy. Compared with offspring from wild-type sows, piglets from hyperglycemic mothers showed impaired glucose tolerance and insulin resistance (homeostatic model assessment of insulin resistance: +3-fold in males; +4.4-fold in females) prior to colostrum uptake. Targeted metabolomics in the fasting and insulin-stimulated state revealed distinct alterations in the plasma metabolic profile of piglets from hyperglycemic mothers. They showed increased levels of acylcarnitines, gluconeogenic precursors such as alanine, phospholipids (in particular lyso-phosphatidylcholines) and α-aminoadipic acid, a potential biomarker for type 2 diabetes. These observations indicate that mild gestational hyperglycemia can cause impaired glucose tolerance, insulin resistance and associated metabolic alterations in neonatal offspring of a large-animal model born at a developmental maturation status comparable to human babies.

Patient’s characteristics and outcomes in necrotising soft-tissue infections: results from a Scandinavian, multicentre, prospective cohort study
Madsen, Martin Bruun ; Skrede, Steinar ; Perner, Anders ; Arnell, Per ; Nekludov, Michael ; Bruun, Trond ; Karlsson, Ylva ; Hansen, Marco Bo ; Polzik, Peter ; Hedetoft, Morten ; Rosén, Anders ; Saccenti, Edoardo ; Bergey, François ; Martins Dos Santos, Vitor A.P. ; Norrby-teglund, Anna ; Hyldegaard, Ole - \ 2019
Intensive Care Medicine 45 (2019)9. - ISSN 0342-4642 - p. 1241 - 1251.
Purpose: Necrotising soft-tissue infections (NSTI) are characterised by necrosis, fast progression, and high rates of morbidity and mortality, but our knowledge is primarily derived from small prospective studies and retrospective studies. Methods: We performed an international, multicentre, prospective cohort study of adults with NSTI describing patient’s characteristics and associations between baseline variables and microbiological findings, amputation, and 90-day mortality. Results: We included 409 patients with NSTI; 402 were admitted to the ICU. Cardiovascular disease [169 patients (41%)] and diabetes [98 (24%)] were the most common comorbidities; 122 patients (30%) had no comorbidity. Before surgery, bruising of the skin [210 patients (51%)] and pain requiring opioids [172 (42%)] were common. The sites most commonly affected were the abdomen/ano-genital area [140 patients (34%)] and lower extremities [126 (31%)]. Monomicrobial infection was seen in 179 patients (44%). NSTI of the upper or lower extremities was associated with monomicrobial group A streptococcus (GAS) infection, and NSTI located to the abdomen/ano-genital area was associated with polymicrobial infection. Septic shock [202 patients (50%)] and acute kidney injury [82 (20%)] were common. Amputation occurred in 22% of patients with NSTI of an extremity and was associated with higher lactate level. All-cause 90-day mortality was 18% (95% CI 14–22); age and higher lactate levels were associated with increased mortality and GAS aetiology with decreased mortality. Conclusions: Patients with NSTI were heterogeneous regarding co-morbidities, initial symptoms, infectious localisation, and microbiological findings. Higher age and lactate levels were associated with increased mortality, and GAS infection with decreased mortality.
How do lianas and trees change their vascular strategy in seasonal versus rain forest?
Dias, Arildo S. ; Oliveira, Rafael S. ; Martins, Fernando R. ; Bongers, F. ; Anten, Niels P.R. ; Sterck, F. - \ 2019
Perspectives in plant ecology, evolution and systematics 40 (2019). - ISSN 1433-8319
Cambial variant - Functional traits - Plant hydraulics - Tropical forests - Wood density - Xylem structure and function

Plants can alter wood anatomy to adjust water supply and mechanical stability demands. However, the different ways in which species can adjust rates of water supply through variation in size and number of vessels in the sapwood, and how this variation is related to the trade-off between hydraulic and mechanical functions remain unclear. We tested the hypothesis that plants with higher investment in mechanical support have relatively less margin to change their potential hydraulic conductivity in terms of vascular strategy: the total area of conducting tissue (vessel lumen fraction) and the combination of vessel sizes and numbers (vessel composition). We measured hydraulic and mechanical traits of xylem tissue and compared the relationship between those traits between trees and lianas co-occurring in a semi-deciduous seasonally dry forest (SDF) and an evergreen rainforest (RF). Along the axis of hydraulic-mechanical trait variation, SDF lianas showed a trait combination towards investment in hydraulic conductivity (higher vessel lumen area, percentage of xylem represented by vessels and potential hydraulic conductivity), whereas trees from both forests were characterized by investment in mechanical support (higher wood density, percentage of xylem represented by fibres and number of vessel per area) and RF lianas were intermediate between these spectrum. The main difference between trees and lianas was in vessel lumen fraction and vessel composition, indicating that not only the vessel size but the distribution between the size and number of vessels is important to explain the higher hydraulic conductivity of lianas. Between forests, trees did not differ in wood density (construction costs). Similarly, lianas did not differ in wood density among forests either; therefore, confirming that differences in potential hydraulic conductivity resulted from changes in the distribution between the size and number of vessels (vascular strategy). Our results suggest that vessel lumen fraction and the vessel composition are important dimensions driving variation in construction costs across woody plants. Thus, what makes lianas hydraulically distinctive from trees is the way vessel lumen fraction and vessel composition vary across environments rather than simply having wider vessels.

Genome-wide association studies for heat stress response in Bos taurus × Bos indicus crossbred cattle
Otto, Pamela I. ; Guimarães, Simone E.F. ; Verardo, Lucas L. ; Azevedo, Ana Luísa S. ; Vandenplas, Jeremie ; Sevillano, Claudia A. ; Marques, Daniele B.D. ; Fatima A. Pires, Maria de; Freitas, Célio de; Verneque, R.S. ; Martins, Marta Fonseca ; Panetto, João Cláudio C. ; Carvalho, Wanessa A. ; Gobo, Diego O.R. ; Silva, Marcos Vinícius G.B. da; Machado, Marco A. - \ 2019
Journal of Dairy Science 102 (2019)9. - ISSN 0022-0302 - p. 8148 - 8158.
crossbred cattle - gene network - heat stress - post-GWAS analyses

Heat stress is an important issue in the global dairy industry. In tropical areas, an alternative to overcome heat stress is the use of crossbred animals or synthetic breeds, such as the Girolando. In this study, we performed a genome-wide association study (GWAS) and post-GWAS analyses for heat stress in an experimental Gir × Holstein F2 population. Rectal temperature (RT) was measured in heat-stressed F2 animals, and the variation between 2 consecutive RT measurements (ΔRT) was used as the dependent variable. Illumina BovineSNP50v1 BeadChip (Illumina Inc., San Diego, CA) and single-SNP approach were used for GWAS. Post-GWAS analyses were performed by gene ontology terms enrichment and gene-transcription factor (TF) networks, generated from enriched TF. The breed origin of marker alleles in the F2 population was assigned using the breed of origin of alleles (BOA) approach. Heritability and repeatability estimates (± standard error) for ΔRT were 0.13 ± 0.08 and 0.29 ± 0.06, respectively. Association analysis revealed 6 SNP significantly associated with ΔRT. Genes involved with biological processes in response to heat stress effects (LIF, OSM, TXNRD2, and DGCR8) were identified as putative candidate genes. After performing the BOA approach, the 10% of F2 animals with the lowest breeding values for ΔRT were classified as low-ΔRT, and the 10% with the highest breeding values for ΔRT were classified as high-ΔRT. On average, 49.4% of low-ΔRT animals had 2 alleles from the Holstein breed (HH), and 39% had both alleles from the Gir breed (GG). In high-ΔRT animals, the average proportion of animals for HH and GG were 1.4 and 50.2%, respectively. This study allowed the identification of candidate genes for ΔRT in Gir × Holstein crossbred animals. According to the BOA approach, Holstein breed alleles could be associated with better response to heat stress effects, which could be explained by the fact that Holstein animals are more affected by heat stress than Gir animals and thus require a genetic architecture to defend the body from the deleterious effects of heat stress. Future studies can provide further knowledge to uncover the genetic architecture underlying heat stress in crossbred cattle.

Pseudomonas putida KT2440 is HV1 certified, not GRAS
Kampers, Linde F.C. ; Volkers, Rita J.M. ; Martins dos Santos, Vitor A.P. - \ 2019
Microbial Biotechnology 12 (2019)5. - ISSN 1751-7907 - p. 845 - 848.

Pseudomonas putida is rapidly becoming a workhorse for industrial production due to its metabolic versatility, genetic accessibility and stress-resistance properties. The P. putida strain KT2440 is often described as Generally Regarded as Safe, or GRAS, indicating the strain is safe to use as food additive. This description is incorrect. P. putida KT2440 is classified by the FDA as HV1 certified, indicating it is safe to use in a P1 or ML1 environment.

Modeling Host-Pathogen Interaction to Elucidate the Metabolic Drug Response of Intracellular Mycobacterium tuberculosis
Rienksma, Rienk A. ; Schaap, Peter J. ; Martins Dos Santos, Vitor A.P. ; Suarez-Diez, Maria - \ 2019
Frontiers in Cellular and Infection Microbiology 9 (2019). - ISSN 2235-2988 - 1 p.
antibiotics - drug response - flux balance analysis - host-pathogen interaction - metabolic model - Mycobacterium tuberculosis

Little is known about the metabolic state of Mycobacterium tuberculosis (Mtb) inside the phagosome, a compartment inside phagocytes for killing pathogens and other foreign substances. We have developed a combined model of Mtb and human metabolism, sMtb-RECON and used this model to predict the metabolic state of Mtb during infection of the host. Amino acids are predicted to be used for energy production as well as biomass formation. Subsequently we assessed the effect of increasing dosages of drugs targeting metabolism on the metabolic state of the pathogen and predict resulting metabolic adaptations and flux rerouting through various pathways. In particular, the TCA cycle becomes more important upon drug application, as well as alanine, aspartate, glutamate, proline, arginine and porphyrin metabolism, while glycine, serine, and threonine metabolism become less important. We modeled the effect of 11 metabolically active drugs. Notably, the effect of eight could be recreated and two major profiles of the metabolic state were predicted. The profiles of the metabolic states of Mtb affected by the drugs BTZ043, cycloserine and its derivative terizidone, ethambutol, ethionamide, propionamide, and isoniazid were very similar, while TMC207 is predicted to have quite a different effect on metabolism as it inhibits ATP synthase and therefore indirectly interferes with a multitude of metabolic pathways.

Capturing the impact of oral processing behaviour on consumption time and dynamic sensory perception of ice creams differing in hardness
Doyennette, Marion ; Aguayo-Mendoza, Monica G. ; Williamson, Ann Marie ; Martins, Sara I.F.S. ; Stieger, Markus - \ 2019
Food Quality and Preference 78 (2019). - ISSN 0950-3293
Consumption time - Eating behaviour - Food oral processing - Ice cream - Self-reporting - Temporal dominance of sensations - Texture - Video recording

Little is known about the oral processing behaviour of ice creams for which the quantification of oral manipulations remains challenging. The impact of oral processing behaviour on dynamic sensory perception of ice creams has not been reported previously, although ice creams are anecdotally known to be consumed following different oral processing strategies. The aims of the study were (1) to compare different methodologies to characterise oral behaviours applied during consumption of ice cream, and (2) to understand how oral processing behaviour influences dynamic sensory perception of ice creams. Oral processing behaviour of ice creams was characterized by self-reporting and video recording of n = 103 consumers. Most consumers applied either tongue movements or combined tongue and jaw oral behaviours. The video recording was clearly better than self-reporting in capturing the actually displayed eating behaviour of ice creams. Consumption time was prolonged considerably when ice cream hardness increased or when oral behaviour was changed during Temporal Dominance of Sensations (TDS) evaluations. When ice creams were consumed by letting them melt in mouth, dominance of sweetness and firmness were significantly prolonged. When ice creams were consumed by chewing, dominance of fruity aroma and coldness were significantly prolonged. We conclude that (1) eating behaviour of ice creams is captured better by video recordings than self-reporting and that (2) oral processing behaviour considerably changes dynamic texture and flavour perception of ice creams. This highlights the importance of controlling oral processing behaviour when quantifying sensory properties of ice creams.

Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcusfuriosus Phosphoglucose Isomerase
Subramanian, Kalyanasundaram ; Mitusińska, Karolina ; Raedts, John ; Almourfi, Feras ; Joosten, Henk Jan ; Hendriks, Sjon ; Sedelnikova, Svetlana E. ; Kengen, Servé W.M. ; Hagen, Wilfred R. ; Góra, Artur ; Martins Dos Santos, Vitor A.P. ; Baker, Patrick J. ; Oost, John van der; Schaap, Peter J. - \ 2019
Biomolecules 9 (2019)6. - ISSN 2218-273X
Comulator - cupin phosphoglucose isomerase - Protein engineering - Pyrococcus furiosus - solvent access

The cupin-type phosphoglucose isomerase (PfPGI) from the hyperthermophilic archaeon Pyrococcus furiosus catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. We investigated PfPGI using protein-engineering bioinformatics tools to select functionally-important residues based on correlated mutation analyses. A pair of amino acids in the periphery of PfPGI was found to be the dominant co-evolving mutation. The position of these selected residues was found to be non-obvious to conventional protein engineering methods. We designed a small smart library of variants by substituting the co-evolved pair and screened their biochemical activity, which revealed their functional relevance. Four mutants were further selected from the library for purification, measurement of their specific activity, crystal structure determination, and metal cofactor coordination analysis. Though the mutant structures and metal cofactor coordination were strikingly similar, variations in their activity correlated with their fine-tuned dynamics and solvent access regulation. Alternative, small smart libraries for enzyme optimization are suggested by our approach, which is able to identify non-obvious yet beneficial mutations.

Risk-Based Bioengineering Strategies for Reliable Bacterial Vaccine Production
Kamminga, Tjerko ; Slagman, Simen Jan ; Martins dos Santos, Vitor A.P. ; Bijlsma, Jetta J.E. ; Schaap, Peter J. - \ 2019
Trends in Biotechnology 37 (2019)8. - ISSN 0167-7799 - p. 805 - 816.
bacterial vaccines - constraint-based - genome-scale metabolic models - process analytical technology - risk-based process design

Design of a reliable process for bacterial antigen production requires understanding of and control over critical process parameters. Current methods for process design use extensive screening experiments for determining ranges of critical process parameters yet fail to give clear insights into how they influence antigen potency. To address this gap, we propose to apply constraint-based, genome-scale metabolic models to reduce the need of experimental screening for strain selection and to optimize strains based on model driven iterative Design–Build–Test–Learn (DBTL) cycles. Application of these systematic methods has not only increased the understanding of how metabolic network properties influence antigen potency, but also allows identification of novel critical process parameters that need to be controlled to achieve high process reliability.

Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions
Odoni, Dorett I. ; Vazquez-Vilar, Marta ; Gaal, Merlijn P. van; Schonewille, Tom ; Martins Dos Santos, Vitor A.P. ; Tamayo-Ramos, Juan Antonio ; Suarez-Diez, Maria ; Schaap, Peter J. - \ 2019
FEMS Microbiology Letters 366 (2019)7. - ISSN 0378-1097
Aspergillus niger - citrate - homology - MDR - transcriptomics - transport

Currently, there is no consensus regarding the mechanism underlying Aspergillus niger citrate biosynthesis and secretion. We hypothesise that depending on the experimental setup, extracellular citrate accumulation can have fundamentally different underlying transcriptomic landscapes. We show that varying the amount and type of supplement of an arginine auxotrophic A. niger strain results in transcriptional down-regulation of citrate metabolising enzymes in the condition in which more citrate is accumulated extracellularly. This contrasts with the transcriptional adaptations when increased citrate production is triggered by iron limitation. By combining gene expression data obtained from these two very distinct experimental setups with hidden Markov models and transporter homology approaches, we were able to compile a shortlist of the most likely citrate transporter candidates. Two candidates (An17g01710 and An09g06720m.01) were heterologously expressed in the yeast Saccharomyces cerevisiae, and one of the resultant mutants showed the ability to secrete citrate. Our findings provide steps in untangling the complex interplay of different mechanisms underlying A. niger citrate accumulation, and we demonstrate how a comparative transcriptomics approach complemented with further bioinformatics analyses can be used to pinpoint a fungal citrate exporter.

Phytosociological study to define restoration measures in a mined area in Minas Gerais, Brazil
Balestrin, Diego ; Martins, Sebastião Venâncio ; Schoorl, Jeroen Machiel ; Teixeira Lopes, Aldo ; Fonseca de Andrade, Christian - \ 2019
Ecological Engineering 135 (2019). - ISSN 0925-8574 - p. 8 - 16.
Environmental restoration - Mining - Sustainability

In this study we describe a case study to evaluate the floristic diversity and the soil conditions of post mined area, currently under 14-years of restoration. The study area is located in the municipality of Descoberto, Minas Gerais State, Brazil, and has one hectare in the process of restoration through the planting of seedlings. The forest inventory of all individuals with Circumference at Breast Height (CBH) ≥15 cm was carried out and the phytosociological parameters were evaluated. The study area shows a high floristic diversity H′ = 3.258 as well as equability (J′ = 0.783), evidencing that the study area is floristically heterogeneous and has low ecological dominance. In addition, this area presented floristic similarity to other restored areas that were already in a more advanced restoration process. Considering soil quality, the restored study area shows higher levels of cation exchange capacity (t), approximate sum base values (SB) and base saturation (V) than those verified in nearby areas. Evaluating the successional characteristics (greater presence of individuals of secondary succession) and the domain of species with dispersion by animals, we can infer that the area is in an advanced stage of restoration, as well as performing its environmental and social functions. Thus, we can conclude that the restoration of mined areas is feasible when the restoration techniques are applied correctly. Furthermore, we can say that these successful restoration measures are improving the environmental sustainability and helping considerably the recovery of losses caused by mining.

Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
Poorter, L. ; Rozendaal, Danaë ; Bongers, F. ; Almeida-Cortez, Jarcilene S. ; Almeyda Zambrano, Angélica María ; Álvarez, Francisco S. ; Andrade, José Luís ; Villa, Luis Felipe Arreola ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Bhaskar, Radika ; Boukili, Vanessa ; Brancalion, Pedro H.S. ; Broadbent, Eben N. ; César, Ricardo Gomes ; Chave, Jerome ; Chazdon, Robin L. ; Colletta, Gabriel Dalla ; Craven, Dylan ; Jong, Ben H.J. de; Denslow, Julie S. ; Dent, Daisy H. ; DeWalt, Saara J. ; García, Elisa Díaz ; Dupuy, Juan M. ; Durán, Sandra M. ; Espírito Santo, Mário Marcos ; Fandiño, María C. ; Fernandes, Geraldo Wilson ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Jakovac, A.C. ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, M.W.M. ; Lopez, Omar R. ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Martins, Sebastião Venâncio ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita ; Mora, Francisco ; Souza Moreno, Vanessa De; Müller, Sandra C. ; Muñoz, Rodrigo ; Muscarella, Robert ; Oliveira Neto, Silvio Nolasco De; Nunes, Yule Roberta Ferreira ; Ochoa-Gaona, Susana ; Paz, Horacio ; Pena Claros, M. ; Piotto, Daniel ; Ruíz, Jorge ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Steininger, Marc K. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Breugel, Michiel van; Wal, Hans van der - \ 2019
secondary succession - community assembly - community-weighted mean - wood density - Neotropics - tropical forest - Latin America
We analyse how community wood density (WD) recovers during secondary tropical forest succession. In wet forests succession proceeds from low to high WD, in dry forests from high to low WD, resulting in convergence of community WD of dry and wet forests over time, as vegetation cover builds up.
Metabolomics in systems medicine: an overview of methods and applications
Karakitsou, Effrosyni ; Foguet, Carles ; Atauri, Pedro de; Kultima, Kim ; Khoonsari, Payam Emami ; Martins dos Santos, Vitor A.P. ; Saccenti, Edoardo ; Rosato, Antonio ; Cascante, Marta - \ 2019
Current Opinion in Systems Biology 15 (2019). - ISSN 2452-3100 - p. 91 - 99.
Constraint-based modelling - Kinetic modellig - Metabolomics - Multiomics - Personalized medicine - Systems medicine

Patient-derived metabolomics offers valuable insights into the metabolic phenotype underlying diseases with a strong metabolic component. Thus, these data sets will be pivotal to the implementation of personalized medicine strategies in health and disease. However, to take full advantage of such data sets, they must be integrated with other omics within a coherent pathophysiological framework to enable improved diagnostics, to identify therapeutic interventions, and to accurately stratify patients. Herein, we provide an overview of the state-of-the-art data analysis and modeling approaches applicable to metabolomics data and of their potential for systems medicine.

Modeling metabolism of Mycobacterium tuberculosis
Rienksma, Rienk A. - \ 2019
Wageningen University. Promotor(en): V.A.P. Martins Dos Santos, co-promotor(en): P.J. Schaap; M. Suárez-Diez. - Wageningen : Wageningen University - ISBN 9789463439190 - 167
Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
Poorter, Lourens ; Rozendaal, Danaë M.A. ; Bongers, Frans ; Almeida-Cortez, Jarcilene S. de; Almeyda Zambrano, Angélica María ; Álvarez, Francisco S. ; Andrade, José Luís ; Villa, Luis Felipe Arreola ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Bhaskar, Radika ; Boukili, Vanessa ; Brancalion, Pedro H.S. ; Broadbent, Eben N. ; César, Ricardo G. ; Chave, Jerome ; Chazdon, Robin L. ; Colletta, Gabriel Dalla ; Craven, Dylan ; Jong, Ben H.J. de; Denslow, Julie S. ; Dent, Daisy H. ; DeWalt, Saara J. ; García, Elisa Díaz ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Espírito Santo, Mário M. ; Fandiño, María C. ; Fernandes, Geraldo Wilson ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Jakovac, Catarina C. ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, Madelon ; Lopez, Omar R. ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Martins, Sebastião V. ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita ; Mora, Francisco ; Souza Moreno, Vanessa de; Müller, Sandra C. ; Muñoz, Rodrigo ; Muscarella, Robert ; Oliveira Neto, Silvio Nolasco de; Nunes, Yule R.F. ; Ochoa-Gaona, Susana ; Paz, Horacio ; Peña-Claros, Marielos ; Piotto, Daniel ; Ruíz, Jorge ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Steininger, Marc K. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Utrera, Luis P. ; Breugel, Michiel van; Sande, Masha T. van der; Wal, Hans van der; Veloso, Maria D.M. ; Vester, Hans F.M. ; Vieira, Ima C.G. ; Villa, Pedro Manuel ; Williamson, G.B. ; Wright, S.J. ; Zanini, Kátia J. ; Zimmerman, Jess K. ; Westoby, Mark - \ 2019
Nature Ecology & Evolution 3 (2019). - ISSN 2397-334X - p. 928 - 934.

Tropical forests are converted at an alarming rate for agricultural use and pastureland, but also regrow naturally through secondary succession. For successful forest restoration, it is essential to understand the mechanisms of secondary succession. These mechanisms may vary across forest types, but analyses across broad spatial scales are lacking. Here, we analyse forest recovery using 1,403 plots that differ in age since agricultural abandonment from 50 sites across the Neotropics. We analyse changes in community composition using species-specific stem wood density (WD), which is a key trait for plant growth, survival and forest carbon storage. In wet forest, succession proceeds from low towards high community WD (acquisitive towards conservative trait values), in line with standard successional theory. However, in dry forest, succession proceeds from high towards low community WD (conservative towards acquisitive trait values), probably because high WD reflects drought tolerance in harsh early successional environments. Dry season intensity drives WD recovery by influencing the start and trajectory of succession, resulting in convergence of the community WD over time as vegetation cover builds up. These ecological insights can be used to improve species selection for reforestation. Reforestation species selected to establish a first protective canopy layer should, among other criteria, ideally have a similar WD to the early successional communities that dominate under the prevailing macroclimatic conditions.

The diurnal transcriptional landscape of the microalga Tetradesmus obliquus
Carreres, Benoit M. ; Mitsue León-Saiki, G. ; Schaap, Peter J. ; Remmers, Ilse M. ; Veen, Douwe van der; Martins dos Santos, Vitor A.P. ; Wijffels, René H. ; Martens, Dirk E. ; Suarez-Diez, Maria - \ 2019
Algal Research 40 (2019). - ISSN 2211-9264
Day/night cycles - Diurnal transcription changes - Microalgae - Photosynthetic efficiency - Scenedesmus obliquus - starchless mutant

Tetradesmus obliquus is a promising oleaginous microalga. We functionally annotated its genome and characterized the transcriptional landscape of T. obliquus adapted to 16:8 h light dark (LD) cycles in turbidostat culture conditions at very high temporal resolution (1 h intervals). Revealing a cycle of cellular events, six distinct expression profiles were obtained, each with transcriptional phenotypes correlating with measurements of biochemical composition. The impact of starch deficiency was studied using the starchless mutant slm1. Significant changes in the transcriptional landscape were observed. Starch deficiency resulted in incapacity to supply energy during the dark period, resulting in a shift of energy demanding processes to an earlier or later time point. Our study provides new perspectives on the role of starch and the adaptation to LD cycles of oleaginous microalgae.

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