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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Conductive thin film drying kinetics relevant to drum drying
Qiu, J. ; Kloosterboer, Koen ; Guo, Yang ; Boom, R.M. ; Schutyser, M.A.I. - \ 2019
Journal of Food Engineering 242 (2019). - ISSN 0260-8774 - p. 68 - 75.
Direct assessment of the kinetics of drum drying operation has been a difficult task as the mass and temperature profiles are hard to monitor. Still, developing better understanding of conductive drying would help to identify new operating windows for this technology. The drying kinetics was investigated by drying maltodextrin and starch suspensions with a novel custom-built laboratory-scale apparatus, which allows on-line monitoring of mass and temperatures. During drying, three separate periods were identified: the heating, the boiling and the conductive drying (declining rate) periods. The duration of the initial heating period was proportional to the film thickness and was responsible for a relatively small amount of water evaporated due to natural convection. During the boiling period, the drying rate kept constant while bubble formation impeded the heat transfer. Larger bubbles were observed for starch suspensions due to its viscoelastic properties. Thus, large temperature gradients between the heating pan and the film were observed for starch suspensions. During the conductive drying period, the initial amount of dry solids per surface area determines the drying rate as it determines the thickness of the semi-moist layer subjected to conductive drying. Application of a thin film is preferred to avoid boiling, especially at increasing solids content. This situation also better approaches double drum drying processes, where boiling occurs in the pool and conductive drying occurs on the drum.
Climate change opens new frontiers for marine species in the Arctic: Current trends and future invasion risks
Chan, Farrah T. ; Stanislawczyk, Keara ; Sneekes, A.C. ; Dvoretsky, Alexander ; Gollasch, Stephan ; Minchin, Dan ; David, Matej ; Jelmert, Anders ; Albretsen, Jon ; Bailey, Sarah A. - \ 2018
Global Change Biology (2018). - ISSN 1354-1013 - 14 p.
alien species - aquaculture - climate warming - fisheries - invasion pathways - invasive species - knowledge gap - nonindigenous species - shipping - vessels
Climate change and increased anthropogenic activities are expected to elevate the potential of introducing nonindigenous species (NIS) into the Arctic. Yet, the knowledge base needed to identify gaps and priorities for NIS research and management is limited. Here, we reviewed primary introduction events to each ecoregion of the marine Arctic realm to identify temporal and spatial patterns, likely source regions of NIS, and the putative introduction pathways. We included 54 introduction events representing 34 unique NIS. The rate of NIS discovery ranged from zero to four species per year between 1960 and 2015. The Iceland Shelf had the greatest number of introduction events (n = 14), followed by the Barents Sea (n = 11), and the Norwegian Sea (n = 11). Sixteen of the 54 introduction records had no known origins. The majority of those with known source regions were attributed to the Northeast Atlantic and the Northwest
Pacific, 19 and 14 records, respectively. Some introduction events were attributed
to multiple possible pathways. For these introductions, vessels transferred the greatest number of aquatic NIS (39%) to the Arctic, followed by natural spread (30%) and aquaculture activities (25%). Similar trends were found for introductions attributed to a single pathway. The phyla Arthropoda and Ochrophyta had the highest number of recorded introduction events, with 19 and 12 records, respectively. Recommendations including vector management, horizon scanning, early detection, rapid response, and a pan‐Arctic biodiversity inventory are considered in this paper. Our study provides a comprehensive record of primary introductions of NIS for marine environments in the
circumpolar Arctic and identifies knowledge gaps and opportunities for NIS research and management. Ecosystems worldwide will face dramatic changes in the coming decades due to global change. Our findings contribute to the knowledge base needed to address two aspects of global change—invasive species and climate change.
Expected and observed genotype complexity in prokaryotes: correlation between 16S-rRNA phylogeny and protein domain content
Koehorst, J.J. ; Schaap, P.J. ; Suarez Diez, M. - \ 2018
16S-rRNA gene phylogeny - Bacterial diversity - Domainome based phylogeny - Heaps's analysis - Horizontal domain transfer - Pan- and core-domainome - Species specific domains
Supplementary files supporting the research performed in Expected and observed genotype complexity in prokaryotes: correlation between 16S-rRNA phylogeny and protein domain content.
Comparative transcriptome analysis of Poncirus trifoliata identifies a core set of genes involved in arbuscular mycorrhizal symbiosis
An, Jianyong ; Sun, Mengqian ; Velzen, Robin van; Ji, Chuanya ; Zheng, Zijun ; Limpens, Erik ; Bisseling, Ton ; Deng, Xiuxin ; Xiao, Shunyuan ; Pan, Zhiyong - \ 2018
Journal of Experimental Botany 69 (2018)21. - ISSN 0022-0957 - p. 5255 - 5264.

The perennial woody plants of citrus are one of the most important fruit crops in the world and largely depends on arbuscular mycorrhizal symbiosis (AMS) to obtain essential nutrients from soil. However, the molecular aspects of AMS in citrus and perennial woody plants in general have largely been understudied. We used RNA-sequencing to identify differentially expressed genes in roots of Poncirus trifoliata upon mycorrhization by the AM fungus Glomus versiforme and evaluated their conservation by comparative transcriptome analyses with four herbaceous model plants. We identified 282 differentially expressed genes in P. trifoliata, including orthologs of 21 genes with characterized roles in AMS and 83 genes that are considered to be conserved in AM-host plants. Comparative transcriptome analysis revealed a 'core set' of 156 genes from P. trifoliata whose orthologous genes from at least three of the five species also exhibited similar transcriptional changes during AMS. Functional analysis of one of these conserved AM-induced genes, a 3-keto-acyl-ACP reductase (FatG) involved in fatty acid biosynthesis, confirmed its involvement in AMS in Medicago truncatula. Our results identify a core transcriptional program for AMS that is largely conserved between P. trifoliata and other plants. The comparative transcriptomics approach adds to previous phylogenomics studies to identify conserved genes required for AMS.

Alstroemeria yellow spot virus (AYSV) : a new orthotospovirus species within a growing Eurasian clade
Hassani-Mehraban, A. ; Dullemans, A.M. ; Verhoeven, J.Th.J. ; Roenhorst, J.W. ; Peters, D. ; Vlugt, R.A.A. van der; Kormelink, R. - \ 2018
Archives of Virology (2018). - ISSN 0304-8608 - 10 p.

An orthotospovirus distinct from all other orthotospoviruses was isolated from naturally infected alstroemeria plants. Disease symptoms caused by this virus mainly consisted of yellow spots on the leaves based on which the name alstroemeria yellow spot virus (AYSV) was coined. A host range analysis was performed and a polyclonal antiserum was produced against purified AYSV ribonucleoproteins which only reacted with the homologous antigen and not with any other (established or tentative) orthotospovirus from a selection of American and Asian species. Upon thrips transmission assays the virus was successfully transmitted by a population of Thrips tabaci. The entire nucleotide sequence of the M and S RNA segments was elucidated by a conventional cloning and sequencing strategy, and contained 4797 respectively 2734 nucleotides (nt). Simultaneously, a next generation sequencing (NGS) approach (RNAseq) was employed and generated contigs covering the entire viral tripartite RNA genome. In addition to the M and S RNA nucleotide sequences, the L RNA (8865 nt) was obtained. The nucleocapsid (N) gene encoded by the S RNA of this virus consisted of 819 nucleotides with a deduced N protein of 272 amino acids and by comparative sequence alignments to other established orthotospovirus species showed highest homology (69.5% identity) to the N protein of polygonum ringspot virus. The data altogether support the proposal of AYSV as a new orthotospovirus species within a growing clade of orthotospoviruses that seem to share the Middle East basin as a region of origin.

Pragmatism is a silent killer when it comes to the climate problem
Turnhout, Esther - \ 2018

An interview with Prof. Esther Turnhout of the Forest and Nature Conservation Policy Group.

Efficient inference of homologs in large eukaryotic pan-proteomes
Sheikhizadeh Anari, Siavash ; Ridder, Dick de; Schranz, M.E. ; Smit, Sandra - \ 2018
BMC Bioinformatics 19 (2018)1. - ISSN 1471-2105 - 11 p.
Homologous genes - k-mer - Orthology - Pan-genome - Protein similarity

BACKGROUND: Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to be continually updated to incorporate new sequences. As new sequences are rapidly being generated, there is a need for efficient standalone tools to detect homologs in novel data.

RESULTS: To address this, we present a fast method for detecting homology groups across a large number of individuals and/or species. We adopted a k-mer based approach which considerably reduces the number of pairwise protein alignments without sacrificing sensitivity. We demonstrate accuracy, scalability, efficiency and applicability of the presented method for detecting homology in large proteomes of bacteria, fungi, plants and Metazoa.

CONCLUSIONS: We clearly observed the trade-off between recall and precision in our homology inference. Favoring recall or precision strongly depends on the application. The clustering behavior of our program can be optimized for particular applications by altering a few key parameters. The program is available for public use at as an extension to our pan-genomic analysis tool, PanTools.

Entangled in scales : Multilevel governance challenges for regional planning strategies
Straalen, F.M. van; Witte, P.A. - \ 2018
Regional Studies, Regional Science 5 (2018)1. - ISSN 2168-1376 - p. 157 - 163.
Fuzzy governance - Regionalisation - Scalar problems - The Netherlands

The academic discourse considers the regional scale as an important planning level to provide for spatial objectives that transcend the boundaries of local authorities. Nonetheless, the problem-solving capacity of the regional planning level is still questioned by both academics and practitioners. This paper studies the tension between formal and informal regional governance and its practical challenges for two cases of Dutch provinces struggling with their position in regional governance networks. These cases entail pan-European development (Trans-European Transport Networks – TEN-T) and regional land development (Bloemendalerpolder). It was found that at the metropolitan scale, formal regional planning powers tend to overrule socially produced regional governance arrangements. Simultaneously, regional planning powers lack support of these socially produced arrangements for their interventions. At the same time, at the supra-regional scale, provinces are a logical stakeholder to fulfil a prominent role in regional governance, but often lack the institutional capacity to act as such. We therefore argue that regional planning authorities need to be granted the power and capacity to take up a more centripetal, intermediate role in governance arrangements. This would provide them more capacity to act in disentangling the difficult practical challenges of scalar problems that many regional governance arrangements currently face.

Denitrification-potential evaluation and nitrate-removal-pathway analysis of aerobic denitrifier strain Marinobacter hydrocarbonoclasticus RAD-2
Kong, Dedong ; Li, Wenbing ; Deng, Yale ; Ruan, Yunjie ; Chen, Guangsuo ; Yu, Jianhai ; Lin, Fucheng - \ 2018
Water 10 (2018)10. - ISSN 2073-4441
Aerobic denitrification - Denitrifying gene expression - Marinobacter hydrocarbonoclasticus RAD-2 - Nitrogen removal - Wastewater treatment

An aerobic denitrifier was isolated from a long-term poly (3-hydroxybutyrate-co-3- hydroxyvalerate) PHBV-supported denitrification reactor that operated under alternate aerobic/anoxic conditions. The strain was identified as Marinobacter hydrocarbonoclasticus RAD-2 based on 16S rRNA-sequence phylogenetic analysis. Morphology was observed by scanning electron microscopy (SEM), and phylogenetic characteristics were analyzed with the API 20NE test. Strain RAD-2 showed efficient aerobic denitrification ability when using NO3 - -N or NO2 --N as its only nitrogen source, while heterotrophic nitrification was not detected. The average NO3 --N and NO2 --N removal rates were 6.47 mg/(L·h)and 6.32 mg/(L·h), respectively. Single-factor experiments indicated that a 5:10 C/N ratio, 25-40 °C temperature, and 100-150 rpm rotation speed were the optimal conditions for aerobic denitrification. Furthermore, the denitrifying gene napA had the highest expression on a transcriptional level, followed by the denitrifying genes nirS and nosZ. The norB gene was found to have significantly low expression during the experiment. Overall, great aerobic denitrification ability makes the RAD-2 strain a potential alternative in enhancing nitrate management for marine recirculating aquaculture system (RAS) practices.

Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data
Koehorst, J.J. ; Dam, J.C.J. van; Heck, R.G.A. van; Saccenti, E. ; Martins dos Santos, V.A.P. ; Suarez Diez, M. ; Schaap, P.J. - \ 2018
database - genome annotation - protein domains - Pseudomonas - semantic web
Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas strains by integrating results from a large scale functional comparison using protein domains with data from six metabolic models, nearly a thousand transcriptome measurements and four large scale transposon mutagenesis experiments. Through heterogeneous data integration we linked gene essentiality, persistence and expression variability. The pan-genome of Pseudomonas is closed indicating a limited role of horizontal gene transfer in the evolutionary history of this genus. A large fraction of essential genes are highly persistent, still non essential genes represent a considerable fraction of the core-genome. Our results emphasize the power of integrating large scale comparative functional genomics with heterogeneous data for exploring bacterial diversity and versatility.
Network Analyses Can Advance Above-Belowground Ecology
Ramirez, Kelly S. ; Geisen, Stefan ; Morriën, Elly ; Snoek, Basten L. ; Putten, Wim H. van der - \ 2018
Trends in Plant Science 23 (2018)9. - ISSN 1360-1385 - p. 759 - 768.
community ecology - global change - species interactions - terrestrial ecology

An understanding of above-belowground (AG-BG) ecology is important for evaluating how plant interactions with enemies, symbionts, and decomposers affect species diversity and will respond to global changes. However, research questions and experiments often focus on only a limited number of interactions, creating an incomplete picture of how entire communities may be involved in AG-BG community ecology. Therefore, a pressing challenge is to formulate hypotheses of AG-BG interactions when considering communities in their full complexity. Here we discuss how network analyses can be a powerful tool to progress AG-BG research, link across scales from individual to community and ecosystem, visualize community interactions between the two (AG and BG) subsystems, and develop testable hypotheses.

Bioaccumulation and Biotransformation of Triclosan and Galaxolide in the Freshwater Oligochaete Limnodrilus hoffmeisteri in a Water/Sediment Microcosm
Peng, Feng-Jiao ; Ying, Guang Guo ; Pan, Chang Gui ; Selck, Henriette ; Salvito, Daniel ; Brink, Paul J. van den - \ 2018
Environmental Science and Technology 52 (2018)15. - ISSN 0013-936X - p. 8390 - 8398.

Personal care products are widely used in our daily life in considerable quantities and discharged via the down-the-drain route to aquatic environments, resulting in potential risks to aquatic organisms. We investigated bioaccumulation and biotransformation of two widely used personal care products, triclosan (TCS) and galaxolide (HHCB) spiked to sediment, in the oligochaete worm Limnodrilus hoffmeisteri in water/sediment microcosms. After 7 days of sediment exposure to 3.1 μg of TCS or HHCB/g of dry weight sediment, the accumulation of TCS and HHCB in L. hoffmeisteri reached equilibrium, at which point the biota-sediment accumulation factors (BSAFs) were 2.07 and 2.50 for TCS and HHCB, respectively. The presence of L. hoffmeisteri significantly accelerated the dissipation of the levels of TCS and HHCB in the microcosms, with approximately 9.03 and 2.90% of TCS and HHCB, respectively, eliminated from the water/sediment systems after exposure for 14 days in the presence of worms. Two biotransformation products, methyl triclosan and triclosan O-sulfate, were identified for TCS in worm tissue, whereas only methyl triclosan was identified in the sediment. Unlike TCS, no evidence of biotransformation products was found for HHCB in either worm tissue or sediment. These experiments demonstrate that L. hoffmeisteri biotransformed TCS through methylation and sulfation, whereas HHCB biotransformation was undetectable.

Supplement use and dietary sources of folate, vitamin D, and n-3 fatty acids during preconception : The GLIMP2 study
Looman, Moniek ; Berg, Claudia van den; Geelen, Anouk ; Samlal, Rahul A.K. ; Heijligenberg, Rik ; Klein Gunnewiek, Jacqueline M.T. ; Balvers, Michiel G.J. ; Leendertz-Eggen, Caroline L. ; Wijnberger, Lia D.E. ; Feskens, Edith J.M. ; Brouwer-Brolsma, Elske M. - \ 2018
Nutrients 10 (2018)8. - ISSN 2072-6643
Diet - Folate - N-3 fatty acids - Preconception - Supplements - Vitamin D

An adequate nutritional status during the preconception period is important, particularly for folate, vitamin D, and n-3 fatty acids (i.e., EPA+DHA). We aimed to determine supplement intake and the main dietary sources of folate, vitamin D, and EPA+DHA using the data of 66 Dutch women aged 18–40 years who wished to become pregnant. Additionally, associations of these intakes with their blood levels were examined. Dietary intake was assessed with a validated food frequency questionnaire, and supplement use with a structured questionnaire. 25-hydroxyvitamin D levels were determined in serum and folate and phospholipid EPA+DHA levels in plasma. Partial Spearman’s correlations, restricted cubic splines and trend analyses over tertiles of nutrient intakes were performed to examine intake-status associations. A large proportion of women did not meet the Dutch recommended intakes of folate (50%), vitamin D (67%), and EPA+DHA (52%). Vegetables were the main contributor to dietary folate intake (25%), oils and fats to dietary vitamin D intake (39%), and fish to dietary EPA+DHA intake (69%). Fourteen percent of the women had an inadequate folate status and 23% an inadequate vitamin D status. Supplemental folate intake, supplemental and dietary vitamin D intake and dietary EPA+DHA intake were significantly associated with their blood levels. In conclusion, even in our highly educated population, a large proportion did not achieve recommended folate, vitamin D and n-3 fatty acid intakes. Promotion of folate and vitamin D supplement use and fish consumption is needed to improve intakes and blood levels of these nutrients in women who wish to become pregnant.

Environmental impacts of experimental production of lactic acid for bioplastics from Ulva spp
Helmes, Roel J.K. ; López-Contreras, Ana M. ; Benoit, Maud ; Abreu, Helena ; Maguire, Julie ; Moejes, Fiona ; Burg, Sander W.K. van den - \ 2018
Sustainability 10 (2018)7. - ISSN 2071-1050
Bioplastics - Lactic acid - Life Cycle Assessment - Seaweed - Ulva spp

An exploratory Life Cycle Assessment (LCA) was carried out to provide insight into the environmental impacts of using the green seaweed Ulva spp. as a feedstock, for production of bioplastic. The study focused on the production of lactic acid as a precursor of polylactic acid. The study was on the production process: (1) The cultivation of Ulva spp., in an Integrated Multitrophic Aquaculture system; (2) the processing of the biomass for solubilization of sugars; (3) the fermentation of the sugars to lactic acid; (4) the isolation of lactic acid from fermentation broth. The study identified environmental hotspots and compared an experimental seaweed production chain with conventional feedstocks. The main hotspot is derived from electricity consumption during seaweed cultivation. The impact of electricity consumption can be lowered by reducing energy use and sourcing renewable energy, and by improving the material efficiency in the product chain. To improve understanding of the process of production's environmental impacts, future studies should broaden the system boundaries and scope of sustainability issues included in the environmental assessment.

Fate and effects of sediment-associated triclosan in subtropical freshwater microcosms
Peng, Feng-Jiao ; Diepens, Noël J. ; Pan, Chang-Gui ; Bracewell, Sally A. ; Ying, Guang-Guo ; Salvito, Daniel ; Selck, Henriette ; Brink, Paul J. Van den - \ 2018
Aquatic Toxicology 202 (2018). - ISSN 0166-445X - p. 117 - 125.
Benthic macroinvertebrates - Bioaccumulation - Dissipation - Partitioning - Toxicity

Triclosan (TCS) is an antibacterial agent that is commonly used in personal care products. Because of its sediment-binding properties, TCS exposure presents a potential threat to sediment-dwelling aquatic organisms. Currently our knowledge of the fate and effects of sediment-associated TCS in aquatic systems is limited. To understand the impact of sediment-associated TCS, we used microcosms to assess effects of TCS exposure on a diverse range of organisms selected to mimic a subtropical community, with an exposure period of 28 days. We included the oligochaete freshwater worm Limnodrilus hoffmeisteri to evaluate the interaction between sediment-associated TCS and sediment-dwelling organisms, including potential loss of TCS from the sediment due to biological activity and bioaccumulation. Benthic macroinvertebrate presence significantly increased the TCS levels from 0.013 ± 0.007 μg/L to 0.613 ± 0.030 μg/L in the overlying water through biological activity, posing a potential additional risk to pelagic species, but it did not result in a significant reduction of the sediment concentration. Furthermore, worms accumulated TCS with estimated Biota-Sediment-Accumulation-Factors (BSAFs) ranging between 0.38–3.55. Other than for algae, TCS at environmental concentrations did not affect the survival of the introduced organisms, including the L. hoffmeisteri. Our results demonstrate that, although TCS at currently detected maximum concentration may not have observable toxic effects on the benthic macroinvertebrates in the short term, it can lead to bioaccumulation in worms.

Circumpolar Arctic Vegetation Classification
Walker, Donald A. ; Daniëls, Fred J.A. ; Matveyeva, Nadezhda V. ; Šibík, Jozef ; Walker, Marilyn D. ; Breen, Amy L. ; Druckenmiller, Lisa A. ; Raynolds, Martha K. ; Bültmann, Helga ; Hennekens, Stephan ; Buchhorn, Marcel ; Epstein, Howard E. ; Ermokhina, Ksenia ; Fosaa, Anna M. ; Heidmarsson, Starri ; Heim, Birgit ; Jónsdóttir, Ingibjörg S. ; Koroleva, Natalia ; Lévesque, Esther ; MacKenzie, William H. ; Henry, Greg H.R. ; Nilsen, Lennart ; Peet, Robert ; Razzhivin, Volodya ; Talbot, Stephen S. ; Telyatnikov, Mikhail ; Thannheiser, Dietbert ; Webber, Patrick J. ; Wirth, Lisa M. - \ 2018
Phytocoenologia 48 (2018)2. - ISSN 0340-269X - p. 181 - 201.
Alaska - Bioclimate gradient - Braun-Blanquet approach - Habitat type - Plant growth form - Plot database - Syntaxon - Tundra - Vegetation mapping

Aims: An Arctic Vegetation Classification (AVC) is needed to address issues related to rapid Arctic-wide changes to climate, land-use, and biodiversity. Location: The 7.1 million km2 Arctic tundra biome. Approach and conclusions: The purpose, scope and conceptual framework for an Arctic Vegetation Archive (AVA) and Classification (AVC) were developed during numerous workshops starting in 1992. The AVA and AVC are modeled after the European vegetation archive (EVA) and classification (EVC). The AVA will use Turboveg for data management. The AVC will use a Braun-Blanquet (Br.-Bl.) classification approach. There are approximately 31,000 Arctic plots that could be included in the AVA. An Alaska AVA (AVA-AK, 24 datasets, 3026 plots) is a prototype for archives in other parts of the Arctic. The plan is to eventually merge data from other regions of the Arctic into a single Turboveg v3 database. We present the pros and cons of using the Br.-Bl. classification approach compared to the EcoVeg (US) and Biogeoclimatic Ecological Classification (Canada) approaches. The main advantages are that the Br.-Bl. approach already has been widely used in all regions of the Arctic, and many described, well-accepted vegetation classes have a pan-Arctic distribution. A crosswalk comparison of Dryas octopetala communities described according to the EcoVeg and the Braun-Blanquet approaches indicates that the non-parallel hierarchies of the two approaches make crosswalks difficult above the plantcommunity level. A preliminary Arctic prodromus contains a list of typical Arctic habitat types with associated described syntaxa from Europe, Greenland, western North America, and Alaska. Numerical clustering methods are used to provide an overview of the variability of habitat types across the range of datasets and to determine their relationship to previously described Braun-Blanquet syntaxa. We emphasize the need for continued maintenance of the Pan-Arctic Species List, and additional plot data to fully sample the variability across bioclimatic subzones, phytogeographic regions, and habitats in the Arctic. This will require standardized methods of plot-data collection, inclusion of physiogonomic information in the numeric analysis approaches to create formal definitions for vegetation units, and new methods of data sharing between the AVA and national vegetation- plot databases.

Removal, biotransformation and toxicity variations of climbazole by freshwater algae Scenedesmus obliquus
Pan, Chang Gui ; Peng, Feng Jiao ; Ying, Guang Guo - \ 2018
Environmental Pollution 240 (2018). - ISSN 0269-7491 - p. 534 - 540.
CBZ-OH - Climbazole - Green algae - Growth inhibition - Kinetics

Climbazole (CBZ) is an antibacterial and antifungal agent widely used in personal care products. In this study, we investigated the interactions between climbazole (CBZ) and freshwater microalgae Scenedesmus obliquus (S. obliquus). Dose-effect relationships between CBZ concentrations and growth inhibitions or chlorophyll a content were observed. After 12 days of incubation, the algae density and chlorophyll a content in 2 mg/L treatment group was 56.6% and 15.8% of those in the control group, respectively. Biotransformation was the predominant way to remove CBZ in the culture solution, whereas the contribution of bioaccumulation and bioadsorption were negligible. More than 88% of CBZ was removed by S. obliquus across all treatments after 12 days of incubation, and the biotransformation of CBZ followed the first order kinetic model with half-lives of approximately 4.5 days at different treatments. CBZ-alcohol (CBZ-OH) was the only biotransformation product identified in algal solution. Moreover, the toxicity of biotransformation products was much lower than its corresponding precursor compound (CBZ). The results of this study revealed that S. obliquus might have a great impact on the environmental fates of CBZ and could be further applied to remove organic pollutants in aquatic environment. S. obliquus can effectively remove CBZ through biotransformation process in algal solution with CBZ-OH as the identified products.

Transcriptome analysis for the scale-down of a CHO cell fed-batch process
Alsayyari, Abdulaziz A. ; Pan, Xiao ; Dalm, Ciska ; Veen, Jochem W. van der; Vriezen, Nienke ; Hageman, Jos A. ; Wijffels, René H. ; Martens, Dirk E. - \ 2018
Journal of Biotechnology 279 (2018). - ISSN 0168-1656 - p. 61 - 72.
Ambr - CHO cell culture - Fed-batch - mAb production - Scale-down - Transcriptome analysis

Transcriptome and metabolism analysis were performed to evaluate the scale-down of a CHO cell fed-batch process from a 10 L bioreactor to an ambr 15® (ambr) system. Two different agitation scale-down principles were applied, resulting in two different agitation rates in the ambr system: 1300 RPM based on the agitator tip speed, and 800 rpm based on the volumetric power input (P/V). Culture performance including cell growth, product titer, glycosylation, and specific consumption/production rates of metabolites was the same for both agitation rates in the ambr and was comparable to that of the 10 L system. The initial variation in gene expression between the inocula for the ambr and 10 L system was no longer present after three days of culture, indicating comparable culture conditions in both systems. Based on principal component analysis, changes in gene expression over time were similar between both scales with less than 6% variation. 2455 genes were uniquely regulated in the ambr system compared to 1604 genes in the 10 L system. Functional analysis of these genes did not reveal their relations with scale or cellular function. This study further strengthens that the ambr system gives representative culture performance for the 10 L bench-scale bioreactor.

Scale-down of CHO cell fed-batch cultures
Pan, Xiao - \ 2018
University. Promotor(en): Rene Wijffels, co-promotor(en): Dirk Martens. - Wageningen : Wageningen University - ISBN 9789463438438 - 157
A possible molecular basis for photoprotection in the minor antenna proteins of plants
Fox, Kieran F. ; Ünlü, Caner ; Balevičius, Vytautas ; Ramdour, Baboo Narottamsing ; Kern, Carina ; Pan, Xiaowei ; Li, Mei ; Amerongen, Herbert van; Duffy, Christopher D.P. - \ 2018
Biochimica et Biophysica Acta. B, Bioenergetics 1859 (2018)7. - ISSN 0005-2728 - p. 471 - 481.
Carotenoids - Light-harvesting - Minor antenna - Non-photochemical quenching - Photoprotection - Photosystem II

The bioenergetics of light-harvesting by photosynthetic antenna proteins in higher plants is well understood. However, investigation into the regulatory non-photochemical quenching (NPQ) mechanism, which dissipates excess energy in high light, has led to several conflicting models. It is generally accepted that the major photosystem II antenna protein, LHCII, is the site of NPQ, although the minor antenna complexes (CP24/26/29) are also proposed as alternative/additional NPQ sites. LHCII crystals were shown to exhibit the short excitation lifetime and several spectral signatures of the quenched state. Subsequent structure-based models showed that this quenching could be explained by slow energy trapping by the carotenoids, in line with one of the proposed models. Using Fluorescence Lifetime Imaging Microscopy (FLIM) we show that the crystal structure of CP29 corresponds to a strongly quenched conformation. Using a structure-based theoretical model we show that this quenching may be explained by the same slow, carotenoid-mediated quenching mechanism present in LHCII crystals.

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